xref: /dports/biology/cufflinks/cufflinks-2.2.1-89-gdc3b0cb/doc/cufflinks.bib

%% This BibTeX bibliography file was created using BibDesk.
%% http://bibdesk.sourceforge.net/


%% Created for Colin Dewey at 2005-10-16 22:47:51 -0700


%% Saved with string encoding ASCII (TeX)


%PASA, alt. splicing graphs, Burge, Sorek, Roderic...



@book{ASCB2005,
    Editor = {L Pachter and B Sturmfels},
    Publisher = {Cambridge University Press},
    Title = {{Algebraic Statistics for Computational Biology}},
    Year = {2005}}

@Article{Rozen2000,
  author = 	 {S Rozen and H J Skaletsky},
  title = 	 {{Primer3 on the WWW for general users and for biolgist programmers}},
  journal = 	 {Methods and Protocols: Methods in Molecular Biology},
  year = 	 {2000},
  OPTkey = 	 {},
  volume = 	 {4},
  OPTnumber = 	 {},
  pages = 	 {365-386},
  OPTmonth = 	 {},
  OPTnote = 	 {},
  OPTannote = 	 {}
}

@Article{Oshlack2009,
  author = 	 {A Oshlack and MJ Wakefield},
  title = 	 {Transcript length bias in {RNA-Seq} data confounds systems biology},
  journal = 	 {Biology Direct},
  year = 	 {2009},
  OPTkey = 	 {},
  volume = 	 {4},
  OPTnumber = 	 {},
  pages = 	 {14},
  OPTmonth = 	 {},
  OPTnote = 	 {},
  OPTannote = 	 {}
}

@book{Agresti1990,
    Address = {New York},
    Author = {A Agresti},
    Isbn = {0-471-85301-1},
    Mrclass = {62H17},
    Mrnumber = {MR1044993 (91k:62055)},
    Mrreviewer = {I. J. Good},
    Note = {A Wiley-Interscience Publication},
    Pages = {xvi+558},
    Publisher = {John Wiley \& Sons Inc.},
    Series = {Wiley Series in Probability and Mathematical Statistics: Applied Probability and Statistics},
    Title = {Categorical Data Analysis},
    Year = {1990}}


@Article{Aroian1978,
  author = 	 {LA Aroian and VS Taneja and LW Cornwell},
  title = 	 {Mathematical forms of the distribution of the product of two normal variables},
  journal = 	 {Communications in Statistics: Theory and Methods},
  year = 	 {1978},
  OPTkey = 	 {},
  volume = 	 {A7},
  OPTnumber = 	 {},
  pages = 	 {165--172},
  OPTmonth = 	 {},
  OPTnote = 	 {},
  OPTannote = 	 {}
}

@article{Bandelt1992,
    Author = {HJ Bandelt and A Dress},
    Date-Modified = {2005-03-01 19:33:42 -0500},
    Journal = {Advances in Mathematics},
    Pages = {47--105},
    Title = {A canonical decomposition theory for metrics on a finite set},
    Volume = {92},
    Year = {1992}}

@article{Bandelt1995,
    Author = {HJ Bandelt and P Forster and BC Sykes and MB Richards},
    Date-Modified = {2005-03-01 19:34:19 -0500},
    Journal = {Genetics},
    Pages = {743--753},
    Title = {Mitochondrial portraits of human population using median networks},
    Volume = {141},
    Year = {1995}}

@inCollection{Barad2003,
  author =       {G Barad},
  title = 	 {Genome rearrangements and algebraic geometry},
  year = 	 {2003},
  OPTkey = 	 {},
  booktitle =    {Knots in Washington XV},
  editor = 	 {K Kobayashi and K Przytycki and Y Rong and S Suzuki and K Taniyama and T Tsukamoto and A Yasuhara},
  OPTvolume = 	 {},
  OPTnumber = 	 {},
  OPTseries = 	 {},
  OPTaddress = 	 {},
  OPTmonth = 	 {},
  OPTorganization = {},
  OPTpublisher = {},
  OPTnote = 	 {},
  OPTannote = 	 {}
}

@Book{Barthelemy1991,
  author = 	 {J-P Barth'{e}l\'{e}my and A Gu\'{e}noche},
  ALTeditor = 	 {},
  title = 	 {Trees and Proximity Representations},
  publisher = 	 {John Wiley \& Sons},
  year = 	 {1991},
  OPTkey = 	 {},
  OPTvolume = 	 {},
  OPTnumber = 	 {},
  OPTseries = 	 {},
  OPTaddress = 	 {},
  OPTedition = 	 {},
  OPTmonth = 	 {},
  OPTnote = 	 {},
  OPTannote = 	 {}
}

@Article{Barthelemy2008,
  author = 	 {J-P Barth'{e}lemy and F Brucker},
  title = 	 {Binary clustering},
  journal = 	 {Discrete Applied Mathematics},
  year = 	 {2008},
  OPTkey = 	 {},
  volume = 	 {156},
  OPTnumber = 	 {8},
  pages = 	 {1237--1250},
  OPTmonth = 	 {},
  OPTnote = 	 {},
  OPTannote = 	 {}
}


@Article{Benjamini1995,
  author = 	 {Y Benjamini and Y Hochberg},
  title = 	 {Controlling the False Discovery Rate: a Practical and Powerful Approach to Multiple Testing},
  journal = 	 {Journal of the Royal Statistical Society, Series B (Methodological)},
  year = 	 {1995},
  OPTkey = 	 {},
  volume = 	 {57},
  OPTnumber = 	 {},
  pages = 	 {289--300},
  OPTmonth = 	 {},
  OPTnote = 	 {},
  OPTannote = 	 {}
}

@Article{Bertrand2002,
  author = 	 {P Bertrand and MF Janowitz},
  title = 	 {Pyramids and weak hierarchies in the ordinal model for clustering},
  journal = 	 {Discrete Applied Mathematics},
  year = 	 {2002},
  OPTkey = 	 {},
  volume = 	 {122},
  OPTnumber = 	 {},
  pages = 	 {55--81},
  OPTmonth = 	 {},
  OPTnote = 	 {},
  OPTannote = 	 {}
}


@book{Bertsekas1999,
    Address = {MA Belmont},
    Author = {D Bertsekas},
    Date-Modified = {2005-02-05 12:49:26 -0800},
    Publisher = {Athena Scientific},
    Title = {Nonlinear Programming},
    Year = {1999}}

@book{Bertsimas1997,
    Author = {D Bertsimas and J Tsitsiklis},
    Date-Modified = {2005-02-05 12:49:26 -0800},
    Publisher = {Athena Scientific},
    Title = {Introduction to Linear Programming},
    Year = {1997}}

@incollection{Berz1991,
    Address = {Philadelphia, PA},
    Author = {M Berz},
    Booktitle = {Automatic differentiation of algorithms: theory, implementation and applications},
    Date-Modified = {2005-02-05 12:49:26 -0800},
    Editor = {A Griewank and G Corliss},
    Pages = {147--156},
    Publisher = {SIAM},
    Title = {Forward algorithms for high orders and many variables with application to beam physics},
    Year = {1991}}

@article{Besag1974,
    Author = {Besag, J.},
    Journal = {Journal of the Royal Statistical Society},
    Pages = {192--236},
    Title = {Spatial interaction and the statistical analysis of lattice systems},
    Volume = {B,36},
    Year = {1974}}


@article{Besag1986,
    Author = {J Besag},
    Journal = {Journal of the Royal Statistical Society},
    Pages = {259--302},
    Title = {On the statistical analysis of dirty pictures},
    Volume = {B 48 No. 3},
    Year = {1986}}

@book{Bickel2000,
    Author = {PJ Bickel and KA Doksum},
    Publisher = {Prentice Hall},
    Title = {Mathematical statistics: Basic Ideas and Selected Topics, Vol I (2nd Edition)},
    Year = {2000}}


@article{Billera2001,
    Author = {LJ Billera and SP Holmes and K Vogtmann},
    Date-Modified = {2005-02-05 13:05:35 -0800},
    Fjournal = {Advances in Applied Mathematics},
    Issn = {0196-8858},
    Journal = {Advances in Applied Mathematics},
    OPTMrclass = {05C90 (92B10)},
    OPTMrnumber = {MR1867931 (2002k:05229)},
    Mrreviewer = {Charles A. Semple},
    OPTNumber = {4},
    Pages = {733--767},
    Title = {Geometry of the space of phylogenetic trees},
    Volume = {27},
    Year = {2001}}

@incollection{Blanchette2000,
    Address = {Providence, RI},
    Author = {D Sankoff and M Blanchette},
    Booktitle = {Stochastic models (Ottawa, ON, 1998)},
    Mrclass = {92D15 (60J27)},
    Mrnumber = {MR1765022 (2002f:92014)},
    Mrreviewer = {Ming-Ying Leung},
    Pages = {399--418},
    Publisher = {American Mathematical Society},
    Series = {Proceedings of the International Conference on Stochstic Models},
    Title = {Comparative genomics via phylogenetic invariants for {J}ukes-{C}antor semigroups},
    Volume = {26},
    Year = {2000}}



@article{Blanchette2004,
    Author = {M Blanchette and WJ Kent and C Riemer and L Elnitski and AFA Smit and KM Roskin and R Baertsch and K Rosenbloom and H Clawson and ED Green and others},
    Journal = {Genome Research},
    Pages = {708--715},
    Title = {Aligning multiple genomic sequences with the threaded blockset aligner},
    Volume = {14},
    Year = {2004}}

@article{Boffelli2003,
    Abstract = {Nonhuman primates represent the most relevant model organisms to understand the biology of Homo sapiens. The recent divergence and associated overall sequence conservation between individual members of this taxon have nonetheless largely precluded the use of primates in comparative sequence studies. We used sequence comparisons of an extensive set of Old World and New World monkeys and hominoids to identify functional regions in the human genome. Analysis of these data enabled the discovery of primate-specific gene regulatory elements and the demarcation of the exons of multiple genes. Much of the information content of the comprehensive primate sequence comparisons could be captured with a small subset of phylogenetically close primates. These results demonstrate the utility of intraprimate sequence comparisons to discover common mammalian as well as primate-specific functional elements in the human genome, which are unattainable through the evaluation of more evolutionarily distant species.},
    Affiliation = {U.S. Department of Energy Joint Genome Institute, Walnut Creek, CA 94598, USA.},
    Aid = {299/5611/1391 {$[$}pii{$]$}},
    Au = {Rubin EM},
    Author = {D Boffelli and J McAuliffe and D Ovcharenko and KD Lewis and I Ovcharenko and L Pachter and EM Rubin},
    Cin = {Science. 2003 Feb 28;299(5611):1331-3. PMID: 12610290},
    Da = {20030228},
    Date-Modified = {2005-02-05 12:49:26 -0800},
    Dcom = {20030314},
    Edat = {2003/03/01 04:00},
    Gr = {R01-HG02362-01/HG/NHGRI},
    Jid = {0404511},
    Journal = {Science},
    Keywords = {Animals and Apolipoproteins A/genetics and Cebidae/genetics and Cercopithecidae/genetics and Computational Biology and Conserved Sequence and DNA-Binding Proteins/metabolism and Electrophoretic Mobility Shift Assay and Evolution and Exons and Gene Expression Regulation and *Genome and *Genome, Human and Hominidae/genetics and Humans and Hylobates/genetics and Likelihood Functions and *Phylogeny and Primates/*genetics and Regulatory Sequences, Nucleic Acid and Research Support, U.S. Gov't, Non-P.H.S. and Research Support, U.S. Gov't, P.H.S. and *Sequence Analysis, DNA and Species Specificity and Tumor Cells, Cultured},
    Language = {eng},
    Lr = {20041117},
    Mhda = {2003/03/15 04:00},
    Number = {5611},
    Own = {NLM},
    Pages = {1391--4},
    Pl = {United States},
    Pmid = {12610304},
    Pst = {ppublish},
    Pt = {Journal Article},
    Pubm = {Print},
    Rn = {0 (DNA-Binding Proteins)},
    Sb = {IM},
    So = {Genome Res 2003 Mar;13(3):496-502.},
    Stat = {MEDLINE},
    Title = {Phylogenetic shadowing of primate sequences to find functional regions of the human genome.},
    Volume = {299},
    Year = {2003}}




@article{Boffelli2004,
    Author = {D Boffelli and MA Nobrega and EM Rubin},
    Journal = {Nature Reviews Genetics},
    Pages = {456--465},
    Title = {Comparative Genomics at the Vertebrate Extremes},
    Volume = {5},
    Year = {2004}}



@article{Boffelli2004a,
    Author = {D Boffelli and CV Weer and L Weng and KD Lewis and MI Shoukry and L Pachter and DN Keys and EM Rubin},
    Journal = {Genome Research},
    Pages = {2406--2411},
    Title = {Intraspecies sequence comparisons for annotating genomes},
    Volume = {14},
    Year = {2004}}

@Misc{Boost,
  key = 	 {Boost library},
  author = 	 {Boost C++ libraries},
  title = 	 {{\tt http://www.boost.org/}},
  OPThowpublished = {},
  OPTmonth = 	 {},
  OPTyear = 	 {},
  OPTnote = 	 {},
  OPTannote = 	 {}
}


@article{Bosma1997,
    Author = {W Bosma and J Cannon and C Playoust},
    Date-Modified = {2005-02-05 12:49:27 -0800},
    Doi = {http://dx.doi.org/10.1006/jsco.1996.0125},
    Issn = {0747-7171},
    Journal = {Journal of Symbolic Computation},
    Number = {3-4},
    Pages = {235--265},
    Publisher = {Academic Press, Inc.},
    Title = {{The MAGMA algebra system I: the user language}},
    Volume = {24},
    Year = {1997}}

@article{Bourque2004,
    Abstract = {Recent analysis of genome rearrangements in human and mouse genomes revealed evidence for more rearrangements than thought previously and shed light on previously unknown features of mammalian evolution, like breakpoint reuse and numerous microrearrangements. However, two-way analysis cannot reveal the genomic architecture of ancestral mammals or assign rearrangement events to different lineages. Thus, the "original synteny" problem introduced by Nadeau and Sankoff previously, remains unsolved, as at least three mammalian genomes are required to derive the ancestral mammalian karyotype. We show that availability of the rat genome allows one to reconstruct a putative genomic architecture of the ancestral murid rodent genome. This reconstruction suggests that this ancestral genome retained many previously postulated chromosome associations in the placental ancestor and reveals others that were beyond the resolution of cytogenetic, radiation hybrid mapping, and chromosome painting techniques. Three-way analysis of rearrangements leads to a reliable reconstruction of the genomic architecture of specific regions in the murid ancestor, including the X chromosome, and for the first time allows one to assign major rearrangement events to one of human, mouse, and rat lineages. Our analysis implies that the rate of rearrangements is much higher in murid rodents than in the human lineage and confirms the existence of rearrangement hot-spots in all three lineages.},
    Affiliation = {Centre de Recherches Mathematiques, Universite de Montreal, Canada H3C 3J7.},
    Aid = {14/4/507 {$[$}pii{$]$}},
    Au = {Tesler G},
    Author = {G Bourque and PA Pevzner and G Tesler},
    Da = {20040402},
    Dcom = {20040505},
    Edat = {2004/04/03 05:00},
    Jid = {9518021},
    Journal = {Genome Research},
    Language = {eng},
    Lr = {20041117},
    Mhda = {2004/05/07 05:00},
    Number = {4},
    Own = {NLM},
    Pages = {507--16},
    Pl = {United States},
    Pmid = {15059991},
    Pst = {ppublish},
    Pt = {Journal Article},
    Pubm = {Print},
    Sb = {IM},
    Stat = {MEDLINE},
    Title = {Reconstructing the genomic architecture of ancestral mammals: lessons from human, mouse, and rat genomes.},
    Volume = {14},
    Year = {2004}}

@article{Boykov1999,
    Author = {Y Boykov and O Veksler and R Zabih},
    Journal = {Intl. Conf. on Computer Vision},
    Title = {Fast approximate energy minimization via graph cuts},
    Year = {1999}}

@article{Bray2003,
    Abstract = {MAVID is a multiple alignment program suitable for many large genomic regions. The MAVID web server allows biomedical researchers to quickly obtain multiple alignments for genomic sequences and to subsequently analyse the alignments for conserved regions. MAVID has been successfully used for the alignment of closely related species such as primates and also for the alignment of more distant organisms such as human and fugu. The server is fast, capable of aligning hundreds of kilobases in less than a minute. The multiple alignment is used to build a phylogenetic tree for the sequences, which is subsequently used as a basis for identifying conserved regions in the alignment. The server can be accessed at http://baboon.math.berkeley.edu/mavid/.},
    Affiliation = {Department of Mathematics, 970 Evans Hall, UC Berkeley, Berkeley, CA 94720, USA.},
    Au = {Pachter L},
    Author = {N Bray and L Pachter},
    Da = {20030625},
    Date-Modified = {2005-02-05 12:49:26 -0800},
    Dcom = {20030818},
    Edat = {2003/06/26 05:00},
    Jid = {0411011},
    Journal = {Nucleic Acids Research},
    Keywords = {Animals and Base Sequence and Conserved Sequence and Genomics/*methods and Humans and Internet and Mice and Molecular Sequence Data and Phylogeny and Rats and Sequence Alignment/*methods and Sequence Analysis, DNA/*methods and *Software and Takifugu/genetics},
    Language = {eng},
    Lr = {20041117},
    Mhda = {2003/08/19 05:00},
    Number = {13},
    Own = {NLM},
    Pages = {3525--6},
    Pl = {England},
    Pmid = {12824358},
    Pst = {ppublish},
    Pt = {Journal Article},
    Pubm = {Print},
    Sb = {IM},
    So = {J Comput Biol 2003;10(3-4):509-20.},
    Stat = {MEDLINE},
    Title = {{MAVID} multiple alignment server.},
    Volume = {31},
    Year = {2003}}



@article{Bray2003a,
    Abstract = {In this paper we describe a new global alignment method called AVID. The method is designed to be fast, memory efficient, and practical for sequence alignments of large genomic regions up to megabases long. We present numerous applications of the method, ranging from the comparison of assemblies to alignment of large syntenic genomic regions and whole genome human/mouse alignments. We have also performed a quantitative comparison of AVID with other popular alignment tools. To this end, we have established a format for the representation of alignments and methods for their comparison. These formats and methods should be useful for future studies. The tools we have developed for the alignment comparisons, as well as the AVID program, are publicly available. See Web Site References section for AVID Web address and Web addresses for other programs discussed in this paper.},
    Affiliation = {Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA.},
    Aid = {10.1101/gr.789803 {$[$}doi{$]$}},
    Au = {Pachter L},
    Author = {N Bray and I Dubchak and L Pachter},
    Da = {20030116},
    Date-Modified = {2005-02-05 12:49:26 -0800},
    Dcom = {20030317},
    Edat = {2003/01/17 04:00},
    Gr = {RO1-HG02362-01/HG/NHGRI},
    Jid = {9518021},
    Journal = {Genome Research},
    Keywords = {Algorithms and Animals and Cats and Cattle and Chickens and Comparative Study and Dogs and Evolution, Molecular and Exons/genetics and Humans and Pan troglodytes and Rats and Repetitive Sequences, Nucleic Acid/genetics and Reproducibility of Results and Research Support, U.S. Gov't, P.H.S. and Sensitivity and Specificity and Sequence Alignment/*methods and *Software and Swine and Time Factors and Untranslated Regions/genetics},
    Language = {eng},
    Lr = {20041117},
    Mhda = {2003/03/18 04:00},
    Number = {1},
    Own = {NLM},
    Pages = {97--102},
    Pl = {United States},
    Pmid = {12529311},
    Pst = {ppublish},
    Pt = {Journal Article},
    Pubm = {Print},
    Rn = {0 (Untranslated Regions)},
    Sb = {IM},
    So = {Science 2003 Feb 28;299(5611):1391-4.},
    Stat = {MEDLINE},
    Title = {{AVID}: A global alignment program.},
    Volume = {13},
    Year = {2003}}

@article{Bray2004,
    Abstract = {We describe a new global multiple-alignment program capable of aligning a large number of genomic regions. Our progressive-alignment approach incorporates the following ideas: maximum-likelihood inference of ancestral sequences, automatic guide-tree construction, protein-based anchoring of ab-initio gene predictions, and constraints derived from a global homology map of the sequences. We have implemented these ideas in the MAVID program, which is able to accurately align multiple genomic regions up to megabases long. MAVID is able to effectively align divergent sequences, as well as incomplete unfinished sequences. We demonstrate the capabilities of the program on the benchmark CFTR region, which consists of 1.8 Mb of human sequence and 20 orthologous regions in marsupials, birds, fish, and mammals. Finally, we describe two large MAVID alignments, an alignment of all the available HIV genomes and a multiple alignment of the entire human, mouse, and rat genomes.},
    Affiliation = {Department of Mathematics, University of California at Berkeley, Berkeley, California 94720, USA.},
    Aid = {14/4/693 {$[$}pii{$]$}},
    Au = {Pachter L},
    Author = {N Bray and L Pachter},
    Da = {20040402},
    Date-Modified = {2005-02-05 12:49:26 -0800},
    Dcom = {20040505},
    Edat = {2004/04/03 05:00},
    Gr = {R01-HG02362-01/HG/NHGRI},
    Jid = {9518021},
    Journal = {Genome Research},
    Keywords = {Animals and Cats and Cattle and Comparative Study and Computational Biology/methods and Cystic Fibrosis Transmembrane Conductance Regulator/genetics and Dogs and *Evolution, Molecular and Fishes/genetics and Genome and Genome, Human and Genome, Viral and HIV-1/genetics and Humans and Mice and Rabbits and Rats and Research Support, U.S. Gov't, P.H.S. and SIV/genetics and Sequence Alignment/*methods/statistics \& numerical data and Software/statistics \& numerical data/*trends and Swine/genetics},
    Language = {eng},
    Lr = {20041117},
    Mhda = {2004/05/07 05:00},
    Number = {4},
    Own = {NLM},
    Pages = {693--9},
    Pl = {United States},
    Pmid = {15060012},
    Pst = {ppublish},
    Pt = {Journal Article},
    Pubm = {Print},
    Rn = {126880-72-6 (Cystic Fibrosis Transmembrane Conductance Regulator)},
    Sb = {IM},
    So = {Genome Res 2004 Apr;14(4):716-20.},
    Stat = {MEDLINE},
    Title = {{MAVID}: constrained ancestral alignment of multiple sequences.},
    Volume = {14},
    Year = {2004}}

@article{Brown1982,
    Author = {WM Brown and EM Prager and A Wang and AC Wilson},
    Date-Modified = {2005-02-05 12:49:26 -0800},
    Journal = {Journal of Molecular Evolution},
    Pages = {225--239},
    Title = {Mitochondrial {DNA} sequences of primates, tempo and mode of evolution},
    Volume = {18},
    Year = {1982}}

@book{Brown2002,
    Author = {TA Brown},
    Publisher = {John Wiley \& Son, Inc.},
    Title = {Genomes 2},
    Year = {2002}}

@article{Brudno2003,
    Author = {M Brudno and S Malde and A Poliakov and C Do and O Couronne and I Dubchak and S Batzoglou},
    Journal = {Special issue on the Proceedings of the ISMB 2003, Bioinformatics},
    Pages = {54i--64i},
    Title = {Glocal alignment: finding rearrangements during alignment},
    Volume = {19},
    Year = {2003}}

@article{Brudno2003a,
    Author = {M Brudno and C Do and G Cooper and MF Kim and E Davydov and ED Green and A Sidow and S Batzoglou},
    Journal = {Genome Research},
    Pages = {721--731},
    Title = {{LAGAN and Multi-LAGAN: efficient tools for large-scale multiple alignment of genomic DNA}},
    Volume = {13},
    Year = {2003}}

@Article{Bruno2000,
  author = {WJ Bruno and ND Socci and AL Halpern},
  title = {Weighted neighbor-joining: a likelihood-based approach to
                  distance-based phylogeny reconstruction},
  journal = {Molecular Biology and Evolution},
  year = {2000},
  OPTkey = {},
  volume = {17},
  number = {1},
  pages = {189--197},
  OPTmonth = {},
  OPTnote = {},
  OPTannote = {}
}

@TechReport{Bryant2003,
  author = 	 {D Bryant and V Moulton},
  title = 	 {Consistency of the {N}eighbor{N}et algorithm for constructing phylogenetic networks},
  institution =  {McGill University},
  year = 	 {2003},
  OPTkey = 	 {},
  OPTtype = 	 {},
  OPTnumber = 	 {},
  OPTaddress = 	 {},
  OPTmonth = 	 {},
  OPTnote = 	 {},
  OPTannote = 	 {}
}

@article{Bryant2004,
    Author = {D Bryant and V Moulton},
    Date-Modified = {2005-03-01 19:59:37 -0500},
    Journal = {Molecular Biology And Evolution},
    Pages = {255--265},
    Title = {{NeighborNet}: An agglomerative method for the construction of planar phylogenetic networks},
    Volume = {21},
    Year = {2004}}

@Article{Bryant2005,
  author = {D Bryant},
  title = {On the uniqueness of the selection criterion in
                  neighbor-joining},
  journal = {Journal of Classification},
  year = {2005},
  OPTkey = {},
  volume = {22},
  number = {1},
  pages = {3--15},
  OPTmonth = {},
  OPTnote = {},
  OPTannote = {}
}

@InCollection{Bryant2005b,
  author = 	 {D Bryant and F Filimon and R Gray},
  title = 	 {Untangling our past: languages, trees, splits and networks},
  booktitle = 	 {The evolution of cultural diversity: phylogenetic approaches},
  OPTcrossref =  {},
  OPTkey = 	 {},
  pages = 	 {69-85},
  publisher = {UCL Press},
  year = 	 {2005},
  editor = 	 {R Mace and C Holden and S Shennan},
  OPTvolume = 	 {},
  OPTnumber = 	 {},
  OPTseries = 	 {},
  OPTtype = 	 {},
  OPTchapter = 	 {},
  OPTaddress = 	 {},
  OPTedition = 	 {},
  OPTmonth = 	 {},
  OPTnote = 	 {},
  OPTannote = 	 {}
}


@InCollection{Bryant2005c,
  author = 	 {D Bryant},
  title = 	 {Extending tree models to split networks},
  booktitle = 	 {Algebraic Statistics for Computational Biology},
  OPTcrossref =  {},
  OPTkey = 	 {},
  pages = 	 {322--334},
  publisher = {Cambridge University Press},
  year = 	 {2005},
  editor = 	 {L Pachter and B Sturmfels},
  OPTvolume = 	 {},
  OPTnumber = 	 {},
  OPTseries = 	 {},
  OPTtype = 	 {},
  OPTchapter = 	 {},
  OPTaddress = 	 {},
  OPTedition = 	 {},
  OPTmonth = 	 {},
  OPTnote = 	 {},
  OPTannote = 	 {}
}

@phdthesis{Buchberger1965,
    Author = {B Buchberger},
    School = {Univ. Innsbruck, Dept. of Math., Innsbruck, Austria},
    Title = {An algorithm for finding a basis for the residue class ring of a zero-dimensional polynomial ideal (in German).},
    Year = {1965}}

@inproceedings{Bucher1996,
    Author = {P Bucher and K Hofmann},
    Booktitle = {Proceedings Intelligent Systems in Molecular Biology},
    Date-Modified = {2005-02-05 12:49:26 -0800},
    Key = {Bucher},
    Title = {A sequence similarity search algorithm based on a probabilistic interpretation of an alignment scoring system},
    Year = {1996}}

@TechReport{Bullard2009,
  author = 	 {JH Bullard and EA Purdom and KD Hansen and S Durinck and S Dudoit},
  title = 	 {Statistical inference in {mRNA-Seq}: exploratory data analysis and differential expression},
  institution =  {UC Berkeley},
  year = 	 {2009},
  OPTkey = 	 {},
  OPTtype = 	 {},
  OPTnumber = 	 {},
  OPTaddress = 	 {},
  OPTmonth = 	 {},
  OPTnote = 	 {},
  OPTannote = 	 {}
}

@Article{Bullard2010,
  author = 	 {JH Bullard and E Purdom and KD Hansen and S Dudoit},
  title = 	 {Evaluation of statistical methods for normalization and differential expression in {mRNA-Seq} experiments},
  journal = 	 {BMC Bioinformatics},
  year = 	 {2010},
  OPTkey = 	 {},
  volume = 	 {11},
  OPTnumber = 	 {},
  pages = 	 {94},
  OPTmonth = 	 {},
  OPTnote = 	 {},
  OPTannote = 	 {}
}

@article{Bulmer1991,
    Author = {D Bulmer},
    Date-Modified = {2005-03-01 20:05:24 -0500},
    Journal = {Molecular Biology and Evolution},
    Number = {6},
    Pages = {868--883},
    Title = {Use of the Method of Generalized Least Squares in Reconstructing Phylogenies from Sequence Data},
    Volume = {8},
    Year = {1991}}

@InCollection{Buneman1971,
  author = 	 {P Buneman},
  title = 	 {The recovery of trees from measures of dissimilarity},
  booktitle = 	 {Mathematics in the Archaeological and Historical Sciences},
  OPTcrossref =  {},
  OPTkey = 	 {},
  pages = 	 {387--395},
  publisher = {Edinburgh University Press},
  year = 	 {1971},
  editor = 	 {FR Hodson and DG Kendall and P Tautu},
  OPTvolume = 	 {},
  OPTnumber = 	 {},
  OPTseries = 	 {},
  OPTtype = 	 {},
  OPTchapter = 	 {},
  OPTaddress = 	 {},
  OPTedition = 	 {},
  OPTmonth = 	 {},
  OPTnote = 	 {},
  OPTannote = 	 {}
}

@article{Burge1997,
    Author = {C Burge and S Karlin},
    Journal = {Journal of Molecular Biology},
    Number = {1},
    Pages = {78--94},
    Title = {{Prediction of complete gene structures in human genomic DNA}},
    Volume = {268},
    Year = {1997}}

@article{Campbell1999,
    Author = {A Campbell and J Mrazek and S Karlin},
    Journal = {Proceedings of the National Academy of Sciences USA},
    Number = {16},
    Pages = {9184--9189},
    Title = {Genome signature comparisons among prokaryote, plasmid and mitochondrial {DNA}},
    Volume = {96},
    Year = {1999}}

@Article{Carr2006,
  author = 	 {M Carr and S Devadoss},
  title = 	 {Coxeter complexes and graph associahedra},
  journal = 	 {Topology and its applications},
  year = 	 {2006},
  OPTkey = 	 {},
  volume = 	 {153},
  OPTnumber = 	 {},
  pages = 	 {2155--2168},
  OPTmonth = 	 {},
  OPTnote = 	 {},
  OPTannote = 	 {}
}

@misc{Casanellas2004,
    Author = {M Casanellas and LD Garcia and S Sullivant},
    Howpublished = {\url{http://www.math.tamu.edu/~lgp/small-trees/}},
    Title = {Small Phylogenetic trees},
    Year = {2004}}

@article{Catalisano2002,
    Author = {MV Catalisano and AV Geramita and A Gimigliano},
    Fjournal = {Linear Algebra and its Applications},
    Journal = {Linear Algebra Appl.},
    Pages = {263--285},
    Title = {Ranks of tensors, secant varieties of {S}egre varieties and fat points},
    Volume = {355},
    Year = {2002}}

@article{Catanese2005,
    Author = {F Catanese and S Ho{\c{s}}ten and A Khetan and B Sturmfels},
    Date-Modified = {2005-02-05 12:49:27 -0800},
    Journal = {American Journal of Mathematics},
    Note = {To appear},
    Title = {The maximum likelihood degree},
    Year = {2005}}



@article{Cavalli-Sforza1967,
    Author = {L Cavalli-Sforza and A Edwards},
    Date-Modified = {2005-03-01 20:03:56 -0500},
    Journal = {Evolution},
    Pages = {550--570},
    Title = {Phylogenetic analysis models and estimation procedures},
    Volume = {32},
    Year = {1967}}

@article{Cavender87,
    Author = {J Cavender and J Felsenstein},
    Journal = {Journal of Classification},
    Pages = {57--71},
    Title = {Invariants of phylogenies in a simple case with discrete states},
    Volume = {4},
    Year = {1987}}

@article{Cawley2003,
    Abstract = {SLAM is a program that simultaneously aligns and annotates pairs of homologous sequences. The SLAM web server integrates SLAM with repeat masking tools and the AVID alignment program to allow for rapid alignment and gene prediction in user submitted sequences. Along with annotations and alignments for the submitted sequences, users obtain a list of predicted conserved non-coding sequences (and their associated alignments). The web site also links to whole genome annotations of the human, mouse and rat genomes produced with the SLAM program. The server can be accessed at http://bio.math.berkeley.edu/slam.},
    Affiliation = {Affymetrix Inc., 6550 Vallejo St, Suite 100, Emeryville, CA 94608, USA. simon_cawley@affymetrix.com},
    Au = {Alexandersson M},
    Author = {S Cawley and L Pachter and M Alexandersson},
    Da = {20030625},
    Date-Modified = {2005-02-05 12:49:27 -0800},
    Dcom = {20030818},
    Edat = {2003/06/26 05:00},
    Gr = {R01-HG02362-01/HG/NHGRI},
    Jid = {0411011},
    Journal = {Nucleic Acids Research},
    Keywords = {Algorithms and Amino Acid Sequence and Animals and Base Sequence and Conserved Sequence and Gene Components and Genomics/*methods and Humans and Internet and Markov Chains and Mice and Peptides/chemistry and RNA, Messenger/chemistry and RNA, Untranslated/chemistry and Rats and Research Support, Non-U.S. Gov't and Research Support, U.S. Gov't, P.H.S. and Sequence Alignment/*methods and Sequence Analysis, DNA/*methods and *Software},
    Language = {eng},
    Lr = {20041117},
    Mhda = {2003/08/19 05:00},
    Number = {13},
    Own = {NLM},
    Pages = {3507--9},
    Pl = {England},
    Pmid = {12824355},
    Pst = {ppublish},
    Pt = {Journal Article},
    Pubm = {Print},
    Rn = {0 (RNA, Untranslated)},
    Sb = {IM},
    So = {Nucleic Acids Res 2003 Jul 1;31(13):3525-6.},
    Stat = {MEDLINE},
    Title = {{SLAM} web server for comparative gene finding and alignment.},
    Volume = {31},
    Year = {2003}}

@article{Cawley2003a,
    Abstract = {The standard method of applying hidden Markov models to biological problems is to find a Viterbi (maximal weight) path through the HMM graph. The Viterbi algorithm reduces the problem of finding the most likely hidden state sequence that explains given observations, to a dynamic programming problem for corresponding directed acyclic graphs. For example, in the gene finding application, the HMM is used to find the most likely underlying gene structure given a DNA sequence. In this note we discuss the applications of sampling methods for HMMs. The standard sampling algorithm for HMMs is a variant of the common forward-backward and backtrack algorithms, and has already been applied in the context of Gibbs sampling methods. Nevetheless, the practice of sampling state paths from HMMs does not seem to have been widely adopted, and important applications have been overlooked. We show how sampling can be used for finding alternative splicings for genes, including alternative splicings that are conserved between genes from related organisms. We also show how sampling from the posterior distribution is a natural way to compute probabilities for predicted exons and gene structures being correct under the assumed model. Finally, we describe a new memory efficient sampling algorithm for certain classes of HMMs which provides a practical sampling alternative to the Hirschberg algorithm for optimal alignment. The ideas presented have applications not only to gene finding and HMMs but more generally to stochastic context free grammars and RNA structure prediction. Key words: suboptimal parses, sampling, hidden Markov model, conserved alternative splicing Contact: lpachter@math.berkeley.edu},
    Affiliation = {Affymetrix, 6550 Vallejo St Suite 100, Emeryville, CA 94608, USA Department of Mathematics, U.C. Berkeley, CA 94720, USA.},
    Au = {Pachter L},
    Author = {S Cawley and L Pachter},
    Da = {20031009},
    Date-Modified = {2005-02-05 12:49:26 -0800},
    Edat = {2003/10/10 05:00},
    Jid = {9808944},
    Journal = {Bioinformatics},
    Language = {eng},
    Mhda = {2003/10/10 05:00},
    Number = {1367-4803},
    Own = {NLM},
    Pages = {II36--II41},
    Pl = {England},
    Pmid = {14534169},
    Pst = {ppublish},
    Pt = {Journal Article},
    Pubm = {Print},
    Sb = {IM},
    So = {Bioinformatics 2004 Aug 12;20(12):1850-60. Epub 2004 Feb 26.},
    Stat = {In-Data-Review},
    Title = {{HMM} sampling and applications to gene finding and alternative splicing.},
    Volume = {19 Suppl 2},
    Year = {2003}}

@article{Chakrabarti2004,
    Abstract = {We introduce a novel genome browser application, the K-BROWSER, that allows intuitive visualization of biological information across an arbitrary number of multiply aligned genomes. In particular, the K-BROWSER simultaneously displays an arbitrary number of genomes both through overlaid annotations and predictions that describe their respective characteristics, and through the multiple alignment that describes their global relationship to one another. The browsing environment has been designed to allow users seamless access to information available in every genome and, furthermore, to allow easy navigation within and between genomes. As of the date of publication, the K-BROWSER has been set up on the human, mouse, and rat genomes.},
    Affiliation = {Department of Computer Science, University of California, Berkeley, Berkeley, California 94720, USA.},
    Aid = {14/4/716 {$[$}pii{$]$}},
    Au = {Pachter L},
    Author = {K Chakrabarti and L Pachter},
    Da = {20040402},
    Date-Modified = {2005-02-05 12:49:27 -0800},
    Dcom = {20040505},
    Edat = {2004/04/03 05:00},
    Gr = {R02-HG02362-01/HG/NHGRI},
    Jid = {9518021},
    Journal = {Genome Research},
    Keywords = {Animals and Computational Biology/methods/trends and Computer Graphics/*trends and Conserved Sequence/genetics and *Genome and Genome, Human and Humans and Mice and Rats and Research Support, Non-U.S. Gov't and Research Support, U.S. Gov't, P.H.S. and Sequence Alignment/*methods/trends and Sequence Homology, Nucleic Acid and Software/*trends},
    Language = {eng},
    Lr = {20041117},
    Mhda = {2004/05/07 05:00},
    Number = {4},
    Own = {NLM},
    Pages = {716--20},
    Pl = {United States},
    Pmid = {15060015},
    Pst = {ppublish},
    Pt = {Journal Article},
    Pubm = {Print},
    Sb = {IM},
    So = {Nucleic Acids Res 2004 Jul 1;32(Web Server issue):W273-9.},
    Stat = {MEDLINE},
    Title = {Visualization of multiple genome annotations and alignments with the {K-BROWSER}.},
    Volume = {14},
    Year = {2004}}

@article{Chargaff1950,
    Author = {E Chargaff},
    Date-Modified = {2005-02-05 12:49:26 -0800},
    Journal = {Experientia},
    Pages = {201--209},
    Title = {Chemical specificity of nucleic acids and mechanism for the enzymatic degradation},
    Volume = {6},
    Year = {1950}}

@inproceedings{Chazelle1991,
    Author = {B Chazelle},
    Booktitle = {Proceedings of the 32nd IEEE Symposium on Foundations of Computer Science},
    Pages = {29--38},
    Title = {An Optimal Convex Hull Algorithm and New Results on Cuttings},
    Year = {1991}}

@article{Chazelle1993,
    Author = {B Chazelle},
    Journal = {Discrete Computational Geometry},
    Pages = {377--409},
    Title = {An optimal convex hull algorithm in any fixed dimension},
    Volume = {10},
    Year = {1993}}

@Article{Chepoi1997,
  author = 	 {V Chepoi and B Fichet},
  title = 	 {Recognition of Robinsonian dissimilarities},
  journal = 	 {Journal of Classification},
  year = 	 {1997},
  OPTkey = 	 {},
  volume = 	 {14},
  OPTnumber = 	 {2},
  pages = 	 {1432--1343},
  OPTmonth = 	 {January},
  OPTnote = 	 {},
  OPTannote = 	 {}
}

@Article{Chepoi1998,
  author = 	 {V Chepoi and B Fichet},
  title = 	 {A note on circular decomposable metrics},
  journal = 	 {Geometrica Dedicata},
  year = 	 {1998},
  OPTkey = 	 {},
  volume = 	 {69},
  OPTnumber = 	 {},
  pages = 	 {237--240},
  OPTmonth = 	 {},
  OPTnote = 	 {},
  OPTannote = 	 {}
}

@InProceedings{Chiaromonte2002,
  author =   {F Chiaromonte and VB Yap and W Miller},
  title =    {Scoring pairwise genomic sequence alignments},
  OPTcrossref =  {},
  OPTkey =   {},
  booktitle = {Proceedings of the Pacific Symposium on Biocomputing},
  pages =    {115--126},
  year =     {2002},
  OPTeditor =    {},
  OPTvolume =    {},
  OPTnumber =    {},
  OPTseries =    {},
  OPTaddress =   {},
  OPTmonth =     {},
  OPTorganization = {},
  OPTpublisher = {},
  OPTnote =      {},
  OPTannote =    {}
}

@incollection{Chickering1996,
    Author = {DM Chickering},
    Booktitle = {Learning from Data: Artificial Intelligence and Statistics V},
    Date-Modified = {2005-02-05 12:49:26 -0800},
    Editor = {D Fisher and H-J Lenz},
    Publisher = {Springer Verlag},
    Title = {Learning {B}ayesian Networks is {NP}-complete},
    Year = {1996}}

@article{Chor2000,
    Author = {B Chor and MD Hendy and BR Holland and D Penny},
    Date-Modified = {2005-02-05 12:49:26 -0800},
    Journal = {Molecular Biology and Evolution},
    Pages = {1529--1541},
    Title = {Multiple maxima of likelihood in phylogenetic trees: an analytic approach},
    Volume = {17},
    Year = {2000}}

@InProceedings{Christopher1996,
  author = 	 {G Christopher and M Farach and M Trick},
  title = 	 {The structure of circular decomposable metrics},
  OPTcrossref =  {},
  OPTkey = 	 {},
  booktitle = {Lecture Notes in Computer Science},
  pages = 	 {406--418},
  year = 	 {1996},
  OPTeditor = 	 {},
  volume = 	 {1136},
  OPTnumber = 	 {},
  OPTseries = 	 {},
  OPTaddress = 	 {},
  OPTmonth = 	 {},
  OPTorganization = {},
  publisher = {Springer, New York},
  OPTnote = 	 {},
  OPTannote = 	 {}
}

@PhdThesis{Christopher1997,
  author = 	 {G Christopher},
  title = 	 {Structure and applications of totally decomposable metrics},
  school = 	 {Carnegie Mellon University},
  year = 	 {1997},
  OPTkey = 	 {},
  OPTtype = 	 {},
  OPTaddress = 	 {},
  OPTmonth = 	 {},
  OPTnote = 	 {},
  OPTannote = 	 {}
}

@article{Cohen1993,
    Author = {JE Cohen and UG Rothblum},
    Coden = {LAAPAW},
    Fjournal = {Linear Algebra and its Applications},
    Issn = {0024-3795},
    Journal = {Linear Algebra Appl.},
    Mrclass = {15A48 (15A23)},
    Mrnumber = {MR1230356 (94i:15015)},
    Mrreviewer = {Thomas L. Markham},
    Pages = {149--168},
    Title = {Nonnegative ranks, decompositions, and factorizations of nonnegative matrices},
    Volume = {190},
    Year = {1993}}

@article{Cohen2004,
    Affiliation = {Laboratory of Populations, Rockefeller and Columbia Universities, New York, New York, USA. cohen@rockefeller.edu},
    Aid = {10.1371/journal.pbio.0020439 {$[$}doi{$]$}},
    Au = {Cohen JE},
    Author = {JE Cohen},
    Da = {20041214},
    Edat = {2004/12/15 09:00},
    Jid = {101183755},
    Journal = {PLoS Biol},
    Language = {eng},
    Mhda = {2004/12/15 09:00},
    Number = {12},
    Own = {NLM},
    Pages = {e439},
    Pl = {United States},
    Pmid = {15597117},
    Pst = {ppublish},
    Pt = {Journal Article},
    Pubm = {Print},
    Sb = {IM},
    Stat = {In-Process},
    Title = {Mathematics is biology's next microscope, only better; biology is mathematics' next physics, only better.},
    Volume = {2},
    Year = {2004}}

@Misc{Concorde,
  key = 	 {Concorde},
  author = 	 {D Applegate and R Bixby and V Chvatal and W Cook},
  title = 	 {{The Concorde TSP solver}},
 howpublished = {{\tt http://www.tsp.gatech.edu/concorde.html/}},
  OPTmonth = 	 {},
  OPTyear = 	 {},
  OPTnote = 	 {},
  OPTannote = 	 {}
}

@InCollection{Contois2005,
  author = 	 {M Contois and D Levy},
  title = 	 {Small trees and generalized neighbor-joining},
  booktitle = 	 {Algebraic Statistics for Computational Biology},
  OPTcrossref =  {},
  OPTkey = 	 {},
  pages = 	 {333--344},
  publisher = {Cambridge University Press},
  year = 	 {2005},
  editor = 	 {L Pachter and B Sturmfels},
  OPTvolume = 	 {},
  OPTnumber = 	 {},
  OPTseries = 	 {},
  OPTtype = 	 {},
  chapter = 	 {18},
  OPTaddress = 	 {},
  OPTedition = 	 {},
  OPTmonth = 	 {},
  OPTnote = 	 {},
  OPTannote = 	 {}
}

@article{Couronne2003,
    Abstract = {The availability of the assembled mouse genome makes possible, for the first time, an alignment and comparison of two large vertebrate genomes. We investigated different strategies of alignment for the subsequent analysis of conservation of genomes that are effective for assemblies of different quality. These strategies were applied to the comparison of the working draft of the human genome with the Mouse Genome Sequencing Consortium assembly, as well as other intermediate mouse assemblies. Our methods are fast and the resulting alignments exhibit a high degree of sensitivity, covering more than 90% of known coding exons in the human genome. We obtained such coverage while preserving specificity. With a view towards the end user, we developed a suite of tools and Web sites for automatically aligning and subsequently browsing and working with whole-genome comparisons. We describe the use of these tools to identify conserved non-coding regions between the human and mouse genomes, some of which have not been identified by other methods.},
    Affiliation = {Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA.},
    Aid = {10.1101/gr.762503 {$[$}doi{$]$}},
    Au = {Pachter L},
    Author = {O Couronne and A Poliakov and N Bray and T Ishkhanov and D Ryaboy and E Rubin and L Pachter and I Dubchak},
    Da = {20030116},
    Date-Modified = {2005-02-05 12:49:27 -0800},
    Dcom = {20030317},
    Edat = {2003/01/17 04:00},
    Jid = {9518021},
    Journal = {Genome Research},
    Keywords = {Algorithms and Animals and Chromosomes/genetics and Chromosomes, Human/genetics and Comparative Study and Computer Communication Networks/instrumentation and Databases, Genetic and *Genome and *Genome, Human and Humans and Internet/instrumentation and Mice and *Research Design and Research Support, U.S. Gov't, Non-P.H.S. and Research Support, U.S. Gov't, P.H.S. and Sequence Alignment/*instrumentation/*methods and Software},
    Language = {eng},
    Lr = {20041117},
    Mhda = {2003/03/18 04:00},
    Number = {1},
    Own = {NLM},
    Pages = {73--80},
    Pl = {United States},
    Pmid = {12529308},
    Pst = {ppublish},
    Pt = {Journal Article},
    Pubm = {Print},
    Sb = {IM},
    So = {Genome Res 2003 Jan;13(1):97-102.},
    Stat = {MEDLINE},
    Title = {Strategies and tools for whole-genome alignments.},
    Volume = {13},
    Year = {2003}}

@book{Cover1991,
    Author = {TM Cover and JA Thomas},
    Date-Modified = {2005-02-05 12:49:26 -0800},
    Publisher = {Wiley},
    Title = {Elements of Information Theory},
    Year = {1991}}

@book{Cowell1999,
    Address = {New York},
    Author = {RG Cowell and AP Dawid and SL Lauritzen and DJ Spiegelhalter},
    Publisher = {Springer-Verlag},
    Series = {Statistics for Engineering and Information Sciences},
    Title = {Probabilistic Networks and Expert Systems},
    Year = {1999}}

@book{Cox1997,
    Address = {New York},
    Author = {D Cox and J Little and D O'Shea},
    Date-Modified = {2005-02-05 13:01:41 -0800},
    Edition = {Second},
    Isbn = {0-387-94680-2},
    Mrclass = {13P10 (13-01 14-01 14Qxx 68Q40)},
    Mrnumber = {MR1417938 (97h:13024)},
    Note = {An introduction to computational algebraic geometry and commutative algebra},
    Pages = {xiv+536},
    Publisher = {Springer-Verlag},
    Series = {Undergraduate Texts in Mathematics},
    Title = {Ideals, Varieties, and Algorithms},
    Year = {1997}}

@article{Craciun2005,
    Author = {G Craciun and M Feinberg},
    Journal = {SIAM Journal of Applied Mathematics},
    Note = {To appear},
    Title = {Multiple Equilibria in Complex Chemical Reaction Networks: I. The Injectivity Property},
    Year = {2005}}

@article{Cuyt2001,
    Author = {A Cuyt and B Verdonk and S Becuwe and P Kuterna},
    Date-Modified = {2005-02-05 12:49:26 -0800},
    Journal = {Computing},
    Pages = {309--320},
    Title = {A remarkable example of catastrophic cancellation unraveled},
    Volume = {66},
    Year = {2001}}

@article{Darling2004,
    Author = {ACE Darling and B Mau and FR Blattner and NT Perna},
    Journal = {Genome Research},
    Pages = {1394--1403},
    Title = {{Mauve: multiple alignment of conserved genomic sequence with rearrangements}},
    Volume = {14},
    Year = {2004}}



@book{Darwin1859,
    Author = {C Darwin},
    Date-Modified = {2005-02-05 12:49:26 -0800},
    Publisher = {John Murray, London},
    Title = {On the Origin of Species by Means of Natural Selection, or the Preservation of Favoured Races in the Struggle for Life},
    Year = {1859}}

@book{Davey2002,
    Address = {New York},
    Author = {BA Davey and HA Priestley},
    Date-Modified = {2005-02-05 12:49:26 -0800},
    Edition = {Second},
    Publisher = {Cambridge University Press},
    Title = {Introduction to Lattices and Order},
    Year = {2002}}

@book{DeConcini1982,
    Address = {Paris},
    Author = {C DeConcini and D Eisenbud and C Procesi},
    Mrclass = {13B99 (13-04 13D10 14M15)},
    Mrnumber = {MR680936 (85d:13009)},
    Mrreviewer = {Melvin Hochster},
    Note = {With a French summary},
    Pages = {87},
    Publisher = {Soci\'et\'e Math\'ematique de France},
    Series = {Ast\'erisque},
    Title = {Hodge algebras},
    Volume = {91},
    Year = {1982}}

@book{DeGroot1970,
    Address = {New York},
    Author = {MH DeGroot},
    Date-Modified = {2005-02-05 12:49:26 -0800},
    Publisher = {McGraw-Hill},
    Title = {Optimal Statistical Decisions},
    Year = {1970}}

@Article{Deineko1998,
  author = 	 {VG Deineko and R Rudolf and GJ Woeginger},
  title = 	 {Sometimes traveling is easy: the master tour problem},
  journal = 	 {SIAM Journal of Discrete Mathematics},
  year = 	 {1998},
  OPTkey = 	 {},
  volume = 	 {11},
  OPTnumber = 	 {1},
  pages = 	 {81--93},
  OPTmonth = 	 {},
  OPTnote = 	 {},
  OPTannote = 	 {}
}

@article{Delcher1999,
    Author = {AL Delcher and S Kasif and RD Fleischmann and J Peterson and O White and AL Salzberg},
    Date-Modified = {2005-02-05 12:49:26 -0800},
    Journal = {Nucleic Acids Research},
    Pages = {2369--2376},
    Title = {Alignment of whole genomes},
    Volume = {27},
    Year = {1999}}

@book{Demmel1997,
    Address = {Philadelphia, PA},
    Author = {JW Demmel},
    Isbn = {0-89871-389-7},
    Mrclass = {65-01 (65Fxx)},
    Mrnumber = {MR1463942 (98m:65001)},
    Mrreviewer = {William W. Hager},
    Pages = {xii+419},
    Publisher = {Society for Industrial and Applied Mathematics (SIAM)},
    Title = {Applied Numerical Linear Algebra},
    Year = {1997}}

@article{Dempster1977,
    Author = {AP Dempster and NM Laird and DB Rubin},
    Journal = {Journal of the Royal Statistical Society},
    Pages = {1--38},
    Title = {Maximum Likelihood from Incomplete Data via the {EM} Algorithm},
    Volume = {39},
    Year = {1977}}

@article{Dermitzakis2003,
    Author = {ET Dermitzakis and A Reymond and N Scamuffa and C Ucla and E Kirkness and C Rossier and SE Antonarakis},
    Date-Modified = {2005-02-05 12:49:26 -0800},
    Journal = {Science},
    Pages = {1033--1035},
    Title = {Evolutionary Discrimination of Mammalian Conserved Non-Genic Sequences ({CNG}s)},
    Volume = {302},
    Year = {2003}}

@article{Desper1999,
    Author = {R Desper and F Jiang and O-P Kallioniemi and H Moch and CH Papadimitriou and AA Sch{\"a}ffer},
    Date-Modified = {2005-02-05 12:49:26 -0800},
    Journal = {Journal of Computational Biology},
    Number = {1},
    Pages = {37--51},
    Title = {Inferring tree models for oncogenesis from comparative genome hybridization data},
    Volume = {6},
    Year = {1999}}

@Article{Desper2002,
  author = 	 {R Desper and O Gascuel},
  title = 	 {Fast and accurate phylogeny reconstruction algorithms based on the minimum-evolution principle},
  journal = 	 {Journal of Computational Biology},
  year = 	 {2002},
  OPTkey = 	 {},
  volume = 	 {19},
  number = 	 {5},
  pages = 	 {687--705},
  OPTmonth = 	 {},
  OPTnote = 	 {},
  OPTannote = 	 {}
}

@Article{Desper2004,
  author = 	 {R Desper and O Gascuel},
  title = 	 {Theoretical foundation of the balanced minimum evolution method of phylogenetic inference and its relationship to weighted least-squares tree fitting},
  journal = 	 {Molecular Biology and Evolution},
  year = 	 {2004},
  OPTkey = 	 {},
  volume = 	 {21},
  OPTnumber = 	 {},
  pages = 	 {587--598},
  OPTmonth = 	 {},
  OPTnote = 	 {},
  OPTannote = 	 {}
}

@InCollection{Desper2005,
  author =   {R Desper and O Gascuel},
  title =    {The minimum evolution distance-based approach to phylogenetic inference},
  booktitle =    {Mathematics of Evolution and Phylogeny},
  OPTcrossref =  {},
  OPTkey =   {},
  OPTpages =     {},
  publisher = {Oxford University Press},
  year =      {2005},
  editor =   {O Gascuel},
  OPTvolume =    {},
  OPTnumber =    {},
  OPTseries =    {},
  OPTtype =      {},
  OPTchapter =   {},
  OPTaddress =   {},
  OPTedition =   {},
  OPTmonth =     {},
  OPTnote =      {},
  OPTannote =    {}
}

@Article{Devadoss1999,
  author = 	 {S Devadoss},
  title = 	 {Tessellations of moduli spaces and the mosaic operad},
  journal = 	 {Contemporary mathematics},
  year = 	 {1999},
  OPTkey = 	 {},
  volume = 	 {239},
  OPTnumber = 	 {},
  pages = 	 {91--114},
  OPTmonth = 	 {},
  OPTnote = 	 {},
  OPTannote = 	 {}
}

@Article{Devadoss2004,
  author = 	 {S Devadoss},
  title = 	 {Combinatorial equivalence of real moduli spaces},
  journal = 	 {Notices of the American Mathematical Society},
  year = 	 {2004},
  OPTkey = 	 {},
  volume = 	 {51},
  OPTnumber = 	 {},
  pages = 	 {620--628},
  OPTmonth = 	 {},
  OPTnote = 	 {},
  OPTannote = 	 {}
}

@article{Develin2003,
    Author = {M Develin and F Santos and B Sturmfels},
    Journal = {MSRI Proceedings},
    Note = {To appear},
    Title = {On the tropical rank of a matrix},
    Year = {2003}}

@article{Develin2004,
    Author = {M Develin and B Sturmfels},
    Date-Modified = {2005-02-05 12:58:09 -0800},
    Fjournal = {Documenta Mathematica},
    Issn = {1431-0643},
    Journal = {Documenta Mathematica},
    Mrclass = {52A30 (52B10)},
    Mrnumber = {MR2054977},
    Pages = {1--27 (electronic)},
    Title = {Tropical convexity},
    Volume = {9},
    Year = {2004}}

@article{Dewey2004,
    Abstract = {We describe a new method for simultaneously identifying novel homologous genes with identical structure in the human, mouse, and rat genomes by combining pairwise predictions made with the SLAM gene-finding program. Using this method, we found 3698 gene triples in the human, mouse, and rat genomes which are predicted with exactly the same gene structure. We show, both computationally and experimentally, that the introns of these triples are predicted accurately as compared with the introns of other ab initio gene prediction sets. Computationally, we compared the introns of these gene triples, as well as those from other ab initio gene finders, with known intron annotations. We show that a unique property of SLAM, namely that it predicts gene structures simultaneously in two organisms, is key to producing sets of predictions that are highly accurate in intron structure when combined with other programs. Experimentally, we performed reverse transcription-polymerase chain reaction (RT-PCR) in both the human and rat to test the exon pairs flanking introns from a subset of the gene triples for which the human gene had not been previously identified. By performing RT-PCR on orthologous introns in both the human and rat genomes, we additionally explore the validity of using RT-PCR as a method for confirming gene predictions.},
    Affiliation = {Department of Electrical Engineering, University of California-Berkeley, Berkeley, California 94720, USA.},
    Aid = {14/4/661 {$[$}pii{$]$}},
    Au = {Pachter L},
    Author = {C Dewey and JQ Wu and S Cawley and M Alexandersson and R Gibbs and L Pachter},
    Da = {20040402},
    Date-Modified = {2005-02-05 12:49:26 -0800},
    Dcom = {20040505},
    Edat = {2004/04/03 05:00},
    Gr = {R01 HG2362-2/HG/NHGRI},
    Jid = {9518021},
    Journal = {Genome Research},
    Keywords = {Animals and Chromosome Mapping/methods and Comparative Study and Computational Biology/methods and Databases, Genetic and Exons/genetics and Genes, Structural/*genetics and Genome and Genome, Human and Humans and Introns/genetics and Mice and Predictive Value of Tests and Rats and Research Support, U.S. Gov't, P.H.S. and Sequence Homology, Nucleic Acid and Software},
    Language = {eng},
    Lr = {20041117},
    Mhda = {2004/05/07 05:00},
    Number = {4},
    Own = {NLM},
    Pages = {661--4},
    Pl = {United States},
    Pmid = {15060007},
    Pst = {ppublish},
    Pt = {Journal Article},
    Pubm = {Print},
    Sb = {IM},
    So = {Genome Res 2004 Apr;14(4):693--9.},
    Stat = {MEDLINE},
    Title = {Accurate identification of novel human genes through simultaneous gene prediction in human, mouse, and rat.},
    Volume = {14},
    Year = {2004}}

@misc{Dewey2005,
    Author = {C Dewey},
    Howpublished = {Software available at \url{http://hanuman.math.berkeley.edu/~cdewey/mercator/}},
    Title = {{MERCATOR}: multiple whole-genome orthology map construction},
    Year = {2005}}

@book{Deza1997,
    Address = {Berlin},
    Author = {MM Deza and M Laurent},
    Isbn = {3-540-61611-X},
    Mrclass = {52-02 (05B30 05C12 51K05 52B12 52C07 68R05 90C28)},
    Mrnumber = {MR1460488 (98g:52001)},
    Mrreviewer = {Alexander I. Barvinok},
    Pages = {xii+587},
    Publisher = {Springer-Verlag},
    Series = {Algorithms and Combinatorics},
    Title = {Geometry of Cuts and Metrics},
    Volume = {15},
    Year = {1997}}

@Book{Deza2006,
  author = 	 {E Deza and MM Deza},
  ALTeditor = 	 {},
  title = 	 {Dictionary of Distances},
  publisher = 	 {Elsevier},
  year = 	 {2006},
  OPTkey = 	 {},
  OPTvolume = 	 {},
  OPTnumber = 	 {},
  OPTseries = 	 {},
  OPTaddress = 	 {},
  OPTedition = 	 {},
  OPTmonth = 	 {},
  OPTnote = 	 {},
  OPTannote = 	 {}
}

@InBook{Diday1986,
  author = 	 {E Diday},
  editor = 	 {J De Leeuw et al.},
  title = 	 {Multidimensional data analysis},
  chapter = 	 {Orders and overlapping clusters by pyramids},
  publisher = 	 {DWO Press, Leiden},
  year = 	 {1986},
  OPTkey = 	 {},
  OPTvolume = 	 {},
  OPTnumber = 	 {},
  OPTseries = 	 {},
  OPTtype = 	 {},
  OPTaddress = 	 {},
  OPTedition = 	 {},
  OPTmonth = 	 {},
  pages = 	 {201--234},
  OPTnote = 	 {},
  OPTannote = 	 {}
}

@Article{Dilworth1950,
  author = 	 {RP Dilworth},
  title = 	 {A decomposition theorem for partially ordered sets},
  journal = 	 {The Annals of Mathematics},
  year = 	 {1950},
  OPTkey = 	 {},
  volume = 	 {51},
  OPTnumber = 	 {},
  pages = 	 {161--166},
  OPTmonth = 	 {},
  OPTnote = 	 {},
  OPTannote = 	 {}
}

@article{Douzery2003,
    Author = {EJP Douzery and F Delsuc and MJ Stanhope and D Huchon},
    Journal = {Molecular Biology and Evolution},
    Pages = {201-213},
    Title = {Local molecular clocks in three nuclear genes: divergence ages of rodents and other mammals, and incompatibility between fossil calibrations},
    Volume = {57},
    Year = {2003}}

@Article{Dress1996,
  author = 	 {A Dress and V Moulton and W Terhalle},
  title = 	 {T-theory: an overview},
  journal = 	 {European Journal Combinatorics},
  year = 	 {1996},
  OPTkey = 	 {},
  volume = 	 {17},
  OPTnumber = 	 {},
  pages = 	 {161--175},
  OPTmonth = 	 {},
  OPTnote = 	 {},
  OPTannote = 	 {}
}

@InCollection{Dress1997,
  author = 	 {A Dress},
  title = 	 {Towards a theory of holistic clustering},
  booktitle = 	 {Mathematical Hierarchies and Biology},
  OPTcrossref =  {},
  OPTkey = 	 {},
  OPTpages = 	 {},
  publisher = {DIMACS},
  year = 	 {1997},
  OPTeditor = 	 {},
  OPTvolume = 	 {},
  OPTnumber = 	 {},
  OPTseries = 	 {},
  OPTtype = 	 {},
  OPTchapter = 	 {},
  OPTaddress = 	 {},
  OPTedition = 	 {},
  OPTmonth = 	 {},
  OPTnote = 	 {},
  OPTannote = 	 {}
}

@inproceedings{Dress1998,
    Author = {A Dress and W Terhalle},
    Booktitle = {Proceedings of the International Congress of Mathematicians},
    Fjournal = {Documenta Mathematica},
    Issn = {1431-0643},
    Journal = {Documenta Mathematica},
    Mrclass = {05B35 (05C05 92B10 92D15)},
    Mrnumber = {MR1648188 (99k:05051)},
    Mrreviewer = {Charles A. Semple},
    Number = {Extra Vol. III},
    Pages = {565--574 (electronic)},
    Series = {Vol. III (Berlin, 1998)},
    Title = {The tree of life and other affine buildings},
    Year = {1998}}

@article{Dress2002,
    Author = {A Dress and JH Koolen and V Moulton},
    Fjournal = {European Journal of Combinatorics},
    Issn = {0195-6698},
    Journal = {European Journal of Combinatorics},
    Mrclass = {52C30 (51M10)},
    Mrnumber = {MR1931939 (2003h:52024)},
    Number = {5},
    Pages = {549--557},
    Title = {On line arrangements in the hyperbolic plane},
    Volume = {23},
    Year = {2002}}

@Article{Dress2004,
  author = 	 {A Dress and DH Huson},
    Journal = {IEEE/ACM Transactions in Computational Biology and Bioinformatics},
  title = 	 {Constructing splits graphs},
  year = 	 {2004},
  OPTkey = 	 {},
  volume = 	 {1},
  OPTnumber = 	 {3},
  pages = 	 {109--115},
  OPTmonth = 	 {},
  OPTnote = 	 {},
  OPTannote = 	 {}
}

@Article{Dress2007,
  author = 	 {A Dress and KT Huber and V Moulton},
  title = 	 {Some uses of the Farris transform in mathematics and phylogenetics-- a review},
  journal = 	 {Annals of Combinatorics},
  year = 	 {2007},
  OPTkey = 	 {},
  volume = 	 {11},
  OPTnumber = 	 {},
  pages = 	 {1--37},
  OPTmonth = 	 {},
  OPTnote = 	 {},
  OPTannote = 	 {}
}

@Article{Drysdale2005,
  author =   {RA Drysdale and MA Crosby and {The Flybase Consortium}},
  title =    {{Flybase: Genes and gene models}},
  journal =      {Nucleic Acids Research},
  year =     {2005},
  OPTkey =   {},
  volume =   {33},
  OPTnumber =    {},
  pages =    {D390--D395},
  OPTmonth =     {},
  OPTnote =      {},
  OPTannote =    {}
}

@article{Dubchak2000,
    Abstract = {Human and mouse genomic sequence comparisons are being increasingly used to search for evolutionarily conserved gene regulatory elements. Large-scale human-mouse DNA comparison studies have discovered numerous conserved noncoding sequences of which only a fraction has been functionally investigated A question therefore remains as to whether most of these noncoding sequences are conserved because of functional constraints or are the result of a lack of divergence time.},
    Affiliation = {Center for Bioinformatics and Computational Genomics, Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA.},
    Au = {Frazer KA},
    Author = {I Dubchak and M Brudno and GG Loots and L Pachter and C Mayor and EM Rubin and KA Frazer},
    Da = {20001017},
    Date-Modified = {2005-02-05 12:49:26 -0800},
    Dcom = {20001017},
    Edat = {2000/09/14 11:00},
    Gr = {GM-5748202/GM/NIGMS},
    Jid = {9518021},
    Journal = {Genome Research},
    Keywords = {Animals and Comparative Study and Conserved Sequence/*genetics and Dogs and Humans and Mice and Molecular Sequence Data and Research Support, U.S. Gov't, Non-P.H.S. and Research Support, U.S. Gov't, P.H.S. and *Sequence Alignment and Species Specificity and Untranslated Regions/*genetics/isolation \& purification},
    Language = {eng},
    Lr = {20041117},
    Mhda = {2000/10/21 11:01},
    Number = {9},
    Own = {NLM},
    Pages = {1304--6},
    Pl = {UNITED STATES},
    Pmid = {10984448},
    Pst = {ppublish},
    Pt = {Journal Article},
    Pubm = {Print},
    Rn = {0 (Untranslated Regions)},
    Sb = {IM},
    Si = {GENBANK/AF276990},
    So = {Bioinformatics 2000 Nov;16(11):1046-7.},
    Stat = {MEDLINE},
    Title = {Active conservation of noncoding sequences revealed by three-way species comparisons.},
    Volume = {10},
    Year = {2000}}

@article{Dubchak2002,
    Abstract = {The explosion in genomic sequence available in public databases has resulted in an unprecedented opportunity for computational whole genome analyses. A number of promising comparative-based approaches have been developed for gene finding, regulatory element discovery and other purposes, and it is clear that these tools will play a fundamental role in analysing the enormous amount of new data that is currently being generated. The synthesis of computationally intensive comparative computational approaches with the requirement for whole genome analysis represents both an unprecedented challenge and opportunity for computational scientists. We focus on a few of these challenges, using by way of example the problems of alignment, gene finding and regulatory element discovery, and discuss the issues that have arisen in attempts to solve these problems in the context of whole genome analysis pipelines.},
    Affiliation = {Lawrence Berkeley National Laboratory, National Energy Resesarch Scientific Computing Center, CA 94720, USA. ildubchak@lbl.gov},
    Au = {Pachter L},
    Author = {I Dubchak and L Pachter},
    Da = {20020510},
    Date-Modified = {2005-02-05 12:49:27 -0800},
    Dcom = {20021024},
    Edat = {2002/05/11 10:00},
    Jid = {100912837},
    Journal = {Brief Bioinform},
    Keywords = {Comparative Study and *Computational Biology and *Genome and Regulatory Sequences, Nucleic Acid and Research Support, U.S. Gov't, P.H.S.},
    Language = {eng},
    Lr = {20041117},
    Mhda = {2002/10/31 04:00},
    Number = {1},
    Own = {NLM},
    Pages = {18--22},
    Pl = {England},
    Pmid = {12002220},
    Pst = {ppublish},
    Pt = {Journal Article},
    Pubm = {Print},
    Sb = {IM},
    So = {J Comput Biol 2002;9(2):389-99.},
    Stat = {MEDLINE},
    Title = {The computational challenges of applying comparative-based computational methods to whole genomes.},
    Volume = {3},
    Year = {2002}}

@Article{Dunn2005,
  author = 	 {M Dunn and A Terrill and G Reesnik and RA Foley and SC Levinson},
  title = 	 {Structural phylogenetics and reconstruction of ancient language history},
  journal = 	 {Science},
  year = 	 {2005},
  OPTkey = 	 {},
  OPTvolume = 	 {309},
  OPTnumber = 	 {},
  pages = 	 {2072--2075},
  OPTmonth = 	 {},
  OPTnote = 	 {},
  OPTannote = 	 {}
}


@book{Durbin1998,
    Author = {R Durbin and S Eddy and A Korgh and G Mitchison},
    Date-Modified = {2005-02-05 12:49:26 -0800},
    Publisher = {Cambridge University Press},
    Title = {{Biological Sequence Analysis: Probabilistic Models of Proteins and Nucleic Acids}},
    Year = {1998}}

@inproceedings{Eddy1995,
    Author = {SR Eddy},
    Booktitle = {Proceedings Intelligent Systems in Molecular Biology},
    Date-Modified = {2005-02-05 12:49:26 -0800},
    Title = {Multiple alignment using hidden {M}arkov models},
    Year = {1995}}

@book {Edelsbrunner1987,
    AUTHOR = {H Edelsbrunner},
     TITLE = {Algorithms in combinatorial geometry},
    SERIES = {EATCS Monographs on Theoretical Computer Science},
    VOLUME = {10},
 PUBLISHER = {Springer-Verlag},
   ADDRESS = {Berlin},
      YEAR = {1987},
     PAGES = {xvi+423},
      ISBN = {3-540-13722-X},
   MRCLASS = {68U05 (52-04 68Q25)},
  MRNUMBER = {MR904271 (89a:68205)},
MRREVIEWER = {D. T. Lee}}

@article{Eichler2003,
    Author = {EE Eichler and D Sankoff},
    Date-Modified = {2005-02-05 12:49:27 -0800},
    Journal = {Science},
    Pages = {793--797},
    Title = {Structural dynamics of eukaryotic chromosome evolution},
    Volume = {301},
    Year = {2003}}

@book{Eisenbud2002,
    Address = {Berlin},
    Date-Modified = {2005-02-05 12:58:09 -0800},
    Editor = {D Eisenbud and DR Grayson and M Stillman},
    Isbn = {3-540-42230-7},
    Mrclass = {14-04 (13-04 13P10 14Q99 68W30)},
    Mrnumber = {MR1949544 (2004b:14002)},
    Mrreviewer = {Luis Miguel Pardo},
    Pages = {xvi+329},
    Publisher = {Springer-Verlag},
    Series = {Algorithms and Computation in Mathematics},
    Title = {Computations in algebraic geometry with {M}acaulay 2},
    Volume = {8},
    Year = {2002}}

@InProceedings{Elias2005,
  author =   {I Elias and J Lagergren},
  title =    {Fast neighbor joining},
  OPTcrossref =  {},
  OPTkey =   {},
  booktitle = {Proceedings of the International Colloquium on
                  Automata, Languages and Programming (ICALP '05)},
  OPTpages =     {},
  year =     {2005},
  OPTeditor =    {},
  OPTvolume =    {},
  OPTnumber =    {},
  OPTseries =    {},
  OPTaddress =   {},
  OPTmonth =     {},
  OPTorganization = {},
  OPTpublisher = {},
  OPTnote =      {},
  OPTannote =    {}
}

@article{Encode2004,
    Abstract = {The ENCyclopedia Of DNA Elements (ENCODE) Project aims to identify all functional elements in the human genome sequence. The pilot phase of the Project is focused on a specified 30 megabases (approximately 1%) of the human genome sequence and is organized as an international consortium of computational and laboratory-based scientists working to develop and apply high-throughput approaches for detecting all sequence elements that confer biological function. The results of this pilot phase will guide future efforts to analyze the entire human genome.},
    Aid = {10.1126/science.1105136 {$[$}doi{$]$}},
    Author = {{ENCODE} Project Consortium},
    Cn = {ENCODE Project Consortium.},
    Da = {20041022},
    Date-Modified = {2005-02-05 12:50:27 -0800},
    Dcom = {20041122},
    Edat = {2004/10/23 09:00},
    Jid = {0404511},
    Journal = {Science},
    Key = {ENCODE},
    Keywords = {Access to Information and Animals and *Computational Biology and Conserved Sequence and Databases, Nucleic Acid and Evolution, Molecular and *Genome, Human and *Genomics and Humans and Information Dissemination and Internet and National Institutes of Health (U.S.) and Pilot Projects and Proteins/genetics and Publishing and Regulatory Sequences, Nucleic Acid and Research Support, Non-U.S. Gov't and Research Support, U.S. Gov't, P.H.S. and Sequence Analysis, DNA and United States},
    Language = {eng},
    Mhda = {2004/12/16 09:00},
    Number = {5696},
    Own = {NLM},
    Pages = {636--40},
    Pl = {United States},
    Pmid = {15499007},
    Pst = {ppublish},
    Pt = {Journal Article},
    Pubm = {Print},
    Rn = {0 (Proteins)},
    Sb = {IM},
    So = {Nature 2003 Aug 14;424(6950):788-93.},
    Stat = {MEDLINE},
    Title = {{The ENCODE (ENCyclopedia Of DNA Elements) Project}},
    Volume = {306},
    Year = {2004}}

@Article{Erdos1999,
  author = {PL Erd\"{o}s and MA Steel and LA Sz\'{e}kely and TJ
                  Warnow},
  title = {A few logs suffice to build (almost) all trees. {I}},
  journal = {Random Structures and Algorithms},
  year = {1999},
  OPTkey = {},
  volume = {14},
  number = {2},
  pages = {153--184},
  OPTmonth = {},
  OPTnote = {},
  OPTannote = {}
}

@Article{Eriksson2008,
  author = 	 {N Eriksson and L Pachter and Y Mitsuya and S-Y Rhee and C Wang and B Gharizadeh and M Ronaghi and RW Shafer and N Beerenwinkel},
  title = 	 {Viral population estimation using pyrosequencing},
  journal = 	 {PLoS Computational Biology},
  year = 	 {2008},
  OPTkey = 	 {},
  volume = 	 {4},
  OPTnumber = 	 {5},
  pages = 	 {e1000074},
  OPTmonth = 	 {},
  OPTnote = 	 {},
  OPTannote = 	 {}
}

@article{Evans1993,
    Author = {S Evans and T Speed},
    Date-Modified = {2005-02-05 12:49:26 -0800},
    Journal = {The Annals of Statistics},
    Pages = {355--377},
    Title = {Invariants of some probability models used in phylogenetic inference},
    Volume = {21},
    Year = {1993}}

@book{Ewens2005,
    Address = {New York},
    Author = {WJ Ewens and GR Grant},
    Edition = {Second},
    Isbn = {0-387-40082-6},
    Mrclass = {92B15 (60J10 62-01 62F10 62F15 62P10)},
    Mrnumber = {MR2107608},
    Pages = {xx+597},
    Publisher = {Springer-Verlag},
    Series = {Statistics for Biology and Health},
    Title = {Statistical Methods in Bioinformatics: An Introduction},
    Year = {2005}}

@article{Faith1992,
    Author = {DP Faith},
    Journal = {Biological Conservation},
    Pages = {1--10},
    Title = {Conservation evaluation and phylogenetic diversity},
    Volume = {61},
    Year = {1992}}

@article{Farris1972,
    Author = {JS Farris},
    Date-Modified = {2005-03-01 20:04:38 -0500},
    Journal = {American Naturalist},
    Pages = {645--668},
    Title = {Estimating phylogenetic trees from distance matrices},
    Volume = {106},
    Year = {1972}}



@InCollection{Farris1977,
  author = 	 {JS Farris},
  title = 	 {On the phenetic approach to vertebrate classification},
  booktitle = 	 {Major patterns in vertebrate evolution},
  OPTcrossref =  {},
  OPTkey = 	 {},
  pages = 	 {823--950},
  publisher = {Plenum, New York},
  year = 	 {1977},
  OPTeditor = 	 {},
  OPTvolume = 	 {},
  OPTnumber = 	 {},
  OPTseries = 	 {},
  OPTtype = 	 {},
  OPTchapter = 	 {},
  OPTaddress = 	 {},
  OPTedition = 	 {},
  OPTmonth = 	 {},
  OPTnote = 	 {},
  OPTannote = 	 {}
}

@Article{Farris1996,
  author = {JS Farris and VA Albert and M K\"{a}llersj\"{o} and D
                  Lipscomb and AG Kluge},
  title = {Parsimony jackknifing outperforms neighbor-joining},
  journal = {Cladistics},
  year = {1996},
  OPTkey = {},
  volume = {12},
  OPTnumber = {},
  pages = {99--124},
  OPTmonth = {},
  OPTnote = {},
  OPTannote = {}
}

@article{Felsenstein1978,
    Author = {J. Felsenstein},
    Journal = {Syst. Zool.},
    Pages = {240-249},
    Title = {Cases in which parsimony or compatibility methods will be positively misleading},
    Volume = {22},
    Year = {1978}}

@article{Felsenstein1981,
    Author = {J Felsenstein},
    Date-Modified = {2005-02-05 12:49:26 -0800},
    Journal = {Journal of Molecular Evolution},
    Pages = {368--376},
    Title = {Evolutionary trees from {DNA} sequences: a maximum likelihood approach},
    Volume = {17},
    Year = {1981}}

@article{Felsenstein1989,
    Author = {J Felsenstein},
    Journal = {Cladistics},
    Pages = {164--166},
    Title = {{PHYLIP -- Phylogeny Inference Package (Version 3.2)}},
    Volume = {5},
    Year = {1989}}

@book{Felsenstein2003,
    Author = {J Felsenstein},
    Date-Modified = {2005-02-05 12:49:26 -0800},
    Publisher = {Sinauer Associates, Inc.},
    Title = {Inferring Phylogenies},
    Year = {2003}}

@misc{Felsenstein2004,
    Author = {J Felsenstein},
    Date-Modified = {2005-02-05 12:49:27 -0800},
    Howpublished = {Distributed by the author, Department of Genome Sciences, University of Washington, Seattle},
    Title = {{PHYLIP (Phylogeny Inference Package) version 3.6}},
    Year = {2004}}

@article{Fernandez-Baca2000,
    Author = {D Fern\'andez-Baca and T Sepp\"al\"ainen and G Slutzki},
    Date-Modified = {2005-02-25 12:49:26 -0800},
    Journal = {Journal of Discrete Algorithms},
    Number = {2},
    Pages = {271--287},
    Title = {Parametric multiple sequence alignment and phylogeny construction},
    Volume = {2},
    Year = {2004}}

@article{Fernandez-Baca2002,
    Author = {D Fern\'andez-Baca and T Sepp\"al\"ainen and G Slutzki},
    Date-Modified = {2005-02-05 12:49:26 -0800},
    Journal = {Discrete Applied Mathematics},
    Pages = {181--198},
    Title = {Bounds for parametric sequence comparison},
    Volume = {118},
    Year = {2002}}

@article{Fernandez-Baca2004,
    Author = {D Fern\'andez-Baca and T Sepp\"al\"ainen and G Slutzki},
    Date-Modified = {2005-10-16 22:07:46 -0700},
    Journal = {Journal of Discrete Algorithms},
    Number = {2},
    Pages = {271--287},
    Title = {Parametric multiple sequence alignment and phylogeny construction},
    Volume = {2},
    Year = {2004}}

@incollection{Fernandez-Baca2005,
    Author = {D Fern\'andez-Baca and B Venkatachalam},
    Booktitle = {To appear in Handbook of Computational Molecular Biology},
    Date-Added = {2005-10-16 22:08:25 -0700},
    Date-Modified = {2005-10-16 22:10:40 -0700},
    Editor = {S Aluru},
    Pages = {271--287},
    Publisher = {Chapman and Hall/CRC Press Computer and Information Science Series},
    Title = {Parametric sequence alignment},
    Volume = {2},
    Year = {2005, in press}}

@article{Ferrari1995,
    Author = {P Ferrari and A Frigessi and P de Sa},
    Journal = {Journal of the Royal Statistical Society},
    Title = {Fast approximate maximum a posteriori restoration of multi-color images},
    Volume = {B,57},
    Year = {1995}}

@article{Fitch1983,
    Abstract = {Current theory is adequate to the task of finding an optimal alignment between two character strings such as nucleic acids. Most algorithms currently in use must fail to find the homologous alignment between a set of codons for the chicken [alpha] - and {beta} -hemoglobin sequence when it is in fact discoverable by a more general treatment of gaps. Fundamental reasons for this are discussed.
},
    Author = {WM Fitch and TF Smith},
    Journal = {PNAS},
    Number = {5},
    Pages = {1382--1386},
    Title = {{Optimal sequence alignments}},
    Url = {http://www.pnas.org/cgi/content/abstract/80/5/1382},
    Volume = {80},
    Year = {1983}}

@article{Fleischmann1995,
    Author = {RD Fleischmann and MD Adams and O White and RA Clayton and EF Kirkness and AR Kerlavage and CJ Bult and JF Tomb and BA Dougherty and JM Merrick et al.},
    Date-Modified = {2005-02-05 12:49:27 -0800},
    Journal = {Science},
    Number = {5223},
    Pages = {496--512},
    Title = {{Whole-genome random sequencing and assembly of {\it Haemophilus influenza} Rd}},
    Volume = {269},
    Year = {1995}}


@article{Floyd1962,
    Author = {RW Floyd},
    Date-Modified = {2005-02-05 12:49:26 -0800},
    Journal = {Communications of ACM},
    Number = {6},
    Pages = {345},
    Title = {Algorithm 97: shortest path},
    Volume = {5},
    Year = {1962}}


@article{Forney1973,
    Author = {GD Forney},
    Date-Modified = {2005-02-05 12:49:27 -0800},
    Journal = {Procedings of the IEEE},
    Number = {3},
    Pages = {268-278},
    Title = {The {V}iterbi Algorithm},
    Volume = {61},
    Year = {1973}}

@article{Frazer2004,
    Abstract = {Comparison of DNA sequences from different species is a fundamental method for identifying functional elements in genomes. Here, we describe the VISTA family of tools created to assist biologists in carrying out this task. Our first VISTA server at http://www-gsd.lbl.gov/vista/ was launched in the summer of 2000 and was designed to align long genomic sequences and visualize these alignments with associated functional annotations. Currently the VISTA site includes multiple comparative genomics tools and provides users with rich capabilities to browse pre-computed whole-genome alignments of large vertebrate genomes and other groups of organisms with VISTA Browser, to submit their own sequences of interest to several VISTA servers for various types of comparative analysis and to obtain detailed comparative analysis results for a set of cardiovascular genes. We illustrate capabilities of the VISTA site by the analysis of a 180 kb interval on human chromosome 5 that encodes for the kinesin family member 3A (KIF3A) protein.},
    Affiliation = {Perlegen Sciences, Inc., 2021 Stierlin Court, Mountain View, CA 94043, USA.},
    Aid = {32/suppl{\_}2/W273 {$[$}pii{$]$}},
    Au = {Dubchak I},
    Author = {KA Frazer and L Pachter and A Poliakov and EM Rubin and I Dubchak},
    Da = {20040624},
    Date-Modified = {2005-02-05 12:49:27 -0800},
    Dcom = {20040820},
    Edat = {2004/06/25 05:00},
    Jid = {0411011},
    Journal = {Nucleic Acids Research},
    Keywords = {Binding Sites and Chromosomes, Human, Pair 5 and *Computational Biology and Genome, Human and *Genomics and Humans and Internet and Kinesin/genetics and Phylogeny and Regulatory Sequences, Nucleic Acid and Sequence Alignment and Sequence Analysis, DNA and *Software and Transcription Factors/metabolism},
    Language = {eng},
    Lr = {20041117},
    Mhda = {2004/08/21 05:00},
    Number = {Web Server issue},
    Own = {NLM},
    Pages = {W273--9},
    Pl = {England},
    Pmid = {15215394},
    Pst = {ppublish},
    Pt = {Journal Article},
    Pubm = {Print},
    Rn = {EC 3.6.1.- (Kinesin)},
    Sb = {IM},
    So = {Proc Natl Acad Sci U S A 2004 Nov 16;101(46):16138-43. Epub 2004 Nov 08.},
    Stat = {MEDLINE},
    Title = {VISTA: computational tools for comparative genomics.},
    Volume = {32},
    Year = {2004}}


@inproceedings{Friedman1997,
    Author = {N Friedman},
    Booktitle = {Proceedings of the International Conference on Machine Learning},
    Date-Modified = {2005-02-05 12:49:26 -0800},
    Title = {Learning belief networks in the presence of missing values and hidden variables},
    Year = {1997}}

@article{Friedman1997a,
    Author = {N Friedman and D Geiger and M Goldszmit},
    Date-Modified = {2005-02-05 12:49:26 -0800},
    Journal = {Machine Learning},
    Pages = {131--163},
    Title = {{Bayesian} Network Classifiers},
    Volume = {29},
    Year = {1997}}

@unpublished{Friedman1999,
    Author = {N Friedman and I Nachman and D Pe{\'e}r},
    Date-Modified = {2005-02-05 12:49:26 -0800},
    Note = {Submitted},
    Title = {Learning of {Bayesian} Network Structure from Massive Datasets: {The} ``Sparse Candidate'' Algorithm},
    Year = {1999}}

@article{Friedman2004,
    Author = {N Friedman},
    Date-Modified = {2005-02-05 12:49:26 -0800},
    Journal = {Science},
    Pages = {799--805},
    Title = {Inferring Cellular Networks Using Probabilistic Graphical Models},
    Volume = {303},
    Year = {2004}}

@inproceedings{Frieze1998,
    Author = {A Frieze and R Kannan and S Vempala},
    Booktitle = {39th Symposium on Foundations of Computing},
    Pages = {370--378},
    Title = {Fast {M}onte {C}arlo algorithms for low rank approximation},
    Year = {1998}}

@InProceedings{Fuglede2004,
  author = 	 {B Fuglede and F Tops{\o}e},
  title = 	 {{Jensen-Shannon divergence and Hilbert space embedding}},
  OPTcrossref =  {},
  OPTkey = 	 {},
  booktitle = {{Proceedings of the IEEE International Symposium on Information Theory}},
  pages = 	 {31},
  year = 	 {2004},
  OPTeditor = 	 {},
  OPTvolume = 	 {},
  OPTnumber = 	 {},
  OPTseries = 	 {},
  OPTaddress = 	 {},
  OPTmonth = 	 {},
  OPTorganization = {},
  OPTpublisher = {},
  OPTnote = 	 {},
  OPTannote = 	 {}
}

@article{Fukuda2004,
    Author = {K Fukuda},
    Fjournal = {Journal of Symbolic Computation},
    Issn = {0747-7171},
    Journal = {Journal of Symbolic Computation},
    Mrclass = {52A39 (52B55 68U05)},
    Mrnumber = {MR2094220},
    Number = {4},
    Pages = {1261--1272},
    Title = {From the zonotope construction to the {M}inkowski addition of convex polytopes},
    Volume = {38},
    Year = {2004}}

@misc{GMP,
    Howpublished = {Available at \url{http://www.swox.com/gmp/}},
    Key = {GMP},
    Title = {{GNU} {M}ultiple {P}recision Arithmetic Library},
    Year = {2004}}

@article{Galtier1998,
    Author = {N Galtier and M Gouy},
    Journal = {Molecular Biology and Evolution},
    Number = {4},
    Pages = {871--879},
    Title = {Inferring pattern and process: maximum likelihood implementation of a non-homogeneous model of {DNA} sequence evolution for phylogenetic analysis.},
    Volume = {154},
    Year = {1998}}

@incollection{Garcia2004,
    Address = {Arlington, VA},
    Author = {LD Garcia},
    Booktitle = {Proceedings of the $20^{th}$ Conference on Uncertainty in Artificial Intelligence},
    Date-Modified = {2005-02-05 12:49:26 -0800},
    Editor = {M Chickering and J Halpern},
    Pages = {177--184},
    Publisher = {AUAI Press},
    Title = {Algebraic Statistics in Model Selection},
    Year = {2004}}

@article{Garcia2004a,
    Author = {Garcia, L. D. and Stillman, M. and Sturmfels, B.},
    Editor = {AM Cohen, G-M Greuel, M-F Roy},
    Fjournal = {Journal of Symbolic Computation, Special issue on the occasion of MEGA 2003},
    Journal = {Journal of Symbolic Computation},
    Note = {Special issue on the occasion of MEGA 2003},
    Pages = {331--355},
    Title = {Algebraic geometry of {B}ayesian networks},
    Volume = {39/3-4},
    Year = {2004}}

@Article{Gascuel1994,
  author =   {O Gascuel},
  title =    {{A note on Sattath and Tversky's, Saitou and Nei's, and Studier and Keppler's Algorithms for Inferring Phylogenies from Evolutionary Distances}},
  journal =      {Molecular Biology and Evolution},
  year =     {1994},
  OPTkey =   {},
  volume =   {11},
  OPTnumber =   {6},
  pages =    {961--963},
  OPTmonth =     {},
  OPTnote =      {},
  OPTannote =    {}
}

@Article{Gascuel1997,
  author = {O Gascuel},
  title = {{BIONJ: an improved version of the NJ algorithm based on a
                  simple model of sequence data}},
  journal = {Molecular Biology and Evolution},
  year = {1997},
  OPTkey = {},
  volume = {14},
  OPTnumber = {7},
  pages = {685--695},
  OPTmonth = {},
  OPTnote = {},
  OPTannote = {}
}

@Article{Gascuel2004,
  author =   {O Gascuel and A McKenzie},
  title =    {Performance analysis of hierarchical clustering algorithms},
  journal =      {Journal of Classification},
  year =     {2004},
  OPTkey =   {},
  volume =   {21},
  OPTnumber =    {},
  pages =    {3--18},
  OPTmonth =     {},
  OPTnote =      {},
  OPTannote =    {}
}


@Article{Gascuel2006,
  author =   {O Gascuel and M Steel},
  title =    {{Neighbor-joining revealed}},
  journal =      {Molecular Biology and Evolution},
  year =     {2006},
  OPTkey =   {},
  volume =    {23},
  OPTnumber =    {11},
  pages =     {1997--2000},
  OPTmonth =     {},
  note =     {},
  OPTannote =    {}
}




@article{Gatermann2005,
    Author = {K Gatermann and M Wolfrum},
    Journal = {Advances in Applied Mathematics},
    Number = {2},
    Pages = {252--294},
    Title = {Bernstein's second theorem and {V}iro's method for sparse polynomial systems in chemistry},
    Volume = {34},
    Year = {2005}}

@incollection{Gaut1998,
    Address = {New York, NY},
    Author = {BS Gaut},
    Booktitle = {Evolutionary Biology, Vol 30},
    Date-Modified = {2005-02-05 12:49:26 -0800},
    Editor = {MK Hecht RJ Macintyre and MT Clegg},
    Pages = {93--120},
    Publisher = {Plenum Press Div Plenum Publishing Corp},
    Title = {Molecular clocks and nucleotide substitution rates in higher plants},
    Year = {1998}}

@incollection{Gawrilow2000,
    Author = {E Gawrilow and M Joswig},
    Booktitle = {Polytopes --- Combinatorics and Computation},
    Date-Modified = {2005-02-05 12:49:26 -0800},
    Editor = {G Kalai and GM Ziegler},
    Pages = {43--74},
    Publisher = {Birkh\"auser},
    Title = {Polymake: a Framework for Analyzing Convex Polytopes},
    Year = {2000}}

@inproceedings{Gawrilow2001,
    Author = {E Gawrilow and M Joswig},
    Booktitle = {Proceedings of the 17th Annual Symposium on Computational Geometry},
    Date-Modified = {2005-02-05 12:49:26 -0800},
    Note = {June 3-5, 2001, Medford, MA},
    Organization = {ACM},
    Pages = {222--231},
    Title = {Polymake: an Approach to Modular Software Design in Computational Geometry},
    Year = {2001}}

@article{Geiger2001,
    Author = {D Geiger and D Heckerman and H King and C Meek},
    Fjournal = {The Annals of Statistics},
    Journal = {The Annals of Statist.},
    Number = {2},
    Pages = {505--529},
    Title = {Stratified exponential families: graphical models and model selection},
    Volume = {29},
    Year = {2001}}

@article{Geiger2005,
    Author = {D Geiger and C Meek and B Sturmfels},
    Date-Modified = {2005-02-05 12:49:26 -0800},
    Institution = {Microsoft Research},
    Journal = {The Annals of Statistics},
    Note = {To appear},
    Title = {On the toric algebra of graphical models},
    Year = {2005}}

@article{Geman1984,
    Author = {S Geman and D Geman},
    Journal = {IEEE Transactions on Pattern Analysis and Machine Intelligence, PAMI-6},
    Pages = {721--741},
    Title = {Stochastic relaxation, Gibbs distributions and the {Bayesian} restoration of images},
    Year = {1984}}

@article{Gentleman2004,
    Author = {RC Gentleman and VJ Carey and DM Bates and B Bolstad and M Dettling and S Dudoit and B Ellis and L Gautier and Y Ge and J Gentry and others},
    Date-Modified = {2005-02-05 12:49:26 -0800},
    Journal = {Genome Biology},
    Pages = {R80},
    Title = {Bioconductor: Open software development for computational biology and bioinformatics},
    Url = {http://genomebiology.com/2004/5/10/R80},
    Volume = {5},
    Year = {2004}}

@article{Gentles2001,
    Author = {AJ Gentles and S Karlin},
    Journal = {Genome Research},
    Pages = {540--546},
    Title = {Genome-scale compositional comparisons in eukaryotes},
    Volume = {4},
    Year = {2001}}

@article{Gibbs2004,
    Abstract = {The laboratory rat (Rattus norvegicus) is an indispensable tool in experimental medicine and drug development, having made inestimable contributions to human health. We report here the genome sequence of the Brown Norway (BN) rat strain. The sequence represents a high-quality 'draft' covering over 90% of the genome. The BN rat sequence is the third complete mammalian genome to be deciphered, and three-way comparisons with the human and mouse genomes resolve details of mammalian evolution. This first comprehensive analysis includes genes and proteins and their relation to human disease, repeated sequences, comparative genome-wide studies of mammalian orthologous chromosomal regions and rearrangement breakpoints, reconstruction of ancestral karyotypes and the events leading to existing species, rates of variation, and lineage-specific and lineage-independent evolutionary events such as expansion of gene families, orthology relations and protein evolution.},
    Affiliation = {Human Genome Sequencing Center, Department of Molecular and Human Genetics, Baylor College of Medicine, MS BCM226, One Baylor Plaza, Houston, Texas 77030, USA <http://www.hgsc.bcm.tmc.edu>.},
    Aid = {nature02426 {$[$}pii{$]$}},
    Au = {Collins F},
    Author = {RA Gibbs and GM Weinstock and ML Metzker and DM Muzny and EJ Sodergren and S Scherer and G Scott and D Steffen and KC Worley and PE Burch and others},
    Cin = {Nature. 2004 Apr 1;428(6982):475-6. PMID: 15057812},
    Cn = {Rat Genome Sequencing Project Consortium.},
    Da = {20040401},
    Date-Modified = {2005-02-05 12:49:26 -0800},
    Dcom = {20040414},
    Edat = {2004/04/02 05:00},
    Jid = {0410462},
    Journal = {Nature},
    Keywords = {Animals and Base Composition and Centromere/genetics and Chromosomes, Mammalian/genetics and CpG Islands/genetics and DNA Transposable Elements/genetics and DNA, Mitochondrial/genetics and *Evolution, Molecular and Gene Duplication and *Genome and *Genomics and Humans and Introns/genetics and Male and Mice and Models, Molecular and Mutagenesis and Polymorphism, Single Nucleotide/genetics and RNA Splice Sites/genetics and RNA, Untranslated/genetics and Rats and Rats, Inbred BN/*genetics and Regulatory Sequences, Nucleic Acid/genetics and Research Support, Non-U.S. Gov't and Research Support, U.S. Gov't, P.H.S. and Retroelements/genetics and Sequence Analysis, DNA and Telomere/genetics},
    Language = {eng},
    Lr = {20041117},
    Mhda = {2004/04/15 05:00},
    Number = {6982},
    Own = {NLM},
    Pages = {493--521},
    Phst = {2004/02/20 {$[$}accepted{$]$}},
    Pl = {England},
    Pmid = {15057822},
    Pst = {ppublish},
    Pt = {Journal Article},
    Pubm = {Print},
    Rn = {0 (Retroelements)},
    Sb = {IM},
    So = {Genome Res 2004 Apr;14(4):574-9.},
    Stat = {MEDLINE},
    Title = {Genome sequence of the Brown Norway rat yields insights into mammalian evolution.},
    Volume = {428},
    Year = {2004}}

@book{Golub1989,
    Author = {GH Golub and CF Van Loan},
    Date-Modified = {2005-02-05 12:49:26 -0800},
    Edition = {second},
    Publisher = {The Johns Hopkins University Press},
    Title = {Matrix Computations},
    Year = {1989}}

@article{Gorban2004,
    Author = {AN Gorban and AY Zinovyev},
    Journal = {arXiv.org:q-bio.GN/0412015},
    Title = {The mystery of two straight lines in bacterial genome statistics},
    Year = {2004}}

@misc{Grayson2002,
    Author = {DR Grayson and ME Stillman},
    Date-Modified = {2005-02-05 12:49:26 -0800},
    Howpublished = {Available at \url{http://www.math.uiuc.edu/Macaulay2/}},
    Title = {Macaulay 2, a software system for research in algebraic geometry},
    Year = {2002}}

@article{Greig1989,
    Author = {DM Greig and BT Porteous and AH Seheult},
    Journal = {Journal of the Royal Statistical Society},
    Pages = {271--279},
    Title = {Exact maximum a posteriori estimation for binary images},
    Volume = {Series B, 51},
    Year = {1989}}

@book{Greuel2002,
    Address = {Berlin and Heidelberg},
    Author = {GM Greuel and G Pfister},
    Date-Modified = {2005-02-05 12:49:26 -0800},
    Publisher = {Springer-Verlag},
    Title = {A Singular Introduction to Commutative Algebra},
    Year = {2002}}

@misc{Greuel2003,
    Author = {GM Greuel and G. Pfister and H. Schoenemann},
    Date-Modified = {2005-02-28 12:49:26 -0800},
    Howpublished = {Available at \url{http://www.singular.uni-kl.de/}},
    Title = {SINGULAR: A Computer Algebra System for Polynomial Computations},
    Year = {2003}}


@article{Griffiths1996,
    Author = {RC Griffiths and P Marjoram},
    Bibsource = {DBLP, http://dblp.uni-trier.de},
    Date-Modified = {2005-03-01 19:23:49 -0500},
    Journal = {Journal of Computational Biology},
    Number = {4},
    Pages = {479--502},
    Title = {Ancestral Inference from Samples of DNA Sequences with Recombination.},
    Volume = {3},
    Year = {1996}}

@article{Gritzmann1993,
    Author = {P Gritzmann and B Sturmfels},
    Journal = {SIAM Journal of Discrete Mathematics},
    Pages = {246--269},
    Title = {{M}inkowski addition of polytopes: {C}omputational complexity and applications to {G}r\"obner bases},
    Volume = {6},
    Year = {1993}}

@book{Grotschel1988,
    Address = {Berlin},
    Author = {M Gr{\"o}tschel and L Lov{\'a}sz and A Schrijver},
    Isbn = {3-540-13624-X},
    Mrclass = {90C27 (05-02 52-02 68Q25)},
    Mrnumber = {MR936633 (89m:90135)},
    Mrreviewer = {J{\"u}rgen K{\"o}hler},
    Pages = {xii+362},
    Publisher = {Springer-Verlag},
    Series = {Algorithms and Combinatorics: Study and Research Texts},
    Title = {Geometric algorithms and combinatorial optimization},
    Volume = {2},
    Year = {1988}}



@book{Grotschel1993,
    Author = {M Gr{\"o}tschel and L Lov{\'a}sz and A Schrijver},
    Isbn = {0-387-56740-2},
    Publisher = {Springer-Verlag},
    Series = {{\rm Algorithms and Combinatorics}},
    Title = {Geometric Algorithms and Combinatorial Optimization},
    Volume = {2},
    Year = {1993}}

@book{Grunbaum2003,
    Address = {New York},
    Author = {B Gr{\"u}nbaum},
    Edition = {Second},
    Isbn = {0-387-00424-6; 0-387-40409-0},
    Mrclass = {52-01 (52Bxx)},
    Mrnumber = {MR1976856 (2004b:52001)},
    Mrreviewer = {Alexander Zvonkin},
    Note = {Prepared and with a preface by Volker Kaibel, Victor Klee and G\"unter M.\ Ziegler},
    Pages = {xvi+468},
    Publisher = {Springer-Verlag},
    Series = {{\rm Graduate Texts in Mathematics}},
    Title = {Convex Polytopes},
    Volume = {221},
    Year = {2003}}

@article{Guigo2004,
    Author = {R Guig\'{o} and E Birbey and M Brent and E Dermitzakis and L Pachter and H Roest Crollius and V Solovyev and MQ Zhang},
    Journal = {arXiv.org:q-bio.GN/0410008},
    Title = {Needed for completion of the human genome: hypothesis driven experiments and biologically realistic mathematical models},
    Year = {2004}}

@article{Gusfield1994,
    Author = {D Gusfield and K Balasubramanian and D Naor},
    Date-Modified = {2005-02-05 12:49:26 -0800},
    Journal = {Algorithmica},
    Pages = {312--326},
    Title = {Parametric optimization of sequence alignment},
    Volume = {12},
    Year = {1994}}

@article{Gusfield1996,
    Author = {D Gusfield and P Stelling},
    Date-Modified = {2005-02-05 12:49:26 -0800},
    Journal = {Methods Enzymology},
    Pages = {481--494},
    Title = {Parametric and inverse-parametric sequence alignment with XPARAL},
    Volume = {266},
    Year = {1996}}

@book{Gusfield1997,
    Author = {D Gusfield},
    Date-Modified = {2005-02-05 12:49:26 -0800},
    Publisher = {Cambridge University Press},
    Title = {Algorithms on Strings, Trees, and Sequences},
    Year = {1997}}

@Article{Haas2003,
  author = 	 {BJ Haas and AL Delcher and SM Mount and JR Wortman and RK Smith and LI Hannick and R Maiti and CM Ronning and DB Rusch and CD Town and SL Salzberg and O White},
  title = 	 {Improving the {{\it Arabidopsis}} genome annotation using maximal transcript alignment assemblies},
  journal = 	 {Nucleic Acids Research},
  year = 	 {2003},
  OPTkey = 	 {},
  volume = 	 {31},
  OPTnumber = 	 {19},
  pages = 	 {5654--5666},
  OPTmonth = 	 {},
  OPTnote = 	 {},
  OPTannote = 	 {}
}

@article{Hacijan1979,
    Author = {LG Ha{\v{c}}ijan},
    Fjournal = {Doklady Akademii Nauk SSSR},
    Issn = {0002-3264},
    Journal = {Dokl. Akad. Nauk SSSR},
    Mrclass = {90C05},
    Mrnumber = {MR522052 (80g:90071)},
    Mrreviewer = {M. Stef{\u{a}}nescu},
    Number = {5},
    Pages = {1093--1096},
    Title = {A polynomial algorithm in linear programming},
    Volume = {244},
    Year = {1979}}

@Article{Hall2005,
  author = {BG Hall},
  title = {Comparison of the accuracies of several phylogenetic
                  methods using protein and {DNA} sequences},
  journal = {Molecular Biology and Evolution},
  year = {2005},
  OPTkey = {},
  volume = {22},
  number = {3},
  pages = {792--802},
  OPTmonth = {},
  OPTnote = {},
  OPTannote = {}
}

@article{Hallgrimsdottir2005,
    Author = {I Hallgr\'{\i}msd\'{o}ttir and B Sturmfels},
    Journal = {Journal of Symbolic Computation},
    Note = {To appear},
    Title = {Resultants in Genetic Linkage Analysis},
    Year = {2005}}

@book{Hammer1995,
    Address = {Berlin},
    Author = {R Hammer and M Hocks and U Kulisch and D Ratz},
    Date-Modified = {2005-02-05 12:49:26 -0800},
    Publisher = {Springer-Verlag},
    Title = {C++ Toolbox for Verified Computing: Basic Numerical Problems},
    Year = {1995}}

@article{Hannenhalli1999,
    Author = {S Hannenhalli and PA Pevzner},
    Journal = {Journal of the ACM},
    Number = {1},
    Pages = {1--27},
    Title = {{Transforming cabbage into turnip: polynomial algorithm for sorting signed permutations by reversals}},
    Volume = {46},
    Year = {1999}}

@article{Hansen1980,
    Author = {E Hansen},
    Date-Modified = {2005-02-05 12:49:26 -0800},
    Journal = {Numerische Mathematik},
    Pages = {247--270},
    Title = {Global optimization using interval analysis -- the multi-dimensional case},
    Volume = {34},
    Year = {1980}}

@article{Hansen1981,
    Author = {E Hansen and S Sengupta},
    Date-Modified = {2005-02-05 12:49:26 -0800},
    Journal = {BIT},
    Pages = {203--211},
    Title = {Bounding solutions of systems of equations using interval analysis},
    Volume = {21},
    Year = {1981}}

@book{Hansen1992,
    Address = {New York},
    Author = {E Hansen},
    Date-Modified = {2005-02-05 12:49:26 -0800},
    Publisher = {Marcel Dekker},
    Title = {Global Optimization using Interval Analysis},
    Year = {1992}}

@book{Hartwell2003,
    Author = {L Hartwell and L Hood and ML Goldberg and LM Silver and RC Veres and A Reynolds},
    Edition = {second},
    Publisher = {McGraw-Hill Science/Engineering/Math},
    Title = {{Genetics: From Genes to Genomes}},
    Year = {2003}}

@article{Hasegawa1985,
    Author = {M Hasegawa and H Kishino and T Yano},
    Date-Modified = {2005-02-05 12:49:26 -0800},
    Journal = {Journal of Molecular Evolution},
    Pages = {160--174},
    Title = {Dating of the human-ape splitting by a molecular clock of mitochondrial {DNA}},
    Volume = {22},
    Year = {1985}}

@article{Heckerman1995,
    Author = {D Heckerman and D Geiger and DM Chickering},
    Date-Modified = {2005-02-05 12:49:26 -0800},
    Journal = {Machine Learning},
    Pages = {197--243},
    Title = {Learning {B}ayesian Networks: {T}he combination of knowledge and statistical data},
    Volume = {20},
    Year = {1995}}

@techreport{Heckerman1995a,
    Author = {D Heckerman},
    Date-Modified = {2005-02-05 12:49:26 -0800},
    Institution = {Microsoft Research},
    Number = {MSR-TR-95-06},
    Title = {A tutorial on learning with {B}ayesian networks},
    Year = {1995}}

@incollection{Heckerman1998,
    Address = {Cambridge, Massachusetts},
    Author = {D Heckerman},
    Booktitle = {Learning in Graphical Models},
    Date-Modified = {2005-02-05 12:49:26 -0800},
    Editor = {MI Jordan},
    Publisher = {MIT Press},
    Title = {A tutorial on learning with {B}ayesian networks},
    Year = {1998}}

@article{Hendy1989,
    Author = {M Hendy and D Penny},
    Date-Added = {2005-03-01 20:20:00 -0500},
    Date-Modified = {2005-03-01 20:20:51 -0500},
    Journal = {Systematic Zoology},
    Number = {4},
    Title = {A framework for the quantitative study of evolutionary trees},
    Volume = {38},
    Year = {1989}}

@article{Hendy1993,
    Author = {MD Hendy and D Penny},
    Journal = {Journal of Classification},
    Pages = {5--24},
    Title = {Spectral analysis of phylogenetic data},
    Volume = {10},
    Year = {1993}}

@article{Heydebreck2004,
    Author = {A von Heydebreck and B Gunawan and L F{\"u}zesi},
    Date-Modified = {2005-02-05 12:49:26 -0800},
    Journal = {Biostatistics},
    Number = {4},
    Pages = {545--556},
    Title = {Maximum likelihood estimation of oncogenetic tree models},
    Url = {http://biostatistics.oupjournals.org/cgi/content/abstract/5/4/545?etoc},
    Volume = {5},
    Year = {2004}}

@article{Hibi1987,
    Author = {T Hibi},
    Journal = {Advanced Studies in Pure Mathematics},
    Pages = {93--109},
    Title = {Distributive Lattices, Affine Semigroup Rings and Algebras with Straightening Laws},
    Volume = {11},
    Year = {1987}}

@Article{Hiller2009,
  author = 	 {D Hiller and H Jiang and W Xu and WH Wong},
  title = 	 {Identifiability of isoform deconvolution from junction arrays and {RNA-Seq}},
  journal = 	 {Bioinformatics},
  year = 	 {2009},
  OPTkey = 	 {},
  volume = 	 {25},
  OPTnumber = 	 {23},
  pages = 	 {3056--3059},
  OPTmonth = 	 {},
  OPTnote = 	 {},
  OPTannote = 	 {}
}

@article{Hillier2004,
    Abstract = {We present here a draft genome sequence of the red jungle fowl, Gallus gallus. Because the chicken is a modern descendant of the dinosaurs and the first non-mammalian amniote to have its genome sequenced, the draft sequence of its genome--composed of approximately one billion base pairs of sequence and an estimated 20,000-23,000 genes--provides a new perspective on vertebrate genome evolution, while also improving the annotation of mammalian genomes. For example, the evolutionary distance between chicken and human provides high specificity in detecting functional elements, both non-coding and coding. Notably, many conserved non-coding sequences are far from genes and cannot be assigned to defined functional classes. In coding regions the evolutionary dynamics of protein domains and orthologous groups illustrate processes that distinguish the lineages leading to birds and mammals. The distinctive properties of avian microchromosomes, together with the inferred patterns of conserved synteny, provide additional insights into vertebrate chromosome architecture.},
    Affiliation = {Genome Sequencing Center, Washington University School of Medicine, Campus Box 8501, 4444 Forest Park Avenue, St Louis, Missouri 63108, USA.},
    Aid = {10.1038/nature03154 {$[$}doi{$]$}},
    Au = {Wilson RK},
    Author = {LW Hillier and W Miller and E Birney and W Warren and RC Hardison and CP Ponting and P Bork and DW Burt and MAM Groenen and ME Delany and others},
    Cin = {Nature. 2004 Dec 9;432(7018):679-80. PMID: 15592391},
    Cn = {International Chicken Genome Sequencing Consortium.},
    Da = {20041216},
    Date-Modified = {2005-02-05 12:49:27 -0800},
    Dcom = {20050105},
    Edat = {2004/12/14 09:00},
    Jid = {0410462},
    Journal = {Nature},
    Keywords = {Animals and Avian Proteins/genetics and Chickens/*genetics and Comparative Study and Conserved Sequence/genetics and DNA Transposable Elements/genetics and *Evolution, Molecular and Gene Duplication and Genes/genetics and *Genome and *Genomics and Humans and Long Interspersed Nucleotide Elements/genetics and Multigene Family/genetics and Mutagenesis/genetics and Physical Chromosome Mapping and Pseudogenes/genetics and RNA, Untranslated/genetics and Research Support, Non-U.S. Gov't and Research Support, U.S. Gov't, Non-P.H.S. and Research Support, U.S. Gov't, P.H.S. and Retroviridae/genetics and Sequence Analysis, DNA and Short Interspersed Nucleotide Elements/genetics and Synteny and Vertebrates/genetics},
    Language = {eng},
    Mhda = {2005/01/06 09:00},
    Number = {7018},
    Own = {NLM},
    Pages = {695-716},
    Phst = {2004/11/01 {$[$}accepted{$]$}},
    Pl = {England},
    Pmid = {15592404},
    Pst = {ppublish},
    Pt = {Journal Article},
    Pubm = {Print},
    Rn = {0 (RNA, Untranslated)},
    Sb = {IM},
    So = {Science 2001 Feb 16;291(5507):1304-51.},
    Stat = {MEDLINE},
    Title = {Sequence and comparative analysis of the chicken genome provide unique perspectives on vertebrate evolution.},
    Volume = {432},
    Year = {2004}}

@article{Hirschberg1975,
    Author = {DS Hirschberg},
    Date-Modified = {2005-02-05 12:49:26 -0800},
    Journal = {CACM},
    Number = {6},
    Pages = {341--343},
    Title = {A Linear Space Algorithm for Computing Maximal Common Subsequences},
    Volume = {18},
    Year = {1975}}

@article{Holland2004,
    Author = {B Holland and KT Huber and V Moulton and P Lockhart},
    Date-Added = {2005-03-01 19:42:44 -0500},
    Date-Modified = {2005-03-01 19:44:00 -0500},
    Journal = {Molecular Biology and Evolution},
    Number = {7},
    Pages = {1459--1461},
    Title = {Using Consensus Networks to Visualize Contradictory Evidence for Species Phylogeny},
    Volume = {21},
    Year = {2004}}

@article{Holmes2001,
    Author = {I Holmes and WJ Bruno},
    Date-Modified = {2005-02-05 12:49:27 -0800},
    Journal = {Bioinformatics},
    Number = {9},
    Pages = {803--820},
    Title = {{Evolutionary HMMs: a Bayesian approach to multiple alignment}},
    Volume = {17},
    Year = {2001}}

@Article{Hopcroft1973,
  author = 	 {JE Hopcroft and RM Karp},
  title = 	 {An $n^{5/2}$ algorithm for maximum matchings in bipartite graphs},
  journal = 	 {SIAM Journal on Computing},
  year = 	 {1973},
  OPTkey = 	 {},
  volume = 	 {2},
  OPTnumber = 	 {4},
  pages = 	 {225--231},
  OPTmonth = 	 {},
  OPTnote = 	 {},
  OPTannote = 	 {}
}

@article{Hosten2005,
    Author = {S Ho{\c{s}}ten and A Khetan and B Sturmfels},
    Date-Modified = {2005-02-05 12:49:27 -0800},
    Journal = {Foundations of Computational Mathematics},
    Note = {To appear},
    Title = {Solving the likelihood equations},
    Year = {2005}}

@article{Huber2002,
    Author = {KT Huber and M Langton and D Penny and V Moulton and M Hendy},
    Date-Added = {2005-03-01 19:35:57 -0500},
    Date-Modified = {2005-03-01 19:39:03 -0500},
    Journal = {Applied Bioinformatics},
    Number = {3},
    Pages = {2041--2059},
    Title = {Spectronet: A package for computing spectra and median networks},
    Volume = {1},
    Year = {2002}}

@Article{Huelsenbeck1993,
  author =   {J Huelsenbeck and D Hillis},
  title =    {Success of phylogenetic methods in the four-taxon case},
  journal =      {Systematic Biology},
  year =     {1993},
  OPTkey =   {},
  volume =   {42},
  number =   {3},
  pages =    {247--264},
  OPTmonth =     {},
  OPTnote =      {},
  OPTannote =    {}
}

@article{Huelsenbeck2000,
    Author = {JP Huelsenbeck and B Larget and DL Swofford},
    Journal = {Genetics},
    Number = {4},
    Pages = {1879--1892},
    Title = {A compound Poisson process for relaxing the molecular clock},
    Volume = {154},
    Year = {2000}}

@article{Hughey1996,
    Author = {R Hughey and A Krogh},
    Date-Modified = {2005-02-05 12:49:26 -0800},
    Journal = {CABIOS},
    Pages = {95--107},
    Title = {Hidden {Markov} models for sequence analysis: {E}xtension and analysis of the basic method},
    Volume = {12},
    Year = {1996}}

@article{Human2004,
    Annote = {10.1038/nature03001},
    Author = {Human Genome Sequencing Consortium, International},
    Date-Modified = {2005-02-12 12:17:12 -0800},
    Ep = {945},
    Journal = {Nature},
    L3 = {http://www.nature.com/nature/journal/v431/n7011/suppinfo/nature03001.html},
    M3 = {10.1038/nature03001},
    Number = {7011},
    Pages = {931--945},
    Sn = {0028-0836},
    Sp = {931},
    Title = {Finishing the euchromatic sequence of the human genome},
    Ty = {JOUR},
    Url = {http://dx.doi.org/10.1038/nature03001},
    Volume = {431},
    Year = {2004}}

@article{Huson1998,
    Author = {D Huson},
    Date-Modified = {2005-03-01 20:26:50 -0500},
    Journal = {Bioinformatics},
    Number = {1},
    Pages = {68--73},
    Title = {SplitsTree - a program for analyzing and visualizing evolutionary data},
    Volume = {14},
    Year = {1998}}

@article{Huson2004,
    Author = {D Huson and T Dezulian and T Kloepper and M Steel},
    Date-Added = {2005-03-01 19:49:09 -0500},
    Date-Modified = {2005-03-01 19:50:40 -0500},
    Journal = {IEEE Transactions on Computational Biology and Bioinformatics},
    Number = {4},
    Pages = {151--158},
    Title = {Phylogenetic super-networks from partial trees},
    Volume = {1},
    Year = {2004}}

@unpublished{Huson2005,
    Author = {D Huson and D Bryant},
    Date-Added = {2005-03-01 19:52:22 -0500},
    Date-Modified = {2005-03-01 19:54:56 -0500},
    Note = {in preparation},
    Title = {{Estimating phylogenetic trees and networks using SplitsTree4}},
    Year = {2005}}

@Article{Huson2005b,
  author = 	 {D Huson and D Bryant},
  title = 	 {Application of phylogenetic networks in evolutionary studies},
  journal = 	 {Molecular Biology and Evolution},
  year = 	 {2005},
  OPTkey = 	 {},
  volume = 	 {23},
  OPTnumber = 	 {},
  pages = 	 {254--267},
  OPTmonth = 	 {},
  OPTnote = 	 {},
  OPTannote = 	 {}
}

@manual{IEEE:p754,
    Date-Modified = {2005-02-05 12:49:27 -0800},
    Key = {IEEE Task P754},
    Note = {A preliminary draft was published in the January 1980 issue of IEEE Computer, together with several companion articles. Available from the IEEE Service Center, Piscataway, NJ, USA.},
    Organization = {IEEE, New York},
    Title = {{ANSI}\slash {IEEE} 754-1985, Standard for Binary Floating-Point Arithmetic},
    Year = {1985}}

@article{Ihaka1996,
    Author = {I Ross and R Gentleman},
    Date-Modified = {2005-02-05 12:49:26 -0800},
    Journal = {Journal of Computational and Graphical Statistics},
    Number = {3},
    Pages = {299--314},
    Title = {R: A Language for Data Analysis and Graphics},
    Url = {http://www.amstat.org/publications/jcgs/},
    Volume = {5},
    Year = {1996}}

@book{Imrich2000,
    Author = {W Imrich and S Klav{\v{z}}ar},
    Date-Modified = {2005-03-01 20:31:05 -0500},
    Isbn = {0-471-37039-8},
    Mrclass = {05-01 (05C75 05C85 05C90 68R10)},
    Mrnumber = {MR1788124 (2001k:05001)},
    Mrreviewer = {Pranava K. Jha},
    Note = {Structure and recognition, With a foreword by Peter Winkler},
    Pages = {xvi+358},
    Publisher = {Wiley--Interscience, New York},
    Series = {Wiley--Interscience Series in Discrete Mathematics and Optimization},
    Title = {Product Graphs},
    Year = {2000}}

@article{International-Human-Genome-Sequencing-Consortium2001,
    Author = {{Human Genome Sequencing Consortium}},
    Date-Modified = {2005-02-05 12:49:27 -0800},
    Journal = {Nature},
    Month = {February},
    Number = {6822},
    Pages = {860--921},
    Title = {{Initial sequencing and analysis of the human genome}},
    Volume = {409},
    Year = {2001}}

@article{Jensen2001,
    Author = {R Jensen},
    Date-Modified = {2005-02-05 12:49:26 -0800},
    Journal = {Genome Biology},
    Number = {8},
    Pages = {1002--1005},
    Title = {Orthologs and Paralogs -- we need to get it right},
    Volume = {2},
    Year = {2001}}

@Article{Jiang2009,
  author = 	 {H Jiang and WH Wong},
  title = 	 {Statistical inferences for isoform expression in {RNA-Seq}},
  journal = 	 {Bioinformatics},
  year = 	 {2009},
  OPTkey = 	 {},
  volume = 	 {25},
  OPTnumber = 	 {},
  pages = 	 {1026--1032},
  OPTmonth = 	 {},
  OPTnote = 	 {},
  OPTannote = 	 {}
}

@Article{Johnson2006,
  author = 	 {O Johnson and J Liu},
  title = 	 {A traveling salesman approach for predicting protein functions},
  journal = 	 {Source Code for Biology and Medicine},
  year = 	 {2006},
  OPTkey = 	 {},
  volume = 	 {1},
  OPTnumber = 	 {3},
  OPTpages = 	 {},
  OPTmonth = 	 {},
  OPTnote = 	 {},
  OPTannote = 	 {}
}

@book{Jordan2005,
    Author = {MI Jordan},
    Publisher = {In preparation},
    Title = {An Introduction to Probabilistic Graphical Models},
    Year = {2005}}

@incollection{Jukes1969,
    Author = {TH Jukes and C Cantor},
    Booktitle = {Mammalian Protein Metabolism},
    Date-Modified = {2005-02-05 12:49:26 -0800},
    Editor = {HN Munro},
    Pages = {21--32},
    Publisher = {New York, Academic Press},
    Title = {Evolution of protein molecules},
    Year = {1969}}

@Article{Kalmanson1975,
  author = 	 {K Kalmanson},
  title = 	 {Edgeconvex circuits and the traveling salesman problem},
  journal = 	 {Canadian Journal of Mathematics},
  year = 	 {1974},
  OPTkey = 	 {},
  volume = 	 {27},
  OPTnumber = 	 {},
  pages = 	 {1000--1010},
  OPTmonth = 	 {},
  OPTnote = 	 {},
  OPTannote = 	 {}
}

@article{Karlin1990,
    Author = {S Karlin and SF Altschul},
    Date-Modified = {2005-02-05 12:49:26 -0800},
    Journal = {Proceedings of the National Academy of Sciences, USA},
    Pages = {2264--2268},
    Title = {Methods for assessing the statistical significance of molecular sequence features by using general scoring schemes},
    Volume = {87},
    Year = {1990}}


@article{Karloff1993,
    Author = {H Karloff},
    Date-Modified = {2005-02-05 12:49:26 -0800},
    Journal = {Information Processing Letters},
    Pages = {53--60},
    Title = {Fast algorithms for approximately counting mismatches},
    Volume = {48},
    Year = {1993}}

@article{Karplus1998,
    Author = {K Karplus and C Barrett and R Hughey},
    Date-Modified = {2005-02-05 12:49:26 -0800},
    Journal = {Bioinformatics},
    Pages = {846--856},
    Title = {Hidden Markov models for detecting remote protein homologies},
    Volume = {14},
    Year = {1998}}

@article{Kellis2004,
    Author = {M Kellis and B Birren and E Lander},
    Date-Modified = {2005-02-05 12:49:26 -0800},
    Journal = {Nature},
    Pages = {617--624},
    Title = {Proof and evolutionary analysis of ancient genome duplication in the yeast Saccharomyces cerevisae},
    Volume = {8},
    Year = {2004}}

@article{Kent2002,
    Author = {WJ Kent},
    Date-Modified = {2005-02-05 12:49:26 -0800},
    Journal = {Genome Biology},
    Number = {4},
    Pages = {656--664},
    Title = {{BLAT- The BLAST like Alignment Tool}},
    Volume = {12},
    Year = {2002}}

@article{Kent2002a,
    Author = {WJ Kent and CW Sugnet and TS Furey and KM Roskin and TH Pringle and AM Zhaler and D Haussler},
    Journal = {Genome Research},
    Number = {6},
    Pages = {996--1006},
    Title = {The human genome browser at {UCSC}},
    Volume = {12},
    Year = {2002}}

@article{Khalil:2009p1195,
	author = {Ahmad M Khalil and Mitchell Guttman and Maite Huarte and Manuel Garber and Arjun Raj and Dianali Rivea Morales and Kelly Thomas and Aviva Presser and Bradley E Bernstein and Alexander van Oudenaarden and Aviv Regev and Eric S Lander and John L Rinn},
	journal = {Proc Natl Acad Sci USA},
	title = {Many human large intergenic noncoding RNAs associate with chromatin-modifying complexes and affect gene expression},
	abstract = {We recently showed that the mammalian genome encodes >1,000 large intergenic noncoding (linc)RNAs that are clearly conserved across mammals and, thus, functional. Gene expression patterns have implicated these lincRNAs in diverse biological processes, including cell-cycle regulation, immune surveillance, and embryonic stem cell pluripotency. However, the mechanism by which these lincRNAs function is unknown. Here, we expand the catalog of human lincRNAs to approximately 3,300 by analyzing chromatin-state maps of various human cell types. Inspired by the observation that the well-characterized lincRNA HOTAIR binds the polycomb repressive complex (PRC)2, we tested whether many lincRNAs are physically associated with PRC2. Remarkably, we observe that approximately 20% of lincRNAs expressed in various cell types are bound by PRC2, and that additional lincRNAs are bound by other chromatin-modifying complexes. Also, we show that siRNA-mediated depletion of certain lincRNAs associated with PRC2 leads to changes in gene expression, and that the up-regulated genes are enriched for those normally silenced by PRC2. We propose a model in which some lincRNAs guide chromatin-modifying complexes to specific genomic loci to regulate gene expression.},
	affiliation = {The Broad Institute of Harvard and Massachusetts Institute of Technology, Cambridge, MA 02142, USA.},
	number = {28},
	pages = {11667--72},
	volume = {106},
	year = {2009},
	month = {Jul},
	language = {eng},
	keywords = {Repressor Proteins, RNA: Untranslated, Gene Expression Profiling, Models: Genetic, Humans, Gene Expression Regulation, Oligonucleotide Array Sequence Analysis, Chromatin, Epigenesis: Genetic},
	date-added = {2009-09-06 15:49:47 -0700},
	date-modified = {2010-02-23 17:02:00 -0800},
	doi = {10.1073/pnas.0904715106},
	pii = {0904715106},
	pmid = {19571010},
	local-url = {file://localhost/Users/cole/Data/Documents/Papers/2009/Khalil/Proc%20Natl%20Acad%20Sci%20USA%202009%20Khalil.pdf},
	uri = {papers://1C45D7C8-DE5F-4BCB-8C6D-9D101AFF5EFF/Paper/p1195},
	read = {Yes},
	rating = {0}
}


@article{Khachiyan1980,
    Author = {LG Khachiyan},
    Journal = {USSR Computational Mathematics and Mathematical Physics},
    Pages = {53--72},
    Title = {Polynomial Algorithms in Linear Programming},
    Volume = {20},
    Year = {1980}}

@article{Kimura1980,
    Author = {M Kimura},
    Date-Modified = {2005-02-05 12:49:26 -0800},
    Journal = {Journal of Molecular Evolution},
    Pages = {111--120},
    Title = {A simple method for estimating evolutionary rates of base substitution through comparative studies of nucleotide sequences},
    Volume = {16},
    Year = {1980}}

@article{Kimura1981,
    Author = {M Kimura},
    Date-Added = {2005-03-01 20:17:11 -0500},
    Date-Modified = {2005-03-01 20:18:29 -0500},
    Journal = {Proceedings of the National Academy of Sciences, USA},
    Pages = {454--458},
    Title = {Estimation of evolutionary sequences between homologous nucleotide sequences},
    Volume = {78},
    Year = {1981}}

@article{Kolmogorov2003,
    Author = {V Kolmogorov and R Zabih},
    Journal = {European Conference on Computer Vision (ECCV)},
    Title = {Multi-camera Scene Reconstruction via Graph Cuts},
    Year = {2003}}

@article{Korf2001,
    Author = {I Korf and P Flicek and D Duan and MR Brent},
    Journal = {Bioinformatics},
    Pages = {S140--8},
    Title = {{Integrating genomic homology into gene structure prediction}},
    Volume = {17 Suppl 1},
    Year = {2001}}

@book{Korf2003,
    Address = {Sebastopol, CA},
    Author = {I Korf and M Yandell and J Bedell},
    Date-Modified = {2005-02-05 12:49:26 -0800},
    Publisher = {O'Reilly \& Associates},
    Title = {BLAST},
    Year = {2003}}

@book{Korner1989,
    Address = {Cambridge},
    Author = {TW K{\"o}rner},
    Date-Modified = {2005-03-01 20:14:52 -0500},
    Edition = {Second},
    Isbn = {0-521-38991-7},
    Mrclass = {42-01},
    Mrnumber = {MR1035216 (90j:42001)},
    Pages = {xii+591},
    Publisher = {Cambridge University Press},
    Title = {Fourier Analysis},
    Year = {1989}}


@Article{Korostensky2000,
  author = 	 {C Korostensky and G Gonnet},
  title = 	 {Using traveling salesman problem algorithms for evolutionary tree construction},
  journal = 	 {Bioinformatics},
  year = 	 {2000},
  OPTkey = 	 {},
  volume = 	 {16},
  OPTnumber = 	 {},
  pages = 	 {619--627},
  OPTmonth = 	 {},
  OPTnote = 	 {},
  OPTannote = 	 {}
}

@article{Krogh1994,
    Author = {A Krogh and M Brown and IS Mian and K Sjolander and DJ Haussler},
    Date-Modified = {2005-02-05 12:49:26 -0800},
    Journal = {Journal of Molecular Biology},
    Pages = {1501--31},
    Title = {Hidden Markov models in computational biology. Applications to protein modeling},
    Volume = {235},
    Year = {1994}}

@article{Kschischang2001,
    Author = {F Kschischang and H Loeliger and B Frey},
    Journal = {IEEE Transactions on Information Theory},
    Month = feb,
    Number = {2},
    Title = {Factor Graphs and the Sum-Product Algorithm},
    Url = {http://citeseer.ist.psu.edu/631022.html},
    Volume = {47},
    Year = {2001}}

@article{Kuhn1955,
    Author = {HW Kuhn},
    Date-Modified = {2005-02-05 12:49:27 -0800},
    Journal = {Naval Research Logistics Quarterly},
    Pages = {83--97},
    Title = {The {H}ungarian method for the assignment problem},
    Volume = {2},
    Year = {1955}}

@Article{Kuhner1994,
  author = {MK Kuhner and J Felsenstein},
  title = {A simulation comparison of phylogeny algorithms under equal
                  and unequal evolutionary rates},
  journal = {Molecular Biology and Evolution},
  year = {1994},
  OPTkey = {},
  volume = {11},
  pages = {459--468},
  OPTpages = {},
  OPTmonth = {},
  OPTnote = {},
  OPTannote = {}
}

@book{Kulisch2001,
    Address = {New York},
    Date-Modified = {2005-02-05 12:49:26 -0800},
    Editor = {U Kulisch and R Lohner and A Facius},
    Publisher = {Springer-Verlag},
    Title = {Perspectives on Enclosure Methods},
    Year = {2001}}

@incollection{Kulisch2001a,
    Address = {New York},
    Author = {U Kulisch},
    Booktitle = {Perspectives on encolsure methods},
    Date-Modified = {2005-02-05 12:49:26 -0800},
    Editor = {U Kulisch and R Lohner and A Facius},
    Pages = {50--70},
    Publisher = {Springer-Verlag},
    Title = {Advanced arithmetic for the digital computer, interval arithmetic revisited},
    Year = {2001}}

@inproceedings{Kulp1996,
    Author = {D Kulp and D Haussler and MG Reese and FH Eeckman},
    Booktitle = {Proceedings of the Fourth International Conference on Intelligent Systems for Molecular Biology},
    Isbn = {1-57735-002-2},
    Pages = {134--142},
    Publisher = {AAAI Press},
    Title = {A Generalized Hidden {M}arkov Model for the Recognition of Human Genes in {DNA}},
    Year = {1996}}

@Article{Kumar2000,
  author = {S Kumar and SR Gadagker},
  title = {Efficiency of the neighbor-joining method in reconstructing
                  evolutionary relationships in large phylogenies},
  journal = {Journal of Molecular Evolution},
  year = {2000},
  OPTkey = {},
  volume = {51},
  OPTnumber = {},
  pages = {544--553},
  OPTmonth = {},
  OPTnote = {},
  OPTannote = {}
}

@article{Kuo2005,
    Author = {E Kuo},
    Journal = {Journal of Symbolic Computation},
    Note = {To appear},
    Title = {Viterbi Sequences and Polytopes},
    Year = {2005}}

@Misc{LEMON,
  key = 	 {Lemon graph library},
  author = 	 {Lemon graph library},
  title = 	 {{\tt http://lemon.cs.elte.hu/trac/lemon}},
  OPThowpublished = {},
  OPTmonth = 	 {},
  OPTyear = 	 {},
  OPTnote = 	 {},
  OPTannote = 	 {}
}

@article{Lake1987,
    Author = {JA Lake},
    Journal = {Molecular Biology and Evolution},
    Pages = {167--191},
    Title = {A rate-independent technique for analysis of nucleaic acid sequences: evolutionary parsimony},
    Volume = {4},
    Year = {1987}}

@article{Lam1994,
    Author = {W Lam and F Bacchus},
    Date-Modified = {2005-02-05 12:49:26 -0800},
    Pages = {269--293},
    Title = {Learning {B}ayesian Belief Networks: {A}n approach based on the {MDL} principle},
    Volume = {10},
    Year = {1994}}

@article{Lam2003,
    Abstract = {The application of Needleman--Wunsch alignment techniques to biological sequences is complicated by two serious problems when the sequences are long: the running time, which scales as the product of the lengths of sequences, and the difficulty in obtaining suitable parameters that produce meaningful alignments. The running time problem is often corrected by reducing the search space, using techniques such as banding, or chaining of high-scoring pairs. The parameter problem is more difficult to fix, partly because the probabilistic model, which Needleman--Wunsch is equivalent to, does not capture a key feature of biological sequence alignments, namely the alternation of conserved blocks and seemingly unrelated nonconserved segments. We present a solution to the problem of designing efficient search spaces for pair hidden Markov models that align biological sequences by taking advantage of their associated features. Our approach leads to an optimization problem, for which we obtain a 2-approximation algorithm, and that is based on the construction of Manhattan networks, which are close relatives of Steiner trees. We describe the underlying theory and show how our methods can be applied to alignment of DNA sequences in practice, successfully reducing the Viterbi algorithm search space of alignment PHMMs by three orders of magnitude.},
    Affiliation = {Department of Mathematics, Massachusetts Institute of Technology, Cambridge, MA 02139, USA.},
    Aid = {10.1089/10665270360688156 {$[$}doi{$]$}},
    Au = {Pachter L},
    Author = {F Lam and M Alexandersson and L Pachter},
    Da = {20030825},
    Date-Modified = {2005-02-05 12:49:26 -0800},
    Dcom = {20040330},
    Edat = {2003/08/26 05:00},
    Jid = {9433358},
    Journal = {J Comput Biol},
    Keywords = {Algorithms and Animals and Antigens, CD4/genetics and Computational Biology/*methods and *Data Interpretation, Statistical and Humans and Markov Chains and Mice and Research Support, Non-U.S. Gov't and Sequence Alignment/*methods},
    Language = {eng},
    Lr = {20041117},
    Mhda = {2004/03/31 05:00},
    Number = {3-4},
    Own = {NLM},
    Pages = {509--20},
    Pl = {United States},
    Pmid = {12935341},
    Pst = {ppublish},
    Pt = {Journal Article},
    Pubm = {Print},
    Rn = {0 (Antigens, CD4)},
    Sb = {IM},
    So = {Bioinformatics 2003 Oct;19 Suppl 2:II36-II41.},
    Stat = {MEDLINE},
    Title = {Picking alignments from (Steiner) trees.},
    Volume = {10},
    Year = {2003}}

@article{Lanave1984,
    Author = {CG Lanave and G Preparata and C Saccone and G Serio},
    Journal = {Journal of Molecular Evolution},
    Pages = {86--93},
    Title = {A new method for calculating evolutionary substitution rates},
    Volume = {20},
    Year = {1984}}

@article{Lander1988,
    Author = {ES Lander and MS Waterman},
    Journal = {Genomics},
    Pages = {231--239},
    Title = {Genomic mapping by fingerprinting random clones: a mathematical analysis},
    Volume = {2},
    Year = {1988}}

@article{Landsberg2004,
    Author = {JM Landsberg and L Manivel},
    Journal = {Foundations of Computational Mathematics},
    Number = {4},
    Pages = {397--422},
    Title = {On the Ideals of Secant Varieties of {Segre} Varieties},
    Volume = {4},
    Year = {2004}}

@Article{Langmead2009,
  author = 	 {B Langmead and C Trapnell and M Pop and SL Salzberg},
  title = 	 {Ultrafast and memory-efficient alignment of short {DNA} sequences to the human genome},
  journal = 	 {Genome Biology},
  year = 	 {2009},
  OPTkey = 	 {},
  volume = 	 {10},
  OPTnumber = 	 {},
  pages = 	 {R25},
  OPTmonth = 	 {},
  OPTnote = 	 {},
  OPTannote = 	 {}
}

@inproceedings{Laubenbacher2003,
    Author = {R Laubenbacher},
    Booktitle = {Proceedings of the 2003 International Symposium on Symbolic and Algebraic Computation},
    Optorganization = {Association for Computing Machinery},
    Title = {A computer algebra approach to biological systems},
    Year = {2003}}

@article{Laubenbacher2004,
    Author = {R Laubenbacher and B Stigler},
    Journal = {Journal of Theoretical Biology},
    Pages = {523--537},
    Title = {A Computational Algebra Approach to the Reverse Engineering of Gene Regulatory Networks},
    Volume = {229},
    Year = {2004}}

@article{Lauritzen1995,
    Author = {SL Lauritzen},
    Date-Modified = {2005-02-05 12:49:27 -0800},
    Journal = {Computational Statistics and Data Analysis},
    Pages = {191--201},
    Title = {The {EM} Algorithm for Graphical Association Models with Missing Data},
    Volume = {19},
    Year = {1995}}

@book{Lauritzen1996,
    Address = {New York},
    Author = {SL Lauritzen},
    Isbn = {0-19-852219-3},
    Mrclass = {62-01 (05C90 60J99 62H05 62H10 62H17 68T30)},
    Mrnumber = {MR1419991 (98g:62001)},
    Mrreviewer = {M. Studen{\'y}},
    Note = {Oxford Science Publications},
    Pages = {x+298},
    Publisher = {The Clarendon Press Oxford University Press},
    Series = {{\rm Oxford Statistical Science Series}},
    Title = {Graphical models},
    Volume = {17},
    Year = {1996}}

@article{Lenstra1983,
    Author = {HW Lenstra},
    Fjournal = {Mathematics of Operations Research},
    Issn = {0364-765X},
    Journal = {Mathematics of Operations Research},
    Mrclass = {90C10},
    Mrnumber = {MR727410 (86f:90106)},
    Number = {4},
    Pages = {538--548},
    Title = {Integer programming with a fixed number of variables},
    Volume = {8},
    Year = {1983}}

@article{Levinson1987,
    Author = {G Levinson and GA Gutman},
    Journal = {Molecular Biology and Evolution},
    Pages = {203--221},
    Title = {Slipped-strand mispairing: a major mechanism for {DNA} sequence evolution},
    Volume = {4},
    Year = {1987}}

@Article{Levy2006,
  Author = {D Levy and R Yoshida and L Pachter},
  title =    {Beyond pairwise distances: neighbor joining with
                  phylogenetic diversity estimates},
  journal =      {Molecular Biology and Evolution},
  year =     {2006},
  OPTkey =   {},
  volume =   {23},
  OPTnumber =    {},
  pages =    {491--498},
  OPTmonth =     {},
  OPTnote =      {},
  OPTannote =    {}
}

@Article{Li2009a,
  author = 	 {H Li and B Handsaker and A Wysoker and T Fennell and J Ruan and N Homer and G Marth and G Abecasis and R Durbin and 1000 Genome Project Data Processing Subgroup},
  title = 	 {The sequence alignment/map format and {SAM}tools},
  journal = 	 {Bioinformatics},
  year = 	 {2009},
  OPTkey = 	 {},
  volume = 	 {25},
  OPTnumber = 	 {16},
  pages = 	 {2078--2079},
  OPTmonth = 	 {},
  OPTnote = 	 {},
  OPTannote = 	 {}
}

@Article{Li2009b,
  author = 	 {B Li and V Ruotti and RM Stewart and JA Thomson and CN Dewey},
  title = 	 {{RNA-Seq} gene expression estimation with read mapping uncertainty},
  journal = 	 {Bioinformatics},
  year = 	 {2009},
  OPTkey = 	 {},
  volume = 	 {26},
  OPTnumber = 	 {},
  pages = 	 {493--500},
  OPTmonth = 	 {},
  OPTnote = 	 {},
  OPTannote = 	 {}
}

@article{Lin2002,
    Author = {YH Lin and PA McLenachan and AR Gore and MJ Phillips and R Ota and MD Hendy and D Penny},
    Journal = {Molecular Phylogenetics and Evolution},
    Pages = {2060-2070},
    Title = {Four new mitochondrial genomes and the increased stability of evolutionary trees of mammals from improved taxon sampling.},
    Volume = {19},
    Year = {2002}}

@article{Litvinov2005,
    Author = {G Litvinov},
    Date-Modified = {2005-02-05 12:49:27 -0800},
    Journal = {arXiv.org:math/0501038},
    Title = {{The Maslov dequantization, idempotent and tropical mathematics: a very brief introduction}},
    Year = {2005}}

@article{Liu1995,
    Author = {JS Liu and CE Lawrence and A Neuwald},
    Date-Modified = {2005-02-05 12:49:27 -0800},
    Journal = {Journal of the American Statistical Association},
    Pages = {1156--70},
    Title = {{Bayesian models for multiple local sequence alignment and its Gibbs sampling strategies}},
    Volume = {90},
    Year = {1995}}

@article{Loh2002,
    Author = {E Loh and GW Walster},
    Date-Modified = {2005-02-05 12:49:26 -0800},
    Journal = {Reliable Computing},
    Pages = {245--248},
    Title = {Rump's example revisited},
    Volume = {8},
    Year = {2002}}

@misc{Loots2002,
    Abstract = {Identifying transcriptional regulatory elements represents a significant challenge in annotating the genomes of higher vertebrates. We have developed a computational tool, rVista, for high-throughput discovery of cis-regulatory elements that combines clustering of predicted transcription factor binding sites (TFBSs) and the analysis of interspecies sequence conservation to maximize the identification of functional sites. To assess the ability of rVista to discover true positive TFBSs while minimizing the prediction of false positives, we analyzed the distribution of several TFBSs across 1 Mb of the well-annotated cytokine gene cluster (Hs5q31; Mm11). Because a large number of AP-1, NFAT, and GATA-3 sites have been experimentally identified in this interval, we focused our analysis on the distribution of all binding sites specific for these transcription factors. The exploitation of the orthologous human-mouse dataset resulted in the elimination of > 95% of the approximately 58,000 binding sites predicted on analysis of the human sequence alone, whereas it identified 88% of the experimentally verified binding sites in this region.},
    Affiliation = {Genome Sciences Department, Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA. ggloots@lbl.gov},
    Aid = {10.1101/gr.225502. Article published online before print in April 2002 [doi]},
    Au = {Rubin EM},
    Author = {GG Loots and I Ovcharenko and L Pachter and I Dubchak and EM Rubin},
    Da = {20020508},
    Date-Modified = {2005-02-05 12:49:27 -0800},
    Dcom = {20020605},
    Edat = {2002/05/09 10:00},
    Jid = {9518021},
    Journal = {Genome Research},
    Keywords = {Animals and Base Sequence/genetics and Binding Sites/genetics and Comparative Study and Computational Biology/methods and Cytokines/chemistry/genetics and Humans and Mice and Multigene Family/genetics and Promoter Regions (Genetics)/genetics and Research Support, U.S. Gov't, Non-P.H.S. and Research Support, U.S. Gov't, P.H.S. and *Software and Transcription Factors/*chemistry/*genetics},
    Language = {eng},
    Lr = {20041117},
    Mhda = {2002/06/06 10:01},
    Number = {5},
    Own = {NLM},
    Pages = {832--9},
    Pl = {United States},
    Pmid = {11997350},
    Pst = {ppublish},
    Pt = {Validation Studies},
    Pubm = {Print},
    Rn = {0 (Transcription Factors)},
    Sb = {IM},
    So = {Brief Bioinform 2002 Mar;3(1):18-22.},
    Stat = {MEDLINE},
    Title = {rVista for comparative sequence-based discovery of functional transcription factor binding sites.},
    Volume = {12},
    Year = {2002}}

@Book{Lovasz2009,
  author = 	 {L L\'{o}vasz and MD Plummer},
  ALTeditor = 	 {},
  title = 	 {{Matching Theory}},
  publisher = 	 {American Mathematical Society Press},
  year = 	 {2009},
  OPTkey = 	 {},
  OPTvolume = 	 {},
  OPTnumber = 	 {},
  OPTseries = 	 {},
  OPTaddress = 	 {},
  OPTedition = 	 {},
  OPTmonth = 	 {},
  OPTnote = 	 {},
  OPTannote = 	 {}
}

@article{MAVID,
    Author = {MAVID},
    Date-Modified = {2005-02-05 12:49:26 -0800},
    Note = {http://baboon.math.berkeley.edu/mavid},
    Title = {http://baboon.math.berkeley.edu/mavid}}

@unpublished{MLAGAN,
    Author = {MLAGAN},
    Date-Modified = {2005-02-05 12:49:26 -0800},
    Note = {http://lagan.stanford.edu/},
    Title = {http://lagan.stanford.edu/}}

@article{Madsen2001,
    Author = {O Madsen and M Scally and CJ Douady and DJ Kao and RW Debry and R Adkins and HM Ambrine and MJ Stanhope and WW DeJong and MS Springer},
    Journal = {Nature},
    Pages = {610-614},
    Title = {{Parallel adaptive radiations in two major clades of placental mammals.}},
    Volume = {409},
    Year = {2001}}

@article{Marcotte1999,
    Author = {EM Marcotte and M Pellegrini and MJ Thompson and T Yeates and D Eisenberg},
    Journal = {Nature},
    Pages = {83--86},
    Title = {A Combined Algorithm for Genome-Wide Prediction of Protein Function},
    Volume = {402},
    Year = {1999}}

@article{Mayor2000,
    Abstract = {Summary: VISTA is a program for visualizing global DNA sequence alignments of arbitrary length. It has a clean output, allowing for easy identification of similarity, and is easily configurable, enabling the visualization of alignments of various lengths at different levels of resolution. It is currently available on the web, thus allowing for easy access by all researchers. Availability: VISTA server is available on the web at http://www-gsd.lbl.gov/vista. The source code is available upon request. Contact: vista@lbl.gov},
    Affiliation = {National Energy Research Scientific Computing Center Genome Sciences Department, Berkeley, CA 94720, USA. vista@lbl.gov},
    Au = {Dubchak I},
    Author = {Mayor, C and Brudno, M and Schwartz, J R and Poliakov, A and Rubin, E M and Frazer, K A and Pachter, L S and Dubchak, I},
    Da = {20010222},
    Date-Modified = {2005-02-05 12:49:27 -0800},
    Dcom = {20010419},
    Edat = {2001/02/13 11:00},
    Gr = {GM-5748202/GM/NIGMS},
    Jid = {9808944},
    Journal = {Bioinformatics},
    Keywords = {Animals and Computational Biology and DNA/*genetics and Humans and Internet and Mice and Rabbits and Research Support, U.S. Gov't, Non-P.H.S. and Research Support, U.S. Gov't, P.H.S. and Sequence Alignment/*statistics \& numerical data and *Software},
    Language = {eng},
    Lr = {20041117},
    Mhda = {2001/04/21 10:01},
    Number = {11},
    Own = {NLM},
    Pages = {1046--7},
    Pl = {England},
    Pmid = {11159318},
    Pst = {ppublish},
    Pt = {Journal Article},
    Pubm = {Print},
    Rn = {9007-49-2 (DNA)},
    Sb = {IM},
    So = {Genome Res 2001 May;11(5):710-30.},
    Stat = {MEDLINE},
    Title = {VISTA : visualizing global DNA sequence alignments of arbitrary length.},
    Volume = {16},
    Year = {2000}}


@article{McAuliffe2004,
    Abstract = {MOTIVATION: Phylogenetic shadowing is a comparative genomics principle that allows for the discovery of conserved regions in sequences from multiple closely related organisms. We develop a formal probabilistic framework for combining phylogenetic shadowing with feature-based functional annotation methods. The resulting model, a generalized hidden {Markov} phylogeny (GHMP), applies to a variety of situations where functional regions are to be inferred from evolutionary constraints. RESULTS: We show how GHMPs can be used to predict complete shared gene structures in multiple primate sequences. We also describe shadower, our implementation of such a prediction system. We find that shadower outperforms previously reported ab initio gene finders, including comparative human-mouse approaches, on a small sample of diverse exonic regions. Finally, we report on an empirical analysis of shadower's performance which reveals that as few as five well-chosen species may suffice to attain maximal sensitivity and specificity in exon demarcation. AVAILABILITY: A Web server is available at http://bonaire.lbl.gov/shadower},
    Affiliation = {Department of Statistics, University of California, 367 Evans Hall, Berkeley, CA 94720, USA.},
    Aid = {bth153 {$[$}pii{$]$}},
    Au = {Jordan MI},
    Author = {JD McAuliffe and L Pachter and MI Jordan},
    Da = {20040812},
    Date-Modified = {2005-02-05 12:49:26 -0800},
    Dep = {20040226},
    Edat = {2004/02/28 05:00},
    Gr = {R01-HG02362-02/HG/NHGRI},
    Jid = {9808944},
    Journal = {Bioinformatics},
    Language = {eng},
    Mhda = {2004/02/28 05:00},
    Number = {12},
    Own = {NLM},
    Pages = {1850-60},
    Phst = {2004/02/26 {$[$}aheadofprint{$]$}},
    Pl = {England},
    Pmid = {14988105},
    Pst = {ppublish},
    Pt = {Journal Article},
    Pubm = {Print-Electronic},
    Sb = {IM},
    So = {Nature 2004 Apr 1;428(6982):493-521.},
    Stat = {In-Process},
    Title = {Multiple-sequence functional annotation and the generalized hidden {M}arkov phylogeny.},
    Volume = {20},
    Year = {2004}}


@article{McMullen1971,
    Author = {P McMullen},
    Date-Modified = {2005-02-05 12:49:27 -0800},
    Journal = {Journal of Combinatorial Theory, Series B},
    Pages = {179--184},
    Title = {The maximum numbers of faces of a convex polytope},
    Volume = {10},
    Year = {1971}}

@article{Megiddo1984,
    Author = {N Megiddo},
    Coden = {JACOAH},
    Fjournal = {Journal of the Association for Computing Machinery},
    Issn = {0004-5411},
    Journal = {Journal of the Association for Computing Machinery},
    Mrclass = {90C05},
    Mrnumber = {MR821388 (87b:90082)},
    Number = {1},
    Pages = {114--127},
    Title = {Linear programming in linear time when the dimension is fixed},
    Volume = {31},
    Year = {1984}}

@unpublished{Mihaescu2005,
    Author = {R Mihaescu},
    Date-Modified = {2005-02-28 12:49:27 -0800},
    Note = {In preparation},
    Title = {The Toric Ideal of the Unhidden {M}arkov Model.},
    Year = {2005}}

@Unpublished{Mihaescu2006,
  author = 	 {R Mihaescu and D Levy and L Pachter},
  title = 	 {Why neighbor joining works},
  note = 	 {arXiv cs.DS/0602041},
  OPTkey = 	 {},
  OPTmonth = 	 {},
  year = 	 {2006},
  OPTannote = 	 {}
}

@article{Miller2001,
    Author = {W Miller},
    Date-Modified = {2005-02-05 12:49:26 -0800},
    Journal = {Bioinformatics},
    Pages = {391--397},
    Title = {Comparison of genomic DNA sequences: solved and unsolved problems},
    Volume = {17},
    Year = {2001}}

@article{Mindell1990,
    Author = {DP Mindell and RL Honeycutt},
    Journal = {Annual Review of Ecology and Systematics},
    Pages = {541--566},
    Title = {Ribosomal {RNA} in vertebrates: evolution and phylogenetic applications.},
    Volume = {21},
    Year = {1990}}

@article{Mitchison1999,
    Author = {GJ Mitchison},
    Date-Modified = {2005-02-05 12:49:26 -0800},
    Journal = {Journal of Molecular Evolution},
    Number = {1},
    Pages = {11--22},
    Title = {A Probabilistic Treatment of Phylogeny and Sequence Alignment},
    Volume = {49},
    Year = {1999}}



@article{Mond2003,
    Author = {DMQ Mond and JQ Smith and D Van Straten},
    Journal = {Proceedings of the Royal Society of London, Series A},
    Pages = {2821--2845},
    Title = {Stochastic factorisations, sandwiched simplices and the topology of the space of explanations},
    Volume = {459},
    Year = {2003}}

@book{Moore1967,
    Address = {Englewood Cliffs, New Jersey},
    Author = {RE Moore},
    Date-Modified = {2005-02-05 12:49:26 -0800},
    Publisher = {Prentice-Hall},
    Title = {Interval Analysis},
    Year = {1967}}

@book{Moore1979,
    Address = {Philadelphia, Pennsylvania},
    Author = {RE Moore},
    Date-Modified = {2005-02-05 12:49:26 -0800},
    Publisher = {SIAM},
    Title = {Methods and Applications of Interval analysis},
    Year = {1979}}

@Article{Moret2004,
  author = 	 {BE Moret and L Nakhleh and T Warnow and CR Linder and A Tholse and A Padolina and J Sun and R Timme},
  title = 	 {Phylogenetic networks: modeling reconstructibility and accuracy},
  journal = 	 {IEEE/ACM Transactions on Computational Biology and Bioinformatics},
  year = 	 {2004},
  OPTkey = 	 {},
  volume = 	 {1},
  OPTnumber = 	 {1},
  pages = 	 {13--23},
  OPTmonth = 	 {},
  OPTnote = 	 {},
  OPTannote = 	 {}
}

@article{Morgenstern1996,
    Author = {B Morgenstern and A Dress and T Werner},
    Date-Modified = {2005-02-05 12:49:26 -0800},
    Journal = {Proceedings of the National Academy of Sciences, USA},
    Pages = {12098--12103},
    Title = {Multiple DNA and protein sequence alignment based on segment-to-segment comparison},
    Volume = {93},
    Year = {1996}}



@article{Morgenstern1999,
    Author = {B Morgenstern},
    Date-Modified = {2005-02-05 12:49:26 -0800},
    Journal = {Bioinformatics},
    Pages = {211--218},
    Title = {DIALIGN 2: Improvement of the segment-to-segment approach to multiple sequence alignment},
    Volume = {15},
    Year = {1999}}




@article{Morgenstern2000,
    Author = {B Morgenstern},
    Date-Modified = {2005-02-05 12:49:26 -0800},
    Journal = {Bioinformatics},
    Pages = {948--949},
    Title = {A space-efficient algorithm for aligning large genomic sequences},
    Volume = {16},
    Year = {2000}}

@Article{Mortazavi2008,
  author = 	 {A Mortazavi and BA Williams and K McCue and L Schaeffer and B Wold},
  title = 	 {Mapping and quantifying mammalian transcriptomes by {RNA-Seq}},
  journal = 	 {Nature Methods},
  year = 	 {2008},
  OPTkey = 	 {},
  volume = 	 {5},
  OPTnumber = 	 {7},
  pages = 	 {585--587},
  OPTmonth = 	 {},
  OPTnote = 	 {},
  OPTannote = 	 {}
}

@article{Mount1982,
    Author = {SM Mount},
    Date-Modified = {2005-02-05 12:49:26 -0800},
    Journal = {Nucleic Acids Research},
    Number = {2},
    Pages = {459--472},
    Title = {A catalogue of splice junction sequence},
    Volume = {10},
    Year = {1982}}

@inproceedings{Murphy1999,
    Author = {KP Murphy and Y Weiss and MI Jordan},
    Booktitle = {Proceedings of the Uncertainty in Artificial Intelligence Conference},
    Date-Modified = {2005-02-05 12:49:26 -0800},
    Pages = {467--475},
    Title = {Loopy belief propagation for approximate inference: an empirical study},
    Year = {1999}}

@article{Murphy2001,
    Author = {WJ Murphy and E Eizirik and WE Johnson and YP Zhang and OA Ryder and SJ O'Brien.},
    Journal = {Nature},
    Pages = {614--618},
    Title = {Molecular phylogenetics and the origins of placental mammals.},
    Volume = {409},
    Year = {2001}}

@article{Myers1999,
    Author = {E Myers},
    Journal = {IEEE Computational Engineering and Science},
    Number = {1},
    Pages = {33--43},
    Title = {Whole-Genome {DNA} Sequencing},
    Volume = {3},
    Year = {1999}}

@book{Na1990,
    Author = {A Neumaier},
    Optaddress = {Cambridge},
    Publisher = {Cambridge university press},
    Title = {Interval Methods for Systems of Equations},
    Year = {1990}}

@article{Nakhleh2003,
    Author = {L Nakhleh and J Sun and T Warnow and CR Linder and BME Moret and A Tholse},
    Date-Modified = {2005-02-05 12:49:27 -0800},
    Journal = {Proceedings of the Eighth Pacific Symposium on Biocomputing (PSB 03)},
    Title = {Towards the Development of Computational Tools for Evaluating Phylogenetic Network Reconstruction Methods},
    Year = {2003}}

@article{Nasrallah2002,
    Author = {JB Nasrallah},
    Date-Modified = {2005-02-05 12:49:26 -0800},
    Journal = {Science},
    Pages = {305--308},
    Title = {Recognition and rejection of self in plant reproduction},
    Volume = {296},
    Year = {2002}}

@article{Needleman1970,
    Author = {SB Needleman and CD Wunsch},
    Date-Modified = {2005-02-05 12:49:26 -0800},
    Journal = {Journal of Molecular Biology},
    Pages = {443--445},
    Title = {A general method applicable to the search for similarities in the amino acid sequence of two proteins},
    Volume = {48},
    Year = {1970}}

@book{Neumaier1990,
    Address = {Cambridge},
    Author = {A Neumaier},
    Date-Modified = {2005-02-05 12:49:26 -0800},
    Publisher = {Cambridge university press},
    Title = {Interval methods for systems of equations},
    Year = {1990}}

@Article{Newberg1996,
  author = 	 {LA Newberg},
  title = 	 {The number of clone orderings},
  journal = 	 {Discrete Applied Mathematics},
  year = 	 {1996},
  OPTkey = 	 {},
  volume = 	 {69},
  OPTnumber = 	 {},
  pages = 	 {233--245},
  OPTmonth = 	 {},
  OPTnote = 	 {},
  OPTannote = 	 {}
}

@incollection{Neyman1971,
    Address = {New York},
    Author = {J Neyman},
    Booktitle = {Statistical Decision Theory and Related Topics},
    Editor = {S Gupta and Y Jackel},
    Pages = {1--27},
    Publisher = {Academic Press},
    Title = {Molecular studies of evolution: {A} source of novel statistical problems},
    Year = {1971}}

@article{Ng1985,
    Author = {SY Ng and P Gunning and R Eddy and P Ponte and J Leavitt and T Shows and L Kedes},
    Journal = {Molecular and Cellular Biology},
    Pages = {2720--2732},
    Title = {Evolution of the functional human beta-actin gene and its multi-pseudogene family: conservation of noncoding regions and chromosomal dispersion of pseudogenes},
    Volume = {5},
    Year = {1985}}

@article{Nobrega2003,
    Author = {MA Nobrega and I Ovcharenko and V Afzal and EM Rubin},
    Eprint = {http://www.sciencemag.org/cgi/reprint/302/5644/413.pdf},
    Journal = {Science},
    Number = {5644},
    Pages = {413-},
    Title = {Scanning Human Gene Deserts for Long-Range Enhancers},
    Url = {\url{http://www.sciencemag.org}},
    Volume = {302},
    Year = {2003}}

@article{Notredame2000,
    Author = {C Notredame and D Higgins and J Heringa},
    Date-Modified = {2005-02-05 12:49:27 -0800},
    Journal = {Journal of Molecular Biology},
    Pages = {205--217},
    Title = {T-Coffee: A novel method for multiple sequence alignments},
    Volume = {302},
    Year = {2000}}


@Article{Olsen1994,
  author = {GJ Olsen and H Matsuda and R Hagstrom and R Overbeek},
  title = {{fastDNAml: A tool for construction of phylogenetic trees
                  of DNA sequences using maximum likelihood}},
  journal = {Computational Applied Biosciences},
  year = {1994},
  OPTkey = {},
  volume = {10},
  OPTnumber = {},
  pages = {41--48},
  OPTmonth = {},
  OPTnote = {},
  OPTannote = {}
}

@article{Ota2000,
    Author = {S Ota and WH Li},
    Journal = {Molecular Biology and Evolution},
    Number = {9},
    Pages = {1401--1409},
    Title = {{NJML}: A Hybrid Algorithm for the Neighbor-Joining and Maximum Likelihood Methods},
    Volume = {17},
    Year = {2000}}

@article{Pachter1999,
    Abstract = {This paper describes a fast and fully automated dictionary-based approach to gene annotation and exon prediction. Two dictionaries are constructed, one from the nonredundant protein OWL database and the other from the dbEST database. These dictionaries are used to obtain O (1) time lookups of tuples in the dictionaries (4 tuples for the OWL database and 11 tuples for the dbEST database). These tuples can be used to rapidly find the longest matches at every position in an input sequence to the database sequences. Such matches provide very useful information pertaining to locating common segments between exons, alternative splice sites, and frequency data of long tuples for statistical purposes. These dictionaries also provide the basis for both homology determination, and statistical approaches to exon prediction.},
    Affiliation = {Department of Mathematics, Massachusetts Institute of Technology, Cambridge 02139, USA.},
    Aid = {10.1089/106652799318364 {$[$}doi{$]$}},
    Au = {Berger B},
    Author = {L Pachter and S Batzoglou and VI Spitkovsky and E Banks and ES Lander and DJ Kleitman and B Berger},
    Da = {19991230},
    Date-Modified = {2005-02-05 12:49:26 -0800},
    Dcom = {19991230},
    Edat = {1999/12/03},
    Jid = {9433358},
    Journal = {J Comput Biol},
    Keywords = {Alternative Splicing and Animals and *Databases, Factual and *Dictionaries and Exons and Expressed Sequence Tags and *Genes and Genetic Techniques and Humans and Proteins/genetics and Research Support, Non-U.S. Gov't and Research Support, U.S. Gov't, P.H.S. and Sequence Alignment/statistics \& numerical data and Software},
    Language = {eng},
    Lr = {20041117},
    Mhda = {1999/12/03 00:01},
    Number = {3-4},
    Own = {NLM},
    Pages = {419--30},
    Pl = {UNITED STATES},
    Pmid = {10582576},
    Pst = {ppublish},
    Pt = {Journal Article},
    Pubm = {Print},
    Rn = {0 (Proteins)},
    Sb = {IM},
    So = {Genome Res 2000 Jul;10(7):950-8.},
    Stat = {MEDLINE},
    Title = {A dictionary-based approach for gene annotation.},
    Volume = {6},
    Year = {1999}}

@article{Pachter2002,
    Abstract = {Hidden Markov models (HMMs) have been successfully applied to a variety of problems in molecular biology, ranging from alignment problems to gene finding and annotation. Alignment problems can be solved with pair HMMs, while gene finding programs rely on generalized HMMs in order to model exon lengths. In this paper, we introduce the generalized pair HMM (GPHMM), which is an extension of both pair and generalized HMMs. We show how GPHMMs, in conjunction with approximate alignments, can be used for cross-species gene finding and describe applications to DNA-cDNA and DNA-protein alignment. GPHMMs provide a unifying and probabilistically sound theory for modeling these problems.},
    Affiliation = {Department of Mathematics, University of California Berkeley, Berkeley, CA 94720, USA. lpachter@math.berkeley.edu},
    Aid = {10.1089/10665270252935520 {$[$}doi{$]$}},
    Au = {Cawley S},
    Author = {L Pachter and M Alexandersson and S Cawley},
    Da = {20020517},
    Date-Modified = {2005-02-05 12:49:26 -0800},
    Dcom = {20021004},
    Edat = {2002/05/23 10:00},
    Jid = {9433358},
    Journal = {J Comput Biol},
    Keywords = {Algorithms and Computational Biology and DNA/genetics and *Markov Chains and Models, Statistical and Proteins/genetics and Research Support, Non-U.S. Gov't and Sequence Alignment/*statistics \& numerical data},
    Language = {eng},
    Lr = {20041117},
    Mhda = {2002/10/09 04:00},
    Number = {2},
    Own = {NLM},
    Pages = {389--99},
    Pl = {United States},
    Pmid = {12015888},
    Pst = {ppublish},
    Pt = {Journal Article},
    Pubm = {Print},
    Rn = {9007-49-2 (DNA)},
    Sb = {IM},
    So = {Nature 2002 Dec 5;420(6915):520-62.},
    Stat = {MEDLINE},
    Title = {{Applications of generalized pair hidden Markov models to alignment and gene finding problems}},
    Volume = {9},
    Year = {2002}}

@article{Pachter2004,
    Author = {L Pachter and D Speyer},
    Coden = {AMLEEL},
    Date-Modified = {2005-02-05 13:00:15 -0800},
    Fjournal = {Applied Mathematics Letters. An International Journal of Rapid Publication},
    Issn = {0893-9659},
    Journal = {Applied Mathematics Letters},
    Mrclass = {05C05 (05C85 92D15)},
    Mrnumber = {MR2064171 (2005b:05066)},
    Number = {6},
    Pages = {615--621},
    Title = {Reconstructing trees from subtree weights},
    Volume = {17},
    Year = {2004}}

@article{Pachter2004b,
    Abstract = {One of the major successes in computational biology has been the unification, by using the graphical model formalism, of a multitude of algorithms for annotating and comparing biological sequences. Graphical models that have been applied to these problems include hidden Markov models for annotation, tree models for phylogenetics, and pair hidden Markov models for alignment. A single algorithm, the sum-product algorithm, solves many of the inference problems that are associated with different statistical models. This article introduces the polytope propagation algorithm for computing the Newton polytope of an observation from a graphical model. This algorithm is a geometric version of the sum-product algorithm and is used to analyze the parametric behavior of maximum a posteriori inference calculations for graphical models.},
    Affiliation = {Department of Mathematics, University of California, Berkeley, CA 94720, USA. lpachter@math.berkeley.edu},
    Aid = {10.1073/pnas.0406011101 {$[$}doi{$]$}},
    Au = {Sturmfels B},
    Author = {L Pachter and B Sturmfels},
    Da = {20041119},
    Date-Modified = {2005-02-05 13:00:15 -0800},
    Dcom = {20041227},
    Dep = {20041108},
    Edat = {2004/11/10 09:00},
    Gr = {R01-HG02362-02/HG/NHGRI},
    Jid = {7505876},
    Journal = {Proc Natl Acad Sci U S A},
    Keywords = {Algorithms and Markov Chains and Models, Statistical and Research Support, Non-U.S. Gov't and Research Support, U.S. Gov't, Non-P.H.S. and Research Support, U.S. Gov't, P.H.S. and Sequence Alignment/statistics \& numerical data and Sequence Analysis/*statistics \& numerical data and Sequence Analysis, DNA/statistics \& numerical data},
    Language = {eng},
    Lr = {20050121},
    Mhda = {2004/12/28 09:00},
    Number = {46},
    Own = {NLM},
    Pages = {16138--43},
    Phst = {2004/11/08 {$[$}aheadofprint{$]$}},
    Pl = {United States},
    Pmid = {15534223},
    Pst = {ppublish},
    Pt = {Journal Article},
    Pubm = {Print-Electronic},
    Sb = {IM},
    So = {Proc Natl Acad Sci U S A 2004 Nov 16;101(46):16132-7. Epub 2004 Nov 08.},
    Stat = {MEDLINE},
    Title = {Parametric inference for biological sequence analysis.},
    Volume = {101},
    Year = {2004}}

@article{Pachter2004c,
    Abstract = {This article presents a unified mathematical framework for inference in graphical models, building on the observation that graphical models are algebraic varieties. From this geometric viewpoint, observations generated from a model are coordinates of a point in the variety, and the sum-product algorithm is an efficient tool for evaluating specific coordinates. Here, we address the question of how the solutions to various inference problems depend on the model parameters. The proposed answer is expressed in terms of tropical algebraic geometry. The Newton polytope of a statistical model plays a key role. Our results are applied to the hidden Markov model and the general Markov model on a binary tree.},
    Affiliation = {Department of Mathematics, University of California, Berkeley, CA 94720, USA.},
    Aid = {10.1073/pnas.0406010101 {$[$}doi{$]$}},
    Au = {Sturmfels B},
    Author = {L Pachter and B Sturmfels},
    Da = {20041119},
    Date-Modified = {2005-02-05 13:00:15 -0800},
    Dcom = {20041227},
    Dep = {20041108},
    Edat = {2004/11/10 09:00},
    Gr = {R01-HG02362-02/HG/NHGRI},
    Jid = {7505876},
    Journal = {Proceedings of the National Academy of Sciences, USA},
    Keywords = {Algorithms and Markov Chains and Mathematics and *Models, Statistical and Research Support, Non-U.S. Gov't and Research Support, U.S. Gov't, Non-P.H.S. and Research Support, U.S. Gov't, P.H.S.},
    Language = {eng},
    Lr = {20050121},
    Mhda = {2004/12/28 09:00},
    Number = {46},
    Own = {NLM},
    Pages = {16132-7},
    Phst = {2004/11/08 {$[$}aheadofprint{$]$}},
    Pl = {United States},
    Pmid = {15534224},
    Pst = {ppublish},
    Pt = {Journal Article},
    Pubm = {Print-Electronic},
    Sb = {IM},
    So = {Nature 2004 Dec 9;432(7018):695-716.},
    Stat = {MEDLINE},
    Title = {Tropical geometry of statistical models.},
    Volume = {101},
    Year = {2004}}

@article{Pachter2005,
    Author = {L Pachter and B Sturmfels},
    Date-Modified = {2005-02-05 13:00:15 -0800},
    Journal = {SIAM Review, in press},
    Title = {The Mathematics of Phylogenomics},
    Year = {2005}}

@article{Park1998,
    Author = {J Park and K Karplus and C Barrett and R Hughey and D Haussler and T Hubbard and C Chothia},
    Date-Modified = {2005-02-05 12:49:27 -0800},
    Journal = {Journal of Molecular Biology},
    Pages = {1201--1210},
    Title = {Sequence Comparisons Using Multiple Sequences Detect Three Times as Many Remote Homolgues as Pairwise Methods},
    Volume = {284},
    Year = {1998}}

@article{Parra2000,
    Author = {G Parra and E Blanco and R Guig\'{o}},
    Journal = {Genome Research},
    Number = {4},
    Pages = {511--515},
    Title = {{GENEID} in Drosophila},
    Volume = {10},
    Year = {2000}}

@Article{Pauplin2000,
  author =   {Y Pauplin},
  title =    {Direct calculation of tree length using a distance matrix},
  journal =      {Journal of Molecular Evolution},
  year =     {2000},
  OPTkey =   {},
  volume =   {51},
  OPTnumber =    {},
  pages =    {41--47},
  OPTmonth =     {},
  OPTnote =      {},
  OPTannote =    {}
}

@Article{Pe'er2004,
  author = 	 {I Pe'er and JS Beckmann},
  title = 	 {Recovering Frequencies of Known Haplotype Blocks From Single-Nucleotide Polymorphism Allele Frequencies},
  journal = 	 {Genetics},
  year = 	 {2004},
  OPTkey = 	 {},
  volume = 	 {166},
  OPTnumber = 	 {},
  pages = 	 {2001--2006},
  OPTmonth = 	 {},
  OPTnote = 	 {},
  OPTannote = 	 {}
}

@book{Pearl1988,
    Address = {San Francisco},
    Author = {J Pearl},
    Date-Modified = {2005-02-05 12:49:26 -0800},
    Publisher = {Morgan Kaufmann},
    Title = {Probabilistic Reasoning in Intelligent Systems},
    Year = {1988}}

@article{Pennacchio2001,
    Author = {LA Pennacchio and EM Rubin},
    Date-Modified = {2005-02-05 12:49:26 -0800},
    Journal = {Nature Review Genetics},
    Pages = {100--109},
    Title = {Genomic strategies to identify mammalian regulatory sequences},
    Volume = {2},
    Year = {2001}}

@article{Peter2002,
    Abstract = {The Drosophila melanogaster genome consists of four chromosomes that contain 165 Mb of DNA, 120 Mb of which are euchromatic. The two Drosophila Genome Projects, in collaboration with Celera Genomics Systems, have sequenced the genome, complementing the previously established physical and genetic maps. In addition, the Berkeley Drosophila Genome Project has undertaken large-scale functional analysis based on mutagenesis by transposable P element insertions into autosomes. Here, we present a large-scale P element insertion screen for vital gene functions and a BAC tiling map for the X chromosome. A collection of 501 X-chromosomal P element insertion lines was used to map essential genes cytogenetically and to establish short sequence tags (STSs) linking the insertion sites to the genome. The distribution of the P element integration sites, the identified genes and transcription units as well as the expression patterns of the P-element-tagged enhancers is described and discussed.},
    Affiliation = {Max-Planck-Institut fur Biophysikalische Chemie, Abt. Molekulare Entwicklungsbiologie, Am Fassberg, 37077 Gottingen, Germany.},
    Aid = {kvf012 {$[$}pii{$]$}},
    Au = {Schafer U},
    Author = {A Peter and P Schottler and M Werner and N Beinert and G Dowe and P Burkert and F Mourkioti and L Dentzer and Y He and P Deak and others},
    Da = {20020118},
    Date-Modified = {2005-02-05 12:49:26 -0800},
    Dcom = {20020923},
    Dep = {20011219},
    Edat = {2001/12/26 10:00},
    Jid = {100963049},
    Journal = {EMBO Rep},
    Keywords = {Animals and *Chromosome Mapping and Chromosomes, Artificial, Bacterial and Contig Mapping and DNA Probes and DNA Transposable Elements and Drosophila melanogaster/*genetics and Female and Genes, Essential and Genes, Insect and Male and Mutagenesis and Research Support, Non-U.S. Gov't and *X Chromosome},
    Language = {eng},
    Lr = {20041117},
    Mhda = {2002/09/30 10:00},
    Number = {1},
    Own = {NLM},
    Pages = {34--8},
    Phst = {2001/12/19 {$[$}aheadofprint{$]$}},
    Pl = {England},
    Pmid = {11751581},
    Pst = {ppublish},
    Pt = {Journal Article},
    Pubm = {Print-Electronic},
    Rn = {0 (DNA Transposable Elements)},
    Sb = {IM},
    So = {Genome Res 2002 May;12(5):832--9.},
    Stat = {MEDLINE},
    Title = {Mapping and identification of essential gene functions on the X chromosome of Drosophila.},
    Volume = {3},
    Year = {2002}}

@article{Peters2000,
    Author = {T Peters and R Dildrop and K Ausmeier and U Ruther},
    Journal = {Genome Research},
    Pages = {1453--1462},
    Title = {Organization of Mouse Iroquois Homeobox Genes in Two Clusters Suggests a Conserved Regulation and Function in Vertebrate Development},
    Volume = {10},
    Year = {2000}}

@article{Pevzner2003,
    Author = {P Pevzner and G Tesler},
    Journal = {Genome Research},
    Pages = {37--45},
    Title = {Genome rearrangements in mammalian evolution: lessons from human and mouse genomes},
    Volume = {13(1)},
    Year = {2003}}

@article{Phillips2003,
    Author = {MJ Phillips and D Penny},
    Journal = {Molecular Phylogenetics and Evolution},
    Pages = {171-185},
    Title = {The root of the mammalian tree inferred from whole mitochondrial genomes.},
    Volume = {28},
    Year = {2003}}

@incollection{Pin1998,
    Address = {Cambridge},
    Author = {Pin, Jean-Eric},
    Booktitle = {Idempotency (Bristol, 1994)},
    Mrclass = {16Y60 (68Q45 68Q70)},
    Mrnumber = {MR1608374 (99a:16045)},
    Mrreviewer = {C. J. Maxson},
    Pages = {50--69},
    Publisher = {Cambridge Univ. Press},
    Series = {Publ. Newton Inst.},
    Title = {Tropical semirings},
    Volume = {11},
    Year = {1998}}

@book{Pistone2000,
    Author = {G Pistone and E Riccomagno and HP Wynn},
    Month = {December},
    Publisher = {Chapman \& Hall/CRC},
    Title = {Algebraic Statistics: Computational Commutative Algebra in Statistics},
    Year = {2000}}

@incollection{Pistone2001,
    Address = {Providence, RI},
    Author = {Pistone, Giovanni and Riccomagno, Eva and Wynn, Henry P.},
    Booktitle = {Algebraic methods in statistics and probability (Notre Dame, IN, 2000)},
    Mrclass = {62B15 (13P99 62H17 62J05 62J12 68W30)},
    Mrnumber = {MR1873681 (2002m:62017)},
    Pages = {267--282},
    Publisher = {American Mathematical Society},
    Series = {Contemporary Mathematics},
    Title = {Computational commutative algebra in discrete statistics},
    Volume = {287},
    Year = {2001}}

@article{Pollard2001,
    Author = {TD Pollard},
    Journal = {Nature},
    Pages = {842--843},
    Title = {Genomics, the cytoskeleton and motility},
    Volume = {409},
    Year = {2001}}



@book{Preparata1985,
    Address = {New York},
    Author = {F Preparata and MI Shamos},
    Isbn = {0-387-96131-3},
    Publisher = {Springer},
    Series = {Texts and Monographs in Computer Science},
    Title = {Computational Geometry: An Introduction},
    Year = {1985}}

@book{Press2002,
    Address = {Cambridge},
    Author = {WH Press and SA Teukolsky and WT Vetterling and BP Flannery},
    Date-Modified = {2005-02-05 13:12:03 -0800},
    Isbn = {0-521-75033-4},
    Mrclass = {65-04},
    Mrnumber = {MR1880993 (2003a:65005)},
    Note = {The art of scientific computing, Second edition, updated for C++},
    Pages = {xxviii+1002},
    Publisher = {Cambridge University Press},
    Title = {Numerical recipes in {C}{\bf++}},
    Year = {2002}}

@manual{R2004,
    Address = {Vienna, Austria},
    Author = {{R Development Core Team}},
    Note = {3-900051-07-0},
    Organization = {R Foundation for Statistical Computing},
    Title = {R: A language and environment for statistical computing},
    Url = {http://www.R-project.org},
    Year = 2004}

@article{Radmacher2001,
    Author = {MD Radmacher and R Simon and R Desper and R Taetle and AA Sch{\"a}ffer and MA Nelson},
    Date-Modified = {2005-02-05 12:49:26 -0800},
    Journal = {Journal of Theoretical Biology},
    Pages = {535--548},
    Title = {Graph models of oncogenesis with an application to melanoma},
    Volume = {212},
    Year = {2001}}

@article{Rahnenfuehrer2005,
    Author = {J Rahnenf{\"u}hrer and N Beerenwinkel and WA Schulz and C Hartmann and A von Deimling and B Wullich and T Lengauer},
    Journal = {Bioinformatics},
    Note = {To appear},
    Title = {Estimating cancer survival and clinical outcome based on genetic tumor progression scores},
    Year = {2005}}

@article{Rahnenfuhrer,
    Author = {J Rahnenf{\"u}hrer and N Beerenwinkel and WA Schulz and C Hartmann and A von Deimling and B Wullich and T Lengauer},
    Date-Modified = {2005-02-05 12:49:26 -0800},
    Journal = {Bioinformatics},
    Note = {Submitted},
    Title = {Estimating cancer survival and clinical outcome based on genetic tumor progression scores}}

@book{Rall1981,
    Address = {New York},
    Author = {LB Rall},
    Date-Modified = {2005-02-05 12:49:26 -0800},
    Publisher = {Springer-Verlag},
    Series = {{\rm Springer Lecture Notes in Computer Science}},
    Title = {Automatic Differentiation, Techniques and Applications},
    Volume = {120},
    Year = {1981}}

@article{Rambaut1997,
    Author = {A Rambaut and NC Grassly},
    Journal = {Comput. Appl. Biosci.},
    Pages = {235--238},
    Title = {{Seq-Gen}: An application for the {M}onte {C}arlo simulation of {DNA} sequence evolution along phylogenetic trees},
    Volume = {13},
    Year = {1997}}

@Article{Ranwez2002,
  author = {V Ranwez and O Gascuel},
  title = {Improvement of distance-based phylogenetic methods by a
                  local maximum likelihood approach using triplets},
  journal = {Molecular Biology and Evolution},
  year = {2002},
  OPTkey = {},
  volume = {19},
  number = {11},
  pages = {1952--1963},
  OPTmonth = {},
  OPTnote = {},
  OPTannote = {}
}

@article{Raphael2004,
    Author = {B Raphael and P Pevzner},
    Journal = {Bioinformatics},
    Pages = {I265--I273},
    Title = {Reconstructing Tumor Amplisomes},
    Volume = {20 Suppl 1, Special ISMB/ECCB 2004 issue},
    Year = {2004}}

@phdthesis{Ratz1992,
    Address = {Karlsruhe, Germany},
    Author = {D Ratz},
    Date-Modified = {2005-02-05 12:49:26 -0800},
    School = {Universit\"{a}t Karlsruhe},
    Title = {Automatische {Ergebnisverifikation} bei globalen {Optimierungsproblemen}},
    Type = {{Ph.D.} Dissertation},
    Year = {1992}}

@article{Richards2005,
    Abstract = {We have sequenced the genome of a second Drosophila species, Drosophila pseudoobscura, and compared this to the genome sequence of Drosophila melanogaster, a primary model organism. Throughout evolution the vast majority of Drosophila genes have remained on the same chromosome arm, but within each arm gene order has been extensively reshuffled, leading to a minimum of 921 syntenic blocks shared between the species. A repetitive sequence is found in the D. pseudoobscura genome at many junctions between adjacent syntenic blocks. Analysis of this novel repetitive element family suggests that recombination between offset elements may have given rise to many paracentric inversions, thereby contributing to the shuffling of gene order in the D. pseudoobscura lineage. Based on sequence similarity and synteny, 10,516 putative orthologs have been identified as a core gene set conserved over 25-55 million years (Myr) since the pseudoobscura/melanogaster divergence. Genes expressed in the testes had higher amino acid sequence divergence than the genome-wide average, consistent with the rapid evolution of sex-specific proteins. Cis-regulatory sequences are more conserved than random and nearby sequences between the species--but the difference is slight, suggesting that the evolution of cis-regulatory elements is flexible. Overall, a pattern of repeat-mediated chromosomal rearrangement, and high coadaptation of both male genes and cis-regulatory sequences emerges as important themes of genome divergence between these species of Drosophila.},
    Affiliation = {Human Genome Sequencing Center and Department of Molecular and Human Genetics, Baylor College of Medicine, Houston Texas 77030, USA. stephenr@bcm.tmc.edu},
    Aid = {10.1101/gr.3059305 {$[$}doi{$]$}},
    Au = {Richards S and Liu Y and Bettencourt BR and Hradecky P and Letovsky S and Nielsen R and Thornton K and Hubisz MJ and Chen R and Meisel RP and others},
    Author = {S Richards and Y Liu and BR Bettencourt and P Hradecky and S Letovsky and R Nielsen and K Thornton and MJ Hubisz and R Chen and RP Meisel and others},
    Da = {20050105},
    Date-Added = {2005-10-16 22:47:25 -0700},
    Date-Modified = {2005-10-16 22:47:25 -0700},
    Dcom = {20050414},
    Edat = {2005/01/06 09:00},
    Gr = {LM007276/LM/NLM},
    Ip = {1},
    Jid = {9518021},
    Journal = {Genome Res},
    Keywords = {Animals, Chromosome Breakage/genetics, Chromosome Mapping/methods, Chromosomes/*genetics, Comparative Study, Conserved Sequence/genetics, Drosophila/*genetics, Drosophila melanogaster/genetics, Enhancer Elements (Genetics), *Evolution, Molecular, Gene Rearrangement/genetics, Genes, Structural, Insect/*genetics, *Genome, Inversion, Chromosome/genetics, Molecular Sequence Data, Predictive Value of Tests, Repetitive Sequences, Nucleic Acid/genetics, Research Support, Non-U.S. Gov't, Research Support, U.S. Gov't, P.H.S., Sequence Analysis, DNA/*methods, Variation (Genetics)/genetics},
    Language = {eng},
    Mhda = {2005/04/15 09:00},
    Own = {NLM},
    Pages = {1-18},
    Pl = {United States},
    Pmid = {15632085},
    Pst = {ppublish},
    Pt = {Journal Article},
    Pubm = {Print},
    Sb = {IM},
    Si = {GENBANK/AY693425},
    So = {Genome Res 2005 Jan;15(1):1-18.},
    Stat = {MEDLINE},
    Title = {Comparative genome sequencing of {Drosophila} pseudoobscura: chromosomal, gene, and cis-element evolution.},
    Volume = {15},
    Year = {2005}}

@inproceedings{Richter-Gebert2003,
    Author = {J Richter-Gebert and B Sturmfels and T Theobald},
    Booktitle = {Proceedings of the Conference on Idempotent Mathematics and Mathematical Physics},
    Editor = {GL Litvinov and VP Maslov},
    Title = {First steps in tropical geometry},
    Year = {2003}}

@Article{Ritchie2008,
  author = 	 {W Ritchie and S Granjeaud and D Puthier and D Gautheret},
  title = 	 {Entropy measures quantify global splicing disorders in cancer},
  journal = 	 {PLoS Computational Biology},
  year = 	 {2008},
  OPTkey = 	 {},
  volume = 	 {4},
  OPTnumber = 	 {3},
  pages = 	 {e1000011},
  OPTmonth = 	 {},
  OPTnote = 	 {},
  OPTannote = 	 {}
}

@article{STjohn2003,
    Author = {K St. John and T Warnow and B Moret and L Vawter},
    Journal = {Journal of Algorithms},
    Pages = {174--193},
    Title = {Performance study of phylogenetic methods: (unweighted) quartet methods and neighbor joining},
    Volume = {48},
    Year = {2003}}

@techreport{Sainudiin2004,
    Author = {R Sainudiin},
    Date-Modified = {2005-02-05 12:49:26 -0800},
    Institution = {Department of Biol.~Stats.~and Comp.~Bio., Cornell University},
    Number = {BU1653-M},
    Title = {Enclosing the maximum likelihood of the simplest {DNA} model evolving on fixed topologies: towards a rigorous framework for phylogenetic inference},
    Year = {2004}}

@article{Sainudiin2005,
    Author = {R Sainudiin and SW Wong and K Yogeeswaran and J Nasrallah and Z Yang and R Nielsen},
    Date-Modified = {2005-02-05 12:49:26 -0800},
    Journal = {Journal of Molecular Evolution},
    Title = {Detecting site-specific physicochemical selective pressures: applications to the class-{I} {HLA} of the human major histocompatibility complex and the {SRK} of the plant sporophytic self-incompatibility system},
    Volume = {in press},
    Year = {2005}}

@article{Saitou1987,
    Author = {N Saitou and M Nei},
    Date-Modified = {2005-02-05 12:49:27 -0800},
    Journal = {Molecular Biology and Evolution},
    OPTNumber = {4},
    Pages = {406--425},
    Title = {The neighbor joining method: a new method for reconstructing phylogenetic trees},
    Volume = {4},
    Year = {1987}}

@inproceedings{Salakhutdinov2003,
    Author = {R Salakhutdinov and S Roweis and Z Ghahramani},
    Booktitle = {Proceedings of the Twentieth International Conference on Machine Learning (ICML-2003)},
    Title = {Optimization with EM and Expectation-Conjugate-Gradient},
    Year = {2003}}

@article{Salakhutdinov2004,
    Author = {R Salakhutdinov and S Roweis and Z Ghahramani},
    Journal = {in preparation},
    Title = {{Relationship between gradient and EM steps in latent variable models}},
    Year = {2004}}

@Misc{Sammeth,
  key = 	 {Flux Capacitor Simulator},
  author = 	 {M Sammeth and V Lacroix and  P Ribeca and R Guig\'{o}},
  title = 	 {Flux Capacitor Simulator: {\tt http://flux.sammeth.net/}},
  OPThowpublished = {},
  OPTmonth = 	 {},
  year = 	 {2009},
  OPTnote = 	 {},
  OPTannote = 	 {}
}

@article{Sandelin2004,
    Author = {A Sandelin and P Bailey and S Bruce and PG Engstr\"{o}m and JM Klos and WW Wasserman and J Ericson and B Lenhard},
    Journal = {BMC Genomics},
    Pages = {99},
    Title = {Arrays of Ultraconserved Non-Coding Regions Span the Loci of Key Developmental Genes in Vertebrate Genomes},
    Volume = {5},
    Year = {2004}}

@article{Sankoff2003,
    Author = {D Sankoff and JH Nadeau},
    Date-Modified = {2005-02-05 12:49:26 -0800},
    Journal = {Proceedings of the National Academy of Sciences, USA},
    Pages = {11188--11189},
    Title = {Chromosome rearrangements in evolution: from gene order to genome sequence and back},
    Volume = {100},
    Year = {2003}}

@Article{Sattath1977,
  author =   {S Sattath and A Tversky},
  title =    {Additive similarity trees},
  journal =      {Psychometrika},
  year =     {1977},
  OPTkey =   {},
  volume =   {42},
  number =   {6},
  pages =    {319--345},
  OPTmonth =     {},
  OPTnote =      {},
  OPTannote =    {}
}

@book{Schenck2003,
    Author = {H Schenck},
    Publisher = {Cambridge University Press},
    Series = {London Mathematical Society Student Texts},
    Title = {Computational Algebraic Geometry},
    Year = {2003}}

@article{Schmitz2003,
    Author = {J Schmitz and H Zischler},
    Journal = {Molecular Phylogenetics and Evolution},
    Pages = {341--349},
    Title = {A novel family of tRNA-derived SINEs in the colugo and two new retrotransposable markers separating dermopterans from primates.},
    Volume = {28},
    Year = {2003}}

@book{Schrijver1986,
    Address = {Chichester},
    Author = {A Schrijver},
    Isbn = {0-471-90854-1},
    Mrclass = {90C05 (90C10)},
    Mrnumber = {MR874114 (88m:90090)},
    Mrreviewer = {J{\"u}rgen K{\"o}hler},
    Note = {A Wiley--Interscience Publication},
    Pages = {xii+471},
    Publisher = {John Wiley \& Sons Ltd.},
    Series = {Wiley-Interscience Series in Discrete Mathematics},
    Title = {Theory of Linear and Integer Programming},
    Year = {1986}}

@article{Schwartz2000,
    Author = {A Schwartz and Z Zhang and KA Frazer and A Smit and C Riemer and J Bouck and R Gibbs and R Hardison and W Miller},
    Date-Modified = {2005-02-05 12:49:26 -0800},
    Journal = {Genome Research},
    Pages = {577--586},
    Title = {PipMaker- A web server for aligning two genomic DNA sequences},
    Volume = {10},
    Year = {2000}}

@article{Schwartz2003,
    Author = {S Schwartz and WJ Kent and A Smit and Z Zhang and R Baertsch and RC Hardison and D Haussler and W Miller},
    Date-Modified = {2005-02-05 12:49:26 -0800},
    Journal = {Genome Research},
    Pages = {103--107},
    Title = {Human--Mouse Alignments with {BLASTZ}},
    Volume = {13},
    Year = {2003}}

@article{Schwarz,
    Author = {G Schwarz},
    Date-Modified = {2005-02-05 12:49:26 -0800},
    Journal = {The Annals of Statistics},
    Pages = {461--464},
    Title = {Estimating the dimension of a model},
    Volume = {6}}

@incollection{Seidel2004,
    Author = {R Seidel},
    Booktitle = {Handbook of Discrete and Computational Geometry},
    Chapter = {22},
    Edition = {Second},
    Editor = {Goodman, Jacob E. and O'Rourke, Joseph},
    Mrclass = {52-00 (00A20 05B25 65D18 68U05)},
    Mrnumber = {MR2082993},
    Publisher = {Chapman \& Hall/CRC, Boca Raton, FL},
    Series = {Discrete Mathematics and its Applications (Boca Raton)},
    Title = {Convex hull computations},
    Year = {2004}}

@book{Semple2003,
    Address = {Oxford},
    Author = {C Semple and M Steel},
    Isbn = {0-19-850942-1},
    OPTMrclass = {92D15 (05C05 05C90 92D40)},
    OPTMrnumber = {MR2060009},
    Pages = {xiv+239},
    Publisher = {Oxford University Press},
    Series = {{\rm Oxford Lecture Series in Mathematics and its Applications}},
    Title = {Phylogenetics},
    Volume = {24},
    Year = {2003}}

@Article{Semple2004,
  author = 	 {C Semple and M Steel},
  title = 	 {Cyclic permutations and evolutionary trees},
  journal = 	 {Advances in Applied Mathematics},
  year = 	 {2004},
  OPTkey = 	 {},
  volume = 	 {32},
  OPTnumber = 	 {},
  pages = 	 {669--680},
  OPTmonth = 	 {},
  OPTnote = 	 {},
  OPTannote = 	 {}
}

@misc{Shoup2004,
    Author = {V Shoup},
    Date-Modified = {2005-02-28 12:49:26 -0800},
    Howpublished = {Available at http://shoup.net/ntl/},
    Title = {{NTL, A Library for doing Number Theory}},
    Year = {2004}}

@article{Siepel2004,
    Author = {A Siepel and D Haussler},
    Date-Modified = {2005-02-05 12:49:26 -0800},
    Journal = {Journal of Computational Biology},
    Pages = {413--428},
    Title = {Combining phylogenetic and hidden Markov models in biosequence analysis},
    Volume = {11},
    Year = {2004}}

@misc{Siepel2005,
    Author = {A Siepel},
    Title = {personal communication},
    Year = {2005}}

@article{Simon2000,
    Author = {R Simon and R Desper and CH Papadimitriou and A Peng and DS Alberts and R Taetle and JM Trent and AA Sch{\"a}ffer},
    Date-Modified = {2005-02-05 12:49:26 -0800},
    Journal = {Genes, Chromosomes \& Cancer},
    Pages = {106--120},
    Title = {Chromosome Abnormalities in Ovarian Adenocarcinoma: {III}. {U}sing Breakpoint Data to Infer and Test Mathematical Models for Oncogenesis},
    Volume = {28},
    Year = {2000}}

@article{Smith1981,
    Author = {TF Smith and MS Waterman},
    Date-Modified = {2005-02-05 12:49:26 -0800},
    Journal = {Journal of Molecular Biology},
    Pages = {195--197},
    Title = {Identification of common molecular sequences},
    Volume = {147},
    Year = {1981}}


@book{Smith1998,
    Author = {JM Smith},
    Edition = {Second},
    Month = {March},
    Publisher = {Oxford University Press},
    Title = {Evolutionary Genetics},
    Year = {1998}}

@book{Sneath1973,
    Address = {San Francisco},
    Author = {PHA Sneath and RR Sokal},
    Date-Modified = {2005-02-05 12:49:26 -0800},
    Publisher = {W.H. Freeman},
    Title = {Numerical Taxonomy: the Principles and Practice of Numerical Classification},
    Year = {1973}}

@article{Speyer2004,
    Author = {D Speyer and B Sturmfels},
    Coden = {AGDEA3},
    Date-Modified = {2005-02-05 12:58:09 -0800},
    Fjournal = {Advances in Geometry},
    Issn = {1615-715X},
    Journal = {Adv. Geom.},
    Mrclass = {14P99 (13J30 14M25)},
    Mrnumber = {MR2071813},
    Mrreviewer = {Meirav Amram-Blei},
    Number = {3},
    Pages = {389--411},
    Title = {The tropical {G}rassmannian},
    Volume = {4},
    Year = {2004}}

@article{Speyer2004a,
    Author = {D Speyer},
    Journal = {Submitted},
    Title = {Tropical Linear Spaces},
    Year = {2004}}

@article{Speyer2004b,
    Author = {D Speyer and L Williams},
    Journal = {Journal of Algebraic Combinatorics, in press},
    Title = {The tropical totally positive {Grassmanian}},
    Year = {2004}}

@book{Stanley1997,
    Address = {Cambridge},
    Author = {RP Stanley},
    Isbn = {0-521-55309-1; 0-521-66351-2},
    OPTMrclass = {05-02 (05A15 06-02 11-02)},
    OPTMrnumber = {MR1442260 (98a:05001)},
    Mrreviewer = {Wayne M. Dymacek},
    OPTNote = {With a foreword by Gian-Carlo Rota, Corrected reprint of the 1986 original},
    Pages = {xii+325},
    Publisher = {Cambridge University Press},
    Series = {{\rm Cambridge Studies in Advanced Mathematics}},
    Title = {Enumerative Combinatorics. {V}ol. 1},
    Volume = {49},
    Year = {1997}}

@book{Stanley1999,
    Address = {Cambridge},
    Author = {RP Stanley},
    Isbn = {0-521-56069-1; 0-521-78987-7},
    OPTMrclass = {05A15 (05-02 05E05 05E10 68R05)},
    OPTMrnumber = {MR1676282 (2000k:05026)},
    OPTMrreviewer = {Ira Gessel},
    OPTNote = {With a foreword by Gian-Carlo Rota and appendix 1 by Sergey Fomin},
    Pages = {xii+581},
    Publisher = {Cambridge University Press},
    Series = {Cambridge Studies in Advanced Mathematics},
    Title = {Enumerative combinatorics. {V}ol. 2},
    Volume = {62},
    Year = {1999}}

@article{Steel1992,
    Author = {MA Steel and MD Hendy and LA Sz{\'e}kely and PL Erd{\H{o}}s},
    Coden = {AMLEEL},
    Date-Modified = {2005-03-01 20:22:22 -0500},
    Fjournal = {Applied Mathematics Letters. An International Journal of Rapid Publication},
    Issn = {0893-9659},
    Journal = {Applied Mathematics Letters},
    Mrclass = {92D15},
    Mrnumber = {MR1345926},
    Number = {6},
    Pages = {63--67},
    Title = {Spectral analysis and a closest tree method for genetic sequences},
    Volume = {5},
    Year = {1992}}

@book{Strachan2004,
    Author = {T Strachan and AP Read},
    Edition = {third},
    Month = {June},
    Publisher = {Garland Press},
    Title = {{Human Molecular Genetics}},
    Year = {2004}}

@article{Strassen1983,
    Author = {V Strassen},
    Coden = {LAAPAW},
    Fjournal = {Linear Algebra and its Applications},
    Issn = {0024-3795},
    Journal = {Linear Algebra Appl.},
    Mrclass = {15A72 (14N99)},
    Mrnumber = {MR709378 (85b:15039)},
    Mrreviewer = {Allen Tannenbaum},
    Pages = {645--685},
    Title = {Rank and optimal computation of generic tensors},
    Volume = {52/53},
    Year = {1983}}

@article{Strimmer1996,
    Author = {K Strimmer and A von Haeseler},
    Journal = {Molecular Biology and Evolution},
    Pages = {964--969},
    Title = {Quartet puzzling: A quartet maximum likelihood method for reconstructing tree topologies},
    Volume = {13},
    Year = {1996}}

@article{Strimmer2000,
    Author = {K Strimmer and V Moulton},
    Date-Added = {2005-03-01 20:10:40 -0500},
    Date-Modified = {2005-03-01 20:11:43 -0500},
    Journal = {Molecular Biology and Evolution},
    Pages = {875-881},
    Title = {Likelihood Analysis of Phylogenetic Networks using directed graphical models},
    Volume = {17},
    Year = {2000}}

@article{Strimmer2001,
    Author = {K Strimmer and C Wiuf and V Moulton},
    Date-Modified = {2005-03-01 20:09:47 -0500},
    Journal = {Molecular Biology and Evolution},
    Pages = {97--99},
    Title = {Recombination analysis using directed graphical models},
    Volume = {18},
    Year = {2001}}

@article{Studier1988,
    Author = {JA Studier and KJ Keppler},
    Date-Modified = {2005-02-05 12:49:26 -0800},
    Journal = {Molecular Biology and Evolution},
    Pages = {729--731},
    Title = {A note on the neighbor-joining method of Saitou and Nei},
    Volume = {5},
    Year = {1988}}

@article{Sturmfels1990,
    Author = {B Sturmfels},
    Coden = {MAZEAX},
    Fjournal = {Mathematische Zeitschrift},
    Issn = {0025-5874},
    Journal = {Mathematische Zeitschrift},
    Mrclass = {14M12 (13P10 68Q40)},
    Mrnumber = {MR1069489 (91m:14076)},
    Mrreviewer = {Piotr Pragacz},
    Number = {1},
    Pages = {137--144},
    Title = {Gr\"obner bases and {S}tanley decompositions of determinantal rings},
    Volume = {205},
    Year = {1990}}

@book{Sturmfels1993,
    Address = {Vienna},
    Author = {B Sturmfels},
    Isbn = {3-211-82445-6},
    Mrclass = {13A50 (13P10 20-01 20-04 20G05)},
    Mrnumber = {MR1255980 (94m:13004)},
    Mrreviewer = {Frank D. Grosshans},
    Pages = {vi+197},
    Publisher = {Springer-Verlag},
    Series = {Texts and Monographs in Symbolic Computation},
    Title = {Algorithms in Invariant Theory},
    Year = {1993}}

@book{Sturmfels2002,
    Author = {B Sturmfels},
    Date-Modified = {2005-02-05 12:58:09 -0800},
    Isbn = {0-8218-3251-4},
    Mrclass = {13P10 (14P99 14Q15 62-09 65H10)},
    Mrnumber = {MR1925796 (2003i:13037)},
    Mrreviewer = {Joseph Gubeladze},
    Pages = {viii+152},
    Publisher = {Published for the Conference Board of the Mathematical Sciences, Washington, DC},
    Series = {CBMS Regional Conference Series in Mathematics},
    Title = {Solving Systems of Polynomial Equations},
    Volume = {97},
    Year = {2002}}

@incollection{Sturmfels2002a,
    Address = {Berlin},
    Author = {B Sturmfels},
    Booktitle = {Computations in algebraic geometry with Macaulay 2},
    Date-Modified = {2005-02-05 12:58:09 -0800},
    Mrclass = {13-04 (14-04)},
    Mrnumber = {MR1949545},
    Pages = {3--15},
    Publisher = {Springer},
    Series = {Algorithms and Computations in Mathematics},
    Title = {Ideals, varieties and {M}acaulay 2},
    Volume = {8},
    Year = {2002}}

@article{Sturmfels2004,
    Author = {B Sturmfels and J Yu},
    Date-Modified = {2005-02-05 12:58:09 -0800},
    Fjournal = {Electronic Journal of Combinatorics},
    Issn = {1077-8926},
    Journal = {Electronic Journal of Combinatorics},
    Mrclass = {51K05 (05C12)},
    Mrnumber = {MR2097310},
    Pages = {Research Paper 44, 16 pp. (electronic)},
    Title = {Classification of six-point metrics},
    Volume = {11},
    Year = {2004}}

@article{Sturmfels2005,
    Author = {B Sturmfels and S Sullivant},
    Journal = {Journal of Computational Biology},
    Pages = {204--228},
    Title = {Toric ideals of phylogenetic invariants},
    Volume = {12},
    Year = {2005}}

@unpublished{Sturmfels2007,
  author = 	 {B Sturmfels and S Sullivant},
  title = 	 {Toric geometry of cuts and splits},
  note  = 	 {arXiv math.AC/0606683},
  year = 	 {2007},
  OPTkey = 	 {},
  OPTvolume = 	 {},
  OPTnumber = 	 {},
  OPTpages = 	 {},
  OPTmonth = 	 {},
  OPTnote = 	 {},
  OPTannote = 	 {}
}

@article{Sun2002,
    Author = {F Sun and D Fern\'andez-Baca and W Yu},
    Date-Modified = {2005-02-23 12:49:26 -0800},
    Journal = {International Computing and Combinatorics Conference (COCOON)},
    Title = {Inverse parametric sequence alignment},
    Year = {2002}}

@article{Susko2003,
    Author = {E Susko},
    Date-Added = {2005-03-01 20:06:38 -0500},
    Date-Modified = {2005-03-01 20:07:08 -0500},
    Journal = {Molecular Biology and Evolution},
    Title = {Confidence Regions and Hypothesis Tests for Topologies Using Generalized Least Squares},
    Year = {2003}}

@manual{Swofford1998,
    Address = {Sunderland Mass.},
    Author = {DL Swofford},
    Publisher = {Sinauer Associates},
    Title = {PAUP*. Phylogenetic Analysis using Parsimony (* and other Methods)},
    Year = {1998}}

@misc{Swox2004,
    Author = {AB Swox},
    Date-Modified = {2005-02-28 12:49:26 -0800},
    Howpublished = {Available at \url{http://swox.com/gmp/}},
    Title = {{GMP, the GNU Multiple Precision Arithmetic Library}},
    Year = {2004}}

@article{Szabo2002,
    Author = {A Szabo and K Boucher},
    Journal = {Mathematical Biosciences},
    Pages = {219--240},
    Title = {Estimating an oncogenetic tree when false negatives and positives are present},
    Volume = {176},
    Year = {2002}}


@article{Szekely1993,
    Author = {LA Sz{\'e}kely and MA Steel and PL Erd{\H{o}}s},
    Date-Modified = {2005-03-01 19:31:08 -0500},
    Fjournal = {Advances in Applied Mathematics},
    Issn = {0196-8858},
    Journal = {Advances in Applied Mathematics},
    Mrclass = {92D15 (42A38)},
    Mrnumber = {MR1218244 (94i:92009)},
    Mrreviewer = {J. Albrycht},
    Number = {2},
    Pages = {200--210},
    Title = {Fourier calculus on evolutionary trees},
    Volume = {14},
    Year = {1993}}

@article{Tamura1993,
    Author = {K Tamura and M Nei},
    Journal = {Molecular Biology and Evolution},
    Pages = {512--526},
    Title = {Estimation of the number of nucleotide substitutions in the control region of mitochondrial {DNA} in humans and chimpanzees},
    Volume = {10},
    Year = {1993}}

@Article{Tamura2004,
  author = {K Tamura and M Nei and S Kumar},
  title = {Prospects for inferring very large phylogenies by using the
                  neighbor-joining method},
  journal = {Proceedings of the National Academy of Sciences},
  year = {2004},
  OPTkey = {},
  volume = {101},
  OPTnumber = {},
  pages = {11030--11035},
  OPTmonth = {},
  OPTnote = {},
  OPTannote = {}
}

@article{Tavare1986,
    Author = {S Tavar\'{e}},
    Journal = {Lectures on the Mathematics in the Life Sciences},
    Pages = {57--86},
    Title = {Some probabilistic and statistical problems in the analysis of {DNA} sequences},
    Volume = {17},
    Year = {1986}}

@article{Terao2002,
    Author = {H Terao},
    Date-Modified = {2005-02-05 12:49:26 -0800},
    Journal = {Journal of Algebra},
    Number = {2},
    Pages = {549--558},
    Title = {Algebras generated by reciprocals of linear forms},
    Volume = {250},
    Year = {2002}}

@article{Tesler2002,
    Author = {G Tesler},
    Journal = {Journal of Computer and System Sciences},
    Number = {3},
    Pages = {587--609},
    Title = {Efficient algorithms for multichromosomal genome rearrangements},
    Volume = {65},
    Year = {2002}}

@article{Thomas2003,
    Abstract = {The systematic comparison of genomic sequences from different organisms represents a central focus of contemporary genome analysis. Comparative analyses of vertebrate sequences can identify coding and conserved non-coding regions, including regulatory elements, and provide insight into the forces that have rendered modern-day genomes. As a complement to whole-genome sequencing efforts, we are sequencing and comparing targeted genomic regions in multiple, evolutionarily diverse vertebrates. Here we report the generation and analysis of over 12 megabases (Mb) of sequence from 12 species, all derived from the genomic region orthologous to a segment of about 1.8 Mb on human chromosome 7 containing ten genes, including the gene mutated in cystic fibrosis. These sequences show conservation reflecting both functional constraints and the neutral mutational events that shaped this genomic region. In particular, we identify substantial numbers of conserved non-coding segments beyond those previously identified experimentally, most of which are not detectable by pair-wise sequence comparisons alone. Analysis of transposable element insertions highlights the variation in genome dynamics among these species and confirms the placement of rodents as a sister group to the primates.},
    Affiliation = {Genome Technology Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland 20892,USA.},
    Aid = {nature01858 {$[$}pii{$]$}},
    Au = {Green ED},
    Author = {JW Thomas and JW Touchman and RW Blakesley and GG Bouffard and SM Beckstrom-Sternberg and EH Margulies and M Blanchette and AC Siepel and PJ Thomas and JC McDowell and others},
    Da = {20030814},
    Date-Modified = {2005-02-05 12:49:26 -0800},
    Dcom = {20030821},
    Edat = {2003/08/15 05:00},
    Jid = {0410462},
    Journal = {Nature},
    Keywords = {Animals and Chromosomes, Human, Pair 7/genetics and Comparative Study and Conserved Sequence/*genetics and Cystic Fibrosis Transmembrane Conductance Regulator/genetics and DNA Transposable Elements/genetics and *Evolution, Molecular and Genome and *Genomics and Humans and Mammals/genetics and Mutagenesis/genetics and Phylogeny and Research Support, Non-U.S. Gov't and Research Support, U.S. Gov't, P.H.S. and Sequence Alignment and Sequence Homology, Nucleic Acid and Species Specificity and Vertebrates/*genetics},
    Language = {eng},
    Lr = {20041117},
    Mhda = {2003/08/22 05:00},
    Number = {6950},
    Own = {NLM},
    Pages = {788--93},
    Phst = {2003/06/16 {$[$}accepted{$]$}},
    Pl = {England},
    Pmid = {12917688},
    Pst = {ppublish},
    Pt = {Journal Article},
    Pubm = {Print},
    Rn = {126880-72-6 (Cystic Fibrosis Transmembrane Conductance Regulator)},
    Sb = {IM},
    So = {Journal of Computational Biology 1999 Fall-Winter;6(3-4):419-30.},
    Stat = {MEDLINE},
    Title = {Comparative analyses of multi-species sequences from targeted genomic regions.},
    Volume = {424},
    Year = {2003}}

@article{Thompson1994,
    Author = {JD Thompson and DG Higgins and TJ Gibseon},
    Date-Modified = {2005-02-05 12:49:26 -0800},
    Journal = {Nucleic Acids Research},
    Pages = {4673--4680},
    Title = {CLUSTALW: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice},
    Volume = {22},
    Year = {1994}}

@article{Tompa2005,
    Annote = {10.1038/nbt1053},
    Author = {M Tompa and N Li and TL Bailey and GM Church and B De Moor and E Eskin and AV Favorov and MC Frith and Y Fu and WJ Kent and others},
    Ep = {144},
    Journal = {Nature Biotechnology},
    L3 = {http://www.nature.com/nbt/journal/v23/n1/suppinfo/nbt1053{\_}S1.html},
    M3 = {10.1038/nbt1053},
    Number = {1},
    Pages = {137--144},
    Sn = {1087-0156},
    Sp = {137},
    Title = {Assessing computational tools for the discovery of transcription factor binding sites},
    Ty = {JOUR},
    Url = {http://dx.doi.org/10.1038/nbt1053},
    Volume = {23},
    Year = {2005}}

@Article{Trapnell2009,
  author = 	 {C Trapnell and L Pachter and S Salzberg},
  title = 	 {{TopHat: discovering splice junctions with RNA-Seq}},
  journal = 	 {Bioinformatics},
  year = 	 {2009},
  OPTkey = 	 {},
  volume = 	 {25},
  OPTnumber = 	 {9},
  pages = 	 {1105--1111},
  OPTmonth = 	 {},
  OPTnote = 	 {},
  OPTannote = 	 {}
}

@Book{Tufte2001,
  author = 	 {Edward R. Tufte},
  ALTeditor = 	 {},
  title = 	 {The Visual Display of Quantitative Information},
  publisher = 	 {Graphics Press},
  year = 	 {2001},
  OPTkey = 	 {},
  OPTvolume = 	 {},
  OPTnumber = 	 {},
  OPTseries = 	 {},
  OPTaddress = 	 {},
  OPTedition = 	 {},
  OPTmonth = 	 {},
  OPTnote = 	 {},
  OPTannote = 	 {}
}

@article{Ureta-Vidal2003,
    Author = {A Ureta-Vidal and L Ettwiller and E Birney},
    Date-Modified = {2005-02-05 12:49:26 -0800},
    Journal = {Nature Review Genetics},
    Pages = {251--262},
    Title = {Comparative Genomics: Genome-wide analysis in metazoan eukaryotes},
    Volume = {4},
    Year = {2003}}

@article{Valiant1979,
    Author = {L Valiant},
    Date-Modified = {2005-02-05 12:49:27 -0800},
    Journal = {Theoretical Computer Science},
    Pages = {189--201},
    Title = {The complexity of computing the permanent},
    Volume = {8},
    Year = {1979}}

@book{Vapnik1995,
    Address = {New York, New York},
    Author = {VN Vapnik},
    Date-Modified = {2005-02-05 12:49:27 -0800},
    Publisher = {Springer-Verlag},
    Title = {The Nature of Statistical Learning Theory},
    Year = {1995}}

@article{Varchenko1995,
    Author = {A Varchenko},
    Coden = {CMPMAF},
    Fjournal = {Compositio Mathematica},
    Issn = {0010-437X},
    Journal = {Compositio Mathematica},
    Mrclass = {32S50 (17B10 32G34 32S40)},
    Mrnumber = {MR1353281 (96j:32053)},
    Mrreviewer = {V. Leksin},
    Number = {3},
    Pages = {385--401},
    Title = {Critical points of the product of powers of linear functions and families of bases of singular vectors},
    Volume = {97},
    Year = {1995}}

@article{Venter2001,
    Abstract = {A 2.91-billion base pair (bp) consensus sequence of the euchromatic portion of the human genome was generated by the whole-genome shotgun sequencing method. The 14.8-billion bp DNA sequence was generated over 9 months from 27,271,853 high-quality sequence reads (5.11-fold coverage of the genome) from both ends of plasmid clones made from the DNA of five individuals. Two assembly strategies-a whole-genome assembly and a regional chromosome assembly-were used, each combining sequence data from Celera and the publicly funded genome effort. The public data were shredded into 550-bp segments to create a 2.9-fold coverage of those genome regions that had been sequenced, without including biases inherent in the cloning and assembly procedure used by the publicly funded group. This brought the effective coverage in the assemblies to eightfold, reducing the number and size of gaps in the final assembly over what would be obtained with 5.11-fold coverage. The two assembly strategies yielded very similar results that largely agree with independent mapping data. The assemblies effectively cover the euchromatic regions of the human chromosomes. More than 90% of the genome is in scaffold assemblies of 100,000 bp or more, and 25% of the genome is in scaffolds of 10 million bp or larger. Analysis of the genome sequence revealed 26,588 protein-encoding transcripts for which there was strong corroborating evidence and an additional approximately 12,000 computationally derived genes with mouse matches or other weak supporting evidence. Although gene-dense clusters are obvious, almost half the genes are dispersed in low G+C sequence separated by large tracts of apparently noncoding sequence. Only 1.1% of the genome is spanned by exons, whereas 24% is in introns, with 75% of the genome being intergenic DNA. Duplications of segmental blocks, ranging in size up to chromosomal lengths, are abundant throughout the genome and reveal a complex evolutionary history. Comparative genomic analysis indicates vertebrate expansions of genes associated with neuronal function, with tissue-specific developmental regulation, and with the hemostasis and immune systems. DNA sequence comparisons between the consensus sequence and publicly funded genome data provided locations of 2.1 million single-nucleotide polymorphisms (SNPs). A random pair of human haploid genomes differed at a rate of 1 bp per 1250 on average, but there was marked heterogeneity in the level of polymorphism across the genome. Less than 1% of all SNPs resulted in variation in proteins, but the task of determining which SNPs have functional consequences remains an open challenge.},
    Affiliation = {Celera Genomics, 45 West Gude Drive, Rockville, MD 20850, USA. humangenome@celera.com},
    Aid = {291/5507/1304 {$[$}pii{$]$}},
    Au = {Zhu X},
    Author = {JC Venter and MD Adams and EW Myers and PW Li and RJ Mural and GG Sutton and HO Smith and M Yandell and CA Evans and RA Holt and others},
    Cin = {Proc Natl Acad Sci U S A. 2003 Mar 18;100(6):3022-4; author reply 3025-6. PMID: 12631699},
    Da = {20010222},
    Date-Modified = {2005-02-05 12:49:27 -0800},
    Dcom = {20010315},
    Edat = {2001/02/22 11:00},
    Ein = {Science 2001 Jun 5;292(5523):1838},
    Jid = {0404511},
    Journal = {Science},
    Keywords = {Algorithms and Animals and Chromosome Banding and Chromosome Mapping and Chromosomes, Artificial, Bacterial and Computational Biology and Consensus Sequence and CpG Islands and DNA, Intergenic and Databases, Factual and Evolution, Molecular and Exons and Female and Gene Duplication and Genes and *Genome, Human and *Human Genome Project and Humans and Introns and Male and Phenotype and Physical Chromosome Mapping and Polymorphism, Single Nucleotide and Proteins/genetics/physiology and Pseudogenes and Repetitive Sequences, Nucleic Acid and Research Support, Non-U.S. Gov't and Retroelements and *Sequence Analysis, DNA/methods and Species Specificity and Variation (Genetics)},
    Language = {eng},
    Lr = {20041117},
    Mhda = {2001/03/17 10:01},
    Number = {5507},
    Own = {NLM},
    Pages = {1304--51},
    Pl = {United States},
    Pmid = {11181995},
    Pst = {ppublish},
    Pt = {Journal Article},
    Pubm = {Print},
    Rn = {0 (Retroelements)},
    Sb = {IM},
    Stat = {MEDLINE},
    Title = {The sequence of the human genome.},
    Volume = {291},
    Year = {2001}}

@article{Viterbi1967,
    Author = {AJ Viterbi},
    Date-Modified = {2005-02-05 12:49:26 -0800},
    Journal = {IEEE Transactions on Information Theory},
    Pages = {260-269},
    Title = {Error Bounds for Convolutional Codes and an Asymptotically Optimum Decoding Algorithm},
    Volume = {13},
    Year = {1967}}

@article{Vogelstein1988,
    Author = {B Vogelstein and E Fearon and S Hamilton},
    Date-Modified = {2005-02-05 12:49:26 -0800},
    Journal = {New England Journal of Medicine},
    Pages = {525--532},
    Title = {Genetic alterations during colorectal-tumor development},
    Volume = {319},
    Year = {1988}}

@article{Vonheydebreck2004,
    Author = {A von Heydebreck and B Gunawan and L F{\"u}zesi},
    Journal = {Biostatistics},
    Number = {4},
    Pages = {545--556},
    Title = {Maximum likelihood estimation of oncogenetic tree models},
    Url = {http://biostatistics.oupjournals.org/cgi/content/abstract/5/4/545?etoc},
    Volume = {5},
    Year = {2004}}

@Article{Wang2008,
  author = 	 {ET Wang and R Sandberg S Luo and I Khrebtukova and L Zhang and C Mayr and SF Kingsmore and GP Schroth and CB Burge},
  title = 	 {Alternative isoform regulation in human tissue transcriptomes},
  journal = 	 {Nature},
  year = 	 {2008},
  OPTkey = 	 {},
  volume = 	 {456},
  OPTnumber = 	 {},
  pages = 	 {470--476},
  OPTmonth = 	 {},
  OPTnote = 	 {},
  OPTannote = 	 {}
}

@article{Warshall1962,
    Author = {S Warshall},
    Date-Modified = {2005-02-05 12:49:26 -0800},
    Journal = {Journal of the ACM},
    Number = {1},
    Pages = {18},
    Title = {A theorem on Boolean matrices},
    Volume = {9},
    Year = {1962}}

@article{Waterman1992,
    Author = {MS Waterman and M Eggert and ES Lander},
    Journal = {Proceedings of the National Academy of Sciences, USA},
    Pages = {6090--6093},
    Title = {Parametric sequence comparisons},
    Volume = {89},
    Year = {1992}}

@book{Waterman1995,
    Author = {MS Waterman},
    Month = {June},
    Publisher = {Chapman \& Hall/CRC},
    Title = {Introduction to Computational Biology: Maps, Sequences and Genomes},
    Year = {1995}}

@article{Waterston2002,
    Abstract = {The sequence of the mouse genome is a key informational tool for understanding the contents of the human genome and a key experimental tool for biomedical research. Here, we report the results of an international collaboration to produce a high-quality draft sequence of the mouse genome. We also present an initial comparative analysis of the mouse and human genomes, describing some of the insights that can be gleaned from the two sequences. We discuss topics including the analysis of the evolutionary forces shaping the size, structure and sequence of the genomes; the conservation of large-scale synteny across most of the genomes; the much lower extent of sequence orthology covering less than half of the genomes; the proportions of the genomes under selection; the number of protein-coding genes; the expansion of gene families related to reproduction and immunity; the evolution of proteins; and the identification of intraspecies polymorphism.},
    Affiliation = {Genome Sequencing Center, Washington University School of Medicine, Campus Box 8501, 4444 Forest Park Avenue, St Louis, Missouri 63108, USA. waterston@gs.washington.edu},
    Aid = {nature01262 {$[$}pii{$]$}},
    Au = {Lander ES},
    Author = {RH Waterston and K Lindblad-Toh and E Birney and J Rogers and JF Abril and P Agarwal and R Agarwala and R Ainscough and M Alexandersson and P An and others},
    Cin = {Nature. 2002 Dec 5;420(6915):515-6. PMID: 12466847},
    Cn = {Mouse Genome Sequencing Consortium.},
    Da = {20021205},
    Date-Modified = {2005-02-05 12:49:26 -0800},
    Dcom = {20021227},
    Edat = {2002/12/06 04:00},
    Jid = {0410462},
    Journal = {Nature},
    Keywords = {Animals and Base Composition and Chromosomes, Mammalian/*genetics and Comparative Study and Conserved Sequence/genetics and CpG Islands/genetics and *Evolution, Molecular and Gene Expression Regulation and Genes/genetics and *Genome and Genome, Human and Genomics and Humans and Mice/classification/*genetics and Mice, Knockout and Mice, Transgenic and Models, Animal and Multigene Family/genetics and Mutagenesis and Neoplasms/genetics and *Physical Chromosome Mapping and Proteome/genetics and Pseudogenes/genetics and Quantitative Trait Loci/genetics and RNA, Untranslated/genetics and Repetitive Sequences, Nucleic Acid/genetics and Research Support, Non-U.S. Gov't and Research Support, U.S. Gov't, Non-P.H.S. and Research Support, U.S. Gov't, P.H.S. and Selection (Genetics) and Sequence Analysis, DNA and Sex Chromosomes/genetics and Species Specificity and Synteny and Variation (Genetics)/genetics},
    Language = {eng},
    Lr = {20041117},
    Mhda = {2002/12/28 04:00},
    Own = {NLM},
    Pages = {520-62},
    Phst = {2002/10/31 {$[$}accepted{$]$}},
    Pl = {England},
    Pmid = {12466850},
    Pst = {ppublish},
    Pt = {Journal Article},
    Pubm = {Print},
    Rn = {0 (RNA, Untranslated)},
    Sb = {IM},
    So = {Genome Res 2003 Jan;13(1):73-80.},
    Stat = {MEDLINE},
    Title = {Initial sequencing and comparative analysis of the mouse genome.},
    Volume = {420},
    Year = {2002}}

@article{Watson1953,
    Author = {J Watson and F Crick},
    Date-Modified = {2005-02-05 12:49:26 -0800},
    Journal = {Nature},
    Pages = {964--967},
    Title = {A structure for deoxyribose nucleic acid},
    Volume = {171},
    Year = {1953}}

@mastersthesis{Wetzel1995,
    Author = {R Wetzel},
    Date-Modified = {2005-03-01 19:55:48 -0500},
    School = {Fakult\"{a}t Mathematik, Universit\"{a}t Bielefeld},
    Title = {Zur {V}isualisierung abstrakter \"{A}hnlichkeitsbeziehungen},
    Year = {1995}}

@article{Winkler1984,
    Author = {P Winkler},
    Date-Added = {2005-03-01 20:01:12 -0500},
    Date-Modified = {2005-03-01 20:02:00 -0500},
    Journal = {Discrete Applied Mathematics},
    Pages = {221--225},
    Title = {Isometric embeddings in products of complete graphs},
    Volume = {7},
    Year = {1984}}

@article{Wolf2000,
    Author = {MJ Wolf and S Easteal and M Kahn and BD McKay and LS Jermiin},
    Journal = {Bioinformatics},
    Pages = {383--394},
    Title = {TrExML: A maximum likelihood program for extensive tree-space exploration},
    Volume = {16},
    Year = {2000}}

@article{Woolfe2005,
    Author = {A Woolfe and M Goodson and DK Goode and P Snell and GK McEwen and T Vavouri and SF Smith and P North and H Callaway and K Kelly and others},
    Journal = {PLoS Biology},
    Pages = {7},
    Title = {Highly Conserved Non-Coding Sequences Are Associated with Vertebrate Development},
    Volume = {3},
    Year = {2005}}

@article{Wu1983,
    Author = {JCF Wu},
    Coden = {ASTSC7},
    Fjournal = {The Annals of Statistics},
    Issn = {0090-5364},
    Journal = {The Annals of Statistics},
    Mrclass = {62F10},
    Mrnumber = {MR684867 (85e:62049)},
    Mrreviewer = {Huynh Huynh},
    Number = {1},
    Pages = {95--103},
    Title = {On the convergence properties of the {EM} algorithm},
    Volume = {11},
    Year = {1983}}

@article{Wu1985,
    Abstract = {When the coding regions of 11 genes from rodents (mouse or rat) and man are compared with those from another mammalian species (usually bovine), it is found that rodents evolve significantly faster than man. The ratio of the number of nucleotide substitutions in the rodent lineage to that in the human lineage since their divergence is 2.0 for synonymous substitutions and 1.3 for nonsynonymous substitutions. Rodents also evolve faster in the 5' and 3' untranslated regions of five different mRNAs; the ratios are 2.6 and 3.1, respectively. The numbers of nucleotide substitutions between members of the {beta} -globin gene family that were duplicated before the man-mouse split are also higher in mouse than in man. The difference is, again, greater for synonymous substitutions than for nonsynonymous substitutions. This tendency is more consistent with the neutralist view of molecular evolution than with the selectionist view. A simple explanation for the higher rates in rodents is that rodents have shorter generation times and, thus, higher mutation rates. The implication of our findings for the study of molecular phylogeny is discussed.
},
    Author = {CI Wu and WH Li},
    Journal = {PNAS},
    Number = {6},
    Pages = {1741-1745},
    Title = {Evidence for Higher Rates of Nucleotide Substitution in Rodents Than in Man},
    Url = {http://www.pnas.org/cgi/content/abstract/82/6/1741},
    Volume = {82},
    Year = {1985}}

@Article{Xing2004,
  author = 	 {Y Xing and A Resch and C Lee},
  title = 	 {The multiassembly problem: reconstructing multiple transcript isoforms from {EST} fragment mixtures},
  journal = 	 {Genome Research},
  year = 	 {2004},
  OPTkey = 	 {},
  volume = 	 {14},
  OPTTnumber = 	 {},
  pages = 	 {426--441},
  OPTmonth = 	 {},
  OPTnote = 	 {},
  OPTannote = 	 {}
}

@Article{Xu2005,
  author =   {Y Xu and W Dai and B Zhu},
  title =    {A lower bound on the edge $l_{\infty}$ radius of {S}aitou and {N}ei's method for phylogenetic reconstruction},
  journal =      {Information Processing Letters},
  year =     {2005},
  OPTkey =   {},
  volume =   {94},
  OPTnumber =    {},
  pages =    {225--230},
  OPTmonth =     {},
  OPTnote =      {},
  OPTannote =    {}
}

@article{Yang1995,
    Author = {Z Yang and D Roberts},
    Journal = {Molecular Biology and Evolution},
    Pages = {451--458},
    Title = {On the use of nucleic acid sequences to infer early branchings in the tree of life},
    Volume = {12},
    Year = {1995}}

@article{Yang1997,
    Author = {Z Yang},
    Howpublished = {Available at \url{http://abacus.gene.ucl.ac.uk/software/paml.html}},
    Journal = {CABIOS},
    Pages = {555--556},
    Title = {{PAML}: A program package for phylogenetic analysis by maximum likelihood},
    Volume = {15},
    Year = {1997}}

@article{Yap2004,
    Abstract = {We describe a whole-genome comparative analysis of the human, mouse, and rat genomes to describe the average substitution patterns of four genomic regions: ancient repeats, rodent-specific DNA, exons, and conserved (coding and noncoding) regions, and to identify rodent evolutionary hotspots. In all types of regions, except the rodent-specific DNA, the rat branch is slightly longer than the mouse branch. Moreover, the mouse-rat distance is longer in the rodent-specific DNA than in the ancient repeats. Analysis of individual conserved regions with different substitution models yielded the conclusion that the Jukes--Cantor model is inadequate, and the Hasegawa-Kishino-Yano model is almost as good as the REV model. Using human as an outgroup, we identified 5055 evolutionary hotspots, which are highly conserved subalignment blocks (each consisting of at least 100 aligned sites and a small fraction of gaps) with a large and statistically significant difference in the branch lengths of the rodent species. The cutoffs used to identify the hotspots are partially based on estimates of the average rates of substitution. The fractions of hotspots overlapping with the rodent RefSeq genes, RefSeq exons, and ESTs are all higher than expected. Still, more than half of the hotspots lie in noncoding regions of the mouse genome. We believe that the hotspots represent biologically interesting regions in the rodent genomes.},
    Affiliation = {Department of Mathematics, University of California, Berkeley, California 94720-3840, USA. vonbing@math.berkeley.edu},
    Aid = {14/4/574 {$[$}pii{$]$}},
    Au = {Pachter L},
    Author = {VB Yap and L Pachter},
    Da = {20040402},
    Date-Modified = {2005-02-05 12:49:26 -0800},
    Dcom = {20040505},
    Edat = {2004/04/03 05:00},
    Gr = {HG02362-01/HG/NHGRI},
    Jid = {9518021},
    Journal = {Genome Research},
    Keywords = {Animals and Comparative Study and Conserved Sequence/genetics and DNA/genetics and *Evolution, Molecular and *Genome and Genome, Human and Humans and Mice and Models, Genetic and Mutation/genetics and Rats and Repetitive Sequences, Nucleic Acid/genetics and Research Support, U.S. Gov't, P.H.S. and Sensitivity and Specificity and Sequence Alignment/methods/statistics \& numerical data and Species Specificity},
    Language = {eng},
    Lr = {20041117},
    Mhda = {2004/05/07 05:00},
    Number = {4},
    Own = {NLM},
    Pages = {574--9},
    Pl = {United States},
    Pmid = {15059998},
    Pst = {ppublish},
    Pt = {Journal Article},
    Pubm = {Print},
    Rn = {9007-49-2 (DNA)},
    Sb = {IM},
    So = {Genome Res 2004 Apr;14(4):661-4.},
    Stat = {MEDLINE},
    Title = {Identification of evolutionary hotspots in the rodent genomes.},
    Volume = {14},
    Year = {2004}}

@inproceedings{Yedidia2000,
    Author = {J Yedidia and W Freeman and Y Weiss},
    Booktitle = {{NIPS}},
    Date-Modified = {2005-02-05 12:49:26 -0800},
    Title = {Generalized Belief Propagation},
    Year = {2000}}

@article{Yoder2000,
    Author = {AD Yoder and Z Yang},
    Journal = {Molecular Biology and Evolution},
    Pages = {1081-1090},
    Title = {Estimation of primate speciation dates using local molecular clocks},
    Volume = {17},
    Year = {2000}}

@article{Yu2002,
    Abstract = {We have produced a draft sequence of the rice genome for the most widely cultivated subspecies in China, {Oryza sativa} {L. ssp. indica}, by whole-genome shotgun sequencing. The genome was 466 megabases in size, with an estimated 46,022 to 55,615 genes. Functional coverage in the assembled sequences was 92.0%. About 42.2% of the genome was in exact 20-nucleotide oligomer repeats, and most of the transposons were in the intergenic regions between genes. Although 80.6% of predicted Arabidopsis thaliana genes had a homolog in rice, only 49.4% of predicted rice genes had a homolog in A. thaliana. The large proportion of rice genes with no recognizable homologs is due to a gradient in the GC content of rice coding sequences.},
    Affiliation = {Beijing Genomics Institute/Center of Genomics and Bioinformatics, Chinese Academy of Sciences, Beijing 101300, China.},
    Aid = {296/5565/79 {$[$}pii{$]$}},
    Au = {Yang H},
    Author = {J Yu and S Hu and J Wang and GKS Wong and S Li and B Liu and Y Deng and L Dai and Y Zhou and X Zhang and others},
    Cin = {Science. 2002 Apr 5;296(5565):92-100. PMID: 11935018},
    Da = {20020405},
    Date-Modified = {2005-02-19 20:05:00 -0800},
    Dcom = {20020423},
    Edat = {2002/04/06 10:00},
    Gr = {1 RO1 ES09909/ES/NIEHS},
    Jid = {0404511},
    Journal = {Science},
    Keywords = {Arabidopsis/genetics and Base Composition and Computational Biology and Contig Mapping and DNA Transposable Elements and DNA, Intergenic and DNA, Plant/chemistry/genetics and Databases, Nucleic Acid and Exons and Gene Duplication and Genes, Plant and *Genome, Plant and Genomics and Introns and Molecular Sequence Data and Oryza sativa/*genetics and Plant Proteins/chemistry/genetics and Polymorphism, Genetic and Repetitive Sequences, Nucleic Acid and Research Support, Non-U.S. Gov't and Research Support, U.S. Gov't, Non-P.H.S. and Research Support, U.S. Gov't, P.H.S. and *Sequence Analysis, DNA and Sequence Homology, Nucleic Acid and Software and Species Specificity and Synteny},
    Language = {eng},
    Lr = {20041117},
    Mhda = {2002/04/24 10:01},
    Number = {5565},
    Own = {NLM},
    Pages = {79--92},
    Pl = {United States},
    Pmid = {11935017},
    Pst = {ppublish},
    Pt = {Journal Article},
    Pubm = {Print},
    Rn = {0 (Plant Proteins)},
    Sb = {IM},
    So = {PLoS Biol 2005 Feb;3(2):e38. Epub 2005 Feb 1.},
    Stat = {MEDLINE},
    Title = {{A draft sequence of the rice genome (Oryza sativa L. ssp. indica)}},
    Volume = {296},
    Year = {2002}}

@Article{bangjensen2004,
  author = 	 {J Bang-Jensen and G Gutin and A Yeo},
  title = 	 {When the greedy algorithm fails},
  journal = 	 {Discrete Optimization},
  year = 	 {2004},
  OPTkey = 	 {},
  volume = 	 {1},
  OPTnumber = 	 {},
  pages = 	 {121--127},
  OPTmonth = 	 {},
  OPTnote = 	 {},
  OPTannote = 	 {}
}

@TECHREPORT{phylip,
  AUTHOR =       {J Felsenstein},
  TITLE =        {{PHYLIP (phylogeny inference package) version 3.5c.}},
  INSTITUTION =  {Department of Genetics, University of Washington, Seattle},
  YEAR =         {1993},
}

@Article{seq_gen,
  author =   {A Rambaut and N C Grassly},
  title =    {{Seq-Gen: an application for the Monte Carlo simulation of DNA sequences evolution along phylogenetic trees}},
  journal =  {Computational Applied Bioscience},
  year =     {1997},
  OPTkey =   {},
  volume =   {13},
  OPTnumber =    {},
  pages =    {235--238},
  OPTmonth =     {},
  OPTnote =      {},
  OPTannote =    {}
}