1@string{AHG = "Annals of Human Genetics"}
2@string{AJHG = "American Journal of Human Genetics"}
3@string{ARB    = "Annual Review of Biochemistry"}
4@string{ARCB   = "Annual Review of Cell Biology"}
5@string{BI = "Bioinformatics"}
6@string{BIOGEN = "Biochemical Genetics"}
7@string{BJLS = "Biological Journal of the Linnean Society"}
8@string{BMB = "Bulletin of Mathematical Biology"}
9@string{CABIOS = "Computer Applications in the Biosciences"}
10@string{CACM   = "Communications of the ACM"}
11@string{COCB   = "Current Opinion in Cell Biology"}
12@string{COSB   = "Current Opinion in Structural Biology"}
13@string{CSHSQB = "Cold Spring Harbor Symposia Quantitative Biology"}
14@string{ComputChem = "Computers and Chemistry"}
15@string{EMBO   = "EMBO Journal"}
16@string{EVO = "Evolution"}
17@string{GEN = "Genetics"}
18@string{JBSD   = "Journal of Biomolecular Structure and Dynamics"}
19@string{JComputBiol = "Journal of Computational Biology"}
20@string{JCB = JComputBiol}
21@string{JMB = "Journal of Molecular Biology"}
22@string{JME = "Journal of Molecular Evolution"}
23@string{JRSS = "Journal of the Royal Statistical Society, B"}
24@string{JTB    = "Journal of Theoretical Biology"}
25@string{MBE = "Molecular Biology and Evolution"}
26@string{MBIO = "Mathematical Biosciences"}
27@string{ME = "Methods in Enzymology"}
28@string{MPE = "Molecular Phylogenetics and Evolution"}
29@string{NAR = "Nucleic Acids Research"}
30@string{NC = "Neural Computation"}
31@string{NNB = "Nature New Biology"}
32@string{Nature = "Nature"}
33@string{PE = "Protein Engineering"}
34@string{PNAS = "Proceedings of the National Academy of Sciences of the USA"}
35@string{PROT = "Proteins"}
36@string{PROTSCI = "Protein Science"}
37@string{SIAM = "SIAM Journal of Applied Mathematics"}
38@string{SYSB = "Systematic Biology"}
39@string{SZ = "Systematic Zoology"}
40@string{Science = "Science"}
41@string{S = Science}
42@string{TIBTECH= "Trends in Biotechnology"}
43@string{TIGS   = "Trends in Genetics"}
44@string{TIBS   = "Trends in Biochemistry"}
45@string{UKSB = "University of Kansas Scientific Bulletin"}
46
47
48@Article{Abrahams90,
49  author = 	 {J. P. Abrahams and M. van den Berg and E. van
50                  Batenburg and C. Pleij},
51  title = 	 {Prediction of {RNA} Secondary Structure, Including
52                  Pseudoknotting, by Computer Simulation},
53  journal = 	 NAR,
54  year = 	 1990,
55  volume =	 18,
56  pages =	 {3035-3044}
57}
58
59
60@inproceedings{AllisonEtal92a,
61  author = "L. Allison and C. S. Wallace and C. N. Yee",
62  title = "Minimum message length encoding, evolutionary trees and
63		  multiple alignment",
64  booktitle = "Hawaii International Conference on System Sciences",
65  year = "1992",
66  volume = "1",
67  pages = "663-674"
68}
69
70@article{AllisonEtal92b,
71  author = "L. Allison and C. S. Wallace and C. N. Yee",
72  title = "Finite-state models in the alignment of macromolecules.",
73  journal = JME,
74  year = "1992",
75  volume = "35",
76  pages = "77-89"
77}
78
79@techreport{AllisonWallace93,
80  author = "L. Allison and C. S. Wallace",
81  title = "The posterior probability distribution of alignments and its
82	application to parameter estimation of evolutionary trees and to
83	optimisation of muliple alignments",
84  institution = "Monash University Computer Science",
85  year = 1993,
86  number = "TR 93/188"
87}
88
89@article{Altschul89,
90  author = "S. F. Altschul",
91  title = "Gap costs for multiple sequence alignment",
92  journal = JTB,
93  volume = 138,
94  pages = "297-309",
95  year = 1989
96}
97
98@Article{Altschul90,
99  author = 	 "S. F. Altschul
100		and W. Gish and W. Miller
101		  and E. W. Myers and D. J. Lipman",
102  title = 	 "Basic Local Alignment Search Tool",
103  journal = 	 JMB,
104  year = 	 1990,
105  volume = 	 215,
106  pages = 	 "403-410"
107}
108
109@Article{Altschul91,
110  author = 	 "S. F. Altschul",
111  title = 	 "Amino Acid Substitution Matrices from an Information
112		  Theoretic Perspective",
113  journal = 	 JMB,
114  year = 	 1991,
115  volume = 	 219,
116  pages = 	 "555-565"
117}
118
119@article{AltschulErickson86,
120  author = "S. F. Altschul and B. W. Erickson",
121  title = "Optimal sequence alignment using affine gap costs",
122  journal = BMB,
123  volume = 48,
124  pages = "603-616",
125  year = 1986
126}
127
128@article{AltschulEtal89,
129  author = "S. F. Altschul and and R. J. Carroll and D. J. Lipman",
130  title = "Weights for Data Related by a Tree",
131  journal = JMB,
132  volume = 207,
133  pages = "647-653",
134  year = 1989
135}
136
137@article{SlonimEtal97,
138  author = "D. Slonim and L. Kruglyak and L. Stein and E. Lander",
139  title  = "Building human genome maps with radiation hybrids",
140  journal = JCB,
141  pages = "487-504",
142  volume = 4,
143  year = 1997,
144}
145
146@article{ThorneEtal96,
147  author = "J. L. Thorne and N. Goldman and D. T. Jones",
148  title  = "Combining protein evolution and secondary structure.",
149  journal = MBE,
150  volume = 13,
151  pages = "666-673",
152  year = 1996,
153}
154
155@article{GoldmanEtal96,
156  author = "N. Goldman and J. L. Thorne and D. T. Jones",
157  title  = "Using evolutionary trees in protein secondary structure prediction and other comparative sequence analyses.",
158  journal = JMB,
159  volume = 263,
160  pages = "196-208",
161  year = 1996,
162}
163
164@article{LioEtal99,
165  author = "P. Lio and J. L. Thorne and N. Goldman and D. T. Jones",
166  title  = "PASSML: combining evolutionary inference and protein secondary structure prediction.",
167  pages  = "726-733",
168  journal = BI,
169  volume = 14,
170  year = 1999,
171}
172
173@article{AltschulGish96,
174author = {S. F. Altschul and W. Gish},
175title = {Local alignment statistics},
176journal = ME,
177volume = 266,
178pages = "460-480",
179year = 1996
180}
181
182@Article{Altschul97,
183  author = 	 {S. F. Altschul and T. L. Madden and A. A. Schaffer and
184                  J. Zhang and Z. Zhang and W. Miller and D. J. Lipman},
185  title = 	 {Gapped {BLAST} and {PSI-BLAST}: a New Generation of
186                  Protein Database Search Programs},
187  journal = 	 NAR,
188  year = 	 1997,
189  volume =	 25,
190  pages =	 {3389-3402}
191}
192
193@Article{AltschulLipman89,
194  author = 	 {S. F. Altschul and D. J. Lipman},
195  title = 	 {Trees, Stars, and Multiple Biological Sequence Alignment},
196  journal = 	 SIAM,
197  year = 	 1989,
198  volume =	 49,
199  pages =	 {197-209}
200}
201
202@article{AsaiEtal93,
203  author = "K. Asai and S. Hayamizu and K. Handa",
204  title = "Prediction of protein secondary structure by the hidden
205	{M}arkov model",
206  journal = CABIOS,
207  year = "1993",
208  volume = "9",
209  number = "2",
210  pages = "141-146"
211}
212
213@book{Asmussen87,
214  author = "S. Asmussen",
215  title = "Applied Probability and Queues",
216  publisher = "Wiley",
217  address = "Chichester, UK",
218  year = 1987
219}
220
221@incollection{Atteson97,
222  author = "K. Atteson",
223  title = "The performance of the neighbor-joining method of phylogeny reconstruction",
224  booktitle = "Mathematical Hierarchies and Biology",
225  pages = "133-148",
226  editor = "B. Mirkin and F. Mc{M}orris and F. Roberts and A. Rzhetsky",
227  publisher = "American Mathematical Society",
228  address = "Providence, RI",
229  year = 1997
230}
231
232@Article{Attwood94,
233  author = 	 {T. K. Attwood and M. E. Beck},
234  title = 	 {{PRINTS} -- A Protein Motif Fingerprint Database},
235  journal = 	 PE,
236  year = 	 1994,
237  volume =	 7,
238  pages =	 {841-848}
239}
240
241@inproceedings{BaileyElkan94,
242  author = "T. L. Bailey and C. Elkan",
243  title = "Fitting a Mixture Model by Expectation Maximization
244	to Discover Motifs in Biopolymers",
245  crossref = "ismb94",
246  pages = "28--36"
247}
248
249@inproceedings{BaileyElkan95,
250  author = "T. L. Bailey and C. Elkan",
251  title = "The value of prior knowledge in discovering motifs with {MEME}",
252  pages = "21-29",
253  crossref = "ismb95"
254}
255
256@inproceedings{BaileyGribskov96,
257  author = "T. L. Bailey and M. Gribskov",
258  title  = "The megaprior heuristic for discovering protein sequence patterns.",
259  pages  = "15-24",
260  crossref = "ismb96",
261}
262
263@inproceedings{BahlEtAl86,
264  author = "L. R. Bahl and P. F. Brown and P. V. de Souza and R. L. Mercer",
265  title = "Maximum Mutual Information Estimation of Hidden {M}arkov
266        Model Parameters for Speech Recognition",
267  booktitle = "Proceedings of ICASSP '86",
268  pages = "49-52",
269  year = "1986",
270  myref = "HMM25"
271}
272
273@Article{Bairoch97b,
274  author = 	 {A. Bairoch and P. Bucher and K. Hofmann},
275  title = 	 {The {\sc PROSITE} Database, Its Status in 1997},
276  journal = 	 NAR,
277  year = 	 1997,
278  volume =	 25,
279  pages =	 {217-221}
280}
281
282% RD says:
283% this is the correct latest swissprot reference to replace
284% BairochApweiler96 in your list - I updated the only \cite{BA96}
285% in the book, in profhmm.
286
287@Article{Bairoch97,
288  author = 	 {A. Bairoch and R. Apweiler},
289  title = 	 {The {\sc SWISS-PROT} Protein Sequence Data Bank and Its
290                  Supplement {TrEMBL}},
291  journal = 	 NAR,
292  year = 	 1997,
293  volume =	 25,
294  pages =	 {31-36}
295}
296
297@book{BaldiBrunak98,
298  author = "P. Baldi and S. Brunak",
299  title = "Bioinformatics -- The Machine Learning Approach",
300  publisher = "MIT Press",
301  address = "Cambridge, MA",
302  year = 1998
303}
304
305@article{BaldiChauvin94,
306  author = "P. Baldi and Y. Chauvin ",
307  title = "Smooth on-line learning algorithms for hidden {M}arkov
308	models",
309  journal = NC,
310  year = 1994,
311  number = 2,
312  volume = 6,
313  pages = "307-318"
314}
315
316@article{bhattacharya99,
317  author = "S. K. Bhattacharya and S. Ramchandani and N. Cervoni and M. Szyf",
318  title = "A mammalian protein with specific demethylase activity for m{C}p{G} {DNA}",
319  journal = Nature,
320  pages = {579-583},
321  volume = 397,
322  year = 1999
323}
324
325@inproceedings{BaldiChauvin95,
326  author = "P. Baldi and Y. Chauvin",
327  title = "Protein modeling with hybrid Hidden {M}arkov Model/neural
328	network architectures",
329  year = "1995",
330  pages = "39-47",
331  crossref = "ismb95"
332}
333
334@article{BaldiEtal94,
335  author = "P. Baldi and Y. Chauvin and T. Hunkapiller and M. A.
336	Mc{C}lure",
337  title = "Hidden {M}arkov models of biological primary sequence
338	information",
339  journal = PNAS,
340  year = "1994",
341  volume = "91",
342  number = "3",
343  pages = "1059-1063"
344}
345
346@article{BaldiEtal96b,
347  author =  {P. Baldi and S. Brunak and Y. Chauvin and A. Krogh},
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349        Human Exons},
350  journal = JMB,
351  volume = 263,
352  pages = "503-510",
353  year = 1996
354}
355
356@article{BandeltDress92,
357  author = "H.-J. Bandelt and A. W. M. Dress",
358  title = "Split decomposition: a new and useful approach to
359		  phylogenetic analysis of distance data",
360  journal = MPE,
361  volume = 1,
362  pages = "242-252",
363  year = 1992
364}
365
366@article{BartonSternberg87,
367  author = "G. J. Barton and M. J. E. Sternberg",
368  title = "A Strategy for the Rapid Multiple Alignment of Protein Sequences",
369  journal = JMB,
370  volume = 198,
371  year = 1987,
372  pages = "327-337"
373}
374
375@article{Barton93,
376  author = "G. J. Barton",
377  title = "An efficient algorithm to locate all locally optimal alignments
378	between two sequences allowing for gaps",
379  journal = CABIOS,
380  volume = 9,
381  number = 6,
382  year = 1993,
383  pages = "729-734"
384}
385
386@article{barton90,
387  author = "G. J. Barton and M. J. Sternberg",
388  title  = "Flexible protein sequence patterns. A sensitive method to detect weak structural similarities.",
389  journal = JMB,
390  volume  = 212,
391  pages   = "389-402",
392  year    = 1990,
393}
394
395@InCollection{Baserga93,
396  author = 	 "S. J. Baserga and J. A. Steitz",
397  title = 	 "The Diverse World of Small Ribonucleoproteins",
398  booktitle =	 "The {RNA} World",
399  publisher =	 "Cold Spring Harbor Press",
400  year =	 1993,
401  editor =	 "R. F. Gesteland and J. F. Atkins",
402  pages =	 "359-381",
403  address =	 "New York"
404}
405
406@article{BashfordEtal87,
407  author = "D. Bashford and C. Chothia and A. M. Lesk",
408  title = "Determinants of a protein fold: unique features of
409        the globin amino acid sequence",
410  journal = JMB,
411  volume = 196,
412  pages = "199-216",
413  year = 1987
414}
415
416@article{Baum72,
417  author =       {L. E. Baum},
418  title =        {An Equality and Associated Maximization Technique
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421  journal =      {Inequalities},
422  year =         1972,
423  volume =       3,
424  pages =        {1-8}
425}
426
427
428@article{BengioEtal92,
429  author = "Y. Bengio and R. De Mori and G. Flammia and R. Kompe",
430  title = "Global optimization of a neural network--hidden {M}arkov
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432  journal = "IEEE Transactions on Neural Networks",
433  year = 1992,
434  number = 2,
435  volume = 3,
436  pages = "252-259"
437}
438
439@book{Berger85,
440  author= "J. O. Berger",
441  title= "Statistical Decision Theory and {B}ayesian Analysis",
442  publisher= "Springer-Verlag",
443  address= "New York",
444  year= 1985
445}
446
447@article{BergerMunson91,
448  author = "M. P. Berger  and P. J. Munson",
449  title = "A novel randomized iterative strategy for aligning
450            multiple protein sequences",
451  journal = CABIOS,
452  volume = 7,
453  pages = "479-484",
454  year = 1991
455}
456
457@Article{Bird87,
458  author = 	 {A. Bird},
459  title = 	 {{CpG} islands as gene markers in the vertebrate nucleus},
460  journal = 	 TIGS,
461  year = 	 1987,
462  volume =	 3,
463  pages =	 {342-347}
464}
465
466@Article{Birney93,
467   author = {E Birney and S. Kumar and A. R.  Krainer},
468   title  = {Analysis of the {RNA}-recognition motif and {RS} and {RGG} domains: conservation in metazoan pre-m{RNA} splicing factors},
469   journal = NAR,
470   year = 1993,
471   pages = {5803-5816}
472}
473
474
475@Article{Birney94,
476   author = {T. J. Gibson and M. Hyvonen and A. Musacchio and M. Saraste and E. Birney},
477   title  = {{PH} domain: the first anniversary},
478   journal = TIBS,
479   year = 1994,
480   volume = 19,
481   pages = {349-353}
482}
483
484@Article{Birney96,
485   author = {E. Birney and J. D. Thompson and T. J. Gibson},
486   title  = {Pairwise and Searchwise: comparison of a protein profile to all three translation frames simultaneously},
487   journal = NAR,
488   year = 1996,
489   volume = 24,
490   pages = {2730-2739}
491}
492
493@inproceedings{BirneyDurbin97,
494  author = "E. Birney and R. Durbin",
495  title = {Dynamite: a flexible code generating language for dynamic
496	programming methods used in sequence comparison},
497  crossref = "ismb97",
498  year = 1997,
499  pages = "56-64"
500}
501
502@article{BishopThompson86,
503author = {M. J. Bishop and E. A. Thompson},
504title = {Maximum Likelihood alignment of {DNA} Sequences},
505journal = JMB,
506year = 1986,
507volume = 190,
508pages = {159-165}
509}
510
511@article{BorodovskyEtal86a,
512  author = "M. Yu. Borodovsky and Yu. A. Sprizhitsky and E. I. Golovanov
513	and A. A. Alexandrov",
514  title = "Statistical Patterns in the Primary Structure of the Functional
515	Regions of the {Escherichia} Coli Genome.
516	{I}. {F}requency Characteristics",
517  journal = "Molecularnaya Biologia",
518  note = "(English translation)",
519  year = 1986,
520  volume = 20,
521  pages = "826--833"
522}
523
524@article{BorodovskyEtal86b,
525  author = "M. Yu. Borodovsky and Yu. A. Sprizhitsky and E. I. Golovanov
526	and A. A. Alexandrov",
527  title = "Statistical Patterns in the Primary Structure of the Functional
528	Regions of the {Escherichia Coli} Genome.
529	{II}. {N}onuniform {M}arkov Models",
530  journal = "Molecularnaya Biologia",
531  note = "(English translation)",
532  year = 1986,
533  volume = 20,
534  pages = "833--840"
535}
536
537@article{BorodovskyEtal86c,
538  author = "M. Yu. Borodovsky and Yu. A. Sprizhitsky and E. I. Golovanov
539	and A. A. Alexandrov",
540  title = "Statistical Patterns in the Primary Structure of the Functional
541	Regions of the {Escherichia Coli} Genome.
542	{III}. {C}omputer Recognition of Coding Regions",
543  journal = "Molecularnaya Biologia",
544  note = "(English translation)",
545  year = 1986,
546  volume = 20,
547  pages = "1144--1150"
548}
549
550@article{BorodovskyMcIninch93,
551  author = "M. Borodovsky and J. Mc{I}ninch",
552  title = "{\sc GENMARK}: parallel Gene Recognition for Both {DNA} strands",
553  journal = ComputChem,
554  year = "1993",
555  volume = 17,
556  number = 2,
557  pages = "123--133",
558  myref = "BIO105"
559}
560
561@article{BowieEtal91,
562  author = "J. U. Bowie and R. Luthy and D. Eisenberg",
563  title = "A method to identify protein sequences that fold into
564	a known three-dimensional structure",
565  journal = Science,
566  year = 1991,
567  volume = 253,
568  pages = "164-170"
569}
570
571@Book{BoxTiao92,
572  author = 	 {G. E. P. Box and G. C. Tiao},
573  title = 	 {Bayesian Inference in Statistical Analysis},
574  publisher = 	 {Wiley-Interscience},
575  year = 	 1992
576}
577
578@Book{Branden91,
579  author = 	 {C. Branden and J. Tooze},
580  title = 	 {Introduction to Protein Structure},
581  publisher = 	 {Garland},
582  year = 	 1991,
583  address =	 {New York}
584}
585
586@Article{Brendel86,
587  author = 	 {V. Brendel and J. S. Beckmann and E. N. Trifonov},
588  title = 	 {Linguistics of Nucleotide Sequences: morphology and
589                  Comparison of Vocabularies},
590  journal = 	 JBSD,
591  year = 	 1986,
592  volume =	 4,
593  pages =	 {11-20},
594  filed =        {Trifonov}
595}
596
597@book{Brooksetal91,
598  author = "D. R. Brooks and D. A. Mc{L}ennan",
599  title = "Phylogeny, Ecology and Behaviour",
600  publisher = "University of Chicago Press",
601  address = "Chicago",
602  year = 1991
603}
604
605@inproceedings{BrownEtal93,
606  author={M. Brown and R. Hughey and A. Krogh and I. S. Mian and
607	K. Sj{\"o}lander and D. Haussler},
608  title="Using {D}irichlet Mixture Priors to Derive Hidden {M}arkov
609	Models for Protein Families",
610  pages= "47-55",
611  crossref = "ismb93"
612}
613
614@Unpublished{BrownWilson95,
615  author = {M. Brown and C. Wilson},
616  title = {{RNA} Pseudoknot Modeling Using Intersections of
617                  Stochastic Context-Free Grammars with Applications
618                  to Database Search},
619  note = {Unpublished manuscript available from
620          http://www.cse.ucsc.edu/research/compbio/pseudoknot.html},
621  year = 1995
622}
623
624@article{BrunakEtal91,
625  author = "S. Brunak and J. Engelbrecht and S. Knudsen",
626  title = "Prediction of human {mRNA} donor and acceptor sites from
627	the {DNA} sequence",
628  journal = JMB,
629  year = "1991",
630  volume = "220",
631  number = "1",
632  pages = "49--65"
633}
634
635@article{BrunakEtal90,
636  author = "S. Brunak and J. Engelbrecht and S. Knudsen",
637  title  = "Iden"
638}
639
640
641@article{BucherEtal96,
642  author = "P. Bucher and K. Karplus and N. Moeri
643	and K. Hofmann",
644  title = "A Flexible Motif Search Technique Based on Generalized
645	Profiles",
646  journal = ComputChem,
647  volume = 20,
648  pages = "3-24",
649  year = 1996
650}
651
652@InProceedings{BucherHofmann96,
653  author = 	 {P. Bucher and K. Hofmann},
654  title = 	 {A Sequence Similarity Search Algorithm Based on a
655                  Probabilistic Interpretation of an Alignment Scoring System},
656  crossref = 	 "ismb96",
657  pages =	 {44-51}
658}
659
660@incollection{Buneman71,
661  author = "P. Buneman",
662  title = "The recovery of trees from measures of dissimilarity",
663  booktitle = "Mathematics in the Archaeological and Historical Sciences",
664  pages = "387-395",
665  editor = "F. R. Hodson and D. G. Kendall and P. Tautu",
666  publisher = "Edinburgh University Press",
667  address = "Edinburgh",
668  year = 1971
669}
670
671@article{BurgeKarlin97,
672  author = "C. Burge and S. Karlin",
673  title = "Prediction of Complete Gene Structures in Human Genomic {DNA}",
674  journal = JMB,
675  volume = 268,
676  year = 1997,
677  pages = "78-94"
678}
679
680@article{CaminSokal65,
681  author = "J. H. Camin and R. R. Sokal",
682  title = "A method for deducing branching sequences in phylogeny",
683  journal = EVO,
684  volume = 19,
685  pages = "311-327",
686  year = 1965
687}
688
689@article{CardonStormo92,
690  author = "L. R. Cardon and G. D. Stormo",
691  title = "Expectation maximization algorithm for identifying
692        protein-binding sites with variable lengths from unaligned
693        {DNA} fragments",
694  journal = JMB,
695  year = 1992,
696  volume = 223,
697  number = 1,
698  pages = "159--170"
699}
700
701@article{CarrilloLipman88,
702  author = "H. Carrillo and D. Lipman",
703  title = "The Multiple Sequence Alignment Problem in Biology",
704  journal = SIAM,
705  volume = 48,
706  pages = "1073-1082",
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