File: alignment.bib

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@string{AHG = "Annals of Human Genetics"}
@string{AJHG = "American Journal of Human Genetics"}
@string{ARB    = "Annual Review of Biochemistry"}
@string{ARCB   = "Annual Review of Cell Biology"}
@string{BI = "Bioinformatics"}
@string{BIOGEN = "Biochemical Genetics"}
@string{BJLS = "Biological Journal of the Linnean Society"}
@string{BMB = "Bulletin of Mathematical Biology"}
@string{CABIOS = "Computer Applications in the Biosciences"}
@string{CACM   = "Communications of the ACM"}
@string{COCB   = "Current Opinion in Cell Biology"}
@string{COSB   = "Current Opinion in Structural Biology"}
@string{CSHSQB = "Cold Spring Harbor Symposia Quantitative Biology"}
@string{ComputChem = "Computers and Chemistry"}
@string{EMBO   = "EMBO Journal"}
@string{EVO = "Evolution"}
@string{GEN = "Genetics"}
@string{JBSD   = "Journal of Biomolecular Structure and Dynamics"}
@string{JComputBiol = "Journal of Computational Biology"}
@string{JCB = JComputBiol}
@string{JMB = "Journal of Molecular Biology"}
@string{JME = "Journal of Molecular Evolution"}
@string{JRSS = "Journal of the Royal Statistical Society, B"}
@string{JTB    = "Journal of Theoretical Biology"}
@string{MBE = "Molecular Biology and Evolution"}
@string{MBIO = "Mathematical Biosciences"}
@string{ME = "Methods in Enzymology"}
@string{MPE = "Molecular Phylogenetics and Evolution"}
@string{NAR = "Nucleic Acids Research"}
@string{NC = "Neural Computation"}
@string{NNB = "Nature New Biology"}
@string{Nature = "Nature"}
@string{PE = "Protein Engineering"}
@string{PNAS = "Proceedings of the National Academy of Sciences of the USA"}
@string{PROT = "Proteins"}
@string{PROTSCI = "Protein Science"}
@string{SIAM = "SIAM Journal of Applied Mathematics"}
@string{SYSB = "Systematic Biology"}
@string{SZ = "Systematic Zoology"}
@string{Science = "Science"}
@string{S = Science}
@string{TIBTECH= "Trends in Biotechnology"}
@string{TIGS   = "Trends in Genetics"}
@string{TIBS   = "Trends in Biochemistry"}
@string{UKSB = "University of Kansas Scientific Bulletin"}


@Article{Abrahams90,
  author = 	 {J. P. Abrahams and M. van den Berg and E. van
                  Batenburg and C. Pleij},
  title = 	 {Prediction of {RNA} Secondary Structure, Including
                  Pseudoknotting, by Computer Simulation},
  journal = 	 NAR,
  year = 	 1990,
  volume =	 18,
  pages =	 {3035-3044}
}


@inproceedings{AllisonEtal92a,
  author = "L. Allison and C. S. Wallace and C. N. Yee",
  title = "Minimum message length encoding, evolutionary trees and
		  multiple alignment",
  booktitle = "Hawaii International Conference on System Sciences",
  year = "1992",
  volume = "1",
  pages = "663-674"
}

@article{AllisonEtal92b,
  author = "L. Allison and C. S. Wallace and C. N. Yee",
  title = "Finite-state models in the alignment of macromolecules.",
  journal = JME,
  year = "1992",
  volume = "35",
  pages = "77-89"
}

@techreport{AllisonWallace93,
  author = "L. Allison and C. S. Wallace",
  title = "The posterior probability distribution of alignments and its
	application to parameter estimation of evolutionary trees and to
	optimisation of muliple alignments",
  institution = "Monash University Computer Science",
  year = 1993,
  number = "TR 93/188"
}

@article{Altschul89,
  author = "S. F. Altschul",
  title = "Gap costs for multiple sequence alignment",
  journal = JTB,
  volume = 138,
  pages = "297-309",
  year = 1989
}

@Article{Altschul90,
  author = 	 "S. F. Altschul
		and W. Gish and W. Miller
		  and E. W. Myers and D. J. Lipman",
  title = 	 "Basic Local Alignment Search Tool",
  journal = 	 JMB,
  year = 	 1990,
  volume = 	 215,
  pages = 	 "403-410"
}

@Article{Altschul91,
  author = 	 "S. F. Altschul",
  title = 	 "Amino Acid Substitution Matrices from an Information
		  Theoretic Perspective",
  journal = 	 JMB,
  year = 	 1991,
  volume = 	 219,
  pages = 	 "555-565"
}

@article{AltschulErickson86,
  author = "S. F. Altschul and B. W. Erickson",
  title = "Optimal sequence alignment using affine gap costs",
  journal = BMB,
  volume = 48,
  pages = "603-616",
  year = 1986
}

@article{AltschulEtal89,
  author = "S. F. Altschul and and R. J. Carroll and D. J. Lipman",
  title = "Weights for Data Related by a Tree",
  journal = JMB,
  volume = 207,
  pages = "647-653",
  year = 1989
}

@article{SlonimEtal97,
  author = "D. Slonim and L. Kruglyak and L. Stein and E. Lander",
  title  = "Building human genome maps with radiation hybrids",
  journal = JCB,
  pages = "487-504",
  volume = 4,
  year = 1997,
}

@article{ThorneEtal96,
  author = "J. L. Thorne and N. Goldman and D. T. Jones",
  title  = "Combining protein evolution and secondary structure.",
  journal = MBE,
  volume = 13,
  pages = "666-673",
  year = 1996,
}

@article{GoldmanEtal96,
  author = "N. Goldman and J. L. Thorne and D. T. Jones",
  title  = "Using evolutionary trees in protein secondary structure prediction and other comparative sequence analyses.",
  journal = JMB,
  volume = 263,
  pages = "196-208",
  year = 1996,
}

@article{LioEtal99,
  author = "P. Lio and J. L. Thorne and N. Goldman and D. T. Jones",
  title  = "PASSML: combining evolutionary inference and protein secondary structure prediction.",
  pages  = "726-733",
  journal = BI,
  volume = 14,
  year = 1999,
}
  
@article{AltschulGish96,
author = {S. F. Altschul and W. Gish},
title = {Local alignment statistics},
journal = ME,
volume = 266,
pages = "460-480",
year = 1996
}

@Article{Altschul97,
  author = 	 {S. F. Altschul and T. L. Madden and A. A. Schaffer and
                  J. Zhang and Z. Zhang and W. Miller and D. J. Lipman},
  title = 	 {Gapped {BLAST} and {PSI-BLAST}: a New Generation of
                  Protein Database Search Programs},
  journal = 	 NAR,
  year = 	 1997,
  volume =	 25,
  pages =	 {3389-3402}
}

@Article{AltschulLipman89,
  author = 	 {S. F. Altschul and D. J. Lipman},
  title = 	 {Trees, Stars, and Multiple Biological Sequence Alignment},
  journal = 	 SIAM,
  year = 	 1989,
  volume =	 49,
  pages =	 {197-209}
}

@article{AsaiEtal93,
  author = "K. Asai and S. Hayamizu and K. Handa",
  title = "Prediction of protein secondary structure by the hidden
	{M}arkov model",
  journal = CABIOS,
  year = "1993",
  volume = "9",
  number = "2",
  pages = "141-146"
}

@book{Asmussen87,
  author = "S. Asmussen",
  title = "Applied Probability and Queues",
  publisher = "Wiley",
  address = "Chichester, UK",
  year = 1987
}

@incollection{Atteson97,
  author = "K. Atteson",
  title = "The performance of the neighbor-joining method of phylogeny reconstruction",
  booktitle = "Mathematical Hierarchies and Biology",
  pages = "133-148",
  editor = "B. Mirkin and F. Mc{M}orris and F. Roberts and A. Rzhetsky",
  publisher = "American Mathematical Society",
  address = "Providence, RI",
  year = 1997
}

@Article{Attwood94,
  author = 	 {T. K. Attwood and M. E. Beck},
  title = 	 {{PRINTS} -- A Protein Motif Fingerprint Database},
  journal = 	 PE,
  year = 	 1994,
  volume =	 7,
  pages =	 {841-848}
}

@inproceedings{BaileyElkan94,
  author = "T. L. Bailey and C. Elkan",
  title = "Fitting a Mixture Model by Expectation Maximization
	to Discover Motifs in Biopolymers",
  crossref = "ismb94",
  pages = "28--36"
}

@inproceedings{BaileyElkan95,
  author = "T. L. Bailey and C. Elkan",
  title = "The value of prior knowledge in discovering motifs with {MEME}",
  pages = "21-29",
  crossref = "ismb95"
}

@inproceedings{BaileyGribskov96,
  author = "T. L. Bailey and M. Gribskov",
  title  = "The megaprior heuristic for discovering protein sequence patterns.",
  pages  = "15-24",
  crossref = "ismb96",
}

@inproceedings{BahlEtAl86,
  author = "L. R. Bahl and P. F. Brown and P. V. de Souza and R. L. Mercer",
  title = "Maximum Mutual Information Estimation of Hidden {M}arkov
        Model Parameters for Speech Recognition",
  booktitle = "Proceedings of ICASSP '86",
  pages = "49-52",
  year = "1986",
  myref = "HMM25"
}

@Article{Bairoch97b,
  author = 	 {A. Bairoch and P. Bucher and K. Hofmann},
  title = 	 {The {\sc PROSITE} Database, Its Status in 1997},
  journal = 	 NAR,
  year = 	 1997,
  volume =	 25,
  pages =	 {217-221}
}

% RD says:
% this is the correct latest swissprot reference to replace
% BairochApweiler96 in your list - I updated the only \cite{BA96} 
% in the book, in profhmm.

@Article{Bairoch97,
  author = 	 {A. Bairoch and R. Apweiler},
  title = 	 {The {\sc SWISS-PROT} Protein Sequence Data Bank and Its
                  Supplement {TrEMBL}},
  journal = 	 NAR,
  year = 	 1997,
  volume =	 25,
  pages =	 {31-36}
}

@book{BaldiBrunak98,
  author = "P. Baldi and S. Brunak",
  title = "Bioinformatics -- The Machine Learning Approach",
  publisher = "MIT Press",
  address = "Cambridge, MA",
  year = 1998
}

@article{BaldiChauvin94,
  author = "P. Baldi and Y. Chauvin ",
  title = "Smooth on-line learning algorithms for hidden {M}arkov
	models",
  journal = NC,
  year = 1994,
  number = 2,
  volume = 6,
  pages = "307-318"
}

@article{bhattacharya99,
  author = "S. K. Bhattacharya and S. Ramchandani and N. Cervoni and M. Szyf",
  title = "A mammalian protein with specific demethylase activity for m{C}p{G} {DNA}",
  journal = Nature,
  pages = {579-583},
  volume = 397,
  year = 1999
}

@inproceedings{BaldiChauvin95,
  author = "P. Baldi and Y. Chauvin",
  title = "Protein modeling with hybrid Hidden {M}arkov Model/neural
	network architectures",
  year = "1995",
  pages = "39-47",
  crossref = "ismb95"
}

@article{BaldiEtal94,
  author = "P. Baldi and Y. Chauvin and T. Hunkapiller and M. A.
	Mc{C}lure",
  title = "Hidden {M}arkov models of biological primary sequence
	information",
  journal = PNAS,
  year = "1994",
  volume = "91",
  number = "3",
  pages = "1059-1063"
}

@article{BaldiEtal96b,
  author =  {P. Baldi and S. Brunak and Y. Chauvin and A. Krogh},
  title  = {Naturally Occurring Nucleosome Positioning Signals in
        Human Exons},
  journal = JMB,
  volume = 263,
  pages = "503-510",
  year = 1996
}

@article{BandeltDress92,
  author = "H.-J. Bandelt and A. W. M. Dress",
  title = "Split decomposition: a new and useful approach to
		  phylogenetic analysis of distance data",
  journal = MPE,
  volume = 1,
  pages = "242-252",
  year = 1992
}

@article{BartonSternberg87,
  author = "G. J. Barton and M. J. E. Sternberg",
  title = "A Strategy for the Rapid Multiple Alignment of Protein Sequences",
  journal = JMB,
  volume = 198,
  year = 1987,
  pages = "327-337"
}

@article{Barton93,
  author = "G. J. Barton",
  title = "An efficient algorithm to locate all locally optimal alignments
	between two sequences allowing for gaps",
  journal = CABIOS,
  volume = 9,
  number = 6,
  year = 1993,
  pages = "729-734"
}

@article{barton90,
  author = "G. J. Barton and M. J. Sternberg",
  title  = "Flexible protein sequence patterns. A sensitive method to detect weak structural similarities.",
  journal = JMB,
  volume  = 212,
  pages   = "389-402",
  year    = 1990,
}

@InCollection{Baserga93,
  author = 	 "S. J. Baserga and J. A. Steitz",
  title = 	 "The Diverse World of Small Ribonucleoproteins",
  booktitle =	 "The {RNA} World",
  publisher =	 "Cold Spring Harbor Press",
  year =	 1993,
  editor =	 "R. F. Gesteland and J. F. Atkins",
  pages =	 "359-381",
  address =	 "New York"
}

@article{BashfordEtal87,
  author = "D. Bashford and C. Chothia and A. M. Lesk",
  title = "Determinants of a protein fold: unique features of
        the globin amino acid sequence",
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  volume = 196,
  pages = "199-216",
  year = 1987
}

@article{Baum72,
  author =       {L. E. Baum},
  title =        {An Equality and Associated Maximization Technique
			in Statistical Estimation for Probabilistic
			Functions of {M}arkov Processes},
  journal =      {Inequalities},
  year =         1972,
  volume =       3,
  pages =        {1-8}
}


@article{BengioEtal92,
  author = "Y. Bengio and R. De Mori and G. Flammia and R. Kompe",
  title = "Global optimization of a neural network--hidden {M}arkov
	model hybrid",
  journal = "IEEE Transactions on Neural Networks",
  year = 1992,
  number = 2,
  volume = 3,
  pages = "252-259"
}
		  
@book{Berger85,
  author= "J. O. Berger",
  title= "Statistical Decision Theory and {B}ayesian Analysis",
  publisher= "Springer-Verlag",
  address= "New York",
  year= 1985
}

@article{BergerMunson91,
  author = "M. P. Berger  and P. J. Munson",
  title = "A novel randomized iterative strategy for aligning 
            multiple protein sequences",
  journal = CABIOS,
  volume = 7,
  pages = "479-484",
  year = 1991
}

@Article{Bird87,
  author = 	 {A. Bird},
  title = 	 {{CpG} islands as gene markers in the vertebrate nucleus},
  journal = 	 TIGS,
  year = 	 1987,
  volume =	 3,
  pages =	 {342-347}
}

@Article{Birney93,
   author = {E Birney and S. Kumar and A. R.  Krainer},
   title  = {Analysis of the {RNA}-recognition motif and {RS} and {RGG} domains: conservation in metazoan pre-m{RNA} splicing factors},
   journal = NAR,
   year = 1993,
   pages = {5803-5816}
}

 
@Article{Birney94,
   author = {T. J. Gibson and M. Hyvonen and A. Musacchio and M. Saraste and E. Birney},
   title  = {{PH} domain: the first anniversary},
   journal = TIBS,
   year = 1994,
   volume = 19,
   pages = {349-353}
}

@Article{Birney96,
   author = {E. Birney and J. D. Thompson and T. J. Gibson},
   title  = {Pairwise and Searchwise: comparison of a protein profile to all three translation frames simultaneously},
   journal = NAR,
   year = 1996,
   volume = 24,
   pages = {2730-2739}
}

@inproceedings{BirneyDurbin97,
  author = "E. Birney and R. Durbin",
  title = {Dynamite: a flexible code generating language for dynamic 
	programming methods used in sequence comparison},
  crossref = "ismb97",
  year = 1997,
  pages = "56-64"
}

@article{BishopThompson86,
author = {M. J. Bishop and E. A. Thompson},
title = {Maximum Likelihood alignment of {DNA} Sequences},
journal = JMB,
year = 1986,
volume = 190,
pages = {159-165}
}

@article{BorodovskyEtal86a,
  author = "M. Yu. Borodovsky and Yu. A. Sprizhitsky and E. I. Golovanov
	and A. A. Alexandrov",
  title = "Statistical Patterns in the Primary Structure of the Functional 
	Regions of the {Escherichia} Coli Genome.
	{I}. {F}requency Characteristics",
  journal = "Molecularnaya Biologia",
  note = "(English translation)",
  year = 1986,
  volume = 20,
  pages = "826--833"
}

@article{BorodovskyEtal86b,
  author = "M. Yu. Borodovsky and Yu. A. Sprizhitsky and E. I. Golovanov
	and A. A. Alexandrov",
  title = "Statistical Patterns in the Primary Structure of the Functional 
	Regions of the {Escherichia Coli} Genome.
	{II}. {N}onuniform {M}arkov Models",
  journal = "Molecularnaya Biologia",
  note = "(English translation)",
  year = 1986,
  volume = 20,
  pages = "833--840"
}

@article{BorodovskyEtal86c,
  author = "M. Yu. Borodovsky and Yu. A. Sprizhitsky and E. I. Golovanov
	and A. A. Alexandrov",
  title = "Statistical Patterns in the Primary Structure of the Functional 
	Regions of the {Escherichia Coli} Genome.
	{III}. {C}omputer Recognition of Coding Regions",
  journal = "Molecularnaya Biologia",
  note = "(English translation)",
  year = 1986,
  volume = 20,
  pages = "1144--1150"
}

@article{BorodovskyMcIninch93,
  author = "M. Borodovsky and J. Mc{I}ninch",
  title = "{\sc GENMARK}: parallel Gene Recognition for Both {DNA} strands",
  journal = ComputChem,
  year = "1993",
  volume = 17,
  number = 2,
  pages = "123--133",
  myref = "BIO105"
}

@article{BowieEtal91,
  author = "J. U. Bowie and R. Luthy and D. Eisenberg",
  title = "A method to identify protein sequences that fold into
	a known three-dimensional structure",
  journal = Science,
  year = 1991,
  volume = 253,
  pages = "164-170"
}

@Book{BoxTiao92,
  author = 	 {G. E. P. Box and G. C. Tiao},
  title = 	 {Bayesian Inference in Statistical Analysis},
  publisher = 	 {Wiley-Interscience},
  year = 	 1992
}

@Book{Branden91,
  author = 	 {C. Branden and J. Tooze},
  title = 	 {Introduction to Protein Structure},
  publisher = 	 {Garland},
  year = 	 1991,
  address =	 {New York}
}

@Article{Brendel86,
  author = 	 {V. Brendel and J. S. Beckmann and E. N. Trifonov},
  title = 	 {Linguistics of Nucleotide Sequences: morphology and
                  Comparison of Vocabularies},
  journal = 	 JBSD,
  year = 	 1986,
  volume =	 4,
  pages =	 {11-20},
  filed =        {Trifonov}
}

@book{Brooksetal91,
  author = "D. R. Brooks and D. A. Mc{L}ennan",
  title = "Phylogeny, Ecology and Behaviour",
  publisher = "University of Chicago Press",
  address = "Chicago",
  year = 1991
}

@inproceedings{BrownEtal93,
  author={M. Brown and R. Hughey and A. Krogh and I. S. Mian and
	K. Sj{\"o}lander and D. Haussler},
  title="Using {D}irichlet Mixture Priors to Derive Hidden {M}arkov
	Models for Protein Families",
  pages= "47-55",
  crossref = "ismb93"
}

@Unpublished{BrownWilson95,
  author = {M. Brown and C. Wilson},
  title = {{RNA} Pseudoknot Modeling Using Intersections of
                  Stochastic Context-Free Grammars with Applications
                  to Database Search},
  note = {Unpublished manuscript available from
          http://www.cse.ucsc.edu/research/compbio/pseudoknot.html},
  year = 1995
}

@article{BrunakEtal91,
  author = "S. Brunak and J. Engelbrecht and S. Knudsen",
  title = "Prediction of human {mRNA} donor and acceptor sites from
	the {DNA} sequence",
  journal = JMB,
  year = "1991",
  volume = "220",
  number = "1",
  pages = "49--65"
}

@article{BrunakEtal90,
  author = "S. Brunak and J. Engelbrecht and S. Knudsen",
  title  = "Iden"
}


@article{BucherEtal96,
  author = "P. Bucher and K. Karplus and N. Moeri
	and K. Hofmann",
  title = "A Flexible Motif Search Technique Based on Generalized
	Profiles",
  journal = ComputChem,
  volume = 20,
  pages = "3-24",
  year = 1996
}

@InProceedings{BucherHofmann96,
  author = 	 {P. Bucher and K. Hofmann},
  title = 	 {A Sequence Similarity Search Algorithm Based on a
                  Probabilistic Interpretation of an Alignment Scoring System},
  crossref = 	 "ismb96",
  pages =	 {44-51}
}

@incollection{Buneman71,
  author = "P. Buneman",
  title = "The recovery of trees from measures of dissimilarity",
  booktitle = "Mathematics in the Archaeological and Historical Sciences",
  pages = "387-395",
  editor = "F. R. Hodson and D. G. Kendall and P. Tautu",
  publisher = "Edinburgh University Press",
  address = "Edinburgh",
  year = 1971
}

@article{BurgeKarlin97,
  author = "C. Burge and S. Karlin",
  title = "Prediction of Complete Gene Structures in Human Genomic {DNA}",
  journal = JMB,
  volume = 268,
  year = 1997,
  pages = "78-94"
}

@article{CaminSokal65,
  author = "J. H. Camin and R. R. Sokal",
  title = "A method for deducing branching sequences in phylogeny",
  journal = EVO,
  volume = 19,
  pages = "311-327",
  year = 1965
}

@article{CardonStormo92,
  author = "L. R. Cardon and G. D. Stormo",
  title = "Expectation maximization algorithm for identifying
        protein-binding sites with variable lengths from unaligned
        {DNA} fragments",
  journal = JMB,
  year = 1992,
  volume = 223,
  number = 1,
  pages = "159--170"
}

@article{CarrilloLipman88,
  author = "H. Carrillo and D. Lipman",
  title = "The Multiple Sequence Alignment Problem in Biology",
  journal = SIAM,
  volume = 48,
  pages = "1073-1082",
  year = "1988"
}


@InProceedings{CaryStormo95,
  author = 	 {R. B. Cary and G. D. Stormo},
  title = 	 {Graph-Theoretic Approach to {RNA} Modeling Using
                  Comparative Data},
  pages =	 {75-80},
  crossref = "ismb95"
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@book{CasellaBerger90,
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@book{Edwards92,
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@inproceedings{FrasconiBengio94,
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@inproceedings{FujiwaraEtal94,
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@Book{Gesteland93,
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% 9518021 (JID) 22202135 (UI) 

@Article{HoweDurbin, Author="Howe,
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% 9808944 (JID) 22263282 (UI) 

@Article{MeyerDurbin, Author="Meyer,
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% 0404511 (JID) 22369169 (UI) 

@Article{Ciona2002, Author="Dehal,
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% 9518021 (JID) 20243852 (UI) 

@Article{Krogh2000, Author="Krogh, A.",
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% 100962779 (JID) 22199598 (UI) 

@Article{Zhang2003, Author="Zhang,
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% 9518021 (JID) 22417281 (UI) 

@Article{SGP2, Author="Parra,
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% 9518021 (JID) 22417273 (UI) 

@Article{Twinscan2003, Author="Flicek,
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% 9808944 (JID) 22425588 (UI) 

@Article{Pedersen2003, Author="Pedersen,
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% 9518021 (JID) 22505432 (UI) 

@Article{Pachter2003,
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