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# This .bib file was distilled from a master bibliography
# by bibdistill.pl. DO NOT EDIT.
#
@string{ARB = "Annu. Rev. Biochem."}
@string{ARBBC = "Annu. Rev. Biophys. Biophys. Chem."}
@string{ARCB = "Annu. Rev. Cell Biol."}
@string{ARG = "Annu. Rev. Genet."}
@string{ARGHG = "Annu. Rev. Genomics Hum. Genet."}
@string{ARI = "Annu. Rev. Immunol."}
@string{ARN = "Annu. Rev. Neurosci."}
@string{ARP = "Annu. Rev. Physiol."}
@string{BBA = "Biochem. Biophys. Acta"}
@string{BBRC = "Biochem. Biophys. Res. Commun."}
@string{CABIOS = "Comput. Applic. Biosci."}
@string{CACM = "Communications of the ACM"}
@string{COCB = "Curr. Opin. Cell Biol."}
@string{COGD = "Curr. Opin. Genet. Dev."}
@string{COM = "Curr. Opin. Microbiol."}
@string{COSB = "Curr. Opin. Struct. Biol."}
@string{CSHSQB = "Cold Spring Harbor Symp. Quant. Biol."}
@string{CURRB = "Curr. Biol."}
@string{DEV = "Development"}
@string{DEVB = "Devel. Biol."}
@string{EMBO = "EMBO J."}
@string{FEBS = "FEBS J."}
@string{FOCS = "Found. Comp. Sci."}
@string{GDEV = "Genes Dev."}
@string{GR = "Genome Res."}
@string{IRC = "Int. Rev. Cytol."}
@string{ISMB = "Proc. Int. Conf. Intell. Syst. Mol. Biol."}
@string{JBACT = "J. Bacteriol."}
@string{JBC = "J. Biol. Chem."}
@string{JBSD = "J. Biomol. Struct. Dyn."}
@string{JCB = "J. Cell. Biol."}
@string{JCompB = "J. Comput. Biol."}
@string{JMB = "J. Mol. Biol."}
@string{JME = "J. Mol. Evol."}
@string{JNEUR = "J. Neurosci."}
@string{JTB = "J. Theor. Biol."}
@string{MBE = "Mol. Bio. Evol."}
@string{MCB = "Mol. Cell. Biol."}
@string{METH = "Meth. Enzymol."}
@string{MGG = "Mol. Gen. Genet."}
@string{NAR = "Nucl. Acids Res."}
@string{NBT = "Nat. Biotechnol."}
@string{NRG = "Nat. Rev. Genet."}
@string{PNARMB = "Prog. Nucl. Acids Res. Mol. Biol."}
@string{PNAS = "Proc. Natl. Acad. Sci. USA"}
@string{PROTS = "Protein Sci."}
@string{PSB = "Pac. Symp. Biocomput."}
@string{SIAMJC = "SIAM Journal of Computing"}
@string{TIBTECH= "Trends Biotech."}
@string{TIBS = "Trends Biochem. Sci."}
@string{TICB = "Trends Cell Biol."}
@string{TIGS = "Trends Genet."}
@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",
filed = "Altschul",
pmid = 2051488,
muid = 91269329,
}
@Article{Bashford87,
author = "Donald Bashford and Cyrus Chothia and Arthur M. Lesk",
title = "Determinants of a Protein Fold: Unique Features of
the Globin Amino Acid Sequences",
journal = JMB,
year = 1987,
volume = 196,
pages = "199-216"
}
@Article{Doolittle81,
author = {R. F. Doolittle},
title = {Similar Amino Acid Sequences: Chance or Common
Ancestry?},
journal = {Science},
year = 1981,
volume = 214,
pages = {149--159},
pmid = 7280687,
}
@Book{Durbin98,
author = {R. Durbin and S. R. Eddy and A. Krogh and G. J. Mitchison},
title = {Biological Sequence Analysis: Probabilistic Models
of Proteins and Nucleic Acids},
publisher = {Cambridge University Press},
address = {Cambridge UK},
year = 1998,
isbn = 0521629713,
reprinturl = {http://eddylab.org/cupbook.html},
lab_keywords = {hmmer},
}
@Article{Eddy08,
author = {S. R. Eddy},
title = {A Probabilistic Model of Local Sequence Alignment
that Simplifies Statistical Significance
Estimation},
journal = {PLOS Comput. Biol.},
year = 2008,
volume = 4,
pages = {e1000069},
pmid = 18516236,
pmcid = {PMC239628},
reprinturl = {http://www.ploscompbiol.org/doi/pcbi.1000069},
lab_keywords = {hmmer},
}
@Article{Eddy11,
author = {S. R. Eddy},
title = {Accelerated profile {HMM} searches},
journal = {PLOS Comp. Biol.},
year = 2011,
volume = 7,
pages = {e1002195},
pmid = 22039361,
pmcid = {PMC3197634},
reprinturl = {http://www.ploscompbiol.org/doi/pcbi.1002195},
lab_keywords = {hmmer},
}
@Article{Gonzalez10,
author = {M. W. Gonzalez and W. R Pearson},
title = {Homologous over-extension: a challenge for iterative similarity searches},
journal = NAR,
year = 2010,
volume = 38,
pages = {2177--2189},
pmid = 20064877,
}
@Article{Gribskov87,
author = "M. Gribskov and A. D. McLachlan and D. Eisenberg",
title = "Profile Analysis: Detection of Distantly Related Proteins",
journal = PNAS,
year = 1987,
volume = 84,
pages = "4355-4358"
}
@PhdThesis{Holmes98,
author = {I. Holmes},
title = {Studies in Probabilistic Sequence Alignment and Evolution},
school = {University of Cambridge},
year = 1998
}
@Article{Karlin90,
author = "S. Karlin and S. F. Altschul",
title = "Methods for Assessing the Statistical Significance
of Molecular Sequence Features by Using General
Scoring Schemes",
journal = PNAS,
year = 1990,
volume = 87,
pages = "2264-2268",
filed = {Karlin},
pmid = 2315319,
}
@Article{Krogh94,
author = {A. Krogh and M. Brown and I. S. Mian and
K. Sj\"olander and D. Haussler},
title = "Hidden {M}arkov Models in Computational Biology:
Applications to Protein Modeling",
journal = JMB,
year = 1994,
volume = 235,
pages = "1501-1531",
pmid = 8107089,
muid = 94149699,
}
@Article{Sonnhammer97,
author = {E. L. L. Sonnhammer and S. R. Eddy and R. Durbin},
title = {Pfam: A Comprehensive Database of Protein Families
Based on Seed Alignments},
journal = {Proteins},
year = 1997,
volume = 28,
pages = {405--420},
pmid = 9223186,
reprinturl = {http://www3.interscience.wiley.com/cgi-bin/abstract/52461/ABSTRACT},
}
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