@article{Abeles1986,
author = "A. L. Abeles",
title = "{P1} Plasmid Replication. {Purification} and {DNA}-binding activity of
  the replication protein {RepA}",
journal = "J. Biol. Chem.",
volume = "261",
pages = "3548-3555",
year = "1986"}

@article{Abeles1989,
author = "A. L. Abeles and L. D. Reaves and S. J. Austin",
title = "Protein-{DNA} Interactions in Regulation of {P1} Plasmid Replication",
journal = "J. Bacteriol.",
volume = "171",
pages = "43-52",
year = "1989"}

@article{Barrett.Sober1991,
author = "M. Barrett and M. J. Donoghue and E. Sober",
title = "{Against Consensus}",
journal = "Syst. Zool.",
volume = "40",
pages = "486--493",
year = "1991"}

@article{Barrett.Sober1993,
author = "M. Barrett and M. J. Donoghue and E. Sober",
title = "{Crusade? A Reply to Nelson}",
journal = "Syst. Biol.",
volume = "42",
pages = "216--217",
year = "1993"}

@article{Basharin1959,
author = "G. P. Basharin",
title = "On a Statistical Estimate for the Entropy of a Sequence of Independent
  Random Variables",
journal = "Theory Probability Appl.",
volume = "4",
pages = "333-336",
comment = "Theory of Probability and its Applications",
year = "1959"}

@inproceedings{Box1979,
author = "George E. P. Box",
title = "Robustness is the Strategy of Scientific Model Building",
pages = "201-236",
editor = "R. L. Launer and G. N. Wilkinson",
booktitle = "Robustness in Statistics",
publisher = "Academic Press",
address = "New York, NY",
note = "`ALL MODELS ARE WRONG BUT SOME ARE USEFUL' is a subheader in the
  chapter on page 202",
comment = "http://www.alceon.com/AnimatePP.4.pdf.
  http://www.google.com/search?q=cache:aNa9PMo729oC:www.alceon.com/AnimatePP.4%
.pdf+George+E.+P.+Box+%2B+All+models+are+wrong&hl=en&ie=UTF-8",
year = "1979"}

@article{Cheng.Kumar1993,
author = "X. Cheng and S. Kumar and J. Posfai and J. W. Pflugrath and R. J.
  Roberts",
title = "Crystal Structure of the {HhaI} {DNA} Methyltransferase Complexed with
  {S-Adenosyl-L-Methionine}",
journal = "Cell",
volume = "74",
pages = "299-307",
year = "1993"}

@article{Day.McMorris1992,
author = "W. H. E. Day and F. R. McMorris",
title = "Critical comparison of consensus methods for molecular sequences",
journal = "Nucleic Acids Res.",
volume = "20",
pages = "1093-1099",
year = "1992"}

@article{Eagleman.Sejnowski2000,
author = "D. M. Eagleman and T. J. Sejnowski",
title = "{Motion integration and postdiction in visual awareness}",
journal = "Science",
volume = "287",
pages = "2036--2038",
year = "2000"}

@article{Fishel1993,
author = "R. Fishel and M. K. Lescoe and M. R. S. Rao and N. G. Copeland and N.
  A. Jenkins and J. Garber and M. Kane and R. Kolodner",
title = "The Human Mutator Gene Homolog {{\em MSH2\/}} and Its Association with
  Hereditary Nonpolyposis Colon Cancer",
journal = "Cell",
volume = "75",
pages = "1027-1038",
year = "1993"}

@article{Gueron.Leroy1987,
author = "M. Gu\'{e}ron and M. Kochoyan and J. L. Leroy",
title = "{A single mode of DNA base-pair opening drives imino proton
  exchange}",
journal = "Nature",
volume = "328",
pages = "89-92",
year = "1987"}

@article{Hengen.fisinfo,
author = "P. N. Hengen and S. L. Bartram and L. E. Stewart and T. D.
  Schneider",
title = "Information Analysis of {Fis} Binding Sites",
journal = "Nucleic Acids Res.",
volume = "25",
pages = "4994-5002",
note = "\htmladdnormallink
  {http://www.lecb.ncifcrf.gov/\~{}toms/paper/fisinfo/}
  {http://www.lecb.ncifcrf.gov/\~{}toms/paper/fisinfo/}",
comment = "fisinfo.tex",
year = "1997"}

@article{Hubner1989b,
author = "P. {H\"{u}bner} and W. Arber",
title = "Mutational analysis of a prokaryotic recombinational enhancer element
  with two functions",
journal = "EMBO J.",
volume = "8",
pages = "577-585",
year = "1989"}

@article{Kendrick.Baldwin1987,
author = "K. M. Kendrick and B. A. Baldwin",
title = "Cells in Temporal Cortex of Conscious Sheep Can Respond Preferentially
  to the Sight of Faces",
journal = "Science",
volume = "236",
pages = "448-450",
comment = "was Kendrick1987",
year = "1987"}

@article{Klimasauskas1994,
author = "S. Klima\v{s}auskas and S. Kumar and R. J. Roberts and X. Cheng",
title = "{HhaI} Methyltransferase Flips Its Target Base out of the {DNA}
  Helix",
journal = "Cell",
volume = "76",
pages = "357-369",
year = "1994"}

@book{Kuhn1970,
author = "T. S. Kuhn",
title = "The Structure of Scientific Revolutions",
publisher = "The University of Chicago Press",
address = "Chicago",
year = "1970"}

@article{Leach1993,
author = "F. S. Leach and N. C. Nicolaides and N. Papadopoulos and B. Liu and
  J. Jen and R. Parsons and P. {Peltom\"{a}ki} and P. Sistonen and L. A.
  Aaltonen and M. {Nystr\"{o}m-Lahti} and X.-Y. Guan and J. Zhang and P. S.
  Meltzer and J.-W. Yu and F.-T. Kao and D. J. Chen and K. M. Cerosaletti and
  R. E. K. Fournier and S. Todd and T. Lewis and R. J. Leach and S. L. Naylor
  and J. Weissenbach and J.-P. Mecklin and H. {J\"{a}rvinen} and G. M. Petersen
  and S. R. Hamilton and J. Green and J. Jass and P. Watson and H. T. Lynch and
  J. M. Trent and A. {de la Chapelle} and K. W. Kinzler and B. Vogelstein",
title = "Mutations of a {{\em mutS\/}} Homolog in Hereditary Nonpolyposis
  Colorectal Cancer",
journal = "Cell",
volume = "75",
pages = "1215-1225",
year = "1993"}

@article{Leroy.Gueron1988,
author = "J. L. Leroy and M. Kochoyan and T. Huynh-Dinh and M. Gu\'{e}ron",
title = "{Characterization of base-pair opening in deoxynucleotide duplexes
  using catalyzed exchange of the imino proton}",
journal = "J. Mol. Biol.",
volume = "200",
pages = "223--238",
year = "1988"}

@book{Lewin1997,
author = "B. Lewin",
title = "Genes VI",
publisher = "Oxford University Press",
address = "Oxford",
comment = "TATAAT consensus: page 303",
year = "1997"}

@article{Lisser1993,
author = "S. Lisser and H. Margalit",
title = "Compilation of {{\em E. coli}} {mRNA} promoter sequences",
journal = "Nucleic Acids Res.",
volume = "21",
pages = "1507-1516",
year = "1993"}

@article{Lyakhov.Schneider2001,
author = "I. G. Lyakhov and P. N. Hengen and D. Rubens and T. D. Schneider",
title = "{The P1 Phage Replication Protein RepA Contacts an Otherwise
  Inaccessible Thymine N3 Proton by DNA Distortion or Base Flipping}",
journal = "Nucl. Acid Res.",
volume = "29",
pages = "4892-4900",
note = "\htmladdnormallink {http://www.lecb.ncifcrf.gov/\~{}toms/paper/repan3/}
  {http://www.lecb.ncifcrf.gov/\~{}toms/paper/repan3/}",
comment = "repan3",
year = "2001"}

@inproceedings{Miller1955,
author = "G. A. Miller",
title = "Note on the Bias of Information Estimates",
pages = "95-100",
editor = "H. Quastler",
booktitle = "Information Theory in Psychology",
publisher = "Free Press",
address = "Glencoe, IL",
year = "1955"}

@article{Nelson1993,
author = "G. Nelson",
title = "{Why Crusade against Consensus? A Reply to Barrett, Donoghue, and
  Sober}",
journal = "Syst. Biol.",
volume = "42",
pages = "215--216",
year = "1993"}

@article{Papp.helixrepa,
author = "P. P. Papp and D. K. Chattoraj and T. D. Schneider",
title = "Information Analysis of Sequences that Bind the Replication Initiator
  {RepA}",
journal = "J. Mol. Biol.",
volume = "233",
pages = "219-230",
comment = "Cover of 233, number 2!",
year = "1993"}

@article{PappChattoraj1994,
author = "P. P. Papp and D. K. Chattoraj",
title = "Missing-base and ethylation interference footprinting of {P1} plasmid
  replication initiator",
journal = "Nucleic Acids Res.",
volume = "22",
pages = "152-157",
year = "1994"}

@article{Pribnow1975,
author = "D. Pribnow",
title = "Nucleotide Sequence of an {RNA} Polymerase Binding Site at an Early
  {T7} Promoter",
journal = "Proc. Natl. Acad. Sci. USA",
volume = "72",
pages = "784-788",
year = "1975"}

@article{Purves.Nundy2002,
author = "D. Purves and R. B. Lotto and S. Nundy",
title = "Why We See What We Do",
journal = "Amer. Sci.",
volume = "90",
pages = "236-243",
note = "\htmladdnormallink
  {http://www.americanscientist.org/articles/02articles/Purves.html}
  {http://www.americanscientist.org/articles/02articles/Purves.html}",
year = "2002"}

@article{Rager.Singer1998,
author = "G. Rager and W. Singer",
title = "{The response of cat visual cortex to flicker stimuli of variable
  frequency}",
journal = "Eur. J. Neurosci.",
volume = "10",
pages = "1856--1877",
year = "1998"}

@article{Reinisch1995,
author = "K. M. Reinisch and L. Chen and G. L. Verdine and W. N. Lipscomb",
title = "The Crystal Structure of {HaeIII} Methyltransferase Covalently
  Complexed to {DNA}: An Extrahelical Cytosine and Rearranged Base Pairing",
journal = "Cell",
volume = "82",
pages = "143-153",
year = "1995"}

@article{Robberson1990,
author = "B. L. Robberson and G. J. Cote and S. M. Berget",
title = "Exon Definition May Facilitate Splice Site Selection in {RNA}s with
  Multiple Exons",
journal = "Mol. Cell. Biol.",
volume = "10",
pages = "84-94",
year = "1990"}

@article{Roberts.Cheng1998,
author = "R. J. Roberts and X. Cheng",
title = "{Base flipping}",
journal = "Annu Rev Biochem",
volume = "67",
pages = "181-198",
year = "1998"}

@article{Roberts1995,
author = "R. J. Roberts",
title = "On Base Flipping",
journal = "Cell",
volume = "82",
pages = "9-12",
year = "1995"}

@article{Rogan.Faux.Schneider1998,
author = "P. K. Rogan and B. M. Faux and T. D. Schneider",
title = "Information analysis of human splice site mutations",
journal = "Human Mutation",
volume = "12",
pages = "153-171",
note = "\htmladdnormallink {http://www.lecb.ncifcrf.gov/\~{}toms/paper/rfs/}
  {http://www.lecb.ncifcrf.gov/\~{}toms/paper/rfs/}",
comment = "submitted, July 1997, formerly called Rogan.Faux.Schneider1996 or
  rfs.tex, got page numbers 1998 June 23, number 3",
year = "1998"}

@article{Rogan.Schneider.hmsh2.1995,
author = "P. K. Rogan and T. D. Schneider",
title = "Using Information Content and Base Frequencies to Distinguish
  Mutations from Genetic Polymorphisms in Splice Junction Recognition Sites",
journal = "Human Mutation",
volume = "6",
pages = "74-76",
note = "\htmladdnormallink
  {http://www.lecb.ncifcrf.gov/\~{}toms/paper/colonsplice/}
  {http://www.lecb.ncifcrf.gov/\~{}toms/paper/colonsplice/}",
year = "1995"}

@article{Schneider.Mastronarde.malign,
author = "T. D. Schneider and D. Mastronarde",
title = "{Fast} multiple alignment of ungapped {DNA} sequences using
  information theory and a relaxation method",
journal = "Discrete Applied Mathematics",
volume = "71",
pages = "259-268",
note = "http://www.lecb.ncifcrf.gov/\~{}toms/paper/malign",
comment = "ftp://ftp.ncifcrf.gov/pub/delila/malign.ps",
year = "1996"}

@article{Schneider.Stephens1990,
author = "T. D. Schneider and R. M. Stephens",
title = "Sequence Logos: A New Way to Display Consensus Sequences",
journal = "Nucleic Acids Res.",
volume = "18",
pages = "6097-6100",
note = "\htmladdnormallink
  {http://www.lecb.ncifcrf.gov/\~{}toms/paper/logopaper/}
  {http://www.lecb.ncifcrf.gov/\~{}toms/paper/logopaper/}",
comment = "formerly Schneider.Stephens.Logo",
year = "1990"}

@article{Schneider.Zen2002,
author = "T. D. Schneider",
title = "{Consensus Sequence Zen}",
journal = "Applied Bioinformatics",
volume = "1",
pages = "111-119",
note = "\htmladdnormallink {http://www.lecb.ncifcrf.gov/\~{}toms/papers/zen/}
  {http://www.lecb.ncifcrf.gov/\~{}toms/papers/zen/}",
year = "2002"}

@article{Schneider.baseflip.2001,
author = "T. D. Schneider",
title = "Strong Minor Groove Base Conservation in Sequence Logos implies {DNA}
  Distortion or Base Flipping during Replication and Transcription Initiation",
journal = "Nucl. Acid Res.",
volume = "29",
pages = "4881-4891",
note = "\htmladdnormallink
  {http://www.lecb.ncifcrf.gov/\~{}toms/paper/baseflip/}
  {http://www.lecb.ncifcrf.gov/\~{}toms/paper/baseflip/}",
comment = "baseflip.tex, journal cover!",
year = "2001"}

@article{Schneider.ev2000,
author = "T. D. Schneider",
title = "Evolution of Biological Information",
journal = "Nucleic Acids Res.",
volume = "28",
pages = "2794-2799",
note = "\htmladdnormallink {http://www.lecb.ncifcrf.gov/\~{}toms/paper/ev/}
  {http://www.lecb.ncifcrf.gov/\~{}toms/paper/ev/}",
comment = "Second issue in the month, July 15, release date July 10",
year = "2000"}

@article{Schneider.oxyr,
author = "T. D. Schneider",
title = "Reading of {DNA} Sequence Logos: Prediction of Major Groove Binding by
  Information Theory",
journal = "Meth. Enzym.",
volume = "274",
pages = "445-455",
note = "\htmladdnormallink {http://www.lecb.ncifcrf.gov/\~{}toms/paper/oxyr/}
  {http://www.lecb.ncifcrf.gov/\~{}toms/paper/oxyr/}",
comment = "ftp://ftp.ncifcrf.gov/pub/delila/oxyr.ps",
year = "1996"}

@article{Schneider.ri,
author = "T. D. Schneider",
title = "Information Content of Individual Genetic Sequences",
journal = "J. Theor. Biol.",
volume = "189",
pages = "427-441",
note = "\htmladdnormallink {http://www.lecb.ncifcrf.gov/\~{}toms/paper/ri/}
  {http://www.lecb.ncifcrf.gov/\~{}toms/paper/ri/}",
comment = "Submitted, April 1997",
year = "1997"}

@article{Schneider.walker,
author = "T. D. Schneider",
title = "Sequence Walkers: a graphical method to display how binding proteins
  interact with {DNA} or {RNA} sequences",
journal = "Nucleic Acids Res.",
volume = "25",
pages = "4408-4415",
note = "\htmladdnormallink {http://www.lecb.ncifcrf.gov/\~{}toms/paper/walker/}
  {http://www.lecb.ncifcrf.gov/\~{}toms/paper/walker/}, erratum: NAR 26(4):
  1135, 1998",
comment = "walker.tex, November 1, issue 21",
year = "1997"}

@article{Schneider1986,
author = "T. D. Schneider and G. D. Stormo and L. Gold and A. Ehrenfeucht",
title = "Information content of binding sites on nucleotide sequences",
journal = "J. Mol. Biol.",
volume = "188",
pages = "415-431",
note = "\htmladdnormallink
  {http://www.lecb.ncifcrf.gov/\~{}toms/paper/schneider1986/}
  {http://www.lecb.ncifcrf.gov/\~{}toms/paper/schneider1986/}",
year = "1986"}

@book{SchneiderPrimer,
author = "T. D. Schneider",
title = "Information Theory Primer",
publisher = "\htmladdnormallink
  {http://www.lecb.ncifcrf.gov/\~{}toms/paper/primer/}
  {http://www.lecb.ncifcrf.gov/\~{}toms/paper/primer/}",
address = "",
comment = "ftp://ftp.ncifcrf.gov/pub/delila/primer.ps",
year = "1995"}

@article{Seeman1976,
author = "N. C. Seeman and J. M. Rosenberg and A. Rich",
title = "Sequence-specific recognition of double helical nucleic acids by
  proteins",
journal = "Proc. Natl. Acad. Sci. USA",
volume = "73",
pages = "804-808",
year = "1976"}

@article{Shannon1948,
author = "C. E. Shannon",
title = "A Mathematical Theory of Communication",
journal = "Bell System Tech. J.",
volume = "27",
pages = "379-423, 623-656",
note = "\htmladdnormallink
  {http://cm.bell-labs.com/cm/ms/what/shannonday/paper.html}
  {http://cm.bell-labs.com/cm/ms/what/shannonday/paper.html}",
year = "1948"}

@article{Slany.Kersten1992,
author = "R. K. Slany and H. Kersten",
title = "The promoter of the {\em tgt/sec\/} operon in {{\em Escherichia
  coli\/}} is preceded by an upstream activation sequence that contains a high
  affinity {FIS} binding site",
journal = "Nucleic Acids Res.",
volume = "20",
pages = "4193-4198",
year = "1992"}

@article{Stephens.Schneider.Splice,
author = "R. M. Stephens and T. D. Schneider",
title = "Features of spliceosome evolution and function inferred from an
  analysis of the information at human splice sites",
journal = "J. Mol. Biol.",
volume = "228",
pages = "1124-1136",
note = "\htmladdnormallink {http://www.lecb.ncifcrf.gov/\~{}toms/paper/splice/}
  {http://www.lecb.ncifcrf.gov/\~{}toms/paper/splice/}",
year = "1992"}

@article{Verdine1994,
author = "G. L. Verdine",
title = "The Flip Side of {DNA} Methylation",
journal = "Cell",
volume = "76",
pages = "197-200",
year = "1994"}

@article{Zheng.Storz.oxyrfur1999,
author = "M. Zheng and B. Doan and T. D. Schneider and G. Storz",
title = "{OxyR and SoxRS regulation of \emph{fur}}",
journal = "J. Bacteriol.",
volume = "181",
pages = "4639-4643",
note = "\htmladdnormallink
  {http://www.lecb.ncifcrf.gov/\~{}toms/paper/oxyrfur/}
  {http://www.lecb.ncifcrf.gov/\~{}toms/paper/oxyrfur/}",
comment = "was Zheng.Storz.fur1999",
year = "1999"}

@article{deQueiroz1993,
author = "A. de Queiroz",
title = "{For Consensus (Sometimes)}",
journal = "Syst. Biol.",
volume = "42",
pages = "368--372",
year = "1993"}