% Tom Schneider's bibliography
%   version = 3.87 of Tom.Schneider.bib.html 2010 Sep 07

% 74
@article{Schneider.brmit,
author = "T. D. Schneider",
title = "A Brief Review of Molecular Information Theory",
journal = "Nano Communication Networks",
volume = "1",
pages = "173--180",
note = "doi:10.1016/j.nancom.2010.09.002 \htmladdnormallink
  {http://dx.doi.org/10.1016/j.nancom.2010.09.002}
  {http://dx.doi.org/10.1016/j.nancom.2010.09.002} \htmladdnormallink
  {http://alum.mit.edu/www/toms/papers/brmit/}
  {http://alum.mit.edu/www/toms/papers/brmit/}",
comment = "brmit.tex",
year = "2010"}

% 73
@article{SchneiderPrimer,
author = "T. D. Schneider",
title = "Information Theory Primer",
journal = "Published on the web at {\textup{\htmladdnormallink
  {http://alum.mit.edu/www/toms/papers/primer/}
  {http://alum.mit.edu/www/toms/papers/primer/}}}",
volume = "",
year = "2010"}

% 72
@article{Hemm.Rudd2008,
author = "M. R. Hemm and B. J. Paul and T. D. Schneider and G. Storz and K. E.
  Rudd",
title = "{Small membrane proteins found by comparative genomics and ribosome
  binding site models}",
journal = "Mol. Microbiol.",
volume = "70",
pages = "1487--1501",
note = "\htmladdnormallink {http://alum.mit.edu/www/toms/papers/smallproteins/}
  {http://alum.mit.edu/www/toms/papers/smallproteins/}",
year = "2008"}

% 71
@article{Inui.Kraemer2008,
author = "H. Inui and K. S. Oh and C. Nadem and T. Ueda and S. G. Khan and A.
  Metin and E. Gozukara and S. Emmert and H. Slor and D. B. Busch and C. C.
  Baker and J. J. Digiovanna and D. Tamura and C. S. Seitz and A. Gratchev and
  W. H. Wu and K. Y. Chung and H. J. Chung and E. Azizi and R. Woodgate and T.
  D. Schneider and K. H. Kraemer",
title = "{Xeroderma Pigmentosum-Variant Patients from America, Europe, and
  Asia}",
journal = "J Invest Dermatol",
volume = "128",
pages = "2055--2068",
note = "\htmladdnormallink {http://alum.mit.edu/www/toms/papers/xpv/}
  {http://alum.mit.edu/www/toms/papers/xpv/}",
year = "2008"}

% 70
@article{Lyakhov.Schneider-p53-2008,
author = "I. Lyakhov and K. Annangarachari and T. D. Schneider",
title = "{Discovery of Novel Tumor Suppressor p53 Response Elements Using
  Information Theory}",
journal = "Nucleic Acids Res.",
volume = "36",
pages = "3828--3833",
note = "\htmladdnormallink {http://alum.mit.edu/www/toms/papers/p53/}
  {http://alum.mit.edu/www/toms/papers/p53/}",
comment = "formerly Annangarachari.Schneider2005: {Information Theoretic p53
  Response Element Model Reveals Mechanism of Down Regulation},
  Lyakhov.Schneider-p532007: {Information Theory Approach to Prediction of
  Novel p53 Response Elements}",
year = "2008"}

% 69
@misc{Schneider.Lyakhov-WHEEL2008,
author = "T. D. Schneider and I. G. Lyakhov",
title = "{MOLECULAR MOTOR}",
note = "US Patent 7,349,834, Australian Patent 784085, European Patent 1204680,
  Canadian Patent 2380611, June 8, 2010. \htmladdnormallink
  {http://alum.mit.edu/www/toms/patent/molecularrotationengine/}
  {http://alum.mit.edu/www/toms/patent/molecularrotationengine/}",
comment = "former names: WHEEL1999, Schneider.Lyakhov-WHEEL2006. invention
  submission 1999. The first US patent may only be for Schneider.",
year = "2008"}

% 68
@article{Chen-Lewis.Schneider2007,
author = "Z. Chen and K. A. Lewis and R. K. Shultzaberger and I. G. Lyakhov and
  M. Zheng and B. Doan and G. Storz and T. D. Schneider",
title = "Discovery of {Fur} binding site clusters in \emph{Escherichia coli} by
  information theory models",
journal = "Nucleic Acids Res.",
volume = "35",
pages = "6762--6777",
note = "\htmladdnormallink {http://alum.mit.edu/www/toms/papers/fur/}
  {http://alum.mit.edu/www/toms/papers/fur/}",
comment = "formerly Lewis.Schneider2002, Lewis.Schneider2003,
  Lewis.Schneider2004, Lewis.Schneider2005, Lewis.Schneider2006,
  Chen-Lewis.Schneider2006",
year = "2007"}

% 67
@article{Shultzaberger.Schneider-flexprom2007,
author = "R. K. Shultzaberger and Zehua Chen and Karen A. Lewis and T. D.
  Schneider",
title = "{Anatomy of \emph{Escherichia coli} $\sigma^{70}$ promoters}",
journal = "Nucleic Acids Res.",
volume = "35",
pages = "771--788",
note = "\htmladdnormallink {http://alum.mit.edu/www/toms/papers/f{l}exprom/}
  {http://alum.mit.edu/www/toms/papers/f{l}exprom/}",
comment = "former names: Shultzaberger.Schneider-flexprom2005,
  Shultzaberger.Schneider-flexprom2006",
year = "2007"}

% 66
@article{Shultzaberger.Schneider-spr2007,
author = "R. K. Shultzaberger and L. R. Roberts and I. G. Lyakhov and I. A.
  Sidorov and A. G. Stephen and R. J. Fisher and T. D. Schneider",
title = "{Correlation between binding rate constants and individual information
  of \emph{E. coli} Fis binding sites}",
journal = "Nucleic Acids Res.",
volume = "35",
pages = "5275-5283",
note = "\htmladdnormallink {http://alum.mit.edu/www/toms/papers/fisbc/}
  {http://alum.mit.edu/www/toms/papers/fisbc/} \htmladdnormallink
  {http://dx.doi.org/10.1093/nar/gkm471}
  {http://dx.doi.org/10.1093/nar/gkm471}",
comment = "fisbc. former names: Shultzaberger.Schneider-spr2005,
  Shultzaberger.Schneider-spr2006",
year = "2007"}

% 65
@article{Bindewald.Shapiro2006,
author = "E. Bindewald and T. D. Schneider and B. A. Shapiro",
title = "{CorreLogo: An online server for 3D sequence logos of RNA and DNA
  alignments}",
journal = "Nucleic Acids Res.",
volume = "34",
pages = "w405-w411",
note = "\htmladdnormallink {http://alum.mit.edu/www/toms/papers/correlogo/}
  {http://alum.mit.edu/www/toms/papers/correlogo/}",
year = "2006"}

% 64
@article{Chen.Schneider-island2006,
author = "Z. Chen and T. D. Schneider",
title = "{Comparative analysis of tandem T7-like promoter containing regions in
  enterobacterial genomes reveals a novel group of genetic islands}",
journal = "Nucleic Acids Res.",
volume = "34",
pages = "1133-1147",
note = "\htmladdnormallink {http://alum.mit.edu/www/toms/papers/t7island/}
  {http://alum.mit.edu/www/toms/papers/t7island/}",
comment = "t7island",
year = "2006"}

% 63
@article{Schneider-aust2002-2006,
author = "T. D. Schneider",
title = "{Twenty years of Delila and molecular information theory}",
journal = "Biological Theory: Integrating Development, Evolution, and
  Cognition",
volume = "1",
pages = "250--260",
comment = "from the meeting in Austria in 2002 aust2002 Werner Callebaut and
  John Collier editors. Thematic issue called Biological Information.",
year = "2006"}

% 62
@misc{Schneider.Rubens2006,
author = "T. D. Schneider and D. Rubens",
title = "{HIGH SPEED PARALLEL MOLECULAR NUCLEIC ACID SEQUENCING}",
note = "US Patent 6,982,146, \htmladdnormallink
  {http://alum.mit.edu/www/toms/patent/dnasequencing/}
  {http://alum.mit.edu/www/toms/patent/dnasequencing/}",
year = "2006"}

% 61
@article{Schneider.shannonbiologist2006,
author = "T. D. Schneider",
title = "{Claude Shannon: Biologist}",
journal = "IEEE Engineering in Medicine and Biology Magazine",
volume = "25",
pages = "30--33",
note = "\htmladdnormallink
  {http://alum.mit.edu/www/toms/papers/shannonbiologist/}
  {http://alum.mit.edu/www/toms/papers/shannonbiologist/}",
year = "2006"}

% 60
@article{Chen.Schneider2005,
author = "Z. Chen and T. D. Schneider",
title = "{Information theory based T7-like promoter models: classification of
  bacteriophages and differential evolution of promoters and their
  polymerases}",
journal = "Nucleic Acids Res.",
volume = "33",
pages = "6172-6187",
note = "\htmladdnormallink {http://alum.mit.edu/www/toms/papers/t7like/}
  {http://alum.mit.edu/www/toms/papers/t7like/}",
comment = "formerly Chen.Schneider2005a",
year = "2005"}

% 59
@article{Lyakhov.Suyazov2005,
author = "I. G. Lyakhov and T. D. Schneider and G. A. Lyakhov and N. V.
  Suyazov",
title = "Orientational Ordering of Protein Micro- and Nanoparticles in a
  Nonuniform Magnetic Field",
journal = "Physics of Wave Phenomena",
volume = "13",
pages = "1-14",
year = "2005"}

% 58
@book{Hancock.Zvelebil2004,
author = "John M. Hancock and Marketa J. Zvelebil",
title = "Dictionary of Bioinformatics and Computational Biology",
publisher = "John Wiley \& Sons, Inc.",
address = "Hoboken, New Jersey",
note = "\htmladdnormallink
  {http://alum.mit.edu/www/toms/papers/Hancock.Zvelebil2004/}
  {http://alum.mit.edu/www/toms/papers/Hancock.Zvelebil2004/}. Thomas D.
  Schneider contributed 50 entries to the dictionary. The web links to Tom
  Schneider's web site are incorrect but this has been handled on the server
  computer. See \htmladdnormallink {http://alum.mit.edu/www/toms/toms/}
  {http://alum.mit.edu/www/toms/toms/}. The entries in the book originated from
  the online page ``A Glossary for Molecular Information Theory and the Delila
  System'', \htmladdnormallink {http://alum.mit.edu/www/toms/glossary.html}
  {http://alum.mit.edu/www/toms/glossary.html}",
year = "2004"}

% 57
@article{Khan.Kraemer2004,
author = "S. G. Khan and A. Metin and E. Gozukara and H. Inui and T. Shahlavi
  and V. Muniz-Medina and C. C. Baker and T. Ueda and J. R. Aiken and T. D.
  Schneider and K. H. Kraemer",
title = "{Two essential splice lariat branchpoint sequences in one intron in a
  xeroderma pigmentosum DNA repair gene: mutations result in reduced XPC mRNA
  levels that correlate with cancer risk}",
journal = "Hum Mol Genet",
volume = "13",
pages = "343--352",
note = "\htmladdnormallink
  {http://hmg.oxfordjournals.org/cgi/content/full/13/3/343}
  {http://hmg.oxfordjournals.org/cgi/content/full/13/3/343}",
year = "2004"}

% 56
@misc{MOCO2004,
author = "T. D. Schneider and P. N. Hengen",
title = "{MOLECULAR COMPUTING ELEMENTS: GATES AND FLIP-FLOPS, \mbox{ United
  States Patent 6,774,222, European Patent 1057118, 2004}}",
note = "US Patent WO 99/42929, PCT/US99/03469. \htmladdnormallink
  {http://alum.mit.edu/www/toms/patent/molecularcomputing/}
  {http://alum.mit.edu/www/toms/patent/molecularcomputing/}",
comment = "formerly MOCO1999, MOCO2003",
year = "2004"}

% 55
@article{Hengen.Schneider2003,
author = "P. N. Hengen and I. G. Lyakhov and L. E. Stewart and T. D.
  Schneider",
title = "Molecular Flip-Flops Formed by Overlapping {Fis} Sites",
journal = "Nucleic Acids Res.",
volume = "31",
pages = "6663-6673",
comment = "fisflipflop.tex, formerly Hengen.fisflipflop",
year = "2003"}

% 54
@inproceedings{Schneider.lessons2003,
author = "T. D. Schneider",
title = "Some Lessons for Molecular Biology from Information Theory",
pages = "229-237",
editor = "Karmeshu",
booktitle = "Entropy Measures, Maximum Entropy Principle and Emerging
  Applications. Special Series on Studies in Fuzziness and Soft Computing.
  (Festschrift Volume in honour of Professor J.N. Kapour, Jawaharlal Nehru
  University, India)",
publisher = "Springer-Verlag",
address = "New York",
note = "\htmladdnormallink {http://alum.mit.edu/www/toms/papers/lessons2003/}
  {http://alum.mit.edu/www/toms/papers/lessons2003/}",
comment = "http://www.springer.de/cgi-bin/search_book.pl?series=2941
  http://www.springer.de/cgi-bin/search_book.pl?isbn=3-540-00242-1, Errata to
  the book: the two figures given in the paper are missing from the book! J.
  Kacprzyk is the editor of the series.",
year = "2003"}

% 53
@article{Khan.Kraemer2002,
author = "S. G. Khan and V. Muniz-Medina and T. Shahlavi and C. C. Baker and H.
  Inui and T. Ueda and S. Emmert and T. D. Schneider and K. H. Kraemer",
title = "{The human \emph{XPC} DNA repair gene: arrangement, splice site
  information content and influence of a single nucleotide polymorphism in a
  splice acceptor site on alternative splicing and function}",
journal = "Nucleic Acids Res.",
volume = "30",
pages = "3624--3631",
year = "2002"}

% 52
@article{Schneider.Zen2002,
author = "T. D. Schneider",
title = "{Consensus Sequence Zen}",
journal = "Applied Bioinformatics",
volume = "1",
pages = "111-119",
note = "\htmladdnormallink {http://alum.mit.edu/www/toms/papers/zen/}
  {http://alum.mit.edu/www/toms/papers/zen/}",
year = "2002"}

% 51
@article{Arnould.Dean2001,
author = "I. Arnould and L. M. Schriml and C. Prades and M.
  Lachtermachter-Triunfol and T. Schneider and C. Maintoux and C. Lemoine and
  D. Debono and C. Devaud and L. Naudin and S. Bauch\'{e} and M. Annat and T.
  Annilo and R. Allikmets and B. Gold and P. Den\`{e}fle and M. Rosier and M.
  Dean",
title = "{Identifying and characterizing a five-gene cluster of ATP-binding
  cassette transporters mapping to human chromosome 17q24: a new subgroup
  within the ABCA subfamily}",
journal = "GeneScreen",
volume = "1",
pages = "157-164",
comment = "it should be Thomas D. Schneider! formerly Schriml.Dean2001",
year = "2001"}

% 50
@article{Emmert.Kraemer2001,
author = "S. Emmert and T. D. Schneider and S. G. Khan and K. H. Kraemer",
title = "{The human XPG gene: gene architecture, alternative splicing and
  single nucleotide polymorphisms}",
journal = "Nucleic Acids Res.",
volume = "29",
pages = "1443--1452",
year = "2001"}

% 49
@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 = "Nucleic Acids Res.",
volume = "29",
pages = "4892-4900",
note = "\htmladdnormallink {http://alum.mit.edu/www/toms/papers/repan3/}
  {http://alum.mit.edu/www/toms/papers/repan3/}",
comment = "repan3",
year = "2001"}

% 48
@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 = "Nucleic Acids Res.",
volume = "29",
pages = "4881-4891",
note = "\htmladdnormallink {http://alum.mit.edu/www/toms/papers/basef{l}ip/}
  {http://alum.mit.edu/www/toms/papers/basef{l}ip/}",
comment = "baseflip.tex, journal cover!",
year = "2001"}

% 47
@article{Shultzaberger.Schneider2001,
author = "R. K. Shultzaberger and R. E. Bucheimer and K. E. Rudd and T. D.
  Schneider",
title = "{Anatomy of \emph{Escherichia coli} Ribosome Binding Sites}",
journal = "J. Mol. Biol.",
volume = "313",
pages = "215-228",
note = "\htmladdnormallink {http://alum.mit.edu/www/toms/papers/f{l}exrbs/}
  {http://alum.mit.edu/www/toms/papers/f{l}exrbs/}",
comment = "Shultzaberger.Schneider.flexrbs",
year = "2001"}

% 46
@article{Zheng.Storz2001,
author = "M. Zheng and X. Wang and B. Doan and K. A. Lewis and T. D. Schneider
  and G. Storz",
title = "{Computation-Directed Identification of OxyR-DNA Binding Sites in
  \emph{Escherichia coli}}",
journal = "J. Bacteriol.",
volume = "183",
pages = "4571--4579",
year = "2001"}

% 45
@article{Kannan.Vishveshwara2000,
author = "N. Kannan and T. D. Schneider and S. Vishveshwara",
title = "Logos for amino acid preferences in different backbone packing density
  regions of protein structural classes",
journal = "Acta Crystallographica Section D",
volume = "56",
pages = "1156-1165",
year = "2000"}

% 44
@article{Schneider.bottle2000,
author = "T. D. Schneider",
title = "The bottle",
journal = "Nature",
volume = "406",
pages = "351",
year = "2000"}

% 43
@article{Schneider.ev2000,
author = "T. D. Schneider",
title = "Evolution of Biological Information",
journal = "Nucleic Acids Res.",
volume = "28",
pages = "2794--2799",
note = "\htmladdnormallink {http://alum.mit.edu/www/toms/papers/ev/}
  {http://alum.mit.edu/www/toms/papers/ev/}",
comment = "Second issue in the month, July 15, release date July 10",
year = "2000"}

% 42
@article{Svojanovsky.Rogan2000,
author = "S. R. Svojanovsky and T. D. Schneider and P. K. Rogan",
title = "{Redundant designations of BRCA1 intron 11 splicing mutation; c.
  4216-2A$>$G; IVS11-2A$>$G; L78833, 37698, A$>$G}",
journal = "Human Mutation",
volume = "16",
pages = "264",
note = "\htmladdnormallink
  {http://www3.interscience.wiley.com/cgi-bin/abstract/73001161/START}
  {http://www3.interscience.wiley.com/cgi-bin/abstract/73001161/START}",
year = "2000"}

% 41
@misc{Schneider.Rogan.walker.patent1999,
author = "T. D. Schneider and P. K. Rogan",
title = "{Computational analysis of nucleic acid information defines binding
  sites, United States Patent 5867402}",
note = "\htmladdnormallink {http://alum.mit.edu/www/toms/patent/walker/}
  {http://alum.mit.edu/www/toms/patent/walker/}",
year = "1999"}

% 40
@article{Shultzaberger.Schneider1999,
author = "R. K. Shultzaberger and T. D. Schneider",
title = "{Using sequence logos and information analysis of {Lrp DNA} binding
  sites to investigate discrepancies between natural selection and {SELEX}}",
journal = "Nucleic Acids Res.",
volume = "27",
pages = "882--887",
note = "\htmladdnormallink {http://alum.mit.edu/www/toms/papers/lrp/}
  {http://alum.mit.edu/www/toms/papers/lrp/}",
year = "1999"}

% 39
@article{Wood.Wolf1999,
author = "T. I. Wood and K. L. Griffith and W. P. Fawcett and K.-W. Jair and T.
  D. Schneider and R. E. Wolf",
title = "Interdependence of the Position and Orientation of {SoxS} Binding
  Sites in the Transcriptional Activation of the Class {I} Subset of
  \emph{Escherichia coli} Superoxide-Inducible Promoters",
journal = "Mol. Microbiol.",
volume = "34",
pages = "414-430",
year = "1999"}

% 38
@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://alum.mit.edu/www/toms/papers/oxyrfur/}
  {http://alum.mit.edu/www/toms/papers/oxyrfur/}",
comment = "was Zheng.Storz.fur1999",
year = "1999"}

% 37
@article{Allikmets.Dean1998,
author = "R. Allikmets and W. W. Wasserman and A. Hutchinson and P. Smallwood
  and J. Nathans and P. K. Rogan and T. D. Schneider and M. Dean",
title = "Organization of the {ABCR} gene: analysis of promoter and splice
  junction sequences",
journal = "Gene",
volume = "215",
pages = "111-122",
note = "\htmladdnormallink {http://alum.mit.edu/www/toms/papers/abcr/}
  {http://alum.mit.edu/www/toms/papers/abcr/}",
year = "1998"}

% 36
@article{Khan.Kraemer1998,
author = "S. G. Khan and H. L. Levy and R. Legerski and E. Quackenbush and J.
  T. Reardon and S. Emmert and A. Sancar and L. Li and T. D. Schneider and J.
  E. Cleaver and K. H. Kraemer",
title = "{Xeroderma Pigmentosum Group C} Splice Mutation Associated with Mutism
  and Hypoglycinemia - {A} New Syndrome?",
journal = "J. Investigative Dermatology",
volume = "111",
pages = "791-796",
year = "1998"}

% 35
@article{Matten.Brusilow1998,
author = "S. R. Matten and T. D. Schneider and S. Ringquist and W. S. A.
  Brusilow",
title = "Identification of an intragenic ribosome binding site that affects
  expression of the \emph{uncB} gene of the \emph{Escherichia coli}
  proton-translocating {ATPase} (\emph{unc}) operon",
journal = "J. Bacteriol.",
volume = "180",
pages = "3940-3945",
comment = "submitted to \emph{J. Bact.}, August 1997",
year = "1998"}

% 34
@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 = "Erratum in: Hum Mutat 1999;13(1):82. \htmladdnormallink
  {http://alum.mit.edu/www/toms/papers/rfs/}
  {http://alum.mit.edu/www/toms/papers/rfs/}",
comment = "submitted, July 1997, formerly Rogan.Faux.Schneider1996 or rfs.tex,
  got page numbers 1998 June 23, number 3",
year = "1998"}

% 33
@article{Tooley.Rogan1998,
author = "P. W. Tooley and J. J. Salvo and T. D. Schneider and P. K. Rogan",
title = "Phylogenetic Inference Based on Information Theory-Based {PCR}
  Amplification",
journal = "Journal of Phytopathology",
volume = "146",
pages = "427-430",
year = "1998"}

% 32
@article{Chattoraj.Schneider1997,
author = "D. K. Chattoraj and T. D. Schneider",
title = "{Replication control of plasmid P1 and its host chromosome: the common
  ground}",
journal = "Prog. Nucl. Acid Res. Mol. Biol.",
volume = "57",
pages = "145-186",
year = "1997"}

% 31
@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://alum.mit.edu/www/toms/papers/f{i}sinfo/}
  {http://alum.mit.edu/www/toms/papers/f{i}sinfo/} \todobf{switch to
  Hengen.Schneider-fisinfo1997}",
comment = "fisinfo.tex",
year = "1997"}

% 30
@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 = "\htmladdnormallink {http://alum.mit.edu/www/toms/papers/malign}
  {http://alum.mit.edu/www/toms/papers/malign}, \htmladdnormallink
  {http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2785095/}
  {http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2785095/}",
year = "1996"}

% 29
@inproceedings{Schneider.Trieste1996,
author = "T. D. Schneider",
title = "New Approaches in Mathematical Biology: Information Theory and
  Molecular Machines",
pages = "313-321",
editor = "Julian Chela-Flores and Francois Raulin",
booktitle = "Chemical Evolution: Physics of the Origin and Evolution of Life",
publisher = "Kluwer Academic Publishers",
address = "Dordrecht, The Netherlands",
comment = "TRIESTE CONFERENCE ON CHEMICAL EVOLUTION, IV: Physics of the Origin
  and Evolution of Life. Cyril Ponnamperuma Memorial, 1995",
year = "1996"}

% 28
@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://alum.mit.edu/www/toms/papers/oxyr/}
  {http://alum.mit.edu/www/toms/papers/oxyr/}",
year = "1996"}

% 27
@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://alum.mit.edu/www/toms/papers/colonsplice/}
  {http://alum.mit.edu/www/toms/papers/colonsplice/}",
year = "1995"}

% 26
@inproceedings{Schneider.Patterns1995,
author = "T. D. Schneider",
title = "Genetic Patterns as shown by Sequence Logos",
pages = "44-45",
editor = "C. Pickover",
booktitle = "The Pattern Book: Fractals, Art and Nature",
publisher = "World Scientific",
address = "River Edge, NJ",
year = "1995"}

% 25
@article{Barrick.ribosomes1994,
author = "D. Barrick and K. Villanueba and J. Childs and R. Kalil and T. D.
  Schneider and C. E. Lawrence and L. Gold and G. D. Stormo",
title = "Quantitative Analysis of Ribosome Binding Sites in {{\em E. coli.}}",
journal = "Nucleic Acids Res.",
volume = "22",
pages = "1287-1295",
comment = "1994 April 11. 22(7)",
year = "1994"}

% 24
@article{Schneider.nano2,
author = "T. D. Schneider",
title = "Sequence Logos, Machine/Channel Capacity, {Maxwell}'s Demon, and
  Molecular Computers: a Review of the Theory of Molecular Machines",
journal = "Nanotechnology",
volume = "5",
pages = "1-18",
note = "\htmladdnormallink {http://alum.mit.edu/www/toms/papers/nano2/}
  {http://alum.mit.edu/www/toms/papers/nano2/}",
comment = "number 1",
year = "1994"}

% 23
@article{Toledano1994,
author = "M. B. Toledano and I. Kullik and F. Trinh and P. T. Baird and T. D.
  Schneider and G. Storz",
title = "Redox-Dependent Shift of {OxyR-DNA} Contacts Along An Extended {DNA}
  Binding Site: A Mechanism for Differential Promoter Selection",
journal = "Cell",
volume = "78",
pages = "897-909",
year = "1994"}

% 22
@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"}

% 21
@inproceedings{Schneider.Keller,
author = "T. D. Schneider",
title = "Protein Patterns as shown by Sequence Logos",
pages = "64",
editor = "P. R. Keller and Mary M. Keller",
booktitle = "Visual Cues - Practical Data Visualization",
publisher = "IEEE Press",
address = "Piscataway, NJ",
year = "1993"}

% 20
@inproceedings{SchneiderPhyCom,
author = "T. D. Schneider",
title = "Use of Information Theory in Molecular Biology",
pages = "102-110",
editor = "D. J. Matzke",
booktitle = "Workshop on Physics and Computation PhysComp '92, Proceedings of
  the Workshop on Physics and computation October 2-4, Dallas, Texas",
publisher = "IEEE Computer Society Press",
address = "Los Alamitos, CA",
comment = "phycom1992.tex, from The Symbiosis of Physics and Computation,
  Physics of Computation Workshop",
year = "1993"}

% 19
@inproceedings{ShanerPrimer,
author = "M. C. Shaner and I. M. Blair and T. D. Schneider",
title = "Sequence Logos: A Powerful, Yet Simple, Tool",
pages = "813-821",
editor = "T. N. Mudge and V. Milutinovic and L. Hunter",
booktitle = "Proceedings of the Twenty-Sixth Annual Hawaii International
  Conference on System Sciences, Volume 1: Architecture and Biotechnology
  Computing",
publisher = "IEEE Computer Society Press",
address = "Los Alamitos, CA",
note = "\htmladdnormallink {http://alum.mit.edu/www/toms/papers/hawaii/}
  {http://alum.mit.edu/www/toms/papers/hawaii/}",
comment = "hawaii.tex. From the ``Alternative Approaches to Sequence
  Representation'' minitrack of the Biotechnology Computing Track, Hawaii
  International Conference on System Sciences - 26, Kauai, Hawaii - January
  5-8, 1993",
year = "1993"}

% 18
@article{Herman.Schneider1992,
author = "N. D. Herman and T. D. Schneider",
title = "High Information Conservation Implies that at Least Three Proteins
  Bind Independently to {F} Plasmid \emph{incD} Repeats",
journal = "J. Bacteriol.",
volume = "174",
pages = "3558-3560",
year = "1992"}

% 17
@inproceedings{Rudd.Schneider1992,
author = "K. E. Rudd and T. D. Schneider",
title = "Compilation of {{\em E. coli\/}} Ribosome Binding Sites",
pages = "17.19-17.45",
editor = "Jeffrey H. Miller",
booktitle = "A Short Course in Bacterial Genetics: A Laboratory Manual and
  Handbook for \emph{Escherichia coli} and Related Bacteria",
publisher = "Cold Spring Harbor Laboratory Press",
address = "Cold Spring Harbor, New York",
year = "1992"}

% 16
@article{Arvidson1991,
author = "D. N. Arvidson and P. Youderian and T. D. Schneider and G. D.
  Stormo",
title = "Automated Kinetic Assay of $\beta$-galactosidase activity",
journal = "BioTechniques",
volume = "11",
pages = "733-738",
year = "1991"}

% 15
@article{Schneider.ccmm,
author = "T. D. Schneider",
title = "Theory of Molecular Machines. {I. Channel} Capacity of Molecular
  Machines",
journal = "J. Theor. Biol.",
volume = "148",
pages = "83-123",
note = "\htmladdnormallink {http://alum.mit.edu/www/toms/papers/ccmm/}
  {http://alum.mit.edu/www/toms/papers/ccmm/}",
comment = "{(Note: The figures were printed out of order! Fig. 1 is on p.
  97)}",
year = "1991"}

% 14
@article{Schneider.edmm,
author = "T. D. Schneider",
title = "Theory of Molecular Machines. {II. Energy} Dissipation from Molecular
  Machines",
journal = "J. Theor. Biol.",
volume = "148",
pages = "125-137",
note = "\htmladdnormallink {http://alum.mit.edu/www/toms/papers/edmm/}
  {http://alum.mit.edu/www/toms/papers/edmm/}",
year = "1991"}

% 13
@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://alum.mit.edu/www/toms/papers/logopaper/}
  {http://alum.mit.edu/www/toms/papers/logopaper/}",
comment = "formerly Schneider.Stephens.Logo",
year = "1990"}

% 12
@article{Schneider1989,
author = "T. D. Schneider and G. D. Stormo",
title = "Excess Information at Bacteriophage {T7} Genomic Promoters Detected by
  a Random Cloning Technique",
journal = "Nucleic Acids Res.",
volume = "17",
pages = "659--674",
year = "1989"}

% 11
@inproceedings{Schneider1988,
author = "T. D. Schneider",
title = "Information and entropy of patterns in genetic switches",
pages = "147-154",
editor = "G. J. Erickson and C. R. Smith",
booktitle = "Maximum-Entropy and Bayesian Methods in Science and Engineering",
publisher = "Kluwer Academic Publishers",
address = "Dordrecht, The Netherlands",
year = "1988"}

% 10
@article{Clift1986,
author = "B. Clift and D. Haussler and R. McConnell and T. D. Schneider and G.
  D. Stormo",
title = "Sequence Landscapes",
journal = "Nucleic Acids Res.",
volume = "14",
pages = "141-158",
year = "1986"}

% 9
@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://alum.mit.edu/www/toms/papers/schneider1986/}
  {http://alum.mit.edu/www/toms/papers/schneider1986/}",
year = "1986"}

% 8
@article{Stormo1986,
author = "G. D. Stormo and T. D. Schneider and L. Gold",
title = "Quantitative analysis of the relationship between nucleotide sequence
  and functional activity",
journal = "Nucleic Acids Res.",
volume = "14",
pages = "6661-6679",
year = "1986"}

% 7
@inproceedings{Childs1985,
author = "J. Childs and K. Villanueba and D. Barrick and T. D. Schneider and G.
  D. Stormo and L. Gold and M. Leitner and M. Caruthers",
title = "Ribosome binding site sequences and function",
pages = "341-350",
editor = "R. Calendar and L. Gold",
booktitle = "Sequence Specificity in Transcription and Translation, UCLA
  Symposia on Molecular and Cellular Biology, {\em Vol. 30}",
publisher = "Alan R. Liss, Inc",
address = "New York",
year = "1985"}

% 6
@inproceedings{Gold1984,
author = "L. Gold and M. Inman and E. Miller and D. Pribnow and T. D. Schneider
  and S. Shinedling and G. Stormo",
title = "Translational Regulation during Bacteriophage {T4} Development",
pages = "379-394",
editor = "B. F. C. Clark and H. U. Petersen",
booktitle = "Gene Expression, Alfred Benzon Symposium 19",
publisher = "Munksgaard",
address = "Copenhagen",
year = "1984"}

% 5
@article{Schneider1984,
author = "T. D. Schneider and G. D. Stormo and M. A. Yarus and L. Gold",
title = "Delila system tools",
journal = "Nucleic Acids Res.",
volume = "12",
pages = "129--140",
year = "1984"}

% 4
@article{Schneider1982,
author = "T. D. Schneider and G. D. Stormo and J. S. Haemer and L. Gold",
title = "A design for computer nucleic-acid sequence storage, retrieval and
  manipulation",
journal = "Nucleic Acids Res.",
volume = "10",
pages = "3013--3024",
year = "1982"}

% 3
@article{StormoInitiation1982,
author = "G. D. Stormo and T. D. Schneider and L. M. Gold",
title = "Characterization of translational initiation sites in {{\em E.
  coli}}",
journal = "Nucleic Acids Res.",
volume = "10",
pages = "2971-2996",
year = "1982"}

% 2
@article{StormoPerceptron1982,
author = "G. D. Stormo and T. D. Schneider and L. Gold and A. Ehrenfeucht",
title = "Use of the {`Perceptron'} algorithm to distinguish translational
  initiation sites in {{\em E. coli}}",
journal = "Nucleic Acids Res.",
volume = "10",
pages = "2997-3011",
year = "1982"}

% 1
@article{Gold1981,
author = "L. Gold and D. Pribnow and T. Schneider and S. Shinedling and B. S.
  Singer and G. Stormo",
title = "Translational initiation in prokaryotes.",
journal = "Annu. Rev. Microbiol.",
volume = "35",
pages = "365-403",
year = "1981"}

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