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  are from my collaborators; I am not an author.
  
• My complete bibliography, containing the complete references for the papers mentioned below and older papers is given in BiBTeX format here.
• Current Bibliography in Medline Molecular Biology Subset. This does not include all papers, but does give many abstracts.
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Theory of Molecular Machines

• Basic Math and Thermodynamics

  primer: Information Theory Primer With an Appendix on Logarithms
  Read this one first to get a solid start on understanding the rest of our papers.

  • The Primer is also in Italian!. Unfortunately it is in an awful, primitive format. :-(

  A Glossary for Molecular Information Theory

  secondlaw: An Equation for the Second Law of Thermodynamics

  Information Is Not Entropy, Information is not Uncertainty!

  Pitfalls in Information Theory

• Reviews

  trieste1996: New Approaches in Mathematical Biology: Information Theory and Molecular Machines A brief 9 page introduction to molecular information theory. 2000 Oct 13: full html, pdf and ps are now available

  T. D. Schneider, Sequence Logos, Machine/Channel Capacity, Maxwell's Demon, and Molecular Computers: a Review of the Theory of Molecular Machines Nanotechnology, 5, 1-18, 1994

  T. D. Schneider, Consensus Sequence Zen, Applied Bioinformatics, 1 (3), 111-119, 2002. as of 2002 Dec 5.

  T. D. Schneider, Some Lessons for Molecular Biology from Information Theory, in Entropy Measures, Maximum Entropy Principle and Emerging Applications, Springer-Verlag, New York, 229-237. as of 2003 April 4.

  T. D. Schneider, Twenty years of Delila and molecular information theory, Biological Theory 1 (3), 250-260. as of 2007 Jan 12.

  T. D. Schneider, A Brief Review of Molecular Information Theory , Nano Communication Networks, 1: 173-180", as of 2011 Aug 11.

• Books

  Visualizing Biological Information by Clifford A. Pickover. @inproceedings{Rogan.Schneider1995, author = "P. K. Rogan and J. J. Salvo and R. M. Stephens and T. D. Schneider", title = "Visual Display of Sequence Conservation as an Aid to Taxonomic Classification Using {PCR} Amplification", editor = "Clifford A. Pickover", booktitle = "Visualizing Biological Information", publisher = "World Scientific", address = "Singapore", pages = "21-32", isbn = "ISBN 981-02-1427-8", year = "1995"}

  	Dictionary of Bioinformatics and Computational Biology, Hancock, John M. / Zvelebil, Marketa J. (eds.). (John Wiley & Sons, Inc., Hoboken, New Jersey, ISBN 0-471-43622-4, 2004.) I (Thomas D. Schneider) am one of the contributors. The entries in the book correspond to some of those in A Glossary for Molecular Information Theory. as of 2004 July 30.
  Please note that there is an error in the web links published in the book!

  ---

• Theory of Molecular Machines Level 0:

  Rsequence and Rfrequency

  T. D. Schneider, G. D. Stormo, L. Gold, and A. Ehrenfeucht, Information content of binding sites on nucleotide sequences, J. Mol. Biol., 188, 415-431, 1986. as of 2001 June 26

  T. D. Schneider, G. J. Erickson and C. R. Smith (eds), Information and entropy of patterns in genetic switches, In: Maximum-Entropy and Bayesian Methods in Science and Engineering, 2, 147-154, Kluwer Academic Publishers, Dordrecht, The Netherlands, 1988.

  T. D. Schneider and G. D. Stormo, Excess Information at Bacteriophage T7 Genomic Promoters Detected by a Random Cloning Technique, Nucl. Acids Res., 17, 659-674, 1989.

  N. D. Herman and T. D. Schneider, High Information Conservation Implies that at Least Three Proteins Bind Independently to F Plasmid incD Repeats, J. Bact., 174, 3558-3560, 1992.

  T. D. Schneider, "Evolution of Biological Information", Nucleic Acids Research, 28(14): 2794-2799, 2000 as of 2000 July 4

  Multiple Alignment

  T. D. Schneider and D. Mastronarde, Fast multiple alignment of ungapped DNA sequences using information theory and a relaxation method, Discrete Applied Mathematics, 71: 259-268, 1996

  Sequence Logos

  T. D. Schneider and R. M. Stephens, Sequence Logos: A New Way to Display Consensus Sequences Nucl. Acids Res., 18: 6097-6100, 1990

  M. C. Shaner I. M. Blair, and T. D. Schneider", (T. N. Mudge and V. Milutinovic and L. Hunter, eds), Sequence Logos: A Powerful, Yet Simple, Tool, Proceedings of the Twenty-Sixth Annual Hawaii International Conference on System Sciences, Volume 1: Architecture and Biotechnology Computing", 813-821", IEEE Computer Society Press", Los Alamitos, CA", 1993 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

  T. D. Schneider, Reading of DNA Sequence Logos: Prediction of Major Groove Binding by Information Theory, Meth. Enzym., 274: 445-455, 1996.

  Advanced Logoology

  R. M. Stephens and T. D. Schneider, Features of spliceosome evolution and function inferred from an analysis of the information at human splice sites, J. Mol. Biol., 228: 1124-1136, 1992

  P. P. Papp, D. K. Chattoraj and T. D. Schneider, Information Analysis of Sequences that Bind the Replication Initiator RepA, J. Mol. Biol., 233, 219-230, 1993. PUBMED

  D. Barrick, K. Villanueba, J. Childs, R. Kalil, T. D. Schneider, C. E. Lawrence, L. Gold and G. D. Stormo Quantitative Analysis of Ribosome Binding Sites in E. coli., Nucleic Acids Res., 22, 1287-1295, 1994.

  M. B. Toledano, I. Kullik, F. Trinh, P. T. Baird, T. D. Schneider, and G. Storz, Redox-Dependent Shift of OxyR-DNA Contacts Along An Extended {DNA} Binding Site: A Mechanism for Differential Promoter Selection, Cell, 78, 897-909, 1994.

  Replication control of plasmid P1 and its host chromosome: the common ground, D. K. Chattoraj and T. D. Schneider, Prog. Nucl. Acid Res. Mol. Biol., 57: 145-186, chapter 5, Moldave (ed), 1997

  R. K. Shultzaberger and T. D. Schneider, Using sequence logos and information analysis of Lrp DNA binding sites to investigate discrepancies between natural selection and SELEX, Nucleic Acids Res, 27 (3): 882-887, 1999. as of 1999 January 4

  N. Kannan, T. D. Schneider and S. Vishveshwara, Logos for amino acid preferences in different backbone packing density regions of protein structural classes, Acta Crystallographica Section D, 56 (9), 1156-1165, 2000 as of 2000 August 25

  2001 December 1 issue of Nucleic Acids Research Copyright ® 2001 Oxford University Press.

  baseflip: Strong Minor Groove Base Conservation in Sequence Logos implies DNA Distortion or Base Flipping during Replication and Transcription Initiation, T. D. Schneider, Nucl. Acid Res., 29, (23), 4881-4891, 2001. as of 2001 Nov 28

  repan3: The P1 Phage Replication Protein RepA Contacts an Otherwise Inaccessible Thymine N3 Proton by DNA Distortion or Base Flipping, I. G. Lyakhov, P. N. Hengen, D. Rubens and T. D. Schneider Nucl. Acid Res., 29, (23), 4892-4900 2001. as of 2001 Nov 28

  Z. Chen and T. D. Schneider, Information theory based T7-like promoter models: classification of bacteriophages and differential evolution of promoters and their polymerases, Nucleic Acids Res, 33, 6172-6187, 2005, as of 2005 Dec 14.

  E. Bindewald, T. D. Schneider and B. A. Shapiro, CorreLogo: An online server for 3D sequence logos of RNA and DNA alignments, Nucleic Acids Res. 34, w405-w411, 2006. as of 2006 Jul 19.

  Individual Information and sequence walkers

  ri: Schneider T. D. Information content of individual genetic sequences. J. Theor. Biol. 189(4): 427-441, 1997.
  as of 1997 Dec 23. was not available prior to 1998 April 26.

  walker: Schneider T. D. Sequence walkers: a graphical method to display how binding proteins interact with DNA or RNA sequences, Nucl. Acids Res. 25: 4408-4415, 1997.
  as of 1997 Nov 24. was not available prior to 1998 April 26.

  fisinfo: P. N. Hengen, S. L. Bartram, L. E. Stewart, T. D. Schneider, Information Analysis of Fis Binding Sites, Nucl. Acids Res. 25(24): 4994-5002, 1997.
  as of 1998 Jan 8. was not available prior to 1998 April 26.

  oxyrfur: M. Zheng, B. Doan, T. D. Schneider, and G. Storz, OxyR and SoxRS Regulation of fur, J. Bact., 181 (15): 4639-4643. as of 1999 July 26

  lrp: Using sequence logos and information analysis of Lrp DNA binding sites to investigate discrepancies between natural selection and SELEX, Nucl. Acids Res. 27(3): 882-887, 1999. as of 2001 Jun 6.

  ridebate: T. D. Schneider, Measuring Molecular Information, Journal of Theoretical Biology 201: 87-92, 1999. as of 1999 November 3

  SoxS: "Interdependence of the Position and Orientation of SoxS Binding Sites in the Transcriptional Activation of the Class I Subset of Escherichia coli Superoxide-Inducible Promoters", T. I. Wood, K. L. Griffith, W. P. Fawcett, K.-W. Jair, T. D. Schneider, and R. E. Wolf, Molec. Microb., 34(3): 414-430. as of 1999 December 20. Supplementary information is available.

  "The human XPG gene: gene architecture, alternative splicing and single nucleotide polymorphisms", Steffen Emmert, Thomas D. Schneider, Sikandar G. Khan and Kenneth H. Kraemer, Nucleic Acids Research, 2001, Vol. 29, No. 7 1443-1452, as of 2001 March 26

  zheng.storz2001. Journal of Bacteriology, August 2001, p. 4571-4579, Vol. 183, No. 15, "Computation-Directed Identification of OxyR DNA Binding Sites in Escherichia coli" Ming Zheng, Xunde Wang, Bernard Doan, Karen A. Lewis, Thomas D. Schneider, and Gisela Storz.

  R. K. Shultzaberger, R. E. Bucheimer, K. E. Rudd and T. D. Schneider, Anatomy of Escherichia coli Ribosome Binding Sites J. Mol. Biol., 313: 215-228, 2001. flexrbs as of 2001 September 25, published 2001 October 16.

  Individual Information: Medical Applications

  colonsplice: P. K. Rogan and T. D. Schneider, Using Information Content and Base Frequencies to Distinguish Mutations from Genetic Polymorphisms in Splice Junction Recognition Sites. Human Mutation, 6: 74-76, 1995

  rfs: P. K. Rogan, B. M. Faux and T. D. Schneider, Information analysis of human splice site mutations Human Mutation 12(3): 153-171 (1998). as of 1998 May 15.

  abcr: Rando Allikmets, Wyeth W. Wasserman, Amy Hutchinson, Philip Smallwood, Jeremy Nathans, Peter K. Rogan, Thomas D. Schneider, Michael Dean, Organization of the ABCR gene: analysis of promoter and splice junction sequences, Gene (215)1: 111-122 , 1998. as of 1998 October 16.

  C. Kannabiran, P. K. Rogan, L. Olmos, S. Basti, G. N. Rao, M. Kaiser-Kupfer, J. F. Hejtmancik. Autosomal dominant zonular cataract with sutural opacities is associated with a splice mutation in the _A3/A1-crystallin gene. Molecular Vision 1998; 4:99
  as of 1998 October 21

  S. G. Kahn, H. L. Levy, R. Legerski, E. Quackenbush, J. T. Reardon, S. Emmert, A. Sancar, L. Li, T. D. Schneider, J. E. Cleaver, and K. H. Kraemer. Xeroderma Pigmentosum Group C splice mutation associated with mutism and hypoglycinemia - A new syndrome? Journal of Investigative Dermatology, 111:791-796, 1998.
  as of 1998 November 2

  J. Patrick O'Neill, Peter K. Rogan, Neal Cariello, Janice A. Nicklas, Mutations that alter RNA splicing of the human HPRT gene: a review of the spectrum, Mutation Research/reviews In Mutation Research (411)3 (1998) pp. 179-214
  as of 1998 November 19

  Splice Site Mutations in Atherosclerosis Candidate Genes: Relating Individual Information to Phenotype. Yskert von Kodolitsch, Reed E. Pyeritz, and Peter K. Rogan, Circulation 100: 693-699, 1999, in press as of 1999 May 27; published as of 1999 August 16

  Exon Skipping in IVD RNA Processing in Isovaleric Acidemia Caused by Point Mutations in the Coding Region of the IVD Gene, Jerry Vockley, Peter K. Rogan, Bambi D. Anderson, Jan Willard, Ratnam S. Seelan, David I. Smith, and Wanguo Liu, American Journal of Human Genetics 66:356-367, 2000 as of 2000 March 2

  Redundant Designations of BRCA1 Intron 11 Splicing Mutation, Stan R. Svojanovsky, Thomas D. Schneider, and Peter K. Rogan. Human Mutation, 16: 264 (2000) as of 2000 Sep 8

  I. Arnould et al, Identifying and characterizing a five-gene cluster of ATP-binding cassette transporters mapping to human chromosome 17q24: a new subgroup within the ABCA subfamily, GeneScreen, 1: 157-164, 2001. as of 2001 November 19.

  Khan.Kraemer2002: Khan SG, Muniz-Medina V, Shahlavi T, Baker CC, Inui H, Ueda T, Emmert S, Schneider TD, Kraemer KH. The human 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. Nucleic Acids Res. 2002 Aug 15;30(16):3624-31. Pubmed PMID: 12177305. as of 2002 August 28.

  Rogan PK, Svojanovsky S, Leeder JS. Information theory-based analysis of CYP2C19, CYP2D6 and CYP3A5 splicing mutations, Pharmacogenetics 2003 13(4): 207-18. as of 2003 April 7.

  

  P. N. Hengen, I. G. Lyakhov, L. E. Stewart and T. D. Schneider, Molecular Flip-Flops Formed by Overlapping Fis Sites, Nucleic Acids Res., 31: 6663-6673, 2003 as of 2003 October 15.

  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, Khan SG, Metin A, Gozukara E, Inui H, Shahlavi T, Muniz-Medina V, Baker CC, Ueda T, Aiken JR, Schneider TD, Kraemer KH, Hum Mol Genet. 2004 Feb 1; 13(3): 343-352. as of 2004 January 18.

  Theory of Molecular Machines

• Theory of Molecular Machines Level 1:

  T. D. Schneider, Theory of Molecular Machines. I. Channel Capacity of Molecular Machines J. Theor. Biol., 148: 83-123, 1991

• Theory of Molecular Machines Level 2:

  T. D. Schneider, Theory of Molecular Machines. II. Energy Dissipation from Molecular Machines J. Theor. Biol., 148: 125-137, 1991

  

  T. D. Schneider, Claude Shannon: Biologist, 25, (1) (January/February), 30-33, 2006, IEEE Engineering in Medicine and Biology Magazine as of 2005 Dec 27.

  T. D. Schneider, 70% efficiency of bistate molecular machines explained by information theory, high dimensional geometry and evolutionary convergence as of 2010 Apr 30.

  T. D. Schneider, A Brief Review of Molecular Information Theory as of 2011 Jul 15.

  Thomas D. Schneider and Vishnu Jejjala Restriction enzymes use a 24 dimensional coding space to recognize 6 base long DNA sequences as of 2020 Mar 16.

Nanotechnology

The bottle, a story published in Nature 406: 351, 27 July 2000 as of 2001 January 24



I. G. Lyakhov, T. D. Schneider, G. A. Lyakhov and N. V. Suyazov, Orientational Ordering of Protein Micro- and Nanoparticles in a Nonuniform Magnetic Field, Physics of Wave Phenomena 13:1-14, 2005.



Patent on how to build a molecular computer: Molecular Computing Elements: Gates and Flip-Flops by TD Schneider and PN Hengen




Patent pending on a molecular motor: Molecular Rotation Engine by Thomas D. Schneider and Ilya G. Lyakhov




Patent pending on a method of molecular sequencing: High Speed Parallel Nucleic Acid Sequencing by Thomas D. Schneider and Denise Rubens.

Schneider Lab
origin: 1996 Feb 15
updated: version = 2.26 of webpapers.html 2020 Mar 16