"Living things are too beautiful
for there not to be a mathematics
that describes them."
--- Tom Schneider

Dr. Matrix SCIENCE Excellence award plaque

A Tour of Molecular Information Theory

Talks about Molecular Information Theory

Molecular Information Theory
and
the Theory of Molecular Machines

by Tom Schneider
schneidt@mail.nih.gov
Molecular Information Theory Group
Center for Cancer Research Nanobiology Program (CCRNP) ^*
National Cancer Institute
National Institutes of Health in Frederick, MD

Molecular information theory is the application of Claude Shannon's information theory to molecular patterns and states.

Geometry for optimal bistate molecular machines

70% efficiency of bistate molecular machines
explained by information theory, high dimensional geometry and evolutionary convergence
published in Nucleic Acids Research 2010; doi: 10.1093/nar/gkq389

What's New? (Forthcoming and Previous Presentations)

frames / noframes

search, glossary

quicklinks

papers

Researchers

If you want to understand life, don't think about vibrant, throbbing gels and oozes, think about information technology.
--- Richard Dawkins, The Blind Watchmaker, 1986, Norton, p. 112.

Nanotechnology Patents
Molecular Rotation Engine U.S. Patent 7,349,834	Molecular Computer U.S. Patent 6,774,222

Medusa^TM Sequencer The claims of the US patent application are allowed!

Rod-Tether Nanoprobe Patent Pending

All Positions are currently closed

What's New? (Forthcoming and Previous Presentations), What's Cool? and What's Old?

Molecular Information Theory

Introduction to the use of information theory in molecular biology.
- Introduction to Tom Schneider's Laboratory
- Suggested Reading in Molecular Information Theory
- Consensus Sequence Zen by Thomas D. Schneider
- Visualizing DNA binding sites: Sequence Logos and Walkers by Paul N. Hengen, Ph.D.
- Poster: Individual Information Theory and Walkers: Sequence Logos, Scan and Walkers as complete replacements for consensus sequences. This is a general purpose method for using information theory to analyze sequences.
- How (and why) to find a needle in a haystack Article in The Economist (April 5th-11th 1997, British version: p. 105-107, American version: p. 73-75, Asian version: p. 79-81).
  Permission to post this article has been granted.
- Pitfalls in Information Theory
Sequence Logos a quantitative graphical display for binding sites and proteins.
- Definition of a Sequence Logo
- Examples of logos
  - Gallery of Logos Go for the Logo!
  - Flicker Logo!
  - Jigglogo!
  - Evolve-a-logo!
- How To Read Sequence Logos
- How Can I Make Logos on My Own Computer?
- The Small Sample Correction for Uncertainty and Information Measures
Sequence Walkers

Web Servers

Delila Server: sequence walkers by Tom Schneider. (ii package)
Weblogo Server Sequence Logos by Steve Brenner's group.
Recommendations for Making Sequence Logos as of 2009 Jan 30.

Automated Splice Site Analysis server by Pete Rogan's group. Further documentation is available in their paper Automated splicing mutation analysis by information theory and on the page Automated Splice Site Analysis.

Publications using this server (PDF) (http://tinyurl.com/splice-server-citations)
This server is recommended by the American College of Medical Genetics.

The Automated Splice Site Analysis server has recently been moved to the following new URL at The University of Western Ontario:
https://splice.uwo.ca See the Corrigendum for further details.

Delila Genome: analyze entire genomes using Delila tools. BMC Bioinformatics 2003 4:38 by Pete Rogan's group
CorreLogo: An online server for 3D sequence logos of RNA and DNA alignments
"3dLOGO: a web server for the identification, analysis and use of conserved protein substructures". link to server (currently down)

Theory of Molecular Machines

Resources
- Papers from the Schneider lab frequently
- Presentations by Tom Schneider and Pete Rogan frequently
- Patents
  - Nanotechnology
  - contacts
- Information Theory Resources
  - Glossary for Molecular Information Theory
  - Biological Information Theory and Chowder Society (BITCS)
  - Biology and Information Theory Researchers as of 2008 Aug 05.
  - Books about Information Theory
  - Information Theory Resources on the web.
- Programs: The Delila System
- Molecular Computation Resources
  - Molecular Computer Patent
  - Molecular Computation Pointers
Other Science Pointers
- Programming Tools
  - by Tom Schneider:
    - ToolKit: Unix tools that I use, including ones listed here.
    - Atchange: eliminate extra mouse moves!
    - slideshow: generate html slide show
    - thethe: catch repeated words in a document
    - usfn: unspacefile name, a script for Unix folks that removes spaces from file names.
    - calaround: unix tool to see the calendar for months around the current one.
    - tailmail/tama: unix tool to extract the last email sent for recording in a log file.
    - nowhere: Now Here! Tools for getting around your files really fast!
    - diffhtml: compare two files visually
    - yvp: direct your browser to a paper by typing just the year, volume and page!
  - useful tools:
    - LaTeX Styles: BiBTeX Bibliography and LaTeX Style Formats for Molecular Biologists
    - LaTeX for Beginners: Beautiful Typesetting!
    - PostScript: an elegant graphics language.
    - vi: still a great editor!
    - wget: grab web pages from the net!
    - Dr. Tom's Simple Introduction to Procmail
    - Why Use Open Source?
    - Quick-Tip: Reusing OpenSSH connections to the same host by Frank Wiles
- Documentation
- Left handed DNA Hall of Fame!
- The Consensus Sequence Hall of Fame!
- Lambda Lunch Schedule weekly
- Scientific Writings
- Sodaplay demonstration of entropic rubber
- Equation Puzzle
- The amazing quincunx
Schneider Lab
- People in the lab
- Collaborators
  - Pete Rogan (University of Western Ontario): Splicing Site Analysis, Transciption Factors, Delila-Genome
  - Jim Ellis (NIH, Bethesda): Splicing Site Analysis.
  - Eric S. Miller (North Carolina State University, Raleigh, NC): bacteriophage T4.
  - Kenneth E. Rudd (University of Miami School of Medicine, Miami, FL): ribosome binding sites
  - Gisela Storz (NIH, Bethesda): OxyR, Fur binding sites.
- Positions
- visits: how to visit the lab
- Schneider Lab Errata and Corrections
- Lab Safety
- Denise's Glass Cleaner
- Lab Feeding Program
NIH
Miscellaneous

I maintain a mailing list for announcements of changes to Delila programs and this web site. If you would like to be on the list, just ask: schneidt@mail.nih.gov

What's New?

Forthcoming and Previous Presentations

Canadian Patent: Molecular Motor 2,380,611 will issue on 2010 June 08 as of 2010 May 17.

Talk: by Tom Schneider. 70% efficiency of bistate molecular machines explained by information theory, high dimensional geometry and evolutionary convergence, at Perspectives in High Dimensions 2-6 August 2010 at Case Western Reserve University in Cleveland. Host: Elizabeth Meckes. Article: Embracing complexity: Theoretical math is the basis for facial recognition programs and modeling of intricate systems new as of 2010 May 15.

Paper: T. D. Schneider emmgeo: 70% efficiency of bistate molecular machines explained by information theory, high dimensional geometry and evolutionary convergence, Nucleic Acids Research 2010; doi: 10.1093/nar/gkq389 (2010) new in press as of 2010 Apr 29, published: as of 2010 Jun 19.

Talk: by Tom Schneider. Efficiency of Molecular Machines, 4 pm at the SIAM Conference on the Life Sciences (LS10 July 12-15, 2010, Pittsburgh, Pennsylvania, The David L. Lawrence Convention Center, MS69, Minisymposium: Information Theory for Bioinformatics, 4:00 PM - 6:00 PM on July 15th, Organizers: Sarosh N. Fatakia (NIDDK, NIH) and Carosh Chow (NIDDK, NIH) new as of 2010 Mar 31.

Presentation: Evolution in a Nutshell at Science UNRESTRICTED 2010 Apr 27. as of 2010 Apr 21.

Talk: by Tom Schneider. "Information theory and molecular biology", at the University of Maryland, Baltimore County Biological Sciences. 2010 April 1. BS 004, 4:00 pm (Additional details will be posted when available.) Host: Ivan Erill. new as of 2010 Mar 09.

Plenary Talk: by Tom Schneider. "Information theory and molecular biology", at the Workshop Information Theory meets Biology (announcement PDF), Workshop Information Theory meets Biology (web site), .16. + 17. 02. 2010 Institute of Telecommunications and Applied Information Theory. Ulm University, Germany. Host: Martin Bossert. new as of 2010 Jan 08.

Talk: by Tom Schneider. "Information theory and molecular biology", at the Systems Biology Colloquium, Humboldt-University and Charitee University Berlin, Germany. 2010 Feb 12. Host: Hanspeter Herzel of the Institute for Theoretical Biology. new as of 2010 Jan 25.

Talk: by Tom Schneider. "Information theory and molecular biology", Thursday, December 10, 2009 2:00pm-3:00pm On the main NIH Campus, Building 38a, B2 NCBI Library (B2N14) Bethesda, Maryland 20892. Host: Eugene Koonin.

Talk: by Tom Schneider. "Information theory and molecular biology", Friday, November 13, 2009 9:00am-10:00am On the main NIH Campus, Building 10 (Clinical Center), Room: Berliner Room (7S235), 10 Center Drive, Bethesda, Maryland 20892. Host: National Heart, Lung, and Blood Institute (NHLBI), Contact Info: 301-496-3187; portneyd@nhlbi.nih.gov

Talk: by Tom Schneider. "Information theory and molecular biology", at the Brooks/Pastor group meeting on September 24, 12pm. Where: 5635 Fishers Lane, Rockville MD. Suite T918, 5635 Fishers Lane. Please enter the building through Fishers Place entrance and their lab is to your right.
Information theory has been applied to molecular biology since 1958 when Yockey, Platzman and Quastler published papers presented at a meeting on the topic. Since then, many attempts have been made to integrate the two subjects. In this talk I will give a semi-historical account of my work starting with the analysis of DNA binding sites which is now widely used as the sequence logo graphic. The logo shows an average picture for a set of sites. This leads to the next graphical technique, sequence walkers, that display the information for individual binding sites. These techniques are quite useful for exploring genomes. The big question, though, is how the information is related to the binding energy. The upper bound on bits per joule is given by the second law of thermodynamics. But when one looks at actual binding sites they do not reach the bound, they only use 70% of the binding energy to make selections. I present my work on explaining why this 70% efficiency appears in many molecular interactions. I promise there will be a really cool surprise at the end about exactly (to 3 decimal places) why the genetic code is degenerate!
new as of 2009 Sep 22.

Herb Schneider Memorial 2009 May 6. as of 2009 Sep 18.

FTP FTP ARCHIVE MOVED:

The FTP archive, containing the Delila programs and other files has been moved to be part of this web site.
The methods archive, containing the Paul Hengen's TIBS articles has been moved to be part of this web site.
The readme has been upgraded. new as of 2009 Jun 25.

Presentation: Evolution in a Nutshell at Science UNRESTRICTED 2009 Mar 31. as of 2009 Feb 13.
Recommendations for Making Sequence Logos as of 2009 Jan 30. as of 2009 Jan 30.
Talk: by Tom Schneider. Jena, Germany Jun 16-21, 2009, the Jena Life Science Forum 2009: The Molecular Language of Life
as of 2010 Jan 19.

Workshop: Workshop on Biological and Bio-Inspired Information Theory to be held in conjunction with the 43rd Annual Conference on Information Sciences and Systems March 18-20, 2009 The Johns Hopkins University, Baltimore, Maryland, USA
Call for Papers. Tom Schneider gave a Plenary talk.
new as of 2008 Nov 07.

Workshop: 2008 NSF Workshop on Molecular Communication/ Biological Communications Technology
The workshop report
The grand research challenges (slides)
as of 2008 Aug 05.
Web page: Daltonized Sequence Logos for Deuteranopes as of 2008 Jul 09.

Paper: Ilya Lyakhov, Annangarachari Krishnamachari and T. D. Schneider p53: Discovery of novel tumor suppressor p53 response elements using information theory , Nucleic Acids Res. 36: 3828-3833 (2008) new as of 2008 May 22.

Article: Ryan Shulzaberger: Enjoying His Life in the March 2008 NCI-Frederick Poster, page 15 as of 2008 May 01.
US Patent: Molecular Motor 7349834 as of 2008 Apr 30.
Presentation: Evolution in a Nutshell at Science UNRESTRICTED 2008 Apr 2. as of 2008 Apr 14.

Paper: Inui H, Oh KS, Nadem C, Ueda T, Khan SG, Metin A, Gozukara E, Emmert S, Slor H, Busch DB, Baker CC, Digiovanna JJ, Tamura D, Seitz CS, Gratchev A, Wu WH, Chung KY, Chung HJ, Azizi E, Woodgate R, Schneider TD, Kraemer KH. xpv: Xeroderma Pigmentosum-Variant Patients from America, Europe, and Asia . J Invest Dermatol. (2008) new as of 2008 Mar 28.

Paper: Z. Chen, K. A. Lewis, R. K. Shultzaberger, I. G. Lyakhov, M. Zheng, B. Doan, G. Storz and T. D. Schneider fur: Discovery of Fur binding site clusters in E. coli by information theory models , Nucleic Acids Res. 35: 6762-6777 (2007) new as of 2007 Oct 06.

Science Fair Posters: the origin of sequence logos: Photographs of Science Fair posters by Mike Stephens and Nate Herman as of 2007 Aug 28.

Paper: R. K. Shultzaberger, L. R. Roberts, I. G. Lyakhov, I. A. Sidorov, A. G. Stephen, R. J. Fisher and T. D. Schneider, fisbc: Correlation between binding rate constants and individual information of E. coli Fis binding sites, Nucleic Acids Res. 35: 5275-5283. This is the "Breakpoint Paper" new as of 2007 Jul 09.

Paper: T. D. Schneider, Information Theory Primer, A German version is now available! as of 2007 Jan 30.
Paper: T. D. Schneider, Twenty years of Delila and molecular information theory, Biological Theory 1 (3), 250-260 (2006). as of 2007 Jan 12.

Paper: R. K. Shultzaberger, Zehua Chen, Karen A. Lewis and T. D. Schneider flexprom: Anatomy of Escherichia coli sigma⁷⁰ promoters, Nucleic Acids Res. 35: 771-788 (2007). new in press as of 2006 Oct 25.

Patent: Molecular Motor, Australian Patent No. 784085 to T.D. Schneider and I. G. Lyakhov. as of 2006 Sep 05.
Talk: at the Keck Graduate Institute by Tom Schneider. Molecular Information Theory: from Clinical Applications to Binding Site Evolution, a seminar on 2006 September 22.

Talk: at the Berkeley Graduate Group in Computational and Genomic Biology by Tom Schneider. Molecular Information Theory: from Clinical Applications to Molecular Machine Efficiency, a seminar on 2006 September 20. The seminar is Wednesday from 4pm until 5pm, at the 101 LSA auditorium. seminar schedule

"Each of your eyes has a blind spot that corresponds to where the optic nerve attaches to your eyeball. So why don't we see some kind of black or gray patch where the blind spot is? Because your brain "hides" the blind spot! This page describes how to fool your brain into revealing where your blind spot is.", new as of 2006 Apr 25.

Paper: 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. new in press as of 2006 Apr 20.

Talk: by Tom Schneider. Molecular Information Theory: from Clinical Applications to Molecular Machine Efficiency, 2006 Feb 15 at the Frederick Faculty Seminar Series Frederick, MD. Announcements: Frederick, NIH. new as of 2006 Feb 13.

Patent Application: Medusa^TM Sequencing by Thomas D. Schneider, Ilya Lyakhov and Danielle Needle. as of 2006 Feb 8.
Patent Application: Rod-Tether Nanoprobes by Ilya Lyakhov, Thomas D. Schneider and Danielle Needle. as of 2006 Feb 8.

Paper: Z. Chen and T. D. Schneider, Comparative analysis of tandem T7-like promoter containing regions in enterobacterial genomes reveals a novel group of genetic islands, Nucleic Acids Res. 34, 1133-1147, 2006 new as of 2006 Jan 31.

Talk: by Tom Schneider. Molecular Information Theory: from Clinical Applications to Molecular Machine Efficiency, 2006 March 28 at the School of Electrical and Computer Engineering -- Cornell University Ithaca, NY 14853-6701. Host: Sergio Servetto of the Cornell Communication Networks Research Group. new as of 2006 Jan 26.

Talk: by Tom Schneider. Molecular Information Theory: Flippers, Flappers and Flip-Flops in DNA Binding, 2006 Feb 22 4:00 pm, at the Department of Chemistry and Biochemistry, University of Maryland, Baltimore County, Baltimore, MD. (This is not part of their Seminar Series.) Host: Ralph Pollack. new as of 2006 Jan 26. Aspects of Self-Organization in Evolution organized by Chris Adami and Claus O. Wilke.

Talk: at the University of Missouri - Kansas City Department of Computer Science and Electrical Engineering (CSEE) Seminar Series by Tom Schneider. Molecular Information Theory: from Clinical Applications to Binding Site Evolution, 2005 November 11. Hosts: Yugyung Lee and Pete Rogan.

Talk: at the FinBioNet 2005 Symposium (symposium website) by Tom Schneider. Molecular Information Theory: from Clinical Applications to Molecular Machine Efficiency. 2005 October 6-7, Hosts: Jaakko Pohjoismaki (google: Jaakko Pohjoismaki)

Paper: at the JCIS 2005/6th International Symposium on Computational Biology and Genome Informatics meeting 2005 July 21-26 by Chengpeng Bi and Peter K. Rogan (2005) Determining thresholds for binding site sequence models using information theory. new as of 2005 April 1.

Talk and Poster: at the International Society of Computational Biology meeting on 2005 June 25-29 by Peter Rogan and Vijay Nalla, "Feasibility of genome-wide recognition of mutant single nucleotide polymorphisms (SNPs) with effects on constitutive mRNA splicing". The poster is by Chengpeng Bi and Peter K. Rogan (2005): "A genetic algorithm for bipartite sequence alignment with application to CAR/RXRalpha binding sites." new as of 2005 April 1.

Talk: at the Wesleyan Biology Department SEMINAR SERIES by Tom Schneider. Molecular Information Theory: from Clinical Applications to Molecular Machine Efficiency. 2005 February 3, Thursday, at 12:00 noon. Hosts: Michael Weir and Jason Wolfe

Article: Molecular OS Gets Upgrade, by Ivan Oransky in The Scientist (Volume 18, Issue 19, 38, Oct. 11, 2004), describes our recently patented method for molecular computing new as of 2004 Oct 11.

Poster: Comparative Analysis of T7-like Promoter Bearing Regions in Bacterial Genomes Reveals a Novel Group of Islands, Z. Chen and T.D. Schneider, at the 2004 NIH Research Fesival new as of 2004 Sep 27.

Poster: A Novel Bacteriophage Lambda Cro Responsive Element in the oop RNA Promoter, I.G. Lyakhov, Z. Chen, and T.D. Schneider, at the 2004 NIH Research Fesival as of 2004 Sep 27.
Talk: Two Essential Splice Lariat Branchpoint Sequences in one Intron in a Xeroderma Pigmentosum DNA Repair Gene Dr. Sikandar Khan, NCI. as of 2004 Sep 10.
US Patent: by Thomas D. Schneider and Paul N. Hengen, Molecular Computing Elements: Gates and Flip-Flops, 2003 August 12.

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. All of my contributed entries are in the online glossary.
new as of 2004 July 30.

Talk Thomas Schneider. The Chemical Theatre of Biological Systems" will be held from 24th - 28th May, 2004 in Bozen, North Italy. The talk will be in the session on "Application of Information Theory to Chemical and Biological Systems" hosted by the Beilstein-Institut. Audio and photos
Talk Thomas Schneider. "Genomes 2004: International Conference on the Analysis of Microbial and Other Genomes" (http://www.tigr.org/conf/mg/) held from April 14-17, 2004 , The Wellcome Trust Conference Centre Hinxton, Cambridge, United Kingdom. (This conference was originally to be held at the Institut Pasteur, France, April 14 - 17th, 2004 www.pasteur.fr/gmp but it was cancelled. It was then located to the UK.)

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. new as of 2003 November 24.

J. E. Cleaver, C. Collins, J. Ellis and S. Volik, "Genome sequence and splice site analysis of low-fidelity DNA polymerases H and I involved in replication of damaged DNA, Genomics", Volume 82, Issue 5, November 2003, Pages 561-570. PubMed Abstract; at www.sciencedirect.com. This paper was written as part of the Splice Junction Analysis Service new as of 2003 November 14.

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 (22): 6663-6673, 2003. as of 2003 October 15.
2003 Oct 7. www.entropysite.com is a site by Frank L. Lambert, who describes it as "More than you want to know about thermodynamic entropy -- BUT all easily readable!"

The full description of each nanotech project is now available:

High Speed Parallel Nucleic Acid Sequencing
Molecular Computing Elements: Gates and Flip-Flops
Molecular Rotation Engine
2003 Oct 6.

Media

Media Mention: "Fear Not Traveling Salesmen, DNA Computing is Here to Save the Day" by Siddharth Srivastava. A very clear description of how the Adleman computer works, quotes yours truely on the future of molecular compters. :-) 2003 Sep 2.

Talk: at the 25th Annual International Conference of the IEEE Engineering in Medicine and Biology Society Cancun, Mexico. Conference Web Site URL 2003 Sep 17 - 21, by Tom Schneider. Molecular Information Theory: from Clinical Applications to Binding Site Evolution. Organizer: Elebeoba (Chi-Chi) May

European Patent: by Thomas D. Schneider Molecular Computing Elements: Gates and Flip-Flops 2003 June 4.

Talk: by Peter K. Rogan. Modeling Splice Site and Transcription Factor Binding Site Variation by Information Theory at the Dept. Pharmaceutical Sciences, St. Jude's Children's Research Hospital, Memphis, TN, 2003 May 15.

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.

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. new as of 2003 April 4.

Dr. Matrix Award for Science Excellence! Award letter. as of 2003 Jan 29. as of 2003 April 4.

Talk: at the Virginia Commonwealth University by Tom Schneider. Molecular Information Theory: from Clinical Applications to Binding Site Evolution. 2003 January 28, Tuesday, 1:00 pm. Host: Gail Christie

Talk: at the University of Richmond by Tom Schneider. Molecular Information Theory: from Clinical Applications to Molecular Machine Efficiency. 2003 January 27, Monday, 4:30 pm. Hosts: Karen Lewis and Peter Smallwood.

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

Talk: at the Center for Advanced Research in Biotechnology CARB (9600 Gudelsky Drive, Rockville, Maryland 20850, contact: Dr. Harold Smith ) by Tom Schneider. Flippers, Flappers and Flip-Flops in DNA Binding. 2002 December 2 Monday, 11:00 am. new as of 2002 October 25.

Talk Institute for Pure and Applied Mathematics (IPAM) Workshop I: Alternative Computing September 30 - October 3, 2002, UCLA, Los Angeles CA. Schneider TD Molecular Information Theory: Molecular Efficiency and Flip-Flops. Wednesday October 2, 2002, 3:30 pm. new as of 2002 September 15.

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. new as of 2002 August 28.

Poster presented at the International Society for the Study of Xenobiotics, 11^th annual meeting, October 27-31, 2002. MODELING PXR/RXR BINDING USING INFORMATION THEORY, Carrie A. Vyhlidal, Peter K. Rogan, and J. Steven Leeder. Division of Pediatric Clinical Pharmacology and Medical Toxicology and Department of Medical Research, Children's Mercy Hospital, Kansas City, MO 64108, USA. new as of 2002 August 12

Talk Photographs from the Altenberg Workshop as of 2002 August 8
Suggested Reading in Molecular Information Theory as of 2002 July 18.
Talk Presentation at the American Neurology Association, Plenary Session on October 15, 2002, NY, NY. ABSTRACT. Peter K. Rogan. as of 2002 June 27

Thompson TE, Rogan PK, Risinger JI, Taylor JA. Splice Variants but not Mutations of DNA Polymerase beta Are Common in Bladder Cancer. Cancer Res. 2002 Jun 1;62(11):3251-3256. Pubmed PMID: 12036941 new as of 2002 June 4.

Schneider Lab Errata and Corrections as of 2002 June 4.
History of the Ev Program, A tribute to Stephen Jay Gould (1941 - 2002) as of 2002 May 22.
Pitfalls in Information Theory as of 2002 March 13.
Molecular Information Theory Glossary Terms as of 2002 Jan 28.

Poster Peter K. Rogan, Ph.D., Modeling Splice Site and Transcription Factor Binding Site Variation by Information Theory. Keystone Symposium in Santa Fe, NM, Genotype to Phenotype: Focus on Disease. 2002 February 19-24. ABSTRACT new as of 2002 Jan 23.

2001 December 1 issue of
Nucleic Acids Research
Copyright � 2001
Oxford University Press. We got the cover!!! The 2001 December 1 issue of Nucleic Acids Research has our cover figure! The issue also contains our back-to-back baseflip and repan3 papers. new as of 2001 November 28. Note: If you don't have a subscription, you won't be able to read the article at NAR for 6 months. HOWEVER, I bought access and you can read it now by using the links the two web pages mentioned above.

Talk Thomas Schneider, Ph.D., National Cancer Institute, NIH, Flippers, Flappers and Flip-Flops in DNA Binding. 2002 Feb 7. Penn State in the Department of Mathematics. new as of 2001 Nov 26

My publications graph has a curious kink in it! as of 2001 November 20.

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. new as of 2001 November 19.

Talk Thomas Schneider, Ph.D., National Cancer Institute, NIH, Flippers, Flappers and Flip-Flops in DNA Binding. 2002 January 17. North Carolina State University in the Microbilogy Department. 10 am. new as of 2001 Nov 7

Talk Thomas Schneider, Ph.D., National Cancer Institute, NIH, Flippers, Flappers and Flip-Flops in DNA Binding. 2001 December 12. Frederick Faculty Seminar Series. Note date change: it will not be December 5th. Building 549 Auditorium, Fort Detrick, MD. new as of 2001 Nov 7

Talk Thomas Schneider, Ph.D., National Cancer Institute, NIH, Flippers, Flappers and Flip-Flops in DNA Binding. 2001 November 6. George Mason University School of Computational Sciences Bioinformatics Colloquium new as of 2001 Oct 29

An Atchange computer! as of 2001 Oct 29

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 new as of 2001 September 25, published 2001 October 16.

Two Posters by Peter K. Rogan at the American Society of Human Genetics meeting, San Diego, California, 2001 October 12-16, as of 2001 October 1
Poster: At the NIH Research Festival 2001 Influence of a single nucleotide polymorphism in an XPC splice acceptor site on alternative splicing October 3, 2001. as of 2001 September 25

Paper: 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. zheng.storz2001 new as of 2001 July 9

Fort Detrick Bicycle Advocacy Group as of 2001 June 21.
slideshow is a Unix csh script that generates an html slide show from a set of images. as of 2001 June 20.

William Dembski, an "Intelligent Design" advocate claims that my simulation of information gain by evolution does not work as claimed. A rebuttal is presented, and a test falsifies his claim new as of 2001 June 6.

A page on The Small Sample Correction for Uncertainty and Information Measures is now available. To allow people to read the details about this topic, my thesis publication (Schneider1986) is also online. Only Figure 1 and the appendix are done, the other figures are still missing. as of 2001 June 1.
The open Postdoctoral position in the Schneider lab for working on T7 promoters is now taken. as of 2001 May 21. (Note: please check the link for whether new positions open up, this message only applies to the date given.)
The Consensus Sequence Hall of Fame as of 2001 April 24

Paper: "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, new as of 2001 March 26

Delila Servers as of 2001 March 26
Tribute To Shannon as of 2001 February 28

Bell Labs Claude Shannon, Father of Information Theory, Dies at 84
Bell Labs Claude Shannon, Father of Information Theory, Dies at 84 as of 2001 February 27
Public Library of Science: open the doors of science to the world! as of 2001 February 23

Public Library of Science
Old news (Olds?)

Keywords for indexing: B-DNA, bioinformatics, biological information, biology, biologist, bionet.info-theory, bit, bits, Boltzmann, cancer, channel capacity, chowder society, consensus sequences, Claude Shannon, Delila, DNA, DNA binding, DNA binding site, entropy, evolutionary theory, Frederick, Gibbs, Herbert Schneider, genetic engineering, gumball machines, information theory, information entropy, left-handed DNA, limits of computers, Maryland, MD, mathematics, mathematics of biology, mathematical biology, Maxwell's Daemon, Maxwell's Demon, microarray, molecular biology, molecular information theory, molecular machines, hMSH2, mutation, Nanobiotechnology, nanotechnology, National Cancer Institute, National Institutes of Health, NCI, NIH, polymorphism, protein, RNA, molecular repertoires, nanotechnology, replication, sequence logo, sequence walker, splice, splicing, statistical mechanics, theory of molecular machines, theory of biology, thermodynamics, Tom Schneider, Thomas Schneider, Thomas D. Schneider, T. D. Schneider, TD Schneider, transcription, translation, uncertainty, what is information, what is information theory, Z-DNA 70% efficiency 70 percent efficiency

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This page is at: http://alum.mit.edu/www/toms. That's what you should be sure is in your bookmarks since it is Tom Schneider's permanent URL at MIT. That URL redirects to the current location of the web site.

A tiny URL for this web page is tinyurl.com/tomschneider

You can view earlier pages with the incredible: Internet Archive WaybackMachine:

http://www-lmmb.ncifcrf.gov/~toms/
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Molecular Information Theory and the Theory of Molecular Machines

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Molecular Information Theory
and
the Theory of Molecular Machines