What's Old?

This list gives the most recent news first. The most recent news is on the main page.

• 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. Slides from all talks. Slides from Tom's talk. Host: Elizabeth Meckes. 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, in press as of 2010 Apr 29, published: as of 2010 Jun 19. Nucleic Acids Research (2010) 38: 5995-6006, doi: 10.1093/nar/gkq389

• 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) 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. 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. 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. 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! 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. 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. 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) as of 2008 May 22.

• Article: Ryan Shulzaberger: Enjoying His Life in the March 2008 NCI at 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) 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) 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" 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). 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.", 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. 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. as of 2006 Feb 13.

• Patent Application: MedusaTM 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 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. 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. 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. 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." 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 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 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. 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. 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 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. as of 2003 April 4.

• Dr. Matrix Award for Science Excellence Award letter. as of 2003 Jan 29. (The original website is gone as of 2018 May 15.) 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. 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. 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. as of 2002 August 28.

• Poster presented at the International Society for the Study of Xenobiotics, 11th 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. 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 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 as of 2002 Jan 23.

• 2001 December 1 issue of Nucleic Acids Research

  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. 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., Flippers, Flappers and Flip-Flops in DNA Binding. 2002 Feb 7. Penn State in the Department of Mathematics. 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. as of 2001 November 19.

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

• Talk	Thomas Schneider, Ph.D., 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. as of 2001 Nov 7

• Talk	Thomas Schneider, Ph.D., Flippers, Flappers and Flip-Flops in DNA Binding. 2001 November 6. George Mason University School of Computational Sciences Bioinformatics Colloquium 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 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 as of 2001 July 9

• 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 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 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, 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

• The bottle, a story published in Nature 406: 351, 27 July 2000 is now available online. as of 2001 January 24

• Delila Programs by Most Recent Update as of 2000 December 19

• Hawaii paper in html as of 2000 December 18

• Easy HTML Lesson as of 2000 December 7

• What is plörk? as of 2000 November 29

• Posters: At the 50th Annual meeting of the American Society of Human Genetics October 3-7, 2000, Peter K. Rogan et al. will present three posters: Tumor suppressor function of the BRCA1 gene has a low threshold for mutation. ABSTRACT Alternative splicing of DNA Polymerase b mRNA in normal tissues and bladder cancer. ABSTRACT Relationship of splice site information content to severity of hemophilia A and B. ABSTRACT as of 2000 September 20

• Paper: "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

• Paper: 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

• Talk Thomas Schneider. "Molecular Information Theory: from Clinical Applications to Molecular Machine Efficiency" at the International Summer School on "DNA and Chromosomes: Physical and Biological Approaches" at the Institut d'Études Scientifiques de Cargése, Cargése, Corsica, France, July 31-August 12, 2000. as of 2000 July 23

• Story: T. D. Schneider, "The bottle", Nature 406: 351, 2000 July 27 as of 2000 July 23

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

• Patent Pending: High Speed Parallel Nucleic Acid Sequencing as of 2000 April 26

• Sodaplay demonstration of entropic rubber

• Paper: 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

• Philosophy and Definition for a Universal Genetic Sequence Database as of 2000 February 29

• Our prediction that the G863A mutation in the ABCR gene creates two forms of mRNA was correct! as of 2000 February 20

• 2000 January 5: Y2K Grqqtings!

• Paper upgrades: The paper ccmm can now be read on line in html. edmm and nano2 have also been improved. as of 1999 December 9

• Talk: Thomas Schneider. 2000 Feb 7: Molecular Information Theory: from Clinical Applications to Molecular Machine Efficiency at the Department of Biochemistry, University of Missouri-Columbia, Columbia MO. as of 1999 November 24

• Talk: Thursday, 1999 Nov. 11, Peter K. Rogan will present "Information analysis of human splice site mutations" at 12 noon at the Cancer Center of the University of Vermont School of Medicine in Burlington. as of 1999 November 9

• Paper: Measuring Molecular Information, T. D. Schneider, Journal of Theoretical Biology 201: 87-92, 1999. as of 1999 October 29

• Patent Pending: Molecular Rotation Engine as of 1999 September 21

• Paper: 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

• Prediction Tools for Protein Homology Domain-Associated Post-Translational Modifications in the RESID Database J.S. Garavelli, D.J. Miller, and G.Y. Srinivasarao, (Protein Information Resource, National Biomedical Research Foundation, Georgetown University Medical Center, Washington, DC 20007, Poster presented at the Protein Society Meeting, July 23 - 27, 1999, Boston, MA) as of 1999 August 5

• Paper: 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

• Paper: "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 July 26

• Introduction to Delila Instructions as of 1999 June 8

• Splice Junction Analysis Service as of 1999 June 4

• Tenure Announcement! as of 1999 June 4

• How the Live program produces the color wave. as of 1999 June 2

• CREATIVE THINKING by J. R. Pierce. A talk at Bell Labs in December, 1951. as of 1999 May 17

  

• HMS Beagle's "Web Pick of the Day as of 1999 May 10

• Talk : Thomas Schneider. Molecular Information Theory, April 27, 1999 at the Transcription Factors Interest Group Conference, Holiday Inn Conference Center, Frederick, MD. as of 1999 April 22

• A Glossary for Molecular Information Theory as of 1999 April 19

• lsc: unix ls in color as of 1999 Mar 1

• A tape recording of my 1999 AAAS presentation "Molecular Information Theory: from Clinical Applications to Molecular Machine Efficiency" is available from AVEN 10532 Greenwood Avenue, Seattle, WA 98133, Phone: 206.440.7989, Fax: 206.440.7990, jason@aven.com, http://www.aven.com/conflist.cfm?ID=153&CompID=1 item AS929. as of 1999 Feb 25

• Papers are now being converted to HTML so that they can now be read directly on the web. If you are reading for the first time, start with the Primer and follow that with the Nanotechnology review.
  
  

  • Theory of Molecular Machines. II. Energy Dissipation from Molecular Machines as of 1999 February 10

  • Sequence Logos, Machine/Channel Capacity, Maxwell's Demon, and Molecular Computers: a Review of the Theory of Molecular Machines as of 1999 February 9

  • Primer on information theory as of 1999 February 9

• Patent 5867402 issued 1999 Feburary 2: Computational analysis of nucleic acid information defines binding sites Schneider; Thomas D., Rogan; Peter K. as of 1999 February 7

• Patent 5849492 issued 1998 December 15: Method for rapid identification of prokaryotic and eukaryotic organisms Rogan; Peter K. as of 1999 February 8

• Paper: 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

• Paper: 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

• The Left Handed DNA Hall of Fame was listed in Science 13 November 1998: 282 (5392): 1223 NetWatch hotpics (The direct link will only work if you have a subscription.) as of 1998 November 16

• Visualizing DNA binding sites: Sequence Logos and Walkers by Paul N. Hengen, Ph.D. as of 1998 November 11

• 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

• Paper: 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

• http://secondlaw.oxy.edu is a light-hearted introduction to the "Mother of all Murphy's Laws":
  as of 1998 October 21
  

• Paper: 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

• Paper: P. K. Rogan, B. M. Faux and T. D. Schneider, Information analysis of human splice site mutations, Human Mutation", 12: 153-171, 1998 as of 1998 August 5

• Paul N. Hengen, former Senior Staff Fellow in Tom Schneider's laboratory, is looking for a new position. See his home page for further information.

  Paul now has a position. 1999 Jan 16.

• RNA Structure Logos by Gorodkin, Heyer, Brunak and Stormo.
  as of 1998 July 11

• Patent Application: Molecular Computing Elements: Gates and Flip-Flops as of 1998 June 16.

• Tapes from the Feb 1998 AAAS Meeting are now available. as of 1998 March 25.

• Sequence logos and walkers. At the top of the figure sequence logos for human donor and acceptor sites depict the DNA sequence conservation by stacks of letters. Within each stack, the height of each letter is proportional to the base frequency at that position in the binding site. The height of each stack is the sequence conservation in bits of information. Below the sequence logos five examples of individual binding sites are shown as walkers. The height of each letter shows its contribution to the average sequence conservation in the sequence logo on the top. This figure is the cover of Nucleic Acids Research Volume 25, Issue 21, 1997.
  

• Large version of this figure
• Movie of a walker
• Papers about walkers:
  • 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.
  • The mathematics for walkers is given in: Schneider TD (1997) Information content of individual genetic sequences. J. Theor. Biol. 189(4): 427-441 as of 1997 Dec 23.
  • A paper applying individual information and walkers to Fis: P. N. Hengen, S. L. Bartram, L. E. Stewart, T. D. Schneider (1997) Information Analysis of Fis Binding Sites, Nucl. Acids Res. 25(24): 4994-5002 as of 1998 Jan 8.
• Further information about walkers and associated software

Schneider Lab
origin:    1998 Oct 16
updated: 2018 Sep 25