What's Old?

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

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

• A Postdoctoral position in the Schneider lab IS currently available as of 2001 January 15

• 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

• Anti creationist page as of 1998 December 30

• 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://www.secondlaw.com 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

• PostDoc Position Available

  This position is now filled. 1999 Jan 16.

• 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: 2008 Apr 07