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.
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.
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!
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.
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.
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.
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:
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
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.
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.
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.
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.
as of 2001 Nov 7
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
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
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.)
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,
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,
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
Thanks for visiting!
For comments, problems, questions or suggestions
please contact
Tom Schneider.
Laboratory of Experimental and Computational Biology (LECB)
has been renamed to:
Center for Cancer Research Nanobiology Program (CCRNP)
effective August 1, 2005
It USED TO BE at
http://www-lmmb.ncifcrf.gov/~toms/,
http://www.lmmb.ncifcrf.gov/~toms/
http://www.lecb.ncifcrf.gov/~toms/
and
http://www.ccrnp.ncifcrf.gov/~toms
which still work but are not recommended for bookmarking.
Consensus Sequence Zen
How (and why) to find a needle in a haystack
Medical Applications of Sequence Walkers
as of 2009 Jan 30.
frequently
Glossary
slideshow
Left handed DNA Hall of Fame!
The Consensus Sequence
Hall of Fame!
Lambda Lunch Schedule
National Institutes of Health (NIH)
as of 2007 Jan 30.
What's that icon?