Abstract

A set of important papers were completed that demonstrate the power, elegance and usefulness of information theory for a variety of molecular systems: We discovered a number of p53, p63 and p73 genes; We analyzed splice site mutations in Xeroderma Pigmentosum variant patients; We characterized sigma 70 promoters in E. coli; We discovered clusters of Fur binding sites in E. coli; We determined the relationship between DNA protein binding on- and off- rates with information of the binding site. This revealed the evidence that DNA binding is a coded function instead of a simple chemical reaction. Further details can be found in the papers, all of which are availabe from www.ccrnp.ncifcrf.gov/toms/ Z01 BC08396-14

  Funding Agency

Agency
National Institute of Health (NIH)
Institute
National Cancer Institute (NCI)
Type
Intramural Research (Z01)
Project #
1Z01BC008396-20
Application #
7732921
Study Section
Project Start
Project End
Budget Start
Budget End
Support Year
20
Fiscal Year
2008
Total Cost
$743,105
Indirect Cost

  Institution

Name
National Cancer Institute Division of Basic Sciences
Department
Type
DUNS #
City
State
Country
United States
Zip Code

  Publications

Jeong, Jae-Ho; Kim, Hyun-Ju; Kim, Kun-Hee et al. (2012) An unusual feature associated with LEE1 P1 promoters in enteropathogenic Escherichia coli (EPEC). Mol Microbiol 83:612-22
Shultzaberger, Ryan K; Chen, Zehua; Lewis, Karen A et al. (2007) Anatomy of Escherichia coli sigma70 promoters. Nucleic Acids Res 35:771-88
Bindewald, Eckart; Schneider, Thomas D; Shapiro, Bruce A (2006) CorreLogo: an online server for 3D sequence logos of RNA and DNA alignments. Nucleic Acids Res 34:W405-11
Schneider, Thomas D (2006) Claude Shannon: biologist. The founder of information theory used biology to formulate the channel capacity. IEEE Eng Med Biol Mag 25:30-3
Schneider, Thomas D (2006) Twenty Years of Delila and Molecular Information Theory: The Altenberg-Austin Workshop in Theoretical Biology Biological Information, Beyond Metaphor: Causality, Explanation, and Unification Altenberg, Austria, 11-14 July 2002. Biol Theory 1:250-260
Chen, Zehua; Schneider, Thomas D (2006) Comparative analysis of tandem T7-like promoter containing regions in enterobacterial genomes reveals a novel group of genetic islands. Nucleic Acids Res 34:1133-47
Khan, Sikandar G; Metin, Ahmet; Gozukara, Engin et al. (2004) 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. Hum Mol Genet 13:343-52
Hengen, Paul N; Lyakhov, Ilya G; Stewart, Lisa E et al. (2003) Molecular flip-flops formed by overlapping Fis sites. Nucleic Acids Res 31:6663-73
Schneider, Thomas D (2002) Consensus sequence Zen. Appl Bioinformatics 1:111-9
Emmert, S; Schneider, T D; Khan, S G et al. (2001) The human XPG gene: gene architecture, alternative splicing and single nucleotide polymorphisms. Nucleic Acids Res 29:1443-52

Showing the most recent 10 out of 20 publications