Abstract

We will use a combination of computer programming and biochemistry to study some interesting questions in molecular biology. Our nucleic-acid sequence library system will be improved to allow the user the powers of recombinant DNA technology available to the biochemist. All of our software will be extensively modularized to facilitate program development and transportation, both of which will hasten improvements. We will continue to expand our collection of programs to analyze sequence-function relationships. This will include improvements to our program of a pattern recognition algorithm (the """"""""perceptron"""""""") and adaptations of multiple regression analyses to nucleic-acid sequence problems. These techniques will be used to make quantitative models for sequence effects on promoter efficiency and mutagenicity. We will generate a large collection of data for sequence effects on translational initiation efficiency using the technologies of recombinant DNA, chemical DNA sysnthesis and DNA sequencing. These data, analyzed by our computer programs, will lead to a quantitative understanding of translational initiation.

  Funding Agency

Agency
National Institute of Health (NIH)
Institute
National Institute of General Medical Sciences (NIGMS)
Type
Research Project (R01)
Project #
5R01GM028755-05
Application #
3276031
Study Section
(SSS)
Project Start
1980-12-01
Project End
1985-11-30
Budget Start
1984-12-01
Budget End
1985-11-30
Support Year
5
Fiscal Year
1985
Total Cost
Indirect Cost

  Institution

Name
University of Colorado at Boulder
Department
Type
Schools of Arts and Sciences
DUNS #
City
Boulder
State
CO
Country
United States
Zip Code
80309

  Publications

Zhou, Yiyong; Cras-Meneur, Corentin; Ohsugi, Mitsuru et al. (2007) A global approach to identify differentially expressed genes in cDNA (two-color) microarray experiments. Bioinformatics 23:2073-9
Liu, Jiajian; Stormo, Gary D (2005) Combining SELEX with quantitative assays to rapidly obtain accurate models of protein-DNA interactions. Nucleic Acids Res 33:e141
Liu, Jiajian; Stormo, Gary D (2005) Quantitative analysis of EGR proteins binding to DNA: assessing additivity in both the binding site and the protein. BMC Bioinformatics 6:176
GuhaThakurta, Debraj; Schriefer, Lawrence A; Waterston, Robert H et al. (2004) Novel transcription regulatory elements in Caenorhabditis elegans muscle genes. Genome Res 14:2457-68
Man, Tsz-Kwong; Yang, Joshua SungWoo; Stormo, Gary D (2004) Quantitative modeling of DNA-protein interactions: effects of amino acid substitutions on binding specificity of the Mnt repressor. Nucleic Acids Res 32:4026-32
Li, Jin Billy; Gerdes, Jantje M; Haycraft, Courtney J et al. (2004) Comparative genomics identifies a flagellar and basal body proteome that includes the BBS5 human disease gene. Cell 117:541-52
Liu, Jiajian; Tan, Kai; Stormo, Gary D (2003) Computational identification of the Spo0A-phosphate regulon that is essential for the cellular differentiation and development in Gram-positive spore-forming bacteria. Nucleic Acids Res 31:6891-903
Benos, Panayiotis V; Bulyk, Martha L; Stormo, Gary D (2002) Additivity in protein-DNA interactions: how good an approximation is it? Nucleic Acids Res 30:4442-51
Silbaq, Fauzi S; Ruttenberg, Steven E; Stormo, Gary D (2002) Specificity of Mnt 'master residue' obtained from in vivo and in vitro selections. Nucleic Acids Res 30:5539-48
Lin, Yiing; Han, Mei; Shimada, Brian et al. (2002) Influence of the period-dependent circadian clock on diurnal, circadian, and aperiodic gene expression in Drosophila melanogaster. Proc Natl Acad Sci U S A 99:9562-7

Showing the most recent 10 out of 36 publications