Integrative Genomics

Mark Gerstein

P Harrison, J Qian, V Alexandrov, P Bertone, R Das, D Greenbaum, R Jansen, W Krebs, N Echols, J Lin, C Wilson, A Drawid, Z Zhang, Y Kluger, N Lan, N Luscombe

Molecular Biophysics & Biochemistry Department
Yale University
New Haven, CT 06520

http://bioinfo.mbb.yale.edu
http://bioinfo.mbb.yale.edu/lectures
http://bioinfo.mbb.yale.edu/genome/

My talk will focus on analyzing genomes and functional genomics data in terms of the finite list of protein "parts". I use the term "part" rather broadly, and depending on context, it can either be a protein family, fold, or motif. I will touch on SOME of the following topics: (i) How one can compare different genomes in terms of the occurrence of parts. (ii) How one can do the exact same operation on the pseudogenome -- the total complement on pseudogenes in an organism. (iii) How this idea can be further extended to compare the representation of parts in the genome versus the transcriptome.

References

J Qian, B Stenger, CA Wilson, J Lin, R Jansen, SA Teichmann, J Park, WG Krebs, H Yu, V Alexandrov, N Echols, M Gerstein (2001). "PartsList: a web-based system for dynamically ranking protein folds based on disparate attributes, including whole-genome expression and interaction information.," Nucleic Acids Res 29: 1750-64

PM Harrison, N Echols, M Gerstein (2001). "Digging for dead genes: an analysis of the characteristics of the pseudogene population in the Caenorhabditis elegans genome.," Nucleic Acids Res 29: 818-30

A Drawid , M Gerstein (2000). "A Bayesian system integrating expression data with sequence patterns for localizing proteins: comprehensive application to the yeast genome." J Mol Biol 301 : 1059-75 .

R Jansen , M Gerstein (2000). "Analysis of the yeast transcriptome with structural and functional categories: characterizing highly expressed proteins." Nucleic Acids Res 28 : 1481-8 .

R Jansen, D Greenbaum, M Gerstein. (in press) "Relating whole-genome expression data with protein-protein interactions." Genome Research.

J Qian, M Dolled-Filhart, J Lin, H Yu, M Gerstein. (2001) "Beyond synexpression relationships: Local Clustering of time-shifted and inverted gene expression profiles identifies new, biologically relevant interactions."
J Mol Biol 314: 1053-1066.