Abstract for talk [I] at Brown

TITLE:

Understanding Protein Function on a Genome-scale using Networks

Mark Gerstein

N Luscombe, Y Xia, H Yu, R Jansen, L Lu, Y Yip, P Kim, S Douglas, A Paccnarro

Yale University

My talk will be concerned with topics in proteomics, in particular predicting
protein function on a genomic scale. We approach this through the prediction and
analysis of biological networks -- both of protein-protein interactions and
transcription-factor-target relationships. I will describe how these networks
can be determined through integration of many genomic features and how
they can be analyzed in terms of various simple topological statistics. I will
discuss the accuracy of various reconstructed quantities.

http://bioinfo.mbb.yale.edu
http://topnet.gersteinlab.org

TopNet: a tool for comparing biological sub-networks, correlating protein
properties with topological statistics.
H Yu, X Zhu, D Greenbaum, J Karro, M Gerstein (2004) Nucleic Acids Res 32: 328-37.

Genomic analysis of regulatory network dynamics reveals large topological changes.
NM Luscombe, MM Babu, H Yu, M Snyder, SA Teichmann, M Gerstein (2004)
Nature 431: 308-12.

Annotation transfer between genomes: protein-protein interologs and protein-DNA
regulogs.
H Yu, NM Luscombe, HX Lu, X Zhu, Y Xia, JD Han, N Bertin, S Chung, M Vidal,
M Gerstein (2004) Genome Res 14: 1107-18.

Genomic analysis of the hierarchical structure of regulatory networks.
H Yu, M Gerstein (2006) Proc Natl Acad Sci U S A

Integrated prediction of the helical membrane protein interactome in yeast.
Y Xia, LJ Lu, M Gerstein (2006) J Mol Biol 357: 339-49.

Relating three-dimensional structures to protein networks provides evolutionary
insights.
PM Kim, LJ Lu, Y Xia, MB Gerstein (2006) Science 314: 1938-41.

The tYNA platform for comparative interactomics: a web tool for managing,
comparing and mining multiple networks.
KY Yip, H Yu, PM Kim, M Schultz, M Gerstein (2006) Bioinformatics 22: 2968-70.

--
Mark.Gerstein@yale.edu * 203 432-6105 *

http://bioinfo.mbb.yale.edu

abstract for talk [I] at McGill

Title: Human Genome Annotation

A central problem for 21st century science will be the analysis and
understanding of the human genome. My talk will be concerned with
topics within this area, in particular annotating pseudogenes (protein
fossils) in the genome. I will discuss a comprehensive pseudogene
identification pipeline and storage database we have built. This has
enabled use to identify >10K pseudogenes in the human and mouse
genomes and analyze their distribution with respect to age, protein
family, and chromosomal location. One interesting finding is the large
number of ribosomal pseudogenes in the human genome, with 80
functional ribosomal proteins giving rise to ~2,000 ribosomal protein
pseudogenes.

I will try to inter-relate our studies on pseudogenes with those on
tiling arrays, which enable one to comprehensively probe the activity
of intergenic regions. At the end I will bring these together, trying
to assess the transcriptional activity of pseudogenes.

Throughout I will try to introduce some of the computational
algorithms and approaches that are required for genome annotation and
tiling arrays -- i.e. the construction of annotation pipelines,
developing algorithms for optimal tiling, and refining approaches for
scoring microarrays.

http://bioinfo.mbb.yale.edu
http://pseudogene.org
http://tiling.gersteinlab.org

Comparative analysis of processed pseudogenes in the mouse and human
genomes.
Z Zhang, N Carriero, M Gerstein (2004) Trends Genet 20: 62-7.

Millions of years of evolution preserved: a comprehensive catalog of
the processed pseudogenes in the human genome.
Z Zhang, PM Harrison, Y Liu, M Gerstein (2003) Genome Res 13: 2541-58.

Patterns of nucleotide substitution, insertion and deletion in the
human genome inferred from pseudogenes. Z Zhang, M Gerstein (2003)
Nucleic Acids Res 31: 5338-48.

Integrated pseudogene annotation for human chromosome 22: evidence for
transcription.
D Zheng, Z Zhang, PM Harrison, J Karro, N Carriero, M Gerstein (2005)
J Mol Biol 349: 27-45.

P. Bertone, F. Schubert, V. Trifonov, J. Rozowsky, O. Emanuelsson,
J. Karro, M-Y Kao, M. Snyder, M. Gerstein. Design optimization methods
for genomic DNA tiling arrays. Genome Research (in press).

TE Royce, JS Rozowsky, P Bertone, M Samanta, V Stolc, S Weissman, M
Snyder, M Gerstein (2005). "Issues in the analysis of oligonucleotide
tiling microarrays for transcript mapping." Trends Genet 21: 466-75.

Pseudogenes in the ENCODE Regions: Consensus Annotation, Analysis of
Transcription and Evolution
D Zheng, A Frankish, R Baertsch, P Kapranov, A Reymond, SW Choo, Y Lu, F
Denoeud, SE Antonarakis, M Snyder, Y Ruan, CL Wei, TR Gingeras, R Guigo, J
Harrow, MB Gerstein (in press) Genome Research.

The ambiguous boundary between genes and pseudogenes: the dead rise up, or do they?
D Zheng, MB Gerstein (2007) Trends Genet

Pseudogene.org: a comprehensive database and comparison platform for pseudogene
annotation.
JE Karro, Y Yan, D Zheng, Z Zhang, N Carriero, P Cayting, P Harrrison, M
Gerstein (2007) Nucleic Acids Res 35: D55-60.

A computational approach for identifying pseudogenes in the ENCODE regions.
D Zheng, MB Gerstein (2006) Genome Biol 7 Suppl 1: S13.1-10.

The real life of pseudogenes.
M Gerstein, D Zheng (2006) Sci Am 295: 48-55.

PseudoPipe: an automated pseudogene identification pipeline.
Z Zhang, N Carriero, D Zheng, J Karro, PM Harrison, M Gerstein (2006)
Bioinformatics 22: 1437-9.