abstract for talk [I] at Cistrome2007

Title: Human Genome Annotation, Focussing on Intergenic Regions

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.