Qian Peng
Department of Computer Science & Engineering
University of California, San Diego
9500 Gilman Drive
La Jolla, CA 92093-0114
Office: EBU3B 4254
Email: qpeng AT cs.ucsd.edu
I am a computer science graduate
student at UC San Diego. I am
working in Pavel Pevzner's
Bioinformatics
Lab at the CSE Department and Joe Ecker's
Plant Biology Lab
at the Salk Institute. My
research is currently funded by NSF PSB IGERT grant.
Research
While a large fraction of eukaryotic
genomes are made up of repetitive sequences, repeats are particularly
prevalent in plants. Previous studies have shown that there were
extensive duplications covering much of the dicot model plant Arabidopsis
thaliana genome, followed by mutations, gene losses and
genomic rearrangements. Further, it is estimated that up to 70% of all
living plant species are of polyploid origin. The widespread
duplications in plants make the study of genome rearrangements
particularly interesting. One of the challenges is the identification
of the homologous regions between chromosomes. Part of the study of
genome rearrangements in mammalian evolution was developing algorithms
for constructing synteny blocks solely from sequence data. While it has
become an active research area, there were very few studies extending
these approaches to a more difficult case of plant genomes.
My research focuses on plant repeat
identification and classification, and the study of whole genome
duplication in plants and comparative genomic architecture.
Publications
Peng Q, Alekseyev M, Tesler G, Pevzner PA "Decoding the Genomic Architecture of Mammalian and Plant Genomes: Synteny Blocks and Large-Scale Duplications", submitted
Chekanova, J.A.*, Gregory, B.D.*, Reverdatto, S.V., Chen, H., Yazaki, J., Li, P., Skiba, N., Peng, Q., Alonso, J., Brukhin, V., Grossniklaus, U., Ecker, J.R., and Belostotsky, D.A. "Genome-Wide High-Resolution Mapping of Exosome Substrates in the Arabidopsis Transcriptome." Cell 2007 131: 1340-1353
Peng Q, Pevzner PA, Tesler G, "The
Fragile Breakage versus Random Breakage Models of Chromosome Evolution."
PLoS Comput Biol. 2006 Feb 24;2(2):e14