Department of Molecular and Cell Biology
1 Cyclotron Road, Mailstop 84-355
Lawrence Berkeley National Lab
Berkeley, CA 94720
dchiang@ocf.berkeley.edu
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Department of Molecular and Cell Biology |
I am a PhD student in Mike Eisen's lab in the Department of Molecular and Cell Biology at the University of California, Berkeley.
I am interested in how information specifying complex patterns of gene expression is encoded in genome sequences. My research aims to discover functional elements in yeast promoter regions, as well as to distill design principles that underlie promoter organization.
Integration of comparative genomics, chromatin immunoprecipitation, and gene expression data yields computational predictions on transcription factors that may work together at the same promoters. I am designing biochemical experiments to validate these predictions and to examine how relative distances between binding sites may constrain productive interactions among transcription factors.
Conservation and evolution of cis-regulatory systems in ascomycete fungi
A.P. Gasch, A.M. Moses, D.Y. Chiang, H.B. Fraser, M. Berardini and M.B. Eisen (2004) Public Library of Science Biology 2: e398.
MONKEY: Identifying conserved transcription-factor binding sites in multiple alignments using a binding site-specific evolutionary model
A.M. Moses, D.Y. Chiang, D.A. Pollard, V.N. Iyer and M.B. Eisen (2004). Genome Biology 5: R98.
Phylogenetic motif detection by expectation-maximization on evolutionary mixtures
A.M. Moses, D.Y. Chiang and M.B. Eisen (2004). Pacific Symposium on Biocomputing 9: 324-335
PDF PS
Position specific variation in the rate of evolution in transcription factor binding sites
A.M. Moses, D.Y. Chiang, M. Kellis, E.S. Lander and M.B. Eisen (2003). BMC Evolutionary Biology 3: 19.
PDF PS Link to journal
Phylogenetically and spatially conserved word pairs associated with gene
expression changes in yeasts
D.Y. Chiang, A.M. Moses, M. Kellis, E.S. Lander and M.B. Eisen (2003).
Genome Biology 4: R43.
PDF PS
Link to journal (see Additional data files)
Visualizing associations between genome sequences and gene expression data using genome-mean expression profiles
D.Y. Chiang, P.O. Brown and M.B. Eisen (2001). Bioinformatics 17: S49-S55.
PDF PS Software
Inferring sequence rules of promoter organization by systematically evaluating biological hypotheses
Systems Biology: Genomic approaches to transcriptional regulation, Cold Spring Harbor, NY 2004. PDF
Phylogenetically and spatially conserved word pairs associated with gene expression changes in yeasts
Research in Computational Molecular Biology, Berlin 2003. PDF
Visualizing associations between genome sequences and gene expression data using genome-mean expression profiles
Intelligent Systems in Molecular Biology, Copenhagen 2001. PDF
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