This page is no longer being updated. Here's a link to my current web page at Rutgers
K. Chen, J. Maaskola, M. L. Siegal and N. Rajewsky. Reexamining microRNA site accessibility in Drosophila: a population genomics study. PLoS ONE 4(5):e5681, 2009.
K. Chen and N. Rajewsky. The evolution of gene regulation by transcription factors and microRNAs. Nature Reviews Genetics 8:93-103, 2007. Supplementary Material
K. Chen and N. Rajewsky. Natural selection on human microRNA binding sites inferred from SNP data . Nature Genetics 38:1452-1456, 2006.
K. Chen and N. Rajewsky. Deep conservation of microRNA-target relationships and 3' UTR motifs in vertebrates, flies and nematodes. Cold Spring Harbor Symposia on Quantitative Biology, Vol. 71, Regulatory RNAs, 2007. PDF
S. Lall, D. Grun, A. Krek, K. Chen, Y. Wang et al. A genome-wide map of conserved microRNA targets in C. elegans . Current Biology 16(5):460-471, 2006
K. Chaudhuri, K. Chen, R. Mihaescu and S. Rao. On the tandem duplication-random loss model of genome rearrangement. SODA 2006.
A. Bachrach, K. Chen, C. Harrelson, R. Mihaescu, S. Rao and A. Shah. Lower Bounds for Maximum Parsimony with Gene Order Data. RECOMB Comparative Genomics, 2005
K. Chen and L. Pachter. Bioinformatics for Whole-Genome Shotgun Sequencing of Microbial Communities. PLoS Computational Biology 1(2):e24, 2005
S. Tringe, C. von Mering, A. Kobayashi, A. Salamov, K. Chen, et al. Comparative Metagenomics of Microbial Communities. Science 308(5721):554-557, 2005.
K. Chen, D.
Durand and M. Farach-Colton. Notung: A Program for Dating Gene
Duplications and Optimizing Gene Family Trees. Journal of Computational
Biology, 7(3/4):429-447, 2000. (Preliminary version in RECOMB 2000 Notung:
Dating Gene Duplications Using Gene Family Trees.
K. Chen and V. Ramachandran. A Space-Efficient Randomized DNA Algorithm for k-SAT. 6th International Meeting on DNA Based Computers, 2000.
K. Chen and E.
Winfree. Error-Correction in DNA
Computing: Misclassification and Strand Loss. DNA
Computers V, American Mathematical Society, 2000, pp 49-63
M. Charikar, K. Chen and M. Farach-Colton. Finding Frequent Items in Data Streams. Theoretical Comp. Sci., 312(1):3-15, 2004 (Preliminary version in ICALP 2002)
K. Chen and S. Rao. An Improved Frequent Items Algorithm with Applications to Web Caching. UC Berkeley Tech Report, UCB-CS-05-1383
K. Chen. Computing
Query Previews in the Flamenco System.
UC Berkeley Tech Report, UCB-CS-04-1303