publications
- B. Viljetic et al. Multiple roles of PIWIL1 in mouse neocorticogenesis, 2017. bioRxiv doi:10.1101/106070
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C. Zhang, J. Song, K. C. Chen and K. Chaudhuri Spectral learning of large structured HMMs for comparative epigenomics. Twenty-ninth Annual Conference on Neural Information Processing Systems (NIPS), Montreal, Canada, 2015.
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J. Song and K. C. Chen. Spectacle: fast chromatin state annotation using spectral learning. Genome Biology, 16:33, 2015 Software and Data
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J. Song, J. Liu, S. Schnakenberg, H. Ha, J. Xing and K. C. Chen. Variation in piRNA and transposable element content in strains of Drosophila melanogaster. Genome Biology and Evolution 6(10):2786-2798, 2014.
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L. Diao, A. Marcais, S. Norton and K. C. Chen. MixMir: microRNA motif discovery from gene expression data using mixed linear models Nucleic Acids Research 42(17):e135, 2014. Software
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H. Ha*, J. Song*, S. Wang, A. Kapusta, C. Feschotte, K. C. Chen and J. Xing. A comprehensive analysis of piRNAs from adult human testis and their relationship with genes and mobile elements, BMC Genomics 15:545, 2014.
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M. R. Friedländer, E. Lizano, A. J. S. Houben, D. Bezdan, M. Bañez-Coronel, G. Kudla, E. Mateu-Huertas, B. Kagerbauer, K. C. Chen, E. M. LeProust, E. Martí, X. Estivill. Evidence for the biogenesis of more than 1,000 novel human microRNAs, Genome Biology, 15:R57, 2014.
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L. Diao and K. Chen. Local ancestry corrects for population structure in S. cerevisiae genome-wide association studies. Genetics, 192(4):1503-11, 2012.
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D. W. Gould, S. Lukic and K. Chen. Selective constraint on copy number variation in human Piwi-interacting RNA loci. PLoS ONE, 7(10): e46611, 2012.
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R. S. Roy, K. Chen, A. M. Sengupta and A. Schliep. SLIQ: Simple linear inequalities for efficient contig scaffolding. Journal of Computational Biology, 19(10): 1162-1175, 2012. Software
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M. S. Kumar and K. Chen. Evolution of animal Piwi-interacting RNAs and prokaryotic CRISPRs. Briefings in Functional Genomics, 11(4):277-88, 2012.
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S. Lukic and K. Chen. Human piRNAs are under selection in Africans and repress transposable elements. Molecular Biology and Evolution, 28:3061-3067, 2011.
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S. Lukic, J. Hey and K. Chen. Non-equilibrium allele frequency spectra via spectral methods. Theoretical Population Biology, 79:203-219, 2011
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J-S. Yang, M. D. Phillips, D. Betel, P. Mu, C. Sander, A. Ventura, A. C. Siepel, K. Chen*, E. C. Lai*. Widespread regulatory activity of vertebrate microRNA* species. RNA 17:312-326, 2011.
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K. Chen*, E. van Nimwegen, N. Rajewsky and M. L. Siegal*. Correlating gene expression variation with cis-regulatory polymorphism in Saccharomyces cerevisiae. Genome Biology and Evolution 2:697-707. 2010
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M. Mangone, et al. The landscape of C. elegans 3’ UTRs. Science 329:432-435, 2010. (see also S. E. Celniker, et al. Unlocking the secrets of the genome. Nature 459:927-30, 2009 and M. B. Gerstein et al. Integrative Analysis of the Caenorhabditis elegans Genome by the modENCODE Project. Science 330:1775-1787, 2010.)
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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.
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K. Chen and N. Rajewsky. The evolution of gene regulation by transcription factors and microRNAs. Nature Reviews Genetics 8:93-103, 2007. Supplementary Material
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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
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K. Chen and N. Rajewsky. Natural selection on human microRNA binding sites inferred from SNP data . Nature Genetics 38:1452-1456, 2006. Data
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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.
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K. Chaudhuri, K. Chen, R. Mihaescu and S. Rao. On the tandem duplication-random loss model of genome rearrangement. SODA 2006.
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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.
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K. Chen* and L. Pachter*. Bioinformatics for whole-genome shotgun sequencing of microbial communities. PLoS Computational Biology 1(2):e24, 2005.
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S. Tringe, C. von Mering, A. Kobayashi, A. Salamov, K. Chen, et al. Comparative metagenomics of microbial communities. Science 308(5721):554-557, 2005.
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M. Charikar, K. Chen and M. Farach-Colton. Finding frequent items in data streams. ICALP 2002 (Journal version: Theoretical Comp. Sci., 312(1):3-15, 2004.)
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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.)
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K. Chen and V. Ramachandran. A space-efficient randomized DNA algorithm for k-SAT. 6th International Meeting on DNA Based Computers, 2000.
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K. Chen and E. Winfree. Error-correction in DNA computing: misclassification and strand loss. DNA Computers V, American Mathematical Society, pp. 49-63, 2000.
Note: On computer science papers, authors are listed strictly alphabetically. Conference papers are peer-reviewed and there is often no subsequent journal article. On biology papers, authors are listed according to their contribution to the paper. An asterisk denotes "corresponding author".