Student Publications

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Hu M, Deng K, Selvaraj S, Qin Z, Ren B, Liu JS. "HiCNorm: removing biases in Hi-C data via Poisson regression." Bioinformatics. 2012;28(23):3131-3.
Xu X, Nagarajan H, Lewis NE, et al. "The genomic sequence of the Chinese hamster ovary (CHO)-K1 cell line." Nat. Biotechnol.. 2011;29(8):735-41.
Chaisson MJ, Brinza D, Pevzner PA. "De novo fragment assembly with short mate-paired reads: Does the read length matter?" Genome Res.. 2009;19(2):336-46.
Kang H M, Zaitlen NA, Wade CM, et al. "Efficient control of population structure in model organism association mapping." Genetics. 2008;178(3):1709-23.
Bashir A, Volik S, Collins C, Bafna V, Raphael BJ. "Evaluation of paired-end sequencing strategies for detection of genome rearrangements in cancer." PLoS Comput. Biol.. 2008;4(4):e1000051.
Bandyopadhyay S, Kelley R, Krogan NJ, Ideker T. "Functional maps of protein complexes from quantitative genetic interaction data." PLoS Comput. Biol.. 2008;4(4):e1000065.
Barrera LO, Li Z, Smith AD, et al. "Genome-wide mapping and analysis of active promoters in mouse embryonic stem cells and adult organs." Genome Res.. 2008;18(1):46-59.
Raphael BJ, Volik S, Yu P, et al. "A sequence-based survey of the complex structural organization of tumor genomes." Genome Biol.. 2008;9(3):R59.
Ye C, Eskin E. "Discovering tightly regulated and differentially expressed gene sets in whole genome expression data." Bioinformatics. 2007;23(2):e84-90.
Bansal V, Bashir A, Bafna V. "Evidence for large inversion polymorphisms in the human genome from HapMap data." Genome Res.. 2007;17(2):219-30.
Bashir A, Liu Y-T, Raphael BJ, Carson D, Bafna V. "Optimization of primer design for the detection of variable genomic lesions in cancer." Bioinformatics. 2007;23(21):2807-15.
Kim T H, Barrera LO, Qu C, et al. "Direct isolation and identification of promoters in the human genome." Genome Res.. 2005;15(6):830-9.
Szpankowski W, Ren W, Szpankowski L. "An optimal DNA segmentation based on the MDL principle." Int J Bioinform Res Appl. 2005;1(1):3-17.