Student Publications

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Nakatsuji T, Chiang H-I, Jiang SB, Nagarajan H, Zengler K, Gallo RL. "The microbiome extends to subepidermal compartments of normal skin." Nat Commun. 2013;4:1431.
Kaikkonen MU, Spann NJ, Heinz S, et al. "Remodeling of the enhancer landscape during macrophage activation is coupled to enhancer transcription." Mol. Cell. 2013;51(3):310-25.
Wagner GA, Pacold ME, Vigil E, et al. "Using ultradeep pyrosequencing to study HIV-1 coreceptor usage in primary and dual infection." J. Infect. Dis.. 2013;208(2):271-4.
Zhou D, Udpa N, Ronen R, et al. "Whole-genome sequencing uncovers the genetic basis of chronic mountain sickness in Andean highlanders." Am. J. Hum. Genet.. 2013;93(3):452-62.
Prlić A, Yates A, Bliven SE, et al. "BioJava: an open-source framework for bioinformatics in 2012." Bioinformatics. 2012;28(20):2693-5.
Kim D, Hong J S-J, Qiu Y, et al. "Comparative analysis of regulatory elements between Escherichia coli and Klebsiella pneumoniae by genome-wide transcription start site profiling." PLoS Genet.. 2012;8(8):e1002867.
Dixon-Salazar TJ, Silhavy JL, Udpa N, et al. "Exome sequencing can improve diagnosis and alter patient management." Sci Transl Med. 2012;4(138):138ra78.
Ruiz S, Diep D, Gore A, et al. "Identification of a specific reprogramming-associated epigenetic signature in human induced pluripotent stem cells." Proc. Natl. Acad. Sci. U.S.A.. 2012;109(40):16196-201.
Diep D, Plongthongkum N, Gore A, Fung H-L, Shoemaker R, Zhang K. "Library-free methylation sequencing with bisulfite padlock probes." Nat. Methods. 2012;9(3):270-2.
Chaisson MJ, Tesler G. "Mapping single molecule sequencing reads using basic local alignment with successive refinement (BLASR): application and theory." BMC Bioinformatics. 2012;13:238.
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.
Pacold M, Smith D, Little S, et al. "Comparison of methods to detect HIV dual infection." AIDS Res. Hum. Retroviruses. 2010;26(12):1291-8.
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.
Butler DM, Pacold ME, Jordan PS, Richman DD, Smith DM. "The efficiency of single genome amplification and sequencing is improved by quantitation and use of a bioinformatics tool." J. Virol. Methods. 2009;162(1-2):280-3.
Veretnik S, Wills C, Youkharibache P, Valas RE, Bourne PE. "Sm/Lsm genes provide a glimpse into the early evolution of the spliceosome." PLoS Comput. Biol.. 2009;5(3):e1000315.
Gupta N, Benhamida J, Bhargava V, et al. "Comparative proteogenomics: combining mass spectrometry and comparative genomics to analyze multiple genomes." Genome Res.. 2008;18(7):1133-42.
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.
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.
Chaisson MJ, Pevzner PA. "Short read fragment assembly of bacterial genomes." Genome Res.. 2008;18(2):324-30.
Zhi D, Keich U, Pevzner P, Heber S, Tang H. "Correcting base-assignment errors in repeat regions of shotgun assembly." IEEE/ACM Trans Comput Biol Bioinform. 2007;4(1):54-64.
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.
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.
Chaisson M, Pevzner P, Tang H. "Fragment assembly with short reads." Bioinformatics. 2004;20(13):2067-74.
Price ND, Papin JA, Schilling CH, Palsson BO. "Genome-scale microbial in silico models: the constraints-based approach." Trends Biotechnol.. 2003;21(4):162-9.