Publications

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Genomics
Kinsella M, Harismendy O, Nakano M, Frazer KA, Bafna V. Sensitive gene fusion detection using ambiguously mapping RNA-Seq read pairs. Bioinformatics. 2011 ;27(8):1068-75.
Kozanitis C, Saunders C, Kruglyak S, Bafna V, Varghese G. Compressing genomic sequence fragments using SlimGene. J Comput Biol. 2011 ;18(3):401-13.
Lo C, Bashir A, Bansal V, Bafna V. Strobe sequence design for haplotype assembly. BMC Bioinformatics. 2011 ;12 Suppl 1:S24.
Brinza D, Schultz M, Tesler G, Bafna V. RAPID detection of gene-gene interactions in genome-wide association studies. Bioinformatics. 2010 ;26(22):2856-62.
Zakov S, Kinsella M, Bafna V. An algorithmic approach for breakage-fusion-bridge detection in tumor genomes. Proc Natl Acad Sci U S A. 2013 ;110(14):5546-51.
Kim S, Medvedev P, Paton TA, Bafna V. Reprever: resolving low-copy duplicated sequences using template driven assembly. Nucleic Acids Res. 2013 .
Kozanitis C, Heiberg A, Varghese G, Bafna V. Using Genome Query Language to uncover genetic variation. Bioinformatics. 2013 .
Zhou D, Udpa N, Ronen R, Stobdan T, Liang J, Appenzeller O, Zhao HW, Yin Y, Du Y, Guo L, 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.
Kim S, Jeong K, Bafna V. Wessim: a whole-exome sequencing simulator based on in silico exome capture. Bioinformatics. 2013 ;29(8):1076-7.
Kim S, Jeong K, Bhutani K, Lee JH, Patel A, Scott E, Nam H, Lee H, Gleeson JG, Bafna V. Virmid: accurate detection of somatic mutations with sample impurity inference. Genome Biol. 2013 ;14(8):R90.
Lo C, Liu R, Lee J, Robasky K, Byrne S, Lucchesi C, Aach J, Church G, Bafna V, Zhang K. On the design of clone-based haplotyping. Genome Biol. 2013 ;14(9):R100.
Udpa N, Ronen R, Zhou D, Liang J, Stobdan T, Appenzeller O, Yin Y, Du Y, Guo L, Cao R, et al. Whole genome sequencing of Ethiopian highlanders reveals conserved hypoxia tolerance genes. Genome Biol. 2014 ;15(2):R36.
Kinsella M, Patel A, Bafna V. The elusive evidence for chromothripsis. Nucleic Acids Res. 2014 ;42(13):8231-42.
Bafna V, Kozanitis C, Deutsch A, Ohno-Machado L, Heiberg A, Varghese G. Abstractions for Genomics. Commun ACM. 2013 ;56(1):83-93.