2017-current

Bansal V et al. Spectrum of mutations in monogenic diabetes genes identified from high-throughput DNA sequencing of 6,888 individuals. in review

Wai Keung Chu, Peter Edge, Ho Suk Lee, Vikas Bansal, Vineet Bafna, Xiaohua Huang, Kun Zhang. Ultra-Accurate Genome Sequencing And Haplotyping Of Single Human Cells. preprint at Bioarxiv. accepted for publication in PNAS

Bansal V. An accurate algorithm for the detection of DNA fragments from dilution pool sequencing experiments. presented at the RECOMB-Seq 2017 conference. published in Bioinformatics, July 2017. [software link]

Tiwari S, Dang J, Qin Y, Lichinchi G,Bansal V, Rana TM. Zika virus infection reprograms global transcription of host cells to allow sustained infection. Emerging Microbes and Infection, April 2017. 

Bansal V. A computational method for estimating the PCR duplication rate in high-throughput DNA sequencing experiments. accepted for presentation at APBC 2017 and published in BMC Bioinformatics, March 2017. PDF [software link] [SLIDES]


2015-2016

Edge P, Bafna V, Bansal V. HapCUT2: robust and accurate haplotype assembly for diverse sequencing technologies, Genome Research, Dec 2016. [software link] 

Patel A, Edge P, Selvaraj S, Bansal V and Bafna V. InPhaDel: Integrative shotgun and proximity-ligation sequencing to phase deletions with single nucleotide polymorphisms. Nucleic Acids Research, 2016. [software link]

Lichinchi G, Gao S, Saletore Y, Gonzalez GM, Bansal V, Wang Y, Mason CE, Rana TM. Dynamics of the human and viral m6A RNA methylomes during HIV-1 infection of T cells. Nature Microbiology, February 2016

Bansal V, Libiger O. Fast individual ancestry inference from DNA sequence data leveraging allele frequencies for multiple populations. BMC Bioinformatics, Jan 2015 [software] [SLIDES] (Note: In Table 1, the column headings for European and African are reversed)



2013-2014

Scott-Van Zeeland AA, Bloss C, Tewhey C, Bansal V, et al “Evidence for the Role of EPHX2 gene variants in Anorexia Nervosa”.   Molecular  Psychiatry, 2014

Selvaraj S, Dixon JR, Bansal V, Ren B. Whole genome haplotype reconstruction using proximity-ligation and shotgun sequencing. Nature Biotechnology 2013

2011-2012

Torkamani A, Pham P, Libiger O, Bansal V, Zhang G, Scott-Van Zeeland AA, Tewhey R, Topol EJ, Schork NJ. Clinical implications of human population differences in genome-wide rates of functional genotypes. Front Genet. 2012;3:211.

Tewhey R, Cannavino CR, Leake JA, Bansal V, Topol EJ, Torkamani A, Bradley JS, Schork NJ. Genetic structure of community acquired methicillin-resistant Staphylococcus aureus USA300. BMC Genomics. 2012 Sep 25;13:508. 

Bansal V, Libiger O. A probabilistic method for the detection and genotyping of small indels from population-scale sequence data. Bioinformatics. 2011 Aug 1;27(15):2047-53. Epub 2011 Jun 7. 


Lo C, Bashir A, Bansal V, Bafna V. Strobe sequence design for haplotype assembly. BMC Bioinformatics. 2011 Feb 15;12 Suppl 1:S24.

Tewhey R, Bansal V, Torkamani A, Topol EJ, Schork NJ. The importance of phase information for human genomics. Nature Review Genetics 2011 Mar;12(3):215-23. 

Bansal V, Tewhey R, Topol EJ, Schork NJ. The next phase in human genetics. Nature Biotechnology 2011 Jan;29(1):38-9. 

Bansal V, Tewhey R, Leproust EM, Schork NJ. Efficient and cost effective population resequencing by pooling and in-solution hybridization. PLoS One. 2011 Mar 30;6(3):e18353. 


2009-2010

Bhatia G, Bansal V, Harismendy O, Schork NJ, Topol EJ, Frazer K, Bafna V. A covering method for detecting genetic associations between rare variants andcommon phenotypes. PLoS Comput Biol. 2010 Oct 14;6(10):e1000954. 

Bansal V. A statistical method for the detection of variants from next-generation resequencing of DNA pools. Bioinformatics. 2010 Jun 15;26(12):i318-24. [CRISP]

Bansal V, Harismendy O, Tewhey R, Murray SS, Schork NJ, Topol EJ, Frazer KA. Accurate detection and genotyping of SNPs utilizing population sequencing data. Genome Res. 2010 Apr;20(4):537-45. [article in Biotechniques] [article in genome technology]

Schork NJ, Bansal V. Not so lost in the genetic crowd. Nature Genetics 2009


2004-2008 (Ph.D. work)

Bansal V, Bafna V. HapCUT: an efficient and accurate algorithm for the haplotype assembly problem. Bioinformatics. 2008 Aug 15;24(16):i153-9.

Bansal V, Halpern AL, Axelrod N, Bafna V. An MCMC algorithm for haplotype assembly from whole-genome sequence data. Genome Res. 2008 Aug;18(8):1336-46.

Levy S, Sutton G, Ng PC, Feuk L, Halpern AL, Walenz BP, Axelrod N, Huang J, Kirkness EF, Denisov G, Lin Y, MacDonald JR, Pang AW, Shago M, Stockwell TB, Tsiamouri A, Bafna V, Bansal V, Kravitz SA, Busam DA, Beeson KY, McIntosh TC, Remington KA, Abril JF, Gill J, Borman J, Rogers YH, Frazier ME, Scherer SW, Strausberg RL, Venter JC. The diploid genome sequence of an individual human. PLoS Biol. 2007 Sep 4;5(10):e254. 

Gusfield D, Bansal V, Bafna V, Song YS. A decomposition theory for phylogenetic networks and incompatible characters. J Comput Biol. 2007 Dec;14(10):1247-72. 

Bansal V, Bashir A, Bafna V. Evidence for large inversion polymorphisms in the human genome from HapMap data. Genome Res. 2007 Feb;17(2):219-30. Epub 2006 Dec 21.

Bafna V, Bansal V. Inference about recombination from haplotype data: lower bounds and recombination hotspots. J Comput Biol. 2006 Mar;13(2):501-21. PubMed PMID: 16597254.


Vikas Bansal, Friedhelm Meyer auf der Heide, Christian Sohler: Labeling Smart Dust. ESA 2004: 77-88