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Prodanov T, Bansal V. A multi-locus approach for accurate variant calling in low-copy repeats using whole-genome sequencing. Bioinformatics Vol 39, June 2023. [ParascopyVC software]


Boehm B, Kratzer W, Bansal V. Whole-genome sequencing of multiple related individuals with type 2 diabetes reveals an atypical likely pathogenic mutation in the PAX6 gene. European journal of Human Genetics, 2022.

Prodanov T, Bansal V. Robust and accurate estimation of paralog-specific copy number for duplicated genes using whole-genome sequencing. Nature Communications 13, 2022. [Parascopy software] [ISMB slides pdf]

Bansal V. HapCUT2: a method for phasing genomes using experimental sequence data. Book chapter in Methods in Molecular Biology (Nov 2022), editors Brock Peters and Radoje Drmanac. [PDF]

Wagner J, Olson N, Harris L et al. Benchmarking challenging small variants with linked and long reads.Cell Genomics, Vol 5(2), 2022


Prodanov T, Bansal V. Sensitive alignment using paralogous sequence variants improves long read mapping and variant calling in segmental duplications. Nucleic Acids Research, 2020 [Duplomap software] [slides PDF]

Chin C, Wagner J, Zeng Q et al. A Diploid Assembly-based Benchmark for Variants in the Major Histocompatibility Complex. Nature Communications 11, 2020.

Chen Z, Pham L, Wu TC et al. Ultra-low input single tube linked-read library method enables short-read NGS systems to generate highly accurate and economical long-range sequencing information for de novo genome assembly and haplotype phasing Genome Research 30: 898-909, June 2020.


Edge P, Bansal V. Longshot: accurate variant calling in diploid genomes using single-molecule long read sequencing. Nature Communications, Oct 2019. [software download]

Scott ER, Bansal V, Meacham C, Scott SA. VarCover: Allele Min-Set Cover Software.The Journal of Molecular Diagnostics, 2019. [software]

Bansal V and Boucher C. Sequencing Technologies and Analyses: Where Have We Been and Where Are We Going? iScience, Aug 2019.

Bansal V. Integrating read-based and population-based phasing for dense and accurate haplotyping of individual genomes. In proceedings of ISMB/ECCB 2019 (published in Bioinformatics, July 2019). [ISMB slides pdf]


Bansal V, Boehm BO, Darvasi A. Identification of a rare missense mutation in the WFS1 gene that causes a mild form of Wolfram syndrome and is associated with risk of type 2 diabetes in Ashkenazi Jewish. Diabetologica, July 2018. [view PDF]

Bakhtiari M, Shleizer-Burko S, Gymrek M, Bansal V, Bafna V. Targeted Genotyping of Variable Number Tandem Repeats with adVNTR. Genome Research, October 2018.


Bansal V, Gassenhuber J, Phillips T, et al. Spectrum of mutations in monogenic diabetes genes identified from high-throughput DNA sequencing of 6,888 individuals. BMC Medicine, 2017 Commentary in BMC Medicine

Chu WK, Edge P, Lee HS, Bansal V, Bafna V, Huang X, Zhang K. Ultra Accurate Genome Sequencing And Haplotyping Of Single Human Cells. PNAS, October 2017.UCSD News article

Bansal V. An accurate algorithm for the detection of DNA fragments from dilution pool sequencing experiments. Bioinformatics 2017. Also presented at the RECOMB-Seq 2017 conference.

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. BMC Bioinformatics, March 2017. [code]


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)

publications from 2014 and before