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Vineet Bafna

TitleResearcher
InstitutionUniversity of California San Diego
DepartmentComputer Science and Engineering
Address9500 Gilman Drive #0404
La Jolla CA 92093
Phone858-822-4978
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    Collapse Research 
    Collapse Research Activities and Funding
    Computational methods for detecting patterns of complex genomic variation
    NIH/NIGMS R01GM114362Jan 1, 2016 - Dec 31, 2019
    Role: Principal Investigator
    Algorithmic strategies for detecting structural variation in genomes
    NIH/NHGRI R01HG004962Apr 1, 2009 - Feb 28, 2014
    Role: Principal Investigator
    Center for Computational Mass Spectrometry
    NIH/NIGMS P41GM103484Sep 20, 2008 - Jun 30, 2019
    Role: Principal Investigator
    Graduate Training Program in Bioinformatics
    NIH/NIGMS T32GM008806Jul 1, 2001 - Jun 30, 2021
    Role: Principal Investigator

    Collapse Bibliographic 
    Collapse Publications
    Publications listed below are automatically derived from MEDLINE/PubMed and other sources, which might result in incorrect or missing publications. Researchers can login to make corrections and additions, or contact us for help.
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    1. Iranmehr A, Stobdan T, Zhou D, Poulsen O, Strohl KP, Aldashev A, Telenti A, Wong EHM, Kirkness EF, Venter JC, Bafna V, Haddad GG. Novel insight into the genetic basis of high-altitude pulmonary hypertension in Kyrgyz highlanders. Eur J Hum Genet. 2018 Sep 25. PMID: 30254217.
      View in: PubMed
    2. Beyter D, Lin MS, Yu Y, Pieper R, Bafna V. ProteoStorm: An Ultrafast Metaproteomics Database Search Framework. Cell Syst. 2018 Sep 24. PMID: 30268435.
      View in: PubMed
    3. Nguyen ND, Deshpande V, Luebeck J, Mischel PS, Bafna V. ViFi: accurate detection of viral integration and mRNA fusion reveals indiscriminate and unregulated transcription in proximal genomic regions in cervical cancer. Nucleic Acids Res. 2018 Mar 20. PMID: 29579309.
      View in: PubMed
    4. Akbari A, Vitti JJ, Iranmehr A, Bakhtiari M, Sabeti PC, Mirarab S, Bafna V. Identifying the favored mutation in a positive selective sweep. Nat Methods. 2018 Apr; 15(4):279-282. PMID: 29457793.
      View in: PubMed
    5. Rozanov DV, Rozanov ND, Chiotti KE, Reddy A, Wilmarth PA, David LL, Cha SW, Woo S, Pevzner P, Bafna V, Burrows GG, Rantala JK, Levin T, Anur P, Johnson-Camacho K, Tabatabaei S, Munson DJ, Bruno TC, Slansky JE, Kappler JW, Hirano N, Boegel S, Fox BA, Egelston C, Simons DL, Jimenez G, Lee PP, Gray JW, Spellman PT. MHC class I loaded ligands from breast cancer cell lines: A potential HLA-I-typed antigen collection. J Proteomics. 2018 Mar 30; 176:13-23. PMID: 29331515.
      View in: PubMed
    6. Stobdan T, Akbari A, Azad P, Zhou D, Poulsen O, Appenzeller O, Gonzales GF, Telenti A, Wong EHM, Saini S, Kirkness EF, Venter JC, Bafna V, Haddad GG. New Insights into the Genetic Basis of Monge's Disease and Adaptation to High-Altitude. Mol Biol Evol. 2017 Dec 01; 34(12):3154-3168. PMID: 29029226.
      View in: PubMed
    7. Chu WK, Edge P, Lee HS, Bansal V, Bafna V, Huang X, Zhang K. Ultraaccurate genome sequencing and haplotyping of single human cells. Proc Natl Acad Sci U S A. 2017 Nov 21; 114(47):12512-12517. PMID: 29078313.
      View in: PubMed
    8. Cha SW, Bonissone S, Na S, Pevzner PA, Bafna V. The Antibody Repertoire of Colorectal Cancer. Mol Cell Proteomics. 2017 Dec; 16(12):2111-2124. PMID: 29046389.
      View in: PubMed
    9. Azad P, Stobdan T, Zhou D, Hartley I, Akbari A, Bafna V, Haddad GG. High-altitude adaptation in humans: from genomics to integrative physiology. J Mol Med (Berl). 2017 Dec; 95(12):1269-1282. PMID: 28951950.
      View in: PubMed
    10. Iranmehr A, Akbari A, Schlötterer C, Bafna V. Clear: Composition of Likelihoods for Evolve and Resequence Experiments. Genetics. 2017 06; 206(2):1011-1023. PMID: 28396506.
      View in: PubMed
    11. Turner KM, Deshpande V, Beyter D, Koga T, Rusert J, Lee C, Li B, Arden K, Ren B, Nathanson DA, Kornblum HI, Taylor MD, Kaushal S, Cavenee WK, Wechsler-Reya R, Furnari FB, Vandenberg SR, Rao PN, Wahl GM, Bafna V, Mischel PS. Extrachromosomal oncogene amplification drives tumour evolution and genetic heterogeneity. Nature. 2017 03 02; 543(7643):122-125. PMID: 28178237.
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    12. Edge P, Bafna V, Bansal V. HapCUT2: robust and accurate haplotype assembly for diverse sequencing technologies. Genome Res. 2017 05; 27(5):801-812. PMID: 27940952.
      View in: PubMed
    13. Ronen R, Tesler G, Akbari A, Zakov S, Rosenberg NA, Bafna V. Correction: Predicting Carriers of Ongoing Selective Sweeps without Knowledge of the Favored Allele. PLoS Genet. 2016 Nov; 12(11):e1006472. PMID: 27902698.
      View in: PubMed
    14. Azad P, Zhao HW, Cabrales PJ, Ronen R, Zhou D, Poulsen O, Appenzeller O, Hsiao YH, Bafna V, Haddad GG. Senp1 drives hypoxia-induced polycythemia via GATA1 and Bcl-xL in subjects with Monge's disease. J Exp Med. 2016 Nov 14; 213(12):2729-2744. PMID: 27821551.
      View in: PubMed
    15. Zhang H, Liu T, Zhang Z, Payne SH, Zhang B, McDermott JE, Zhou JY, Petyuk VA, Chen L, Ray D, Sun S, Yang F, Chen L, Wang J, Shah P, Cha SW, Aiyetan P, Woo S, Tian Y, Gritsenko MA, Clauss TR, Choi C, Monroe ME, Thomas S, Nie S, Wu C, Moore RJ, Yu KH, Tabb DL, Fenyö D, Bafna V, Wang Y, Rodriguez H, Boja ES, Hiltke T, Rivers RC, Sokoll L, Zhu H, Shih IM, Cope L, Pandey A, Zhang B, Snyder MP, Levine DA, Smith RD, Chan DW, Rodland KD. Integrated Proteogenomic Characterization of Human High-Grade Serous Ovarian Cancer. Cell. 2016 Jul 28; 166(3):755-765. PMID: 27372738; PMCID: PMC4967013 [Available on 07/28/17].
    16. Patel A, Edge P, Selvaraj S, Bansal V, Bafna V. InPhaDel: integrative shotgun and proximity-ligation sequencing to phase deletions with single nucleotide polymorphisms. Nucleic Acids Res. 2016 07 08; 44(12):e111. PMID: 27105843; PMCID: PMC4937317.
    17. Beyter D, Tang PZ, Becker S, Hoang T, Bilgin D, Lim YW, Peterson TC, Mayfield S, Haerizadeh F, Shurin JB, Bafna V, McBride R. Diversity, Productivity, and Stability of an Industrial Microbial Ecosystem. Appl Environ Microbiol. 2016 Apr; 82(8):2494-2505. PMID: 26896141.
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    18. Rawson R, Anilkumar A, Newbury RO, Bafna V, Aquino M, Palmquist J, Hoffman HM, Mueller JL, Dohil R, Broide DH, Aceves SS. The TGFß1 Promoter SNP C-509T and Food Sensitization Promote Esophageal Remodeling in Pediatric Eosinophilic Esophagitis. PLoS One. 2015; 10(12):e0144651. PMID: 26656423; PMCID: PMC4678166.
    19. Ronen R, Tesler G, Akbari A, Zakov S, Rosenberg NA, Bafna V. Predicting Carriers of Ongoing Selective Sweeps without Knowledge of the Favored Allele. PLoS Genet. 2015 Sep; 11(9):e1005527. PMID: 26402243; PMCID: PMC4581834.
    20. Flannery EL, Wang T, Akbari A, Corey VC, Gunawan F, Bright AT, Abraham M, Sanchez JF, Santolalla ML, Baldeviano GC, Edgel KA, Rosales LA, Lescano AG, Bafna V, Vinetz JM, Winzeler EA. Next-Generation Sequencing of Plasmodium vivax Patient Samples Shows Evidence of Direct Evolution in Drug-Resistance Genes. ACS Infect Dis. 2015 Aug 14; 1(8):367-79. PMID: 26719854; PMCID: PMC4692371.
    21. Stobdan T, Zhou D, Ao-Ieong E, Ortiz D, Ronen R, Hartley I, Gan Z, McCulloch AD, Bafna V, Cabrales P, Haddad GG. Endothelin receptor B, a candidate gene from human studies at high altitude, improves cardiac tolerance to hypoxia in genetically engineered heterozygote mice. Proc Natl Acad Sci U S A. 2015 Aug 18; 112(33):10425-30. PMID: 26240367; PMCID: PMC4547246.
    22. Woo S, Cha SW, Bonissone S, Na S, Tabb DL, Pevzner PA, Bafna V. Advanced Proteogenomic Analysis Reveals Multiple Peptide Mutations and Complex Immunoglobulin Peptides in Colon Cancer. J Proteome Res. 2015 Sep 04; 14(9):3555-67. PMID: 26139413; PMCID: PMC4868822.
    23. Zakov S, Bafna V. Reconstructing breakage fusion bridge architectures using noisy copy numbers. J Comput Biol. 2015 Jun; 22(6):577-94. PMID: 26020441; PMCID: PMC4449712.
    24. Woo S, Cha SW, Na S, Guest C, Liu T, Smith RD, Rodland KD, Payne S, Bafna V. Proteogenomic strategies for identification of aberrant cancer peptides using large-scale next-generation sequencing data. Proteomics. 2014 Dec; 14(23-24):2719-30. PMID: 25263569; PMCID: PMC4256132.
    25. Chen HS, Hutter CM, Mechanic LE, Amos CI, Bafna V, Hauser ER, Hernandez RD, Li C, Liberles DA, McAllister K, Moore JH, Paltoo DN, Papanicolaou GJ, Peng B, Ritchie MD, Rosenfeld G, Witte JS, Gillanders EM, Feuer EJ. Genetic simulation tools for post-genome wide association studies of complex diseases. Genet Epidemiol. 2015 Jan; 39(1):11-19. PMID: 25371374.
      View in: PubMed
    26. Ronen R, Zhou D, Bafna V, Haddad GG. The genetic basis of chronic mountain sickness. Physiology (Bethesda). 2014 Nov; 29(6):403-12. PMID: 25362634; PMCID: PMC4280153.
    27. Kelkar DS, Provost E, Chaerkady R, Muthusamy B, Manda SS, Subbannayya T, Selvan LD, Wang CH, Datta KK, Woo S, Dwivedi SB, Renuse S, Getnet D, Huang TC, Kim MS, Pinto SM, Mitchell CJ, Madugundu AK, Kumar P, Sharma J, Advani J, Dey G, Balakrishnan L, Syed N, Nanjappa V, Subbannayya Y, Goel R, Prasad TS, Bafna V, Sirdeshmukh R, Gowda H, Wang C, Leach SD, Pandey A. Annotation of the zebrafish genome through an integrated transcriptomic and proteomic analysis. Mol Cell Proteomics. 2014 Nov; 13(11):3184-98. PMID: 25060758; PMCID: PMC4223501.
    28. Kinsella M, Patel A, Bafna V. The elusive evidence for chromothripsis. Nucleic Acids Res. 2014 Jul; 42(13):8231-42. PMID: 24939897; PMCID: PMC4117757.
    29. Kramer M, Dutkowski J, Yu M, Bafna V, Ideker T. Inferring gene ontologies from pairwise similarity data. Bioinformatics. 2014 Jun 15; 30(12):i34-42. PMID: 24932003; PMCID: PMC4058954.
    30. Udpa N, Ronen R, Zhou D, Liang J, Stobdan T, Appenzeller O, Yin Y, Du Y, Guo L, Cao R, Wang Y, Jin X, Huang C, Jia W, Cao D, Guo G, Claydon VE, Hainsworth R, Gamboa JL, Zibenigus M, Zenebe G, Xue J, Liu S, Frazer KA, Li Y, Bafna V, Haddad GG. Whole genome sequencing of Ethiopian highlanders reveals conserved hypoxia tolerance genes. Genome Biol. 2014 Feb 20; 15(2):R36. PMID: 24555826; PMCID: PMC4054780.
    31. Patel A, Schwab R, Liu YT, Bafna V. Amplification and thrifty single-molecule sequencing of recurrent somatic structural variations. Genome Res. 2014 Feb; 24(2):318-28. PMID: 24307551; PMCID: PMC3912422.
    32. Castellana NE, Shen Z, He Y, Walley JW, Cassidy CJ, Briggs SP, Bafna V. An automated proteogenomic method uses mass spectrometry to reveal novel genes in Zea mays. Mol Cell Proteomics. 2014 Jan; 13(1):157-67. PMID: 24142994; PMCID: PMC3879611.
    33. Kim S, Jeong K, Bhutani K, Lee J, 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 Aug 29; 14(8):R90. PMID: 23987214; PMCID: PMC4054681.
    34. Zhou D, Udpa N, Ronen R, Stobdan T, Liang J, Appenzeller O, Zhao HW, Yin Y, Du Y, Guo L, Cao R, Wang Y, Jin X, Huang C, Jia W, Cao D, Guo G, Gamboa JL, Villafuerte F, Callacondo D, Xue J, Liu S, Frazer KA, Li Y, Bafna V, Haddad GG. Whole-genome sequencing uncovers the genetic basis of chronic mountain sickness in Andean highlanders. Am J Hum Genet. 2013 Sep 05; 93(3):452-62. PMID: 23954164; PMCID: PMC3769925.
    35. Woo S, Cha SW, Merrihew G, He Y, Castellana N, Guest C, MacCoss M, Bafna V. Proteogenomic database construction driven from large scale RNA-seq data. J Proteome Res. 2014 Jan 03; 13(1):21-8. PMID: 23802565; PMCID: PMC4034692.
    36. Ronen R, Udpa N, Halperin E, Bafna V. Learning natural selection from the site frequency spectrum. Genetics. 2013 Sep; 195(1):181-93. PMID: 23770700; PMCID: PMC3761300.
    37. Kozanitis C, Heiberg A, Varghese G, Bafna V. Using Genome Query Language to uncover genetic variation. Bioinformatics. 2014 Jan 01; 30(1):1-8. PMID: 23751181; PMCID: PMC3866549.
    38. Kim S, Medvedev P, Paton TA, Bafna V. Reprever: resolving low-copy duplicated sequences using template driven assembly. Nucleic Acids Res. 2013 Jul; 41(12):e128. PMID: 23658221; PMCID: PMC3695505.
    39. Lo C, Kim S, Zakov S, Bafna V. Evaluating genome architecture of a complex region via generalized bipartite matching. BMC Bioinformatics. 2013; 14 Suppl 5:S13. PMID: 23734567; PMCID: PMC3622632.
    40. 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 Apr 02; 110(14):5546-51. PMID: 23503850; PMCID: PMC3619374.
    41. Kim S, Jeong K, Bafna V. Wessim: a whole-exome sequencing simulator based on in silico exome capture. Bioinformatics. 2013 Apr 15; 29(8):1076-7. PMID: 23413434; PMCID: PMC3624799.
    42. 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. PMID: 24028704; PMCID: PMC4053695.
    43. Bafna V, Kozanitis C, Deutsch A, Ohno-Machado L, Heiberg A, Varghese G. Abstractions for Genomics. Commun ACM. 2013 Jan; 56(1):83-93. PMID: 25284821.
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    44. Lee JH, Huynh M, Silhavy JL, Kim S, Dixon-Salazar T, Heiberg A, Scott E, Bafna V, Hill KJ, Collazo A, Funari V, Russ C, Gabriel SB, Mathern GW, Gleeson JG. De novo somatic mutations in components of the PI3K-AKT3-mTOR pathway cause hemimegalencephaly. Nat Genet. 2012 Jun 24; 44(8):941-5. PMID: 22729223; PMCID: PMC4417942.
    45. Dixon-Salazar TJ, Silhavy JL, Udpa N, Schroth J, Bielas S, Schaffer AE, Olvera J, Bafna V, Zaki MS, Abdel-Salam GH, Mansour LA, Selim L, Abdel-Hadi S, Marzouki N, Ben-Omran T, Al-Saana NA, Sonmez FM, Celep F, Azam M, Hill KJ, Collazo A, Fenstermaker AG, Novarino G, Akizu N, Garimella KV, Sougnez C, Russ C, Gabriel SB, Gleeson JG. Exome sequencing can improve diagnosis and alter patient management. Sci Transl Med. 2012 Jun 13; 4(138):138ra78. PMID: 22700954; PMCID: PMC4442637.
    46. Liu X, Mammana A, Bafna V. Speeding up tandem mass spectral identification using indexes. Bioinformatics. 2012 Jul 01; 28(13):1692-7. PMID: 22543365; PMCID: PMC3381964.
    47. Kinsella M, Bafna V. Combinatorics of the breakage-fusion-bridge mechanism. J Comput Biol. 2012 Jun; 19(6):662-78. PMID: 22506505; PMCID: PMC3375649.
    48. Dost B, Bandeira N, Li X, Shen Z, Briggs SP, Bafna V. Accurate mass spectrometry based protein quantification via shared peptides. J Comput Biol. 2012 Apr; 19(4):337-48. PMID: 22414154; PMCID: PMC3317402.
    49. Abad-Grau MM, Medina-Medina N, Montes-Soldado R, Matesanz F, Bafna V. Sample reproducibility of genetic association using different multimarker TDTs in genome-wide association studies: characterization and a new approach. PLoS One. 2012; 7(2):e29613. PMID: 22363405.
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    50. Hon GC, Hawkins RD, Caballero OL, Lo C, Lister R, Pelizzola M, Valsesia A, Ye Z, Kuan S, Edsall LE, Camargo AA, Stevenson BJ, Ecker JR, Bafna V, Strausberg RL, Simpson AJ, Ren B. Global DNA hypomethylation coupled to repressive chromatin domain formation and gene silencing in breast cancer. Genome Res. 2012 Feb; 22(2):246-58. PMID: 22156296; PMCID: PMC3266032.
    51. Udpa N, Zhou D, Haddad GG, Bafna V. Tests of selection in pooled case-control data: an empirical study. Front Genet. 2011; 2:83. PMID: 22303377; PMCID: PMC3268381.
    52. Ohno-Machado L, Bafna V, Boxwala AA, Chapman BE, Chapman WW, Chaudhuri K, Day ME, Farcas C, Heintzman ND, Jiang X, Kim H, Kim J, Matheny ME, Resnic FS, Vinterbo SA. iDASH: integrating data for analysis, anonymization, and sharing. J Am Med Inform Assoc. 2012 Mar-Apr; 19(2):196-201. PMID: 22081224; PMCID: PMC3277627.
    53. Liu X, Sirotkin Y, Shen Y, Anderson G, Tsai YS, Ting YS, Goodlett DR, Smith RD, Bafna V, Pevzner PA. Protein identification using top-down. Mol Cell Proteomics. 2012 Jun; 11(6):M111.008524. PMID: 22027200; PMCID: PMC3433905.
    54. Bruand J, Alexandrov T, Sistla S, Wisztorski M, Meriaux C, Becker M, Salzet M, Fournier I, Macagno E, Bafna V. AMASS: algorithm for MSI analysis by semi-supervised segmentation. J Proteome Res. 2011 Oct 07; 10(10):4734-43. PMID: 21800894; PMCID: PMC3190602.
    55. Dost B, Wu C, Su A, Bafna V. TCLUST: a fast method for clustering genome-scale expression data. IEEE/ACM Trans Comput Biol Bioinform. 2011 May-Jun; 8(3):808-18. PMID: 20479508.
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    56. Bruand J, Sistla S, Mériaux C, Dorrestein PC, Gaasterland T, Ghassemian M, Wisztorski M, Fournier I, Salzet M, Macagno E, Bafna V. Automated querying and identification of novel peptides using MALDI mass spectrometric imaging. J Proteome Res. 2011 Apr 01; 10(4):1915-28. PMID: 21332220; PMCID: PMC4845900.
    57. Kozanitis C, Saunders C, Kruglyak S, Bafna V, Varghese G. Compressing genomic sequence fragments using SlimGene. J Comput Biol. 2011 Mar; 18(3):401-13. PMID: 21385043; PMCID: PMC3123913.
    58. Kinsella M, Harismendy O, Nakano M, Frazer KA, Bafna V. Sensitive gene fusion detection using ambiguously mapping RNA-Seq read pairs. Bioinformatics. 2011 Apr 15; 27(8):1068-75. PMID: 21330288; PMCID: PMC3072550.
    59. Lo C, Bashir A, Bansal V, Bafna V. Strobe sequence design for haplotype assembly. BMC Bioinformatics. 2011 Feb 15; 12 Suppl 1:S24. PMID: 21342554; PMCID: PMC3044279.
    60. Zhou D, Udpa N, Gersten M, Visk DW, Bashir A, Xue J, Frazer KA, Posakony JW, Subramaniam S, Bafna V, Haddad GG. Experimental selection of hypoxia-tolerant Drosophila melanogaster. Proc Natl Acad Sci U S A. 2011 Feb 08; 108(6):2349-54. PMID: 21262834; PMCID: PMC3038716.
    61. Castellana NE, McCutcheon K, Pham VC, Harden K, Nguyen A, Young J, Adams C, Schroeder K, Arnott D, Bafna V, Grogan JL, Lill JR. Resurrection of a clinical antibody: template proteogenomic de novo proteomic sequencing and reverse engineering of an anti-lymphotoxin-a antibody. Proteomics. 2011 Feb; 11(3):395-405. PMID: 21268269; PMCID: PMC3253889.
    62. Meier JL, Patel AD, Niessen S, Meehan M, Kersten R, Yang JY, Rothmann M, Cravatt BF, Dorrestein PC, Burkart MD, Bafna V. Practical 4'-phosphopantetheine active site discovery from proteomic samples. J Proteome Res. 2011 Jan 07; 10(1):320-9. PMID: 21067235; PMCID: PMC3042426.
    63. Harismendy O, Bansal V, Bhatia G, Nakano M, Scott M, Wang X, Dib C, Turlotte E, Sipe JC, Murray SS, Deleuze JF, Bafna V, Topol EJ, Frazer KA. Population sequencing of two endocannabinoid metabolic genes identifies rare and common regulatory variants associated with extreme obesity and metabolite level. Genome Biol. 2010; 11(11):R118. PMID: 21118518; PMCID: PMC3156957.
    64. Bhatia G, Bansal V, Harismendy O, Schork NJ, Topol EJ, Frazer K, Bafna V. A covering method for detecting genetic associations between rare variants and common phenotypes. PLoS Comput Biol. 2010 Oct 14; 6(10):e1000954. PMID: 20976246.
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    65. Brinza D, Schultz M, Tesler G, Bafna V. RAPID detection of gene-gene interactions in genome-wide association studies. Bioinformatics. 2010 Nov 15; 26(22):2856-62. PMID: 20871107; PMCID: PMC3493125.
    66. Liu X, Inbar Y, Dorrestein PC, Wynne C, Edwards N, Souda P, Whitelegge JP, Bafna V, Pevzner PA. Deconvolution and database search of complex tandem mass spectra of intact proteins: a combinatorial approach. Mol Cell Proteomics. 2010 Dec; 9(12):2772-82. PMID: 20855543; PMCID: PMC3101958.
    67. Castellana N, Bafna V. Proteogenomics to discover the full coding content of genomes: a computational perspective. J Proteomics. 2010 Oct 10; 73(11):2124-35. PMID: 20620248; PMCID: PMC2949459.
    68. Macagno ER, Gaasterland T, Edsall L, Bafna V, Soares MB, Scheetz T, Casavant T, Da Silva C, Wincker P, Tasiemski A, Salzet M. Construction of a medicinal leech transcriptome database and its application to the identification of leech homologs of neural and innate immune genes. BMC Genomics. 2010 Jun 25; 11:407. PMID: 20579359; PMCID: PMC2996935.
    69. Bashir A, Bansal V, Bafna V. Designing deep sequencing experiments: detecting structural variation and estimating transcript abundance. BMC Genomics. 2010 Jun 18; 11:385. PMID: 20565853; PMCID: PMC3091630.
    70. Hormozdiari F, Salari R, Bafna V, Sahinalp SC. Protein-protein interaction network evaluation for identifying potential drug targets. J Comput Biol. 2010 May; 17(5):669-84. PMID: 20500021.
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    71. Bashir A, Lu Q, Carson D, Raphael BJ, Liu YT, Bafna V. Optimizing PCR assays for DNA-based cancer diagnostics. J Comput Biol. 2010 Mar; 17(3):369-81. PMID: 20377451; PMCID: PMC3213025.
    72. Castellana NE, Pham V, Arnott D, Lill JR, Bafna V. Template proteogenomics: sequencing whole proteins using an imperfect database. Mol Cell Proteomics. 2010 Jun; 9(6):1260-70. PMID: 20164058; PMCID: PMC2877985.
    73. Watrous J, Burns K, Liu WT, Patel A, Hook V, Bafna V, Barry CE, Bark S, Dorrestein PC. Expansion of the mycobacterial "PUPylome". Mol Biosyst. 2010 Feb; 6(2):376-85. PMID: 20094657.
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    74. Kalaev M, Bafna V, Sharan R. Fast and accurate alignment of multiple protein networks. J Comput Biol. 2009 Aug; 16(8):989-99. PMID: 19624266.
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    75. McKernan KJ, Peckham HE, Costa GL, McLaughlin SF, Fu Y, Tsung EF, Clouser CR, Duncan C, Ichikawa JK, Lee CC, Zhang Z, Ranade SS, Dimalanta ET, Hyland FC, Sokolsky TD, Zhang L, Sheridan A, Fu H, Hendrickson CL, Li B, Kotler L, Stuart JR, Malek JA, Manning JM, Antipova AA, Perez DS, Moore MP, Hayashibara KC, Lyons MR, Beaudoin RE, Coleman BE, Laptewicz MW, Sannicandro AE, Rhodes MD, Gottimukkala RK, Yang S, Bafna V, Bashir A, MacBride A, Alkan C, Kidd JM, Eichler EE, Reese MG, De La Vega FM, Blanchard AP. Sequence and structural variation in a human genome uncovered by short-read, massively parallel ligation sequencing using two-base encoding. Genome Res. 2009 Sep; 19(9):1527-41. PMID: 19546169; PMCID: PMC2752135.
    76. Castellana NE, Payne SH, Shen Z, Stanke M, Bafna V, Briggs SP. Discovery and revision of Arabidopsis genes by proteogenomics. Proc Natl Acad Sci U S A. 2008 Dec 30; 105(52):21034-8. PMID: 19098097.
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    77. Dost B, Shlomi T, Gupta N, Ruppin E, Bafna V, Sharan R. QNet: a tool for querying protein interaction networks. J Comput Biol. 2008 Sep; 15(7):913-25. PMID: 18707533.
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    78. Bansal V, Bafna V. HapCUT: an efficient and accurate algorithm for the haplotype assembly problem. Bioinformatics. 2008 Aug 15; 24(16):i153-9. PMID: 18689818.
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    79. 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. PMID: 18676820; PMCID: PMC2493424.
    80. Payne SH, Yau M, Smolka MB, Tanner S, Zhou H, Bafna V. Phosphorylation-specific MS/MS scoring for rapid and accurate phosphoproteome analysis. J Proteome Res. 2008 Aug; 7(8):3373-81. PMID: 18563926; PMCID: PMC2566938.
    81. Han B, Dost B, Bafna V, Zhang S. Structural alignment of pseudoknotted RNA. J Comput Biol. 2008 Jun; 15(5):489-504. PMID: 18549303.
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    82. 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 Apr 25; 4(4):e1000051. PMID: 18404202; PMCID: PMC2278375.
    83. Gupta N, Benhamida J, Bhargava V, Goodman D, Kain E, Kerman I, Nguyen N, Ollikainen N, Rodriguez J, Wang J, Lipton MS, Romine M, Bafna V, Smith RD, Pevzner PA. Comparative proteogenomics: combining mass spectrometry and comparative genomics to analyze multiple genomes. Genome Res. 2008 Jul; 18(7):1133-42. PMID: 18426904; PMCID: PMC2493402.
    84. Albuquerque CP, Smolka MB, Payne SH, Bafna V, Eng J, Zhou H. A multidimensional chromatography technology for in-depth phosphoproteome analysis. Mol Cell Proteomics. 2008 Jul; 7(7):1389-96. PMID: 18407956; PMCID: PMC2493382.
    85. 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. PMID: 18047426; PMCID: PMC2581772.
    86. Tanner S, Payne SH, Dasari S, Shen Z, Wilmarth PA, David LL, Loomis WF, Briggs SP, Bafna V. Accurate annotation of peptide modifications through unrestrictive database search. J Proteome Res. 2008 Jan; 7(1):170-81. PMID: 18034453.
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    87. 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 04; 5(10):e254. PMID: 17803354; PMCID: PMC1964779.
    88. Bashir A, Liu YT, Raphael BJ, Carson D, Bafna V. Optimization of primer design for the detection of variable genomic lesions in cancer. Bioinformatics. 2007 Nov 01; 23(21):2807-15. PMID: 17766270.
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    89. Gupta N, Tanner S, Jaitly N, Adkins JN, Lipton M, Edwards R, Romine M, Osterman A, Bafna V, Smith RD, Pevzner PA. Whole proteome analysis of post-translational modifications: applications of mass-spectrometry for proteogenomic annotation. Genome Res. 2007 Sep; 17(9):1362-77. PMID: 17690205; PMCID: PMC1950905.
    90. Ideker T, Bafna V, Lemberger T. Integrating scientific cultures. Mol Syst Biol. 2007; 3:105. PMID: 17437030; PMCID: PMC1865587.
    91. Yooseph S, Sutton G, Rusch DB, Halpern AL, Williamson SJ, Remington K, Eisen JA, Heidelberg KB, Manning G, Li W, Jaroszewski L, Cieplak P, Miller CS, Li H, Mashiyama ST, Joachimiak MP, van Belle C, Chandonia JM, Soergel DA, Zhai Y, Natarajan K, Lee S, Raphael BJ, Bafna V, Friedman R, Brenner SE, Godzik A, Eisenberg D, Dixon JE, Taylor SS, Strausberg RL, Frazier M, Venter JC. The Sorcerer II Global Ocean Sampling expedition: expanding the universe of protein families. PLoS Biol. 2007 Mar; 5(3):e16. PMID: 17355171; PMCID: PMC1821046.
    92. Tanner S, Shen Z, Ng J, Florea L, Guigó R, Briggs SP, Bafna V. Improving gene annotation using peptide mass spectrometry. Genome Res. 2007 Feb; 17(2):231-9. PMID: 17189379; PMCID: PMC1781355.
    93. 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. PMID: 17185644; PMCID: PMC1781354.
    94. Zhang S, Borovok I, Aharonowitz Y, Sharan R, Bafna V. A sequence-based filtering method for ncRNA identification and its application to searching for riboswitch elements. Bioinformatics. 2006 Jul 15; 22(14):e557-65. PMID: 16873520.
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    95. Bafna V, Tang H, Zhang S. Consensus folding of unaligned RNA sequences revisited. J Comput Biol. 2006 Mar; 13(2):283-95. PMID: 16597240.
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    96. Bafna V, Bansal V. Inference about recombination from haplotype data: lower bounds and recombination hotspots. J Comput Biol. 2006 Mar; 13(2):501-21. PMID: 16597254.
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    97. Tanner S, Pevzner PA, Bafna V. Unrestrictive identification of post-translational modifications through peptide mass spectrometry. Nat Protoc. 2006; 1(1):67-72. PMID: 17406213.
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    98. Tsur D, Tanner S, Zandi E, Bafna V, Pevzner PA. Identification of post-translational modifications by blind search of mass spectra. Nat Biotechnol. 2005 Dec; 23(12):1562-7. PMID: 16311586.
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    99. Zhang S, Haas B, Eskin E, Bafna V. Searching genomes for noncoding RNA using FastR. IEEE/ACM Trans Comput Biol Bioinform. 2005 Oct-Dec; 2(4):366-79. PMID: 17044173.
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    100. Tanner S, Shu H, Frank A, Wang LC, Zandi E, Mumby M, Pevzner PA, Bafna V. InsPecT: identification of posttranslationally modified peptides from tandem mass spectra. Anal Chem. 2005 Jul 15; 77(14):4626-39. PMID: 16013882.
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    101. Frank A, Tanner S, Bafna V, Pevzner P. Peptide sequence tags for fast database search in mass-spectrometry. J Proteome Res. 2005 Jul-Aug; 4(4):1287-95. PMID: 16083278.
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    102. Bashir A, Ye C, Price AL, Bafna V. Orthologous repeats and mammalian phylogenetic inference. Genome Res. 2005 Jul; 15(7):998-1006. PMID: 15998912; PMCID: PMC1172044.
    103. Tsur D, Tanner S, Zandi E, Bafna V, Pevzner PA. Identification of post-translational modifications via blind search of mass-spectra. Proc IEEE Comput Syst Bioinform Conf. 2005; 157-66. PMID: 16447973.
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    104. Bandeira N, Tang H, Bafna V, Pevzner P. Shotgun protein sequencing by tandem mass spectra assembly. Anal Chem. 2004 Dec 15; 76(24):7221-33. PMID: 15595863.
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    105. Halldórsson BV, Bafna V, Lippert R, Schwartz R, De La Vega FM, Clark AG, Istrail S. Optimal haplotype block-free selection of tagging SNPs for genome-wide association studies. Genome Res. 2004 Aug; 14(8):1633-40. PMID: 15289481; PMCID: PMC509273.
    106. Bafna V, Bansal V. The number of recombination events in a sample history: conflict graph and lower bounds. IEEE/ACM Trans Comput Biol Bioinform. 2004 Apr-Jun; 1(2):78-90. PMID: 17048383.
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    107. Bafna V, Gusfield D, Hannenhalli S, Yooseph S. A note on efficient computation of haplotypes via perfect phylogeny. J Comput Biol. 2004; 11(5):858-66. PMID: 15700406.
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    108. Bafna V, Zhang S. FastR: fast database search tool for non-coding RNA. Proc IEEE Comput Syst Bioinform Conf. 2004; 52-61. PMID: 16447999.
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    109. Kirkness EF, Bafna V, Halpern AL, Levy S, Remington K, Rusch DB, Delcher AL, Pop M, Wang W, Fraser CM, Venter JC. The dog genome: survey sequencing and comparative analysis. Science. 2003 Sep 26; 301(5641):1898-903. PMID: 14512627.
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    110. Bafna V, Gusfield D, Lancia G, Yooseph S. Haplotyping as perfect phylogeny: a direct approach. J Comput Biol. 2003; 10(3-4):323-40. PMID: 12935331.
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    111. Schwartz R, Halldórsson BV, Bafna V, Clark AG, Istrail S. Robustness of inference of haplotype block structure. J Comput Biol. 2003; 10(1):13-9. PMID: 12676048.
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