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Vineet Bafna

Title(s)Professor, Computer Science and Engineering
SchoolVc-academic Affairs
Address9500 Gilman Drive #
La Jolla CA 92093
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    Collapse Research 
    Collapse Research Activities and Funding
    Refining Mendelian disease analysis via detection of clinically relevant repeat variants
    NIH/NHGRI R01HG010149Sep 14, 2018 - Jun 30, 2022
    Role: Co-Principal Investigator
    Computational methods for detecting patterns of complex genomic variation
    NIH/NIGMS R01GM114362Jan 1, 2016 - Dec 31, 2023
    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. to make corrections and additions.
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    Altmetrics Details PMC Citations indicate the number of times the publication was cited by articles in PubMed Central, and the Altmetric score represents citations in news articles and social media. (Note that publications are often cited in additional ways that are not shown here.) Fields are based on how the National Library of Medicine (NLM) classifies the publication's journal and might not represent the specific topic of the publication. Translation tags are based on the publication type and the MeSH terms NLM assigns to the publication. Some publications (especially newer ones and publications not in PubMed) might not yet be assigned Field or Translation tags.) Click a Field or Translation tag to filter the publications.
    1. AmpliconReconstructor integrates NGS and optical mapping to resolve the complex structures of focal amplifications. Nat Commun. 2020 09 01; 11(1):4374. Luebeck J, Coruh C, Dehkordi SR, Lange JT, Turner KM, Deshpande V, Pai DA, Zhang C, Rajkumar U, Law JA, Mischel PS, Bafna V. PMID: 32873787.
      View in: PubMed   Mentions:    Fields:    Translation:HumansCells
    2. Extrachromosomal DNA is associated with oncogene amplification and poor outcome across multiple cancers. Nat Genet. 2020 Aug 17. Kim H, Nguyen NP, Turner K, Wu S, Gujar AD, Luebeck J, Liu J, Deshpande V, Rajkumar U, Namburi S, Amin SB, Yi E, Menghi F, Schulte JH, Henssen AG, Chang HY, Beck CR, Mischel PS, Bafna V, Verhaak RGW. PMID: 32807987.
      View in: PubMed   Mentions: 1     Fields:    
    3. Beyond DNA barcoding: The unrealized potential of genome skim data in sample identification. Mol Ecol. 2020 Jul; 29(14):2521-2534. Bohmann K, Mirarab S, Bafna V, Gilbert MTP. PMID: 32542933.
      View in: PubMed   Mentions: 1     Fields:    
    4. Author Correction: Longitudinal assessment of tumor development using cancer avatars derived from genetically engineered pluripotent stem cells. Nat Commun. 2020 04 20; 11(1):1958. Koga T, Chaim IA, Benitez JA, Markmiller S, Parisian AD, Hevner RF, Turner KM, Hessenauer FM, D'Antonio M, Nguyen ND, Saberi S, Ma J, Miki S, Boyer AD, Ravits J, Frazer KA, Bafna V, Chen CC, Mischel PS, Yeo GW, Furnari FB. PMID: 32312984.
      View in: PubMed   Mentions:    Fields:    
    5. The impact of contaminants on the accuracy of genome skimming and the effectiveness of exclusion read filters. Mol Ecol Resour. 2020 May; 20(3). Rachtman E, Balaban M, Bafna V, Mirarab S. PMID: 31943790.
      View in: PubMed   Mentions: 2     Fields:    
    6. Longitudinal assessment of tumor development using cancer avatars derived from genetically engineered pluripotent stem cells. Nat Commun. 2020 Jan 28; 11(1):550. Koga T, Chaim IA, Benitez JA, Markmiller S, Parisian AD, Hevner RF, Turner KM, Hessenauer FM, D'Antonio M, Nguyen ND, Saberi S, Ma J, Miki S, Boyer AD, Ravits J, Frazer KA, Bafna V, Chen CC, Mischel PS, Yeo GW, Furnari FB. PMID: 31992716.
      View in: PubMed   Mentions: 3     Fields:    Translation:HumansAnimalsCells
    7. Circular ecDNA promotes accessible chromatin and high oncogene expression. Nature. 2019 11; 575(7784):699-703. Wu S, Turner KM, Nguyen N, Raviram R, Erb M, Santini J, Luebeck J, Rajkumar U, Diao Y, Li B, Zhang W, Jameson N, Corces MR, Granja JM, Chen X, Coruh C, Abnousi A, Houston J, Ye Z, Hu R, Yu M, Kim H, Law JA, Verhaak RGW, Hu M, Furnari FB, Chang HY, Ren B, Bafna V, Mischel PS. PMID: 31748743.
      View in: PubMed   Mentions: 11     Fields:    Translation:HumansCells
    8. EcSeg: Semantic Segmentation of Metaphase Images Containing Extrachromosomal DNA. iScience. 2019 Nov 22; 21:428-435. Rajkumar U, Turner K, Luebeck J, Deshpande V, Chandraker M, Mischel P, Bafna V. PMID: 31706138.
      View in: PubMed   Mentions:
    9. Computing the Statistical Significance of Overlap between Genome Annotations with iStat. Cell Syst. 2019 06 26; 8(6):523-529.e4. Sarmashghi S, Bafna V. PMID: 31202632.
      View in: PubMed   Mentions:    Fields:    Translation:Humans
    10. Proteogenomic Annotation of Chinese Hamsters Reveals Extensive Novel Translation Events and Endogenous Retroviral Elements. J Proteome Res. 2019 06 07; 18(6):2433-2445. Li S, Cha SW, Heffner K, Hizal DB, Bowen MA, Chaerkady R, Cole RN, Tejwani V, Kaushik P, Henry M, Meleady P, Sharfstein ST, Betenbaugh MJ, Bafna V, Lewis NE. PMID: 31020842.
      View in: PubMed   Mentions: 2     Fields:    Translation:AnimalsCells
    11. Extrachromosomal oncogene amplification in tumour pathogenesis and evolution. Nat Rev Cancer. 2019 05; 19(5):283-288. Verhaak RGW, Bafna V, Mischel PS. PMID: 30872802.
      View in: PubMed   Mentions: 11     Fields:    Translation:HumansAnimalsCells
    12. NAD metabolic dependency in cancer is shaped by gene amplification and enhancer remodelling. Nature. 2019 05; 569(7757):570-575. Chowdhry S, Zanca C, Rajkumar U, Koga T, Diao Y, Raviram R, Liu F, Turner K, Yang H, Brunk E, Bi J, Furnari F, Bafna V, Ren B, Mischel PS. PMID: 31019297.
      View in: PubMed   Mentions: 17     Fields:    Translation:HumansAnimalsCells
    13. Skmer: assembly-free and alignment-free sample identification using genome skims. Genome Biol. 2019 02 13; 20(1):34. Sarmashghi S, Bohmann K, P Gilbert MT, Bafna V, Mirarab S. PMID: 30760303.
      View in: PubMed   Mentions: 4     Fields:    Translation:Animals
    14. Exploring the landscape of focal amplifications in cancer using AmpliconArchitect. Nat Commun. 2019 01 23; 10(1):392. Deshpande V, Luebeck J, Nguyen ND, Bakhtiari M, Turner KM, Schwab R, Carter H, Mischel PS, Bafna V. PMID: 30674876.
      View in: PubMed   Mentions: 7     Fields:    Translation:HumansCells
    15. Targeted genotyping of variable number tandem repeats with adVNTR. Genome Res. 2018 11; 28(11):1709-1719. Bakhtiari M, Shleizer-Burko S, Gymrek M, Bansal V, Bafna V. PMID: 30352806.
      View in: PubMed   Mentions: 3     Fields:    Translation:HumansCells
    16. ProteoStorm: An Ultrafast Metaproteomics Database Search Framework. Cell Syst. 2018 10 24; 7(4):463-467.e6. Beyter D, Lin MS, Yu Y, Pieper R, Bafna V. PMID: 30268435.
      View in: PubMed   Mentions: 1     Fields:    Translation:Humans
    17. Novel insight into the genetic basis of high-altitude pulmonary hypertension in Kyrgyz highlanders. Eur J Hum Genet. 2019 01; 27(1):150-159. Iranmehr A, Stobdan T, Zhou D, Poulsen O, Strohl KP, Aldashev A, Telenti A, Wong EHM, Kirkness EF, Venter JC, Bafna V, Haddad GG. PMID: 30254217.
      View in: PubMed   Mentions: 1     Fields:    Translation:Humans
    18. 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 04 20; 46(7):3309-3325. Nguyen ND, Deshpande V, Luebeck J, Mischel PS, Bafna V. PMID: 29579309.
      View in: PubMed   Mentions: 1     Fields:    Translation:HumansCells
    19. Identifying the favored mutation in a positive selective sweep. Nat Methods. 2018 04; 15(4):279-282. Akbari A, Vitti JJ, Iranmehr A, Bakhtiari M, Sabeti PC, Mirarab S, Bafna V. PMID: 29457793.
      View in: PubMed   Mentions: 4     Fields:    Translation:HumansCells
    20. MHC class I loaded ligands from breast cancer cell lines: A potential HLA-I-typed antigen collection. J Proteomics. 2018 03 30; 176:13-23. 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. PMID: 29331515.
      View in: PubMed   Mentions: 5     Fields:    Translation:HumansCells
    21. 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. 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. PMID: 29029226.
      View in: PubMed   Mentions: 5     Fields:    Translation:HumansAnimals
    22. Ultraaccurate genome sequencing and haplotyping of single human cells. Proc Natl Acad Sci U S A. 2017 11 21; 114(47):12512-12517. Chu WK, Edge P, Lee HS, Bansal V, Bafna V, Huang X, Zhang K. PMID: 29078313.
      View in: PubMed   Mentions: 10     Fields:    Translation:HumansCells
    23. The Antibody Repertoire of Colorectal Cancer. Mol Cell Proteomics. 2017 Dec; 16(12):2111-2124. Cha SW, Bonissone S, Na S, Pevzner PA, Bafna V. PMID: 29046389.
      View in: PubMed   Mentions: 1     Fields:    Translation:HumansCells
    24. High-altitude adaptation in humans: from genomics to integrative physiology. J Mol Med (Berl). 2017 Dec; 95(12):1269-1282. Azad P, Stobdan T, Zhou D, Hartley I, Akbari A, Bafna V, Haddad GG. PMID: 28951950.
      View in: PubMed   Mentions: 8     Fields:    Translation:Humans
    25. Clear: Composition of Likelihoods for Evolve and Resequence Experiments. Genetics. 2017 06; 206(2):1011-1023. Iranmehr A, Akbari A, Schlötterer C, Bafna V. PMID: 28396506.
      View in: PubMed   Mentions: 5     Fields:    Translation:Animals
    26. Extrachromosomal oncogene amplification drives tumour evolution and genetic heterogeneity. Nature. 2017 03 02; 543(7643):122-125. 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. PMID: 28178237.
      View in: PubMed   Mentions: 72     Fields:    Translation:HumansCells
    27. HapCUT2: robust and accurate haplotype assembly for diverse sequencing technologies. Genome Res. 2017 05; 27(5):801-812. Edge P, Bafna V, Bansal V. PMID: 27940952.
      View in: PubMed   Mentions: 32     Fields:    Translation:Humans
    28. Correction: Predicting Carriers of Ongoing Selective Sweeps without Knowledge of the Favored Allele. PLoS Genet. 2016 Nov; 12(11):e1006472. Ronen R, Tesler G, Akbari A, Zakov S, Rosenberg NA, Bafna V. PMID: 27902698.
      View in: PubMed   Mentions:    Fields:    
    29. Senp1 drives hypoxia-induced polycythemia via GATA1 and Bcl-xL in subjects with Monge's disease. J Exp Med. 2016 11 14; 213(12):2729-2744. Azad P, Zhao HW, Cabrales PJ, Ronen R, Zhou D, Poulsen O, Appenzeller O, Hsiao YH, Bafna V, Haddad GG. PMID: 27821551.
      View in: PubMed   Mentions: 5     Fields:    Translation:HumansCells
    30. Integrated Proteogenomic Characterization of Human High-Grade Serous Ovarian Cancer. Cell. 2016 Jul 28; 166(3):755-765. 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. PMID: 27372738.
      View in: PubMed   Mentions: 177     Fields:    Translation:HumansCells
    31. InPhaDel: integrative shotgun and proximity-ligation sequencing to phase deletions with single nucleotide polymorphisms. Nucleic Acids Res. 2016 07 08; 44(12):e111. Patel A, Edge P, Selvaraj S, Bansal V, Bafna V. PMID: 27105843.
      View in: PubMed   Mentions: 1     Fields:    Translation:Humans
    32. Diversity, Productivity, and Stability of an Industrial Microbial Ecosystem. Appl Environ Microbiol. 2016 Apr; 82(8):2494-2505. Beyter D, Tang PZ, Becker S, Hoang T, Bilgin D, Lim YW, Peterson TC, Mayfield S, Haerizadeh F, Shurin JB, Bafna V, McBride R. PMID: 26896141.
      View in: PubMed   Mentions: 5     Fields:    Translation:AnimalsCellsPHPublic Health
    33. The TGFß1 Promoter SNP C-509T and Food Sensitization Promote Esophageal Remodeling in Pediatric Eosinophilic Esophagitis. PLoS One. 2015; 10(12):e0144651. Rawson R, Anilkumar A, Newbury RO, Bafna V, Aquino M, Palmquist J, Hoffman HM, Mueller JL, Dohil R, Broide DH, Aceves SS. PMID: 26656423.
      View in: PubMed   Mentions: 10     Fields:    Translation:HumansCells
    34. Predicting Carriers of Ongoing Selective Sweeps without Knowledge of the Favored Allele. PLoS Genet. 2015 Sep; 11(9):e1005527. Ronen R, Tesler G, Akbari A, Zakov S, Rosenberg NA, Bafna V. PMID: 26402243.
      View in: PubMed   Mentions: 5     Fields:    Translation:Humans
    35. 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. 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. PMID: 26719854.
      View in: PubMed   Mentions: 11     Fields:    
    36. 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. Stobdan T, Zhou D, Ao-Ieong E, Ortiz D, Ronen R, Hartley I, Gan Z, McCulloch AD, Bafna V, Cabrales P, Haddad GG. PMID: 26240367.
      View in: PubMed   Mentions: 16     Fields:    Translation:HumansAnimals
    37. Advanced Proteogenomic Analysis Reveals Multiple Peptide Mutations and Complex Immunoglobulin Peptides in Colon Cancer. J Proteome Res. 2015 Sep 04; 14(9):3555-67. Woo S, Cha SW, Bonissone S, Na S, Tabb DL, Pevzner PA, Bafna V. PMID: 26139413.
      View in: PubMed   Mentions: 10     Fields:    Translation:HumansCells
    38. Reconstructing breakage fusion bridge architectures using noisy copy numbers. J Comput Biol. 2015 Jun; 22(6):577-94. Zakov S, Bafna V. PMID: 26020441.
      View in: PubMed   Mentions: 2     Fields:    Translation:HumansCells
    39. Proteogenomic strategies for identification of aberrant cancer peptides using large-scale next-generation sequencing data. Proteomics. 2014 Dec; 14(23-24):2719-30. Woo S, Cha SW, Na S, Guest C, Liu T, Smith RD, Rodland KD, Payne S, Bafna V. PMID: 25263569.
      View in: PubMed   Mentions: 22     Fields:    Translation:Humans
    40. Genetic simulation tools for post-genome wide association studies of complex diseases. Genet Epidemiol. 2015 Jan; 39(1):11-19. 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. PMID: 25371374.
      View in: PubMed   Mentions: 9     Fields:    Translation:Humans
    41. The genetic basis of chronic mountain sickness. Physiology (Bethesda). 2014 Nov; 29(6):403-12. Ronen R, Zhou D, Bafna V, Haddad GG. PMID: 25362634.
      View in: PubMed   Mentions: 12     Fields:    Translation:Humans
    42. Annotation of the zebrafish genome through an integrated transcriptomic and proteomic analysis. Mol Cell Proteomics. 2014 Nov; 13(11):3184-98. 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. PMID: 25060758.
      View in: PubMed   Mentions: 13     Fields:    Translation:AnimalsCells
    43. The elusive evidence for chromothripsis. Nucleic Acids Res. 2014 Jul; 42(13):8231-42. Kinsella M, Patel A, Bafna V. PMID: 24939897.
      View in: PubMed   Mentions: 13     Fields:    
    44. Inferring gene ontologies from pairwise similarity data. Bioinformatics. 2014 Jun 15; 30(12):i34-42. Kramer M, Dutkowski J, Yu M, Bafna V, Ideker T. PMID: 24932003.
      View in: PubMed   Mentions: 20     Fields:    Translation:Animals
    45. Whole genome sequencing of Ethiopian highlanders reveals conserved hypoxia tolerance genes. Genome Biol. 2014 Feb 20; 15(2):R36. 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. PMID: 24555826.
      View in: PubMed   Mentions: 31     Fields:    Translation:HumansAnimalsCells
    46. Amplification and thrifty single-molecule sequencing of recurrent somatic structural variations. Genome Res. 2014 Feb; 24(2):318-28. Patel A, Schwab R, Liu YT, Bafna V. PMID: 24307551.
      View in: PubMed   Mentions: 8     Fields:    Translation:HumansCells
    47. An automated proteogenomic method uses mass spectrometry to reveal novel genes in Zea mays. Mol Cell Proteomics. 2014 Jan; 13(1):157-67. Castellana NE, Shen Z, He Y, Walley JW, Cassidy CJ, Briggs SP, Bafna V. PMID: 24142994.
      View in: PubMed   Mentions: 20     Fields:    Translation:HumansAnimals
    48. Virmid: accurate detection of somatic mutations with sample impurity inference. Genome Biol. 2013 Aug 29; 14(8):R90. Kim S, Jeong K, Bhutani K, Lee J, Patel A, Scott E, Nam H, Lee H, Gleeson JG, Bafna V. PMID: 23987214.
      View in: PubMed   Mentions: 25     Fields:    Translation:Humans
    49. 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. 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. PMID: 23954164.
      View in: PubMed   Mentions: 36     Fields:    Translation:HumansAnimalsCells
    50. Proteogenomic database construction driven from large scale RNA-seq data. J Proteome Res. 2014 Jan 03; 13(1):21-8. Woo S, Cha SW, Merrihew G, He Y, Castellana N, Guest C, MacCoss M, Bafna V. PMID: 23802565.
      View in: PubMed   Mentions: 35     Fields:    Translation:AnimalsCells
    51. Learning natural selection from the site frequency spectrum. Genetics. 2013 Sep; 195(1):181-93. Ronen R, Udpa N, Halperin E, Bafna V. PMID: 23770700.
      View in: PubMed   Mentions: 24     Fields:    Translation:HumansAnimals
    52. Using Genome Query Language to uncover genetic variation. Bioinformatics. 2014 Jan 01; 30(1):1-8. Kozanitis C, Heiberg A, Varghese G, Bafna V. PMID: 23751181.
      View in: PubMed   Mentions: 6     Fields:    Translation:Humans
    53. Reprever: resolving low-copy duplicated sequences using template driven assembly. Nucleic Acids Res. 2013 Jul; 41(12):e128. Kim S, Medvedev P, Paton TA, Bafna V. PMID: 23658221.
      View in: PubMed   Mentions: 3     Fields:    Translation:Humans
    54. Evaluating genome architecture of a complex region via generalized bipartite matching. BMC Bioinformatics. 2013; 14 Suppl 5:S13. Lo C, Kim S, Zakov S, Bafna V. PMID: 23734567.
      View in: PubMed   Mentions:    Fields:    Translation:Humans
    55. 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. Zakov S, Kinsella M, Bafna V. PMID: 23503850.
      View in: PubMed   Mentions: 13     Fields:    
    56. Wessim: a whole-exome sequencing simulator based on in silico exome capture. Bioinformatics. 2013 Apr 15; 29(8):1076-7. Kim S, Jeong K, Bafna V. PMID: 23413434.
      View in: PubMed   Mentions: 12     Fields:    Translation:Humans
    57. On the design of clone-based haplotyping. Genome Biol. 2013; 14(9):R100. Lo C, Liu R, Lee J, Robasky K, Byrne S, Lucchesi C, Aach J, Church G, Bafna V, Zhang K. PMID: 24028704.
      View in: PubMed   Mentions: 10     Fields:    Translation:HumansCells
    58. Abstractions for Genomics. Commun ACM. 2013 Jan; 56(1):83-93. Bafna V, Kozanitis C, Deutsch A, Ohno-Machado L, Heiberg A, Varghese G. PMID: 25284821.
      View in: PubMed   Mentions:
    59. De novo somatic mutations in components of the PI3K-AKT3-mTOR pathway cause hemimegalencephaly. Nat Genet. 2012 Jun 24; 44(8):941-5. 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. PMID: 22729223.
      View in: PubMed   Mentions: 185     Fields:    Translation:HumansCells
    60. Exome sequencing can improve diagnosis and alter patient management. Sci Transl Med. 2012 Jun 13; 4(138):138ra78. 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. PMID: 22700954.
      View in: PubMed   Mentions: 102     Fields:    Translation:Humans
    61. Speeding up tandem mass spectral identification using indexes. Bioinformatics. 2012 Jul 01; 28(13):1692-7. Liu X, Mammana A, Bafna V. PMID: 22543365.
      View in: PubMed   Mentions: 6     Fields:    Translation:HumansCells
    62. Combinatorics of the breakage-fusion-bridge mechanism. J Comput Biol. 2012 Jun; 19(6):662-78. Kinsella M, Bafna V. PMID: 22506505.
      View in: PubMed   Mentions: 6     Fields:    Translation:Humans
    63. Accurate mass spectrometry based protein quantification via shared peptides. J Comput Biol. 2012 Apr; 19(4):337-48. Dost B, Bandeira N, Li X, Shen Z, Briggs SP, Bafna V. PMID: 22414154.
      View in: PubMed   Mentions: 16     Fields:    Translation:AnimalsCells
    64. 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. Abad-Grau MM, Medina-Medina N, Montes-Soldado R, Matesanz F, Bafna V. PMID: 22363405.
      View in: PubMed   Mentions: 2     Fields:    Translation:Humans
    65. Global DNA hypomethylation coupled to repressive chromatin domain formation and gene silencing in breast cancer. Genome Res. 2012 Feb; 22(2):246-58. 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. PMID: 22156296.
      View in: PubMed   Mentions: 191     Fields:    Translation:HumansCells
    66. Tests of selection in pooled case-control data: an empirical study. Front Genet. 2011; 2:83. Udpa N, Zhou D, Haddad GG, Bafna V. PMID: 22303377.
      View in: PubMed   Mentions:
    67. iDASH: integrating data for analysis, anonymization, and sharing. J Am Med Inform Assoc. 2012 Mar-Apr; 19(2):196-201. 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. PMID: 22081224.
      View in: PubMed   Mentions: 59     Fields:    
    68. Protein identification using top-down. Mol Cell Proteomics. 2012 Jun; 11(6):M111.008524. Liu X, Sirotkin Y, Shen Y, Anderson G, Tsai YS, Ting YS, Goodlett DR, Smith RD, Bafna V, Pevzner PA. PMID: 22027200.
      View in: PubMed   Mentions: 54     Fields:    Translation:AnimalsCells
    69. AMASS: algorithm for MSI analysis by semi-supervised segmentation. J Proteome Res. 2011 Oct 07; 10(10):4734-43. Bruand J, Alexandrov T, Sistla S, Wisztorski M, Meriaux C, Becker M, Salzet M, Fournier I, Macagno E, Bafna V. PMID: 21800894.
      View in: PubMed   Mentions: 12     Fields:    Translation:Animals
    70. TCLUST: a fast method for clustering genome-scale expression data. IEEE/ACM Trans Comput Biol Bioinform. 2011 May-Jun; 8(3):808-18. Dost B, Wu C, Su A, Bafna V. PMID: 20479508.
      View in: PubMed   Mentions: 1     Fields:    Translation:Animals
    71. Automated querying and identification of novel peptides using MALDI mass spectrometric imaging. J Proteome Res. 2011 Apr 01; 10(4):1915-28. Bruand J, Sistla S, Mériaux C, Dorrestein PC, Gaasterland T, Ghassemian M, Wisztorski M, Fournier I, Salzet M, Macagno E, Bafna V. PMID: 21332220.
      View in: PubMed   Mentions: 10     Fields:    Translation:AnimalsCells
    72. Compressing genomic sequence fragments using SlimGene. J Comput Biol. 2011 Mar; 18(3):401-13. Kozanitis C, Saunders C, Kruglyak S, Bafna V, Varghese G. PMID: 21385043.
      View in: PubMed   Mentions: 34     Fields:    Translation:Humans
    73. Sensitive gene fusion detection using ambiguously mapping RNA-Seq read pairs. Bioinformatics. 2011 Apr 15; 27(8):1068-75. Kinsella M, Harismendy O, Nakano M, Frazer KA, Bafna V. PMID: 21330288.
      View in: PubMed   Mentions: 26     Fields:    Translation:HumansCells
    74. Strobe sequence design for haplotype assembly. BMC Bioinformatics. 2011 Feb 15; 12 Suppl 1:S24. Lo C, Bashir A, Bansal V, Bafna V. PMID: 21342554.
      View in: PubMed   Mentions: 9     Fields:    Translation:Humans
    75. Experimental selection of hypoxia-tolerant Drosophila melanogaster. Proc Natl Acad Sci U S A. 2011 Feb 08; 108(6):2349-54. Zhou D, Udpa N, Gersten M, Visk DW, Bashir A, Xue J, Frazer KA, Posakony JW, Subramaniam S, Bafna V, Haddad GG. PMID: 21262834.
      View in: PubMed   Mentions: 56     Fields:    Translation:AnimalsCells
    76. 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. Castellana NE, McCutcheon K, Pham VC, Harden K, Nguyen A, Young J, Adams C, Schroeder K, Arnott D, Bafna V, Grogan JL, Lill JR. PMID: 21268269.
      View in: PubMed   Mentions: 12     Fields:    Translation:AnimalsCells
    77. Practical 4'-phosphopantetheine active site discovery from proteomic samples. J Proteome Res. 2011 Jan 07; 10(1):320-9. Meier JL, Patel AD, Niessen S, Meehan M, Kersten R, Yang JY, Rothmann M, Cravatt BF, Dorrestein PC, Burkart MD, Bafna V. PMID: 21067235.
      View in: PubMed   Mentions: 6     Fields:    Translation:Cells
    78. 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. 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. PMID: 21118518.
      View in: PubMed   Mentions: 12     Fields:    Translation:HumansCells
    79. A covering method for detecting genetic associations between rare variants and common phenotypes. PLoS Comput Biol. 2010 Oct 14; 6(10):e1000954. Bhatia G, Bansal V, Harismendy O, Schork NJ, Topol EJ, Frazer K, Bafna V. PMID: 20976246.
      View in: PubMed   Mentions: 49     Fields:    
    80. RAPID detection of gene-gene interactions in genome-wide association studies. Bioinformatics. 2010 Nov 15; 26(22):2856-62. Brinza D, Schultz M, Tesler G, Bafna V. PMID: 20871107.
      View in: PubMed   Mentions: 11     Fields:    
    81. Deconvolution and database search of complex tandem mass spectra of intact proteins: a combinatorial approach. Mol Cell Proteomics. 2010 Dec; 9(12):2772-82. Liu X, Inbar Y, Dorrestein PC, Wynne C, Edwards N, Souda P, Whitelegge JP, Bafna V, Pevzner PA. PMID: 20855543.
      View in: PubMed   Mentions: 53     Fields:    Translation:Cells
    82. Proteogenomics to discover the full coding content of genomes: a computational perspective. J Proteomics. 2010 Oct 10; 73(11):2124-35. Castellana N, Bafna V. PMID: 20620248.
      View in: PubMed   Mentions: 55     Fields:    Translation:HumansAnimals
    83. 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. Macagno ER, Gaasterland T, Edsall L, Bafna V, Soares MB, Scheetz T, Casavant T, Da Silva C, Wincker P, Tasiemski A, Salzet M. PMID: 20579359.
      View in: PubMed   Mentions: 22     Fields:    Translation:HumansAnimals
    84. Designing deep sequencing experiments: detecting structural variation and estimating transcript abundance. BMC Genomics. 2010 Jun 18; 11:385. Bashir A, Bansal V, Bafna V. PMID: 20565853.
      View in: PubMed   Mentions: 12     Fields:    Translation:Humans
    85. Protein-protein interaction network evaluation for identifying potential drug targets. J Comput Biol. 2010 May; 17(5):669-84. Hormozdiari F, Salari R, Bafna V, Sahinalp SC. PMID: 20500021.
      View in: PubMed   Mentions: 9     Fields:    Translation:HumansCells
    86. Optimizing PCR assays for DNA-based cancer diagnostics. J Comput Biol. 2010 Mar; 17(3):369-81. Bashir A, Lu Q, Carson D, Raphael BJ, Liu YT, Bafna V. PMID: 20377451.
      View in: PubMed   Mentions: 3     Fields:    Translation:HumansCells
    87. Template proteogenomics: sequencing whole proteins using an imperfect database. Mol Cell Proteomics. 2010 Jun; 9(6):1260-70. Castellana NE, Pham V, Arnott D, Lill JR, Bafna V. PMID: 20164058.
      View in: PubMed   Mentions: 16     Fields:    Translation:AnimalsCells
    88. Expansion of the mycobacterial "PUPylome". Mol Biosyst. 2010 Feb; 6(2):376-85. Watrous J, Burns K, Liu WT, Patel A, Hook V, Bafna V, Barry CE, Bark S, Dorrestein PC. PMID: 20094657.
      View in: PubMed   Mentions: 34     Fields:    Translation:Cells
    89. Fast and accurate alignment of multiple protein networks. J Comput Biol. 2009 Aug; 16(8):989-99. Kalaev M, Bafna V, Sharan R. PMID: 19624266.
      View in: PubMed   Mentions: 16     Fields:    Translation:Animals
    90. 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. 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. PMID: 19546169.
      View in: PubMed   Mentions: 235     Fields:    Translation:HumansCells
    91. Discovery and revision of Arabidopsis genes by proteogenomics. Proc Natl Acad Sci U S A. 2008 Dec 30; 105(52):21034-8. Castellana NE, Payne SH, Shen Z, Stanke M, Bafna V, Briggs SP. PMID: 19098097.
      View in: PubMed   Mentions: 108     Fields:    Translation:Animals
    92. QNet: a tool for querying protein interaction networks. J Comput Biol. 2008 Sep; 15(7):913-25. Dost B, Shlomi T, Gupta N, Ruppin E, Bafna V, Sharan R. PMID: 18707533.
      View in: PubMed   Mentions: 22     Fields:    Translation:HumansAnimalsCells
    93. HapCUT: an efficient and accurate algorithm for the haplotype assembly problem. Bioinformatics. 2008 Aug 15; 24(16):i153-9. Bansal V, Bafna V. PMID: 18689818.
      View in: PubMed   Mentions: 78     Fields:    Translation:Cells
    94. An MCMC algorithm for haplotype assembly from whole-genome sequence data. Genome Res. 2008 Aug; 18(8):1336-46. Bansal V, Halpern AL, Axelrod N, Bafna V. PMID: 18676820.
      View in: PubMed   Mentions: 40     Fields:    Translation:Humans
    95. Phosphorylation-specific MS/MS scoring for rapid and accurate phosphoproteome analysis. J Proteome Res. 2008 Aug; 7(8):3373-81. Payne SH, Yau M, Smolka MB, Tanner S, Zhou H, Bafna V. PMID: 18563926.
      View in: PubMed   Mentions: 31     Fields:    Translation:AnimalsCells
    96. Structural alignment of pseudoknotted RNA. J Comput Biol. 2008 Jun; 15(5):489-504. Han B, Dost B, Bafna V, Zhang S. PMID: 18549303.
      View in: PubMed   Mentions: 2     Fields:    Translation:Cells
    97. Evaluation of paired-end sequencing strategies for detection of genome rearrangements in cancer. PLoS Comput Biol. 2008 Apr 25; 4(4):e1000051. Bashir A, Volik S, Collins C, Bafna V, Raphael BJ. PMID: 18404202.
      View in: PubMed   Mentions: 37     Fields:    Translation:HumansCells
    98. Comparative proteogenomics: combining mass spectrometry and comparative genomics to analyze multiple genomes. Genome Res. 2008 Jul; 18(7):1133-42. 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. PMID: 18426904.
      View in: PubMed   Mentions: 44     Fields:    Translation:Cells
    99. A multidimensional chromatography technology for in-depth phosphoproteome analysis. Mol Cell Proteomics. 2008 Jul; 7(7):1389-96. Albuquerque CP, Smolka MB, Payne SH, Bafna V, Eng J, Zhou H. PMID: 18407956.
      View in: PubMed   Mentions: 213     Fields:    Translation:AnimalsCells
    100. A decomposition theory for phylogenetic networks and incompatible characters. J Comput Biol. 2007 Dec; 14(10):1247-72. Gusfield D, Bansal V, Bafna V, Song YS. PMID: 18047426.
      View in: PubMed   Mentions: 9     Fields:    
    101. Accurate annotation of peptide modifications through unrestrictive database search. J Proteome Res. 2008 Jan; 7(1):170-81. Tanner S, Payne SH, Dasari S, Shen Z, Wilmarth PA, David LL, Loomis WF, Briggs SP, Bafna V. PMID: 18034453.
      View in: PubMed   Mentions: 20     Fields:    Translation:Cells
    102. The diploid genome sequence of an individual human. PLoS Biol. 2007 Sep 04; 5(10):e254. 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. PMID: 17803354.
      View in: PubMed   Mentions: 687     Fields:    Translation:HumansCells
    103. Optimization of primer design for the detection of variable genomic lesions in cancer. Bioinformatics. 2007 Nov 01; 23(21):2807-15. Bashir A, Liu YT, Raphael BJ, Carson D, Bafna V. PMID: 17766270.
      View in: PubMed   Mentions: 6     Fields:    Translation:Humans
    104. Whole proteome analysis of post-translational modifications: applications of mass-spectrometry for proteogenomic annotation. Genome Res. 2007 Sep; 17(9):1362-77. Gupta N, Tanner S, Jaitly N, Adkins JN, Lipton M, Edwards R, Romine M, Osterman A, Bafna V, Smith RD, Pevzner PA. PMID: 17690205.
      View in: PubMed   Mentions: 81     Fields:    Translation:Cells
    105. Integrating scientific cultures. Mol Syst Biol. 2007; 3:105. Ideker T, Bafna V, Lemberger T. PMID: 17437030.
      View in: PubMed   Mentions: 4     Fields:    Translation:Humans
    106. The Sorcerer II Global Ocean Sampling expedition: expanding the universe of protein families. PLoS Biol. 2007 Mar; 5(3):e16. 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. PMID: 17355171.
      View in: PubMed   Mentions: 297     Fields:    Translation:PHPublic Health
    107. Improving gene annotation using peptide mass spectrometry. Genome Res. 2007 Feb; 17(2):231-9. Tanner S, Shen Z, Ng J, Florea L, Guigó R, Briggs SP, Bafna V. PMID: 17189379.
      View in: PubMed   Mentions: 83     Fields:    Translation:HumansCells
    108. Evidence for large inversion polymorphisms in the human genome from HapMap data. Genome Res. 2007 Feb; 17(2):219-30. Bansal V, Bashir A, Bafna V. PMID: 17185644.
      View in: PubMed   Mentions: 31     Fields:    Translation:Humans
    109. Age-related changes in human crystallins determined from comparative analysis of post-translational modifications in young and aged lens: does deamidation contribute to crystallin insolubility? J Proteome Res. 2006 Oct; 5(10):2554-66. Wilmarth PA, Tanner S, Dasari S, Nagalla SR, Riviere MA, Bafna V, Pevzner PA, David LL. PMID: 17022627.
      View in: PubMed   Mentions: 102     Fields:    Translation:HumansCells
    110. A sequence-based filtering method for ncRNA identification and its application to searching for riboswitch elements. Bioinformatics. 2006 Jul 15; 22(14):e557-65. Zhang S, Borovok I, Aharonowitz Y, Sharan R, Bafna V. PMID: 16873520.
      View in: PubMed   Mentions: 8     Fields:    Translation:Cells
    111. Consensus folding of unaligned RNA sequences revisited. J Comput Biol. 2006 Mar; 13(2):283-95. Bafna V, Tang H, Zhang S. PMID: 16597240.
      View in: PubMed   Mentions: 11     Fields:    Translation:Cells
    112. Inference about recombination from haplotype data: lower bounds and recombination hotspots. J Comput Biol. 2006 Mar; 13(2):501-21. Bafna V, Bansal V. PMID: 16597254.
      View in: PubMed   Mentions: 3     Fields:    Translation:HumansCells
    113. Unrestrictive identification of post-translational modifications through peptide mass spectrometry. Nat Protoc. 2006; 1(1):67-72. Tanner S, Pevzner PA, Bafna V. PMID: 17406213.
      View in: PubMed   Mentions: 15     Fields:    Translation:Cells
    114. Identification of post-translational modifications by blind search of mass spectra. Nat Biotechnol. 2005 Dec; 23(12):1562-7. Tsur D, Tanner S, Zandi E, Bafna V, Pevzner PA. PMID: 16311586.
      View in: PubMed   Mentions: 86     Fields:    Translation:Cells
    115. Searching genomes for noncoding RNA using FastR. IEEE/ACM Trans Comput Biol Bioinform. 2005 Oct-Dec; 2(4):366-79. Zhang S, Haas B, Eskin E, Bafna V. PMID: 17044173.
      View in: PubMed   Mentions: 14     Fields:    Translation:AnimalsCells
    116. InsPecT: identification of posttranslationally modified peptides from tandem mass spectra. Anal Chem. 2005 Jul 15; 77(14):4626-39. Tanner S, Shu H, Frank A, Wang LC, Zandi E, Mumby M, Pevzner PA, Bafna V. PMID: 16013882.
      View in: PubMed   Mentions: 237     Fields:    Translation:Cells
    117. Peptide sequence tags for fast database search in mass-spectrometry. J Proteome Res. 2005 Jul-Aug; 4(4):1287-95. Frank A, Tanner S, Bafna V, Pevzner P. PMID: 16083278.
      View in: PubMed   Mentions: 44     Fields:    Translation:Cells
    118. Orthologous repeats and mammalian phylogenetic inference. Genome Res. 2005 Jul; 15(7):998-1006. Bashir A, Ye C, Price AL, Bafna V. PMID: 15998912.
      View in: PubMed   Mentions: 10     Fields:    Translation:HumansAnimalsCells
    119. Identification of post-translational modifications via blind search of mass-spectra. Proc IEEE Comput Syst Bioinform Conf. 2005; 157-66. Tsur D, Tanner S, Zandi E, Bafna V, Pevzner PA. PMID: 16447973.
      View in: PubMed   Mentions: 7     Fields:    Translation:Cells
    120. Shotgun protein sequencing by tandem mass spectra assembly. Anal Chem. 2004 Dec 15; 76(24):7221-33. Bandeira N, Tang H, Bafna V, Pevzner P. PMID: 15595863.
      View in: PubMed   Mentions: 16     Fields:    Translation:Cells
    121. Optimal haplotype block-free selection of tagging SNPs for genome-wide association studies. Genome Res. 2004 Aug; 14(8):1633-40. Halldórsson BV, Bafna V, Lippert R, Schwartz R, De La Vega FM, Clark AG, Istrail S. PMID: 15289481.
      View in: PubMed   Mentions: 22     Fields:    Translation:HumansCells
    122. 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. Bafna V, Bansal V. PMID: 17048383.
      View in: PubMed   Mentions: 3     Fields:    Translation:Animals
    123. A note on efficient computation of haplotypes via perfect phylogeny. J Comput Biol. 2004; 11(5):858-66. Bafna V, Gusfield D, Hannenhalli S, Yooseph S. PMID: 15700406.
      View in: PubMed   Mentions: 2     Fields:    
    124. FastR: fast database search tool for non-coding RNA. Proc IEEE Comput Syst Bioinform Conf. 2004; 52-61. Bafna V, Zhang S. PMID: 16447999.
      View in: PubMed   Mentions: 10     Fields:    Translation:Cells
    125. The dog genome: survey sequencing and comparative analysis. Science. 2003 Sep 26; 301(5641):1898-903. Kirkness EF, Bafna V, Halpern AL, Levy S, Remington K, Rusch DB, Delcher AL, Pop M, Wang W, Fraser CM, Venter JC. PMID: 14512627.
      View in: PubMed   Mentions: 147     Fields:    Translation:HumansAnimalsCells
    126. Haplotyping as perfect phylogeny: a direct approach. J Comput Biol. 2003; 10(3-4):323-40. Bafna V, Gusfield D, Lancia G, Yooseph S. PMID: 12935331.
      View in: PubMed   Mentions: 11     Fields:    
    127. Robustness of inference of haplotype block structure. J Comput Biol. 2003; 10(1):13-9. Schwartz R, Halldórsson BV, Bafna V, Clark AG, Istrail S. PMID: 12676048.
      View in: PubMed   Mentions: 16     Fields:    Translation:Humans
    128. The sequence of the human genome. Science. 2001 Feb 16; 291(5507):1304-51. Venter JC, Adams MD, Myers EW, Li PW, Mural RJ, Sutton GG, Smith HO, Yandell M, Evans CA, Holt RA, Gocayne JD, Amanatides P, Ballew RM, Huson DH, Wortman JR, Zhang Q, Kodira CD, Zheng XH, Chen L, Skupski M, Subramanian G, Thomas PD, Zhang J, Gabor Miklos GL, Nelson C, Broder S, Clark AG, Nadeau J, McKusick VA, Zinder N, Levine AJ, Roberts RJ, Simon M, Slayman C, Hunkapiller M, Bolanos R, Delcher A, Dew I, Fasulo D, Flanigan M, Florea L, Halpern A, Hannenhalli S, Kravitz S, Levy S, Mobarry C, Reinert K, Remington K, Abu-Threideh J, Beasley E, Biddick K, Bonazzi V, Brandon R, Cargill M, Chandramouliswaran I, Charlab R, Chaturvedi K, Deng Z, Di Francesco V, Dunn P, Eilbeck K, Evangelista C, Gabrielian AE, Gan W, Ge W, Gong F, Gu Z, Guan P, Heiman TJ, Higgins ME, Ji RR, Ke Z, Ketchum KA, Lai Z, Lei Y, Li Z, Li J, Liang Y, Lin X, Lu F, Merkulov GV, Milshina N, Moore HM, Naik AK, Narayan VA, Neelam B, Nusskern D, Rusch DB, Salzberg S, Shao W, Shue B, Sun J, Wang Z, Wang A, Wang X, Wang J, Wei M, Wides R, Xiao C, Yan C, Yao A, Ye J, Zhan M, Zhang W, Zhang H, Zhao Q, Zheng L, Zhong F, Zhong W, Zhu S, Zhao S, Gilbert D, Baumhueter S, Spier G, Carter C, Cravchik A, Woodage T, Ali F, An H, Awe A, Baldwin D, Baden H, Barnstead M, Barrow I, Beeson K, Busam D, Carver A, Center A, Cheng ML, Curry L, Danaher S, Davenport L, Desilets R, Dietz S, Dodson K, Doup L, Ferriera S, Garg N, Gluecksmann A, Hart B, Haynes J, Haynes C, Heiner C, Hladun S, Hostin D, Houck J, Howland T, Ibegwam C, Johnson J, Kalush F, Kline L, Koduru S, Love A, Mann F, May D, McCawley S, McIntosh T, McMullen I, Moy M, Moy L, Murphy B, Nelson K, Pfannkoch C, Pratts E, Puri V, Qureshi H, Reardon M, Rodriguez R, Rogers YH, Romblad D, Ruhfel B, Scott R, Sitter C, Smallwood M, Stewart E, Strong R, Suh E, Thomas R, Tint NN, Tse S, Vech C, Wang G, Wetter J, Williams S, Williams M, Windsor S, Winn-Deen E, Wolfe K, Zaveri J, Zaveri K, Abril JF, Guigó R, Campbell MJ, Sjolander KV, Karlak B, Kejariwal A, Mi H, Lazareva B, Hatton T, Narechania A, Diemer K, Muruganujan A, Guo N, Sato S, Bafna V, Istrail S, Lippert R, Schwartz R, Walenz B, Yooseph S, Allen D, Basu A, Baxendale J, Blick L, Caminha M, Carnes-Stine J, Caulk P, Chiang YH, Coyne M, Dahlke C, Mays A, Dombroski M, Donnelly M, Ely D, Esparham S, Fosler C, Gire H, Glanowski S, Glasser K, Glodek A, Gorokhov M, Graham K, Gropman B, Harris M, Heil J, Henderson S, Hoover J, Jennings D, Jordan C, Jordan J, Kasha J, Kagan L, Kraft C, Levitsky A, Lewis M, Liu X, Lopez J, Ma D, Majoros W, McDaniel J, Murphy S, Newman M, Nguyen T, Nguyen N, Nodell M, Pan S, Peck J, Peterson M, Rowe W, Sanders R, Scott J, Simpson M, Smith T, Sprague A, Stockwell T, Turner R, Venter E, Wang M, Wen M, Wu D, Wu M, Xia A, Zandieh A, Zhu X. PMID: 11181995.
      View in: PubMed   Mentions: 2634     Fields:    Translation:HumansAnimalsCells
    129. SCOPE: a probabilistic model for scoring tandem mass spectra against a peptide database. Bioinformatics. 2001; 17 Suppl 1:S13-21. Bafna V, Edwards N. PMID: 11472988.
      View in: PubMed   Mentions: 36     Fields:    Translation:Cells
    130. Ligand-receptor pairing via tree comparison. J Comput Biol. 2000 Feb-Apr; 7(1-2):59-70. Bafna V, Hannenhalli S, Rice K, Vawter L. PMID: 10890388.
      View in: PubMed   Mentions:    Fields:    
    131. The conserved exon method for gene finding. Proc Int Conf Intell Syst Mol Biol. 2000; 8:3-12. Bafna V, Huson DH. PMID: 10977061.
      View in: PubMed   Mentions: 18     Fields:    Translation:HumansAnimalsCells
    132. Human beta-defensin 2 is a salt-sensitive peptide antibiotic expressed in human lung. J Clin Invest. 1998 Sep 01; 102(5):874-80. Bals R, Wang X, Wu Z, Freeman T, Bafna V, Zasloff M, Wilson JM. PMID: 9727055.
      View in: PubMed   Mentions: 145     Fields:    Translation:HumansCells
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