Vineet Bafna - Publications

Affiliations: 
Computer Science and Engineering University of California, San Diego, La Jolla, CA 
Area:
Computer Science, Bioinformatics Biology

147 high-probability publications. We are testing a new system for linking publications to authors. You can help! If you notice any inaccuracies, please sign in and mark papers as correct or incorrect matches. If you identify any major omissions or other inaccuracies in the publication list, please let us know.

Year Citation  Score
2019 Li S, Cha SW, Hefner 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. Proteogenomic annotation of the Chinese hamster reveals extensive novel translation events and endogenous retroviral elements. Journal of Proteome Research. PMID 31020842 DOI: 10.1021/acs.jproteome.8b00935  1
2019 Deshpande V, Luebeck J, Nguyen ND, Bakhtiari M, Turner KM, Schwab R, Carter H, Mischel PS, Bafna V. Exploring the landscape of focal amplifications in cancer using AmpliconArchitect. Nature Communications. 10: 392. PMID 30674876 DOI: 10.1038/s41467-018-08200-y  0.72
2018 Bakhtiari M, Shleizer-Burko S, Gymrek M, Bansal V, Bafna V. Targeted genotyping of variable number tandem repeats with adVNTR. Genome Research. PMID 30352806 DOI: 10.1101/gr.235119.118  1
2018 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. European Journal of Human Genetics : Ejhg. PMID 30254217 DOI: 10.1038/s41431-018-0270-8  1
2018 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 Research. PMID 29579309 DOI: 10.1093/nar/gky180  0.72
2018 Akbari A, Vitti JJ, Iranmehr A, Bakhtiari M, Sabeti PC, Mirarab S, Bafna V. Identifying the favored mutation in a positive selective sweep. Nature Methods. PMID 29457793 DOI: 10.1038/nmeth.4606  1
2018 Rozanov DV, Rozanov ND, Chiotti K, 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, et al. MHC class I loaded ligands from breast cancer cell lines: A potential HLA-I-typed antigen collection. Journal of Proteomics. PMID 29331515 DOI: 10.1016/j.jprot.2018.01.004  1
2017 Chu WK, Edge P, Lee HS, Bansal V, Bafna V, Huang X, Zhang K. Ultraaccurate genome sequencing and haplotyping of single human cells. Proceedings of the National Academy of Sciences of the United States of America. PMID 29078313 DOI: 10.1073/pnas.1707609114  1
2017 Cha SW, Bonissone S, Na S, Pevzner PA, Bafna V. The antibody repertoire of colorectal cancer. Molecular & Cellular Proteomics : McP. PMID 29046389 DOI: 10.1074/mcp.RA117.000397  1
2017 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. Molecular Biology and Evolution. PMID 29029226 DOI: 10.1093/molbev/msx239  1
2017 Azad P, Stobdan T, Zhou D, Hartley I, Akbari A, Bafna V, Haddad GG. High-altitude adaptation in humans: from genomics to integrative physiology. Journal of Molecular Medicine (Berlin, Germany). PMID 28951950 DOI: 10.1007/s00109-017-1584-7  1
2017 Iranmehr A, Akbari A, Schlötterer C, Bafna V. CLEAR: Composition of Likelihoods for Evolve And Resequence Experiments. Genetics. PMID 28396506 DOI: 10.1534/genetics.116.197566  1
2017 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, ... ... Bafna V, et al. Extrachromosomal oncogene amplification drives tumour evolution and genetic heterogeneity. Nature. PMID 28178237 DOI: 10.1038/nature21356  0.72
2016 Edge P, Bafna V, Bansal V. HapCUT2: robust and accurate haplotype assembly for diverse sequencing technologies. Genome Research. PMID 27940952 DOI: 10.1101/gr.213462.116  1
2016 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 Genetics. 12: e1006472. PMID 27902698 DOI: 10.1371/journal.pgen.1006472  1
2016 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. The Journal of Experimental Medicine. PMID 27821551 DOI: 10.1084/jem.20151920  1
2016 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 Research. PMID 27105843 DOI: 10.1093/nar/gkw281  1
2015 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, et al. Next-Generation Sequencing of Plasmodium vivax Patient Samples Shows Evidence of Direct Evolution in Drug-Resistance Genes. Acs Infectious Diseases. 1: 367-379. PMID 26719854 DOI: 10.1021/acsinfecdis.5b00049  1
2015 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 Genetics. 11: e1005527. PMID 26402243 DOI: 10.1371/journal.pgen.1005527  1
2015 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. Proceedings of the National Academy of Sciences of the United States of America. 112: 10425-30. PMID 26240367 DOI: 10.1073/pnas.1507486112  1
2015 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. Journal of Proteome Research. 14: 3555-67. PMID 26139413 DOI: 10.1021/acs.jproteome.5b00264  1
2015 Zakov S, Bafna V. Reconstructing breakage fusion bridge architectures using noisy copy numbers. Journal of Computational Biology : a Journal of Computational Molecular Cell Biology. 22: 577-94. PMID 26020441 DOI: 10.1089/cmb.2014.0166  1
2015 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, et al. Genetic simulation tools for post-genome wide association studies of complex diseases. Genetic Epidemiology. 39: 11-9. PMID 25371374 DOI: 10.1002/gepi.21870  1
2015 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 Proceedings of the National Academy of Sciences of the United States of America. 112: 10425-10430. DOI: 10.1073/pnas.1507486112  1
2015 Ronen R, Tesler G, Akbari A, Zakov S, Rosenberg NA, Bafna V. Haplotype Allele Frequency (HAF) score: Predicting carriers of ongoing selective sweeps without knowledge of the adaptive allele Lecture Notes in Computer Science (Including Subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics). 9029: 276-280. DOI: 10.1007/978-3-319-16706-0_28  1
2014 Ronen R, Zhou D, Bafna V, Haddad GG. The genetic basis of chronic mountain sickness. Physiology (Bethesda, Md.). 29: 403-12. PMID 25362634 DOI: 10.1152/physiol.00008.2014  1
2014 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. 14: 2719-30. PMID 25263569 DOI: 10.1002/pmic.201400206  1
2014 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, ... ... Bafna V, et al. Annotation of the zebrafish genome through an integrated transcriptomic and proteomic analysis. Molecular & Cellular Proteomics : McP. 13: 3184-98. PMID 25060758 DOI: 10.1074/mcp.M114.038299  1
2014 Kinsella M, Patel A, Bafna V. The elusive evidence for chromothripsis. Nucleic Acids Research. 42: 8231-42. PMID 24939897 DOI: 10.1093/nar/gku525  1
2014 Kramer M, Dutkowski J, Yu M, Bafna V, Ideker T. Inferring gene ontologies from pairwise similarity data. Bioinformatics (Oxford, England). 30: i34-42. PMID 24932003 DOI: 10.1093/bioinformatics/btu282  1
2014 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, ... ... Bafna V, et al. Whole genome sequencing of Ethiopian highlanders reveals conserved hypoxia tolerance genes. Genome Biology. 15: R36. PMID 24555826 DOI: 10.1186/gb-2014-15-2-r36  1
2014 Patel A, Schwab R, Liu YT, Bafna V. Amplification and thrifty single-molecule sequencing of recurrent somatic structural variations. Genome Research. 24: 318-28. PMID 24307551 DOI: 10.1101/gr.161497.113  1
2014 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. Molecular & Cellular Proteomics : McP. 13: 157-67. PMID 24142994 DOI: 10.1074/mcp.M113.031260  1
2014 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. Journal of Proteome Research. 13: 21-8. PMID 23802565 DOI: 10.1021/pr400294c  1
2014 Kozanitis C, Heiberg A, Varghese G, Bafna V. Using Genome Query Language to uncover genetic variation. Bioinformatics (Oxford, England). 30: 1-8. PMID 23751181 DOI: 10.1093/bioinformatics/btt250  1
2013 Bafna V, Kozanitis C, Deutsch A, Ohno-Machado L, Heiberg A, Varghese G. Abstractions for Genomics. Communications of the Acm. 56: 83-93. PMID 25284821 DOI: 10.1145/2398356.2398376  1
2013 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 Biology. 14: R100. PMID 24028704 DOI: 10.1186/gb-2013-14-9-r100  1
2013 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 Biology. 14: R90. PMID 23987214 DOI: 10.1186/gb-2013-14-8-r90  1
2013 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, ... ... Bafna V, et al. Whole-genome sequencing uncovers the genetic basis of chronic mountain sickness in Andean highlanders. American Journal of Human Genetics. 93: 452-62. PMID 23954164 DOI: 10.1016/j.ajhg.2013.07.011  1
2013 Ronen R, Udpa N, Halperin E, Bafna V. Learning natural selection from the site frequency spectrum. Genetics. 195: 181-93. PMID 23770700 DOI: 10.1534/genetics.113.152587  1
2013 Lo C, Kim S, Zakov S, Bafna V. Evaluating genome architecture of a complex region via generalized bipartite matching. Bmc Bioinformatics. 14: S13. PMID 23734567 DOI: 10.1186/1471-2105-14-S5-S13  1
2013 Kim S, Medvedev P, Paton TA, Bafna V. Reprever: resolving low-copy duplicated sequences using template driven assembly. Nucleic Acids Research. 41: e128. PMID 23658221 DOI: 10.1093/nar/gkt339  1
2013 Zakov S, Kinsella M, Bafna V. An algorithmic approach for breakage-fusion-bridge detection in tumor genomes. Proceedings of the National Academy of Sciences of the United States of America. 110: 5546-51. PMID 23503850 DOI: 10.1073/pnas.1220977110  1
2013 Kim S, Jeong K, Bafna V. Wessim: a whole-exome sequencing simulator based on in silico exome capture. Bioinformatics (Oxford, England). 29: 1076-7. PMID 23413434 DOI: 10.1093/bioinformatics/btt074  1
2013 Deshpande V, Fung EDK, Pham S, Bafna V. Cerulean: A hybrid assembly using high throughput short and long reads Lecture Notes in Computer Science (Including Subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics). 8126: 349-363. DOI: 10.1007/978-3-642-40453-5_27  1
2012 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. Nature Genetics. 44: 941-5. PMID 22729223 DOI: 10.1038/ng.2329  1
2012 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, et al. Exome sequencing can improve diagnosis and alter patient management. Science Translational Medicine. 4: 138ra78. PMID 22700954 DOI: 10.1126/scitranslmed.3003544  1
2012 Liu X, Mammana A, Bafna V. Speeding up tandem mass spectral identification using indexes. Bioinformatics (Oxford, England). 28: 1692-7. PMID 22543365 DOI: 10.1093/bioinformatics/bts244  1
2012 Kinsella M, Bafna V. Combinatorics of the breakage-fusion-bridge mechanism. Journal of Computational Biology : a Journal of Computational Molecular Cell Biology. 19: 662-78. PMID 22506505 DOI: 10.1089/cmb.2012.0020  1
2012 Dost B, Bandeira N, Li X, Shen Z, Briggs SP, Bafna V. Accurate mass spectrometry based protein quantification via shared peptides. Journal of Computational Biology : a Journal of Computational Molecular Cell Biology. 19: 337-48. PMID 22414154 DOI: 10.1089/cmb.2009.0267  1
2012 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. 7: e29613. PMID 22363405 DOI: 10.1371/journal.pone.0029613  1
2012 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, et al. Global DNA hypomethylation coupled to repressive chromatin domain formation and gene silencing in breast cancer. Genome Research. 22: 246-58. PMID 22156296 DOI: 10.1101/gr.125872.111  1
2012 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, et al. iDASH: integrating data for analysis, anonymization, and sharing. Journal of the American Medical Informatics Association : Jamia. 19: 196-201. PMID 22081224 DOI: 10.1136/amiajnl-2011-000538  1
2012 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. Molecular & Cellular Proteomics : McP. 11: M111.008524. PMID 22027200 DOI: 10.1074/mcp.M111.008524  1
2012 Joshi KS, Pathak HA, Dayal RK, Bafna VK, Kimihiro I, Barabash V. General and crevice corrosion study of the materials for ITER vacuum vessel inwall shield Ieee Transactions On Plasma Science. 40: 2274-2278. DOI: 10.1109/TPS.2012.2208657  1
2012 Joshi KS, Pathak HA, Dayal RK, Bafna VK, Kimihiro I, Barabash V. General and crevice corrosion study of the in-wall shielding materials for ITER vacuum vessel Journal of Physics: Conference Series. 390. DOI: 10.1088/1742-6596/390/1/012038  1
2012 Kinsella M, Bafna V. Modeling the breakage-fusion-bridge mechanism: Combinatorics and cancer genomics Lecture Notes in Computer Science (Including Subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics). 7262: 148-162. DOI: 10.1007/978-3-642-29627-7_13  1
2011 Udpa N, Zhou D, Haddad GG, Bafna V. Tests of selection in pooled case-control data: an empirical study. Frontiers in Genetics. 2: 83. PMID 22303377 DOI: 10.3389/fgene.2011.00083  1
2011 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. Journal of Proteome Research. 10: 4734-43. PMID 21800894 DOI: 10.1021/pr2005378  1
2011 Kozanitis C, Saunders C, Kruglyak S, Bafna V, Varghese G. Compressing genomic sequence fragments using SlimGene. Journal of Computational Biology : a Journal of Computational Molecular Cell Biology. 18: 401-13. PMID 21385043 DOI: 10.1089/cmb.2010.0253  1
2011 Lo C, Bashir A, Bansal V, Bafna V. Strobe sequence design for haplotype assembly. Bmc Bioinformatics. 12: S24. PMID 21342554 DOI: 10.1186/1471-2105-12-S1-S24  1
2011 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. Journal of Proteome Research. 10: 1915-28. PMID 21332220 DOI: 10.1021/pr101159e  1
2011 Kinsella M, Harismendy O, Nakano M, Frazer KA, Bafna V. Sensitive gene fusion detection using ambiguously mapping RNA-Seq read pairs. Bioinformatics (Oxford, England). 27: 1068-75. PMID 21330288 DOI: 10.1093/bioinformatics/btr085  1
2011 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-α antibody. Proteomics. 11: 395-405. PMID 21268269 DOI: 10.1002/pmic.201000487  1
2011 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. Proceedings of the National Academy of Sciences of the United States of America. 108: 2349-54. PMID 21262834 DOI: 10.1073/pnas.1010643108  1
2011 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. Journal of Proteome Research. 10: 320-9. PMID 21067235 DOI: 10.1021/pr100953b  1
2011 Dost B, Wu C, Su A, Bafna V. TCLUST: a fast method for clustering genome-scale expression data. Ieee/Acm Transactions On Computational Biology and Bioinformatics / Ieee, Acm. 8: 808-18. PMID 20479508 DOI: 10.1109/TCBB.2010.34  1
2011 Joshi KS, Pathak HA, Dayal RK, Bafna VK, Kimihiro I, Barabash V. General and crevice corrosion study of the materials for ITER vacuum vessel in-wall shield Proceedings - Symposium On Fusion Engineering. DOI: 10.1109/SOFE.2011.6052259  1
2011 Bafna V. Preface: Satellite workshop on comparative genomics, Research in Computational Molecular Biology (RECOMB-CG 2010) Preface Journal of Computational Biology. 18: 1369. DOI: 10.1089/cmb.2011.009p  1
2011 Elberfeld M, Bafna V, Gamzu I, Medvedovsky A, Segev D, Silverbush D, Zwick U, Sharan R. On the approximability of reachability-preserving network orientations Internet Mathematics. 7: 209-232. DOI: 10.1080/15427951.2011.604554  1
2010 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 Biology. 11: R118. PMID 21118518 DOI: 10.1186/gb-2010-11-11-r118  1
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 and common phenotypes. Plos Computational Biology. 6: e1000954. PMID 20976246 DOI: 10.1371/journal.pcbi.1000954  1
2010 Brinza D, Schultz M, Tesler G, Bafna V. RAPID detection of gene-gene interactions in genome-wide association studies. Bioinformatics (Oxford, England). 26: 2856-62. PMID 20871107 DOI: 10.1093/bioinformatics/btq529  1
2010 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. Molecular & Cellular Proteomics : McP. 9: 2772-82. PMID 20855543 DOI: 10.1074/mcp.M110.002766  1
2010 Castellana N, Bafna V. Proteogenomics to discover the full coding content of genomes: a computational perspective. Journal of Proteomics. 73: 2124-35. PMID 20620248 DOI: 10.1016/j.jprot.2010.06.007  1
2010 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. 11: 407. PMID 20579359 DOI: 10.1186/1471-2164-11-407  1
2010 Bashir A, Bansal V, Bafna V. Designing deep sequencing experiments: detecting structural variation and estimating transcript abundance. Bmc Genomics. 11: 385. PMID 20565853 DOI: 10.1186/1471-2164-11-385  1
2010 Hormozdiari F, Salari R, Bafna V, Sahinalp SC. Protein-protein interaction network evaluation for identifying potential drug targets. Journal of Computational Biology : a Journal of Computational Molecular Cell Biology. 17: 669-84. PMID 20500021 DOI: 10.1089/cmb.2009.0032  1
2010 Bashir A, Lu Q, Carson D, Raphael BJ, Liu YT, Bafna V. Optimizing PCR assays for DNA-based cancer diagnostics. Journal of Computational Biology : a Journal of Computational Molecular Cell Biology. 17: 369-81. PMID 20377451 DOI: 10.1089/cmb.2009.0203  1
2010 Castellana NE, Pham V, Arnott D, Lill JR, Bafna V. Template proteogenomics: sequencing whole proteins using an imperfect database. Molecular & Cellular Proteomics : McP. 9: 1260-70. PMID 20164058 DOI: 10.1074/mcp.M900504-MCP200  1
2010 Watrous J, Burns K, Liu WT, Patel A, Hook V, Bafna V, Barry CE, Bark S, Dorrestein PC. Expansion of the mycobacterial "PUPylome". Molecular Biosystems. 6: 376-85. PMID 20094657 DOI: 10.1039/b916104j  1
2009 Kalaev M, Bafna V, Sharan R. Fast and accurate alignment of multiple protein networks. Journal of Computational Biology : a Journal of Computational Molecular Cell Biology. 16: 989-99. PMID 19624266 DOI: 10.1089/cmb.2009.0136  1
2009 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, ... ... Bafna V, et al. Sequence and structural variation in a human genome uncovered by short-read, massively parallel ligation sequencing using two-base encoding. Genome Research. 19: 1527-41. PMID 19546169 DOI: 10.1101/gr.091868.109  1
2009 Dost B, Bandeira N, Li X, Shen Z, Briggs S, Bafna V. Shared peptides in mass spectrometry based protein quantification Lecture Notes in Computer Science (Including Subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics). 5541: 356-371. DOI: 10.1007/978-3-642-02008-7_26  1
2009 Bashir A, Lu Q, Carson D, Raphael B, Liu YT, Bafna V. Optimizing PCR assays for DNA based cancer diagnostics Lecture Notes in Computer Science (Including Subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics). 5541: 220-235. DOI: 10.1007/978-3-642-02008-7_17  1
2008 Castellana NE, Payne SH, Shen Z, Stanke M, Bafna V, Briggs SP. Discovery and revision of Arabidopsis genes by proteogenomics. Proceedings of the National Academy of Sciences of the United States of America. 105: 21034-8. PMID 19098097 DOI: 10.1073/pnas.0811066106  1
2008 Dost B, Shlomi T, Gupta N, Ruppin E, Bafna V, Sharan R. QNet: a tool for querying protein interaction networks. Journal of Computational Biology : a Journal of Computational Molecular Cell Biology. 15: 913-25. PMID 18707533 DOI: 10.1089/cmb.2007.0172  1
2008 Bansal V, Bafna V. HapCUT: an efficient and accurate algorithm for the haplotype assembly problem. Bioinformatics (Oxford, England). 24: i153-9. PMID 18689818 DOI: 10.1093/bioinformatics/btn298  1
2008 Bansal V, Halpern AL, Axelrod N, Bafna V. An MCMC algorithm for haplotype assembly from whole-genome sequence data. Genome Research. 18: 1336-46. PMID 18676820 DOI: 10.1101/gr.077065.108  1
2008 Payne SH, Yau M, Smolka MB, Tanner S, Zhou H, Bafna V. Phosphorylation-specific MS/MS scoring for rapid and accurate phosphoproteome analysis. Journal of Proteome Research. 7: 3373-81. PMID 18563926 DOI: 10.1021/pr800129m  1
2008 Han B, Dost B, Bafna V, Zhang S. Structural alignment of pseudoknotted RNA. Journal of Computational Biology : a Journal of Computational Molecular Cell Biology. 15: 489-504. PMID 18549303 DOI: 10.1089/cmb.2007.0214  1
2008 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 Research. 18: 1133-42. PMID 18426904 DOI: 10.1101/gr.074344.107  1
2008 Albuquerque CP, Smolka MB, Payne SH, Bafna V, Eng J, Zhou H. A multidimensional chromatography technology for in-depth phosphoproteome analysis. Molecular & Cellular Proteomics : McP. 7: 1389-96. PMID 18407956 DOI: 10.1074/mcp.M700468-MCP200  1
2008 Bashir A, Volik S, Collins C, Bafna V, Raphael BJ. Evaluation of paired-end sequencing strategies for detection of genome rearrangements in cancer. Plos Computational Biology. 4: e1000051. PMID 18404202 DOI: 10.1371/journal.pcbi.1000051  1
2008 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. Journal of Proteome Research. 7: 170-81. PMID 18034453 DOI: 10.1021/pr070444v  1
2008 Medvedovsky A, Bafna V, Zwick U, Sharan R. An algorithm for orienting graphs based on cause-effect pairs and its applications to orienting protein networks Lecture Notes in Computer Science (Including Subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics). 5251: 222-232. DOI: 10.1007/978-3-540-87361-7_19  1
2007 Gusfield D, Bansal V, Bafna V, Song YS. A decomposition theory for phylogenetic networks and incompatible characters. Journal of Computational Biology : a Journal of Computational Molecular Cell Biology. 14: 1247-72. PMID 18047426 DOI: 10.1089/cmb.2006.0137  1
2007 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, ... ... Bafna V, et al. The diploid genome sequence of an individual human. Plos Biology. 5: e254. PMID 17803354 DOI: 10.1371/journal.pbio.0050254  1
2007 Bashir A, Liu YT, Raphael BJ, Carson D, Bafna V. Optimization of primer design for the detection of variable genomic lesions in cancer. Bioinformatics (Oxford, England). 23: 2807-15. PMID 17766270 DOI: 10.1093/bioinformatics/btm390  1
2007 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 Research. 17: 1362-77. PMID 17690205 DOI: 10.1101/gr.6427907  1
2007 Ideker T, Bafna V, Lemberger T. Integrating scientific cultures. Molecular Systems Biology. 3: 105. PMID 17437030 DOI: 10.1038/msb4100145  1
2007 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, ... ... Bafna V, et al. The Sorcerer II Global Ocean Sampling expedition: expanding the universe of protein families. Plos Biology. 5: e16. PMID 17355171 DOI: 10.1371/journal.pbio.0050016  1
2007 Tanner S, Shen Z, Ng J, Florea L, Guigó R, Briggs SP, Bafna V. Improving gene annotation using peptide mass spectrometry. Genome Research. 17: 231-9. PMID 17189379 DOI: 10.1101/gr.5646507  1
2007 Bansal V, Bashir A, Bafna V. Evidence for large inversion polymorphisms in the human genome from HapMap data. Genome Research. 17: 219-30. PMID 17185644 DOI: 10.1101/gr.5774507  1
2007 Bafna V, Ideker T. Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics): Preface Lecture Notes in Computer Science (Including Subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics). 4532: vi.  1
2006 Tanner S, Pevzner PA, Bafna V. Unrestrictive identification of post-translational modifications through peptide mass spectrometry. Nature Protocols. 1: 67-72. PMID 17406213 DOI: 10.1038/nprot.2006.10  1
2006 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 (Oxford, England). 22: e557-65. PMID 16873520 DOI: 10.1093/bioinformatics/btl232  1
2006 Bafna V, Bansal V. Inference about recombination from haplotype data: lower bounds and recombination hotspots. Journal of Computational Biology : a Journal of Computational Molecular Cell Biology. 13: 501-21. PMID 16597254 DOI: 10.1089/cmb.2006.13.501  1
2006 Bafna V, Tang H, Zhang S. Consensus folding of unaligned RNA sequences revisited. Journal of Computational Biology : a Journal of Computational Molecular Cell Biology. 13: 283-95. PMID 16597240 DOI: 10.1089/cmb.2006.13.283  1
2005 Zhang S, Haas B, Eskin E, Bafna V. Searching genomes for noncoding RNA using FastR. Ieee/Acm Transactions On Computational Biology and Bioinformatics / Ieee, Acm. 2: 366-79. PMID 17044173 DOI: 10.1109/TCBB.2005.57  1
2005 Tsur D, Tanner S, Zandi E, Bafna V, Pevzner PA. Identification of post-translational modifications via blind search of mass-spectra. Proceedings / Ieee Computational Systems Bioinformatics Conference, Csb. Ieee Computational Systems Bioinformatics Conference. 157-66. PMID 16447973 DOI: 10.1109/CSB.2005.34  1
2005 Tsur D, Tanner S, Zandi E, Bafna V, Pevzner PA. Identification of post-translational modifications by blind search of mass spectra. Nature Biotechnology. 23: 1562-7. PMID 16311586 DOI: 10.1038/nbt1168  1
2005 Frank A, Tanner S, Bafna V, Pevzner P. Peptide sequence tags for fast database search in mass-spectrometry. Journal of Proteome Research. 4: 1287-95. PMID 16083278 DOI: 10.1021/pr050011x  1
2005 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. Analytical Chemistry. 77: 4626-39. PMID 16013882 DOI: 10.1021/ac050102d  1
2005 Bashir A, Ye C, Price AL, Bafna V. Orthologous repeats and mammalian phylogenetic inference. Genome Research. 15: 998-1006. PMID 15998912 DOI: 10.1101/gr.3493405  1
2005 Bafna V, Istrail S, Lancia G, Rizzi R. Polynomial and APX-hard cases of the individual haplotyping problem Theoretical Computer Science. 335: 109-125. DOI: 10.1016/j.tcs.2004.12.017  1
2005 Bafna V, Bansal V. Improved recombination lower bounds for haplotype data Lecture Notes in Bioinformatics (Subseries of Lecture Notes in Computer Science). 3500: 569-584.  1
2004 Bafna V, Bansal V. The number of recombination events in a sample history: conflict graph and lower bounds. Ieee/Acm Transactions On Computational Biology and Bioinformatics / Ieee, Acm. 1: 78-90. PMID 17048383 DOI: 10.1109/TCBB.2004.23  1
2004 Bafna V, Zhang S. FastR: fast database search tool for non-coding RNA. Proceedings / Ieee Computational Systems Bioinformatics Conference, Csb. Ieee Computational Systems Bioinformatics Conference. 52-61. PMID 16447999  1
2004 Bafna V, Gusfield D, Hannenhalli S, Yooseph S. A note on efficient computation of haplotypes via perfect phylogeny. Journal of Computational Biology : a Journal of Computational Molecular Cell Biology. 11: 858-66. PMID 15700406 DOI: 10.1089/cmb.2004.11.858  1
2004 Bandeira N, Tang H, Bafna V, Pevzner P. Shotgun protein sequencing by tandem mass spectra assembly. Analytical Chemistry. 76: 7221-33. PMID 15595863 DOI: 10.1021/ac0489162  1
2004 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 Research. 14: 1633-40. PMID 15289481 DOI: 10.1101/gr.2570004  1
2004 Halldórsson BV, Bafna V, Edwards N, Lippert R, Yooseph S, Istrail S. A Survey of Computational Methods for Determining Haplotypes Lecture Notes in Computer Science (Including Subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics). 2983: 26-47.  1
2003 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 (New York, N.Y.). 301: 1898-903. PMID 14512627 DOI: 10.1126/science.1086432  1
2003 Bafna V, Gusfield D, Lancia G, Yooseph S. Haplotyping as perfect phylogeny: a direct approach. Journal of Computational Biology : a Journal of Computational Molecular Cell Biology. 10: 323-40. PMID 12935331 DOI: 10.1089/10665270360688048  0.44
2003 Schwartz R, Halldórsson BV, Bafna V, Clark AG, Istrail S. Robustness of inference of haplotype block structure. Journal of Computational Biology : a Journal of Computational Molecular Cell Biology. 10: 13-9. PMID 12676048 DOI: 10.1089/106652703763255642  1
2003 Bafna V, Edwards N. On de novo interpretation of tandem mass spectra for peptide identification Proceedings of the Annual International Conference On Computational Molecular Biology, Recomb. 9-18.  1
2003 Bafna V, Halldórsson BV, Schwartz R, Clark AG, Istrail S. Haplotypes and informative SNP selection algorithms: Don't block out information Proceedings of the Annual International Conference On Computational Molecular Biology, Recomb. 19-27.  1
2003 Halldórsson BV, Bafna V, Edwards N, Lippert R, Yooseph S, Istrail S. Combinatorial problems arising in SNP and haplotype analysis Lecture Notes in Computer Science (Including Subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics). 2731: 26-47.  1
2002 Rizzi R, Bafna V, Istrail S, Lancia G. Practical algorithms and fixed-parameter tractability for the single individual SNP haplotyping problem Lecture Notes in Computer Science (Including Subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics). 2452: 29-43.  1
2001 Bafna V, Edwards N. SCOPE: A probabilistic model for scoring tandem mass spectra against a peptide database Bioinformatics. 17. PMID 11472988  1
2001 Lancia G, Bafna V, Istrail S, Lippert R, Schwartz R. SNPs problems, complexity, and algorithms Lecture Notes in Computer Science (Including Subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics). 2161: 182-193.  1
2000 Bafna V, Huson DH. The conserved exon method for gene finding. Proceedings / ... International Conference On Intelligent Systems For Molecular Biology ; Ismb. International Conference On Intelligent Systems For Molecular Biology. 8: 3-12. PMID 10977061  1
2000 Bafna V, Hannenhalli S, Rice K, Vawter L. Ligand-receptor pairing via tree comparison Journal of Computational Biology. 7: 59-70. PMID 10890388 DOI: 10.1089/10665270050081388  1
2000 Wu BY, Lancia G, Bafna V, Chao KM, Ravi R, Tang CY. A polynomial-time approximation scheme for minimum routing cost spanning trees Siam Journal On Computing. 29: 761-778.  1
1999 Bafna V, Berman P, Fujito T. A 2-Approximation algorithm for the undirected feedback vertex set problem Siam Journal On Discrete Mathematics. 12: 289-297.  1
1999 Agarwala R, Bafna V, Farach M, Paterson M, Thorup M. On the approximability of numerical taxonomy (fitting distances by tree metrics) Siam Journal On Computing. 28: 1073-1085.  1
1998 Agarwal P, Bafna V. The ribosome scanning model for translation initiation: implications for gene prediction and full-length cDNA detection Proceedings / ... International Conference On Intelligent Systems For Molecular Biology ; Ismb. International Conference On Intelligent Systems For Molecular Biology. 6: 2-7. PMID 9783203  1
1998 Bals R, Wang X, Wu Z, Freeman T, Bafna V, Zasloff M, Wilson JM. Human beta-defensin 2 is a salt-sensitive peptide antibiotic expressed in human lung. The Journal of Clinical Investigation. 102: 874-80. PMID 9727055 DOI: 10.1172/JCI2410  1
1998 Bafna V, Pevzner PA. Sorting by transpositions Siam Journal On Discrete Mathematics. 11: 224-240.  1
1997 Bafna V, Lawler EL, Pevzner PA. Approximation algorithms for multiple sequence alignment Theoretical Computer Science. 182: 233-244.  1
1996 Bafna V, Pevzner PA. Genome rearrangements and sorting by reversals Siam Journal On Computing. 25: 272-289.  1
1996 Bafna V, Narayanan B, Ravi R. Nonoverlapping local alignments (weighted independent sets of axis-parallel rectangles) Discrete Applied Mathematics. 71: 41-53.  1
1995 Bafna V, Narayanan B, Ravi R. Nonoverlapping local alignments (Weighted independent sets of axis parallel rectangles) Lecture Notes in Computer Science (Including Subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics). 955: 506-517. DOI: 10.1007/3-540-60220-8_89  1
1995 Bafna V, Pevzner PA. Sorting by reversals: Genome rearrangements in plant organelles and evolutionary history of X chromosome Molecular Biology and Evolution. 12: 239-246.  1
1995 Bafna V, Berman P, Fujito T. Constant ratio approximations of the weighted feedback vertex set problem for undirected graphs Lecture Notes in Computer Science (Including Subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics). 1004: 142-151.  1
1994 Bafna V, Kalyanasundaram B, Pruhs K. Not all insertion methods yield constant approximate tours in the Euclidean plane Theoretical Computer Science. 125: 345-353. DOI: 10.1016/0304-3975(94)90257-7  1
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