| Year |
Citation |
Score |
| 2024 |
Zhu K, Jones MG, Luebeck J, Bu X, Yi H, Hung KL, Wong IT, Zhang S, Mischel PS, Chang HY, Bafna V. CoRAL accurately resolves extrachromosomal DNA genome structures with long-read sequencing. Biorxiv : the Preprint Server For Biology. PMID 38405779 DOI: 10.1101/2024.02.15.580594 |
0.31 |
|
| 2023 |
Dehkordi SR, Wong IT, Ni J, Luebeck J, Zhu K, Prasad G, Krockenberger L, Xu G, Chowdhury B, Rajkumar U, Caplin A, Muliaditan D, Coruh C, Jin Q, Turner K, ... ... Bafna V, et al. Breakage fusion bridge cycles drive high oncogene copy number, but not intratumoral genetic heterogeneity or rapid cancer genome change. Biorxiv : the Preprint Server For Biology. PMID 38168210 DOI: 10.1101/2023.12.12.571349 |
0.308 |
|
| 2021 |
Sarmashghi S, Balaban M, Rachtman E, Touri B, Mirarab S, Bafna V. Estimating repeat spectra and genome length from low-coverage genome skims with RESPECT. Plos Computational Biology. 17: e1009449. PMID 34780468 DOI: 10.1371/journal.pcbi.1009449 |
0.302 |
|
| 2021 |
Rachtman E, Bafna V, Mirarab S. CONSULT: accurate contamination removal using locality-sensitive hashing. Nar Genomics and Bioinformatics. 3: lqab071. PMID 34377979 DOI: 10.1093/nargab/lqab071 |
0.33 |
|
| 2020 |
Luebeck J, Coruh C, Dehkordi SR, Lange JT, Turner KM, Deshpande V, Pai DA, Zhang C, Rajkumar U, Law JA, Mischel PS, Bafna V. AmpliconReconstructor integrates NGS and optical mapping to resolve the complex structures of focal amplifications. Nature Communications. 11: 4374. PMID 32873787 DOI: 10.1038/S41467-020-18099-Z |
0.803 |
|
| 2020 |
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, ... ... Bafna V, et al. Extrachromosomal DNA is associated with oncogene amplification and poor outcome across multiple cancers. Nature Genetics. PMID 32807987 DOI: 10.1038/S41588-020-0678-2 |
0.788 |
|
| 2020 |
Bohmann K, Mirarab S, Bafna V, Gilbert MTP. Beyond DNA barcoding: The unrealised potential of genome skim data in sample identification. Molecular Ecology. PMID 32542933 DOI: 10.1111/Mec.15507 |
0.447 |
|
| 2020 |
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, ... ... Bafna V, et al. Longitudinal assessment of tumor development using cancer avatars derived from genetically engineered pluripotent stem cells. Nature Communications. 11: 550. PMID 31992716 DOI: 10.1038/S41467-020-14312-1 |
0.302 |
|
| 2020 |
Rachtman E, Balaban M, Bafna V, Mirarab S. On the impact of contaminants on the accuracy of genome skimming and the effectiveness of exclusion read filters. Molecular Ecology Resources. PMID 31943790 DOI: 10.1111/1755-0998.13135 |
0.434 |
|
| 2019 |
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, ... ... Bafna V, et al. Circular ecDNA promotes accessible chromatin and high oncogene expression. Nature. PMID 31748743 DOI: 10.1038/S41586-019-1763-5 |
0.408 |
|
| 2019 |
Rajkumar U, Turner K, Luebeck J, Deshpande V, Chandraker M, Mischel P, Bafna V. EcSeg: Semantic Segmentation of Metaphase Images Containing Extrachromosomal DNA. Iscience. 21: 428-435. PMID 31706138 DOI: 10.1016/J.Isci.2019.10.035 |
0.79 |
|
| 2019 |
Sarmashghi S, Bafna V. Computing the Statistical Significance of Overlap between Genome Annotations with iStat. Cell Systems. PMID 31202632 DOI: 10.1016/J.Cels.2019.05.006 |
0.426 |
|
| 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 |
0.444 |
|
| 2019 |
Verhaak RGW, Bafna V, Mischel PS. Extrachromosomal oncogene amplification in tumour pathogenesis and evolution. Nature Reviews. Cancer. PMID 30872802 DOI: 10.1038/S41568-019-0128-6 |
0.3 |
|
| 2019 |
Sarmashghi S, Bohmann K, P Gilbert MT, Bafna V, Mirarab S. Skmer: assembly-free and alignment-free sample identification using genome skims. Genome Biology. 20: 34. PMID 30760303 DOI: 10.1186/S13059-019-1632-4 |
0.457 |
|
| 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 |
0.807 |
|
| 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 |
0.598 |
|
| 2018 |
Beyter D, Lin MS, Yu Y, Pieper R, Bafna V. ProteoStorm: An Ultrafast Metaproteomics Database Search Framework. Cell Systems. PMID 30268435 DOI: 10.1016/J.Cels.2018.08.009 |
0.346 |
|
| 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 |
0.404 |
|
| 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 |
0.802 |
|
| 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 |
0.527 |
|
| 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 |
0.596 |
|
| 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 |
0.604 |
|
| 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 |
0.366 |
|
| 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 |
0.311 |
|
| 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 |
0.372 |
|
| 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 |
0.797 |
|
| 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 |
0.599 |
|
| 2016 |
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, ... ... Bafna V, et al. Integrated Proteogenomic Characterization of Human High-Grade Serous Ovarian Cancer. Cell. PMID 27372738 DOI: 10.1016/J.Cell.2016.05.069 |
0.645 |
|
| 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 |
0.503 |
|
| 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 |
0.331 |
|
| 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 |
0.321 |
|
| 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 |
0.592 |
|
| 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 |
0.464 |
|
| 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 |
0.329 |
|
| 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 |
0.674 |
|
| 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 |
0.47 |
|
| 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 |
0.798 |
|
| 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 |
0.347 |
|
| 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 |
0.447 |
|
| 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 |
0.441 |
|
| 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 |
0.778 |
|
| 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 |
0.744 |
|
| 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 |
0.801 |
|
| 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 |
0.786 |
|
| 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 |
0.418 |
|
| 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 |
0.568 |
|
| 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 |
0.389 |
|
| 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 |
0.306 |
|
| 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 |
0.475 |
|
| 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 |
0.465 |
|
| 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 |
0.807 |
|
| 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 |
0.62 |
|
| 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 |
0.766 |
|
| 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 |
0.312 |
|
| 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 |
0.797 |
|
| 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 |
0.775 |
|
| 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 |
0.328 |
|
| 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 |
0.583 |
|
| 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 |
0.316 |
|
| 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 |
0.335 |
|
| 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 |
0.313 |
|
| 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 |
0.796 |
|
| 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 |
0.694 |
|
| 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 |
0.372 |
|
| 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 |
0.785 |
|
| 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 |
0.706 |
|
| 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 |
0.558 |
|
| 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 |
0.381 |
|
| 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 |
0.688 |
|
| 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 |
0.351 |
|
| 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 |
0.532 |
|
| 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 |
0.552 |
|
| 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 |
0.35 |
|
| 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 |
0.595 |
|
| 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 |
0.772 |
|
| 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 |
0.45 |
|
| 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 |
0.7 |
|
| 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 |
0.59 |
|
| 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 |
0.78 |
|
| 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 |
0.309 |
|
| 2010 |
Harismendy O, Bhatia G, Rahim NG, Bansal V, Nakano M, Scott M, Wang X, Dib C, Turlotte E, Heintzman N, Murray SS, Deleuze J, Sipe JC, Ren B, Bafna V, et al. Deciphering the genetic basis of common diseases by integrated functional annotation of common and rare variants Genome Biology. 11. DOI: 10.1186/Gb-2010-11-S1-I8 |
0.531 |
|
| 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 |
0.658 |
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| 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 |
0.683 |
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| 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 |
0.545 |
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| 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 |
0.793 |
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| 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 |
0.731 |
|
| 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 |
0.499 |
|
| 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 |
0.603 |
|
| 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 |
0.79 |
|
| 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 |
0.738 |
|
| 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 |
0.719 |
|
| 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 |
0.56 |
|
| 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 |
0.663 |
|
| 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 |
0.803 |
|
| 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 |
0.501 |
|
| 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 |
0.603 |
|
| 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 |
0.594 |
|
| 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 |
0.824 |
|
| 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 |
0.368 |
|
| 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 |
0.825 |
|
| 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 |
0.701 |
|
| 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 |
0.795 |
|
| 2006 |
Wilmarth PA, Tanner S, Dasari S, Nagalla SR, Riviere MA, Bafna V, Pevzner PA, David LL. 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? Journal of Proteome Research. 5: 2554-66. PMID 17022627 DOI: 10.1021/Pr050473A |
0.765 |
|
| 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 |
0.392 |
|
| 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 |
0.53 |
|
| 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 |
0.309 |
|
| 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 |
0.425 |
|
| 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 |
0.782 |
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| 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 |
0.788 |
|
| 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 |
0.818 |
|
| 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 |
0.798 |
|
| 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 |
0.604 |
|
| 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. |
0.437 |
|
| 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 |
0.47 |
|
| 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 |
0.725 |
|
| 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 |
0.36 |
|
| 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 |
0.451 |
|
| 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 |
0.344 |
|
| 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. DOI: 10.1007/3-540-45066-1_3 |
0.357 |
|
| 2001 |
Bafna V, Edwards N. SCOPE: A probabilistic model for scoring tandem mass spectra against a peptide database Bioinformatics. 17. PMID 11472988 DOI: 10.1093/Bioinformatics/17.Suppl_1.S13 |
0.391 |
|
| 2001 |
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, ... ... Bafna V, et al. The sequence of the human genome. Science (New York, N.Y.). 291: 1304-51. PMID 11181995 DOI: 10.1126/Science.1058040 |
0.485 |
|
| 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 |
0.314 |
|
| 1998 |
Bafna V, Pevzner PA. Sorting by transpositions Siam Journal On Discrete Mathematics. 11: 224-240. DOI: 10.1137/S089548019528280X |
0.609 |
|
| 1997 |
Bafna V, Lawler EL, Pevzner PA. Approximation algorithms for multiple sequence alignment Theoretical Computer Science. 182: 233-244. DOI: 10.1016/S0304-3975(97)00023-6 |
0.521 |
|
| 1996 |
Bafna V, Pevzner PA. Genome rearrangements and sorting by reversals Siam Journal On Computing. 25: 272-289. DOI: 10.1137/S0097539793250627 |
0.606 |
|
| 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. DOI: 10.1093/Oxfordjournals.Molbev.A040208 |
0.583 |
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