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Proteogenomic Annotation of Chinese Hamsters Reveals Extensive Novel Translation Events and Endogenous Retroviral Elements.

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.

J Proteome Res. 2019 Jun 7;18(6):2433-2445. doi: 10.1021/acs.jproteome.8b00935. Epub 2019 May 8.


NAD metabolic dependency in cancer is shaped by gene amplification and enhancer remodelling.

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.

Nature. 2019 May;569(7757):570-575. doi: 10.1038/s41586-019-1150-2. Epub 2019 Apr 24.


Case report on hypersensitivity to methotrexate infusion in a pediatric acute lymphoblastic leukaemia patient.

Sajith M, Pawar A, Bafna V, Bartakke S.

J Oncol Pharm Pract. 2019 Apr 8:1078155219839219. doi: 10.1177/1078155219839219. [Epub ahead of print]


Extrachromosomal oncogene amplification in tumour pathogenesis and evolution.

Verhaak RGW, Bafna V, Mischel PS.

Nat Rev Cancer. 2019 May;19(5):283-288. doi: 10.1038/s41568-019-0128-6. Review.


Skmer: assembly-free and alignment-free sample identification using genome skims.

Sarmashghi S, Bohmann K, P Gilbert MT, Bafna V, Mirarab S.

Genome Biol. 2019 Feb 13;20(1):34. doi: 10.1186/s13059-019-1632-4.


Exploring the landscape of focal amplifications in cancer using AmpliconArchitect.

Deshpande V, Luebeck J, Nguyen ND, Bakhtiari M, Turner KM, Schwab R, Carter H, Mischel PS, Bafna V.

Nat Commun. 2019 Jan 23;10(1):392. doi: 10.1038/s41467-018-08200-y.


Targeted genotyping of variable number tandem repeats with adVNTR.

Bakhtiari M, Shleizer-Burko S, Gymrek M, Bansal V, Bafna V.

Genome Res. 2018 Nov;28(11):1709-1719. doi: 10.1101/gr.235119.118. Epub 2018 Oct 23.


ProteoStorm: An Ultrafast Metaproteomics Database Search Framework.

Beyter D, Lin MS, Yu Y, Pieper R, Bafna V.

Cell Syst. 2018 Oct 24;7(4):463-467.e6. doi: 10.1016/j.cels.2018.08.009. Epub 2018 Sep 26.


Novel insight into the genetic basis of high-altitude pulmonary hypertension in Kyrgyz highlanders.

Iranmehr A, Stobdan T, Zhou D, Poulsen O, Strohl KP, Aldashev A, Telenti A, Wong EHM, Kirkness EF, Venter JC, Bafna V, Haddad GG.

Eur J Hum Genet. 2019 Jan;27(1):150-159. doi: 10.1038/s41431-018-0270-8. Epub 2018 Sep 25.


ViFi: accurate detection of viral integration and mRNA fusion reveals indiscriminate and unregulated transcription in proximal genomic regions in cervical cancer.

Nguyen ND, Deshpande V, Luebeck J, Mischel PS, Bafna V.

Nucleic Acids Res. 2018 Apr 20;46(7):3309-3325. doi: 10.1093/nar/gky180.


Identifying the favored mutation in a positive selective sweep.

Akbari A, Vitti JJ, Iranmehr A, Bakhtiari M, Sabeti PC, Mirarab S, Bafna V.

Nat Methods. 2018 Apr;15(4):279-282. doi: 10.1038/nmeth.4606. Epub 2018 Feb 19.


'Quality of Life' of Parents of Children Suffering from Pediatric Malignancies in a Low Income Setting.

Bafna VS, Bafna TA, Sampagar A, Rupavataram SR.

Indian J Pediatr. 2018 Sep;85(9):718-722. doi: 10.1007/s12098-018-2626-z. Epub 2018 Jan 25.


MHC class I loaded ligands from breast cancer cell lines: A potential HLA-I-typed antigen collection.

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.

J Proteomics. 2018 Mar 30;176:13-23. doi: 10.1016/j.jprot.2018.01.004. Epub 2018 Jan 10.


Human Leukocyte Antigen-B27: The Genetic Predisposition Leading to Reactive Arthritis during Induction Phase Chemotherapy for Acute Myeloid Leukemia.

Bartakke SP, Sampagar AA, Bafna VS, Patel P.

Indian J Med Paediatr Oncol. 2017 Jul-Sep;38(3):377-379. doi: 10.4103/ijmpo.ijmpo_8_17.


Ultraaccurate genome sequencing and haplotyping of single human cells.

Chu WK, Edge P, Lee HS, Bansal V, Bafna V, Huang X, Zhang K.

Proc Natl Acad Sci U S A. 2017 Nov 21;114(47):12512-12517. doi: 10.1073/pnas.1707609114. Epub 2017 Oct 24.


The Antibody Repertoire of Colorectal Cancer.

Cha SW, Bonissone S, Na S, Pevzner PA, Bafna V.

Mol Cell Proteomics. 2017 Dec;16(12):2111-2124. doi: 10.1074/mcp.RA117.000397. Epub 2017 Oct 18.


New Insights into the Genetic Basis of Monge's Disease and Adaptation to High-Altitude.

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.

Mol Biol Evol. 2017 Dec 1;34(12):3154-3168. doi: 10.1093/molbev/msx239.


High-altitude adaptation in humans: from genomics to integrative physiology.

Azad P, Stobdan T, Zhou D, Hartley I, Akbari A, Bafna V, Haddad GG.

J Mol Med (Berl). 2017 Dec;95(12):1269-1282. doi: 10.1007/s00109-017-1584-7. Epub 2017 Sep 26. Review.


Clear: Composition of Likelihoods for Evolve and Resequence Experiments.

Iranmehr A, Akbari A, Schlötterer C, Bafna V.

Genetics. 2017 Jun;206(2):1011-1023. doi: 10.1534/genetics.116.197566. Epub 2017 Apr 10.


Extrachromosomal oncogene amplification drives tumour evolution and genetic heterogeneity.

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.

Nature. 2017 Mar 2;543(7643):122-125. doi: 10.1038/nature21356. Epub 2017 Feb 8.


Juvenile granulosa cell tumor associated with Ollier disease.

Sampagar AA, Jahagirdar RR, Bafna VS, Bartakke SP.

Indian J Med Paediatr Oncol. 2016 Oct-Dec;37(4):293-295. doi: 10.4103/0971-5851.195749.


HapCUT2: robust and accurate haplotype assembly for diverse sequencing technologies.

Edge P, Bafna V, Bansal V.

Genome Res. 2017 May;27(5):801-812. doi: 10.1101/gr.213462.116. Epub 2016 Dec 9.


Correction: Predicting Carriers of Ongoing Selective Sweeps without Knowledge of the Favored Allele.

Ronen R, Tesler G, Akbari A, Zakov S, Rosenberg NA, Bafna V.

PLoS Genet. 2016 Nov 30;12(11):e1006472. doi: 10.1371/journal.pgen.1006472. eCollection 2016 Nov.


Senp1 drives hypoxia-induced polycythemia via GATA1 and Bcl-xL in subjects with Monge's disease.

Azad P, Zhao HW, Cabrales PJ, Ronen R, Zhou D, Poulsen O, Appenzeller O, Hsiao YH, Bafna V, Haddad GG.

J Exp Med. 2016 Nov 14;213(12):2729-2744. Epub 2016 Nov 7.


Integrated Proteogenomic Characterization of Human High-Grade Serous Ovarian Cancer.

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; CPTAC Investigators.

Cell. 2016 Jul 28;166(3):755-765. doi: 10.1016/j.cell.2016.05.069. Epub 2016 Jun 29.


InPhaDel: integrative shotgun and proximity-ligation sequencing to phase deletions with single nucleotide polymorphisms.

Patel A, Edge P, Selvaraj S, Bansal V, Bafna V.

Nucleic Acids Res. 2016 Jul 8;44(12):e111. doi: 10.1093/nar/gkw281. Epub 2016 Apr 21.


Diversity, Productivity, and Stability of an Industrial Microbial Ecosystem.

Beyter D, Tang PZ, Becker S, Hoang T, Bilgin D, Lim YW, Peterson TC, Mayfield S, Haerizadeh F, Shurin JB, Bafna V, McBride R.

Appl Environ Microbiol. 2016 Apr 4;82(8):2494-2505. doi: 10.1128/AEM.03965-15. Print 2016 Apr.


Next-Generation Sequencing of Plasmodium vivax Patient Samples Shows Evidence of Direct Evolution in Drug-Resistance Genes.

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.

ACS Infect Dis. 2015 Aug 14;1(8):367-79. doi: 10.1021/acsinfecdis.5b00049. Epub 2015 Aug 3.


The TGFβ1 Promoter SNP C-509T and Food Sensitization Promote Esophageal Remodeling in Pediatric Eosinophilic Esophagitis.

Rawson R, Anilkumar A, Newbury RO, Bafna V, Aquino M, Palmquist J, Hoffman HM, Mueller JL, Dohil R, Broide DH, Aceves SS.

PLoS One. 2015 Dec 14;10(12):e0144651. doi: 10.1371/journal.pone.0144651. eCollection 2015.


Predicting Carriers of Ongoing Selective Sweeps without Knowledge of the Favored Allele.

Ronen R, Tesler G, Akbari A, Zakov S, Rosenberg NA, Bafna V.

PLoS Genet. 2015 Sep 24;11(9):e1005527. doi: 10.1371/journal.pgen.1005527. eCollection 2015 Sep. Erratum in: PLoS Genet. 2016 Nov 30;12 (11):e1006472.


Endothelin receptor B, a candidate gene from human studies at high altitude, improves cardiac tolerance to hypoxia in genetically engineered heterozygote mice.

Stobdan T, Zhou D, Ao-Ieong E, Ortiz D, Ronen R, Hartley I, Gan Z, McCulloch AD, Bafna V, Cabrales P, Haddad GG.

Proc Natl Acad Sci U S A. 2015 Aug 18;112(33):10425-30. doi: 10.1073/pnas.1507486112. Epub 2015 Aug 3.


Advanced Proteogenomic Analysis Reveals Multiple Peptide Mutations and Complex Immunoglobulin Peptides in Colon Cancer.

Woo S, Cha SW, Bonissone S, Na S, Tabb DL, Pevzner PA, Bafna V.

J Proteome Res. 2015 Sep 4;14(9):3555-67. doi: 10.1021/acs.jproteome.5b00264. Epub 2015 Jul 21.


Reconstructing breakage fusion bridge architectures using noisy copy numbers.

Zakov S, Bafna V.

J Comput Biol. 2015 Jun;22(6):577-94. doi: 10.1089/cmb.2014.0166.


Genetic simulation tools for post-genome wide association studies of complex diseases.

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.

Genet Epidemiol. 2015 Jan;39(1):11-19. doi: 10.1002/gepi.21870. Epub 2014 Nov 4.


The genetic basis of chronic mountain sickness.

Ronen R, Zhou D, Bafna V, Haddad GG.

Physiology (Bethesda). 2014 Nov;29(6):403-12. doi: 10.1152/physiol.00008.2014. Review.


Proteogenomic strategies for identification of aberrant cancer peptides using large-scale next-generation sequencing data.

Woo S, Cha SW, Na S, Guest C, Liu T, Smith RD, Rodland KD, Payne S, Bafna V.

Proteomics. 2014 Dec;14(23-24):2719-30. doi: 10.1002/pmic.201400206. Epub 2014 Nov 17.


Annotation of the zebrafish genome through an integrated transcriptomic and proteomic analysis.

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.

Mol Cell Proteomics. 2014 Nov;13(11):3184-98. doi: 10.1074/mcp.M114.038299. Epub 2014 Jul 24.


The elusive evidence for chromothripsis.

Kinsella M, Patel A, Bafna V.

Nucleic Acids Res. 2014 Jul;42(13):8231-42. doi: 10.1093/nar/gku525. Epub 2014 Jun 17.


Inferring gene ontologies from pairwise similarity data.

Kramer M, Dutkowski J, Yu M, Bafna V, Ideker T.

Bioinformatics. 2014 Jun 15;30(12):i34-42. doi: 10.1093/bioinformatics/btu282.


Whole genome sequencing of Ethiopian highlanders reveals conserved hypoxia tolerance genes.

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.

Genome Biol. 2014 Feb 20;15(2):R36. doi: 10.1186/gb-2014-15-2-r36.


Amplification and thrifty single-molecule sequencing of recurrent somatic structural variations.

Patel A, Schwab R, Liu YT, Bafna V.

Genome Res. 2014 Feb;24(2):318-28. doi: 10.1101/gr.161497.113. Epub 2013 Dec 4.


An automated proteogenomic method uses mass spectrometry to reveal novel genes in Zea mays.

Castellana NE, Shen Z, He Y, Walley JW, Cassidy CJ, Briggs SP, Bafna V.

Mol Cell Proteomics. 2014 Jan;13(1):157-67. doi: 10.1074/mcp.M113.031260. Epub 2013 Oct 18.


On the design of clone-based haplotyping.

Lo C, Liu R, Lee J, Robasky K, Byrne S, Lucchesi C, Aach J, Church G, Bafna V, Zhang K.

Genome Biol. 2013;14(9):R100.


Virmid: accurate detection of somatic mutations with sample impurity inference.

Kim S, Jeong K, Bhutani K, Lee J, Patel A, Scott E, Nam H, Lee H, Gleeson JG, Bafna V.

Genome Biol. 2013 Aug 29;14(8):R90. doi: 10.1186/gb-2013-14-8-r90.


Whole-genome sequencing uncovers the genetic basis of chronic mountain sickness in Andean highlanders.

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.

Am J Hum Genet. 2013 Sep 5;93(3):452-62. doi: 10.1016/j.ajhg.2013.07.011. Epub 2013 Aug 15.


Proteogenomic database construction driven from large scale RNA-seq data.

Woo S, Cha SW, Merrihew G, He Y, Castellana N, Guest C, MacCoss M, Bafna V.

J Proteome Res. 2014 Jan 3;13(1):21-8. doi: 10.1021/pr400294c. Epub 2013 Jul 17.


Learning natural selection from the site frequency spectrum.

Ronen R, Udpa N, Halperin E, Bafna V.

Genetics. 2013 Sep;195(1):181-93. doi: 10.1534/genetics.113.152587. Epub 2013 Jun 14.


Evaluating genome architecture of a complex region via generalized bipartite matching.

Lo C, Kim S, Zakov S, Bafna V.

BMC Bioinformatics. 2013;14 Suppl 5:S13. doi: 10.1186/1471-2105-14-S5-S13. Epub 2013 Apr 10.


Using Genome Query Language to uncover genetic variation.

Kozanitis C, Heiberg A, Varghese G, Bafna V.

Bioinformatics. 2014 Jan 1;30(1):1-8. doi: 10.1093/bioinformatics/btt250. Epub 2013 Jun 10.


Reprever: resolving low-copy duplicated sequences using template driven assembly.

Kim S, Medvedev P, Paton TA, Bafna V.

Nucleic Acids Res. 2013 Jul;41(12):e128. doi: 10.1093/nar/gkt339. Epub 2013 May 8.

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