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    Results: 1 to 20 of 45

    1.

    Fast and accurate alignment of multiple protein networks.

    Kalaev M, Bafna V, Sharan R.

    J Comput Biol. 2009 Aug;16(8):989-99.PMID: 19624266 [PubMed - indexed for MEDLINE]Related articles

    2.

    Sequence and structural variation in a human genome uncovered by short-read, massively parallel ligation sequencing using two-base encoding.

    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.

    Genome Res. 2009 Sep;19(9):1527-41. Epub 2009 Jun 22.PMID: 19546169 [PubMed - in process]Related articlesFree article

    3.

    Discovery and revision of Arabidopsis genes by proteogenomics.

    Castellana NE, Payne SH, Shen Z, Stanke M, Bafna V, Briggs SP.

    Proc Natl Acad Sci U S A. 2008 Dec 30;105(52):21034-8. Epub 2008 Dec 19.PMID: 19098097 [PubMed - indexed for MEDLINE]Related articlesFree article

    4.

    QNet: a tool for querying protein interaction networks.

    Dost B, Shlomi T, Gupta N, Ruppin E, Bafna V, Sharan R.

    J Comput Biol. 2008 Sep;15(7):913-25.PMID: 18707533 [PubMed - indexed for MEDLINE]Related articles

    5.

    HapCUT: an efficient and accurate algorithm for the haplotype assembly problem.

    Bansal V, Bafna V.

    Bioinformatics. 2008 Aug 15;24(16):i153-9.PMID: 18689818 [PubMed - indexed for MEDLINE]Related articlesFree article

    6.

    An MCMC algorithm for haplotype assembly from whole-genome sequence data.

    Bansal V, Halpern AL, Axelrod N, Bafna V.

    Genome Res. 2008 Aug;18(8):1336-46.PMID: 18676820 [PubMed - indexed for MEDLINE]Related articlesFree article

    7.

    Phosphorylation-specific MS/MS scoring for rapid and accurate phosphoproteome analysis.

    Payne SH, Yau M, Smolka MB, Tanner S, Zhou H, Bafna V.

    J Proteome Res. 2008 Aug;7(8):3373-81. Epub 2008 Jun 19.PMID: 18563926 [PubMed - indexed for MEDLINE]Related articlesFree article

    8.

    Structural alignment of pseudoknotted RNA.

    Han B, Dost B, Bafna V, Zhang S.

    J Comput Biol. 2008 Jun;15(5):489-504.PMID: 18549303 [PubMed - indexed for MEDLINE]Related articles

    9.

    Comparative proteogenomics: combining mass spectrometry and comparative genomics to analyze multiple genomes.

    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.

    Genome Res. 2008 Jul;18(7):1133-42. Epub 2008 Apr 21.PMID: 18426904 [PubMed - indexed for MEDLINE]Related articlesFree article

    10.

    A multidimensional chromatography technology for in-depth phosphoproteome analysis.

    Albuquerque CP, Smolka MB, Payne SH, Bafna V, Eng J, Zhou H.

    Mol Cell Proteomics. 2008 Jul;7(7):1389-96. Epub 2008 Apr 11.PMID: 18407956 [PubMed - indexed for MEDLINE]Related articlesFree article

    11.

    Evaluation of paired-end sequencing strategies for detection of genome rearrangements in cancer.

    Bashir A, Volik S, Collins C, Bafna V, Raphael BJ.

    PLoS Comput Biol. 2008 Apr 25;4(4):e1000051.PMID: 18404202 [PubMed - indexed for MEDLINE]Related articlesFree article

    12.

    A decomposition theory for phylogenetic networks and incompatible characters.

    Gusfield D, Bansal V, Bafna V, Song YS.

    J Comput Biol. 2007 Dec;14(10):1247-72.PMID: 18047426 [PubMed - indexed for MEDLINE]Related articlesFree article

    13.

    Accurate annotation of peptide modifications through unrestrictive database search.

    Tanner S, Payne SH, Dasari S, Shen Z, Wilmarth PA, David LL, Loomis WF, Briggs SP, Bafna V.

    J Proteome Res. 2008 Jan;7(1):170-81. Epub 2007 Nov 23.PMID: 18034453 [PubMed - indexed for MEDLINE]Related articles

    14.

    The diploid genome sequence of an individual human.

    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.

    PLoS Biol. 2007 Sep 4;5(10):e254.PMID: 17803354 [PubMed - indexed for MEDLINE]Related articlesFree article

    15.

    Optimization of primer design for the detection of variable genomic lesions in cancer.

    Bashir A, Liu YT, Raphael BJ, Carson D, Bafna V.

    Bioinformatics. 2007 Nov 1;23(21):2807-15. Epub 2007 Aug 30.PMID: 17766270 [PubMed - indexed for MEDLINE]Related articlesFree article

    16.

    Whole proteome analysis of post-translational modifications: applications of mass-spectrometry for proteogenomic annotation.

    Gupta N, Tanner S, Jaitly N, Adkins JN, Lipton M, Edwards R, Romine M, Osterman A, Bafna V, Smith RD, Pevzner PA.

    Genome Res. 2007 Sep;17(9):1362-77. Epub 2007 Aug 9.PMID: 17690205 [PubMed - indexed for MEDLINE]Related articlesFree article

    17.

    Integrating scientific cultures.

    Ideker T, Bafna V, Lemberger T.

    Mol Syst Biol. 2007;3:105. Epub 2007 Apr 17. No abstract available. PMID: 17437030 [PubMed - indexed for MEDLINE]Related articlesFree article

    18.

    Unrestrictive identification of post-translational modifications through peptide mass spectrometry.

    Tanner S, Pevzner PA, Bafna V.

    Nat Protoc. 2006;1(1):67-72.PMID: 17406213 [PubMed - indexed for MEDLINE]Related articles

    19.

    The Sorcerer II Global Ocean Sampling expedition: expanding the universe of protein families.

    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.

    PLoS Biol. 2007 Mar;5(3):e16.PMID: 17355171 [PubMed - indexed for MEDLINE]Related articlesFree article

    20.

    Improving gene annotation using peptide mass spectrometry.

    Tanner S, Shen Z, Ng J, Florea L, Guigó R, Briggs SP, Bafna V.

    Genome Res. 2007 Feb;17(2):231-9. Epub 2006 Dec 22.PMID: 17189379 [PubMed - indexed for MEDLINE]Related articlesFree article

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