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Items: 1 to 20 of 107

1.

Effective Leveraging of Targeted Search Spaces for Improving Peptide Identification in Tandem Mass Spectrometry Based Proteomics.

Shanmugam AK, Nesvizhskii AI.

J Proteome Res. 2015 Dec 4;14(12):5169-78. doi: 10.1021/acs.jproteome.5b00504. Epub 2015 Nov 24.

2.

Two-pass alignment improves novel splice junction quantification.

Veeneman BA, Shukla S, Dhanasekaran SM, Chinnaiyan AM, Nesvizhskii AI.

Bioinformatics. 2016 Jan 1;32(1):43-9. doi: 10.1093/bioinformatics/btv642. Epub 2015 Oct 30.

3.

Large-Scale Analysis of Kinase Signaling in Yeast Pseudohyphal Development Identifies Regulation of Ribonucleoprotein Granules.

Shively CA, Kweon HK, Norman KL, Mellacheruvu D, Xu T, Sheidy DT, Dobry CJ, Sabath I, Cosky EE, Tran EJ, Nesvizhskii A, Andrews PC, Kumar A.

PLoS Genet. 2015 Oct 8;11(10):e1005564. doi: 10.1371/journal.pgen.1005564. eCollection 2015 Oct.

4.

mapDIA: Preprocessing and statistical analysis of quantitative proteomics data from data independent acquisition mass spectrometry.

Teo G, Kim S, Tsou CC, Collins B, Gingras AC, Nesvizhskii AI, Choi H.

J Proteomics. 2015 Nov 3;129:108-120. doi: 10.1016/j.jprot.2015.09.013. Epub 2015 Sep 15.

5.

QPROT: Statistical method for testing differential expression using protein-level intensity data in label-free quantitative proteomics.

Choi H, Kim S, Fermin D, Tsou CC, Nesvizhskii AI.

J Proteomics. 2015 Nov 3;129:121-126. doi: 10.1016/j.jprot.2015.07.036. Epub 2015 Aug 4.

6.

Mining Missing Membrane Proteins by High-pH Reverse-Phase StageTip Fractionation and Multiple Reaction Monitoring Mass Spectrometry.

Kitata RB, Dimayacyac-Esleta BR, Choong WK, Tsai CF, Lin TD, Tsou CC, Weng SH, Chen YJ, Yang PC, Arco SD, Nesvizhskii AI, Sung TY, Chen YJ.

J Proteome Res. 2015 Sep 4;14(9):3658-69. doi: 10.1021/acs.jproteome.5b00477. Epub 2015 Aug 6.

7.

Research Resource: Androgen Receptor Activity Is Regulated Through the Mobilization of Cell Surface Receptor Networks.

Hsiao JJ, Ng BH, Smits MM, Martinez HD, Jasavala RJ, Hinkson IV, Fermin D, Eng JK, Nesvizhskii AI, Wright ME.

Mol Endocrinol. 2015 Aug;29(8):1195-218. doi: 10.1210/me.2015-1021. Epub 2015 Jul 16.

8.

Metrics for the Human Proteome Project 2015: Progress on the Human Proteome and Guidelines for High-Confidence Protein Identification.

Omenn GS, Lane L, Lundberg EK, Beavis RC, Nesvizhskii AI, Deutsch EW.

J Proteome Res. 2015 Sep 4;14(9):3452-60. doi: 10.1021/acs.jproteome.5b00499. Epub 2015 Jul 30.

9.

The landscape of antisense gene expression in human cancers.

Balbin OA, Malik R, Dhanasekaran SM, Prensner JR, Cao X, Wu YM, Robinson D, Wang R, Chen G, Beer DG, Nesvizhskii AI, Chinnaiyan AM.

Genome Res. 2015 Jul;25(7):1068-79. doi: 10.1101/gr.180596.114. Epub 2015 Jun 10.

10.

Proteomic profiling of naïve multiple myeloma patient plasma cells identifies pathways associated with favourable response to bortezomib-based treatment regimens.

Dytfeld D, Rosebeck S, Kandarpa M, Mayampurath A, Mellacheruvu D, Alonge MM, Ngoka L, Jasielec J, Richardson PG, Volchenboum S, Nesvizhskii AI, Sreekumar A, Jakubowiak AJ.

Br J Haematol. 2015 Jul;170(1):66-79. doi: 10.1111/bjh.13394. Epub 2015 Mar 30.

11.

Targeting the MLL complex in castration-resistant prostate cancer.

Malik R, Khan AP, Asangani IA, Cieślik M, Prensner JR, Wang X, Iyer MK, Jiang X, Borkin D, Escara-Wilke J, Stender R, Wu YM, Niknafs YS, Jing X, Qiao Y, Palanisamy N, Kunju LP, Krishnamurthy PM, Yocum AK, Mellacheruvu D, Nesvizhskii AI, Cao X, Dhanasekaran SM, Feng FY, Grembecka J, Cierpicki T, Chinnaiyan AM.

Nat Med. 2015 Apr;21(4):344-52. doi: 10.1038/nm.3830. Epub 2015 Mar 30.

12.

Large-scale determination of absolute phosphorylation stoichiometries in human cells by motif-targeting quantitative proteomics.

Tsai CF, Wang YT, Yen HY, Tsou CC, Ku WC, Lin PY, Chen HY, Nesvizhskii AI, Ishihama Y, Chen YJ.

Nat Commun. 2015 Mar 27;6:6622. doi: 10.1038/ncomms7622.

13.

DIA-Umpire: comprehensive computational framework for data-independent acquisition proteomics.

Tsou CC, Avtonomov D, Larsen B, Tucholska M, Choi H, Gingras AC, Nesvizhskii AI.

Nat Methods. 2015 Mar;12(3):258-64, 7 p following 264. doi: 10.1038/nmeth.3255. Epub 2015 Jan 19.

14.

Analysis of Protein Stability by the Cycloheximide Chase Assay.

Kao SH, Wang WL, Chen CY, Chang YL, Wu YY, Wang YT, Wang SP, Nesvizhskii AI, Chen YJ, Hong TM, Yang PC.

Bio Protoc. 2015 Jan 5;5(1). pii: e1374. doi: 10.21769/BioProtoc.1374.

15.

LuciPHOr2: site localization of generic post-translational modifications from tandem mass spectrometry data.

Fermin D, Avtonomov D, Choi H, Nesvizhskii AI.

Bioinformatics. 2015 Apr 1;31(7):1141-3. doi: 10.1093/bioinformatics/btu788. Epub 2014 Nov 25.

16.

Proteogenomics: concepts, applications and computational strategies.

Nesvizhskii AI.

Nat Methods. 2014 Nov;11(11):1114-25. doi: 10.1038/nmeth.3144. Review.

17.

Utility of RNA-seq and GPMDB protein observation frequency for improving the sensitivity of protein identification by tandem MS.

Shanmugam AK, Yocum AK, Nesvizhskii AI.

J Proteome Res. 2014 Sep 5;13(9):4113-9. doi: 10.1021/pr500496p. Epub 2014 Jul 28.

18.

Global phosphoproteomic profiling reveals distinct signatures in B-cell non-Hodgkin lymphomas.

Rolland D, Basrur V, Conlon K, Wolfe T, Fermin D, Nesvizhskii AI, Lim MS, Elenitoba-Johnson KS.

Am J Pathol. 2014 May;184(5):1331-42. doi: 10.1016/j.ajpath.2014.01.036. Epub 2014 Mar 22.

19.

The yeast Sks1p kinase signaling network regulates pseudohyphal growth and glucose response.

Johnson C, Kweon HK, Sheidy D, Shively CA, Mellacheruvu D, Nesvizhskii AI, Andrews PC, Kumar A.

PLoS Genet. 2014 Mar 6;10(3):e1004183. doi: 10.1371/journal.pgen.1004183. eCollection 2014 Mar.

20.

SAINTexpress: improvements and additional features in Significance Analysis of INTeractome software.

Teo G, Liu G, Zhang J, Nesvizhskii AI, Gingras AC, Choi H.

J Proteomics. 2014 Apr 4;100:37-43. doi: 10.1016/j.jprot.2013.10.023. Epub 2013 Oct 26.

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