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Results: 1 to 20 of 88


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. doi: 10.1038/nmeth.3255. Epub 2015 Jan 19.


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

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

Bioinformatics. 2014 Nov 25. pii: btu788. [Epub ahead of print]


Proteogenomics: concepts, applications and computational strategies.

Nesvizhskii AI.

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


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.


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.


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.


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.


Reconstructing targetable pathways in lung cancer by integrating diverse omics data.

Balbin OA, Prensner JR, Sahu A, Yocum A, Shankar S, Malik R, Fermin D, Dhanasekaran SM, Chandler B, Thomas D, Beer DG, Cao X, Nesvizhskii AI, Chinnaiyan AM.

Nat Commun. 2013;4:2617. doi: 10.1038/ncomms3617.


Comprehensive analysis of protein digestion using six trypsins reveals the origin of trypsin as a significant source of variability in proteomics.

Walmsley SJ, Rudnick PA, Liang Y, Dong Q, Stein SE, Nesvizhskii AI.

J Proteome Res. 2013 Dec 6;12(12):5666-80. doi: 10.1021/pr400611h. Epub 2013 Nov 14.


The CRAPome: a contaminant repository for affinity purification-mass spectrometry data.

Mellacheruvu D, Wright Z, Couzens AL, Lambert JP, St-Denis NA, Li T, Miteva YV, Hauri S, Sardiu ME, Low TY, Halim VA, Bagshaw RD, Hubner NC, Al-Hakim A, Bouchard A, Faubert D, Fermin D, Dunham WH, Goudreault M, Lin ZY, Badillo BG, Pawson T, Durocher D, Coulombe B, Aebersold R, Superti-Furga G, Colinge J, Heck AJ, Choi H, Gstaiger M, Mohammed S, Cristea IM, Bennett KL, Washburn MP, Raught B, Ewing RM, Gingras AC, Nesvizhskii AI.

Nat Methods. 2013 Aug;10(8):730-6. doi: 10.1038/nmeth.2557. Epub 2013 Jul 7.


LuciPHOr: algorithm for phosphorylation site localization with false localization rate estimation using modified target-decoy approach.

Fermin D, Walmsley SJ, Gingras AC, Choi H, Nesvizhskii AI.

Mol Cell Proteomics. 2013 Nov;12(11):3409-19. doi: 10.1074/mcp.M113.028928. Epub 2013 Aug 5.


GSK3β controls epithelial-mesenchymal transition and tumor metastasis by CHIP-mediated degradation of Slug.

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

Oncogene. 2014 Jun 12;33(24):3172-82. doi: 10.1038/onc.2013.279. Epub 2013 Jul 15.


Fusion peptides from oncogenic chimeric proteins as putative specific biomarkers of cancer.

Conlon KP, Basrur V, Rolland D, Wolfe T, Nesvizhskii AI, MacCoss MJ, Lim MS, Elenitoba-Johnson KS.

Mol Cell Proteomics. 2013 Oct;12(10):2714-23. doi: 10.1074/mcp.M113.029926. Epub 2013 Jul 8.


The functional interactome landscape of the human histone deacetylase family.

Joshi P, Greco TM, Guise AJ, Luo Y, Yu F, Nesvizhskii AI, Cristea IM.

Mol Syst Biol. 2013;9:672. doi: 10.1038/msb.2013.26.


Combining results of multiple search engines in proteomics.

Shteynberg D, Nesvizhskii AI, Moritz RL, Deutsch EW.

Mol Cell Proteomics. 2013 Sep;12(9):2383-93. doi: 10.1074/mcp.R113.027797. Epub 2013 May 29. Review.


Sparsely correlated hidden Markov models with application to genome-wide location studies.

Choi H, Fermin D, Nesvizhskii AI, Ghosh D, Qin ZS.

Bioinformatics. 2013 Mar 1;29(5):533-41. doi: 10.1093/bioinformatics/btt012. Epub 2013 Jan 16.


A statistical model-building perspective to identification of MS/MS spectra with PeptideProphet.

Ma K, Vitek O, Nesvizhskii AI.

BMC Bioinformatics. 2012;13 Suppl 16:S1. doi: 10.1186/1471-2105-13-S16-S1. Epub 2012 Nov 5.


Using ProHits to store, annotate, and analyze affinity purification-mass spectrometry (AP-MS) data.

Liu G, Zhang J, Choi H, Lambert JP, Srikumar T, Larsen B, Nesvizhskii AI, Raught B, Tyers M, Gingras AC.

Curr Protoc Bioinformatics. 2012 Sep;Chapter 8:Unit8.16. doi: 10.1002/0471250953.bi0816s39.


Analyzing protein-protein interactions from affinity purification-mass spectrometry data with SAINT.

Choi H, Liu G, Mellacheruvu D, Tyers M, Gingras AC, Nesvizhskii AI.

Curr Protoc Bioinformatics. 2012 Sep;Chapter 8:Unit8.15. doi: 10.1002/0471250953.bi0815s39.


A dual role for receptor-interacting protein kinase 2 (RIP2) kinase activity in nucleotide-binding oligomerization domain 2 (NOD2)-dependent autophagy.

Homer CR, Kabi A, Marina-García N, Sreekumar A, Nesvizhskii AI, Nickerson KP, Chinnaiyan AM, Nuñez G, McDonald C.

J Biol Chem. 2012 Jul 20;287(30):25565-76. doi: 10.1074/jbc.M111.326835. Epub 2012 Jun 4.

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