Alexey I. Nesvizhskii, Ph.D. - Publications

Affiliations: 
2001 University of Washington, Seattle, Seattle, WA 
Area:
Condensed Matter Physics

114 high-probability publications. We are testing a new system for linking publications to authors. You can help! If you notice any innacuracies, please sign in and mark papers as correct or incorrect matches. If you identify any major omissions or other inaccuracies in the publication list, please let us know.

Year Citation  Score
2016 Avtonomov DM, Raskind A, Nesvizhskii AI. BatMass: a Java software platform for LC/MS data visualization in proteomics and metabolomics. Journal of Proteome Research. PMID 27306858 DOI: 10.1021/acs.jproteome.6b00021  1
2016 Tsou CC, Tsai CF, Teo G, Chen YJ, Nesvizhskii AI. Untargeted, spectral library-free analysis of data independent acquisition proteomics data generated using Orbitrap mass spectrometers. Proteomics. PMID 27246681 DOI: 10.1002/pmic.201500526  1
2016 Kochen MA, Chambers MC, Holman JD, Nesvizhskii AI, Weintraub ST, Belisle JT, Islam N, Tabb DL. Greazy: open-source software for automated phospholipid MS/MS identification. Analytical Chemistry. PMID 27186799 DOI: 10.1021/acs.analchem.6b00021  1
2016 Zhang H, Gayen S, Xiong J, Zhou B, Shanmugam AK, Sun Y, Karatas H, Liu L, Rao RC, Wang S, Nesvizhskii AI, Kalantry S, Dou Y. MLL1 Inhibition Reprograms Epiblast Stem Cells to Naive Pluripotency. Cell Stem Cell. PMID 26996599 DOI: 10.1016/j.stem.2016.02.004  1
2016 Veeneman BA, Shukla S, Dhanasekaran SM, Chinnaiyan AM, Nesvizhskii AI. Two-pass alignment improves novel splice junction quantification. Bioinformatics (Oxford, England). 32: 43-9. PMID 26519505 DOI: 10.1093/bioinformatics/btv642  1
2015 Shanmugam AK, Nesvizhskii AI. Effective Leveraging of Targeted Search Spaces for Improving Peptide Identification in Tandem Mass Spectrometry Based Proteomics. Journal of Proteome Research. PMID 26569054 DOI: 10.1021/acs.jproteome.5b00504  1
2015 Teo G, Kim S, Tsou CC, Collins B, Gingras AC, Nesvizhskii AI, Choi H. mapDIA: Preprocessing and Statistical Analysis of Quantitative Proteomics Data from Data Independent Acquisition Mass Spectrometry. Journal of Proteomics. PMID 26381204 DOI: 10.1016/j.jprot.2015.09.013  1
2015 Choi H, Kim S, Fermin D, Tsou CC, Nesvizhskii AI. QPROT: Statistical method for testing differential expression using protein-level intensity data in label-free quantitative proteomics. Journal of Proteomics. PMID 26254008 DOI: 10.1016/j.jprot.2015.07.036  1
2015 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. Mining Missing Membrane Proteins by High-pH Reverse-Phase StageTip Fractionation and Multiple Reaction Monitoring Mass Spectrometry. Journal of Proteome Research. 14: 3658-69. PMID 26202522 DOI: 10.1021/acs.jproteome.5b00477  1
2015 Hsiao JJ, Ng BH, Smits MM, Martinez HD, Jasavala RJ, Hinkson IV, Fermin D, Eng JK, Nesvizhskii AI, Wright ME. Research Resource: Androgen Receptor Activity is Regulated through the Mobilization of Cell Surface Receptor Networks. Molecular Endocrinology (Baltimore, Md.). me20151021. PMID 26181434 DOI: 10.1210/me.2015-1021  1
2015 Omenn GS, Lane L, Lundberg EK, Beavis RC, Nesvizhskii AI, Deutsch EW. Metrics for the Human Proteome Project 2015: Progress on the Human Proteome and Guidelines for High-Confidence Protein Identification. Journal of Proteome Research. 14: 3452-60. PMID 26155816 DOI: 10.1021/acs.jproteome.5b00499  1
2015 Balbin OA, Malik R, Dhanasekaran SM, Prensner JR, Cao X, Wu YM, Robinson D, Wang R, Chen G, Beer DG, Nesvizhskii AI, Chinnaiyan AM. The landscape of antisense gene expression in human cancers. Genome Research. 25: 1068-79. PMID 26063736 DOI: 10.1101/gr.180596.114  1
2015 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. Proteomic profiling of naïve multiple myeloma patient plasma cells identifies pathways associated with favourable response to bortezomib-based treatment regimens. British Journal of Haematology. 170: 66-79. PMID 25824111 DOI: 10.1111/bjh.13394  1
2015 Malik R, Khan AP, Asangani IA, Cie?lik M, Prensner JR, Wang X, Iyer MK, Jiang X, Borkin D, Escara-Wilke J, Stender R, Wu YM, Niknafs YS, Jing X, Qiao Y, ... ... Nesvizhskii AI, et al. Targeting the MLL complex in castration-resistant prostate cancer. Nature Medicine. 21: 344-52. PMID 25822367 DOI: 10.1038/nm.3830  1
2015 Tsai CF, Wang YT, Yen HY, Tsou CC, Ku WC, Lin PY, Chen HY, Nesvizhskii AI, Ishihama Y, Chen YJ. Large-scale determination of absolute phosphorylation stoichiometries in human cells by motif-targeting quantitative proteomics. Nature Communications. 6: 6622. PMID 25814448 DOI: 10.1038/ncomms7622  1
2015 Tsou CC, Avtonomov D, Larsen B, Tucholska M, Choi H, Gingras AC, Nesvizhskii AI. DIA-Umpire: comprehensive computational framework for data-independent acquisition proteomics. Nature Methods. 12: 258-64, 7 p followin. PMID 25599550 DOI: 10.1038/nmeth.3255  1
2015 Fermin D, Avtonomov D, Choi H, Nesvizhskii AI. LuciPHOr2: site localization of generic post-translational modifications from tandem mass spectrometry data. Bioinformatics (Oxford, England). 31: 1141-3. PMID 25429062 DOI: 10.1093/bioinformatics/btu788  1
2014 Nesvizhskii AI. Proteogenomics: concepts, applications and computational strategies. Nature Methods. 11: 1114-25. PMID 25357241 DOI: 10.1038/nmeth.3144  1
2014 Shanmugam AK, Yocum AK, Nesvizhskii AI. Utility of RNA-seq and GPMDB protein observation frequency for improving the sensitivity of protein identification by tandem MS. Journal of Proteome Research. 13: 4113-9. PMID 25026199 DOI: 10.1021/pr500496p  1
2014 Rolland D, Basrur V, Conlon K, Wolfe T, Fermin D, Nesvizhskii AI, Lim MS, Elenitoba-Johnson KS. Global phosphoproteomic profiling reveals distinct signatures in B-cell non-Hodgkin lymphomas. The American Journal of Pathology. 184: 1331-42. PMID 24667141 DOI: 10.1016/j.ajpath.2014.01.036  1
2014 Johnson C, Kweon HK, Sheidy D, Shively CA, Mellacheruvu D, Nesvizhskii AI, Andrews PC, Kumar A. The yeast Sks1p kinase signaling network regulates pseudohyphal growth and glucose response. Plos Genetics. 10: e1004183. PMID 24603354 DOI: 10.1371/journal.pgen.1004183  1
2014 Teo G, Liu G, Zhang J, Nesvizhskii AI, Gingras AC, Choi H. SAINTexpress: improvements and additional features in Significance Analysis of INTeractome software. Journal of Proteomics. 100: 37-43. PMID 24513533 DOI: 10.1016/j.jprot.2013.10.023  1
2014 Kao SH, Wang WL, Chen CY, Chang YL, Wu YY, Wang YT, Wang SP, Nesvizhskii AI, Chen YJ, Hong TM, Yang PC. GSK3β controls epithelial-mesenchymal transition and tumor metastasis by CHIP-mediated degradation of Slug. Oncogene. 33: 3172-82. PMID 23851495 DOI: 10.1038/onc.2013.279  1
2013 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. Reconstructing targetable pathways in lung cancer by integrating diverse omics data. Nature Communications. 4: 2617. PMID 24135919 DOI: 10.1038/ncomms3617  1
2013 Walmsley SJ, Rudnick PA, Liang Y, Dong Q, Stein SE, Nesvizhskii AI. Comprehensive analysis of protein digestion using six trypsins reveals the origin of trypsin as a significant source of variability in proteomics. Journal of Proteome Research. 12: 5666-80. PMID 24116745 DOI: 10.1021/pr400611h  1
2013 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, ... ... Nesvizhskii AI, et al. The CRAPome: a contaminant repository for affinity purification-mass spectrometry data. Nature Methods. 10: 730-6. PMID 23921808 DOI: 10.1038/nmeth.2557  1
2013 Fermin D, Walmsley SJ, Gingras AC, Choi H, Nesvizhskii AI. LuciPHOr: algorithm for phosphorylation site localization with false localization rate estimation using modified target-decoy approach. Molecular & Cellular Proteomics : McP. 12: 3409-19. PMID 23918812 DOI: 10.1074/mcp.M113.028928  1
2013 Conlon KP, Basrur V, Rolland D, Wolfe T, Nesvizhskii AI, MacCoss MJ, Lim MS, Elenitoba-Johnson KSJ. Fusion peptides from oncogenic chimeric proteins as putative specific biomarkers of cancer Molecular and Cellular Proteomics. 12: 2714-2723. PMID 23836920 DOI: 10.1074/mcp.M113.029926  1
2013 Joshi P, Greco TM, Guise AJ, Luo Y, Yu F, Nesvizhskii AI, Cristea IM. The functional interactome landscape of the human histone deacetylase family. Molecular Systems Biology. 9: 672. PMID 23752268 DOI: 10.1038/msb.2013.26  1
2013 Shteynberg D, Nesvizhskii AI, Moritz RL, Deutsch EW. Combining results of multiple search engines in proteomics. Molecular & Cellular Proteomics : McP. 12: 2383-93. PMID 23720762 DOI: 10.1074/mcp.R113.027797  1
2013 Choi H, Fermin D, Nesvizhskii AI, Ghosh D, Qin ZS. Sparsely correlated hidden Markov models with application to genome-wide location studies. Bioinformatics (Oxford, England). 29: 533-41. PMID 23325620 DOI: 10.1093/bioinformatics/btt012  1
2012 Ma K, Vitek O, Nesvizhskii AI. A statistical model-building perspective to identification of MS/MS spectra with PeptideProphet. Bmc Bioinformatics. 13: S1. PMID 23176103 DOI: 10.1186/1471-2105-13-S16-S1  1
2012 Liu G, Zhang J, Choi H, Lambert JP, Srikumar T, Larsen B, Nesvizhskii AI, Raught B, Tyers M, Gingras AC. Using ProHits to store, annotate, and analyze affinity purification-mass spectrometry (AP-MS) data. Current Protocols in Bioinformatics / Editoral Board, Andreas D. Baxevanis ... [Et Al.]. Unit8.16. PMID 22948730 DOI: 10.1002/0471250953.bi0816s39  1
2012 Choi H, Liu G, Mellacheruvu D, Tyers M, Gingras AC, Nesvizhskii AI. Analyzing protein-protein interactions from affinity purification-mass spectrometry data with SAINT. Current Protocols in Bioinformatics / Editoral Board, Andreas D. Baxevanis ... [Et Al.]. Unit8.15. PMID 22948729 DOI: 10.1002/0471250953.bi0815s39  1
2012 Homer CR, Kabi A, Marina-García N, Sreekumar A, Nesvizhskii AI, Nickerson KP, Chinnaiyan AM, Nuñez G, McDonald C. A dual role for receptor-interacting protein kinase 2 (RIP2) kinase activity in nucleotide-binding oligomerization domain 2 (NOD2)-dependent autophagy. The Journal of Biological Chemistry. 287: 25565-76. PMID 22665475 DOI: 10.1074/jbc.M111.326835  1
2012 Nesvizhskii AI. Computational and informatics strategies for identification of specific protein interaction partners in affinity purification mass spectrometry experiments. Proteomics. 12: 1639-55. PMID 22611043 DOI: 10.1002/pmic.201100537  1
2012 Richmond AL, Kabi A, Homer CR, Marina-García N, Nickerson KP, Nesvizhskii AI, Sreekumar A, Chinnaiyan AM, Nuñez G, McDonald C. The nucleotide synthesis enzyme CAD inhibits NOD2 antibacterial function in human intestinal epithelial cells. Gastroenterology. 142: 1483-92.e6. PMID 22387394 DOI: 10.1053/j.gastro.2012.02.040  1
2012 Choi H, Glatter T, Gstaiger M, Nesvizhskii AI. SAINT-MS1: protein-protein interaction scoring using label-free intensity data in affinity purification-mass spectrometry experiments. Journal of Proteome Research. 11: 2619-24. PMID 22352807 DOI: 10.1021/pr201185r  1
2012 Ning K, Fermin D, Nesvizhskii AI. Comparative analysis of different label-free mass spectrometry based protein abundance estimates and their correlation with RNA-Seq gene expression data. Journal of Proteome Research. 11: 2261-71. PMID 22329341 DOI: 10.1021/pr201052x  1
2012 Rodríguez-Piñeiro AM, van der Post S, Johansson ME, Thomsson KA, Nesvizhskii AI, Hansson GC. Proteomic study of the mucin granulae in an intestinal goblet cell model. Journal of Proteome Research. 11: 1879-90. PMID 22248381 DOI: 10.1021/pr2010988  1
2011 Glatter T, Schittenhelm RB, Rinner O, Roguska K, Wepf A, Jünger MA, Köhler K, Jevtov I, Choi H, Schmidt A, Nesvizhskii AI, Stocker H, Hafen E, Aebersold R, Gstaiger M. Modularity and hormone sensitivity of the Drosophila melanogaster insulin receptor/target of rapamycin interaction proteome. Molecular Systems Biology. 7: 547. PMID 22068330 DOI: 10.1038/msb.2011.79  1
2011 Shteynberg D, Deutsch EW, Lam H, Eng JK, Sun Z, Tasman N, Mendoza L, Moritz RL, Aebersold R, Nesvizhskii AI. iProphet: multi-level integrative analysis of shotgun proteomic data improves peptide and protein identification rates and error estimates. Molecular & Cellular Proteomics : McP. 10: M111.007690. PMID 21876204 DOI: 10.1074/mcp.M111.007690  1
2011 Bayona JC, Nakayasu ES, Laverrière M, Aguilar C, Sobreira TJ, Choi H, Nesvizhskii AI, Almeida IC, Cazzulo JJ, Alvarez VE. SUMOylation pathway in Trypanosoma cruzi: functional characterization and proteomic analysis of target proteins. Molecular & Cellular Proteomics : McP. 10: M110.007369. PMID 21832256 DOI: 10.1074/mcp.M110.007369  1
2011 Bergerat A, Decano J, Wu CJ, Choi H, Nesvizhskii AI, Moran AM, Ruiz-Opazo N, Steffen M, Herrera VL. Prestroke proteomic changes in cerebral microvessels in stroke-prone, transgenic[hCETP]-Hyperlipidemic, Dahl salt-sensitive hypertensive rats. Molecular Medicine (Cambridge, Mass.). 17: 588-98. PMID 21519634 DOI: 10.2119/molmed.2010.00228  1
2011 Kwon T, Choi H, Vogel C, Nesvizhskii AI, Marcotte EM. MSblender: A probabilistic approach for integrating peptide identifications from multiple database search engines. Journal of Proteome Research. 10: 2949-58. PMID 21488652 DOI: 10.1021/pr2002116  1
2011 Vareed SK, Bhat VB, Thompson C, Vasu VT, Fermin D, Choi H, Creighton CJ, Gayatri S, Lan L, Putluri N, Thangjam GS, Kaur P, Shabahang M, Giri JG, Nesvizhskii AI, et al. Metabolites of purine nucleoside phosphorylase (NP) in serum have the potential to delineate pancreatic adenocarcinoma. Plos One. 6: e17177. PMID 21448452 DOI: 10.1371/journal.pone.0017177  1
2011 Skarra DV, Goudreault M, Choi H, Mullin M, Nesvizhskii AI, Gingras AC, Honkanen RE. Label-free quantitative proteomics and SAINT analysis enable interactome mapping for the human Ser/Thr protein phosphatase 5 Proteomics. 11: 1508-1516. PMID 21360678 DOI: 10.1002/pmic.201000770  1
2011 Fermin D, Basrur V, Yocum AK, Nesvizhskii AI. Abacus: a computational tool for extracting and pre-processing spectral count data for label-free quantitative proteomic analysis. Proteomics. 11: 1340-5. PMID 21360675 DOI: 10.1002/pmic.201000650  1
2011 Emmer BT, Nakayasu ES, Souther C, Choi H, Sobreira TJ, Epting CL, Nesvizhskii AI, Almeida IC, Engman DM. Global analysis of protein palmitoylation in African trypanosomes. Eukaryotic Cell. 10: 455-63. PMID 21193548 DOI: 10.1128/EC.00248-10  1
2011 Choi H, Larsen B, Lin ZY, Breitkreutz A, Mellacheruvu D, Fermin D, Qin ZS, Tyers M, Gingras AC, Nesvizhskii AI. SAINT: probabilistic scoring of affinity purification-mass spectrometry data. Nature Methods. 8: 70-3. PMID 21131968 DOI: 10.1038/nmeth.1541  1
2010 Ning K, Nesvizhskii AI. The utility of mass spectrometry-based proteomic data for validation of novel alternative splice forms reconstructed from RNA-Seq data: a preliminary assessment. Bmc Bioinformatics. 11: S14. PMID 21172049 DOI: 10.1186/1471-2105-11-S11-S14  1
2010 Liu G, Zhang J, Larsen B, Stark C, Breitkreutz A, Lin ZY, Breitkreutz BJ, Ding Y, Colwill K, Pasculescu A, Pawson T, Wrana JL, Nesvizhskii AI, Raught B, Tyers M, et al. ProHits: integrated software for mass spectrometry-based interaction proteomics. Nature Biotechnology. 28: 1015-7. PMID 20944583 DOI: 10.1038/nbt1010-1015  1
2010 Ning K, Ng HK, Srihari S, Leong HW, Nesvizhskii AI. Examination of the relationship between essential genes in PPI network and hub proteins in reverse nearest neighbor topology. Bmc Bioinformatics. 11: 505. PMID 20939873 DOI: 10.1186/1471-2105-11-505  1
2010 Nesvizhskii AI. A survey of computational methods and error rate estimation procedures for peptide and protein identification in shotgun proteomics. Journal of Proteomics. 73: 2092-123. PMID 20816881 DOI: 10.1016/j.jprot.2010.08.009  1
2010 Choi H, Kim S, Gingras AC, Nesvizhskii AI. Analysis of protein complexes through model-based biclustering of label-free quantitative AP-MS data. Molecular Systems Biology. 6: 385. PMID 20571534 DOI: 10.1038/msb.2010.41  1
2010 Vellaichamy A, Dezso Z, JeBailey L, Chinnaiyan AM, Sreekumar A, Nesvizhskii AI, Omenn GS, Bugrim A. "Topological significance" analysis of gene expression and proteomic profiles from prostate cancer cells reveals key mechanisms of androgen response. Plos One. 5: e10936. PMID 20532174 DOI: 10.1371/journal.pone.0010936  1
2010 Breitkreutz A, Choi H, Sharom JR, Boucher L, Neduva V, Larsen B, Lin ZY, Breitkreutz BJ, Stark C, Liu G, Ahn J, Dewar-Darch D, Reguly T, Tang X, Almeida R, ... ... Nesvizhskii AI, et al. A global protein kinase and phosphatase interaction network in yeast. Science (New York, N.Y.). 328: 1043-6. PMID 20489023 DOI: 10.1126/science.1176495  1
2010 Ning K, Fermin D, Nesvizhskii AI. Computational analysis of unassigned high-quality MS/MS spectra in proteomic data sets. Proteomics. 10: 2712-8. PMID 20455209 DOI: 10.1002/pmic.200900473  1
2010 Saleem RA, Rogers RS, Ratushny AV, Dilworth DJ, Shannon PT, Shteynberg D, Wan Y, Moritz RL, Nesvizhskii AI, Rachubinski RA, Aitchison JD. Integrated phosphoproteomics analysis of a signaling network governing nutrient response and peroxisome induction. Molecular & Cellular Proteomics : McP. 9: 2076-88. PMID 20395639 DOI: 10.1074/mcp.M000116-MCP201  1
2010 Deutsch EW, Mendoza L, Shteynberg D, Farrah T, Lam H, Tasman N, Sun Z, Nilsson E, Pratt B, Prazen B, Eng JK, Martin DB, Nesvizhskii AI, Aebersold R. A guided tour of the Trans-Proteomic Pipeline. Proteomics. 10: 1150-9. PMID 20101611 DOI: 10.1002/pmic.200900375  1
2010 Khan AP, Poisson LM, Bhat VB, Fermin D, Zhao R, Kalyana-Sundaram S, Michailidis G, Nesvizhskii AI, Omenn GS, Chinnaiyan AM, Sreekumar A. Quantitative proteomic profiling of prostate cancer reveals a role for miR-128 in prostate cancer. Molecular & Cellular Proteomics : McP. 9: 298-312. PMID 19955085 DOI: 10.1074/mcp.M900159-MCP200  1
2010 Vellaichamy A, Lin CY, Aye TT, Kunde GR, Nesvizhskii AI, Liu ET, Sze SK. A chloroform-assisted protein isolation method followed by capillary NanoLC-MS identify estrogen-regulated proteins from MCF7 cells Journal of Proteomics and Bioinformatics. 3: 212-220. DOI: 10.4172/jpb.1000142  1
2009 Vellaichamy A, Sreekumar A, Strahler JR, Rajendiran T, Yu J, Varambally S, Li Y, Omenn GS, Chinnaiyan AM, Nesvizhskii AI. Proteomic interrogation of androgen action in prostate cancer cells reveals roles of aminoacyl tRNA synthetases. Plos One. 4: e7075. PMID 19763266 DOI: 10.1371/journal.pone.0007075  1
2009 Choi H, Nesvizhskii AI, Ghosh D, Qin ZS. Hierarchical hidden Markov model with application to joint analysis of ChIP-chip and ChIP-seq data. Bioinformatics (Oxford, England). 25: 1715-21. PMID 19447789 DOI: 10.1093/bioinformatics/btp312  1
2009 Ho L, Ronan JL, Wu J, Staahl BT, Chen L, Kuo A, Lessard J, Nesvizhskii AI, Ranish J, Crabtree GR. An embryonic stem cell chromatin remodeling complex, esBAF, is essential for embryonic stem cell self-renewal and pluripotency. Proceedings of the National Academy of Sciences of the United States of America. 106: 5181-6. PMID 19279220 DOI: 10.1073/pnas.0812889106  1
2009 Ulintz PJ, Yocum AK, Bodenmiller B, Aebersold R, Andrews PC, Nesvizhskii AI. Comparison of MS(2)-only, MSA, and MS(2)/MS(3) methodologies for phosphopeptide identification. Journal of Proteome Research. 8: 887-99. PMID 19072539 DOI: 10.1021/pr800535h  1
2009 Goudreault M, D'Ambrosio LM, Kean MJ, Mullin MJ, Larsen BG, Sanchez A, Chaudhry S, Chen GI, Sicheri F, Nesvizhskii AI, Aebersold R, Raught B, Gingras AC. A PP2A phosphatase high density interaction network identifies a novel striatin-interacting phosphatase and kinase complex linked to the cerebral cavernous malformation 3 (CCM3) protein. Molecular & Cellular Proteomics : McP. 8: 157-71. PMID 18782753 DOI: 10.1074/mcp.M800266-MCP200  1
2008 Ding Y, Choi H, Nesvizhskii AI. Adaptive discriminant function analysis and reranking of MS/MS database search results for improved peptide identification in shotgun proteomics. Journal of Proteome Research. 7: 4878-89. PMID 18788775 DOI: 10.1021/pr800484x  1
2008 Cao X, Nesvizhskii AI. Improved sequence tag generation method for peptide identification in tandem mass spectrometry. Journal of Proteome Research. 7: 4422-34. PMID 18785767 DOI: 10.1021/pr800400q  1
2008 Choi H, Fermin D, Nesvizhskii AI. Significance analysis of spectral count data in label-free shotgun proteomics. Molecular & Cellular Proteomics : McP. 7: 2373-85. PMID 18644780 DOI: 10.1074/mcp.M800203-MCP200  1
2008 Marelli M, Nesvizhskii AI, Aitchison JD. Identifying bona fide components of an organelle by isotope-coded labeling of subcellular fractions : an example in peroxisomes. Methods in Molecular Biology (Clifton, N.J.). 432: 357-71. PMID 18370030 DOI: 10.1007/978-1-59745-028-7_24  1
2008 Searle BC, Turner M, Nesvizhskii AI. Improving sensitivity by probabilistically combining results from multiple MS/MS search methodologies. Journal of Proteome Research. 7: 245-53. PMID 18173222 DOI: 10.1021/pr070540w  1
2008 Choi H, Nesvizhskii AI. Semisupervised model-based validation of peptide identifications in mass spectrometry-based proteomics. Journal of Proteome Research. 7: 254-65. PMID 18159924 DOI: 10.1021/pr070542g  1
2008 Choi H, Ghosh D, Nesvizhskii AI. Statistical validation of peptide identifications in large-scale proteomics using the target-decoy database search strategy and flexible mixture modeling. Journal of Proteome Research. 7: 286-92. PMID 18078310 DOI: 10.1021/pr7006818  1
2008 Taylor BS, Pal M, Yu J, Laxman B, Kalyana-Sundaram S, Zhao R, Menon A, Wei JT, Nesvizhskii AI, Ghosh D, Omenn GS, Lubman DM, Chinnaiyan AM, Sreekumar A. Humoral response profiling reveals pathways to prostate cancer progression. Molecular & Cellular Proteomics : McP. 7: 600-11. PMID 18077443 DOI: 10.1074/mcp.M700263-MCP200  1
2008 Choi H, Nesvizhskii AI. False discovery rates and related statistical concepts in mass spectrometry-based proteomics. Journal of Proteome Research. 7: 47-50. PMID 18067251 DOI: 10.1021/pr700747q  1
2008 Ulintz PJ, Bodenmiller B, Andrews PC, Aebersold R, Nesvizhskii AI. Investigating MS2/MS3 matching statistics: a model for coupling consecutive stage mass spectrometry data for increased peptide identification confidence. Molecular & Cellular Proteomics : McP. 7: 71-87. PMID 17872894 DOI: 10.1074/mcp.M700128-MCP200  1
2008 Marelli M, Nesvizhskii AI, Aitchison JD. Identifying bona fide components of an organelle by isotope-coded labeling of subcellular fractions: An example in peroxisomes Methods in Molecular Biology. 432: 357-371. DOI: 10.1007/978-1-59745-28-7_24  1
2007 Kim B, Nesvizhskii AI, Rani PG, Hahn S, Aebersold R, Ranish JA. The transcription elongation factor TFIIS is a component of RNA polymerase II preinitiation complexes. Proceedings of the National Academy of Sciences of the United States of America. 104: 16068-73. PMID 17913884 DOI: 10.1073/pnas.0704573104  1
2007 Nesvizhskii AI, Vitek O, Aebersold R. Analysis and validation of proteomic data generated by tandem mass spectrometry. Nature Methods. 4: 787-97. PMID 17901868 DOI: 10.1038/nmeth1088  1
2007 Yoo C, Patwa TH, Kreunin P, Miller FR, Huber CG, Nesvizhskii AI, Lubman DM. Comprehensive analysis of proteins of pH fractionated samples using monolithic LC/MS/MS, intact MW measurement and MALDI-QIT-TOF MS. Journal of Mass Spectrometry : Jms. 42: 312-34. PMID 17206599 DOI: 10.1002/jms.1163  1
2007 Nesvizhskii AI. Protein identification by tandem mass spectrometry and sequence database searching. Methods in Molecular Biology (Clifton, N.J.). 367: 87-119. PMID 17185772 DOI: 10.1385/1-59745-275-0:87  1
2006 King NL, Deutsch EW, Ranish JA, Nesvizhskii AI, Eddes JS, Mallick P, Eng J, Desiere F, Flory M, Martin DB, Kim B, Lee H, Raught B, Aebersold R. Analysis of the Saccharomyces cerevisiae proteome with PeptideAtlas. Genome Biology. 7: R106. PMID 17101051 DOI: 10.1186/gb-2006-7-11-r106  1
2006 Malmström J, Lee H, Nesvizhskii AI, Shteynberg D, Mohanty S, Brunner E, Ye M, Weber G, Eckerskorn C, Aebersold R. Optimized peptide separation and identification for mass spectrometry based proteomics via free-flow electrophoresis. Journal of Proteome Research. 5: 2241-9. PMID 16944936 DOI: 10.1021/pr0600632  1
2006 Desiere F, Deutsch EW, King NL, Nesvizhskii AI, Mallick P, Eng J, Chen S, Eddes J, Loevenich SN, Aebersold R. The PeptideAtlas project. Nucleic Acids Research. 34: D655-8. PMID 16381952 DOI: 10.1093/nar/gkj040  1
2006 Nesvizhskii AI, Roos FF, Grossmann J, Vogelzang M, Eddes JS, Gruissem W, Baginsky S, Aebersold R. Dynamic spectrum quality assessment and iterative computational analysis of shotgun proteomic data: toward more efficient identification of post-translational modifications, sequence polymorphisms, and novel peptides. Molecular & Cellular Proteomics : McP. 5: 652-70. PMID 16352522 DOI: 10.1074/mcp.M500319-MCP200  1
2006 Martens L, Nesvizhskii AI, Hermjakob H, Adamski M, Omenn GS, Vandekerckhove J, Gevaert K. Do we want our data raw? Including binary mass spectrometry data in public proteomics data repositories Exploring the Human Plasma Proteome. 323-328. DOI: 10.1002/9783527609482.ch15  1
2006 Deutsch EW, Eng JK, Zhang H, King NL, Nesvizhskii AI, Lin B, Lee H, Yi EC, Ossola R, Aebersold R. Human Plasma PeptideAtlas Exploring the Human Plasma Proteome. 317-322. DOI: 10.1002/9783527609482.ch14  1
2005 Martin DB, Eng JK, Nesvizhskii AI, Gemmill A, Aebersold R. Investigation of neutral loss during collision-induced dissociation of peptide ions. Analytical Chemistry. 77: 4870-82. PMID 16053300 DOI: 10.1021/ac050701k  1
2005 Deutsch EW, Eng JK, Zhang H, King NL, Nesvizhskii AI, Lin B, Lee H, Yi EC, Ossola R, Aebersold R. Human Plasma PeptideAtlas. Proteomics. 5: 3497-500. PMID 16052627 DOI: 10.1002/pmic.200500160  1
2005 Nesvizhskii AI, Aebersold R. Interpretation of shotgun proteomic data: the protein inference problem. Molecular & Cellular Proteomics : McP. 4: 1419-40. PMID 16009968 DOI: 10.1074/mcp.R500012-MCP200  1
2005 Desiere F, Deutsch EW, Nesvizhskii AI, Mallick P, King NL, Eng JK, Aderem A, Boyle R, Brunner E, Donohoe S, Fausto N, Hafen E, Hood L, Katze MG, Kennedy KA, et al. Integration with the human genome of peptide sequences obtained by high-throughput mass spectrometry. Genome Biology. 6: R9. PMID 15642101 DOI: 10.1186/gb-2004-6-1-r9  1
2004 Marelli M, Smith JJ, Jung S, Yi E, Nesvizhskii AI, Christmas RH, Saleem RA, Tam YY, Fagarasanu A, Goodlett DR, Aebersold R, Rachubinski RA, Aitchison JD. Quantitative mass spectrometry reveals a role for the GTPase Rho1p in actin organization on the peroxisome membrane. The Journal of Cell Biology. 167: 1099-112. PMID 15596542 DOI: 10.1083/jcb.200404119  1
2004 Wollscheid B, von Haller PD, Yi E, Donohoe S, Vaughn K, Keller A, Nesvizhskii AI, Eng J, Li XJ, Goodlett DR, Aebersold R, Watts JD. Lipid raft proteins and their identification in T lymphocytes. Sub-Cellular Biochemistry. 37: 121-52. PMID 15376619  1
2004 Nesvizhskii AI, Aebersold R. Analysis, statistical validation and dissemination of large-scale proteomics datasets generated by tandem MS. Drug Discovery Today. 9: 173-81. PMID 14960397 DOI: 10.1016/S1359-6446(03)02978-7  1
2003 Nesvizhskii AI, Keller A, Kolker E, Aebersold R. A statistical model for identifying proteins by tandem mass spectrometry. Analytical Chemistry. 75: 4646-58. PMID 14632076 DOI: 10.1021/ac0341261  1
2003 Kolker E, Purvine S, Galperin MY, Stolyar S, Goodlett DR, Nesvizhskii AI, Keller A, Xie T, Eng JK, Yi E, Hood L, Picone AF, Cherny T, Tjaden BC, Siegel AF, et al. Initial proteome analysis of model microorganism Haemophilus influenzae strain Rd KW20. Journal of Bacteriology. 185: 4593-602. PMID 12867470 DOI: 10.1128/JB.185.15.4593-4602.2003  1
2003 von Haller PD, Yi E, Donohoe S, Vaughn K, Keller A, Nesvizhskii AI, Eng J, Li XJ, Goodlett DR, Aebersold R, Watts JD. The application of new software tools to quantitative protein profiling via isotope-coded affinity tag (ICAT) and tandem mass spectrometry: II. Evaluation of tandem mass spectrometry methodologies for large-scale protein analysis, and the application of statistical tools for data analysis and interpretation. Molecular & Cellular Proteomics : McP. 2: 428-42. PMID 12832459 DOI: 10.1074/mcp.M300041-MCP200  1
2003 von Haller PD, Yi E, Donohoe S, Vaughn K, Keller A, Nesvizhskii AI, Eng J, Li XJ, Goodlett DR, Aebersold R, Watts JD. The application of new software tools to quantitative protein profiling via isotope-coded affinity tag (ICAT) and tandem mass spectrometry: I. Statistically annotated datasets for peptide sequences and proteins identified via the application of ICAT and tandem mass spectrometry to proteins copurifying with T cell lipid rafts. Molecular & Cellular Proteomics : McP. 2: 426-7. PMID 12832456 DOI: 10.1074/mcp.D300002-MCP200  1
2003 Ankudinov AL, Nesvizhskii AI, Rehr JJ. Dynamic screening effects in x-ray absorption spectra Physical Review B - Condensed Matter and Materials Physics. 67: 1151201-1151206.  1
2002 Keller A, Nesvizhskii AI, Kolker E, Aebersold R. Empirical statistical model to estimate the accuracy of peptide identifications made by MS/MS and database search. Analytical Chemistry. 74: 5383-92. PMID 12403597 DOI: 10.1021/ac025747h  1
2002 Keller A, Purvine S, Nesvizhskii AI, Stolyar S, Goodlett DR, Kolker E. Experimental protein mixture for validating tandem mass spectral analysis. Omics : a Journal of Integrative Biology. 6: 207-12. PMID 12143966 DOI: 10.1089/153623102760092805  1
2002 Keller AD, Nesvizhskii AI, Kolker E, Aebersold R. Empirical statistical model to estimate the accuracy of protein identifications made by MS/MS and database search Proceedings 50th Asms Conference On Mass Spectrometry and Allied Topics. 37-38.  1
2001 Ankudinov AL, Nesvizhskii AI, Rehr JJ. Hole counts from X-ray absorption spectra. Journal of Synchrotron Radiation. 8: 92-5. PMID 11512979 DOI: 10.1107/S0909049500016435  1
2001 Hsu LS, Nesvizhskii AI. Experimental and theoretical study of the electronic structure of AuAl2 Journal of Physics and Chemistry of Solids. 62: 1047-1054. DOI: 10.1016/S0022-3697(00)00275-4  1
2001 Nesvizhskii AI, Ankudinov AL, Rehr JJ. Normalization and convergence of x-ray absorption sum rules Physical Review B - Condensed Matter and Materials Physics. 63: 944121-944125.  1
2000 Nesvizhskii AI, Ankudinov AL, Rehr JJ, Baberschke K. Interpretation of x-ray magnetic circular dichroism and x-ray absorption near-edge structure in Ni Physical Review B - Condensed Matter and Materials Physics. 62: 15295-15298. DOI: 10.1103/PhysRevB.62.15295  1
1999 Nesvizhskii AI, Rehr JJ. L-edge XANES of 3d-transition metals. Journal of Synchrotron Radiation. 6: 315-6. PMID 15263292 DOI: 10.1107/S0909049599001697  1
1996 Winkler R, Nesvizhskii AI. Anisotropic hole subband states and interband optical absorption in [mmn]-oriented quantum wells Physical Review B - Condensed Matter and Materials Physics. 53: 9984-9992.  1
1996 Ivchenko EL, Kaliteevski MA, Kavokin AV, Nesvizhskii AI. Reflection and absorption spectra from microcavities with resonant Bragg quantum wells Journal of the Optical Society of America B: Optical Physics. 13: 1061-1068.  1
1995 Seisyan RP, Kavokin AV, Kokhanovskii SI, Nesvizhskii AI, Sasin ME, Sinitzin MA, Yavich BS. The excitonic structure of absorption and magnetoabsorption spectra near the type I-II transition in strained (In, Ga)As/GaAs heterostructures Semiconductor Science and Technology. 10: 611-615. DOI: 10.1088/0268-1242/10/5/007  1
1995 Cao SM, Willander M, Ivchenko EL, Nesvizhskii AI, Toropov AA. Electrons and excitons in an imperfect superlattice in electric fields Superlattices and Microstructures. 17: 97. DOI: 10.1006/spmi.1995.1020  1
1994 Kavokin AV, Nesvizhskii AI. Stark effect near the type-I-type-II transition point in semiconductor quantum wells Physical Review B. 49: 17055-17058. DOI: 10.1103/PhysRevB.49.17055  1
1994 Ivchenko EL, Nesvizhskii AI, Jorda S. Resonant Bragg reflection from quantum-well structures Superlattices and Microstructures. 16: 17-20. DOI: 10.1006/spmi.1994.1101  1
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