Publications


See Publication list in Google Scholar


Representative Recent Publications

  • Computational and informatics strategies for identification of specific protein interaction partners in affinity purification mass spectrometry experiments. (2012). Nesvizhskii AI. Proteomics, vol 12(10):1639-55. PMID:22611043

  • Comparative analysis of different label-free mass spectrometry based protein abundance estimates and their correlation with RNA-Seq gene expression data. (2012). Ning K, Fermin D, Nesvizhskii AI. Journal of proteome research, vol 11(4):2261-71. PMID:22329341

  • SAINT: probabilistic scoring of affinity purification-mass spectrometry data. (2011). Choi H, Larsen B, Lin ZY, Breitkreutz A, Mellacheruvu D, Fermin D, Qin ZS, Tyers M, Gingras AC, Nesvizhskii AI. Nature methods, vol 8(1):70-3. PMID:21131968

  • The utility of mass spectrometry-based proteomic data for validation of novel alternative splice forms reconstructed from RNA-Seq data: a preliminary assessment. (2011). Ning K, Nesvizhskii AI. BMC bioinformatics, vol 11 Suppl 11():S14. PMID:21172049

  • Examination of the relationship between essential genes in PPI network and hub proteins in reverse nearest neighbor topology. (2011). Ning K, Ng HK, Srihari S, Leong HW, Nesvizhskii AI. BMC bioinformatics, vol 11():505. PMID:20939873

  • A survey of computational methods and error rate estimation procedures for peptide and protein identification in shotgun proteomics. (2011). Nesvizhskii AI. Journal of proteomics, vol 73(11):2092-123. PMID:20816881

  • Analysis of protein complexes through model-based biclustering of label-free quantitative AP-MS data. (2010). Choi H, Kim S, Gingras AC, Nesvizhskii AI. Molecular systems biology, vol 6():385. PMID:20571534

  • Proteomic interrogation of androgen action in prostate cancer cells reveals roles of aminoacyl tRNA synthetases. (2010). Vellaichamy A, Sreekumar A, Strahler JR, Rajendiran T, Yu J, Varambally S, Li Y, Omenn GS, Chinnaiyan AM, Nesvizhskii AI. PloS one, vol 4(9):e7075. PMID:19763266

  • Computational analysis of unassigned high-quality MS/MS spectra in proteomic data sets. (2010). Ning K, Fermin D, Nesvizhskii AI. Proteomics, vol 10(14):2712-8. PMID:20455209

  • Hierarchical hidden Markov model with application to joint analysis of ChIP-chip and ChIP-seq data. (2009). Choi H, Nesvizhskii AI, Ghosh D, Qin ZS. Bioinformatics (Oxford, England), vol 25(14):1715-21. PMID:19447789

  • An embryonic stem cell chromatin remodeling complex, esBAF, is essential for embryonic stem cell self-renewal and pluripotency. (2009). Ho L, Ronan JL, Wu J, Staahl BT, Chen L, Kuo A, Lessard J, Nesvizhskii AI, Ranish J, Crabtree GR. Proceedings of the National Academy of Sciences of the United States of America, vol 106(13):5181-6. PMID:19279220

  • Comparison of MS(2)-only, MSA, and MS(2)/MS(3) methodologies for phosphopeptide identification. (2009). Ulintz PJ, Yocum AK, Bodenmiller B, Aebersold R, Andrews PC, Nesvizhskii AI. Journal of proteome research, vol 8(2):887-99. PMID:19072539

  • Significance analysis of spectral count data in label-free shotgun proteomics. (2008). Choi H, Fermin D, Nesvizhskii AI. Molecular & cellular proteomics : MCP, vol 7(12):2373-85. PMID:18644780

  • Statistical validation of peptide identifications in large-scale proteomics using the target-decoy database search strategy and flexible mixture modeling. (2007). Choi H, Ghosh D, Nesvizhskii AI. Journal of proteome research, vol 7(1):286-92. PMID:18078310

  • False discovery rates and related statistical concepts in mass spectrometry-based proteomics. (2007). Choi H, Nesvizhskii AI. Journal of proteome research, vol 7(1):47-50. PMID:18067251

  • Analysis and validation of proteomic data generated by tandem mass spectrometry. (2007). Nesvizhskii AI, Vitek O, Aebersold R. Nature methods, vol 4(10):787-97. PMID:17901868

  • A role for the MLL fusion partner ENL in transcriptional elongation and chromatin modification. (2007). Mueller D, Bach C, Zeisig D, Garcia-Cuellar MP, Monroe S, Sreekumar A, Zhou R, Nesvizhskii A, Chinnaiyan A, Hess JL, Slany RK. Blood, vol 110(13):4445-54. PMID:17855633

  • 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. (2005). Nesvizhskii AI, Roos FF, Grossmann J, Vogelzang M, Eddes JS, Gruissem W, Baginsky S, Aebersold R. Molecular & cellular proteomics : MCP, vol 5(4):652-70. PMID:16352522

  • Interpretation of shotgun proteomic data: the protein inference problem. (2005). Nesvizhskii AI, Aebersold R. Molecular & cellular proteomics : MCP, vol 4(10):1419-40. PMID:16009968

  • Integration with the human genome of peptide sequences obtained by high-throughput mass spectrometry. (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, Kregenow F, Lee H, Lin B, Martin D, Ranish JA, Rawlings DJ, Samelson LE, Shiio Y, Watts JD, Wollscheid B, Wright ME, Yan W, Yang L, Yi EC, Zhang H, Aebersold R. Genome biology, vol 6(1):R9. PMID:15642101


All Recent Publications in PubMed

  • SAINTexpress: Improvements and additional features in Significance Analysis of INTeractome software. (2014). Teo G, Liu G, Zhang J, Nesvizhskii AI, Gingras AC, Choi H. Journal of proteomics, vol 100():37-43. PMID:24513533

  • Global Phosphoproteomic Profiling Reveals Distinct Signatures in B-Cell Non-Hodgkin Lymphomas. (2014). Rolland D, Basrur V, Conlon K, Wolfe T, Fermin D, Nesvizhskii AI, Lim MS, Elenitoba-Johnson KS. The American journal of pathology, vol ():. PMID:24667141

  • The yeast Sks1p kinase signaling network regulates pseudohyphal growth and glucose response. (2014). Johnson C, Kweon HK, Sheidy D, Shively CA, Mellacheruvu D, Nesvizhskii AI, Andrews PC, Kumar A. PLoS genetics, vol 10(3):e1004183. PMID:24603354

  • Toward more transparent and reproducible omics studies through a common metadata checklist and data publications. (2014). Kolker E, Özdemir V, Martens L, Hancock W, Anderson G, Anderson N, Aynacioglu S, Baranova A, Campagna SR, Chen R, Choiniere J, Dearth SP, Feng WC, Ferguson L, Fox G, Frishman D, Grossman R, Heath A, Higdon R, Hutz MH, Janko I, Jiang L, Joshi S, Kel A, Kemnitz JW, Kohane IS, Kolker N, Lancet D, Lee E, Li W, Lisitsa A, Llerena A, Macnealy-Koch C, Marshall JC, Masuzzo P, May A, Mias G, Monroe M, Montague E, Mooney S, Nesvizhskii A, Noronha S, Omenn G, Rajasimha H, Ramamoorthy P, Sheehan J, Smarr L, Smith CV, Smith T, Snyder M, Rapole S, Srivastava S, Stanberry L, Stewart E, Toppo S, Uetz P, Verheggen K, Voy BH, Warnich L, Wilhelm SW, Yandl G. Omics : a journal of integrative biology, vol 18(1):10-4. PMID:24456465

  • Comprehensive analysis of protein digestion using six trypsins reveals the origin of trypsin as a significant source of variability in proteomics. (2013). Walmsley SJ, Rudnick PA, Liang Y, Dong Q, Stein SE, Nesvizhskii AI. Journal of proteome research, vol 12(12):5666-80. PMID:24116745

  • Hands-on workshops as an effective means of learning advanced technologies including genomics, proteomics and bioinformatics. (2014). Reisdorph N, Stearman R, Kechris K, Phang TL, Reisdorph R, Prenni J, Erle DJ, Coldren C, Schey K, Nesvizhskii A, Geraci M. Genomics, proteomics & bioinformatics, vol 11(6):368-77. PMID:24316330

  • LuciPHOr: algorithm for phosphorylation site localization with false localization rate estimation using modified target-decoy approach. (2014). Fermin D, Walmsley SJ, Gingras AC, Choi H, Nesvizhskii AI. Molecular & cellular proteomics : MCP, vol 12(11):3409-19. PMID:23918812

  • Fusion peptides from oncogenic chimeric proteins as putative specific biomarkers of cancer. (2014). Conlon KP, Basrur V, Rolland D, Wolfe T, Nesvizhskii AI, MacCoss MJ, Lim MS, Elenitoba-Johnson KS. Molecular & cellular proteomics : MCP, vol 12(10):2714-23. PMID:23836920

  • Combining results of multiple search engines in proteomics. (2014). Shteynberg D, Nesvizhskii AI, Moritz RL, Deutsch EW. Molecular & cellular proteomics : MCP, vol 12(9):2383-93. PMID:23720762

  • The CRAPome: a contaminant repository for affinity purification-mass spectrometry data. (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, 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. Nature methods, vol 10(8):730-6. PMID:23921808

  • Genetic networks inducing invasive growth in Saccharomyces cerevisiae identified through systematic genome-wide overexpression. (2013). Shively CA, Eckwahl MJ, Dobry CJ, Mellacheruvu D, Nesvizhskii A, Kumar A. Genetics, vol 193(4):1297-310. PMID:23410832

  • Sparsely correlated hidden Markov models with application to genome-wide location studies. (2013). Choi H, Fermin D, Nesvizhskii AI, Ghosh D, Qin ZS. Bioinformatics (Oxford, England), vol 29(5):533-41. PMID:23325620

  • The functional interactome landscape of the human histone deacetylase family. (2013). Joshi P, Greco TM, Guise AJ, Luo Y, Yu F, Nesvizhskii AI, Cristea IM. Molecular systems biology, vol 9():672. PMID:23752268

  • Reconstructing targetable pathways in lung cancer by integrating diverse omics data. (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. Nature communications, vol 4():2617. PMID:24135919

  • Using ProHits to store, annotate, and analyze affinity purification-mass spectrometry (AP-MS) data. (2012). Liu G, Zhang J, Choi H, Lambert JP, Srikumar T, Larsen B, Nesvizhskii AI, Raught B, Tyers M, Gingras AC. Current protocols in bioinformatics / editoral board, Andreas D. Baxevanis ... [et al.], vol Chapter 8():Unit8.16. PMID:22948730

  • Analyzing protein-protein interactions from affinity purification-mass spectrometry data with SAINT. (2012). Choi H, Liu G, Mellacheruvu D, Tyers M, Gingras AC, Nesvizhskii AI. Current protocols in bioinformatics / editoral board, Andreas D. Baxevanis ... [et al.], vol Chapter 8():Unit8.15. PMID:22948729

  • A dual role for receptor-interacting protein kinase 2 (RIP2) kinase activity in nucleotide-binding oligomerization domain 2 (NOD2)-dependent autophagy. (2012). Homer CR, Kabi A, Marina-García N, Sreekumar A, Nesvizhskii AI, Nickerson KP, Chinnaiyan AM, Nuñez G, McDonald C. The Journal of biological chemistry, vol 287(30):25565-76. PMID:22665475

  • The nucleotide synthesis enzyme CAD inhibits NOD2 antibacterial function in human intestinal epithelial cells. (2012). Richmond AL, Kabi A, Homer CR, Marina-García N, Nickerson KP, Nesvizhskii AI, Sreekumar A, Chinnaiyan AM, Nuñez G, McDonald C. Gastroenterology, vol 142(7):1483-92.e6. PMID:22387394

  • Protein complexes and interaction networks. (2012). Gingras AC, Nesvizhskii A. Proteomics, vol 12(10):1475-7. PMID:22711591

  • Computational and informatics strategies for identification of specific protein interaction partners in affinity purification mass spectrometry experiments. (2012). Nesvizhskii AI. Proteomics, vol 12(10):1639-55. PMID:22611043

  • SAINT-MS1: protein-protein interaction scoring using label-free intensity data in affinity purification-mass spectrometry experiments. (2012). Choi H, Glatter T, Gstaiger M, Nesvizhskii AI. Journal of proteome research, vol 11(4):2619-24. PMID:22352807

  • Comparative analysis of different label-free mass spectrometry based protein abundance estimates and their correlation with RNA-Seq gene expression data. (2012). Ning K, Fermin D, Nesvizhskii AI. Journal of proteome research, vol 11(4):2261-71. PMID:22329341

  • Proteomic study of the mucin granulae in an intestinal goblet cell model. (2012). Rodríguez-Piñeiro AM, van der Post S, Johansson ME, Thomsson KA, Nesvizhskii AI, Hansson GC. Journal of proteome research, vol 11(3):1879-90. PMID:22248381

  • A statistical model-building perspective to identification of MS/MS spectra with PeptideProphet. (2013). Ma K, Vitek O, Nesvizhskii AI. BMC bioinformatics, vol 13 Suppl 16():S1. PMID:23176103

  • iProphet: multi-level integrative analysis of shotgun proteomic data improves peptide and protein identification rates and error estimates. (2012). Shteynberg D, Deutsch EW, Lam H, Eng JK, Sun Z, Tasman N, Mendoza L, Moritz RL, Aebersold R, Nesvizhskii AI. Molecular & cellular proteomics : MCP, vol 10(12):M111.007690. PMID:21876204

  • SUMOylation pathway in Trypanosoma cruzi: functional characterization and proteomic analysis of target proteins. (2012). Bayona JC, Nakayasu ES, Laverrière M, Aguilar C, Sobreira TJ, Choi H, Nesvizhskii AI, Almeida IC, Cazzulo JJ, Alvarez VE. Molecular & cellular proteomics : MCP, vol 10(12):M110.007369. PMID:21832256

  • Modularity and hormone sensitivity of the Drosophila melanogaster insulin receptor/target of rapamycin interaction proteome. (2012). 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. Molecular systems biology, vol 7():547. PMID:22068330

  • Advancing next-generation proteomics through computational research. (2011). Bandeira N, Nesvizhskii A, McIntosh M. Journal of proteome research, vol 10(7):2895. PMID:21627070

  • MSblender: A probabilistic approach for integrating peptide identifications from multiple database search engines. (2011). Kwon T, Choi H, Vogel C, Nesvizhskii AI, Marcotte EM. Journal of proteome research, vol 10(7):2949-58. PMID:21488652

  • Label-free quantitative proteomics and SAINT analysis enable interactome mapping for the human Ser/Thr protein phosphatase 5. (2011). Skarra DV, Goudreault M, Choi H, Mullin M, Nesvizhskii AI, Gingras AC, Honkanen RE. Proteomics, vol 11(8):1508-16. PMID:21360678

  • Abacus: a computational tool for extracting and pre-processing spectral count data for label-free quantitative proteomic analysis. (2011). Fermin D, Basrur V, Yocum AK, Nesvizhskii AI. Proteomics, vol 11(7):1340-5. PMID:21360675

  • Metabolites of purine nucleoside phosphorylase (NP) in serum have the potential to delineate pancreatic adenocarcinoma. (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, Asea AA, Cashikar AG, Rao A, McLoughlin J, Sreekumar A. PloS one, vol 6(3):e17177. PMID:21448452

  • Global analysis of protein palmitoylation in African trypanosomes. (2011). Emmer BT, Nakayasu ES, Souther C, Choi H, Sobreira TJ, Epting CL, Nesvizhskii AI, Almeida IC, Engman DM. Eukaryotic cell, vol 10(3):455-63. PMID:21193548

  • Prestroke proteomic changes in cerebral microvessels in stroke-prone, transgenic[hCETP]-Hyperlipidemic, Dahl salt-sensitive hypertensive rats. (2011). Bergerat A, Decano J, Wu CJ, Choi H, Nesvizhskii AI, Moran AM, Ruiz-Opazo N, Steffen M, Herrera VL. Molecular medicine (Cambridge, Mass.), vol 17(7-8):588-98. PMID:21519634

  • SAINT: probabilistic scoring of affinity purification-mass spectrometry data. (2011). Choi H, Larsen B, Lin ZY, Breitkreutz A, Mellacheruvu D, Fermin D, Qin ZS, Tyers M, Gingras AC, Nesvizhskii AI. Nature methods, vol 8(1):70-3. PMID:21131968

  • Phosphoproteomic analysis reveals interconnected system-wide responses to perturbations of kinases and phosphatases in yeast. (2011). Bodenmiller B, Wanka S, Kraft C, Urban J, Campbell D, Pedrioli PG, Gerrits B, Picotti P, Lam H, Vitek O, Brusniak MY, Roschitzki B, Zhang C, Shokat KM, Schlapbach R, Colman-Lerner A, Nolan GP, Nesvizhskii AI, Peter M, Loewith R, von Mering C, Aebersold R. Science signaling, vol 3(153):rs4. PMID:21177495

  • The utility of mass spectrometry-based proteomic data for validation of novel alternative splice forms reconstructed from RNA-Seq data: a preliminary assessment. (2011). Ning K, Nesvizhskii AI. BMC bioinformatics, vol 11 Suppl 11():S14. PMID:21172049

  • Examination of the relationship between essential genes in PPI network and hub proteins in reverse nearest neighbor topology. (2011). Ning K, Ng HK, Srihari S, Leong HW, Nesvizhskii AI. BMC bioinformatics, vol 11():505. PMID:20939873

  • A survey of computational methods and error rate estimation procedures for peptide and protein identification in shotgun proteomics. (2011). Nesvizhskii AI. Journal of proteomics, vol 73(11):2092-123. PMID:20816881

  • ProHits: integrated software for mass spectrometry-based interaction proteomics. (2011). 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, Gingras AC. Nature biotechnology, vol 28(10):1015-7. PMID:20944583

  • Integrated phosphoproteomics analysis of a signaling network governing nutrient response and peroxisome induction. (2011). Saleem RA, Rogers RS, Ratushny AV, Dilworth DJ, Shannon PT, Shteynberg D, Wan Y, Moritz RL, Nesvizhskii AI, Rachubinski RA, Aitchison JD. Molecular & cellular proteomics : MCP, vol 9(9):2076-88. PMID:20395639

  • Computational analysis of unassigned high-quality MS/MS spectra in proteomic data sets. (2010). Ning K, Fermin D, Nesvizhskii AI. Proteomics, vol 10(14):2712-8. PMID:20455209

  • Analysis of protein complexes through model-based biclustering of label-free quantitative AP-MS data. (2010). Choi H, Kim S, Gingras AC, Nesvizhskii AI. Molecular systems biology, vol 6():385. PMID:20571534

  • "Topological significance" analysis of gene expression and proteomic profiles from prostate cancer cells reveals key mechanisms of androgen response. (2010). Vellaichamy A, Dezso Z, JeBailey L, Chinnaiyan AM, Sreekumar A, Nesvizhskii AI, Omenn GS, Bugrim A. PloS one, vol 5(6):e10936. PMID:20532174

  • A global protein kinase and phosphatase interaction network in yeast. (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, Qin ZS, Pawson T, Gingras AC, Nesvizhskii AI, Tyers M. Science (New York, N.Y.), vol 328(5981):1043-6. PMID:20489023

  • A guided tour of the Trans-Proteomic Pipeline. (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. Proteomics, vol 10(6):1150-9. PMID:20101611

  • Quantitative proteomic profiling of prostate cancer reveals a role for miR-128 in prostate cancer. (2010). Khan AP, Poisson LM, Bhat VB, Fermin D, Zhao R, Kalyana-Sundaram S, Michailidis G, Nesvizhskii AI, Omenn GS, Chinnaiyan AM, Sreekumar A. Molecular & cellular proteomics : MCP, vol 9(2):298-312. PMID:19955085

  • Proteomic interrogation of androgen action in prostate cancer cells reveals roles of aminoacyl tRNA synthetases. (2010). Vellaichamy A, Sreekumar A, Strahler JR, Rajendiran T, Yu J, Varambally S, Li Y, Omenn GS, Chinnaiyan AM, Nesvizhskii AI. PloS one, vol 4(9):e7075. PMID:19763266

  • Hierarchical hidden Markov model with application to joint analysis of ChIP-chip and ChIP-seq data. (2009). Choi H, Nesvizhskii AI, Ghosh D, Qin ZS. Bioinformatics (Oxford, England), vol 25(14):1715-21. PMID:19447789

  • Recommendations from the 2008 International Summit on Proteomics Data Release and Sharing Policy: the Amsterdam principles. (2009). Rodriguez H, Snyder M, Uhlén M, Andrews P, Beavis R, Borchers C, Chalkley RJ, Cho SY, Cottingham K, Dunn M, Dylag T, Edgar R, Hare P, Heck AJ, Hirsch RF, Kennedy K, Kolar P, Kraus HJ, Mallick P, Nesvizhskii A, Ping P, Pontén F, Yang L, Yates JR, Stein SE, Hermjakob H, Kinsinger CR, Apweiler R. Journal of proteome research, vol 8(7):3689-92. PMID:19344107

  • An embryonic stem cell chromatin remodeling complex, esBAF, is essential for embryonic stem cell self-renewal and pluripotency. (2009). Ho L, Ronan JL, Wu J, Staahl BT, Chen L, Kuo A, Lessard J, Nesvizhskii AI, Ranish J, Crabtree GR. Proceedings of the National Academy of Sciences of the United States of America, vol 106(13):5181-6. PMID:19279220

  • Comparison of MS(2)-only, MSA, and MS(2)/MS(3) methodologies for phosphopeptide identification. (2009). Ulintz PJ, Yocum AK, Bodenmiller B, Aebersold R, Andrews PC, Nesvizhskii AI. Journal of proteome research, vol 8(2):887-99. PMID:19072539

  • 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. (2008). 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. Molecular & cellular proteomics : MCP, vol 8(1):157-71. PMID:18782753

  • Significance analysis of spectral count data in label-free shotgun proteomics. (2008). Choi H, Fermin D, Nesvizhskii AI. Molecular & cellular proteomics : MCP, vol 7(12):2373-85. PMID:18644780

  • Adaptive discriminant function analysis and reranking of MS/MS database search results for improved peptide identification in shotgun proteomics. (2008). Ding Y, Choi H, Nesvizhskii AI. Journal of proteome research, vol 7(11):4878-89. PMID:18788775

  • Improved sequence tag generation method for peptide identification in tandem mass spectrometry. (2008). Cao X, Nesvizhskii AI. Journal of proteome research, vol 7(10):4422-34. PMID:18785767

  • Humoral response profiling reveals pathways to prostate cancer progression. (2007). 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. Molecular & cellular proteomics : MCP, vol 7(3):600-11. PMID:18077443

  • Improving sensitivity by probabilistically combining results from multiple MS/MS search methodologies. (2008). Searle BC, Turner M, Nesvizhskii AI. Journal of proteome research, vol 7(1):245-53. PMID:18173222

  • Semisupervised model-based validation of peptide identifications in mass spectrometry-based proteomics. (2007). Choi H, Nesvizhskii AI. Journal of proteome research, vol 7(1):254-65. PMID:18159924

  • Statistical validation of peptide identifications in large-scale proteomics using the target-decoy database search strategy and flexible mixture modeling. (2007). Choi H, Ghosh D, Nesvizhskii AI. Journal of proteome research, vol 7(1):286-92. PMID:18078310

  • False discovery rates and related statistical concepts in mass spectrometry-based proteomics. (2007). Choi H, Nesvizhskii AI. Journal of proteome research, vol 7(1):47-50. PMID:18067251

  • Identifying bona fide components of an organelle by isotope-coded labeling of subcellular fractions : an example in peroxisomes. (2008). Marelli M, Nesvizhskii AI, Aitchison JD. Methods in molecular biology (Clifton, N.J.), vol 432():357-71. PMID:18370030

  • Investigating MS2/MS3 matching statistics: a model for coupling consecutive stage mass spectrometry data for increased peptide identification confidence. (2007). Ulintz PJ, Bodenmiller B, Andrews PC, Aebersold R, Nesvizhskii AI. Molecular & cellular proteomics : MCP, vol 7(1):71-87. PMID:17872894

  • A role for the MLL fusion partner ENL in transcriptional elongation and chromatin modification. (2007). Mueller D, Bach C, Zeisig D, Garcia-Cuellar MP, Monroe S, Sreekumar A, Zhou R, Nesvizhskii A, Chinnaiyan A, Hess JL, Slany RK. Blood, vol 110(13):4445-54. PMID:17855633

  • The transcription elongation factor TFIIS is a component of RNA polymerase II preinitiation complexes. (2007). Kim B, Nesvizhskii AI, Rani PG, Hahn S, Aebersold R, Ranish JA. Proceedings of the National Academy of Sciences of the United States of America, vol 104(41):16068-73. PMID:17913884

  • Analysis and validation of proteomic data generated by tandem mass spectrometry. (2007). Nesvizhskii AI, Vitek O, Aebersold R. Nature methods, vol 4(10):787-97. PMID:17901868

  • Comprehensive analysis of proteins of pH fractionated samples using monolithic LC/MS/MS, intact MW measurement and MALDI-QIT-TOF MS. (2007). Yoo C, Patwa TH, Kreunin P, Miller FR, Huber CG, Nesvizhskii AI, Lubman DM. Journal of mass spectrometry : JMS, vol 42(3):312-34. PMID:17206599

  • Protein identification by tandem mass spectrometry and sequence database searching. (2006). Nesvizhskii AI. Methods in molecular biology (Clifton, N.J.), vol 367():87-119. PMID:17185772

  • Optimized peptide separation and identification for mass spectrometry based proteomics via free-flow electrophoresis. (2006). Malmström J, Lee H, Nesvizhskii AI, Shteynberg D, Mohanty S, Brunner E, Ye M, Weber G, Eckerskorn C, Aebersold R. Journal of proteome research, vol 5(9):2241-9. PMID:16944936

  • 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. (2005). Nesvizhskii AI, Roos FF, Grossmann J, Vogelzang M, Eddes JS, Gruissem W, Baginsky S, Aebersold R. Molecular & cellular proteomics : MCP, vol 5(4):652-70. PMID:16352522

  • Analysis of the Saccharomyces cerevisiae proteome with PeptideAtlas. (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. Genome biology, vol 7(11):R106. PMID:17101051

  • The PeptideAtlas project. (2005). Desiere F, Deutsch EW, King NL, Nesvizhskii AI, Mallick P, Eng J, Chen S, Eddes J, Loevenich SN, Aebersold R. Nucleic acids research, vol 34(Database issue):D655-8. PMID:16381952

  • Interpretation of shotgun proteomic data: the protein inference problem. (2005). Nesvizhskii AI, Aebersold R. Molecular & cellular proteomics : MCP, vol 4(10):1419-40. PMID:16009968

  • Investigation of neutral loss during collision-induced dissociation of peptide ions. (2005). Martin DB, Eng JK, Nesvizhskii AI, Gemmill A, Aebersold R. Analytical chemistry, vol 77(15):4870-82. PMID:16053300

  • Human Plasma PeptideAtlas. (2005). Deutsch EW, Eng JK, Zhang H, King NL, Nesvizhskii AI, Lin B, Lee H, Yi EC, Ossola R, Aebersold R. Proteomics, vol 5(13):3497-500. PMID:16052627

  • Do we want our data raw? Including binary mass spectrometry data in public proteomics data repositories. (2005). Martens L, Nesvizhskii AI, Hermjakob H, Adamski M, Omenn GS, Vandekerckhove J, Gevaert K. Proteomics, vol 5(13):3501-5. PMID:16041670

  • Integration with the human genome of peptide sequences obtained by high-throughput mass spectrometry. (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, Kregenow F, Lee H, Lin B, Martin D, Ranish JA, Rawlings DJ, Samelson LE, Shiio Y, Watts JD, Wollscheid B, Wright ME, Yan W, Yang L, Yi EC, Zhang H, Aebersold R. Genome biology, vol 6(1):R9. PMID:15642101

  • Quantitative mass spectrometry reveals a role for the GTPase Rho1p in actin organization on the peroxisome membrane. (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. The Journal of cell biology, vol 167(6):1099-112. PMID:15596542

  • The need for guidelines in publication of peptide and protein identification data: Working Group on Publication Guidelines for Peptide and Protein Identification Data. (2004). Carr S, Aebersold R, Baldwin M, Burlingame A, Clauser K, Nesvizhskii A, . Molecular & cellular proteomics : MCP, vol 3(6):531-3. PMID:15075378

  • Analysis, statistical validation and dissemination of large-scale proteomics datasets generated by tandem MS. (2004). Nesvizhskii AI, Aebersold R. Drug discovery today, vol 9(4):173-81. PMID:14960397

  • Lipid raft proteins and their identification in T lymphocytes. (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. Sub-cellular biochemistry, vol 37():121-52. PMID:15376619

  • A statistical model for identifying proteins by tandem mass spectrometry. (2003). Nesvizhskii AI, Keller A, Kolker E, Aebersold R. Analytical chemistry, vol 75(17):4646-58. PMID:14632076

  • Initial proteome analysis of model microorganism Haemophilus influenzae strain Rd KW20. (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, Reilly TJ, Makarova KS, Palsson BO, Smith AL. Journal of bacteriology, vol 185(15):4593-602. PMID:12867470

  • 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. (2003). von Haller PD, Yi E, Donohoe S, Vaughn K, Keller A, Nesvizhskii AI, Eng J, Li XJ, Goodlett DR, Aebersold R, Watts JD. Molecular & cellular proteomics : MCP, vol 2(7):428-42. PMID:12832459

  • 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. (2003). von Haller PD, Yi E, Donohoe S, Vaughn K, Keller A, Nesvizhskii AI, Eng J, Li XJ, Goodlett DR, Aebersold R, Watts JD. Molecular & cellular proteomics : MCP, vol 2(7):426-7. PMID:12832456

  • Empirical statistical model to estimate the accuracy of peptide identifications made by MS/MS and database search. (2002). Keller A, Nesvizhskii AI, Kolker E, Aebersold R. Analytical chemistry, vol 74(20):5383-92. PMID:12403597

  • Experimental protein mixture for validating tandem mass spectral analysis. (2002). Keller A, Purvine S, Nesvizhskii AI, Stolyar S, Goodlett DR, Kolker E. Omics : a journal of integrative biology, vol 6(2):207-12. PMID:12143966