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Alexey Nesvizhskii

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Christian A Shively; Craig J Dobry; Matthew J Eckwahl; Dattatreya Mellacheruvu; Alexey I Nesvizhskii; Anuj Kumar
Genetic networks inducing invasive growth in Saccharomyces cerevisiae identified through systematic genome-wide overexpression.
Hyungwon Choi; Damian Fermin; Debashis Ghosh; Alexey I Nesvizhskii; Zhaohui S Qin
Sparsely correlated hidden Markov models with application to genome-wide location studies.
Guomin Liu; Alexey I Nesvizhskii; Brian Raught; Tharan Srikumar; Mike Tyers; Jianping Zhang; Hyungwon Choi; Jean-Philippe Lambert; Brett Larsen; Anne-Claude Gingras
Using ProHits to store, annotate, and analyze affinity purification-mass spectrometry (AP-MS) data.

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2013: Christian A Shively; Craig J Dobry; Matthew J Eckwahl; Dattatreya Mellacheruvu; Alexey I Nesvizhskii; Anuj Kumar
Genetic networks inducing invasive growth in Saccharomyces cerevisiae identified through systematic genome-wide overexpression.
Genetics 2013;193(4):1297-310.
2013: Hyungwon Choi; Damian Fermin; Debashis Ghosh; Alexey I Nesvizhskii; Zhaohui S Qin
Sparsely correlated hidden Markov models with application to genome-wide location studies.
Bioinformatics (Oxford, England) 2013;29(5):533-41.
2012: Guomin Liu; Alexey I Nesvizhskii; Brian Raught; Tharan Srikumar; Mike Tyers; Jianping Zhang; Hyungwon Choi; Jean-Philippe Lambert; Brett Larsen; Anne-Claude Gingras
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.] 2012;Chapter 8():Unit8.16.
2012: Hyungwon Choi; Anne-Claude Gingras; Guomin Liu; Dattatreya Mellacheruvu; Mike Tyers; Alexey I Nesvizhskii
Analyzing protein-protein interactions from affinity purification-mass spectrometry data with SAINT.
Current protocols in bioinformatics / editoral board, Andreas D. Baxevanis ... [et al.] 2012;Chapter 8():Unit8.15.
2012: Craig R Homer; Amrita Kabi; Noemí Marina-García; Alexey I Nesvizhskii; Kourtney P Nickerson; Gabriel Nuñez; Arun Sreekumar; Arul M Chinnaiyan; Christine McDonald
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 2012;287(30):25565-76.
2012: Amy L Richmond; Arun Sreekumar; Alexey I Nesvizhskii; Kourtney P Nickerson; Gabriel Nuñez; Arul M Chinnaiyan; Craig R Homer; Amrita Kabi; Noemí Marina-García; Christine McDonald
The nucleotide synthesis enzyme CAD inhibits NOD2 antibacterial function in human intestinal epithelial cells.
Gastroenterology 2012;142(7):1483-92.e6.
2012: Anne-Claude Gingras; Alexey I Nesvizhskii
Protein complexes and interaction networks.
Proteomics 2012;12(10):1475-7.
2012: Alexey I Nesvizhskii
Computational and informatics strategies for identification of specific protein interaction partners in affinity purification mass spectrometry experiments.
Proteomics 2012;12(10):1639-55.
2012: Hyungwon Choi; Timo Glatter; Mathias Gstaiger; Alexey I Nesvizhskii
SAINT-MS1: protein-protein interaction scoring using label-free intensity data in affinity purification-mass spectrometry experiments.
Journal of proteome research 2012;11(4):2619-24.
2012: Kang Ning; Damian Fermin; Alexey I Nesvizhskii
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 2012;11(4):2261-71.
2012: Ana M Rodríguez-Piñeiro; Kristina A Thomsson; Sjoerd van der Post; Malin E V Johansson; Alexey I Nesvizhskii; Gunnar C Hansson
Proteomic study of the mucin granulae in an intestinal goblet cell model.
Journal of proteome research 2012;11(3):1879-90.
2012: Kelvin Ma; Olga Vitek; Alexey I Nesvizhskii
A statistical model-building perspective to identification of MS/MS spectra with PeptideProphet.
BMC bioinformatics 2012;13 Suppl 16():S1.
2011: David Shteynberg; Zhi Sun; Natalie Tasman; Ruedi Aebersold; Eric Deutsch; Jimmy K Eng; Henry Lam; Luis Mendoza; Robert L Moritz; Alexey I Nesvizhskii
iProphet: multi-level integrative analysis of shotgun proteomic data improves peptide and protein identification rates and error estimates.
Molecular & cellular proteomics : MCP 2011;10(12):M111.007690.
2011: Julio C Bayona; Juan J Cazzulo; Hyungwon Choi; Marc Laverrière; Ernesto S Nakayasu; Alexey I Nesvizhskii; Tiago J P Sobreira; Clemente Aguilar; Igor Almeida; Vanina E Alvarez
SUMOylation pathway in Trypanosoma cruzi: functional characterization and proteomic analysis of target proteins.
Molecular & cellular proteomics : MCP 2011;10(12):M110.007369.
2011: Nuno Bandeira; Alexey I Nesvizhskii; Martin McIntosh
Advancing next-generation proteomics through computational research.
Journal of proteome research 2011;10(7):2895.
2011: Taejoon Kwon; Alexey I Nesvizhskii; Christine Vogel; Hyungwon Choi; Edward M Marcotte
MSblender: A probabilistic approach for integrating peptide identifications from multiple database search engines.
Journal of proteome research 2011;10(7):2949-58.
2011: Dana V Skarra; Marilyn Goudreault; Hyungwon Choi; Michael Mullin; Alexey I Nesvizhskii; Anne-Claude Gingras; Richard E Honkanen
Label-free quantitative proteomics and SAINT analysis enable interactome mapping for the human Ser/Thr protein phosphatase 5.
Proteomics 2011;11(8):1508-16.
2011: Damian Fermin; venkatesha basrur; Anastasia K Yocum; Alexey I Nesvizhskii
Abacus: a computational tool for extracting and pre-processing spectral count data for label-free quantitative proteomic analysis.
Proteomics 2011;11(7):1340-5.
2011: Brian T Emmer; Ernesto S Nakayasu; Christina Souther; Hyungwon Choi; Tiago Sobreira; Conrad L Epting; Alexey I Nesvizhskii; Igor Almeida; David M Engman
Global analysis of protein palmitoylation in African trypanosomes.
Eukaryotic cell 2011;10(3):455-63.
2011: Timo Glatter; Ruedi Aebersold; Hyungwon Choi; Ernst Hafen; Irena Jevtov; Martin A Jünger; Katja Köhler; Alexey I Nesvizhskii; Oliver Rinner; Katarzyna Roguska; Ralf B Schittenhelm; Alexander Schmidt; Hugo Stocker; Alexander Wepf; Matthias Gstaiger
Modularity and hormone sensitivity of the Drosophila melanogaster insulin receptor/target of rapamycin interaction proteome.
Molecular systems biology 2011;7():547.
2011: Agnes Bergerat; Hyungwon Choi; Julius Decano; Ann Marie Moran; Alexey I Nesvizhskii; Nelson Ruiz-Opazo; Martin Steffen; Chang-Jiun Wu; Victoria Lm Herrera
Prestroke proteomic changes in cerebral microvessels in stroke-prone, transgenic[hCETP]-Hyperlipidemic, Dahl salt-sensitive hypertensive rats.
Molecular medicine (Cambridge, Mass.) 2011;17(7-8):588-98.
2011: Shaiju K Vareed; Vadiraja B Bhat; Christopher Thompson; Vihas T Vasu; Damian Fermin; Hyungwon Choi; Chad J Creighton; Sitaram Gayatri; Ling Lan; Nagireddy Putluri; Gagan Singh Thangjam; Punit Kaur; Mohsen Shabahang; Judith Goldstein Giri; Alexey I Nesvizhskii; Alexzander Asea; Anil Govind Cashikar; Arundhati Rao; James M. McLoughlin; Arun Sreekumar
Metabolites of purine nucleoside phosphorylase (NP) in serum have the potential to delineate pancreatic adenocarcinoma.
PloS one 2011;6(3):e17177.
2011: Hyungwon Choi; Brett Larsen; Zhen-Yuan Lin; Ashton Breitkreutz; Dattatreya Mellacheruvu; Damian Fermin; Zhaohui S Qin; Mike Tyers; Anne-Claude Gingras; Alexey I Nesvizhskii
SAINT: probabilistic scoring of affinity purification-mass spectrometry data.
Nature methods 2011;8(1):70-3.
2010: Alexey I Nesvizhskii
A survey of computational methods and error rate estimation procedures for peptide and protein identification in shotgun proteomics.
Journal of proteomics 2010;73(11):2092-123.
2010: Guomin Liu; Jianping Zhang; Brett Larsen; Chris Stark; Ashton Breitkreutz; Zhen-Yuan Lin; Bobby-Joe Breitkreutz; Yongmei Ding; Karen Colwill; Adrian Pasculescu; Tony Pawson; Jeffrey L Wrana; Alexey I Nesvizhskii; Brian Raught; Mike Tyers; Anne-Claude Gingras
ProHits: integrated software for mass spectrometry-based interaction proteomics.
Nature biotechnology 2010;28(10):1015-7.
2010: Ramsey A Saleem; Richard S Rogers; Alexander V Ratushny; David J Dilworth; Paul T Shannon; David Shteynberg; Yakun Wan; Robert L Moritz; Alexey I Nesvizhskii; Richard A Rachubinski; John D Aitchison
Integrated phosphoproteomics analysis of a signaling network governing nutrient response and peroxisome induction.
Molecular & cellular proteomics : MCP 2010;9(9):2076-88.
2010: Kang Ning; Damian Fermin; Alexey I Nesvizhskii
Computational analysis of unassigned high-quality MS/MS spectra in proteomic data sets.
Proteomics 2010;10(14):2712-8.
2010: Hyungwon Choi; Sinae Kim; Anne-Claude Gingras; Alexey I Nesvizhskii
Analysis of protein complexes through model-based biclustering of label-free quantitative AP-MS data.
Molecular systems biology 2010;6():385.
2010: Ashton Breitkreutz; Hyungwon Choi; Jeffrey R Sharom; Lorrie Boucher; Victor Neduva; Brett Larsen; Zhen-Yuan Lin; Bobby-Joe Breitkreutz; Chris Stark; Guomin Liu; Jessica Ahn; Danielle Dewar-Darch; Teresa Reguly; Xiaojing Tang; Ricardo Almeida; Zhaohui Steve Qin; Tony Pawson; Anne-Claude Gingras; Alexey I Nesvizhskii; Mike Tyers
A global protein kinase and phosphatase interaction network in yeast.
Science (New York, N.Y.) 2010;328(5981):1043-6.
2010: Eric Deutsch; Luis Mendoza; David Shteynberg; Terry Farrah; Henry Lam; Natalie Tasman; Zhi Sun; Erik Nilsson; Brian Pratt; Bryan Prazen; Jimmy K Eng; Daniel B Martin; Alexey I Nesvizhskii; Ruedi Aebersold
A guided tour of the Trans-Proteomic Pipeline.
Proteomics 2010;10(6):1150-9.
2010: Amjad P Khan; Laila M Poisson; Vadiraja B Bhat; Damian Fermin; Rong Zhao; Shanker Kalyana-Sundaram; George Michailidis; Alexey I Nesvizhskii; Gilbert S Omenn; Arul M Chinnaiyan; Arun Sreekumar
Quantitative proteomic profiling of prostate cancer reveals a role for miR-128 in prostate cancer.
Molecular & cellular proteomics : MCP 2010;9(2):298-312.
2010: Bernd Bodenmiller; Stefanie Wanka; Claudine Kraft; Jörg Urban; David Campbell; Patrick G Pedrioli; Bertran Gerrits; Paola Picotti; Henry Lam; Olga Vitek; Mi-Youn Brusniak; Bernd Roschitzki; Chao Zhang; Kevan M Shokat; Ralph Schlapbach; Alejandro Colman-Lerner; Garry P Nolan; Alexey I Nesvizhskii; Matthias Peter; Robbie Loewith; Christian von Mering; Ruedi Aebersold
Phosphoproteomic analysis reveals interconnected system-wide responses to perturbations of kinases and phosphatases in yeast.
Science signaling 2010;3(153):rs4.
2010: Kang Ning; Alexey I Nesvizhskii
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 2010;11 Suppl 11():S14.
2010: Kang Ning; Hoong Kee Ng; Sriganesh Srihari; Kang Ning; Alexey I Nesvizhskii
Examination of the relationship between essential genes in PPI network and hub proteins in reverse nearest neighbor topology.
BMC bioinformatics 2010;11():505.
2010: Adaikkalam Vellaichamy; Zoltán Dezso; Lellean JeBailey; Arul M Chinnaiyan; Arun Sreekumar; Alexey I Nesvizhskii; Gilbert S Omenn; Andrej Bugrim
"Topological significance" analysis of gene expression and proteomic profiles from prostate cancer cells reveals key mechanisms of androgen response.
PloS one 2010;5(6):e10936.
2009: Hyungwon Choi; Alexey I Nesvizhskii; Debashis Ghosh; Zhaohui S Qin
Hierarchical hidden Markov model with application to joint analysis of ChIP-chip and ChIP-seq data.
Bioinformatics (Oxford, England) 2009;25(14):1715-21.
2009: Henry Rodriguez; Mike Snyder; Mathias Uhlén; Philip C Andrews; Ronald Beavis; Christoph Borchers; Robert J Chalkley; Sang Yun Cho; Katie Cottingham; Michael Dunn; Tomasz Dylag; Ron Edgar; Peter Hare; Albert J R Heck; Roland F Hirsch; Karen Kennedy; Patrik Kolar; Hans-Joachim Kraus; Parag Mallick; Alexey I Nesvizhskii; Peipei Ping; Fredrik Pontén; Liming Yang; John R Yates; Stephen E Stein; Henning Hermjakob; Christopher R Kinsinger; Rolf Apweiler
Recommendations from the 2008 International Summit on Proteomics Data Release and Sharing Policy: the Amsterdam principles.
Journal of proteome research 2009;8(7):3689-92.
2009: Lena Ho; Jehnna L Ronan; Jiang Wu; Brett T Staahl; Lei Chen; Ann Kuo; Julie Lessard; Alexey I Nesvizhskii; Jeffrey A Ranish; Gerald R Crabtree
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 2009;106(13):5181-6.
2009: Peter Ulintz; Anastasia K Yocum; Bernd Bodenmiller; Ruedi Aebersold; Philip C Andrews; Alexey I Nesvizhskii
Comparison of MS(2)-only, MSA, and MS(2)/MS(3) methodologies for phosphopeptide identification.
Journal of proteome research 2009;8(2):887-99.
2009: Adaikkalam Vellaichamy; Arun Sreekumar; John R Strahler; Thekkelnaycke Rajendiran; Jindan YU; Sooryanarayana Lnu; Yong Li; Gilbert S Omenn; Arul M Chinnaiyan; Alexey I Nesvizhskii
Proteomic interrogation of androgen action in prostate cancer cells reveals roles of aminoacyl tRNA synthetases.
PloS one 2009;4(9):e7075.
2009: Marilyn Goudreault; Lisa M D'Ambrosio; Michelle J Kean; Michael J Mullin; Brett G Larsen; Amy Sanchez; Sidharth Chaudhry; Ginny I Chen; Frank Sicheri; Alexey I Nesvizhskii; Ruedi Aebersold; Brian Raught; Anne-Claude Gingras
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 2009;8(1):157-71.
2008: Hyungwon Choi; Damian Fermin; Alexey I Nesvizhskii
Significance analysis of spectral count data in label-free shotgun proteomics.
Molecular & cellular proteomics : MCP 2008;7(12):2373-85.
2008: Ying Ding; Hyungwon Choi; Alexey I Nesvizhskii
Adaptive discriminant function analysis and reranking of MS/MS database search results for improved peptide identification in shotgun proteomics.
Journal of proteome research 2008;7(11):4878-89.
2008: Xia Cao; Alexey I Nesvizhskii
Improved sequence tag generation method for peptide identification in tandem mass spectrometry.
Journal of proteome research 2008;7(10):4422-34.
2008: Barry S Taylor; Manoj Pal; Jianjun Yu; Bharathi Laxman; Shanker Kalyana-Sundaram; Rong Zhao; Anjana Menon; John T Wei; Alexey I Nesvizhskii; Debashis Ghosh; Gilbert S Omenn; David M Lubman; Arul M Chinnaiyan; Arun Sreekumar
Humoral response profiling reveals pathways to prostate cancer progression.
Molecular & cellular proteomics : MCP 2008;7(3):600-11.
2008: Marcello Marelli; Alexey I Nesvizhskii; John D Aitchison
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.) 2008;432():357-71.
2008: Brian C Searle; Mark Turner; Alexey I Nesvizhskii
Improving sensitivity by probabilistically combining results from multiple MS/MS search methodologies.
Journal of proteome research 2008;7(1):245-53.
2008: Hyungwon Choi; Alexey I Nesvizhskii
Semisupervised model-based validation of peptide identifications in mass spectrometry-based proteomics.
Journal of proteome research 2008;7(1):254-65.
2008: Hyungwon Choi; Debashis Ghosh; Alexey I Nesvizhskii
Statistical validation of peptide identifications in large-scale proteomics using the target-decoy database search strategy and flexible mixture modeling.
Journal of proteome research 2008;7(1):286-92.
2008: Hyungwon Choi; Alexey I Nesvizhskii
False discovery rates and related statistical concepts in mass spectrometry-based proteomics.
Journal of proteome research 2008;7(1):47-50.
2008: Peter Ulintz; Bernd Bodenmiller; Philip C Andrews; Ruedi Aebersold; Alexey I Nesvizhskii
Investigating MS2/MS3 matching statistics: a model for coupling consecutive stage mass spectrometry data for increased peptide identification confidence.
Molecular & cellular proteomics : MCP 2008;7(1):71-87.
2007: Dorothee Mueller; Christian Bach; Deniz T Zeisig; Maria-Paz Garcia-Cuellar; Sara Monroe; Arun Sreekumar; Rong Zhou; Alexey I Nesvizhskii; Arul M Chinnaiyan; Jay L Hess; Robert K Slany
A role for the MLL fusion partner ENL in transcriptional elongation and chromatin modification.
Blood 2007;110(13):4445-54.
2007: Bong Kim; Alexey I Nesvizhskii; P Geetha Rani; Steven Hahn; Ruedi Aebersold; Jeffrey A Ranish
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 2007;104(41):16068-73.
2007: Alexey I Nesvizhskii; Olga Vitek; Ruedi Aebersold
Analysis and validation of proteomic data generated by tandem mass spectrometry.
Nature methods 2007;4(10):787-97.
2007: Chul Yoo; Tasneem H Patwa; Paweena Kreunin; Fred R Miller; Christian G. Huber; Alexey I Nesvizhskii; David M Lubman
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 2007;42(3):312-34.
2007: Alexey I Nesvizhskii
Protein identification by tandem mass spectrometry and sequence database searching.
Methods in molecular biology (Clifton, N.J.) 2007;367():87-119.
2006: Johan Malmström; Hookeun Lee; Alexey I Nesvizhskii; David Shteynberg; Sonali Mohanty; Erich Brunner; Mingliang Ye; Gerhard Weber; Christoph Eckerskorn; Ruedi Aebersold
Optimized peptide separation and identification for mass spectrometry based proteomics via free-flow electrophoresis.
Journal of proteome research 2006;5(9):2241-9.
2006: Alexey I Nesvizhskii; Franz F Roos; Jonas Grossmann; Mathijs Vogelzang; James S Eddes; Wilhelm Gruissem; Sacha Baginsky; Ruedi Aebersold
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 2006;5(4):652-70.
2006: Nichole L King; Eric Deutsch; Jeffrey A Ranish; Alexey I Nesvizhskii; James S Eddes; Parag Mallick; Jimmy Eng; Frank Desiere; Mark R Flory; Daniel B Martin; Bong Kim; Hookeun Lee; Brian Raught; Ruedi Aebersold
Analysis of the Saccharomyces cerevisiae proteome with PeptideAtlas.
Genome biology 2006;7(11):R106.
2006: Frank Desiere; Eric Deutsch; Nichole L King; Alexey I Nesvizhskii; Parag Mallick; Jimmy Eng; Sharon Chen; James S Eddes; Sandra N Loevenich; Ruedi Aebersold
The PeptideAtlas project.
Nucleic acids research 2006;34(Database issue):D655-8.
2005: Alexey I Nesvizhskii; Ruedi Aebersold
Interpretation of shotgun proteomic data: the protein inference problem.
Molecular & cellular proteomics : MCP 2005;4(10):1419-40.
2005: Daniel B Martin; Jimmy K Eng; Alexey I Nesvizhskii; Andrew Gemmill; Ruedi Aebersold
Investigation of neutral loss during collision-induced dissociation of peptide ions.
Analytical chemistry 2005;77(15):4870-82.
2005: Eric Deutsch; Jimmy K Eng; HUI ZHANG; Nichole L King; Alexey I Nesvizhskii; Lin Biao; Hookeun Lee; Eugene C Yi; Reto Ossola; Ruedi Aebersold
Human Plasma PeptideAtlas.
Proteomics 2005;5(13):3497-500.
2005: Lennart Martens; Alexey I Nesvizhskii; Henning Hermjakob; Marcin Adamski; Gilbert S Omenn; Joël Vandekerckhove; Kris Gevaert
Do we want our data raw? Including binary mass spectrometry data in public proteomics data repositories.
Proteomics 2005;5(13):3501-5.
2005: Frank Desiere; Eric W Deutsch; Alexey I Nesvizhskii; Parag Mallick; Nichole L King; Jimmy K Eng; Alan Aderem; Rose Boyle; Erich Brunner; Samuel Donohoe; Nelson Fausto; Ernst Hafen; Lee Hood; Michael G Katze; Kathleen A Kennedy; Floyd Kregenow; Hookeun Lee; Lin Biao; Dan Martin; Jeffrey A Ranish; David J Rawlings; Lawrence E Samelson; Yuzuru Shiio; Julian D Watts; Bernd Wollscheid; Michael E Wright; Wei Yan; Lihong Yang; Eugene C Yi; HUI ZHANG; Ruedi Aebersold
Integration with the human genome of peptide sequences obtained by high-throughput mass spectrometry.
Genome biology 2005;6(1):R9.
2004: Marcello Marelli; Jennifer J Smith; Sunhee Jung; Eugene Yi; Alexey I Nesvizhskii; Rowan H Christmas; Ramsey A Saleem; Yuen Yi C Tam; Andrei Fagarasanu; David R Goodlett; Ruedi Aebersold; Richard A Rachubinski; John D Aitchison
Quantitative mass spectrometry reveals a role for the GTPase Rho1p in actin organization on the peroxisome membrane.
The Journal of cell biology 2004;167(6):1099-112.
2004: Steven Carr; Ruedi Aebersold; Michael Baldwin; Al L Burlingame; Karl Clauser; Alexey I Nesvizhskii
The need for guidelines in publication of peptide and protein identification data: Working Group on Publication Guidelines for Peptide and Protein Identification Data.
Molecular & cellular proteomics : MCP 2004;3(6):531-3.
2004: Alexey I Nesvizhskii; Ruedi Aebersold
Analysis, statistical validation and dissemination of large-scale proteomics datasets generated by tandem MS.
Drug discovery today 2004;9(4):173-81.
2004: Bernd Wollscheid; Priska D von Haller; Eugene Yi; Samuel Donohoe; Kelly Vaughn; Andrew Keller; Alexey I Nesvizhskii; Jimmy Eng; Xiao-jun Li; David R Goodlett; Ruedi Aebersold; Julian D Watts
Lipid raft proteins and their identification in T lymphocytes.
Sub-cellular biochemistry 2004;37():121-52.
2003: Alexey I Nesvizhskii; Andrew Keller; Eugene Kolker; Ruedi Aebersold
A statistical model for identifying proteins by tandem mass spectrometry.
Analytical chemistry 2003;75(17):4646-58.
2003: Eugene Kolker; Samuel O Purvine; Michael Galperin; Sergey Stolyar; David R Goodlett; Alexey I Nesvizhskii; Andrew Keller; Tao Xie; Jimmy K Eng; Eugene Yi; Leroy Hood; Alex F Picone; Tim Cherny; Brian C Tjaden; Andrew F Siegel; Thomas J Reilly; Kira S Makarova; Bernhard Ø Palsson; Arnold L. Smith
Initial proteome analysis of model microorganism Haemophilus influenzae strain Rd KW20.
Journal of bacteriology 2003;185(15):4593-602.
2003: Priska D von Haller; Eugene Yi; Samuel Donohoe; Kelly Vaughn; Andrew Keller; Alexey I Nesvizhskii; Jimmy Eng; Xiao-jun Li; David R Goodlett; Ruedi Aebersold; Julian D Watts
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 2003;2(7):428-42.
2003: Priska D von Haller; Eugene Yi; Samuel Donohoe; Kelly Vaughn; Andrew Keller; Alexey I Nesvizhskii; Jimmy Eng; Xiao-jun Li; David R Goodlett; Ruedi Aebersold; Julian D Watts
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 2003;2(7):426-7.
2002: Andrew Keller; Alexey I Nesvizhskii; Eugene Kolker; Ruedi Aebersold
Empirical statistical model to estimate the accuracy of peptide identifications made by MS/MS and database search.
Analytical chemistry 2002;74(20):5383-92.
2002: Andrew Keller; Samuel O Purvine; Alexey I Nesvizhskii; Sergey Stolyar; David R Goodlett; Eugene Kolker
Experimental protein mixture for validating tandem mass spectral analysis.
Omics : a journal of integrative biology 2002;6(2):207-12.
2001: AL Ankudinov; Alexey I Nesvizhskii; JJ Rehr
Hole counts from X-ray absorption spectra.
Journal of synchrotron radiation 2001;8(Pt 2):92-5.
1999: Alexey I Nesvizhskii; JJ Rehr
L-edge XANES of 3d-transition metals.
Journal of synchrotron radiation 1999;6(Pt 3):315-6.