| Year |
Citation |
Score |
| 2024 |
Li K, Teo GC, Yang KL, Yu F, Nesvizhskii AI. diaTracer enables spectrum-centric analysis of diaPASEF proteomics data. Biorxiv : the Preprint Server For Biology. PMID 38854051 DOI: 10.1101/2024.05.25.595875 |
0.324 |
|
| 2023 |
Kweon HK, Kong AT, Hersberger KE, Huang S, Nesvizhskii AI, Wang Y, Hakansson K, Andrews PC. Sulfoproteomics Workflow with Precursor Ion Accurate Mass Shift Analysis Reveals Novel Tyrosine Sulfoproteins in the Golgi. Journal of Proteome Research. PMID 38112105 DOI: 10.1021/acs.jproteome.3c00323 |
0.318 |
|
| 2023 |
Rojas Ramírez C, Espino JA, Jones LM, Polasky DA, Nesvizhskii AI. Efficient Analysis of Proteome-Wide FPOP Data by FragPipe. Analytical Chemistry. 95: 16131-16137. PMID 37878603 DOI: 10.1021/acs.analchem.3c02388 |
0.331 |
|
| 2023 |
Yu F, Teo GC, Kong AT, Fröhlich K, Li GX, Demichev V, Nesvizhskii AI. Analysis of DIA proteomics data using MSFragger-DIA and FragPipe computational platform. Nature Communications. 14: 4154. PMID 37438352 DOI: 10.1038/s41467-023-39869-5 |
0.328 |
|
| 2023 |
Ramírez CR, Espino JA, Jones LM, Polasky DA, Nesvizhskii AI. Efficient Analysis of Proteome-wide FPOP Data by FragPipe. Biorxiv : the Preprint Server For Biology. PMID 37333157 DOI: 10.1101/2023.06.01.543263 |
0.326 |
|
| 2023 |
Polasky DA, Geiszler DJ, Yu F, Li K, Teo GC, Nesvizhskii AI. MSFragger-Labile: A Flexible Method to Improve Labile PTM Analysis in Proteomics. Molecular & Cellular Proteomics : McP. 100538. PMID 37004988 DOI: 10.1016/j.mcpro.2023.100538 |
0.305 |
|
| 2020 |
Yu F, Haynes SE, Teo GC, Avtonomov DM, Polasky DA, Nesvizhskii AI. Fast Quantitative Analysis of timsTOF PASEF Data with MSFragger and IonQuant. Molecular & Cellular Proteomics : McP. 19: 1575-1585. PMID 33451737 DOI: 10.1074/mcp.TIR120.002048 |
0.336 |
|
| 2020 |
Choi M, Carver J, Chiva C, Tzouros M, Huang T, Tsai TH, Pullman B, Bernhardt OM, Hüttenhain R, Teo GC, Perez-Riverol Y, Muntel J, Müller M, Goetze S, Pavlou M, ... ... Nesvizhskii AI, et al. MassIVE.quant: a community resource of quantitative mass spectrometry-based proteomics datasets. Nature Methods. PMID 32929271 DOI: 10.1038/S41592-020-0955-0 |
0.37 |
|
| 2020 |
Yu F, Teo GC, Kong AT, Haynes SE, Avtonomov DM, Geiszler DJ, Nesvizhskii AI. Identification of modified peptides using localization-aware open search. Nature Communications. 11: 4065. PMID 32792501 DOI: 10.1038/S41467-020-17921-Y |
0.361 |
|
| 2020 |
da Veiga Leprevost F, Haynes SE, Avtonomov DM, Chang HY, Shanmugam AK, Mellacheruvu D, Kong AT, Nesvizhskii AI. Philosopher: a versatile toolkit for shotgun proteomics data analysis. Nature Methods. PMID 32669682 DOI: 10.1038/S41592-020-0912-Y |
0.358 |
|
| 2020 |
Gillette MA, Satpathy S, Cao S, Dhanasekaran SM, Vasaikar SV, Krug K, Petralia F, Li Y, Liang WW, Reva B, Krek A, Ji J, Song X, Liu W, Hong R, ... ... Nesvizhskii AI, et al. Proteogenomic Characterization Reveals Therapeutic Vulnerabilities in Lung Adenocarcinoma. Cell. 182: 200-225.e35. PMID 32649874 DOI: 10.1016/J.Cell.2020.06.013 |
0.315 |
|
| 2020 |
Yu F, Haynes SE, Teo GC, Avtonomov DM, Polasky DA, Nesvizhskii AI. Fast quantitative analysis of timsTOF PASEF data with MSFragger and IonQuant. Molecular & Cellular Proteomics : McP. PMID 32616513 DOI: 10.1074/Mcp.Tir120.002048 |
0.438 |
|
| 2020 |
Park SS, Ponce-Balbuena D, Kuick R, Guerrero-Serna G, Yoon J, Mellacheruvu D, Conlon KP, Basrur V, Nesvizhskii AI, Jalife J, Rual JF. Kir2.1 interactome mapping uncovers PKP4 as a modulator of the Kir2.1-regulated inward rectifier potassium currents. Molecular & Cellular Proteomics : McP. PMID 32541000 DOI: 10.1074/Mcp.Ra120.002071 |
0.303 |
|
| 2020 |
Chang HY, Kong AT, da Veiga Leprevost F, Avtonomov DM, Haynes SE, Nesvizhskii AI. Crystal-C: A computational tool for refinement of open search results. Journal of Proteome Research. PMID 32338005 DOI: 10.1021/Acs.Jproteome.0C00119 |
0.402 |
|
| 2020 |
Djomehri SI, Gonzalez ME, da Veiga Leprevost F, Tekula SR, Chang HY, White MJ, Cimino-Mathews A, Burman B, Basrur V, Argani P, Nesvizhskii AI, Kleer CG. Quantitative proteomic landscape of metaplastic breast carcinoma pathological subtypes and their relationship to triple-negative tumors. Nature Communications. 11: 1723. PMID 32265444 DOI: 10.1038/S41467-020-15283-Z |
0.359 |
|
| 2020 |
Dou Y, Kawaler EA, Cui Zhou D, Gritsenko MA, Huang C, Blumenberg L, Karpova A, Petyuk VA, Savage SR, Satpathy S, Liu W, Wu Y, Tsai CF, Wen B, Li Z, ... ... Nesvizhskii AI, et al. Proteogenomic Characterization of Endometrial Carcinoma. Cell. PMID 32059776 DOI: 10.1016/J.Cell.2020.01.026 |
0.308 |
|
| 2020 |
Cho KC, Clark DJ, Schnaubelt M, Teo GC, Leprevost FDV, Bocik W, Boja E, Hiltke T, Nesvizhskii A, Zhang H. Deep Proteomics using Two Dimensional Data Independent Acquisition Mass Spectrometry. Analytical Chemistry. PMID 32058701 DOI: 10.1021/Acs.Analchem.9B04418 |
0.426 |
|
| 2019 |
Clark DJ, Dhanasekaran SM, Petralia F, Pan J, Song X, Hu Y, da Veiga Leprevost F, Reva B, Lih TM, Chang HY, Ma W, Huang C, Ricketts CJ, Chen L, Krek A, ... ... Nesvizhskii AI, et al. Integrated Proteogenomic Characterization of Clear Cell Renal Cell Carcinoma. Cell. 179: 964-983.e31. PMID 31675502 DOI: 10.1016/J.Cell.2019.10.007 |
0.32 |
|
| 2019 |
Parker BW, Goncz EJ, Krist DT, Statsyuk AV, Nesvizhskii AI, Weiss EL. Mapping low-affinity/high-specificity peptide-protein interactions using ligand-footprinting mass spectrometry. Proceedings of the National Academy of Sciences of the United States of America. PMID 31578253 DOI: 10.1073/Pnas.1819533116 |
0.389 |
|
| 2019 |
Shi J, Wang X, Zhu H, Jiang H, Wang D, Nesvizhskii A, Zhu HJ. Response to the comments on "Determining Allele-Specific Protein Expression (ASPE) Using a Novel QconCAT-Based Proteomics Method". Journal of Proteome Research. PMID 30616350 DOI: 10.1021/Acs.Jproteome.8B00940 |
0.347 |
|
| 2018 |
Avtonomov DM, Kong A, Nesvizhskii AI. DeltaMass: Automated detection and visualization of mass shifts in proteomic open search results. Journal of Proteome Research. PMID 30523686 DOI: 10.1021/Acs.Jproteome.8B00728 |
0.382 |
|
| 2018 |
Shi J, Wang X, Zhu H, Jiang H, Wang D, Nesvizhskii A, Zhu HJ. Determining Allele-Specific Protein Expression (ASPE) Using a Novel QconCAT-Based Proteomics Method. Journal of Proteome Research. PMID 30141943 DOI: 10.1021/Acs.Jproteome.8B00620 |
0.341 |
|
| 2018 |
Khoriaty R, Hesketh GG, Bernard A, Weyand AC, Mellacheruvu D, Zhu G, Hoenerhoff MJ, McGee B, Everett L, Adams EJ, Zhang B, Saunders TL, Nesvizhskii AI, Klionsky DJ, Shavit JA, et al. Functions of the COPII gene paralogs SEC23A and SEC23B are interchangeable in vivo. Proceedings of the National Academy of Sciences of the United States of America. PMID 30065114 DOI: 10.1073/Pnas.1805784115 |
0.306 |
|
| 2018 |
Glazier AA, Hafeez N, Mellacheruvu D, Basrur V, Nesvizhskii AI, Lee LM, Shao H, Tang V, Yob JM, Gestwicki JE, Helms AS, Day SM. HSC70 is a chaperone for wild-type and mutant cardiac myosin binding protein C. Jci Insight. 3. PMID 29875314 DOI: 10.1172/Jci.Insight.99319 |
0.324 |
|
| 2018 |
Ropa J, Saha N, Chen Z, Serio J, Chen W, Mellacheruvu D, Zhao L, Basrur V, Nesvizhskii AI, Muntean AG. PAF1 complex interactions with SETDB1 mediate promoter H3K9 methylation and transcriptional repression of and in acute myeloid leukemia. Oncotarget. 9: 22123-22136. PMID 29774127 DOI: 10.18632/Oncotarget.25204 |
0.354 |
|
| 2018 |
Hawkins AG, Basrur V, da Veiga Leprevost F, Pedersen E, Sperring C, Nesvizhskii AI, Lawlor ER. The Ewing sarcoma secretome and its response to activation of Wnt/beta-catenin signaling. Molecular & Cellular Proteomics : McP. PMID 29386236 DOI: 10.1074/Mcp.Ra118.000596 |
0.323 |
|
| 2017 |
Avtonomov DM, Polasky DA, Ruotolo BT, Nesvizhskii AI. IMTBX and Grppr: Software for Top-Down Proteomics Utilizing Ion Mobility-Mass Spectrometry. Analytical Chemistry. PMID 29278491 DOI: 10.1021/Acs.Analchem.7B04999 |
0.363 |
|
| 2017 |
Shao W, Pedrioli PGA, Wolski W, Scurtescu C, Schmid E, Vizcaíno JA, Courcelles M, Schuster H, Kowalewski D, Marino F, Arlehamn CSL, Vaughan K, Peters B, Sette A, Ottenhoff THM, ... ... Nesvizhskii AI, et al. The SysteMHC Atlas project. Nucleic Acids Research. PMID 28985418 DOI: 10.1093/Nar/Gkx664 |
0.387 |
|
| 2017 |
Rosenberger G, Bludau I, Schmitt U, Heusel M, Hunter CL, Liu Y, MacCoss MJ, MacLean BX, Nesvizhskii AI, Pedrioli PGA, Reiter L, Röst HL, Tate S, Ting YS, Collins BC, et al. Statistical control of peptide and protein error rates in large-scale targeted data-independent acquisition analyses. Nature Methods. PMID 28825704 DOI: 10.1038/Nmeth.4398 |
0.438 |
|
| 2017 |
Meyer JG, Mukkamalla S, Steen H, Nesvizhskii AI, Gibson BW, Schilling B. PIQED: automated identification and quantification of protein modifications from DIA-MS data. Nature Methods. 14: 646-647. PMID 28661500 DOI: 10.1038/Nmeth.4334 |
0.404 |
|
| 2017 |
Rolland DCM, Basrur V, Jeon YK, McNeil-Schwalm C, Fermin D, Conlon KP, Zhou Y, Ng SY, Tsou CC, Brown NA, Thomas DG, Bailey NG, Omenn GS, Nesvizhskii AI, Root DE, et al. Functional proteogenomics reveals biomarkers and therapeutic targets in lymphomas. Proceedings of the National Academy of Sciences of the United States of America. PMID 28607076 DOI: 10.1073/Pnas.1701263114 |
0.343 |
|
| 2017 |
Kong AT, Leprevost FV, Avtonomov DM, Mellacheruvu D, Nesvizhskii AI. MSFragger: ultrafast and comprehensive peptide identification in mass spectrometry-based proteomics. Nature Methods. PMID 28394336 DOI: 10.1038/Nmeth.4256 |
0.438 |
|
| 2017 |
Bruderer R, Sondermann J, Tsou CC, Barrantes-Freer A, Stadelmann C, Nesvizhskii AI, Schmidt M, Reiter L, Gomez-Varela D. New targeted approaches for the quantification of data-independent acquisition mass spectrometry. Proteomics. PMID 28319648 DOI: 10.1002/Pmic.201700021 |
0.379 |
|
| 2017 |
Hawkins A, Sperring C, Basrur V, Nesvizhskii A, Lawlor E. Abstract 5836: Activation of Wnt/beta-catenin alters the Ewing sarcoma secretome - Implications for tumor:tumor microenvironment crosstalk Cancer Research. 77: 5836-5836. DOI: 10.1158/1538-7445.Am2017-5836 |
0.304 |
|
| 2016 |
Navarro P, Kuharev J, Gillet LC, Bernhardt OM, MacLean B, Röst HL, Tate SA, Tsou CC, Reiter L, Distler U, Rosenberger G, Perez-Riverol Y, Nesvizhskii AI, Aebersold R, Tenzer S. A multicenter study benchmarks software tools for label-free proteome quantification. Nature Biotechnology. PMID 27701404 DOI: 10.1038/Nbt.3685 |
0.408 |
|
| 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 |
0.364 |
|
| 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 |
0.405 |
|
| 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 |
0.379 |
|
| 2016 |
Liu G, Knight JD, Zhang JP, Tsou CC, Wang J, Lambert JP, Larsen B, Tyers M, Raught B, Bandeira N, Nesvizhskii AI, Choi H, Gingras AC. Data Independent Acquisition analysis in ProHits 4.0. Journal of Proteomics. PMID 27132685 DOI: 10.1016/J.Jprot.2016.04.042 |
0.403 |
|
| 2016 |
Dimitrakopoulos L, Prassas I, Diamandis EP, Nesvizhskii A, Kislinger T, Jaffe J, Drabovich A. Proteogenomics: Opportunities and Caveats. Clinical Chemistry. 62: 551-7. PMID 26817480 DOI: 10.1373/Clinchem.2015.247858 |
0.388 |
|
| 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 |
0.38 |
|
| 2015 |
Shively CA, Kweon HK, Norman KL, Mellacheruvu D, Xu T, Sheidy DT, Dobry CJ, Sabath I, Cosky EE, Tran EJ, Nesvizhskii A, Andrews PC, Kumar A. Large-Scale Analysis of Kinase Signaling in Yeast Pseudohyphal Development Identifies Regulation of Ribonucleoprotein Granules. Plos Genetics. 11: e1005564. PMID 26447709 DOI: 10.1371/Journal.Pgen.1005564 |
0.331 |
|
| 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 |
0.43 |
|
| 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 |
0.384 |
|
| 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 |
0.382 |
|
| 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 |
0.403 |
|
| 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 |
0.309 |
|
| 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 |
0.439 |
|
| 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 |
0.329 |
|
| 2015 |
Rolland DC, Basrur V, Jeon YK, McNeil-Schwalm C, Fermin D, Conlon K, Tsou C, Brown NA, Thomas DG, Bailey NG, Omenn GS, Nesvizhskii AI, Lim MS, Elenitoba-Johnson KS. N-Glycoproteomic Landscape of Human Lymphoid Cancers Reveals Novel Biomarkers and Potential Therapeutic Targets Blood. 126: 697-697. DOI: 10.1182/Blood.V126.23.697.697 |
0.325 |
|
| 2015 |
Lambert J, Zhou Y, Couzens A, Tsou C, Picaud S, Ivosev G, Tate S, Nesvizhskii A, Filippakopoulos P, Gingras A. Abstract IA19: Regulation of signaling interactomes in cancer Cancer Research. 75. DOI: 10.1158/1538-7445.Compsysbio-Ia19 |
0.397 |
|
| 2014 |
Nesvizhskii AI. Proteogenomics: concepts, applications and computational strategies. Nature Methods. 11: 1114-25. PMID 25357241 DOI: 10.1038/Nmeth.3144 |
0.419 |
|
| 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 |
0.432 |
|
| 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 |
0.322 |
|
| 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 |
0.404 |
|
| 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 |
0.315 |
|
| 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 |
0.362 |
|
| 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 |
0.414 |
|
| 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 |
0.428 |
|
| 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 |
0.312 |
|
| 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 |
0.358 |
|
| 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 |
0.327 |
|
| 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 |
0.316 |
|
| 2013 |
Balbin AO, Prensner J, Sahu A, Yocum A, Shankar S, Dhanasekaran M, Cao X, Nesvizhskii A, Chinnaiyan A. Abstract 5214: Reconstructing targetable pathways in KRAS dependent lung cancer by integrating transcriptome, proteome and phosphoproteome. Cancer Research. 73: 5214-5214. DOI: 10.1158/1538-7445.Am2013-5214 |
0.346 |
|
| 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 |
0.381 |
|
| 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 |
0.395 |
|
| 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 |
0.402 |
|
| 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 |
0.44 |
|
| 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 |
0.433 |
|
| 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 |
0.403 |
|
| 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 |
0.359 |
|
| 2012 |
Balbin AO, Presner J, Shankar S, Sahu A, Yocum A, Iyer M, Dhanasekaran M, Robinson D, Cao X, Nesvizhskii A, Chinnaiyan A. Abstract LB-35: Reconstructing targetable pathways in lung cancer by integrating transcriptome, proteome and phosphoproteome Cancer Research. 72. DOI: 10.1158/1538-7445.Am2012-Lb-35 |
0.38 |
|
| 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 |
0.322 |
|
| 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 |
0.443 |
|
| 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 |
0.371 |
|
| 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 |
0.378 |
|
| 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 |
0.392 |
|
| 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 |
0.403 |
|
| 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 |
0.364 |
|
| 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 |
0.432 |
|
| 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 |
0.403 |
|
| 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 |
0.427 |
|
| 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 |
0.311 |
|
| 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 |
0.423 |
|
| 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 |
0.388 |
|
| 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 |
0.308 |
|
| 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 |
0.389 |
|
| 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 |
0.329 |
|
| 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 |
0.394 |
|
| 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 |
0.414 |
|
| 2010 |
Dytfeld D, Kandarpa M, Strahler JR, Mellacheruvu D, Subramani S, Kraftson SJ, Ngoka L, Nesvizhskii A, Sreekumar A, Richardson PG, Jakubowiak AJ. Proteomic Profiling of Multiple Myeloma (MM) Cells Using iTRAQ and Label-Free Quantitative Proteomics for the Prediction of Complete or near Complete Response (CR/nCR) In Frontline Treatment with Lenalidomide, Bortezomib, and Dexamethasone Blood. 116: 618-618. DOI: 10.1182/Blood.V116.21.618.618 |
0.417 |
|
| 2010 |
Dytfeld D, Kandarpa M, Kraftson SJ, Strahler JR, Mellacheruvu D, Subramani S, Nesvizhskii A, Jakubowiak AJ. Proteomic Profiling of Multiple Myeloma Plasma Cells and Normal Plasma Cells Reveals Differential Expression of Clu1 and Basp1 Proteins Blood. 116: 4034-4034. DOI: 10.1182/Blood.V116.21.4034.4034 |
0.39 |
|
| 2010 |
Dytfeld D, Kandarpa M, Strahler JR, Mellacheruvu D, Subramani S, Kraftson SJ, Ngoka L, Nesvizhskii A, Sreekumar A, Jakubowiak AJ. Proteomic Signature Predicting Achievement of Very Good Partial Response In Patients with Multiple Myeloma Based On Complementary Label-Free and iTRAQ Quantitative Proteome Analysis Blood. 116: 1902-1902. DOI: 10.1182/Blood.V116.21.1902.1902 |
0.428 |
|
| 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 |
0.351 |
|
| 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, ... ... Nesvizhskii A, et al. Recommendations from the 2008 International Summit on Proteomics Data Release and Sharing Policy: the Amsterdam principles. Journal of Proteome Research. 8: 3689-92. PMID 19344107 DOI: 10.1021/Pr900023Z |
0.3 |
|
| 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 |
0.385 |
|
| 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 |
0.368 |
|
| 2009 |
Dytfeld D, Hari M, Strahler J, Mellacheruvu D, Subramani S, Nesvizhskii A, Sreekumar A, Jakubowiak AJ. Proteomic Profiling of Multiple Myeloma Using iTRAQ Labeling Followed by Multidimensional Liquid Chromatography and Tandem Mass Spectrometry. Blood. 114: 4865-4865. DOI: 10.1182/Blood.V114.22.4865.4865 |
0.402 |
|
| 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 |
0.426 |
|
| 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 |
0.374 |
|
| 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 |
0.391 |
|
| 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 |
0.385 |
|
| 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 |
0.405 |
|
| 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 |
0.423 |
|
| 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 |
0.417 |
|
| 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 |
0.389 |
|
| 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 |
0.39 |
|
| 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 |
0.386 |
|
| 2007 |
Mueller D, Bach C, Zeisig D, Garcia-Cuellar MP, Monroe S, Sreekumar A, Zhou R, Nesvizhskii A, Chinnaiyan A, Hess JL, Slany RK. A role for the MLL fusion partner ENL in transcriptional elongation and chromatin modification. Blood. 110: 4445-54. PMID 17855633 DOI: 10.1182/Blood-2007-05-090514 |
0.317 |
|
| 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 |
0.417 |
|
| 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 |
0.422 |
|
| 2007 |
Elenitoba-Johnson KS, Basrur V, Kronk A, Seiler C, Fermin D, Nesvizhskii A, Lim MS. Analysis of T-Cell Leukemia/Lymphoma (TCL1) Oncoprotein Interacting Proteins by Immunoprecipitation and Tandem Mass Spectrometry. Blood. 110: 3566-3566. DOI: 10.1182/Blood.V110.11.3566.3566 |
0.414 |
|
| 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 |
0.406 |
|
| 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 |
0.376 |
|
| 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 |
0.424 |
|
| 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 |
0.408 |
|
| 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 |
0.33 |
|
| 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 |
0.357 |
|
| 2005 |
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. Proteomics. 5: 3501-5. PMID 16041670 DOI: 10.1002/Pmic.200401302 |
0.366 |
|
| 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 |
0.445 |
|
| 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 |
0.408 |
|
| 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 |
0.375 |
|
| 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 DOI: 10.1007/978-1-4757-5806-1_3 |
0.359 |
|
| 2004 |
Carr S, Aebersold R, Baldwin M, Burlingame A, Clauser K, Nesvizhskii A. 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. 3: 531-3. PMID 15075378 DOI: 10.1074/Mcp.T400006-Mcp200 |
0.449 |
|
| 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 |
0.411 |
|
| 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 |
0.447 |
|
| 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 |
0.427 |
|
| 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 |
0.459 |
|
| 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 |
0.426 |
|
| 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. DOI: 10.1103/Physrevb.67.115120 |
0.471 |
|
| 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 |
0.401 |
|
| 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 |
0.397 |
|
| 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 |
0.471 |
|
| 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. DOI: 10.1103/Physrevb.63.094412 |
0.471 |
|
| 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 |
0.471 |
|
| 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 |
0.356 |
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