Alexey I Nesvizhskii : rechercher sur Z-Library

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1

Analysis and validation of proteomic data generated by tandem mass spectrometry

Nesvizhskii, Alexey I, Vitek, Olga, Aebersold, Ruedi

Journal:

Année:

2007

Langue:

english

Fichier:

PDF, 576 KB

english, 2007

2

False Discovery Rates and Related Statistical Concepts in Mass Spectrometry-Based Proteomics

Choi, Hyungwon, Nesvizhskii, Alexey I.

Journal:

Journal of Proteome Research

Année:

2008

Langue:

english

Fichier:

PDF, 82 KB

english, 2008

3

Hands-on Workshops as An Effective Means of Learning Advanced Technologies Including Genomics, Proteomics and Bioinformatics

Reisdorph, Nichole, Stearman, Robert, Kechris, Katerina, Phang, Tzu Lip, Reisdorph, Richard, Prenni, Jessica, Erle, David J., Coldren, Christopher, Schey, Kevin, Nesvizhskii, Alexey, Geraci, Mark

Journal:

Genomics, Proteomics & Bioinformatics

Année:

2013

Langue:

english

Fichier:

PDF, 889 KB

english, 2013

4

Proteogenomics: concepts, applications and computational strategies

Nesvizhskii, Alexey I

Journal:

Année:

2014

Langue:

english

Fichier:

PDF, 641 KB

english, 2014

5

Large-scale determination of absolute phosphorylation stoichiometries in human cells by motif-targeting quantitative proteomics

Tsai, Chia-Feng, Wang, Yi-Ting, Yen, Hsin-Yung, Tsou, Chih-Chiang, Ku, Wei-Chi, Lin, Pei-Yi, Chen, Hsuan-Yu, Nesvizhskii, Alexey I., Ishihama, Yasushi, Chen, Yu-Ju

Journal:

Nature Communications

Année:

2015

Langue:

english

Fichier:

PDF, 1.50 MB

english, 2015

6

MLL1 Inhibition Reprograms Epiblast Stem Cells to Naive Pluripotency

Zhang, Hui, Gayen, Srimonta, Xiong, Jie, Zhou, Bo, Shanmugam, Avinash K., Sun, Yuqing, Karatas, Hacer, Liu, Liu, Rao, Rajesh C., Wang, Shaomeng, Nesvizhskii, Alexey I., Kalantry, Sundeep, Dou, Yali

Journal:

Année:

2016

Langue:

english

Fichier:

PDF, 4.99 MB

english, 2016

7

MSFragger: ultrafast and comprehensive peptide identification in mass spectrometry–based proteomics

Kong, Andy T, Leprevost, Felipe V, Avtonomov, Dmitry M, Mellacheruvu, Dattatreya, Nesvizhskii, Alexey I

Journal:

Année:

2017

Langue:

english

Fichier:

PDF, 805 KB

english, 2017

8

Fast and comprehensive N- and O-glycoproteomics analysis with MSFragger-Glyco

Polasky, Daniel A., Yu, Fengchao, Teo, Guo Ci, Nesvizhskii, Alexey I.

Journal:

Année:

2020

Fichier:

PDF, 3.59 MB

2020

9

Comprehensive analysis of proteins of pH fractionated samples using monolithic LC/MS/MS, intact MW measurement and MALDI-QIT-TOF MS

Chul Yoo, Tasneem H. Patwa, Paweena Kreunin, Fred R. Miller, Christian G. Huber, Alexey I. Nesvizhskii, David M. Lubman

Journal:

Journal of Mass Spectrometry

Année:

2007

Langue:

english

Fichier:

PDF, 402 KB

english, 2007

10

A survey of computational methods and error rate estimation procedures for peptide and protein identification in shotgun proteomics

Alexey I. Nesvizhskii

Journal:

Journal of Proteomics

Année:

2010

Langue:

english

Fichier:

PDF, 4.00 MB

english, 2010

11

Do we want our data raw? Including binary mass spectrometry data in public proteomics data repositories

Lennart Martens, Alexey I. Nesvizhskii, Henning Hermjakob, Marcin Adamski, Gilbert S. Omenn, Joël Vandekerckhove, Kris Gevaert

Journal:

Année:

2005

Langue:

english

Fichier:

PDF, 270 KB

english, 2005

12

Human Plasma PeptideAtlas

Eric W. Deutsch, Jimmy K. Eng, Hui Zhang, Nichole L. King, Alexey I. Nesvizhskii, Biaoyang Lin, Hookeun Lee, Eugene C. Yi, Reto Ossola, Ruedi Aebersold

Journal:

Année:

2005

Langue:

english

Fichier:

PDF, 85 KB

english, 2005

13

A guided tour of the Trans-Proteomic Pipeline

Eric W. 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

Journal:

Année:

2010

Langue:

english

Fichier:

PDF, 244 KB

english, 2010

14

Computational analysis of unassigned high-quality MS/MS spectra in proteomic data sets

Kang Ning, Damian Fermin, Alexey I. Nesvizhskii

Journal:

Année:

2010

Langue:

english

Fichier:

PDF, 227 KB

english, 2010

15

Abacus: A computational tool for extracting and pre-processing spectral count data for label-free quantitative proteomic analysis

Damian Fermin, Venkatesha Basrur, Anastasia K. Yocum, Alexey I. Nesvizhskii

Journal:

Année:

2011

Langue:

english

Fichier:

PDF, 253 KB

english, 2011

16

Label-free quantitative proteomics and SAINT analysis enable interactome mapping for the human Ser/Thr protein phosphatase 5

Dana V. Skarra, Marilyn Goudreault, Hyungwon Choi, Michael Mullin, Alexey I. Nesvizhskii, Anne-Claude Gingras, Richard E. Honkanen

Journal:

Année:

2011

Langue:

english

Fichier:

PDF, 224 KB

english, 2011

17

SAINT: probabilistic scoring of affinity purification–mass spectrometry data

Choi, Hyungwon, Larsen, Brett, Lin, Zhen-Yuan, Breitkreutz, Ashton, Mellacheruvu, Dattatreya, Fermin, Damian, Qin, Zhaohui S, Tyers, Mike, Gingras, Anne-Claude, Nesvizhskii, Alexey I

Journal:

Année:

2010

Langue:

english

Fichier:

PDF, 666 KB

english, 2010

18

Comparative Analysis of Different Label-Free Mass Spectrometry Based Protein Abundance Estimates and Their Correlation with RNA-Seq Gene Expression Data

Ning, Kang, Fermin, Damian, Nesvizhskii, Alexey I.

Journal:

Journal of Proteome Research

Année:

2012

Langue:

english

Fichier:

PDF, 2.93 MB

english, 2012

19

Statistical Validation of Peptide Identifications in Large-Scale Proteomics Using the Target-Decoy Database Search Strategy and Flexible Mixture Modeling

Choi, Hyungwon, Ghosh, Debashis, Nesvizhskii, Alexey I.

Journal:

Journal of Proteome Research

Année:

2008

Langue:

english

Fichier:

PDF, 240 KB

english, 2008

20

Semisupervised Model-Based Validation of Peptide Identifications in Mass Spectrometry-Based Proteomics

Choi, Hyungwon, Nesvizhskii, Alexey I.

Journal:

Journal of Proteome Research

Année:

2008

Langue:

english

Fichier:

PDF, 790 KB

english, 2008

21

Computational and informatics strategies for identification of specific protein interaction partners in affinity purification mass spectrometry experiments

Alexey I. Nesvizhskii

Journal:

Année:

2012

Langue:

english

Fichier:

PDF, 1.16 MB

english, 2012

22

Analysis, statistical validation and dissemination of large-scale proteomics datasets generated by tandem MS

Alexey I Nesvizhskii, Ruedi Aebersold

Journal:

Drug Discovery Today

Année:

2004

Langue:

english

Fichier:

PDF, 201 KB

english, 2004

23

Examination of the relationship between essential genes in PPI network and hub proteins in reverse nearest neighbor topology

Kang Ning, Hoong Kee Ng, Sriganesh Srihari, Hon Wai Leong, Alexey I Nesvizhskii

Journal:

BMC Bioinformatics

Année:

2010

Langue:

english

Fichier:

PDF, 864 KB

english, 2010

24

The utility of mass spectrometry-based proteomic data for validation of novel alternative splice forms reconstructed from RNA-Seq data: a preliminary assessment

Kang Ning, Alexey I Nesvizhskii

Journal:

BMC Bioinformatics

Année:

2010

Langue:

english

Fichier:

PDF, 342 KB

english, 2010

25

Experimental Protein Mixture for Validating Tandem Mass Spectral Analysis

Keller, Andrew, Purvine, Samuel, Nesvizhskii, Alexey I., Stolyar, Sergey, Goodlett, David R., Kolker, Eugene

Journal:

Omics A Journal of Integrative Biology

Année:

2002

Langue:

english

Fichier:

PDF, 160 KB

english, 2002

26

SAINT-MS1: Protein–Protein Interaction Scoring Using Label-free Intensity Data in Affinity Purification-Mass Spectrometry Experiments

Choi, Hyungwon, Glatter, Timo, Gstaiger, Mathias, Nesvizhskii, Alexey I.

Journal:

Journal of Proteome Research

Année:

2012

Langue:

english

Fichier:

PDF, 753 KB

english, 2012

27

Analysis of protein complexes through model-based biclustering of label-free quantitative AP-MS data

Choi, Hyungwon, Kim, Sinae, Gingras, Anne-Claude, Nesvizhskii, Alexey I

Journal:

Molecular Systems Biology

Année:

2010

Langue:

english

Fichier:

PDF, 1.62 MB

english, 2010

28

360 CAD, a Nucleotide Synthesis Enzyme, Inhibits NOD2 Anti-Bacterial Function in Human Intestinal Epithelial Cells

Amy L. Richmond, Amrita Kabi, Craig R. Homer, Kourtney P. Nickerson, Alexey I. Nesvizhskii, Arun Sreekumar, Arul Chinnaiyan, Gabriel Nunez, Christine McDonald

Journal:

Gastroenterology

Année:

2012

Langue:

english

Fichier:

PDF, 66 KB

english, 2012

29

The Nucleotide Synthesis Enzyme CAD Inhibits NOD2 Antibacterial Function in Human Intestinal Epithelial Cells

Amy L. Richmond, Amrita Kabi, Craig R. Homer, Noemí Marina–García, Kourtney P. Nickerson, Alexey I. Nesvizhskii, Arun Sreekumar, Arul M. Chinnaiyan, Gabriel Nuñez, Christine McDonald

Journal:

Gastroenterology

Année:

2012

Langue:

english

Fichier:

PDF, 4.19 MB

english, 2012

30

Optimized Peptide Separation and Identification for Mass Spectrometry Based Proteomics via Free-Flow Electrophoresis

Malmström, Johan, Lee, Hookeun, Nesvizhskii, Alexey I., Shteynberg, David, Mohanty, Sonali, Brunner, Erich, Ye, Mingliang, Weber, Gerhard, Eckerskorn, Christoph, Aebersold, Ruedi

Journal:

Journal of Proteome Research

Année:

2006

Langue:

english

Fichier:

PDF, 356 KB

english, 2006

31

Empirical Statistical Model To Estimate the Accuracy of Peptide Identifications Made by MS/MS and Database Search

Keller, Andrew, Nesvizhskii, Alexey I., Kolker, Eugene, Aebersold, Ruedi

Journal:

Analytical Chemistry

Année:

2002

Langue:

english

Fichier:

PDF, 147 KB

english, 2002

32

A Statistical Model for Identifying Proteins by Tandem Mass Spectrometry

Nesvizhskii, Alexey I., Keller, Andrew, Kolker, Eugene, Aebersold, Ruedi

Journal:

Analytical Chemistry

Année:

2003

Langue:

english

Fichier:

PDF, 206 KB

english, 2003

33

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

Kelvin Ma, Olga Vitek, Alexey I Nesvizhskii

Journal:

BMC Bioinformatics

Année:

2012

Langue:

english

Fichier:

PDF, 1.56 MB

english, 2012

34

Analysis of theSaccharomyces cerevisiaeproteome with PeptideAtlas

Nichole L King, Eric W Deutsch, Jeffrey A Ranish, Alexey I Nesvizhskii…

Journal:

Année:

2006

Langue:

english

Fichier:

PDF, 1.93 MB

english, 2006

35

Integration with the human genome of peptide sequences obtained by high-throughput mass spectrometry

Frank Desiere, Eric W Deutsch, Alexey I Nesvizhskii, Parag Mallick…

Journal:

Année:

2005

Langue:

english

Fichier:

PDF, 4.61 MB

english, 2005

36

Improving Sensitivity by Probabilistically Combining Results from Multiple MS/MS Search Methodologies

Searle, Brian C., Turner, Mark, Nesvizhskii, Alexey I.

Journal:

Journal of Proteome Research

Année:

2008

Langue:

english

Fichier:

PDF, 1.47 MB

english, 2008

37

Investigation of Neutral Loss during Collision-Induced Dissociation of Peptide Ions

Martin, Daniel B., Eng, Jimmy K., Nesvizhskii, Alexey I., Gemmill, Andrew, Aebersold, Ruedi

Journal:

Analytical Chemistry

Année:

2005

Langue:

english

Fichier:

PDF, 802 KB

english, 2005

38

Global Phosphoproteomic Profiling Reveals Distinct Signatures in B-Cell Non-Hodgkin Lymphomas

Rolland, Delphine, Basrur, Venkatesha, Conlon, Kevin, Wolfe, Thomas, Fermin, Damian, Nesvizhskii, Alexey I., Lim, Megan S., Elenitoba-Johnson, Kojo S.J.

Journal:

The American Journal of Pathology

Année:

2014

Langue:

english

Fichier:

PDF, 2.16 MB

english, 2014

39

SAINTexpress: Improvements and additional features in Significance Analysis of INTeractome software

Teo, Guoci, Liu, Guomin, Zhang, Jianping, Nesvizhskii, Alexey I., Gingras, Anne-Claude, Choi, Hyungwon

Journal:

Journal of Proteomics

Année:

2014

Langue:

english

Fichier:

PDF, 667 KB

english, 2014

40

Comprehensive Analysis of Protein Digestion Using Six Trypsins Reveals the Origin of Trypsin As a Significant Source of Variability in Proteomics

Walmsley, Scott J., Rudnick, Paul A., Liang, Yuxue, Dong, Qian, Stein, Stephen E., Nesvizhskii, Alexey I.

Journal:

Journal of Proteome Research

Année:

2013

Langue:

english

Fichier:

PDF, 2.78 MB

english, 2013

41

Improved Sequence Tag Generation Method for Peptide Identification in Tandem Mass Spectrometry

Cao, Xia, Nesvizhskii, Alexey I.

Journal:

Journal of Proteome Research

Année:

2008

Langue:

english

Fichier:

PDF, 1.70 MB

english, 2008

42

MSblender: A Probabilistic Approach for Integrating Peptide Identifications from Multiple Database Search Engines

Kwon, Taejoon, Choi, Hyungwon, Vogel, Christine, Nesvizhskii, Alexey I., Marcotte, Edward M.

Journal:

Journal of Proteome Research

Année:

2011

Langue:

english

Fichier:

PDF, 3.98 MB

english, 2011

43

Advancing Next-Generation Proteomics through Computational Research

Bandeira, Nuno, Nesvizhskii, Alexey, McIntosh, Martin

Journal:

Journal of Proteome Research

Année:

2011

Langue:

english

Fichier:

PDF, 611 KB

english, 2011

44

Utility of RNA-seq and GPMDB Protein Observation Frequency for Improving the Sensitivity of Protein Identification by Tandem MS

Shanmugam, Avinash K., Yocum, Anastasia K., Nesvizhskii, Alexey I.

Journal:

Journal of Proteome Research

Année:

2014

Langue:

english

Fichier:

PDF, 1.08 MB

english, 2014

45

Comparison of MS 2 -Only, MSA, and MS 2 /MS 3 Methodologies for Phosphopeptide Identification

Ulintz, Peter J., Yocum, Anastasia K., Bodenmiller, Bernd, Aebersold, Ruedi, Andrews, Philip C., Nesvizhskii, Alexey I.

Journal:

Journal of Proteome Research

Année:

2009

Langue:

english

Fichier:

PDF, 1.11 MB

english, 2009

46

Proteomic Study of the Mucin Granulae in an Intestinal Goblet Cell Model

Rodríguez-Piñeiro, Ana M., Post, Sjoerd van der, Johansson, Malin E. V., Thomsson, Kristina A., Nesvizhskii, Alexey I., Hansson, Gunnar C.

Journal:

Journal of Proteome Research

Année:

2012

Langue:

english

Fichier:

PDF, 6.14 MB

english, 2012

47

DIA-Umpire: comprehensive computational framework for data-independent acquisition proteomics

Tsou, Chih-Chiang, Avtonomov, Dmitry, Larsen, Brett, Tucholska, Monika, Choi, Hyungwon, Gingras, Anne-Claude, Nesvizhskii, Alexey I

Journal:

Année:

2015

Langue:

english

Fichier:

PDF, 1.62 MB

english, 2015

48

The landscape of antisense gene expression in human cancers

Balbin, O. Alejandro, Malik, Rohit, Dhanasekaran, Saravana M., Prensner, John R., Cao, Xuhong, Wu, Yi-Mi, Robinson, Dan, Wang, Rui, Chen, Guoan, Beer, David G., Nesvizhskii, Alexey I., Chinnaiyan, Aru

Journal:

Genome Research

Année:

2015

Langue:

english

Fichier:

PDF, 1.11 MB

english, 2015

49

The Yeast Sks1p Kinase Signaling Network Regulates Pseudohyphal Growth and Glucose Response

Johnson, Cole, Kweon, Hye Kyong, Sheidy, Daniel, Shively, Christian A., Mellacheruvu, Dattatreya, Nesvizhskii, Alexey I., Andrews, Philip C., Kumar, Anuj, Erdman, Scott

Journal:

Année:

2014

Langue:

english

Fichier:

PDF, 6.33 MB

english, 2014

50

Metrics for the Human Proteome Project 2015: Progress on the Human Proteome and Guidelines for High-Confidence Protein Identification

Omenn, Gilbert S., Lane, Lydie, Lundberg, Emma K., Beavis, Ronald C., Nesvizhskii, Alexey I., Deutsch, Eric W.

Journal:

Journal of Proteome Research

Année:

2015

Langue:

english

Fichier:

PDF, 523 KB

english, 2015