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1

Calculating block diagram reliability: Parallel industrial objects with backup

V. I. Mushtaev, F. A. Nesvizhskii, V. S. Shubin, N. P. Lozovaya

Journal:

Chemical and Petroleum Engineering

Year:

2004

Language:

english

File:

PDF, 43 KB

english, 2004

2

Analysis and validation of proteomic data generated by tandem mass spectrometry

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

Journal:

Year:

2007

Language:

english

File:

PDF, 576 KB

english, 2007

3

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

Choi, Hyungwon, Nesvizhskii, Alexey I.

Journal:

Journal of Proteome Research

Year:

2008

Language:

english

File:

PDF, 82 KB

english, 2008

4

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

Year:

2013

Language:

english

File:

PDF, 889 KB

english, 2013

5

Proteogenomics: concepts, applications and computational strategies

Nesvizhskii, Alexey I

Journal:

Year:

2014

Language:

english

File:

PDF, 641 KB

english, 2014

6

Stark effect near the type-I–type-II transition point in semiconductor quantum wells

Kavokin, A. V., Nesvizhskii, A. I.

Journal:

Physical Review B

Year:

1994

Language:

english

File:

PDF, 197 KB

english, 1994

7

Anisotropic hole subband states and interband optical absorption in [ mmn ]-oriented quantum wells

Winkler, R., Nesvizhskii, A. I.

Journal:

Physical Review B

Year:

1996

Language:

english

File:

PDF, 247 KB

english, 1996

8

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

Year:

2015

Language:

english

File:

PDF, 1.50 MB

english, 2015

9

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:

Year:

2016

Language:

english

File:

PDF, 4.99 MB

english, 2016

10

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:

Year:

2017

Language:

english

File:

PDF, 805 KB

english, 2017

11

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

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

Journal:

Year:

2020

File:

PDF, 3.59 MB

2020

12

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

Year:

2007

Language:

english

File:

PDF, 402 KB

english, 2007

13

Resonant Bragg reflection from quantum-well structures

E.L. Ivchenko, A.I. Nesvizhskii, S. Jorda

Journal:

Superlattices and Microstructures

Year:

1994

File:

PDF, 154 KB

1994

14

Electrons and excitons in an imperfect superlattice in electric fields

S.M. Cao, M. Willander, E.L. Ivchenko, A.I. Nesvizhskii, A.A. Toropov

Journal:

Superlattices and Microstructures

Year:

1995

File:

PDF, 314 KB

1995

15

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

Year:

2010

Language:

english

File:

PDF, 4.00 MB

english, 2010

16

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:

Year:

2005

Language:

english

File:

PDF, 270 KB

english, 2005

17

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:

Year:

2005

Language:

english

File:

PDF, 85 KB

english, 2005

18

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:

Year:

2010

Language:

english

File:

PDF, 244 KB

english, 2010

19

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

Kang Ning, Damian Fermin, Alexey I. Nesvizhskii

Journal:

Year:

2010

Language:

english

File:

PDF, 227 KB

english, 2010

20

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:

Year:

2011

Language:

english

File:

PDF, 253 KB

english, 2011

21

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:

Year:

2011

Language:

english

File:

PDF, 224 KB

english, 2011

22

Patterns of phenotypic variation in DNA autoantibody levels in healthy persons

Yu. V. Nesvizhskii, L. G. Sibiryakova, D. V. Korogodin, A. A. Vorob'ev

Journal:

Bulletin of Experimental Biology and Medicine

Year:

1988

Language:

english

File:

PDF, 336 KB

english, 1988

23

Book reviews

M. Yu. Lur'e, B. M. Gusev, F. A. Nesvizhskii

Journal:

Chemical and Petroleum Engineering

Year:

1974

Language:

english

File:

PDF, 155 KB

english, 1974

24

Reliability of manufacturing processes in chemical engineering

Yu. A. Zakharova, V. I. Mushtaev, V. S. Shubin, F. A. Nesvizhskii, O. P. Nikiforova

Journal:

Chemical and Petroleum Engineering

Year:

1999

Language:

english

File:

PDF, 258 KB

english, 1999

25

The “familial” factor and the microbiocenosis of the normal human intestine

A. A. Vorob'ev, Yu. V. Nesvizhskii, E. V. Budanova, L. O. Inozemtseva

Journal:

Bulletin of Experimental Biology and Medicine

Year:

1994

Language:

english

File:

PDF, 606 KB

english, 1994

26

Pattern of age variability of the autoantibody levels in (NZB×NZW) F1 mice

Yu. V. Nesvizhskii, D. V. Korogodin, A. A. Vorob'ev

Journal:

Bulletin of Experimental Biology and Medicine

Year:

1994

Language:

english

File:

PDF, 389 KB

english, 1994

27

Factors influencing the manifestation of skin allergic reaction to microorganism antigens in healthy subjects

Yu. V. Nesvizhskii, L. O. Inozemtseva, D. O. Meshkov, A. A. Vorob'ev

Journal:

Bulletin of Experimental Biology and Medicine

Year:

1995

Language:

english

File:

PDF, 341 KB

english, 1995

28

Contribution of the disease process to phenotypic variability of human colon microflora

A. A. Vorob’ev, L. O. Inozemtseva, Yu. V. Nesvizhskii, E. V. Budanova, N. A. Mukhin, O. A. Belokrinitskaya

Journal:

Bulletin of Experimental Biology and Medicine

Year:

1997

Language:

english

File:

PDF, 323 KB

english, 1997

29

Experimental and theoretical study of the electronic structures of Ni3Al, Ni3Ga, Ni3In, and NiGa

L.-S. Hsu, A.I. Nesvizhskii

Journal:

Journal of Physics and Chemistry of Solids

Year:

2001

Language:

english

File:

PDF, 237 KB

english, 2001

30

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:

Year:

2010

Language:

english

File:

PDF, 666 KB

english, 2010

31

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

Year:

2012

Language:

english

File:

PDF, 2.93 MB

english, 2012

32

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

Year:

2008

Language:

english

File:

PDF, 240 KB

english, 2008

33

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

Choi, Hyungwon, Nesvizhskii, Alexey I.

Journal:

Journal of Proteome Research

Year:

2008

Language:

english

File:

PDF, 790 KB

english, 2008

34

Initial Proteome Analysis of Model Microorganism Haemophilus influenzae Strain Rd KW20

Kolker, E., Purvine, S., Galperin, M. Y., Stolyar, S., Goodlett, D. R., Nesvizhskii, A. I., Keller, A., Xie, T., Eng, J. K., Yi, E.

Journal:

Journal of Bacteriology

Year:

2003

Language:

english

File:

PDF, 475 KB

english, 2003

35

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

Alexey I. Nesvizhskii

Journal:

Year:

2012

Language:

english

File:

PDF, 1.16 MB

english, 2012

36

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

Alexey I Nesvizhskii, Ruedi Aebersold

Journal:

Drug Discovery Today

Year:

2004

Language:

english

File:

PDF, 201 KB

english, 2004

37

Orbital magnetism of 2D chaotic lattices

A. I. Nesvizhskii, A. Yu. Zyuzin

Journal:

Year:

1996

Language:

english

File:

PDF, 95 KB

english, 1996

38

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

Year:

2010

Language:

english

File:

PDF, 864 KB

english, 2010

39

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

Year:

2010

Language:

english

File:

PDF, 342 KB

english, 2010

40

Reflection and absorption spectra from microcavities with resonant Bragg quantum wells

Ivchenko, E. L., Kaliteevski, M. A., Kavokin, A. V., Nesvizhskii, A. I., Ioffe, A. F.

Journal:

Journal of the Optical Society of America B

Year:

1996

Language:

english

File:

PDF, 453 KB

english, 1996

41

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

Year:

2002

Language:

english

File:

PDF, 160 KB

english, 2002

42

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

Year:

2012

Language:

english

File:

PDF, 753 KB

english, 2012

43

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

Year:

2010

Language:

english

File:

PDF, 1.62 MB

english, 2010

44

B480 Proteomic Alterations Caused by Treatment with Velcade, Doxorubicin, and Dexamethasone in Myeloma

Sreekumar, A, Jakubowiak, AJ, Hari, M, Nesvizhskii, A

Journal:

Clinical Lymphoma & Myeloma

Year:

2009

Language:

english

File:

PDF, 81 KB

english, 2009

45

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

Year:

2012

Language:

english

File:

PDF, 66 KB

english, 2012

46

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

Year:

2012

Language:

english

File:

PDF, 4.19 MB

english, 2012

47

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

Year:

2006

Language:

english

File:

PDF, 356 KB

english, 2006

48

Genetic Networks Inducing Invasive Growth in Saccharomyces cerevisiae Identified Through Systematic Genome-Wide Overexpression

Shively, C. A., Eckwahl, M. J., Dobry, C. J., Mellacheruvu, D., Nesvizhskii, A., Kumar, A.

Journal:

Year:

2013

Language:

english

File:

PDF, 9.53 MB

english, 2013

49

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

Year:

2002

Language:

english

File:

PDF, 147 KB

english, 2002

50

A Statistical Model for Identifying Proteins by Tandem Mass Spectrometry

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

Journal:

Analytical Chemistry

Year:

2003

Language:

english

File:

PDF, 206 KB

english, 2003

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