Alexey I. Nesvizhskii

发表

ProHits: an integrated software platform for mass spectrometry-based interaction proteomics

Tony Pawson, Guomin Liu, Brett Larsen, 2010, Nature Biotechnology.

SAINT: Probabilistic Scoring of Affinity Purification - Mass Spectrometry Data

Hyungwon Choi, Brett Larsen, Mike Tyers, 2010, Nature Methods.

PIQED: Automated Identification And Quantification Of Protein Modifications From DIA-MS Data

Hanno Steen, Birgit Schilling, Bradford W. Gibson, 2017 .

LuciPHOr2: site localization of generic post-translational modifications from tandem mass spectrometry data

Hyungwon Choi, Alexey I. Nesvizhskii, Damian Fermin, 2015, Bioinform..

Omics Discovery Index - Discovering and Linking Public ‘Omics’ Datasets

Christoph Steinbeck, Yasset Perez-Riverol, Juan Antonio Vizcaíno, 2016, bioRxiv.

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

Olga Vitek, Alexey I. Nesvizhskii, Kelvin Ma, 2012, BMC Bioinformatics.

A Web Resource for Improved Analysis of AP-MS Protein Interaction Data.

Tony Pawson, Hyungwon Choi, Jean-Philippe Lambert, 2013 .

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

Guo Ci Teo, Fengchao Yu, Alexey I. Nesvizhskii, 2020, Nature Methods.

Identification of modified peptides using localization-aware open search

Fengchao Yu, Guo Ci Teo, Alexey I. Nesvizhskii, 2020, Nature Communications.

Exciton structure of absorption and magneto-absorption spectra near type I-type II transition in the strained heterostructures

Victor M. Ustinov, Alexey I. Nesvizhskii, Alexey Kavokin, 1995, Other Conferences.

DIA-Pipe: Identification and Quantification of Post-Translational Modifications using exclusively Data-Independent Acquisition

Birgit Schilling, Bradford W. Gibson, Alexey I. Nesvizhskii, 2017 .

BioContainers: an open-source and community-driven framework for software standardization

Harald Barsnes, Johannes Griss, Rafael C. Jimenez, 2017, Bioinform..

Toward More Transparent and Reproducible Omics Studies Through a Common Metadata Checklist and Data Publications

Lennart Martens, Stefano Toppo, Geoffrey C. Fox, 2013, Big Data.

The SysteMHC Atlas project

Roman A. Zubarev, Emanuel Schmid, Witold Wolski, 2017, Nucleic Acids Res..

IonQuant Enables Accurate and Sensitive Label-Free Quantification With FDR-Controlled Match-Between-Runs

Fengchao Yu, Alexey I. Nesvizhskii, Sarah E. Haynes, 2020, bioRxiv.

Hyungwon Choi, Debashis Ghosh, Alexey I. Nesvizhskii, 2013, Bioinform..

Philosopher: a versatile toolkit for shotgun proteomics data analysis

Alexey I. Nesvizhskii, Andy T. Kong, Sarah E. Haynes, 2020, Nature Methods.

How to Generate High Quality Protein Interaction Maps

Anne-Claude Gingras, Alexey I. Nesvizhskii, 2013 .

Diamagnetic excitons (magneto-excitons) in multiple quantum well (MQW) heterosystem

Alexey I. Nesvizhskii, Alexey Kavokin, R. P. Seisyan, 1995, Other Conferences.

Using MSFragger for ultrafast database searching

Alexey I. Nesvizhskii, Dattatreya Mellacheruvu, Felipe da Veiga Leprevost, 2017 .

Hierarchical hidden Markov model with application to joint analysis of ChIP-chip and ChIP-seq data

Hyungwon Choi, Debashis Ghosh, Alexey I. Nesvizhskii, 2009, Bioinform..

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, A. Nesvizhskii, 2010, BMC Bioinformatics.

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

Katerina Kechris, Alexey I. Nesvizhskii, Richard Reisdorph, 2013, Genom. Proteom. Bioinform..

Two-pass alignment improves novel splice junction quantification

Alexey I. Nesvizhskii, Brendan A. Veeneman, Saravana M. Dhanasekaran, 2015, Bioinform..

iProphet: A new tool for combining PeptideProphet results from multiple search engines improves spectrum validation

Henry H N Lam, Ruedi Aebersold, Alexey I. Nesvizhskii, 2008 .

Computational Analysis and Comparison of Continuous and Count-based Label-free Quantitative Proteomic Data

Brian C. Searle, Alexey I. Nesvizhskii, Ming Li, 2012 .

A multi-center study benchmarks software tools for label-free proteome quantification

Yasset Perez-Riverol, Brendan MacLean, Ruedi Aebersold, 2016, Nature Biotechnology.

The PeptideAtlas project

Eric W. Deutsch, Alexey I. Nesvizhskii, Jimmy K. Eng, 2005, Nucleic Acids Res..

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

Hon Wai Leong, Kang Ning, Sriganesh Srihari, 2010, BMC Bioinformatics.

Combining Results of Multiple Search Engines in Proteomics*

Eric W. Deutsch, Alexey I. Nesvizhskii, Robert L. Moritz, 2013, Molecular & Cellular Proteomics.

Fast quantitative analysis of timsTOF PASEF data with MSFragger and IonQuant

Guo Ci Teo, Fengchao Yu, Alexey I. Nesvizhskii, 2020, bioRxiv.

Magneto-optical study of band parameters in the GaAs/(Al,Ga)As MQW heterosystem

Alexey I. Nesvizhskii, Alexey Kavokin, R. P. Seisyan, 1993, Other Conferences.

iProphet: Improved statistical validation of peptide and protein identifications in shotgun proteomics

Henry H N Lam, Luis Mendoza, Ruedi Aebersold, 2011 .

Dynamic screening effects in x-ray absorption spectra

Alexey I. Nesvizhskii, John J. Rehr, A. Nesvizhskii, 2003 .

iProphet: improved validation of peptide identification in shotgun proteomics

Henry H N Lam, Ruedi Aebersold, Alexey I. Nesvizhskii, 2008 .

The Application of New Software Tools to Quantitative Protein Profiling Via Isotope-coded Affinity Tag (ICAT) and Tandem Mass Spectrometry

Ruedi Aebersold, Alexey I. Nesvizhskii, David R. Goodlett, 2003, Molecular & Cellular Proteomics.

Reconstructing targetable pathways in lung cancer by integrating diverse omics data

Alexey I. Nesvizhskii, Damian Fermin, Arul M. Chinnaiyan, 2013, Nature Communications.

Proteogenomic Characterization of Endometrial Carcinoma

Peter B. McGarvey, Ying Wang, Li Ding, 2020, Cell.

LuciPHOr 2 : site localization of generic post-translational modifications from tandem mass spectrometry data

Hyungwon Choi, Alexey I. Nesvizhskii, Damian Fermin, 2015 .

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*S

Brian Raught, Anne-Claude Gingras, Ruedi Aebersold, 2009, Molecular & Cellular Proteomics.

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

Alexey I. Nesvizhskii, Sjoerd van der Post, Gunnar C. Hansson, 2012, Journal of proteome research.

Combining Results of Multiple Search Engines

Alexey I. Nesvizhskii, Robert L. Moritz, David Shteynberg, 2013 .

Quantitative proteomic landscape of metaplastic breast carcinoma pathological subtypes and their relationship to triple-negative tumors

Alexey I. Nesvizhskii, Felipe da Veiga Leprevost, Venkatesha Basrur, 2020, Nature Communications.

Quantitative mass spectrometry reveals a role for the GTPase Rho1p in actin organization on the peroxisome membrane

Ruedi Aebersold, Alexey I. Nesvizhskii, David R. Goodlett, 2004, The Journal of cell biology.