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List of works by Alexey I. Nesvizhskii

"Topological significance" analysis of gene expression and proteomic profiles from prostate cancer cells reveals key mechanisms of androgen response

scientific article (publication date: 3 June 2010)

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

scientific article

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

scientific article published in May 2013

A data-independent acquisition-based global phosphoproteomics system enables deep profiling

scientific article published on 05 May 2021

A dual role for receptor-interacting protein kinase 2 (RIP2) kinase activity in nucleotide-binding oligomerization domain 2 (NOD2)-dependent autophagy

scientific article

A global protein kinase and phosphatase interaction network in yeast.

scientific article

A guided tour of the Trans-Proteomic Pipeline

scientific article

A role for the MLL fusion partner ENL in transcriptional elongation and chromatin modification

scientific article

A statistical model for identifying proteins by tandem mass spectrometry

scientific article (publication date: September 2003)

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

scientific article

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

scientific article published on September 8, 2010

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

scientific article

Adaptive discriminant function analysis and reranking of MS/MS database search results for improved peptide identification in shotgun proteomics

scientific article published on 13 September 2008

Advancing next-generation proteomics through computational research

scientific article published on 31 May 2011

An embryonic stem cell chromatin remodeling complex, esBAF, is essential for embryonic stem cell self-renewal and pluripotency

scholarly article

Analysis and validation of proteomic data generated by tandem mass spectrometry

scientific article

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

scientific article

Analysis of the Saccharomyces cerevisiae proteome with PeptideAtlas

scientific article published on January 2006

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

scientific article published on February 2004

Analyzing protein-protein interactions from affinity purification-mass spectrometry data with SAINT

scientific article

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

scientific article published on 01 April 1996

BatMass: a Java Software Platform for LC-MS Data Visualization in Proteomics and Metabolomics.

scientific article

Combining results of multiple search engines in proteomics

scientific article published on 29 May 2013

Comparative analysis of different label-free mass spectrometry based protein abundance estimates and their correlation with RNA-Seq gene expression data

scientific article

Comparison of MS(2)-only, MSA, and MS(2)/MS(3) methodologies for phosphopeptide identification

scientific article published on February 2009

Comprehensive analysis of protein digestion using six trypsins reveals the origin of trypsin as a significant source of variability in proteomics

scientific article

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

scientific article

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

scientific article

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

scientific article (publication date: May 2012)

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

scientific article

Data Independent Acquisition analysis in ProHits 4.0.

scientific article

Deep-Learning-Derived Evaluation Metrics Enable Effective Benchmarking of Computational Tools for Phosphopeptide Identification

scientific article published on 01 November 2021

Discovering and linking public omics data sets using the Omics Discovery Index.

scientific article

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

scientific article

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

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

scientific article published on 12 December 2005

Empirical statistical model to estimate the accuracy of peptide identifications made by MS/MS and database search

scientific article (publication date: 15 October 2002)

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

scientific article

False discovery rates and related statistical concepts in mass spectrometry-based proteomics

scientific article published on 8 December 2007

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

scientific article published on 05 October 2020

Fast quantitative analysis of timsTOF PASEF data with MSFragger and IonQuant

scientific article published on 02 July 2020

Fusion peptides from oncogenic chimeric proteins as putative specific biomarkers of cancer.

scientific article published on 8 July 2013

GSK3β controls epithelial-mesenchymal transition and tumor metastasis by CHIP-mediated degradation of Slug

scientific article

Genetic networks inducing invasive growth in Saccharomyces cerevisiae identified through systematic genome-wide overexpression

scientific article published on 14 February 2013

Global analysis of protein palmitoylation in African trypanosomes.

scientific article

Global phosphoproteomic profiling reveals distinct signatures in B-cell non-Hodgkin lymphomas

scientific article published on 22 March 2014

Hands-on workshops as an effective means of learning advanced technologies including genomics, proteomics and bioinformatics

scientific article

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

scientific article

Hole counts from X-ray absorption spectra

scientific article published on 01 March 2001

Human Plasma PeptideAtlas

scientific article published on August 2005

Humoral response profiling reveals pathways to prostate cancer progression

scientific article published on 11 December 2007

Identification of modified peptides using localization-aware open search

scientific article published on 13 August 2020

Immunopeptidomics-based identification of naturally presented non-canonical circRNA-derived peptides

scientific article published in 2024

Improved sequence tag generation method for peptide identification in tandem mass spectrometry

scientific article published on 12 September 2008

Improving sensitivity by probabilistically combining results from multiple MS/MS search methodologies

scientific article published in January 2008

Initial proteome analysis of model microorganism Haemophilus influenzae strain Rd KW20.

scientific article

Integrated phosphoproteomics analysis of a signaling network governing nutrient response and peroxisome induction

scientific article

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

scientific article

Interpretation of shotgun proteomic data: the protein inference problem

scientific article

Investigating MS2/MS3 matching statistics: a model for coupling consecutive stage mass spectrometry data for increased peptide identification confidence

scientific article

Investigation of neutral loss during collision-induced dissociation of peptide ions

scientific article

Kinesin-binding protein remodels the kinesin motor to prevent microtubule binding

scientific article published on 19 November 2021

Kir2.1 interactome mapping uncovers PKP4 as a modulator of the Kir2.1-regulated inward rectifier potassium currents

scientific article published on 15 June 2020

L-edge XANES of 3d-transition metals

scientific article published on 01 May 1999

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

scientific article

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

scientific article

Light-mediated discovery of surfaceome nanoscale organization and intercellular receptor interaction networks

scientific article published on 02 December 2021

Lipid raft proteins and their identification in T lymphocytes.

scientific article published in January 2004

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

scientific article

LuciPHOr: algorithm for phosphorylation site localization with false localization rate estimation using modified target-decoy approach

scientific article

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

scientific article published on 10 April 2017

MSblender: A probabilistic approach for integrating peptide identifications from multiple database search engines

scientific article

MassIVE.quant: a community resource of quantitative mass spectrometry-based proteomics datasets

scientific article published on 14 September 2020

Metabolites of purine nucleoside phosphorylase (NP) in serum have the potential to delineate pancreatic adenocarcinoma

scientific article

Modularity and hormone sensitivity of the Drosophila melanogaster insulin receptor/target of rapamycin interaction proteome

scientific article published on 8 November 2011

Omics Discovery Index - Discovering and Linking Public Omics Datasets

Optimized peptide separation and identification for mass spectrometry based proteomics via free-flow electrophoresis

scientific article published in September 2006

PIQED: automated identification and quantification of protein modifications from DIA-MS data

scientific article

PTM-Shepherd: analysis and summarization of post-translational and chemical modifications from open search results

scientific article published on 01 December 2020

Parthenolide Destabilizes Microtubules by Covalently Modifying Tubulin

scientific article published on 21 January 2021

Phosphoproteomic analysis reveals interconnected system-wide responses to perturbations of kinases and phosphatases in yeast

scientific article

Prestroke proteomic changes in cerebral microvessels in stroke-prone, transgenic[hCETP]-Hyperlipidemic, Dahl salt-sensitive hypertensive rats

scientific article

ProHits-viz: a suite of web tools for visualizing interaction proteomics data.

scientific article

ProHits: integrated software for mass spectrometry-based interaction proteomics

scientific article

Protein Complexes and Interaction Networks ⬇️

scientific article published on 01 May 2012

Protein identification by tandem mass spectrometry and sequence database searching

scientific article

Proteogenomics: concepts, applications and computational strategies

scientific article

Proteomic interrogation of androgen action in prostate cancer cells reveals roles of aminoacyl tRNA synthetases

scientific article

Proteomic profiling of naïve multiple myeloma patient plasma cells identifies pathways associated with favourable response to bortezomib-based treatment regimens

scientific article published on 30 March 2015

Proteomic study of the mucin granulae in an intestinal goblet cell model

scientific article published on 2 February 2012

QPROT: Statistical method for testing differential expression using protein-level intensity data in label-free quantitative proteomics.

scientific article

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

scientific article

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

scientific article published on 07 April 2020

Quantitative proteomic profiling of prostate cancer reveals a role for miR-128 in prostate cancer

scientific article

Recommendations from the 2008 International Summit on Proteomics Data Release and Sharing Policy: the Amsterdam principles

scientific article (publication date: July 2009)

Reconstructing targetable pathways in lung cancer by integrating diverse omics data

scientific article

Regulation of ALT-associated homology-directed repair by polyADP-ribosylation

scientific article published on 12 October 2020

SAINT-MS1: protein-protein interaction scoring using label-free intensity data in affinity purification-mass spectrometry experiments

scientific article

SAINT: probabilistic scoring of affinity purification-mass spectrometry data

scientific article

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

scientific article

SP3-Enabled Rapid and High Coverage Chemoproteomic Identification of Cell-State-Dependent Redox-Sensitive Cysteines

scientific article published on 25 February 2022

SUMOylation pathway in Trypanosoma cruzi: functional characterization and proteomic analysis of target proteins

scientific article published on 10 August 2011

Semisupervised model-based validation of peptide identifications in mass spectrometry-based proteomics

scientific article published on 27 December 2007

Significance analysis of spectral count data in label-free shotgun proteomics

scientific article

Sparsely correlated hidden Markov models with application to genome-wide location studies

scientific article published on 16 January 2013

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

scientific article published on 01 June 1994

Statistical validation of peptide identifications in large-scale proteomics using the target-decoy database search strategy and flexible mixture modeling

scientific article

Targeting SWI/SNF ATPases in enhancer-addicted prostate cancer

scientific article published on 22 December 2021

Targeting the MLL complex in castration-resistant prostate cancer

scientific article

The CRAPome: a contaminant repository for affinity purification-mass spectrometry data

scientific article

The PeptideAtlas project

scientific article

The SysteMHC Atlas project

scientific article published on 29 July 2017

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

scientific article published on 25 June 2003

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 applicatio

scientific article

The functional interactome landscape of the human histone deacetylase family

scientific article

The need for guidelines in publication of peptide and protein identification data: Working Group on Publication Guidelines for Peptide and Protein Identification Data

scientific article published on 9 April 2004

The nucleotide synthesis enzyme CAD inhibits NOD2 antibacterial function in human intestinal epithelial cells

scientific article published on 28 February 2012

The transcription elongation factor TFIIS is a component of RNA polymerase II preinitiation complexes

scientific article

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

scientific article

The yeast Sks1p kinase signaling network regulates pseudohyphal growth and glucose response

scientific article

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

scientific article

Toward more transparent and reproducible omics studies through a common metadata checklist and data publications

scientific article (publication date: 2014)

Untargeted, spectral library-free analysis of data-independent acquisition proteomics data generated using Orbitrap mass spectrometers

scientific article

Using ProHits to store, annotate, and analyze affinity purification-mass spectrometry (AP-MS) data

scientific article

Utility of RNA-seq and GPMDB protein observation frequency for improving the sensitivity of protein identification by tandem MS

scientific article

iProphet: multi-level integrative analysis of shotgun proteomic data improves peptide and protein identification rates and error estimates

scientific article

mapDIA: Preprocessing and statistical analysis of quantitative proteomics data from data independent acquisition mass spectrometry

scientific article

p38-mediated phosphorylation at T367 induces EZH2 cytoplasmic localization to promote breast cancer metastasis

scientific article published in Nature Communications

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