Research Explorer

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Researcher

Robbin Bouwmeester

21 Results

2022

FAVA: High-quality functional association networks inferred from scRNA-seq and proteomics data

Robbin BouwmeesterLennart Martens

How sticky are our proteins? Quantifying hydrophobicity of the human proteome

Robbin Bouwmeester

A2 Journal Article in BIOINFORMATICS ADVANCES

Ionbot : a novel, innovative and sensitive machine learning approach to LC-MS/MS peptide identification

Sven DegroeveRalf GabrielsKevin VelgheRobbin BouwmeesterNatalia TichshenkoLennart Martens

MS2Rescore : data-driven rescoring dramatically boosts immunopeptide identification rates

Arthur DeclercqRobbin BouwmeesterSven DegroeveLennart MartensRalf Gabriels

A1 Journal Article in MOLECULAR & CELLULAR PROTEOMICS

Machine learning on large-scale proteomics data identifies tissue- and cell type-specific proteins

Tine ClaeysRobbin BouwmeesterKris GevaertLennart Martens

ProteomicsML: An Online Platform for Community-Curated Datasets and Tutorials for Machine Learning in Proteomics

Ralf GabrielsRobbin Bouwmeester

Sensitive and specific spectral library searching with CompOmics Spectral library Searching tool and Percolator

Genet Abay ShiferawRalf GabrielsRobbin BouwmeesterTim Van Den BosscheElien VandermarliereLennart MartensPieter-Jan Volders

A1 Journal Article in JOURNAL OF PROTEOME RESEARCH

psm_utils: A high level Python API for parsing and handling peptide-spectrum-matches and proteomics search results

Ralf GabrielsArthur DeclercqRobbin BouwmeesterSven DegroeveLennart Martens

2021

Cov-MS : a community-based template assay for mass-spectrometry-based protein detection in SARS-CoV-2 patients

Bart Van PuyveldeKatleen Van UytfangheOlivier TytgatRalf GabrielsRobbin BouwmeesterSimon DaledTim Van Den BosschePathmanaban RamasamySigrid VerhelstLaura De ClerckLaura CorveleynSander WillemsNathan DebunneEvelien WynendaeleBart De SpiegeleerPéter JudákKris RoelsLaurie De WildePeter Van EenooTim ReynsMarc CherletSurya GuptaSven DegroeveChristophe StoveDieter DeforceLennart MartensMaarten Dhaenens

A2 Journal Article in JACS AU

DeepLC can predict retention times for peptides that carry as-yet unseen modifications

Robbin BouwmeesterRalf GabrielsNiels HulstaertLennart MartensSven Degroeve

A1 Journal Article in NATURE METHODS

MS²DIP : highly accurate MS2 spectrum prediction for modified peptides & MS²Rescore : data-driven rescoring dramatically boosts immunopeptide identification rates

Ralf GabrielsRobbin BouwmeesterJasper ZuallaertLennart MartensSven Degroeve

Massively parallel interrogation of protein fragment secretability using SECRiFY reveals features influencing secretory system transit

Morgane BoonePathmanaban RamasamyJasper ZuallaertRobbin BouwmeesterBerre Van MoerDavy MaddeleinDemet TuranNiels HulstaertHannah EeckhautElien VandermarliereLennart MartensSven DegroeveNico Callewaert

A1 Journal Article in NATURE COMMUNICATIONS

Personalized proteome : comparing proteogenomics and open variant search approaches for single amino acid variant detection

Robbin BouwmeesterRalf GabrielsSven DegroeveLennart MartensPieter-Jan Volders

A1 Journal Article in JOURNAL OF PROTEOME RESEARCH

Sensitive and specific spectral library searching with COSS and Percolator

Genet Abay ShiferawRalf GabrielsRobbin BouwmeesterTim Van Den BosscheElien VandermarliereLennart MartensPieter-Jan Volders

2020

Cov-MS : a community-based template assay for clinical MS-based protein detection in SARS-CoV-2 patients

Bart Van PuyveldeKatleen Van UytfangheOlivier TytgatRalf GabrielsRobbin BouwmeesterSimon DaledTim Van Den BosschePathmanaban RamasamySigrid VerhelstLaura De ClerckLaura CorveleynNathan DebunneEvelien WynendaeleBart De SpiegeleerPéter JudákKris RoelsLaurie De WildePeter Van EenooTim ReynsMarc CherletSurya GuptaSven DegroeveChristophe StoveDieter DeforceLennart MartensMaarten Dhaenens

Generalized calibration across liquid chromatography setups for generic prediction of small-molecule retention times

Robbin BouwmeesterLennart MartensSven Degroeve

A1 Journal Article in ANALYTICAL CHEMISTRY

The age of data-driven proteomics : how machine learning enables novel workflows

Robbin BouwmeesterRalf GabrielsTim Van Den BosscheLennart MartensSven Degroeve

A1 Journal Article in PROTEOMICS

The difference is in the details : predicting the LC-IM-MS behaviour of metabolites and peptides

Robbin BouwmeesterLennart MartensSven Degroeve

2019

A comparison of collision cross section values obtained via travelling wave ion mobility-mass spectrometry and ultra high performance liquid chromatography-ion mobility-mass spectrometry : application to the characterisation of metabolites in rat urine

Robbin BouwmeesterLennart Martens

A1 Journal Article in JOURNAL OF CHROMATOGRAPHY A

Accurate peptide fragmentation predictions allow data driven approaches to replace and improve upon proteomics search engine scoring functions

Ana Sílvia Ferreira Diamantino Coelho e SilvaRobbin BouwmeesterLennart MartensSven Degroeve

A1 Journal Article in BIOINFORMATICS

Comprehensive and empirical evaluation of machine learning algorithms for small molecule LC retention time prediction

Robbin BouwmeesterLennart MartensSven Degroeve

A1 Journal Article in ANALYTICAL CHEMISTRY