Research Explorer

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Researcher

Robbin Bouwmeester

23 Results

2023

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

Tine ClaeysMaxime MenuRobbin BouwmeesterKris GevaertLennart Martens

A1 Journal Article in JOURNAL OF PROTEOME RESEARCH

PhosphoLingo : protein language models for phosphorylation site prediction

Jasper ZuallaertPathmanaban RamasamyRobbin BouwmeesterNico CallewaertSven Degroeve

ProteomicsML : an online platform for community-curated data sets and tutorials for machine learning in proteomics

Tobias G. RehfeldtRalf GabrielsRobbin BouwmeesterSiegfried GessulatBenjamin A. NeelyMagnus PalmbladYasset Perez-RiverolTobias SchmidtJuan Antonio VizcaínoEric W. Deutsch

A1 Journal Article in JOURNAL OF PROTEOME RESEARCH

Toward an integrated machine learning model of a proteomics experiment

Benjamin A. NeelyViktoria DorferLennart MartensIsabell BludauRobbin BouwmeesterSven DegroeveEric W. DeutschSiegfried GessulatLukas KaellPawel Palczynski et al.

A1 Journal Article in JOURNAL OF PROTEOME RESEARCH

2022

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

Mikaela KoutrouliPau Piera LíndezRobbin BouwmeesterLennart MartensLars Juhl Jensen

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

Juami Hermine Mariama van GilsDea GogishviliJan van EckRobbin BouwmeesterErik van DijkSanne Abeln

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 BouwmeesterAurélie HirschlerChristine CarapitoSven 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 ClaeysMaxime MenuRobbin BouwmeesterKris GevaertLennart Martens

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

A1 Journal Article in JOURNAL OF PROTEOME RESEARCH

2021

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

Bart Van PuyveldeKatleen Van UytfangheOlivier TytgatLaurence Van OudenhoveRalf GabrielsRobbin BouwmeesterSimon DaledTim Van Den BosschePathmanaban RamasamySigrid Verhelst et al.

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 Vandermarliere et al.

A1 Journal Article in NATURE COMMUNICATIONS

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

Renee SalzRobbin BouwmeesterRalf GabrielsSven DegroeveLennart MartensPieter-Jan VoldersPeter A.C. ’t Hoen

A1 Journal Article in JOURNAL OF PROTEOME RESEARCH

2020

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

Bart Van PuyveldeKatleen Van UytfangheOlivier TytgatL. Van OudenhoveRalf GabrielsRobbin BouwmeesterSimon DaledTim Van Den BosschePathmanaban RamasamySigrid Verhelst et al.

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

Leanne C NyeJonathan P WilliamsNyasha C MunjomaMarine PM LetertreMuireann CoenRobbin BouwmeesterLennart MartensJonathan R SwannJeremy K NicholsonRobert S Plumb et al.

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