Research Explorer

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Researcher

Tim Van Den Bossche

33 Results

2023

Proteomics standards initiative at twenty years : current activities and future work

Eric W. DeutschJuan Antonio VizcaínoAndrew R. JonesPierre-Alain BinzHenry LamJoshua KleinWout BittremieuxYasset Perez-RiverolDavid L. TabbMathias Walzer et al.

A1 Journal Article in JOURNAL OF PROTEOME RESEARCH

The European Bioinformatics Community for Mass Spectrometry (EuBIC‐MS) : an open community for bioinformatics training and research

Wout BittremieuxDavid BouyssiéViktoria DorferMarie Locard‐PauletYasset Perez‐RiverolVeit SchwämmleJulian UszkoreitTim Van Den Bossche

A1 Journal Article in RAPID COMMUNICATIONS IN MASS SPECTROMETRY

2022

Benchmark and improving methods in metaproteomics informatics

Tim Van Den BosscheLennart MartensBart MesuereThilo Muth

Pout2Prot : an efficient tool to create protein (sub)groups from Percolator Output Files

Kay SchallertPieter VerschaffeltBart MesuereDirk BenndorfLennart MartensTim Van Den Bossche

A1 Journal Article in JOURNAL OF PROTEOME RESEARCH

Proteomics standards initiative’s ProForma 2.0 : unifying the encoding of proteoforms and peptidoforms

Richard D. LeDucEric W. DeutschPierre-Alain BinzRyan T. FellersAnthony J. CesnikJoshua A. KleinTim Van Den BosscheRalf GabrielsArshika YalavarthiYasset Perez-Riverol et al.

A1 Journal Article in JOURNAL OF PROTEOME RESEARCH

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

2021

A proteomics sample metadata representation for multiomics integration and big data analysis

Chengxin DaiAnja FüllgrabeJulianus PfeufferElizaveta M. SolovyevaJingwen DengPablo MorenoSelvakumar KamatchinathanDeepti Jaiswal KunduNancy GeorgeSilvie Fexova et al.

A1 Journal Article in NATURE COMMUNICATIONS

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

Critical Assessment of MetaProteome Investigation (CAMPI) : a multi-laboratory comparison of established workflows

Tim Van Den BosscheBenoit J. KunathKay SchallertStephanie S. SchäpePaul E. AbrahamJean ArmengaudMagnus Ø. ArntzenAriane BassignaniDirk BenndorfStephan Fuchs et al.

A1 Journal Article in NATURE COMMUNICATIONS

Critical assessment of metaproteome investigation (CAMPI) : a multi-lab comparison of established workflows

Tim Van Den BosscheBenoit J. KunathKay SchallertStephanie S. SchäpePaul E. AbrahamJean ArmengaudMagnus Ø. ArntzenAriane BassignaniDirk BenndorfStephan Fuchs et al.

MegaGO : a fast yet powerful approach to assess functional gene ontology similarity across meta-omics data sets

Pieter VerschaffeltTim Van Den BosscheWassim GabrielMichał BurdukiewiczAlessio SoggiuLennart MartensBernhard Y. RenardHenning SchiebenhoeferBart Mesuere

A1 Journal Article in JOURNAL OF PROTEOME RESEARCH

Pout2Prot : an efficient tool to create protein (sub)groups from Percolator output files

Tim Van Den BosscheKay SchallertPieter VerschaffeltBart MesuereDirk BenndorfLennart Martens

Proteomics standards initiatives ProForma 2.0 unifying the encoding of proteoforms and peptidoforms

Richard D. LeDucEric W. DeutschPierre-Alain BinzRyan T. FellersAnthony J. CesnikJoshua A. KleinTim Van Den BosscheRalf GabrielsArshika YalavarthiYasset Perez-Riverol et al.

Research culture : science from bench to society

Lorenzo CantiAnna ChrzanowskaMaria Giulia DoglioLia MartinaTim Van Den Bossche

A1 Journal Article in BIOLOGY OPEN

The Metaproteomics Initiative: a coordinated approach for propelling the functional characterization of microbiomes

Tim Van Den BosscheMagnus Ø. ArntzenDörte BecherDirk BenndorfVincent G. H. EijsinkCéline HenryPratik D. JagtapNico JehmlichCatherine JusteBenoit J. Kunath et al.

A1 Journal Article in MICROBIOME

Unipept Desktop : a faster, more powerful metaproteomics results analysis tool

Pieter VerschaffeltTim Van Den BosscheLennart MartensPeter DawyndtBart Mesuere

A1 Journal Article in JOURNAL OF PROTEOME RESEARCH

Universal Spectrum Identifier for mass spectra

Eric W. DeutschYasset Perez-RiverolJeremy CarverShin KawanoLuis MendozaTim Van Den BosscheRalf GabrielsPierre-Alain BinzBenjamin PullmanZhi Sun et al.

A1 Journal Article in NATURE METHODS

2020

An unforgettable PhD conference : VIBes2020

Tim Van Den BosscheMaria Giulia DoglioAnna Chrzanowska

Connecting MetaProteomeAnalyzer and PeptideShaker to Unipept for seamless end-to-end metaproteomics data analysis

Tim Van Den BosschePieter VerschaffeltKay SchallertHarald BarsnesPeter DawyndtDirk BenndorfBernhard Y. RenardBart MesuereLennart MartensThilo Muth

A1 Journal Article in JOURNAL OF PROTEOME RESEARCH

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.

Extracellular vesicles in patients in the acute phase of psychosis and after clinical improvement : an explorative study

Mette Elise TunsetHanne Haslene-HoxTim Van Den BosscheArne Einar VaalerEinar SulheimDaniel Kondziella

A1 Journal Article in PEERJ

Proceedings of the EuBIC-MS 2020 Developers’ Meeting

Christopher AshwoodWout BittremieuxEric W. DeutschNadezhda T. DonchevaViktoria DorferRalf GabrielsVladimir GorshkovSurya GuptaAndrew R. JonesLukas Käll et al.

A2 Journal Article in EUPA OPEN PROTEOMICS

The HUPO-PSI standardized spectral library format

Ralf GabrielsNuno BandeiraWout BittremieuxJeremy J CarverMatthew ChambersShin KawanoHenry LamTytus MakYasset Perez-RiverolBenjamin J Pullman et al.

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

Unipept CLI 2.0 : adding support for visualizations and functional annotations

Pieter VerschaffeltPhilippe Van ThienenTim Van Den BosscheFelix Van der JeugtCaroline De TenderLennart MartensPeter DawyndtBart Mesuere

A1 Journal Article in BIOINFORMATICS

gNOMO : a multi-omics pipeline for integrated host and microbiome analysis of non-model organisms

Maria Muñoz-BenaventFelix HartkopfTim Van Den BosscheVitor C PiroCarlos García-FerrisAmparo LatorreBernhard Y RenardThilo Muth

A2 Journal Article in NAR GENOMICS AND BIOINFORMATICS

gNOMO : a multi-omics pipeline for integrated host and microbiome analysis of non-model organisms (vol 2, 10.1093/nargab/lqaa058, 2020)

Maria Munoz-BenaventFelix HartkopfTim Van Den BosscheVitor C. PiroCarlos Garcia-FerrisAmparo LatorreBernhard Y. RenardThilo Muth

2019

Challenges and promise at the interface of metaproteomics and genomics : an overview of recent progress in metaproteogenomic data analysis

Henning SchiebenhoeferTim Van Den BosscheStephan FuchsBernhard Y RenardThilo MuthLennart Martens

A1 Journal Article in EXPERT REVIEW OF PROTEOMICS

Prediction-based reduction of the search space in metaproteomics

Tim Van Den BosscheLennart Martens

Proteomics Standards Initiative extended FASTA format

Pierre-Alain BinzJim ShofstahlJuan Antonio VizcaínoHarald BarsnesRobert J ChalkleyGerben MenschaertEmanuele AlpiKarl ClauserJimmy K EngLydie Lane et al.

A1 Journal Article in JOURNAL OF PROTEOME RESEARCH

Rescoring peptide-to-spectrum-matches based on predicted fragment ion intensities leads to an increased identification rate in metaproteomics

Tim Van Den BosscheAna Sílvia Ferreira Diamantino Coelho e SilvaBernhard Y RenardThilo MuthLennart Martens

2018

Prediction-based reduction of the search space in metaproteomics

Tim Van Den BosscheLennart Martens

Prediction-based reduction of the search space in metaproteomics

Tim Van Den BosscheLennart Martens