Research Explorer

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Researcher

Tim Van Den Bossche

Publications & Research Data

Awards & Distinctions

60 Results

2026

BioSamples database : the global hub for sample metadata and multi-omics integration

Dipayan GuptaIsuru LiyanageYasset Perez-RiverolEnrique Sapena VenturaWei Kheng TehTim Van Den BosscheSenthilnathan VijayarajaAmnon KhenUgis SarkansTony Burdett et al.

A1 Journal Article in NUCLEIC ACIDS RESEARCH

The Escherichia coli PeptideAtlas build : characterizing the observed Escherichia coli pan-proteome and its post-translational modifications

Caroline JachmannZhi SunKevin VelgheFlorence Arsène-PloetzeAurélie HirschlerJasper ZuallaertChristine CarapitoRobbin BouwmeesterKay NieseltEric W. Deutsch et al.

A1 Journal Article in JOURNAL OF PROTEOME RESEARCH

Unlocking the next decade of proteomics with standardized, structured metadata

Tim Van Den BosscheAnanth PrakashTine ClaeysJuan Antonio VizcaínoLennart Martens

A1 Journal Article in JOURNAL OF PROTEOME RESEARCH

2025

Creating a supportive academic culture by preventing and responding to transgressive behavior

Tim Van Den BosscheDries BostynFemke De BackereSean Bex

A2 Journal Article in NATURE MENTAL HEALTH

Critical Assessment of MetaProteome Investigation 2 (CAMPI-2) : multi-laboratory assessment of sample processing methods to stabilize fecal microbiome for functional analysis

Alessandro TancaKay SchallertLucia GrengaSamantha L. PetersMarcello AbbondioLaura De DiegoMaria Antonietta DeleddaSven-Bastiaan HaangeGuylaine MiotelloJohan S. Sáenz et al.

A1 Journal Article in MICROBIOME

Emergence and global spread of Mpox Clade Ib : challenges and the role of wastewater and environmental surveillance

Ananda TiwariThierry KalonjiTaru MillerTim Van Den BosscheAdriana KrolickaHypolite Muhindo-MavokoPatrick MitashiMarc Christian TahitaRolf LoodTarja Pitkänen et al.

Editorial material

Establishing the ELIXIR microbiome community

Robert D. FinnBachir BalechJosephine BurginPhysilia ChuaErwan CorreCymon J. CoxClaudio DonatiVitor Martins dos SantosBruno FossoJohn Hancock et al.

A2 Journal Article in F1000RESEARCH

Illuminating the invisible : green fluorescent protein as a beacon for antibiotic-induced phage activity in Escherichia coli

Maria João SilvaTim Van Den BosscheMattias CollinRolf Lood

A1 Journal Article in ANTIBIOTICS-BASEL

Metaproteomics in the One Health framework for unraveling microbial effectors in microbiomes

Robert HeyerMaximilian WolfDirk BenndorfSergio UzzauJana SeifertLucia GrengaMartin PabstHeike SchmittBart MesuereTim Van Den Bossche et al.

Editorial material

MzPeak : designing a scalable, interoperable, and future-ready mass spectrometry data format

Tim Van Den BosscheTheodore AlexandrovAivett BilbaoWout BittremieuxFederico Ivan BriganteMatthew Chase ChambersJoshua CharkowEric DeutschAndrew W. DowseyYasin El Abiead et al.

A1 Journal Article in JOURNAL OF PROTEOME RESEARCH

PathwayPilot : a user-friendly tool for visualizing and navigating metabolic pathways

Tibo Vande MoortelePieter VerschaffeltQingyao HuangNadezhda T. DonchevaTanja HolsteinCaroline JachmannPeter DawyndtLennart MartensBart MesuereTim Van Den Bossche

A1 Journal Article in MOLECULAR & CELLULAR PROTEOMICS

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

The microbiologist's guide to metaproteomics

Tim Van Den BosscheJean ArmengaudDirk BenndorfJose Alfredo Blakeley‐RuizMadita BrauerKai ChengMarybeth CreskeyDaniel FigeysLucia GrengaTimothy J. Griffin et al.

A1 Journal Article in IMETA

The microbiologist’s guide to metaproteomics

Tim Van Den BosscheJean ArmengaudDirk BenndorfJose Alfredo Blakeley-RuizMadita BrauerKai ChengMarybeth CreskeyDaniel FigeysLucia GrengaTimothy J Griffin et al.

TIMS2Rescore : a data dependent acquisition-parallel accumulation and serial fragmentation-optimized data-driven rescoring pipeline based on MS2Rescore

Arthur DeclercqRobbe DevreeseJonas ScheidCaroline JachmannTim Van Den BosscheAnnica PreikschatDavid Gomez-ZepedaJeewan Babu RijalAurelie HirschlerJonathan R. Krieger et al.

A1 Journal Article in JOURNAL OF PROTEOME RESEARCH

Unipept in 2024 : expanding metaproteomics analysis with support for missed cleavages and semitryptic and nontryptic peptides

Tibo Vande MoorteleBram DevlaminckSimon Van de VyverTim Van Den BosscheLennart MartensPeter DawyndtBart MesuerePieter Verschaffelt

A1 Journal Article in JOURNAL OF PROTEOME RESEARCH

2024

Biodiversity analysis of metaproteomics samples with Unipept : a comprehensive tutorial

Tim Van Den BosschePieter VerschaffeltTibo Vande MoortelePeter DawyndtLennart MartensBart Mesuere

Bookchapter in Protein bioinformatics

Communicating mass spectrometry quality information in mzQC with Python, R, and Java

Chris BielowNils HoffmannDavid Jimenez-MoralesTim Van Den BosscheJuan Antonio VizcainoDavid L. TabbWout BittremieuxMathias Walzer

A1 Journal Article in JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY

ECCB2024 : the 23rd European Conference on Computational Biology

Anu Kukkonen-MacchiSampsa HautaniemiKatharina F HeilMerja HeinäniemiLars Juhl JensenSini JunttilaLukas KällAsta LaihoPeter MaccallumMatti Nykter et al.

A1 Journal Article in BIOINFORMATICS

Enzymatic machinery of wood-inhabiting fungi that degrade temperate tree species

Lydia KippingNico JehmlichJulia MollMatthias NollMartin M GossnerTim Van Den BosschePascal EdelmannWerner BorkenMartin HofrichterHarald Kellner

A1 Journal Article in ISME JOURNAL

Proceedings of the EuBIC-MS developers meeting 2023

Pedro BeltraoTim Van Den BosscheRalf GabrielsTanja HolsteinTobias KockmannAlireza NameniChristian PanseRalph SchlapbachLudwig LautenbacherMatthias Mattanovich et al.

A1 Journal Article in JOURNAL OF PROTEOMICS

The Peptonizer2000 : bringing confidence to metaproteomics

Tanja HolsteinPieter VerschaffeltTim Van Den BosscheSimon Van de VyverLennart MartensBart MesuereThilo Muth

The proteomics standards initiative standardized formats for spectral libraries and fragment ion peak annotations : mzSpecLib and mzPAF

Joshua KleinHenry LamTytus D. MakWout BittremieuxYasset Perez-RiverolRalf GabrielsJim ShofstahlHelge HechtPierre-Alain BinzShin Kawano et al.

A1 Journal Article in ANALYTICAL CHEMISTRY

2023

Blood-borne extracellular vesicles of bacteria and intestinal cells in patients with psychotic disorders

Mette Elise TunsetHanne Haslene-HoxTim Van Den BosscheSusan MalekiArne VaalerDaniel Kondziella

A1 Journal Article in NORDIC JOURNAL OF PSYCHIATRY

lesSDRF is more : maximizing the value of proteomics data through streamlined metadata annotation

Tine ClaeysTim Van Den BosscheYasset Perez-RiverolKris GevaertJuan Antonio VizcaínoLennart Martens

A1 Journal Article in NATURE COMMUNICATIONS

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 nutritional composition and cell size of microbial biomass for food applications are defined by the growth conditions

Myrsini SakarikaFrederiek-Maarten KerckhofLotte Van PeteghemAlexandra Pinto Martins PereiraTim Van Den BosscheRobbin BouwmeesterRalf GabrielsDelphi Van HaverBarbara UlčarLennart Martens et al.

A1 Journal Article in MICROBIAL CELL FACTORIES

Unipept Desktop 2.0 : construction of targeted reference protein databases for metaproteogenomics analyses

Pieter VerschaffeltAlessandro TancaMarcello AbbondioTim Van Den BosscheTibo Vande MoortelePeter DawyndtLennart MartensBart Mesuere

A1 Journal Article in JOURNAL OF PROTEOME RESEARCH

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-lab comparison of established workflows

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

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

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

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

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

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

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 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 HUPO-PSI standardized spectral library format

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

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

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

Proteomics standards initiative extended FASTA format (PEFF)

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

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

The hindfoot alignment in total knee arthroplasty : a systematic review

Arne BurssensDries De RoosAlexej BargTim Van Den BosscheDaniel PfeuferCharles L. SaltzmanJan Victor

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

The influence of a total knee arthroplasty on hindfoot alignment and vice versa : a systematic review

Dries De RoosTim Van Den BosscheArne BurssensJan Victor