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Researcher
Lennart Martens
Profile
Projects
Publications
Activities
Awards & Distinctions
309
Results
2024
MS²Rescore 3.0 is a modular, flexible, and user-friendly platform to boost peptide identifications, as showcased with MS Amanda 3.0
Louise M. Buur
Arthur Declercq
Marina Strobl
Robbin Bouwmeester
Sven Degroeve
Lennart Martens
Viktoria Dorfer
Ralf Gabriels
A1
Journal Article
in
JOURNAL OF PROTEOME RESEARCH
2024
Novel statistical strategies for differential PTM abundance analysis in proteomics
Nina Demeulemeester
Lennart Martens
Lieven Clement
Dissertation
2024
Thunder-DDA-PASEF enables high-coverage immunopeptidomics and is boosted by MS2Rescore with MS2PIP timsTOF fragmentation prediction model
David Gomez-Zepeda
Danielle Arnold-Schild
Julian Beyrle
Arthur Declercq
Ralf Gabriels
Elena Kumm
Annica Preikschat
Mateusz Krzysztof Łącki
Aurélie Hirschler
Jeewan Babu Rijal
et al.
A1
Journal Article
in
NATURE COMMUNICATIONS
2024
msqrob2PTM : differential abundance and differential usage analysis of MS-based proteomics data at the post-translational modification and peptidoform level
Nina Demeulemeester
Marie Gébelin
Lucas Caldi Gomes
Paul Lingor
Christine Carapito
Lennart Martens
Lieven Clement
A1
Journal Article
in
MOLECULAR & CELLULAR PROTEOMICS
2024
2023
Building the Unipept Ecosystem : empowering high-throughput metaproteomics data analysis for characterizing complex microbial communities
Pieter Verschaffelt
Peter Dawyndt
Lennart Martens
Bart Mesuere
Dissertation
2023
FAVA : high-quality functional association networks inferred from scRNA-seq and proteomics data
Mikaela Koutrouli
Pau Piera Líndez
Katerina Nastou
Robbin Bouwmeester
Simon Rasmussen
Lennart Martens
Lars Juhl Jensen
Preprint
2023
Ionmob : a Python package for prediction of peptide collisional cross-section values
David Teschner
David Gomez-Zepeda
Arthur Declercq
Mateusz K Łącki
Seymen Avci
Konstantin Bob
Ute Distler
Thomas Michna
Lennart Martens
Stefan Tenzer
et al.
A1
Journal Article
in
BIOINFORMATICS
2023
Machine learning on large-scale proteomics data identifies tissue and cell-type specific proteins
Tine Claeys
Maxime Menu
Robbin Bouwmeester
Kris Gevaert
Lennart Martens
A1
Journal Article
in
JOURNAL OF PROTEOME RESEARCH
2023
Quality control for the target decoy approach for peptide identification
Elke Debrie
Milan Malfait
Ralf Gabriels
Arthur Declercq
Adriaan Sticker
Lennart Martens
Lieven Clement
A1
Journal Article
in
JOURNAL OF PROTEOME RESEARCH
2023
The nutritional composition and cell size of microbial biomass for food applications are defined by the growth conditions
Myrsini Sakarika
Frederiek-Maarten Kerckhof
Lotte Van Peteghem
Alexandra Pinto Martins Pereira
Tim Van Den Bossche
Robbin Bouwmeester
Ralf Gabriels
Delphi Van Haver
Barbara Ulčar
Lennart Martens
et al.
A1
Journal Article
in
MICROBIAL CELL FACTORIES
2023
Toward an integrated machine learning model of a proteomics experiment
Benjamin A. Neely
Viktoria Dorfer
Lennart Martens
Isabell Bludau
Robbin Bouwmeester
Sven Degroeve
Eric W. Deutsch
Siegfried Gessulat
Lukas Kaell
Pawel Palczynski
et al.
A1
Journal Article
in
JOURNAL OF PROTEOME RESEARCH
2023
Unipept Desktop 2.0 : construction of targeted reference protein databases for metaproteogenomics analyses
Pieter Verschaffelt
Alessandro Tanca
Marcello Abbondio
Tim Van Den Bossche
Tibo Vande Moortele
Peter Dawyndt
Lennart Martens
Bart Mesuere
A1
Journal Article
in
JOURNAL OF PROTEOME RESEARCH
2023
Updated MS²PIP web server supports cutting-edge proteomics applications
Arthur Declercq
Robbin Bouwmeester
Cristina Chiva
Eduard Sabido
Aurelie Hirschler
Christine Carapito
Lennart Martens
Sven Degroeve
Ralf Gabriels
A1
Journal Article
in
NUCLEIC ACIDS RESEARCH
2023
lesSDRF is more : maximizing the value of proteomics data through streamlined metadata annotation
Tine Claeys
Tim Van Den Bossche
Yasset Perez-Riverol
Kris Gevaert
Juan Antonio Vizcaíno
Lennart Martens
A1
Journal Article
in
NATURE COMMUNICATIONS
2023
2022
A comprehensive LFQ benchmark dataset on modern day acquisition strategies in proteomics
Bart Van Puyvelde
Simon Daled
Sander Willems
Ralf Gabriels
Anne Gonzalez de Peredo
Karima Chaoui
Emmanuelle Mouton-Barbosa
David Bouyssié
Kurt Boonen
Christopher J. Hughes
et al.
A1
Journal Article
in
SCIENTIFIC DATA
2022
An interactive mass spectrometry atlas of histone posttranslational modifications in T-cell acute leukemia
Lien Provez
Bart Van Puyvelde
Laura Corveleyn
Nina Demeulemeester
Sigrid Verhelst
Beatrice Lintermans
Simon Daled
Juliette Roels
Lieven Clement
Lennart Martens
et al.
A1
Journal Article
in
SCIENTIFIC DATA
2022
Benchmark and improving methods in metaproteomics informatics
Tim Van Den Bossche
Lennart Martens
Bart Mesuere
Thilo Muth
Dissertation
2022
Cov²MS : an automated and quantitative matrix-independent assay for mass spectrometric measurement of SARS-CoV-2 nucleocapsid protein
Bart Van Puyvelde
Katleen Van Uytfanghe
Laurence Van Oudenhove
Ralf Gabriels
Tessa Van Royen
Arne Matthys
Morteza Razavi
Richard Yip
Terry Pearson
Nicolas Drouin
et al.
A1
Journal Article
in
ANALYTICAL CHEMISTRY
2022
Data mining and modelling to understand cell migration heterogeneity and plasticity
Gwendolien Sergeant
Lennart Martens
Dissertation
2022
Immunopeptidomics-based design of mRNA vaccine formulations against Listeria monocytogenes
Rupert Mayer
Rein Verbeke
Caroline Asselman
Ilke Aernout
Adillah Gul
Denzel Eggermont
Katie Boucher
Fabien Henri Thery
Teresa Maia
Hans Demol
et al.
A1
Journal Article
in
NATURE COMMUNICATIONS
2022
Ionbot : a novel, innovative and sensitive machine learning approach to LC-MS/MS peptide identification
Sven Degroeve
Ralf Gabriels
Kevin Velghe
Robbin Bouwmeester
Natalia Tichshenko
Lennart Martens
Preprint
2022
MS2Rescore : data-driven rescoring dramatically boosts immunopeptide identification rates
Arthur Declercq
Robbin Bouwmeester
Aurélie Hirschler
Christine Carapito
Sven Degroeve
Lennart Martens
Ralf Gabriels
A1
Journal Article
in
MOLECULAR & CELLULAR PROTEOMICS
2022
Machine learning on large-scale proteomics data identifies tissue- and cell type-specific proteins
Tine Claeys
Maxime Menu
Robbin Bouwmeester
Kris Gevaert
Lennart Martens
Preprint
2022
Machine learning to the rescue : enabling novel proteomics workflows with data-driven bioinformatics methods
Ralf Gabriels
Lennart Martens
Sven Degroeve
Dissertation
2022
Orthogonal proteomics methods to unravel the HOTAIR interactome
Louis Delhaye
Edith De Bruycker
Pieter-Jan Volders
Daria Fijalkowska
Delphine De Sutter
Sven Degroeve
Lennart Martens
Pieter Mestdagh
Sven Eyckerman
A1
Journal Article
in
SCIENTIFIC REPORTS
2022
Orthogonal proteomics methods to unravel the HOTAIR interactome
Louis Delhaye
Edith De Bruycker
Pieter-Jan Volders
Daria Fijalkowska
Delphine De Sutter
Sven Degroeve
Lennart Martens
Pieter Mestdagh
Sven Eyckerman
C3
Conference
2022
Pout2Prot : an efficient tool to create protein (sub)groups from Percolator Output Files
Kay Schallert
Pieter Verschaffelt
Bart Mesuere
Dirk Benndorf
Lennart Martens
Tim Van Den Bossche
A1
Journal Article
in
JOURNAL OF PROTEOME RESEARCH
2022
Psm_utils : a high level Python API for parsing and handling peptide-spectrum-matches and proteomics search results
Ralf Gabriels
Arthur Declercq
Robbin Bouwmeester
Sven Degroeve
Lennart Martens
Preprint
2022
Sensitive and specific spectral library searching with CompOmics Spectral library Searching tool and Percolator
Genet Abay Shiferaw
Ralf Gabriels
Robbin Bouwmeester
Tim Van Den Bossche
Elien Vandermarliere
Lennart Martens
Pieter-Jan Volders
A1
Journal Article
in
JOURNAL OF PROTEOME RESEARCH
2022
Uncovering new knowledge on protein post-translational modifications by large-scale reprocessing and analysis of public proteomics data
Pathmanaban Ramasamy
Lennart Martens
Wim F. Vranken
Dissertation
2022
Unipept visualizations : an interactive visualization library for biological data
Pieter Verschaffelt
James Collier
Alexander Botzki
Lennart Martens
Peter Dawyndt
Bart Mesuere
A1
Journal Article
in
BIOINFORMATICS
2022
psm_utils : a high-level python API for parsing and handling peptide-spectrum matches and proteomics search results
Ralf Gabriels
Arthur Declercq
Robbin Bouwmeester
Sven Degroeve
Lennart Martens
A1
Journal Article
in
JOURNAL OF PROTEOME RESEARCH
2022
2021
Cov-MS : a community-based template assay for mass-spectrometry-based protein detection in SARS-CoV-2 patients
Bart Van Puyvelde
Katleen Van Uytfanghe
Olivier Tytgat
Laurence Van Oudenhove
Ralf Gabriels
Robbin Bouwmeester
Simon Daled
Tim Van Den Bossche
Pathmanaban Ramasamy
Sigrid Verhelst
et al.
A2
Journal Article
in
JACS AU
2021
Critical Assessment of MetaProteome Investigation (CAMPI) : a multi-laboratory comparison of established workflows
Tim Van Den Bossche
Benoit J. Kunath
Kay Schallert
Stephanie S. Schäpe
Paul E. Abraham
Jean Armengaud
Magnus Ø. Arntzen
Ariane Bassignani
Dirk Benndorf
Stephan Fuchs
et al.
A1
Journal Article
in
NATURE COMMUNICATIONS
2021
Critical assessment of metaproteome investigation (CAMPI) : a multi-lab comparison of established workflows
Tim Van Den Bossche
Benoit J. Kunath
Kay Schallert
Stephanie S. Schäpe
Paul E. Abraham
Jean Armengaud
Magnus Ø. Arntzen
Ariane Bassignani
Dirk Benndorf
Stephan Fuchs
et al.
Preprint
2021
DeepLC can predict retention times for peptides that carry as-yet unseen modifications
Robbin Bouwmeester
Ralf Gabriels
Niels Hulstaert
Lennart Martens
Sven Degroeve
A1
Journal Article
in
NATURE METHODS
2021
MS²DIP : highly accurate MS2 spectrum prediction for modified peptides & MS²Rescore : data-driven rescoring dramatically boosts immunopeptide identification rates
Ralf Gabriels
Robbin Bouwmeester
Jasper Zuallaert
Lennart Martens
Sven Degroeve
C3
Conference
2021
Massively parallel interrogation of protein fragment secretability using SECRiFY reveals features influencing secretory system transit
Morgane Boone
Pathmanaban Ramasamy
Jasper Zuallaert
Robbin Bouwmeester
Berre Van Moer
Davy Maddelein
Demet Turan
Niels Hulstaert
Hannah Eeckhaut
Elien Vandermarliere
et al.
A1
Journal Article
in
NATURE COMMUNICATIONS
2021
MegaGO : a fast yet powerful approach to assess functional gene ontology similarity across meta-omics data sets
Pieter Verschaffelt
Tim Van Den Bossche
Wassim Gabriel
Michał Burdukiewicz
Alessio Soggiu
Lennart Martens
Bernhard Y. Renard
Henning Schiebenhoefer
Bart Mesuere
A1
Journal Article
in
JOURNAL OF PROTEOME RESEARCH
2021
Personalized proteome : comparing proteogenomics and open variant search approaches for single amino acid variant detection
Renee Salz
Robbin Bouwmeester
Ralf Gabriels
Sven Degroeve
Lennart Martens
Pieter-Jan Volders
Peter A.C. ’t Hoen
A1
Journal Article
in
JOURNAL OF PROTEOME RESEARCH
2021
Pout2Prot : an efficient tool to create protein (sub)groups from Percolator output files
Tim Van Den Bossche
Kay Schallert
Pieter Verschaffelt
Bart Mesuere
Dirk Benndorf
Lennart Martens
Preprint
2021
Spectral prediction features as a solution for the search space size problem in proteogenomics
Steven Verbruggen
Siegfried Gessulat
Ralf Gabriels
Anna Matsaroki
Hendrik Van de Voorde
Bernhard Kuster
Sven Degroeve
Lennart Martens
Wim Van Criekinge
Mathias Wilhelm
et al.
A1
Journal Article
in
MOLECULAR & CELLULAR PROTEOMICS
2021
The RNA landscape of the human placenta in health and disease
Sungsam Gong
Francesca Gaccioli
Justyna Dopierala
Ulla Sovio
Emma Cook
Pieter-Jan Volders
Lennart Martens
Paul D. W. Kirk
Sylvia Richardson
Gordon C. S. Smith
et al.
A1
Journal Article
in
NATURE COMMUNICATIONS
2021
Unipept Desktop : a faster, more powerful metaproteomics results analysis tool
Pieter Verschaffelt
Tim Van Den Bossche
Lennart Martens
Peter Dawyndt
Bart Mesuere
A1
Journal Article
in
JOURNAL OF PROTEOME RESEARCH
2021
2020
Anatomy and evolution of database search engines : a central component of mass spectrometry based proteomic workflows
Kenneth Verheggen
Helge Raeder
Frode S Berven
Lennart Martens
Harald Barsnes
Marc Vaudel
A1
Journal Article
in
MASS SPECTROMETRY REVIEWS
2020
COSS : a fast and user-friendly tool for spectral library searching
Genet Abay Shiferaw
Elien Vandermarliere
Niels Hulstaert
Ralf Gabriels
Lennart Martens
Pieter-Jan Volders
A1
Journal Article
in
JOURNAL OF PROTEOME RESEARCH
2020
Community standards for open cell migration data
Alejandra N. Gonzalez-Beltran
Paola Masuzzo
Christophe Ampe
Gert-Jan Bakker
Sébastien Besson
Robert H Eibl
Peter Friedl
Matthias Gunzer
Mark Kittisopikul
Sylvia E. Le Dévédec
et al.
A1
Journal Article
in
GIGASCIENCE
2020
Connecting MetaProteomeAnalyzer and PeptideShaker to Unipept for seamless end-to-end metaproteomics data analysis
Tim Van Den Bossche
Pieter Verschaffelt
Kay Schallert
Harald Barsnes
Peter Dawyndt
Dirk Benndorf
Bernhard Y. Renard
Bart Mesuere
Lennart Martens
Thilo Muth
A1
Journal Article
in
JOURNAL OF PROTEOME RESEARCH
2020
Generalized calibration across liquid chromatography setups for generic prediction of small-molecule retention times
Robbin Bouwmeester
Lennart Martens
Sven Degroeve
A1
Journal Article
in
ANALYTICAL CHEMISTRY
2020
MSqRob takes the missing hurdle : uniting intensity- and count-based proteomics
Ludger Goeminne
Adriaan Sticker
Lennart Martens
Kris Gevaert
Lieven Clement
A1
Journal Article
in
ANALYTICAL CHEMISTRY
2020
Pitfalls in re-analysis of observational omics studies: a post-mortem of the human pathology atlas
Jeroen Gilis
Steff Taelman
Lucas Davey
Lennart Martens
Lieven Clement
Preprint
2020
Precursor intensity-based label-free quantification software tools for proteomic and multi-omic analysis within the galaxy platform
Subina Mehta
Caleb W. Easterly
Ray Sajulga
Robert J. Millikin
Andrea Argentini
Ignacio Eguinoa
Lennart Martens
Michael R. Shortreed
Lloyd M. Smith
Thomas McGowan
et al.
A2
Journal Article
in
PROTEOMES
2020
Removing the hidden data dependency of DIA with predicted spectral libraries
Bart Van Puyvelde
Sander Willems
Ralf Gabriels
Simon Daled
Laura De Clerck
Sofie Vande Casteele
An Staes
Francis Impens
Dieter Deforce
Lennart Martens
et al.
A1
Journal Article
in
PROTEOMICS
2020
Robust summarization and inference in proteome-wide label-free quantification
Adriaan Sticker
Ludger Goeminne
Lennart Martens
Lieven Clement
A1
Journal Article
in
MOLECULAR & CELLULAR PROTEOMICS
2020
Scop3P : a comprehensive resource of human phosphosites within their full context
Pathmanaban Ramasamy
Demet Turan
Natalia Tichshenko
Niels Hulstaert
Elien Vandermarliere
Wim Vranken
Lennart Martens
A1
Journal Article
in
JOURNAL OF PROTEOME RESEARCH
2020
Simple peptide quantification approach for MS-based proteomics quality control
Teresa Maia
An Staes
Kim Plasman
Jarne Pauwels
Katie Boucher
Andrea Argentini
Lennart Martens
Tony Montoye
Kris Gevaert
Francis Impens
A1
Journal Article
in
ACS OMEGA
2020
The CEP5 peptide promotes abiotic stress tolerance, as revealed by quantitative proteomics, and attenuates the AUX/IAA equilibrium in Arabidopsis
Stephanie Smith
Shanshuo Zhu
Lisa Joos
Ianto Roberts
Natalia Nikonorova
Lam Dai Vu
Elisabeth Stes
Hyunwoo Cho
Antoine Larrieu
Wei Xuan
et al.
A1
Journal Article
in
MOLECULAR & CELLULAR PROTEOMICS
2020
The age of data-driven proteomics : how machine learning enables novel workflows
Robbin Bouwmeester
Ralf Gabriels
Tim Van Den Bossche
Lennart Martens
Sven Degroeve
A1
Journal Article
in
PROTEOMICS
2020
The difference is in the details : predicting the LC-IM-MS behaviour of metabolites and peptides
Robbin Bouwmeester
Lennart Martens
Sven Degroeve
Dissertation
2020
ThermoRawFileParser : modular, scalable and cross-platform RAW file conversion
Niels Hulstaert
Jim Shofstahl
Timo Sachsenberg
Mathias Walzer
Harald Barsnes
Lennart Martens
Yasset Perez-Riverol
A1
Journal Article
in
JOURNAL OF PROTEOME RESEARCH
2020
Unipept CLI 2.0 : adding support for visualizations and functional annotations
Pieter Verschaffelt
Philippe Van Thienen
Tim Van Den Bossche
Felix Van der Jeugt
Caroline De Tender
Lennart Martens
Peter Dawyndt
Bart Mesuere
A1
Journal Article
in
BIOINFORMATICS
2020
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 Nye
Jonathan P Williams
Nyasha C Munjoma
Marine PM Letertre
Muireann Coen
Robbin Bouwmeester
Lennart Martens
Jonathan R Swann
Jeremy K Nicholson
Robert S Plumb
et al.
A1
Journal Article
in
JOURNAL OF CHROMATOGRAPHY A
2019
A time of enlightenment : straightforward identification of protein modifications
Lennart Martens
C3
Conference
2019
Accurate peptide fragmentation predictions allow data driven approaches to replace and improve upon proteomics search engine scoring functions
Ana Sílvia Ferreira Diamantino Coelho e Silva
Robbin Bouwmeester
Lennart Martens
Sven Degroeve
A1
Journal Article
in
BIOINFORMATICS
2019
An update on the moFF algorithm for label-free quantitative proteomics
Andrea Argentini
An Staes
Björn Andreas Grüning
Subina Mehta
Caleb Easterly
Timothy Griffin
Pratik Jagtap
Francis Impens
Lennart Martens
A1
Journal Article
in
JOURNAL OF PROTEOME RESEARCH
2019
Challenges and promise at the interface of metaproteomics and genomics : an overview of recent progress in metaproteogenomic data analysis
Henning Schiebenhoefer
Tim Van Den Bossche
Stephan Fuchs
Bernhard Y Renard
Thilo Muth
Lennart Martens
A1
Journal Article
in
EXPERT REVIEW OF PROTEOMICS
2019
Comprehensive and empirical evaluation of machine learning algorithms for small molecule LC retention time prediction
Robbin Bouwmeester
Lennart Martens
Sven Degroeve
A1
Journal Article
in
ANALYTICAL CHEMISTRY
2019
Data-driven approaches for improved mass spectrometry-based analyte identification
Ana Sílvia Ferreira Diamantino Coelho e Silva
Lennart Martens
Sven Degroeve
Dissertation
2019
DoRes within CellMissy : dose-response analysis on cell migration and related data
Gwendolien Sergeant
Lennart Martens
Marleen Van Troys
Paola Masuzzo
A1
Journal Article
in
BIOINFORMATICS
2019
Fast and accurate MS² peak intensity predictions for multiple fragmentation methods, instruments and labeling techniques
Ralf Gabriels
Lennart Martens
Sven Degroeve
C3
Conference
2019
Keeping up appearances in the mumps vaccine : do antigenic differences matter?
Tessa Vermeire
Lennart Martens
Steven Van Gucht
Paul Rota
Elien Vandermarliere
Dissertation
2019
LNCipedia 5 : towards a reference set of human long non-coding RNAs
Pieter-Jan Volders
Jasper Anckaert
Kenneth Verheggen
Justine Nuytens
Lennart Martens
Pieter Mestdagh
Jo Vandesompele
A1
Journal Article
in
NUCLEIC ACIDS RESEARCH
2019
MS²PIP : fast and accurate MS² peak intensity prediction for multiple fragmentation methods, instruments and labeling techniques
Ralf Gabriels
Lennart Martens
Sven Degroeve
C3
Conference
2019
Prediction-based reduction of the search space in metaproteomics
Tim Van Den Bossche
Lennart Martens
C3
Conference
2019
Rescoring peptide-to-spectrum-matches based on predicted fragment ion intensities leads to an increased identification rate in metaproteomics
Tim Van Den Bossche
Ana Sílvia Ferreira Diamantino Coelho e Silva
Bernhard Y Renard
Thilo Muth
Lennart Martens
C3
Conference
2019
Robust summarisation and inference for Label-Free Quantification
Adriaan Sticker
Ludger Goeminne
Lennart Martens
Lieven Clement
C3
Conference
2019
Unipept 4.0 : functional analysis of metaproteome data
Robbert Gurdeep Singh
Alessandro Tanca
Antonio Palomba
Felix Van der Jeugt
Pieter Verschaffelt
Sergio Uzzau
Lennart Martens
Peter Dawyndt
Bart Mesuere
A1
Journal Article
in
JOURNAL OF PROTEOME RESEARCH
2019
Updated MS²PIP web server delivers fast and accurate MS² peak intensity prediction for multiple fragmentation methods, instruments and labeling techniques
Ralf Gabriels
Lennart Martens
Sven Degroeve
A1
Journal Article
in
NUCLEIC ACIDS RESEARCH
2019
2018
Adding new nodes to the protein association network
Surya Gupta
Lennart Martens
Jan Tavernier
Dissertation
2018
Analysis of invasion dynamics of matrix-embedded cells in a multisample format
Marleen Van Troys
Paola Masuzzo
Lynn Huyck
Karima Bakkali
Davy Waterschoot
Lennart Martens
Christophe Ampe
Bookchapter
in
Cell migration : methods and protocols
2018
Complementary use of ribosome profiling and proteomics for mapping the translation landscape
Elvis Ndah
Petra Van Damme
Gerben Menschaert
Lennart Martens
Dissertation
2018
Cross-linked peptide identification : a computational forest of algorithms
Sule Yilmaz-Rumpf
Genet Abay Shiferaw
Josep Rayo
Anastassios Economou
Lennart Martens
Elien Vandermarliere
A1
Journal Article
in
MASS SPECTROMETRY REVIEWS
2018
Data-driven rescoring of metabolite annotations significantly improves sensitivity
Ana Sílvia Ferreira Diamantino Coelho e Silva
Andrew Palmer
Vitaly Kovalev
Artem Tarasov
Theodore Alexandrov
Lennart Martens
Sven Degroeve
A1
Journal Article
in
ANALYTICAL CHEMISTRY
2018
Differences in antigenic sites and other functional regions between genotype A and G mumps virus surface proteins
Sigrid Gouma
Tessa Vermeire
Steven Van Gucht
Lennart Martens
Veronik Hutse
Jeroen Cremer
Paul A Rota
Geert Leroux-Roels
Marion Koopmans
Rob van Binnendijk
et al.
A1
Journal Article
in
SCIENTIFIC REPORTS
2018
High-throughput metaproteomics data analysis with Unipept : a tutorial
Bart Mesuere
Felix Van der Jeugt
Toon Willems
Tom Naessens
Bart Devreese
Lennart Martens
Peter Dawyndt
A1
Journal Article
in
JOURNAL OF PROTEOMICS
2018
How to till a growing field : large-scale re-analysis of public proteomics data
Kenneth Verheggen
Lennart Martens
Harald Barsnes
Dissertation
2018
Prediction-based reduction of the search space in metaproteomics
Tim Van Den Bossche
Lennart Martens
C3
Conference
2018
Prediction-based reduction of the search space in metaproteomics
Tim Van Den Bossche
Lennart Martens
C3
Conference
2018
SQANTI : extensive characterization of long-read transcript sequences for quality control in full-length transcriptome identification and quantification
Manuel Tardaguila
Lorena de la Fuente
Cristina Marti
Cécile Pereira
Francisco Jose Pardo-Palacios
Hector del Risco
Marc Ferrell
Maravillas Mellado
Marissa Macchietto
Kenneth Verheggen
et al.
A1
Journal Article
in
GENOME RESEARCH
2018
Surveillance of myelodysplastic syndrome via migration analyses of blood neutrophils : a potential prognostic tool
Marc Schuster
Mischa Moeller
Lea Bornemann
Clara Bessen
Charlyn Sobczak
Saskia Schmitz
Laura Witjes
Katja Kruithoff
Christina Kohn
Olga Just
et al.
A1
Journal Article
in
JOURNAL OF IMMUNOLOGY
2018
The mutational landscape of MYCN, Lin28b and ALKF1174L driven murine neuroblastoma mimics human disease
Bram De Wilde
Anneleen Beckers
Sven Lindner
Kristina Althoff
Katleen De Preter
Pauline Depuydt
Pieter Mestdagh
Tom Sante
Steve Lefever
Falk Hertwig
et al.
A2
Journal Article
in
ONCOTARGET
2018
The online Tabloid Proteome : an annotated database of protein associations
Surya Gupta
Demet Turan
Jan Tavernier
Lennart Martens
A1
Journal Article
in
NUCLEIC ACIDS RESEARCH
2018
The study of degradation mechanisms of glyco-engineered plant produced anti-rabies monoclonal antibodies E559 and 62-71-3
Sindisiwe G Buthelezi
Heini W Dirr
Ereck Chakauya
Rachel Chikwamba
Lennart Martens
Tsepo L Tsekoa
Elien Vandermarliere
Stoyan H Stoychev
A1
Journal Article
in
PLOS ONE
2018
2017
A community proposal to integrate proteomics activities in ELIXIR
Juan Antonio Vizcaíno
Mathias Walzer
Rafael C Jiménez
Wout Bittremieux
David Bouyssié
Christine Carapito
Fernando Corrales
Myriam Ferro
Albert JR Heck
Peter Horvatovich
et al.
A2
Journal Article
in
F1000RESEARCH
2017
A golden age for working with public proteomics data
Lennart Martens
Juan Antonio Vizcaíno
A1
Journal Article
in
TRENDS IN BIOCHEMICAL SCIENCES
2017
An accessible proteogenomics informatics resource for cancer researchers
Matthew C Chambers
Pratik D Jagtap
James E Johnson
Thomas McGowan
Praveen Kumar
Getiria Onsongo
Candace R Guerrero
Harald Barsnes
Marc Vaudel
Lennart Martens
et al.
A1
Journal Article
in
CANCER RESEARCH
2017
An end-to-end software solution for the analysis of high-throughput single-cell migration data
Paola Masuzzo
Lynn Huyck
Aleksandra Simiczyjew
Christophe Ampe
Lennart Martens
Marleen Van Troys
A1
Journal Article
in
SCIENTIFIC REPORTS
2017
Computational quality control tools for mass spectrometry proteomics
Wout Bittremieux
Dirk Valkenborg
Lennart Martens
Kris Laukens
A1
Journal Article
in
PROTEOMICS
2017
MAPPI-DAT : data management and analysis for protein-protein interaction data from the high-throughput MAPPIT cell microarray platform
Surya Gupta
Veronic De Puysseleyr
José Van Der Heyden
Davy Maddelein
Irma Lemmens
Sam Lievens
Sven Degroeve
Jan Tavernier
Lennart Martens
A1
Journal Article
in
BIOINFORMATICS
2017
MPA Portable : a stand-alone software package for analyzing metaproteome samples on the go
Thilo Muth
Fabian Kohrs
Robert Heyer
Dirk Benndorf
Erdmann Rapp
Udo Reichl
Lennart Martens
Bernhard Y Renard
A1
Journal Article
in
ANALYTICAL CHEMISTRY
2017
Mass spectrometrists should search for all peptides, but assess only the ones they care about
Adriaan Sticker
Lennart Martens
Lieven Clement
A1
Journal Article
in
NATURE METHODS
2017
Methods to calculate spectrum similarity
Sule Yilmaz-Rumpf
Elien Vandermarliere
Lennart Martens
Bookchapter
in
Proteome bioinformatics
2017
N-terminal proteomics assisted profiling of the unexplored translation initiation landscape in Arabidopsis thaliana
Patrick Willems
Elvis Ndah
Veronique Jonckheere
Simon Stael
Adriaan Sticker
Lennart Martens
Frank Van Breusegem
Kris Gevaert
Petra Van Damme
A1
Journal Article
in
MOLECULAR & CELLULAR PROTEOMICS
2017
Noncoding after all : biases in proteomics data do not explain observed absence of lncRNA translation products
Kenneth Verheggen
Pieter-Jan Volders
Pieter Mestdagh
Gerben Menschaert
Petra Van Damme
Kris Gevaert
Lennart Martens
Jo Vandesompele
A1
Journal Article
in
JOURNAL OF PROTEOME RESEARCH
2017
Novel algorithms for two interesting challenges in proteomics : unsequenced organisms and cross-linked peptide identification
Sule Yilmaz-Rumpf
Lennart Martens
Elien Vandermarliere
Dissertation
2017
Protein complex analysis : from raw protein lists to protein interaction networks
Pieter Meysman
Kevin Titeca
Sven Eyckerman
Jan Tavernier
Bart Goethals
Lennart Martens
Dirk Valkenborg
Kris Laukens
A1
Journal Article
in
MASS SPECTROMETRY REVIEWS
2017
Quality control in mass spectrometry-based proteomics
Wout Bittremieux
David L Tabb
Francis Impens
An Staes
Evy Timmerman
Lennart Martens
Kris Laukens
A1
Journal Article
in
MASS SPECTROMETRY REVIEWS
2017
Unbiased protein association study on the public human proteome reveals biological connections between co-occurring protein pairs
Surya Gupta
Kenneth Verheggen
Jan Tavernier
Lennart Martens
A1
Journal Article
in
JOURNAL OF PROTEOME RESEARCH
2017
sfinx : an R package for the elimination of false positives from affinity purification-mass spectrometry datasets
Kevin Titeca
Pieter Meysman
Kris Laukens
Lennart Martens
Jan Tavernier
Sven Eyckerman
A1
Journal Article
in
BIOINFORMATICS
2017
2016
A pipeline for differential proteomics in unsequenced species
Sule Yilmaz-Rumpf
Bjorn Victor
Niels Hulstaert
Elien Vandermarliere
Harald Barsnes
Sven Degroeve
Surya Gupta
Adriaan Sticker
Sarah Gabriël
Pierre Dorny
et al.
A1
Journal Article
in
JOURNAL OF PROTEOME RESEARCH
2016
An extra dimension in protein tagging by quantifying universal proteotypic peptides using targeted proteomics
Giel Vandemoortele
An Staes
Giulia Gonnelli
Noortje Samyn
Delphine De Sutter
Elien Vandermarliere
Evy Timmerman
Kris Gevaert
Lennart Martens
Sven Eyckerman
A1
Journal Article
in
SCIENTIFIC REPORTS
2016
Database search engines : paradigms, challenges and solutions
Kenneth Verheggen
Lennart Martens
Frode S. Berven
Harald Barsnes
Marc Vaudel
A1
Journal Article
in
Modern proteomics : sample preparation, analysis and practical applications
2016
Designing biomedical proteomics experiments : state-of-the-art and future perspectives
Evelyne Maes
Pieter Kelchtermans
Wout Bittremieux
Kurt De Grave
Sven Degroeve
Jef Hooyberghs
Inge Mertens
Geert Baggerman
Jan Ramon
Kris Laukens
et al.
A1
Journal Article
in
EXPERT REVIEW OF PROTEOMICS
2016
Exploring the potential of public proteomics data
Marc Vaudel
Kenneth Verheggen
Attila Csordas
Helge Raeder
Frode S Berven
Lennart Martens
Juan A Vizcaíno
Harald Barsnes
A1
Journal Article
in
PROTEOMICS
2016
Human proteome project mass spectrometry data interpretation guidelines 2.1
Eric W Deutsch
Christopher M Overall
Jennifer E Van Eyk
Mark S Baker
Young-Ki Paik
Susan T Weintraub
Lydie Lane
Lennart Martens
Yves Vandenbrouck
Ulrike Kusebauch
et al.
Editorial material
2016
Identification of quantitative proteomic differences between Mycobacterium tuberculosis lineages with altered virulence
Julian S Peters
Bridget Calder
Giulia Gonnelli
Sven Degroeve
Elinambinina Rajaonarifara
Nicola Mulder
Nelson C Soares
Lennart Martens
Jonathan M Blackburn
A1
Journal Article
in
FRONTIERS IN MICROBIOLOGY
2016
Metaproteomic data analysis at a glance : advances in computational microbial community proteomics
Thilo Muth
Bernhard Y Renard
Lennart Martens
A1
Journal Article
in
EXPERT REVIEW OF PROTEOMICS
2016
Proteome-scale binary interactomics in human cells
Sam Lievens
José Van Der Heyden
Delphine Masschaele
Leentje De Ceuninck
Ioanna Petta
Surya Gupta
Veronic De Puysseleyr
Virginie Vauthier
Irma Lemmens
Dries De Clercq
et al.
A1
Journal Article
in
MOLECULAR & CELLULAR PROTEOMICS
2016
Resolution of protein structure by mass spectrometry
Elien Vandermarliere
Elisabeth Stes
Kris Gevaert
Lennart Martens
A1
Journal Article
in
MASS SPECTROMETRY REVIEWS
2016
SFINX : straightforward filtering index for affinity purification mass spectrometry data analysis
Kevin Titeca
Pieter Meysman
Kris Gevaert
Jan Tavernier
Kris Laukens
Lennart Martens
Sven Eyckerman
A1
Journal Article
in
JOURNAL OF PROTEOME RESEARCH
2016
Taking aim at moving targets in computational cell migration
Paola Masuzzo
Marleen Van Troys
Christophe Ampe
Lennart Martens
A1
Journal Article
in
TRENDS IN CELL BIOLOGY
2016
The Lyssavirus glycoprotein : a key to cross-immunity
Sindisiwe G Buthelezi
Heini W Dirr
Ereck Chakauya
Rachel Chikwamba
Lennart Martens
Tsepo L Tsekoa
Stoyan H Stoychev
Elien Vandermarliere
A1
Journal Article
in
VIROLOGY
2016
The impact of sequence database choice on metaproteomic results in gut microbiota studies
Alessandro Tanca
Antonio Palomba
Cristina Fraumene
Daniela Pagnozzi
Valeria Manghina
Massimo Deligios
Thilo Muth
Erdmann Rapp
Lennart Martens
Maria Filippa Addis
et al.
A1
Journal Article
in
MICROBIOME
2016
Towards an open data exchange ecosystem : forging a new path for cell migration data analysis and mining
Paola Masuzzo
Christophe Ampe
Lennart Martens
Marleen Van Troys
Dissertation
2016
Unsupervised quality assessment of mass spectrometry proteomics experiments by multivariate quality control metrics
Wout Bittremieux
Pieter Meysman
Lennart Martens
Dirk Valkenborg
Kris Laukens
A1
Journal Article
in
JOURNAL OF PROTEOME RESEARCH
2016
Up-to-date workflow for plant (phospho)proteomics identifies differential drought-responsive phosphorylation events in maize leaves
Lam Dai Vu
Elisabeth Stes
Michiel Van Bel
Hilde Nelissen
Davy Maddelein
Dirk Inzé
Frederik Coppens
Lennart Martens
Kris Gevaert
Ive De Smet
A1
Journal Article
in
JOURNAL OF PROTEOME RESEARCH
2016
Xilmass: a new approach toward the identification of cross-linked peptides
Sule Yilmaz-Rumpf
Friedel Drepper
Niels Hulstaert
Maša Černič
Kris Gevaert
Anastassios Economou
Bettina Warscheid
Lennart Martens
Elien Vandermarliere
A1
Journal Article
in
ANALYTICAL CHEMISTRY
2016
moFF : a robust and automated approach to extract peptide ion intensities
Andrea Argentini
Ludger Goeminne
Kenneth Verheggen
Niels Hulstaert
An Staes
Lieven Clement
Lennart Martens
A1
Journal Article
in
NATURE METHODS
2016
2015
A decoy-free approach to the identification of peptides
Giulia Gonnelli
Michiel Stock
Jan Verwaeren
Davy Maddelein
Bernard De Baets
Lennart Martens
Sven Degroeve
A1
Journal Article
in
JOURNAL OF PROTEOME RESEARCH
2015
An improved toolbox to unravel the plant cellular machinery by tandem affinity purification of Arabidopsis protein complexes
Jelle Van Leene
Dominique Eeckhout
Bernard Cannoot
Nancy De Winne
Geert Persiau
Eveline Van De Slijke
Leen Vercruysse
Maarten Dedecker
Aurine Verkest
Klaas Vandepoele
et al.
A1
Journal Article
in
NATURE PROTOCOLS
2015
An open data ecosystem for cell migration research
Paola Masuzzo
Lennart Martens
the 2014 Cell Migration workshop participants
Christophe Ampe
Olivier De Wever
Marleen Van Troys
Editorial material
2015
An update on LNCipedia : a database for annotated human lncRNA sequences
Pieter-Jan Volders
Kenneth Verheggen
Gerben Menschaert
Klaas Vandepoele
Lennart Martens
Jo Vandesompele
Pieter Mestdagh
A1
Journal Article
in
NUCLEIC ACIDS RESEARCH
2015
Ariadne's thread : a robust software solution leading to automated absolute and relative quantification of SRM data
Sara Nasso
Sandra Goetze
Lennart Martens
A1
Journal Article
in
JOURNAL OF PROTEOME RESEARCH
2015
Colonic metaproteomic signatures of active bacteria and the host in obesity
Carolin A Kolmeder
Jarmo Ritari
Froukje J Verdam
Thilo Muth
Salla Keskitalo
Markku Varjosalo
Susana Fuentes
Jan Willem Greve
Wim A Buurman
Udo Reichl
et al.
A1
Journal Article
in
PROTEOMICS
2015
JSparklines : making tabular proteomics data come alive
Harald Barsnes
Marc Vaudel
Lennart Martens
A1
Journal Article
in
PROTEOMICS
2015
Limited proteolysis combined with stable isotope labeling reveals conformational changes in protein (pseudo)kinases upon binding small molecules
Michela Di Michele
Elisabeth Stes
Elien Vandermarliere
Rohit Arora
Juan Astorga-Wells
Jonathan Vandenbussche
Erika van Heerde
Roman Zubarev
Pascal Bonnet
Joannes TM Linders
et al.
A1
Journal Article
in
JOURNAL OF PROTEOME RESEARCH
2015
MS²PIP prediction server : compute and visualize MS² peak intensity predictions for CID and HCD fragmentation
Sven Degroeve
Davy Maddelein
Lennart Martens
A1
Journal Article
in
NUCLEIC ACIDS RESEARCH
2015
Managing expectations when publishing tools and methods for computational proteomics
Lennart Martens
Oliver Kohlbacher
Susan T Weintraub
Editorial material
2015
Navigating through metaproteomics data : a logbook of database searching
Thilo Muth
Carolin A Kolmeder
Jarkko Salojärvi
Salla Keskitalo
Markku Varjosalo
Froukje J Verdam
Sander S Rensen
Udo Reichl
Willem M de Vos
Erdmann Rapp
et al.
A1
Journal Article
in
PROTEOMICS
2015
On the assessment of the reliability of peptide-to-spectrum matches in mass-spectrometry-based proteomics
Giulia Gonnelli
Lennart Martens
Bernard De Baets
Dissertation
2015
Open-source, platform-independent library and online scripting environment for accessing thermo scientific RAW files
Pieter Kelchtermans
Ana Sílvia Ferreira Diamantino Coelho e Silva
Andrea Argentini
An Staes
Jonathan Vandenbussche
Kris Laukens
Dirk Valkenborg
Lennart Martens
A1
Journal Article
in
JOURNAL OF PROTEOME RESEARCH
2015
PepShell : visualization of conformational proteomics data
Elien Vandermarliere
Davy Maddelein
Niels Hulstaert
Elisabeth Stes
Michela Di Michele
Kris Gevaert
Edgar Jacoby
Dirk Brehmer
Lennart Martens
A1
Journal Article
in
JOURNAL OF PROTEOME RESEARCH
2015
PeptideShaker enables reanalysis of MS-derived proteomics data sets
Marc Vaudel
Julia M Burkhart
René P Zahedi
Eystein Oveland
Frode S Berven
Albert Sickmann
Lennart Martens
Harald Barsnes
A1
Journal Article
in
NATURE BIOTECHNOLOGY
2015
Phospho-iTRAQ : assessing isobaric labels for the large-scale study of phosphopeptide stoichiometry
Pieter Glibert
Paulien Meert
Katleen Van Steendam
Filip Van Nieuwerburgh
Dieter De Coninck
Lennart Martens
Maarten Dhaenens
Dieter Deforce
A1
Journal Article
in
JOURNAL OF PROTEOME RESEARCH
2015
Phospho-iTRAQ data article : assessing isobaric labels for the large-scale study of phosphopeptide stoichiometry
Pieter Glibert
Paulien Meert
Katleen Van Steendam
Lennart Martens
Dieter Deforce
Maarten Dhaenens
A2
Journal Article
in
DATA IN BRIEF
2015
Pladipus enables universal distributed computing in proteomics bioinformatics
Kenneth Verheggen
Davy Maddelein
Niels Hulstaert
Lennart Martens
Harald Barsnes
Marc Vaudel
A1
Journal Article
in
JOURNAL OF PROTEOME RESEARCH
2015
Ryanodine receptors are targeted by anti-apoptotic Bcl-X-L involving its BH4 domain and Lys87 from its BH3 domain
Tim Vervliet
Irma Lemmens
Elien Vandermarliere
Elke Decrock
Hristina Ivanova
Giovanni Monaco
Vincenzo Sorrentino
Nael Nadif Kasri
Ludwig Missiaen
Lennart Martens
et al.
A1
Journal Article
in
SCIENTIFIC REPORTS
2015
Scop3D : three-dimensional visualization of sequence conservation
Tessa Vermeire
Stijn Vermaere
Bert Schepens
Xavier Saelens
Steven Van Gucht
Lennart Martens
Elien Vandermarliere
A1
Journal Article
in
PROTEOMICS
2015
Structural investigation of B-Raf paradox breaker and inducer inhibitors
Rohit Arora
Michela Di Michele
Elisabeth Stes
Elien Vandermarliere
Lennart Martens
Kris Gevaert
Erika Van Heerde
Joannes TM Linders
Dirk Brehmer
Edgar Jacoby
et al.
A1
Journal Article
in
JOURNAL OF MEDICINAL CHEMISTRY
2015
Summarization vs. peptide-based models in label-free quantitative proteomics : performance, pitfalls, and data analysis guidelines
Ludger Goeminne
Andrea Argentini
Lennart Martens
Lieven Clement
A1
Journal Article
in
JOURNAL OF PROTEOME RESEARCH
2015
The MetaProteomeAnalyzer : a powerful open-source software suite for metaproteomics data analysis and interpretation
Thilo Muth
Alexander Behne
Robert Heyer
Fabian Kohrs
Dirk Benndorf
Marcus Hoffmann
Miro Lehteva
Udo Reichl
Lennart Martens
Erdmann Rapp
A1
Journal Article
in
JOURNAL OF PROTEOME RESEARCH
2015
The iceLogo web server and SOAP service for determining protein consensus sequences
Davy Maddelein
Niklaas Colaert
Iain Buchanan
Niels Hulstaert
Kris Gevaert
Lennart Martens
A1
Journal Article
in
NUCLEIC ACIDS RESEARCH
2015
Viewing the proteome : how to visualize proteomics data?
Eystein Oveland
Thilo Muth
Erdmann Rapp
Lennart Martens
Frode S Berven
Harald Barsnes
A1
Journal Article
in
PROTEOMICS
2015
iMonDB : mass spectrometry quality control through instrument monitoring
Wout Bittremieux
Hanny Willems
Pieter Kelchtermans
Lennart Martens
Kris Laukens
Dirk Valkenborg
A1
Journal Article
in
JOURNAL OF PROTEOME RESEARCH
2015
sORFs.org : a repository of small ORFs identified by ribosome profiling
Volodimir Olexiouk
Jeroen Crappé
Steven Verbruggen
Kenneth Verheggen
Lennart Martens
Gerben Menschaert
A1
Journal Article
in
NUCLEIC ACIDS RESEARCH
2015
2014
DeNovoGUI: an open source graphical user interface for de novo sequencing of tandem mass spectra
Thilo Muth
Lisa Weilnböck
Erdmann Rapp
Christian G Huber
Lennart Martens
Marc Vaudel
Harald Barsnes
A1
Journal Article
in
JOURNAL OF PROTEOME RESEARCH
2014
Distributed computing and data storage in proteomics: many hands make light work, and a stronger memory
Kenneth Verheggen
Harald Barsnes
Lennart Martens
A1
Journal Article
in
PROTEOMICS
2014
Informaticawetenschappen in het leerplichtonderwijs
Giovanni Samaey
Jacques Van Remortel
Hugues Bersini
Yvan Bruynseraede
Jan Dekelver
Frederik De Laender
Dirk Deschoolmeester
Paul Gistelinck
Bern Martens
Lennart Martens
et al.
Theatrereview
2014
Introduction to opportunities and pitfalls in functional mass spectrometry based proteomics
Marc Vaudel
Albert Sickmann
Lennart Martens
A1
Journal Article
in
BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS
2014
Machine learning applications in proteomics research: how the past can boost the future
Pieter Kelchtermans
Wout Bittremieux
Kurt De Grave
Sven Degroeve
Jan Ramon
Kris Laukens
Dirk Valkenborg
Harald Barsnes
Lennart Martens
A1
Journal Article
in
PROTEOMICS
2014
ProteomeXchange provides globally coordinated proteomics data submission and dissemination
Juan A Vizcaino
Eric W Deutsch
Rui Wang
Attila Csordas
Florian Reisinger
Daniel Ríos
José A Dianes
Zhi Sun
Terry Farrah
Nuno Bandeira
et al.
A1
Journal Article
in
NATURE BIOTECHNOLOGY
2014
Shedding light on black boxes in protein identification
Marc Vaudel
A Saskia Venne
Frode S Berven
René P Zahedi
Lennart Martens
Harald Barsnes
A1
Journal Article
in
PROTEOMICS
2014
Time-resolved characterization of cAMP/PKA-dependent signaling reveals that platelet inhibition is a concerted process involving multiple signaling pathways
Florian Beck
Jörg Geiger
Stepan Gambaryan
Johannes Veit
Marc Vaudel
Peter Nollau
Oliver Kohlbacher
Lennart Martens
Ulrich Walter
Albert Sickmann
et al.
A1
Journal Article
in
BLOOD
2014
Toward more transparent and reproducible omics studies through a common metadata checklist and data publications
Eugene Kolker
Vural Özdemir
Lennart Martens
William Hancock
Gordon Anderson
Nathaniel Anderson
Sukru Aynacioglu
Ancha Baranova
Shawn R Campagna
Rui Chen
et al.
Editorial material
2014
Unraveling the specificities of the different human methionine sulfoxide reductases
Elien Vandermarliere
Bart Ghesquière
Veronique Jonckheere
Kris Gevaert
Lennart Martens
A1
Journal Article
in
PROTEOMICS
2014
jqcML: an open-source Java API for mass spectrometry quality control data in the qcML format
Wout Bittremieux
Pieter Kelchtermans
Dirk Vakenborg
Lennart Martens
Kris Laukens
A1
Journal Article
in
JOURNAL OF PROTEOME RESEARCH
2014
qcML: an exchange format for quality control metrics from mass spectrometry experiments
Mathias Walzer
Lucia Espona Pernas
Sara Nasso
Wout Bittremieux
Sven Nahnsen
Pieter Kelchtermans
Peter Pichler
Henk WP van den Toorn
An Staes
Jonathan Vandenbussche
et al.
A1
Journal Article
in
MOLECULAR & CELLULAR PROTEOMICS
2014
2013
About dice, bouldering, and team empowerment: running the CompOmics group at VIB and Ghent University, Belgium
Lennart Martens
A1
Journal Article
in
PLOS COMPUTATIONAL BIOLOGY
2013
Asn₃, a reliable, robust, and universal lock mass for improved accuracy in LC-MS and LC-MS/MS
An Staes
Jonathan Vandenbussche
Hans Demol
Marc Goethals
Sule Yilmaz-Rumpf
Niels Hulstaert
Sven Degroeve
Pieter Kelchtermans
Lennart Martens
Kris Gevaert
A1
Journal Article
in
ANALYTICAL CHEMISTRY
2013
Bringing proteomics into the clinic: the need for the field to finally take itself seriously
Lennart Martens
A1
Journal Article
in
PROTEOMICS CLINICAL APPLICATIONS
2013
CellMissy: a tool for management, storage and analysis of cell migration data produced in wound healing-like assays
Paola Masuzzo
Niels Hulstaert
Lynn Huyck
Christophe Ampe
Marleen Van Troys
Lennart Martens
A1
Journal Article
in
BIOINFORMATICS
2013
Computational proteomics pitfalls and challenges: HavanaBioinfo 2012 Workshop report
Yasset Perez-Riverol
Henning Hermjakob
Oliver Kohlbacher
Lennart Martens
David Creasy
Jürgen Cox
Felipe Leprevost
Baozhen Paul Shan
Violeta I Pérez-Nueno
Michal Blazejczyk
et al.
A1
Journal Article
in
JOURNAL OF PROTEOMICS
2013
Crowdsourcing in proteomics: public resources lead to better experiments
Harald Barsnes
Lennart Martens
A1
Journal Article
in
AMINO ACIDS
2013
D-score: a search engine independent MD-score
Marc Vaudel
Daniela Breiter
Florian Beck
Jörg Rahnenführer
Lennart Martens
René P Zahedi
A1
Journal Article
in
PROTEOMICS
2013
Delsa workshop IV : launching the Quantified Human Initiative
Elizabeth Stewart
Todd Smith
Andrea De Souza
Jack Faris
Lennart Martens
Sophie Mohin
Vural Ozdemir
Courtney MacNealy-Koch
Eugene Kolker
A1
Journal Article
in
BIG DATA
2013
Early targets of MIR-34A in neuroblastoma
P De Antonellis
M Carotenuto
G De Vita
Jonathan Vandenbussche
C Medaglia
J Vandesopele
P Mestdagh
Lennart Martens
An Staes
Kathleen Moens
et al.
C3
Conference
2013
Getting intimate with trypsin, the leading protease in proteomics
Elien Vandermarliere
Michael Mueller
Lennart Martens
A1
Journal Article
in
MASS SPECTROMETRY REVIEWS
2013
In praise of open research measures
Eugene Kolker
Ilkay Altintas
Philip Bourne
Jack Faris
Geoffrey Fox
Dmitrij Frishman
Christy Geraci
William Hancock
Biaoyang Lin
Doron Lancet
et al.
A1
Journal Article
in
NATURE
2013
LNCipedia 2.0: a database for annotated human lncRNA transcript sequences and structures
Pieter-Jan Volders
Kenny Helsens
Xiaowei Wang
Lennart Martens
Kris Gevaert
Jo Vandesompele
Pieter Mestdagh
C3
Conference
2013
LNCipedia 2.0: a database for annotated human lncRNA transcript sequences and structures
Pieter-Jan Volders
Kenny Helsens
Xiaowei Wang
Lennart Martens
Kris Gevaert
Jo Vandesompele
Pieter Mestdagh
C3
Conference
2013
LNCipedia : a database for annotated human lncRNA transcript sequences and structures
Pieter-Jan Volders
Kenny Helsens
Xiaowei Wang
Björn Menten
Lennart Martens
Kris Gevaert
Jo Vandesompele
Pieter Mestdagh
A1
Journal Article
in
NUCLEIC ACIDS RESEARCH
2013
LNCipedia: a database for annotated human lncRNA transcript sequences and structures
Pieter-Jan Volders
Kenny Helsens
Xiaowei Wang
Lennart Martens
Kris Gevaert
Jo Vandesompele
Pieter Mestdagh
C3
Conference
2013
MS²PIP: a tool for MS/MS peak intensity prediction
Sven Degroeve
Lennart Martens
A1
Journal Article
in
BIOINFORMATICS
2013
PiTRAQ, a strategy to simultaneously correlate protein expression and phosphorylation stoichiometry between different samples: evaluation on different mass spectrometers
Pieter Glibert
Maarten Dhaenens
Paulien Meert
Niklaas Colaert
Filip Van Nieuwerburgh
Lennart Martens
Dieter Deforce
C3
Conference
2013
Predicting tryptic cleavage from proteomics data using decision tree ensembles
Thomas Fannes
Elien Vandermarliere
Leander Schietgat
Sven Degroeve
Lennart Martens
Jan Ramon
A1
Journal Article
in
JOURNAL OF PROTEOME RESEARCH
2013
Pride-asap: automatic fragment ion annotation of identified PRIDE spectra
Niels Hulstaert
Florian Reisinger
Jonathan Rameseder
Harald Barsnes
Juan Antonio Vizcaíno
Lennart Martens
A1
Journal Article
in
JOURNAL OF PROTEOMICS
2013
Protein structure as a means to triage proposed PTM sites
Elien Vandermarliere
Lennart Martens
A1
Journal Article
in
PROTEOMICS
2013
ProteoCloud: a full-featured open source proteomics cloud computing pipeline
Thilo Muth
Julian Peters
Jonathan Blackburn
Erdmann Rapp
Lennart Martens
A1
Journal Article
in
JOURNAL OF PROTEOMICS
2013
Proteome-derived peptide libraries to study the substrate specificity profiles of carboxypeptidases
Sebastian Tanco
Julia Lorenzo
Javier Garcia-Pardo
Sven Degroeve
Lennart Martens
Francesc Xavier Aviles
Kris Gevaert
Petra Van Damme
A1
Journal Article
in
MOLECULAR & CELLULAR PROTEOMICS
2013
Resilience in the proteomics data ecosystem: how the field cares for its data
Lennart Martens
A1
Journal Article
in
PROTEOMICS
2013
Searching for a needle in a stack of needles: challenges in metaproteomics data analysis
Thilo Muth
Dirk Benndorf
Udo Reichl
Erdmann Rapp
Lennart Martens
A1
Journal Article
in
MOLECULAR BIOSYSTEMS
2013
The Online Protein Processing Resource (TOPPR) : a database and analysis platform for protein processing events
Niklaas Colaert
Davy Maddelein
Francis Impens
Petra Van Damme
Kim Plasman
Kenny Helsens
Niels Hulstaert
Joël Vandekerckhove
Kris Gevaert
Lennart Martens
A1
Journal Article
in
NUCLEIC ACIDS RESEARCH
2013
2012
A complex standard for protein identification, designed by evolution
Marc Vaudel
Julia M Burkhart
Daniela Breiter
René P Zahedi
Albert Sickmann
Lennart Martens
A1
Journal Article
in
JOURNAL OF PROTEOME RESEARCH
2012
Chromatographic retention time prediction for posttranslationally modified peptides
Luminita Moruz
An Staes
Joseph M Foster
Maria Hatzou
Evy Timmerman
Lennart Martens
Lukas Käll
A1
Journal Article
in
PROTEOMICS
2012
Current methods for global proteome identification
Marc Vaudel
Albert Sickmann
Lennart Martens
A1
Journal Article
in
EXPERT REVIEW OF PROTEOMICS
2012
Detailed analysis of the blood platelet proteome through the use of innovative bioinformatics methods for protein identification, quantification and post-translational modification localization
Marc Vaudel
Lennart Martens
Albert Sickmann
Dissertation
2012
Enabling computational proteomics by public and local data management systems
Kenny Helsens
Lennart Martens
A1
Journal Article
in
CIRCULATION-CARDIOVASCULAR GENETICS
2012
Evaluation of a strategy for parallel protein phosphorylation and expression analysis
Pieter Glibert
Maarten Dhaenens
Paulien Meert
Niklaas Colaert
Filip Van Nieuwerburgh
Lennart Martens
Dieter Deforce
C3
Conference
2012
Integral quantification accuracy estimation for reporter ion-based quantitative proteomics (iQuARI)
Marc Vaudel
Julia M Burkhart
Sonja Radau
René P Zahedi
Lennart Martens
Albert Sickmann
A1
Journal Article
in
JOURNAL OF PROTEOME RESEARCH
2012
Lncipedia: a novel database for annotated lncRNA sequences and structures
Pieter-Jan Volders
Kenny Helsens
Xiaowei Wang
Lennart Martens
Kris Gevaert
Jo Vandesompele
Pieter Mestdagh
C3
Conference
2012
PRIDE Inspector: a tool to visualize and validate MS proteomics data
Rui Wang
Antonio Fabregat
Daniel Ríos
David Ovelleiro
Joseph M Foster
Richard G Côté
Johannes Griss
Attila Csordas
Yasset Perez-Riverol
Florian Reisinger
et al.
A1
Journal Article
in
NATURE BIOTECHNOLOGY
2012
Sigpep: calculating unique peptide signature transition sets in a complete proteome background
Kenny Helsens
Michael Mueller
Niels Hulstaert
Lennart Martens
A1
Journal Article
in
PROTEOMICS
2012
The HUPO initiative on Model Organism Proteomes, iMOP
Alexandre ME Jones
Ruedi Aebersold
Christian H Ahrens
Rolf Apweiler
Katja Baerenfaller
Mark Baker
Emøke Bendixen
Steve Briggs
Philip Brownridge
Erich Brunner
et al.
A1
Journal Article
in
PROTEOMICS
2012
The PRoteomics IDEntification (PRIDE) converter 2 framework: an improved suite of tools to facilitate data submission to the PRIDE database and the ProteomeXchange consortium
Richard G Côté
Johannes Griss
José A Dianes
Rui Wang
James C Wright
Henk WP van den Toorn
Bas van Breukelen
Albert JR Heck
Niels Hulstaert
Lennart Martens
et al.
A1
Journal Article
in
MOLECULAR & CELLULAR PROTEOMICS
2012
The effect of peptide identification search algorithms on MS2-based label-free protein quantification
Sven Degroeve
An Staes
Pieter-Jan De Bock
Lennart Martens
A1
Journal Article
in
OMICS-A JOURNAL OF INTEGRATIVE BIOLOGY
2012
The first comprehensive and quantitative analysis of human platelet protein composition allows the comparative analysis of structural and functional pathways
Julia M Burkhart
Marc Vaudel
Stepan Gambaryan
Sonja Radau
Ulrich Walter
Lennart Martens
Jörg Geiger
Albert Sickmann
René P Zahedi
A1
Journal Article
in
BLOOD
2012
Towards a human proteomics atlas
Giulia Gonnelli
Niels Hulstaert
Sven Degroeve
Lennart Martens
A1
Journal Article
in
ANALYTICAL AND BIOANALYTICAL CHEMISTRY
2012
TraML: a standard format for exchange of selected reaction monitoring transition lists
Eric W Deutsch
Matthew Chambers
Steffen Neumann
Fredrik Levander
Pierre-Alain Binz
Jim Shofstahl
David S Campbell
Luis Mendoza
David Ovelleiro
Kenny Helsens
et al.
A1
Journal Article
in
MOLECULAR & CELLULAR PROTEOMICS
2012
iTRAQ data interpretation
Marc Vaudel
Julia Maria Burkhart
René Peiman Zahedi
Lennart Martens
Albert Sickmann
Bookchapter
in
Quantitative methods in proteomics
2012
2011
'4D Biology for health and disease' workshop report
Jan-Pieter Abrahams
Rolf Apweiler
Rudi Balling
Michela G Bertero
Janusz M Bujnicki
Naomi E Chayen
Patrick Chène
Gary L Corthals
Tomasz Dyląg
Friedrich Förster
et al.
A1
Journal Article
in
NEW BIOTECHNOLOGY
2011
A case study on the comparison of different software tools for automated quantification of peptides
Niklaas Colaert
Joël Vandekerckhove
Lennart Martens
Kris Gevaert
Bookchapter
in
Gel-free proteomics : methods and protocols
2011
A comparison of MS2-based label-free quantitative proteomic techniques with regards to accuracy and precision
Niklaas Colaert
Joël Vandekerckhove
Kris Gevaert
Lennart Martens
A1
Journal Article
in
PROTEOMICS
2011
A global analysis of peptide fragmentation variability
Harald Barsnes
Ingvar Eidhammer
Lennart Martens
A1
Journal Article
in
PROTEOMICS
2011
A posteriori quality control for the curation and reuse of public proteomics data
Joseph M Foster
Sven Degroeve
Laurent Gatto
Matthieu Visser
Rui Wang
Johannes Griss
Rolf Apweiler
Lennart Martens
A1
Journal Article
in
PROTEOMICS
2011
A reproducibility-based evaluation procedure for quantifying the differences between MS/MS peak intensity normalization methods
Sven Degroeve
Niklaas Colaert
Joël Vandekerckhove
Kris Gevaert
Lennart Martens
A1
Journal Article
in
PROTEOMICS
2011
Analysis of the resolution limitations of peptide identification algorithms
Niklaas Colaert
Sven Degroeve
Kenny Helsens
Lennart Martens
A1
Journal Article
in
JOURNAL OF PROTEOME RESEARCH
2011
Bioinformatics analysis of a Saccharomyces cerevisiae N-terminal proteome provides evidence of alternative translation initiation and post-translational N-terminal acetylation
Kenny Helsens
Petra Van Damme
Sven Degroeve
Lennart Martens
Thomas Arnesen
Joël Vandekerckhove
Kris Gevaert
A1
Journal Article
in
JOURNAL OF PROTEOME RESEARCH
2011
Combining quantitative proteomics data processing workflows for greater sensitivity
Niklaas Colaert
Christophe Van Huele
Sven Degroeve
An Staes
Joël Vandekerckhove
Kris Gevaert
Lennart Martens
A1
Journal Article
in
NATURE METHODS
2011
Digging deeper in the data, novel approaches and analysis methods in quantitative peptide-centric proteomics
Niklaas Colaert
Kris Gevaert
Lennart Martens
Dissertation
2011
N-Terminal combined fractional diagonal chromatographic (COFRADIC) analysis of the human platelet proteome
Francis Impens
Kenny Helsens
Niklaas Colaert
Lennart Martens
Joël Vandekerckhove
Kris Gevaert
Bookchapter
in
Platelet proteomics : principles, analysis, and applications
2011
Peptide identification quality control
Marc Vaudel
Julia M Burkhart
Albert Sickmann
Lennart Martens
Rene P Zahedi
A1
Journal Article
in
PROTEOMICS
2011
Quality control in proteomics
Lennart Martens
Juan Antonio Vizcaino
Roz Banks
Editorial material
2011
RIBAR and xRIBAR: methods for reproducible relative MS/MS-based label-free protein quantification
Niklaas Colaert
Kris Gevaert
Lennart Martens
A1
Journal Article
in
JOURNAL OF PROTEOME RESEARCH
2011
SearchGUI: an open-source graphical user interface for simultaneous OMSSA and X!Tandem searches
Marc Vaudel
Harald Barsnes
Frode S Berven
Albert Sickmann
Lennart Martens
A1
Journal Article
in
PROTEOMICS
2011
compomics-utilities: an open-source Java library for computational proteomics
Harald Barsnes
Marc Vaudel
Niklaas Colaert
Kenny Helsens
Albert Sickmann
Frode S Berven
Lennart Martens
A1
Journal Article
in
BMC BIOINFORMATICS
2011
iTRAQ protein quantification: a quality-controlled workflow
Julia M Burkhart
Marc Vaudel
ReneP Zahedi
Lennart Martens
Albert Sickmann
A1
Journal Article
in
PROTEOMICS
2011
jTraML: an open source Java API for TraML, the PSI standard for sharing SRM transitions
Kenny Helsens
Mi-Youn Brusniak
Eric Deutsch
Robert L Moritz
Lennart Martens
A1
Journal Article
in
JOURNAL OF PROTEOME RESEARCH
2011
mzML: a community standard for mass spectrometry data
Lennart Martens
Matthew Chambers
Marc Sturm
Darren Kessner
Fredrik Levander
Jim Shofstahl
Wilfred H Tang
Andreas Ropp
Steffen Neumann
Angel D Pizarro
et al.
A1
Journal Article
in
MOLECULAR & CELLULAR PROTEOMICS
2011
thermo-msf-parser: an open source Java library to parse and visualize Thermo Proteome Discoverer msf files
Niklaas Colaert
Harald Barsnes
Marc Vaudel
Kenny Helsens
Evy Timmerman
Albert Sickmann
Kris Gevaert
Lennart Martens
A1
Journal Article
in
JOURNAL OF PROTEOME RESEARCH
2011
2010
A report on the ESF workshop on quality control in proteomics
Lennart Martens
Editorial material
2010
FragmentationAnalyzer: an open-source tool to analyze MS/MS fragmentation data
Harald Barsnes
Ingvar Eidhammer
Lennart Martens
A1
Journal Article
in
PROTEOMICS
2010
High-throughput proteomics and bioinformatics : joined at the hip
Lennart Martens
Henning Hermjakob
Editorial material
2010
Increasing the specificity and the sensitivity in peptide centric proteomics
Kenny Helsens
Kris Gevaert
Lennart Martens
Dissertation
2010
OLS Dialog : an open-source front end to the Ontology Lookup Service
Harald Barsnes
Richard G Côté
Ingvar Eidhammer
Lennart Martens
A1
Journal Article
in
BMC BIOINFORMATICS
2010
Peptide and protein quantification: A map of the minefield
Marc Vaudel
Albert Sickmann
Lennart Martens
A1
Journal Article
in
PROTEOMICS
2010
Proteomics data repositories: providing a safe haven for your data and acting as a springboard for further research
Juan Antonio Vizcaíno
Joseph M Foster
Lennart Martens
A1
Journal Article
in
JOURNAL OF PROTEOMICS
2010
The Ontology Lookup Service : bigger and better
Richard Côté
Florian Reisinger
Lennart Martens
Harald Barsnes
Juan Antonio Vizcaíno
Henning Hermjakob
A1
Journal Article
in
NUCLEIC ACIDS RESEARCH
2010
The Proteomics Identifications database : 2010 update
Juan Antonio Vizcaíno
Richard Côté
Florian Reisinger
Harald Barsnes
Joseph M Foster
Jonathan Rameseder
Henning Hermjakob
Lennart Martens
A1
Journal Article
in
NUCLEIC ACIDS RESEARCH
2010
XTandem parser: an open-source library to parse and analyse X!Tandem MS/MS search results
Thilo Muth
Marc Vaudel
Harald Barsnes
Lennart Martens
Albert Sickmann
A1
Journal Article
in
PROTEOMICS
2010
jTraqX: a free, platform independent tool for isobaric tag quantitation at the protein level
Thilo Muth
Daniela Keller
Stephanie Michaela Puetz
Lennart Martens
Albert Sickmann
Andreas M Boehm
A1
Journal Article
in
PROTEOMICS
2010
jmzML, an open-source Java API for mzML, the PSI standard for MS data
Richard G Côté
Florian Reisinger
Lennart Martens
A1
Journal Article
in
PROTEOMICS
2010
ms_lims, a simple yet powerful open source laboratory information management system for MS-driven proteomics
Kenny Helsens
Niklaas Colaert
Harald Barsnes
Thilo Muth
Kristian Flikka
An Staes
Evy Timmerman
Steffi Wortelkamp
Albert Sickmann
Joël Vandekerckhove
et al.
A1
Journal Article
in
PROTEOMICS
2010
2009
A HUPO test sample study reveals common problems in mass spectrometry-based proteomics
Alexander W Bell
Eric W Deutsch
Catherine E Au
Robert E Kearney
Ron Beavis
Salvatore Sechi
Tommy Nilsson
John J M Bergeron
- HUPO Test Sample Working Group
Lennart Martens
A1
Journal Article
in
NATURE METHODS
2009
A guide to the Proteomics Identifications Database proteomics data repository
JA Vizcaino
R Cote
F Reisinger
JM Foster
M Mueller
J Rameseder
H Hermjakob
Lennart Martens
A1
Journal Article
in
PROTEOMICS
2009
Charting online OMICS resources: a navigational chart for clinical researchers
Juan Antonio Vizca
Michael Mueller
Henning Hermjakob
Lennart Martens
A1
Journal Article
in
PROTEOMICS CLINICAL APPLICATIONS
2009
Database on Demand: an online tool for the custom generation of FASTA-formatted sequence databases
Florian Reisinger
Lennart Martens
A1
Journal Article
in
PROTEOMICS
2009
Getting a grip on proteomics data: Proteomics Data Collection (ProDaC)
Martin Eisenacher
Lennart Martens
Michael Kohl
Harald Barsnes
Kenny Helsens
Jari Häkkinen
Fredrik Levander
Ruedi Aebersold
Joël Vandekerckhove
Michael J. Dunn
et al.
A1
Journal Article
in
PROTEOMICS
2009
Improved visualization of protein consensus sequences by iceLogo
Niklaas Colaert
Kenny Helsens
Lennart Martens
Joël Vandekerckhove
Kris Gevaert
A1
Journal Article
in
NATURE METHODS
2009
OMSSA Parser: an open-source library to parse and extract data from OMSSA MS/MS search results
Harald Barsnes
Steffen Huber
Albert Sickmann
Ingvar Eidhammer
Lennart Martens
A1
Journal Article
in
PROTEOMICS
2009
PRIDE Converter: making proteomics data-sharing easy
Harald Barsnes
Juan Antonio Vizcaíno
Ingvar Eidhammer
Lennart Martens
A1
Journal Article
in
NATURE BIOTECHNOLOGY
2009
Proteomics data collection : 4th ProDaC workshop: 15 August 2008, Amsterdam, The Netherlands
Martin Eisenacher
Michael Kohl
Lennart Martens
Harald Barsnes
Tanja Hardt
Fredrik Levander
Jari Häkkinen
Rolf Apweiler
Helmut E Meyer
Christian Stephan
Editorial material
2009
Proteomics data collection: 5th ProDaC workshop: 4 March 2009, Kolympari, Crete, Greece
Martin Eisenacher
Lennart Martens
Harald Barsnes
Tanja Hardt
Michael Kohl
Jari Häkkinen
Rolf Apweiler
Helmut E Meyer
Christian Stephan
A1
Journal Article
in
PROTEOMICS
2009
The PSI semantic validator: a framework to check MIAPE compliance of proteomics data
Luisa Montecchi-Palazzi
Samuel Kerrien
Florian Reisinger
Bruno Aranda
Andrew R Jones
Lennart Martens
Henning Hermjakob
A1
Journal Article
in
PROTEOMICS
2009
Toward a successful clinical neuroproteomics : the 11th HUPO Brain Proteome Project Workshop 3 March, 2009, Kolymbari, Greece
Young Hye Kim
Katrin Marcus
Lea Tenenholz Grinberg
Heike Goehler
Jens Wiltfang
Christian Stephan
Martin Eisenacher
Tanja Hardt
Lennart Martens
Michael J Dunn
et al.
A1
Journal Article
in
PROTEOMICS CLINICAL APPLICATIONS
2009
2008
6th HUPO Annual World Congress : Proteomics Standards Initiative Workshop 6-10 October 2007, Seoul, Korea
Sandra Orchard
Lennart Martens
Joshua Tasman
Pierre-Alain Binz
Juan Pablo Albar
Henning Hermjakob
Editorial material
2008
Analysis of the experimental detection of central nervous system-related genes in human brain and cerebrospinal fluid datasets
Michael Mueller
Juan Antonio Vizcaíno
Philip Jones
Richard Côté
David Thorneycroft
Rolf Apweiler
Henning Hermjakob
Lennart Martens
A1
Journal Article
in
PROTEOMICS
2008
Analyzing large-scale proteomics projects with latent semantic indexing
Sebastian Klie
Lennart Martens
Juan Antonio Vizcaíno
Richard Côté
Phil Jones
Rolf Apweiler
Alexander Hinneburg
Henning Hermjakob
A1
Journal Article
in
JOURNAL OF PROTEOME RESEARCH
2008
Human Proteinpedia enables sharing of human protein data
Suresh Mathivanan
Mukhtar Ahmed
Natalie G Ahn
Hainard Alexandre
Ramars Amanchy
Philip C Andrews
Joel S Bader
Brian M Balgley
Marcus Bantscheff
Keiryn L Bennett
et al.
A1
Journal Article
in
NATURE BIOTECHNOLOGY
2008
OMSSAGUI: an open-source user interface component to configure and run the OMSSA search engine
Ravi Tharakan
Lennart Martens
Jennifer E Van Eyk
David R Graham
A1
Journal Article
in
PROTEOMICS
2008
PRIDE : new developments and new datasets
Philip Jones
Richard G Côté
Sang Yun Cho
Sebastian Klie
Lennart Martens
Antony F Quinn
David Thorneycroft
Henning Hermjakob
A1
Journal Article
in
NUCLEIC ACIDS RESEARCH
2008
Peptizer: a tool for assessing false positive peptide identifications and manually validating selected results
Kenny Helsens
Evy Timmerman
Joël Vandekerckhove
Kris Gevaert
Lennart Martens
A1
Journal Article
in
MOLECULAR & CELLULAR PROTEOMICS
2008
Proteomics data collection : 2nd ProDaC workshop : 5 October 2007, Seoul, Korea
Martin Eisenacher
Tanja Hardt
Michael Hamacher
Lennart Martens
Jari Häkkinen
Fredrik Levander
Rolf Apweiler
Helmut E Meyer
Christian Stephan
A1
Journal Article
in
PROTEOMICS
2008
Proteomics data collection: 3rd ProDaC workshop April 22nd 2008, Toledo, Spain
Martin Eisenacher
Tanja Hardt
Lennart Martens
Jari Häkkinen
Rolf Apweiler
Michael Hamacher
Helmut E Meyer
Christian Stephan
A1
Journal Article
in
PROTEOMICS
2008
The HUPO Brain Proteome project wish list : summary of the 9th HUPO BPP Workshop 9-10 January 2008, Barbados
Michael Hamacher
Martin Eisenacher
Florian Tribl
Christian Stephan
Katrin Marcus
Tanja Hardt
Jens Wiltfang
Lennart Martens
Dominic Desiderio
Howard Gutstein
et al.
A1
Journal Article
in
PROTEOMICS
2008
The Ontology Lookup Service : more data and better tools for controlled vocabulary queries
Richard G Côté
Philip Jones
Lennart Martens
Rolf Apweiler
Henning Hermjakob
A1
Journal Article
in
NUCLEIC ACIDS RESEARCH
2008
2007
A la carte proteomics with an emphasis on gel-free techniques
Kris Gevaert
Petra Van Damme
Bart Ghesquière
Francis Impens
Lennart Martens
Kenny Helsens
Joël Vandekerckhove
A1
Journal Article
in
PROTEOMICS
2007
Annotating the human proteome: beyond establishing a parts list
Michael Mueller
Lennart Martens
Rolf Apweiler
A1
Journal Article
in
BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS
2007
High performance proteomics : 7th HUPO Brain Proteome project workshop, March 7-9, 2007, Wellcome Trust Conference Centre, Hinxton, UK
Michael Hamacher
Christian Stephan
Martin Eisenacher
Piotr Lewczuk
Jens Wiltfang
Lennart Martens
Juan Antonio Vizcaíno
Kyung-Hoon Kwon
Jong Shin Yoo
Young Mok Park
et al.
Editorial material
2007
Human Proteome Organization Proteomics Standards Initiative: data standardization, a view on developments and policy
Lennart Martens
Sandra Orchard
Rolf Apweiler
Henning Hermjakob
A1
Journal Article
in
MOLECULAR & CELLULAR PROTEOMICS
2007
Implementation and application of a versatile clustering tool for tandem mass spectrometry data
Kristian Flikka
Jeroen Meukens
Kenny Helsens
Joël Vandekerckhove
Ingvar Eidhammer
Kris Gevaert
Lennart Martens
A1
Journal Article
in
PROTEOMICS
2007
Large-scale identification of N-terminal peptides in the halophilic archaea Halobacterium salinarum and Natronomonas pharaonis
Michalis Aivaliotis
Kris Gevaert
Michaela Falb
Andreas Tebbe
Kosta Konstantinidis
Birgit Bisle
Christian Klein
Lennart Martens
An Staes
Evy Timmerman
et al.
A1
Journal Article
in
JOURNAL OF PROTEOME RESEARCH
2007
MascotDatfile: an open-source library to fully parse and analyse MASCOT MS/MS search results
Kenny Helsens
Lennart Martens
Joël Vandekerckhove
Kris Gevaert
A1
Journal Article
in
PROTEOMICS
2007
Proteomics data collection : the 1st ProDaC workshop: 26 April 2007, Ecole Normale Supérieur, Lyon, France
Martin Eisenacher
Tanja Hardt
Michael Hamacher
Lennart Martens
Jari Häkkinen
Fredrik Levander
Rolf Apweiler
Helmut E Meyer
Christian Stephan
A1
Journal Article
in
PROTEOMICS
2007
Proteomics data validation: why all must provide data
Lennart Martens
Henning Hermjakob
A1
Journal Article
in
MOLECULAR BIOSYSTEMS
2007
Proteomics for everyday use : activities of the HUPO Brain Proteome project during the 5th HUPO world congress
Michael Hamacher
Christian Stephan
Martin Eisenacher
Andre van Hall
Katrin Marcus
Lennart Martens
Young Mok Park
Howard B Gutstein
Friedrich Herberg
Helmut E Meyer
Editorial material
2007
The PSI formal document process and its implementation on the PSI website
Juan Antonio Vizcaíno
Lennart Martens
Henning Hermjakob
Randall K Julian
Norman W Paton
A1
Journal Article
in
PROTEOMICS
2007
The Protein Identifier Cross-Referencing (PICR) service : reconciling protein identifiers across multiple source databases
Richard G Côté
Philip Jones
Lennart Martens
Samuel Kerrien
Florian Reisinger
Quan Lin
Rasko Leinonen
Rolf Apweiler
Henning Hermjakob
A1
Journal Article
in
BMC BIOINFORMATICS
2007
The minimum information about a proteomics experiment (MIAPE)
Chris F Taylor
Norman W Paton
Kathryn S Lilley
Pierre-Alain Binz
Randall K, Jr Julian
Andrew R Jones
Weimin Zhu
Rolf Apweiler
Ruedi Aebersold
Eric W Deutsch
et al.
A1
Journal Article
in
NATURE BIOTECHNOLOGY
2007
2006
A comparison of the HUPO Brain Proteome project pilot with other proteomics studies
Lennart Martens
Michael Müller
Christian Stephan
Michael Hamacher
Kai A Reidegeld
Helmut E Meyer
Martin Blüggel
Joël Vandekerckhove
Kris Gevaert
Rolf Apweiler
A1
Journal Article
in
PROTEOMICS
2006
A new functional, chemical proteomics technology to identify purine nucleotide binding sites in complex proteomes
Xavier Hanoulle
Jozef Van Damme
An Staes
Lennart Martens
Marc Goethals
Joël Vandekerckhove
Kris Gevaert
A1
Journal Article
in
JOURNAL OF PROTEOME RESEARCH
2006
Automated reprocessing pipeline for searching heterogeneous mass spectrometric data of the HUPO Brain Proteome project pilot phase
Christian Stephan
Kai A Reidegeld
Michael Hamacher
André van Hall
Katrin Marcus
Chris Taylor
Philip Jones
Michael Müller
Rolf Apweiler
Lennart Martens
et al.
A1
Journal Article
in
PROTEOMICS
2006
Cell_motility : a cross-platform, open source application for the study of cell motion paths
Lennart Martens
Geert Monsieur
Christophe Ampe
Kris Gevaert
Joël Vandekerckhove
A1
Journal Article
in
BMC BIOINFORMATICS
2006
Four stage liquid chromatographic selection of methionyl peptides for peptide-centric proteome analysis: the proteome of human multipotent adult progenitor cells
Kris Gevaert
Jozef Pinxteren
Hans Demol
Koen Hugelier
An Staes
Jozef Van Damme
Lennart Martens
Joël Vandekerckhove
A1
Journal Article
in
JOURNAL OF PROTEOME RESEARCH
2006
Functional annotation of proteins identified in human brain during the HUPO Brain Proteome project pilot study
Michael Mueller
Lennart Martens
Kai A Reidegeld
Michael Hamacher
Christian Stephan
Martin Blüggel
Gerhard Körting
Daniel Chamrad
Christian Scheer
Katrin Marcus
et al.
A1
Journal Article
in
PROTEOMICS
2006
HUPO Brain Proteome Project : summary of the pilot phase and introduction of a comprehensive data reprocessing strategy
Michael Hamacher
Rolf Apweiler
Georg Arnold
Albert Becker
Martin Blüggel
Odile Carrette
Christine Colvis
Michael J Dunn
Thomas Fröhlich
Michael Fountoulakis
et al.
Editorial material
2006
HUPO Brain Proteome Project : summary of the pilot phase and introduction of a comprehensive data reprocessing strategy
Michael Hamacher
Rolf Apweiler
Georg Arnold
Albert Becker
Martin Blüggel
Odile Carrette
Christine Colvis
Michael J. Dunn
Thomas Fröhlich
Michael Fountoulakis
et al.
Correction
2006
Improving the reliability and throughput of mass spectrometry-based proteomics by spectrum quality filtering
Kristian Flikka
Lennart Martens
Joël Vandekerckhove
Kris Gevaert
Ingvar Eidhammer
A1
Journal Article
in
PROTEOMICS
2006
Novel bioinformatics tools assisting targeted peptide-centric proteomics and global proteomics data dissemination
Lennart Martens
J Vandekerckhove
Dissertation
2006
PRIDE : a public repository of protein and peptide identifications for the proteomics community
Philip Jones
Richard G Côté
Lennart Martens
Antony F Quinn
Chris F Taylor
William Derache
Henning Hermjakob
Rolf Apweiler
A1
Journal Article
in
NUCLEIC ACIDS RESEARCH
2006
Proteome-wide characterization of N-glycosylation events by diagonal chromatography
Bart Ghesquière
Jozef Van Damme
Lennart Martens
Joël Vandekerckhove
Kris Gevaert
A1
Journal Article
in
JOURNAL OF PROTEOME RESEARCH
2006
The HUPO Brain Proteome Project
Kai Reidegeld
Hemut Meyer
Christian Stephan
Martin Blüggel
Gerhard Körting
Daniel Chamrad
Christian Scheer
Herbert Thiele
Bruker Daltonik
Chris Taylor
et al.
A2
Journal Article
in
EUROPEAN PHARMACEUTICAL REVIEW
2006
The HUPO Brain Proteome project jamboree: centralised summary of the pilot studies
Michael Hamacher
Christian Stephan
Martin Blüggel
Daniel Chamrad
Gerhard Körting
Lennart Martens
Michael Müller
Henning Hermjakob
David Parkinson
Andrew Dowsey
et al.
A1
Journal Article
in
PROTEOMICS
2006
The power of cooperative investigation: summary and comparison of the HUPO Brain Proteome project pilot study results
Kai A Reidegeld
Michael Müller
Christian Stephan
Martin Blüggel
Michael Hamacher
Lennart Martens
Gerhard Körting
Daniel C Chamrad
David Parkinson
Rolf Apweiler
et al.
A1
Journal Article
in
PROTEOMICS
2006
2005
5th HUPO BPP bioinformatics meeting at the European Bioinformatics Institute in Hinxton, UK : setting the analysis frame
Christian Stephan
Michael Hamacher
Martin Blüggel
Gerhard Körting
Daniel Chamrad
Christian Scheer
Katrin Marcus
Kai A Reidegeld
Christiane Lohaus
Heike Schäfer
et al.
A1
Journal Article
in
PROTEOMICS
2005
Caspase-specific and nonspecific in vivo protein processing during Fas-induced apoptosis
Petra Van Damme
Lennart Martens
Jozef Van Damme
Koen Hugelier
An Staes
Joël Vandekerckhove
Kris Gevaert
A1
Journal Article
in
NATURE METHODS
2005
DBToolkit: processing protein databases for peptide-centric proteomics
Lennart Martens
Joël Vandekerckhove
Kris Gevaert
A1
Journal Article
in
BIOINFORMATICS
2005
Data management and preliminary data analysis in the pilot phase of the HUPO Plasma Proteome project
Marcin Adamski
Thomas Blackwell
Rajasree Menon
Lennart Martens
Henning Hermjakob
Chris Taylor
Gilbert S Omenn
David J States
A1
Journal Article
in
PROTEOMICS
2005
Diagonal reverse-phase chromatography applications in peptide-centric proteomics: ahead of catalogue-omics?
Kris Gevaert
Petra Van Damme
Lennart Martens
Joël Vandekerckhove
A1
Journal Article
in
ANALYTICAL BIOCHEMISTRY
2005
Do we want our data raw?: including binary mass spectrometry data in public proteomics data repositories
Lennart Martens
Alexey I Nesvizhskii
Henning Hermjakob
Marcin Adamski
Gilbert S Omenn
Joël Vandekerckhove
Kris Gevaert
A1
Journal Article
in
PROTEOMICS
2005
Global phosphoproteome analysis on human HepG2 hepatocytes using reversed-phase diagonal LC
Kris Gevaert
An Staes
Jozef Van Damme
Sara De Groot
Koen Hugelier
Hans Demol
Lennart Martens
Marc Goethals
Joël Vandekerckhove
A1
Journal Article
in
PROTEOMICS
2005
PRIDE: The proteomics identification database (vol 5, pg 3537, 2005)
Lennart Martens
Correction
2005
PRIDE: the proteomics identifications database
Lennart Martens
Henning Hermjakob
Philip Jones
Marcin Adamski
Chris Taylor
David States
Kris Gevaert
Joël Vandekerckhove
Rolf Apweiler
A1
Journal Article
in
PROTEOMICS
2005
The human platelet proteome mapped by peptide-centric proteomics: a functional protein profile
Lennart Martens
Petra Van Damme
Jozef Van Damme
An Staes
Evy Timmerman
Bart Ghesquière
Grégoire R Thomas
Joël Vandekerckhove
Kris Gevaert
A1
Journal Article
in
PROTEOMICS
2005
2004
Global differential non-gel proteomics by quantitative and stable labeling of tryptic peptides with oxygen-18
An Staes
Hans Demol
Jozef Van Damme
Lennart Martens
Joël Vandekerckhove
Kris Gevaert
A1
Journal Article
in
JOURNAL OF PROTEOME RESEARCH
2004
Reversible labeling of cysteine-containing peptides allows their specific chromatographic isolation for non-gel proteome studies
Kris Gevaert
Bart Ghesquière
An Staes
Lennart Martens
Jozef Van Damme
Grégoire Thomas
Joël Vandekerckhove
A1
Journal Article
in
PROTEOMICS
2004
2003
Exploring proteomes and analyzing protein processing by mass spectrometric identification of sorted N-terminal peptides
Kris Gevaert
Marc Goethals
Lennart Martens
Jozef Van Damme
An Staes
Grégoire Thomas
Joël Vandekerckhove
A1
Journal Article
in
NATURE BIOTECHNOLOGY
2003
IL-29 Is proteomics heading towards medicine?
Joël Vandekerckhove
Jozef Van Damme
Lennart Martens
Grégoire Thomas
An Staes
Marc Goethals
Bart Ghesquière
Magda Puype
Hans Demol
Kris Gevaert
A2
Journal Article
in
PIGMENT CELL RESEARCH
2003
2002
Chromatographic isolation of methionine-containing peptides for gel-free proteome analysis: identification of more than 800 Escherichia coli proteins
Kris Gevaert
Jozef Van Damme
Marc Goethals
Grégoire Thomas
Bart Hoorelbeke
Hans Demol
Lennart Martens
Magda Puype
An Staes
Joël Vandekerckhove
A1
Journal Article
in
MOLECULAR & CELLULAR PROTEOMICS
2002
2001
Protein identification based on matrix assisted laser desorption/ionization-post source decay-mass spectrometry.
Kris Gevaert
Hans Demol
Lennart Martens
B HOORELBEKE
Magda Puype
M GOETHALS
Jozef Van Damme
Stefaan De Boeck
Joël Vandekerckhove
A1
Journal Article
in
ELECTROPHORESIS
2001