G
Gerben Menschaert
Researcher at Ghent University
Publications - 81
Citations - 3182
Gerben Menschaert is an academic researcher from Ghent University. The author has contributed to research in topics: Ribosome profiling & Proteogenomics. The author has an hindex of 27, co-authored 77 publications receiving 2492 citations. Previous affiliations of Gerben Menschaert include Katholieke Universiteit Leuven & University of Illinois at Urbana–Champaign.
Papers
More filters
Journal ArticleDOI
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 +6 more
TL;DR: Assessment of the protein-coding potential of LNCipedia entries is improved with state-of-the art methods that include large-scale reprocessing of publicly available proteomics data, and a high-confidence set of lncRNA transcripts with low coding potential is defined and made available for download.
Journal ArticleDOI
PubMeth: a cancer methylation database combining text-mining and expert annotation
Maté Ongenaert,Leander Van Neste,Tim De Meyer,Gerben Menschaert,Sofie Bekaert,Wim Van Criekinge +5 more
TL;DR: PubMeth is a cancer methylation database that includes genes that are reported to be methylated in various cancer types that is based on text-mining of Medline/PubMed abstracts, combined with manual reading and annotation of preselected abstracts.
Journal ArticleDOI
Deep Proteome Coverage Based on Ribosome Profiling Aids Mass Spectrometry-based Protein and Peptide Discovery and Provides Evidence of Alternative Translation Products and Near-cognate Translation Initiation Events*
Gerben Menschaert,Wim Van Criekinge,Tineke Notelaers,Alexander Koch,Jeroen Crappé,Kris Gevaert,Petra Van Damme +6 more
TL;DR: This proteogenomic approach constructing a custom protein sequence search space, built from both Swiss-Prot- and RIBO-seq-derived translation products, applicable for MS/MS spectrum identification increases the overall protein identification rate 2.5% as compared with only searching UniProtKB-SwissProt.
Journal ArticleDOI
An update on sORFs.org: a repository of small ORFs identified by ribosome profiling.
TL;DR: This update elaborates on the major improvements implemented since the initial release of sORFs.org, and a full PRIDE-ReSpin pipeline was now released, reprocessing publicly available MS-based proteomics PRIDE datasets, reporting on true translation events.
Journal ArticleDOI
PROTEOFORMER: deep proteome coverage through ribosome profiling and MS integration
Jeroen Crappé,Elvis Ndah,Alexander Koch,Sandra Steyaert,Daria Gawron,Sarah De Keulenaer,Ellen De Meester,Tim De Meyer,Wim Van Criekinge,Petra Van Damme,Gerben Menschaert +10 more
TL;DR: The PROTEOFORMER tool is developed, which automatically processes data of the recently developed ribosome profiling method, resulting in genome-wide visualization of Ribosome occupancy, and enables proteome-wide detection of 5′-extended proteoforms, upstream ORF translation and near-cognate translation start sites.