Gerben Menschaert

Affiliations

BioBix, Lab of Bioinformatics and Computational Genomics, Department of Mathematical Modelling, Statistics and Bioinformatics, Faculty of Bioscience Engineering, Ghent University, Coupure Links 653, Ghent 9000, Belgium. Electronic address: Gerben.Menschaert@UGent.be.

Publications (21)

mQC: A post-mapping data exploration tool for ribosome profiling.

Computer methods and programs in biomedicine

Avec: Steven Verbruggen ,

CpG Transformer for imputation of single-cell methylomes.

Bioinformatics (Oxford, England)

Avec: Gaetan De Waele , Jim Clauwaert , Willem Waegeman

Functional role of Tet-mediated RNA hydroxymethylcytosine in mouse ES cells and during differentiation.

Nature communications

Avec: Jie Lan , Nicholas Rajan , Martin Bizet , Audrey Penning , Nitesh K Singh , Diana Guallar , Emilie Calonne , Andrea Li Greci , Elise Bonvin , Rachel Deplus , Phillip J Hsu , Sigrid Nachtergaele , Chengjie Ma , Renhua Song , Alejandro Fuentes-Iglesias , Bouchra Hassabi , Pascale Putmans , Frédérique Mies , Justin J L Wong , Jianlong Wang , Miguel Fidalgo , Bifeng Yuan , François Fuks

Proteomics Standards Initiative Extended FASTA Format.

Journal of proteome research

Avec: Pierre-Alain Binz , Jim Shofstahl , Juan Antonio Vizcaíno , Harald Barsnes , Robert J Chalkley , Emanuele Alpi , Karl Clauser , Jimmy K Eng , Lydie Lane , Sean L Seymour , Luis Francisco Hernández Sánchez , Gerhard Mayer , Martin Eisenacher , Yasset Perez-Riverol , Eugene A Kapp , Luis Mendoza , Peter R Baker , Andrew Collins , Tim Van Den Bossche , Eric W Deutsch

A methodology for discovering novel brain-relevant peptides: Combination of ribosome profiling and peptidomics.

Neuroscience research

Avec: Ravi Tharakan , Simion Kreimer , Ceereena Ubaida-Mohien , Joelle Lavoie , Volodimir Olexiouk , Nicholas T Ingolia , Robert N Cole , Koko Ishizuka , Akira Sawa , Leslie G Nucifora

Spectral Prediction Features as a Solution for the Search Space Size Problem in Proteogenomics.

Molecular & cellular proteomics : MCP

Avec: Steven Verbruggen , Siegfried Gessulat , Ralf Gabriels , Anna Matsaroki , Hendrik Van de Voorde , Bernhard Kuster , Sven Degroeve , Lennart Martens , Wim Van Criekinge , Mathias Wilhelm ,

Identification of Non-Canonical Translation Products in

Frontiers in genetics

Avec: Bhavesh S Parmar , Marlies K R Peeters , Kurt Boonen , Ellie C Clark , Geert Baggerman , Liesbet Temmerman

High-quality peptide evidence for annotating non-canonical open reading frames as human proteins.

bioRxiv : the preprint server for biology

Avec: Eric W Deutsch , Leron W Kok , Jonathan M Mudge , Jorge Ruiz-Orera , Ivo Fierro-Monti , Zhi Sun , Jennifer G Abelin , M Mar Alba , Julie L Aspden , Ariel A Bazzini , Elspeth A Bruford , Marie A Brunet , Lorenzo Calviello , Steven A Carr , Anne-Ruxandra Carvunis , Sonia Chothani , Jim Clauwaert , Kellie Dean , Pouya Faridi , Adam Frankish , Norbert Hubner , Nicholas T Ingolia , Michele Magrane , Maria Jesus Martin , Thomas F Martinez , Uwe Ohler , Sandra Orchard , Owen Rackham , Xavier Roucou , Sarah A Slavoff , Eivind Valen , Aaron Wacholder , Jonathan S Weissman , Wei Wu , Zhi Xie , Jyoti Choudhary , Michal Bassani-Sternberg , Juan Antonio Vizcaíno , Nicola Ternette , Robert L Moritz , John R Prensner , Sebastiaan van Heesch

A combined strategy of neuropeptide prediction and tandem mass spectrometry identifies evolutionarily conserved ancient neuropeptides in the sea anemone Nematostella vectensis.

PloS one

Avec: Eisuke Hayakawa , Hiroshi Watanabe , Thomas W Holstein , Geert Baggerman , Liliane Schoofs

DeepRibo: a neural network for precise gene annotation of prokaryotes by combining ribosome profiling signal and binding site patterns.

Nucleic acids research

Avec: Jim Clauwaert , Willem Waegeman

Using the sORFs.Org Database.

Current protocols in bioinformatics

Avec: Volodimir Olexiouk ,

Explainability in transformer models for functional genomics.

Briefings in bioinformatics

Avec: Jim Clauwaert , Willem Waegeman

Downregulation of the FTO m

Nature cancer

Avec: Jana Jeschke , Evelyne Collignon , Clémence Al Wardi , Mohammad Krayem , Martin Bizet , Yan Jia , Soizic Garaud , Zéna Wimana , Emilie Calonne , Bouchra Hassabi , Renato Morandini , Rachel Deplus , Pascale Putmans , Gaurav Dube , Nitesh Kumar Singh , Alexander Koch , Kateryna Shostak , Lara Rizzotto , Robert L Ross , Christine Desmedt , Yacine Bareche , Françoise Rothé , Jacqueline Lehmann-Che , Martine Duterque-Coquillaud , Xavier Leroy , Luis Teixeira , Mingzhou Guo , Patrick A Limbach , Pierre Close , Alain Chariot , Eleonora Leucci , Ghanem Ghanem , Bi-Feng Yuan , Karen Willard-Gallo , Christos Sotiriou , Jean-Christophe Marine , François Fuks

The hunt for sORFs: A multidisciplinary strategy.

Experimental cell research

Avec: Marlies K R Peeters ,

Beyond Genes: Re-Identifiability of Proteomic Data and Its Implications for Personalized Medicine.

Genes

Avec: Kurt Boonen , Kristien Hens , Geert Baggerman , Dirk Valkenborg , Gokhan Ertaylan

Multiple solvent elution, a method to counter the effects of coelution and ion suppression in LC-MS analysis in bottom up proteomics.

Journal of chromatography. B, Analytical technologies in the biomedical and life sciences

Avec: Harshavardhan Budamgunta , Evelyne Maes , Hanny Willems , Karin Schildermans , Ajay Anand Kumar , Kurt Boonen , Geert Baggerman

PROTEOFORMER 2.0: Further Developments in the Ribosome Profiling-assisted Proteogenomic Hunt for New Proteoforms.

Molecular & cellular proteomics : MCP

Avec: Steven Verbruggen , Elvis Ndah , Wim Van Criekinge , Siegfried Gessulat , Bernhard Kuster , Mathias Wilhelm , Petra Van Damme ,

Mitochondrial peptide BRAWNIN is essential for vertebrate respiratory complex III assembly.

Nature communications

Avec: Shan Zhang , Boris Reljić , Chao Liang , Baptiste Kerouanton , Joel Celio Francisco , Jih Hou Peh , Camille Mary , Narendra Suhas Jagannathan , Volodimir Olexiouk , Claire Tang , Gio Fidelito , Srikanth Nama , Ruey-Kuang Cheng , Caroline Lei Wee , Loo Chien Wang , Paula Duek Roggli , Prabha Sampath , Lydie Lane , Enrico Petretto , Radoslaw M Sobota , Suresh Jesuthasan , Lisa Tucker-Kellogg , Bruno Reversade , Lei Sun , David A Stroud , Lena Ho

Ion Mobility Coupled to a Time-of-Flight Mass Analyzer Combined With Fragment Intensity Predictions Improves Identification of Classical Bioactive Peptides and Small Open Reading Frame-Encoded Peptides.

Frontiers in cell and developmental biology

Avec: Marlies K R Peeters , Geert Baggerman , Ralf Gabriels , Elise Pepermans , Kurt Boonen

TIS Transformer: remapping the human proteome using deep learning.

NAR genomics and bioinformatics

Avec: Jim Clauwaert , Zahra McVey , Ramneek Gupta ,

Deep learning to decode sites of RNA translation in normal and cancerous tissues.

bioRxiv : the preprint server for biology

Avec: Jim Clauwaert , Zahra McVey , Ramneek Gupta , Ian Yannuzzi , John R Prensner

Réseau de co-auteurs

Jim Clauwaert 6 collaborations

Geert Baggerman 5 collaborations

Kurt Boonen 4 collaborations

Steven Verbruggen 3 collaborations

Willem Waegeman 3 collaborations

Volodimir Olexiouk 3 collaborations

Marlies K R Peeters 3 collaborations

Martin Bizet 2 collaborations

Emilie Calonne 2 collaborations

Rachel Deplus 2 collaborations

Bouchra Hassabi 2 collaborations

Pascale Putmans 2 collaborations

François Fuks 2 collaborations

Juan Antonio Vizcaíno 2 collaborations

Lydie Lane 2 collaborations

Eric W Deutsch 2 collaborations

Nicholas T Ingolia 2 collaborations

Siegfried Gessulat 2 collaborations

Ralf Gabriels 2 collaborations

Bernhard Kuster 2 collaborations

Wim Van Criekinge 2 collaborations

Mathias Wilhelm 2 collaborations

John R Prensner 2 collaborations

Zahra McVey 2 collaborations

Ramneek Gupta 2 collaborations

Gaetan De Waele 1 collaboration

Jie Lan 1 collaboration

Nicholas Rajan 1 collaboration

Audrey Penning 1 collaboration

Nitesh K Singh 1 collaboration

Diana Guallar 1 collaboration

Andrea Li Greci 1 collaboration

Elise Bonvin 1 collaboration

Phillip J Hsu 1 collaboration

Sigrid Nachtergaele 1 collaboration

Chengjie Ma 1 collaboration

Renhua Song 1 collaboration

Alejandro Fuentes-Iglesias 1 collaboration

Frédérique Mies 1 collaboration

Justin J L Wong 1 collaboration

Jianlong Wang 1 collaboration

Miguel Fidalgo 1 collaboration

Bifeng Yuan 1 collaboration

Pierre-Alain Binz 1 collaboration

Jim Shofstahl 1 collaboration

Harald Barsnes 1 collaboration

Robert J Chalkley 1 collaboration

Emanuele Alpi 1 collaboration

Karl Clauser 1 collaboration

Jimmy K Eng 1 collaboration

Sean L Seymour 1 collaboration

Luis Francisco Hernández Sánchez 1 collaboration

Gerhard Mayer 1 collaboration

Martin Eisenacher 1 collaboration

Yasset Perez-Riverol 1 collaboration

Eugene A Kapp 1 collaboration

Luis Mendoza 1 collaboration

Peter R Baker 1 collaboration

Andrew Collins 1 collaboration

Tim Van Den Bossche 1 collaboration

Ravi Tharakan 1 collaboration

Simion Kreimer 1 collaboration

Ceereena Ubaida-Mohien 1 collaboration

Joelle Lavoie 1 collaboration

Robert N Cole 1 collaboration

Koko Ishizuka 1 collaboration

Akira Sawa 1 collaboration

Leslie G Nucifora 1 collaboration

Anna Matsaroki 1 collaboration

Hendrik Van de Voorde 1 collaboration

Sven Degroeve 1 collaboration

Lennart Martens 1 collaboration

Bhavesh S Parmar 1 collaboration

Ellie C Clark 1 collaboration

Liesbet Temmerman 1 collaboration

Leron W Kok 1 collaboration

Jonathan M Mudge 1 collaboration

Jorge Ruiz-Orera 1 collaboration

Ivo Fierro-Monti 1 collaboration

Zhi Sun 1 collaboration

Jennifer G Abelin 1 collaboration

M Mar Alba 1 collaboration

Julie L Aspden 1 collaboration

Ariel A Bazzini 1 collaboration

Elspeth A Bruford 1 collaboration

Marie A Brunet 1 collaboration

Lorenzo Calviello 1 collaboration

Steven A Carr 1 collaboration

Anne-Ruxandra Carvunis 1 collaboration

Sonia Chothani 1 collaboration

Kellie Dean 1 collaboration

Pouya Faridi 1 collaboration

Adam Frankish 1 collaboration

Norbert Hubner 1 collaboration

Michele Magrane 1 collaboration

Maria Jesus Martin 1 collaboration

Thomas F Martinez 1 collaboration

Uwe Ohler 1 collaboration

Sandra Orchard 1 collaboration

Owen Rackham 1 collaboration

Xavier Roucou 1 collaboration

Sarah A Slavoff 1 collaboration

Eivind Valen 1 collaboration

Aaron Wacholder 1 collaboration

Jonathan S Weissman 1 collaboration

Wei Wu 1 collaboration

Zhi Xie 1 collaboration

Jyoti Choudhary 1 collaboration

Michal Bassani-Sternberg 1 collaboration

Nicola Ternette 1 collaboration

Robert L Moritz 1 collaboration

Sebastiaan van Heesch 1 collaboration

Eisuke Hayakawa 1 collaboration

Hiroshi Watanabe 1 collaboration

Thomas W Holstein 1 collaboration

Liliane Schoofs 1 collaboration

Jana Jeschke 1 collaboration

Evelyne Collignon 1 collaboration

Clémence Al Wardi 1 collaboration

Mohammad Krayem 1 collaboration

Yan Jia 1 collaboration

Soizic Garaud 1 collaboration

Zéna Wimana 1 collaboration

Renato Morandini 1 collaboration

Gaurav Dube 1 collaboration

Nitesh Kumar Singh 1 collaboration

Alexander Koch 1 collaboration

Kateryna Shostak 1 collaboration

Lara Rizzotto 1 collaboration

Robert L Ross 1 collaboration

Christine Desmedt 1 collaboration

Yacine Bareche 1 collaboration

Françoise Rothé 1 collaboration

Jacqueline Lehmann-Che 1 collaboration

Martine Duterque-Coquillaud 1 collaboration

Xavier Leroy 1 collaboration

Luis Teixeira 1 collaboration

Mingzhou Guo 1 collaboration

Patrick A Limbach 1 collaboration

Pierre Close 1 collaboration

Alain Chariot 1 collaboration

Eleonora Leucci 1 collaboration

Ghanem Ghanem 1 collaboration

Bi-Feng Yuan 1 collaboration

Karen Willard-Gallo 1 collaboration

Christos Sotiriou 1 collaboration

Jean-Christophe Marine 1 collaboration

Kristien Hens 1 collaboration

Dirk Valkenborg 1 collaboration

Gokhan Ertaylan 1 collaboration

Harshavardhan Budamgunta 1 collaboration

Evelyne Maes 1 collaboration

Hanny Willems 1 collaboration

Karin Schildermans 1 collaboration

Ajay Anand Kumar 1 collaboration

Elvis Ndah 1 collaboration

Petra Van Damme 1 collaboration

Shan Zhang 1 collaboration

Boris Reljić 1 collaboration

Chao Liang 1 collaboration

Baptiste Kerouanton 1 collaboration

Joel Celio Francisco 1 collaboration

Jih Hou Peh 1 collaboration

Camille Mary 1 collaboration

Narendra Suhas Jagannathan 1 collaboration

Claire Tang 1 collaboration

Gio Fidelito 1 collaboration

Srikanth Nama 1 collaboration

Ruey-Kuang Cheng 1 collaboration

Caroline Lei Wee 1 collaboration

Loo Chien Wang 1 collaboration

Paula Duek Roggli 1 collaboration

Prabha Sampath 1 collaboration

Enrico Petretto 1 collaboration

Radoslaw M Sobota 1 collaboration

Suresh Jesuthasan 1 collaboration

Lisa Tucker-Kellogg 1 collaboration

Bruno Reversade 1 collaboration

Lei Sun 1 collaboration

David A Stroud 1 collaboration

Lena Ho 1 collaboration

Elise Pepermans 1 collaboration

Ian Yannuzzi 1 collaboration