Yves Van de Peer

Publication Activity (10 Years)

Years Active: 1993-2023
Publications (10 Years): 14

Top Topics

Error Correction

Comparative Genomics

Event Extraction

Top Venues

Nucleic Acids Res.

IEEE ACM Trans. Comput. Biol. Bioinform.

Publications

Fabricio Almeida-Silva, Tao Zhao, Kristian K. Ullrich, M. Eric Schranz, Yves Van de Peer
syntenet: an R/Bioconductor package for the inference and analysis of synteny networks. Bioinform. 39 (1) (2023)
Pieter Meysman, Yvan Saeys, Ehsan Sabaghian, Wout Bittremieux, Yves Van de Peer, Bart Goethals, Kris Laukens
Mining the Enriched Subgraphs for Specific Vertices in a Biological Graph. IEEE ACM Trans. Comput. Biol. Bioinform. 16 (5) (2019)
Arthur Zwaenepoel, Yves Van de Peer
wgd - simple command line tools for the analysis of ancient whole-genome duplications. Bioinform. 35 (12) (2019)
Mahdi Heydari, Giles Miclotte, Yves Van de Peer, Jan Fostier
Illumina error correction near highly repetitive DNA regions improves de novo genome assembly. BMC Bioinform. 20 (1) (2019)
Ine Melckenbeeck, Pieter Audenaert, Thomas Van Parys, Yves Van de Peer, Didier Colle, Mario Pickavet
Optimising orbit counting of arbitrary order by equation selection. BMC Bioinform. 20 (1) (2019)
Mahdi Heydari, Giles Miclotte, Yves Van de Peer, Jan Fostier
BrownieAligner: accurate alignment of Illumina sequencing data to de Bruijn graphs. BMC Bioinform. 19 (1) (2018)
Michiel Van Bel, Tim Diels, Emmelien Vancaester, Lukasz Kreft, Alexander Botzki, Yves Van de Peer, Frederik Coppens, Klaas Vandepoele
PLAZA 4.0: an integrative resource for functional, evolutionary and comparative plant genomics. Nucleic Acids Res. 46 (Database-Issue) (2018)
Thomas Van Parys, Ine Melckenbeeck, Maarten Houbraken, Pieter Audenaert, Didier Colle, Mario Pickavet, Piet Demeester, Yves Van de Peer
A Cytoscape app for motif enumeration with ISMAGS. Bioinform. 33 (3) (2017)
Mahdi Heydari, Giles Miclotte, Piet Demeester, Yves Van de Peer, Jan Fostier
Evaluation of the impact of Illumina error correction tools on de novo genome assembly. BMC Bioinform. 18 (1) (2017)
Yao Yao, Yves Van de Peer
Simulating Biological Complexity through Artificial Evolution. CYBCONF (2017)
Giles Miclotte, Stéphane Plaisance, Stephane Rombauts, Yves Van de Peer, Pieter Audenaert, Jan Fostier
OMSim: a simulator for optical map data. Bioinform. 33 (17) (2017)
Giles Miclotte, Mahdi Heydari, Piet Demeester, Stephane Rombauts, Yves Van de Peer, Pieter Audenaert, Jan Fostier
Jabba: hybrid error correction for long sequencing reads. Algorithms Mol. Biol. 11 (2016)
Suwisa Kaewphan, Sofie Van Landeghem, Tomoko Ohta, Yves Van de Peer, Filip Ginter, Sampo Pyysalo
Cell line name recognition in support of the identification of synthetic lethality in cancer from text. Bioinform. 32 (2) (2016)
Sofie Van Landeghem, Thomas Van Parys, Marieke Dubois, Dirk Inzé, Yves Van de Peer
Diffany: an ontology-driven framework to infer, visualise and analyse differential molecular networks. BMC Bioinform. 17 (2016)
Sebastian Proost, Michiel Van Bel, Dries Vaneechoutte, Yves Van de Peer, Dirk Inzé, Bernd Mueller-Roeber, Klaas Vandepoele
PLAZA 3.0: an access point for plant comparative genomics. Nucleic Acids Res. 43 (Database-Issue) (2015)
Kai Hakala, Sofie Van Landeghem, Tapio Salakoski, Yves Van de Peer, Filip Ginter
Application of the EVEX resource to event extraction and network construction: Shared Task entry and result analysis. BMC Bioinform. 16 (S16) (2015)
Panayotis Vlastaridis, Stephen G. Oliver, Yves Van de Peer, Grigoris D. Amoutzias
The Challenges of Interpreting Phosphoproteomics Data: A Critical View Through the Bioinformatics Lens. CIBB (2015)
Mushthofa Mushthofa, Gustavo Torres, Yves Van de Peer, Kathleen Marchal, Martine De Cock
ASP-G: an ASP-based method for finding attractors in genetic regulatory networks. Bioinform. 30 (21) (2014)
Yao Yao, Kathleen Marchal, Yves Van de Peer
Using novel bio-inspired principles to improve adaptability of evolutionary robots in dynamically changing environments. ECAL (2013)
James E. Galagan, Kyle J. Minch, Matthew Peterson, Anna Lyubetskaya, Elham Azizi, Linsday Sweet, Antonio Gomes, Tige R. Rustad, Gregory Dolganov, Irina Glotova, Thomas Abeel, Chris Mahwinney, Adam D. Kennedy, René Allard, William Brabant, Andrew Krueger, Suma Jaini, Brent Honda, Wen-Han Yu, Mark J. Hickey, Jeremy Zucker, Christopher Garay, Brian Weiner, Peter Sisk, Christian Stolte, Jessica K. Winkler, Yves Van de Peer, Paul Iazzetti, Diogo Camacho, Jonathan M. Dreyfuss, Yang Liu, Anca Dorhoi, Hans-Joachim Mollenkopf, Paul Drogaris, Julie Lamontagne, Yiyong Zhou, Julie Piquenot, Sang Tae Park, Sahadevan Raman, Stefan H. E. Kaufmann, Robert P. Mohney, Daniel Chelsky, D. Branch Moody, David R. Sherman, Gary K. Schoolnik
regulatory network and hypoxia. Nat. 499 (7457) (2013)
Sofie Van Landeghem, Suwisa Kaewphan, Filip Ginter, Yves Van de Peer
Evaluating Large-scale Text Mining Applications Beyond the Traditional Numeric Performance Measures. BioNLP@ACL (2013)
Kai Hakala, Sofie Van Landeghem, Tapio Salakoski, Yves Van de Peer, Filip Ginter
EVEX in ST'13: Application of a large-scale text mining resource to event extraction and network construction. BioNLP@ACL (Shared Task) (2013)
Sofie Van Landeghem, Kai Hakala, Samuel Rönnqvist, Tapio Salakoski, Yves Van de Peer, Filip Ginter
Exploring Biomolecular Literature with EVEX: Connecting Genes through Events, Homology, and Indirect Associations. Adv. Bioinformatics 2012 (2012)
Sofie Van Landeghem, Jari Björne, Thomas Abeel, Bernard De Baets, Tapio Salakoski, Yves Van de Peer
Semantically linking molecular entities in literature through entity relationships. BMC Bioinform. 13 (S-11) (2012)
Jari Björne, Sofie Van Landeghem, Sampo Pyysalo, Tomoko Ohta, Filip Ginter, Yves Van de Peer, Sophia Ananiadou, Tapio Salakoski
PubMed-Scale Event Extraction for Post-Translational Modifications, Epigenetics and Protein Structural Relations. BioNLP@HLT-NAACL (2012)
Rubén Armañanzas, Yvan Saeys, Iñaki Inza, Miguel García-Torres, Concha Bielza, Yves Van de Peer, Pedro Larrañaga
Peakbin Selection in Mass Spectrometry Data Using a Consensus Approach with Estimation of Distribution Algorithms. IEEE ACM Trans. Comput. Biol. Bioinform. 8 (3) (2011)
Yao Yao, Guy Baele, Yves Van de Peer
A bio-inspired agent-based system for controlling robot behaviour. IEEE IA (2011)
Sofie Van Landeghem, Filip Ginter, Yves Van de Peer, Tapio Salakoski
EVEX: A PubMed-Scale Resource for Homology-Based Generalization of Text Mining Predictions. BioNLP@ACL (2011)
Yoshinobu Kano, Jari Björne, Filip Ginter, Tapio Salakoski, Ekaterina Buyko, Udo Hahn, K. Bretonnel Cohen, Karin Verspoor, Christophe Roeder, Lawrence E. Hunter, Halil Kilicoglu, Sabine Bergler, Sofie Van Landeghem, Thomas Van Parys, Yves Van de Peer, Makoto Miwa, Sophia Ananiadou, Mariana L. Neves, Alberto D. Pascual-Montano, Arzucan Özgür, Dragomir R. Radev, Sebastian Riedel, Rune Sætre, Hong-Woo Chun, Jin-Dong Kim, Sampo Pyysalo, Tomoko Ohta, Jun'ichi Tsujii
U-Compare bio-event meta-service: compatible BioNLP event extraction services. BMC Bioinform. 12 (2011)
Sofie Van Landeghem, Thomas Abeel, Bernard De Baets, Yves Van de Peer
Detecting Entity Relations as a Supporting Task for Bio-Molecular Event Extraction. BioNLP@ACL (Shared Task) (2011)
Pieter Audenaert, Thomas Van Parys, Florian Brondel, Mario Pickavet, Piet Demeester, Yves Van de Peer, Tom Michoel
CyClus3D: a Cytoscape plugin for clustering network motifs in integrated networks. Bioinform. 27 (11) (2011)
Sofie Van Landeghem, Bernard De Baets, Yves Van de Peer, Yvan Saeys
High-Precision Bio-molecular Event Extraction from Text Using Parallel Binary Classifiers. Comput. Intell. 27 (4) (2011)
Jan Fostier, Sebastian Proost, Bart Dhoedt, Yvan Saeys, Piet Demeester, Yves Van de Peer, Klaas Vandepoele
A greedy, graph-based algorithm for the alignment of multiple homologous gene lists. Bioinform. 27 (6) (2011)
Thomas Abeel, Sofie Van Landeghem, Roser Morante, Vincent Van Asch, Yves Van de Peer, Walter Daelemans, Yvan Saeys
Highlights of the BioTM 2010 workshop on advances in bio text mining. BMC Bioinform. 11 (S-5) (2010)
Thomas Abeel, Thibault Helleputte, Yves Van de Peer, Pierre Dupont, Yvan Saeys
Robust biomarker identification for cancer diagnosis with ensemble feature selection methods. Bioinform. 26 (3) (2010)
Eric Bonnet, Ying He, Kenny Billiau, Yves Van de Peer
TAPIR, a web server for the prediction of plant microRNA targets, including target mimics. Bioinform. 26 (12) (2010)
Yvan Saeys, Sofie Van Landeghem, Yves Van de Peer
Event based text mining for integrated network construction. MLSB (2010)
Sofie Van Landeghem, Sampo Pyysalo, Tomoko Ohta, Yves Van de Peer
Integration of Static Relations to Enhance Event Extraction from Text. BioNLP@ACL (2010)
Eric Bonnet, Tom Michoel, Yves Van de Peer
Prediction of a gene regulatory network linked to prostate cancer from gene expression, microRNA and clinical data. Bioinform. 26 (18) (2010)
Sofie Van Landeghem, Thomas Abeel, Yvan Saeys, Yves Van de Peer
Discriminative and informative features for biomolecular text mining with ensemble feature selection. Bioinform. 26 (18) (2010)
Tom Michoel, Riet De Smet, Anagha Joshi, Yves Van de Peer, Kathleen Marchal
Comparative analysis of module-based versus direct methods for reverse-engineering transcriptional regulatory networks. BMC Syst. Biol. 3 (2009)
Thomas Abeel, Yves Van de Peer, Yvan Saeys
Toward a gold standard for promoter prediction evaluation. Bioinform. 25 (12) (2009)
Anagha Joshi, Riet De Smet, Kathleen Marchal, Yves Van de Peer, Tom Michoel
Module networks revisited: computational assessment and prioritization of model predictions. Bioinform. 25 (4) (2009)
Sofie Van Landeghem, Yvan Saeys, Bernard De Baets, Yves Van de Peer
Analyzing text in search of bio-molecular events: a high-precision machine learning framework. BioNLP@HLT-NAACL (Shared Task) (2009)
Thomas Abeel, Yves Van de Peer, Yvan Saeys
Java-ML: A Machine Learning Library. J. Mach. Learn. Res. 10 (2009)
Guy Baele, Nicolas Bredèche, Evert Haasdijk, Steven Maere, Nico K. Michiels, Yves Van de Peer, Thomas Schmickl, Christopher S. F. Schwarzer, Ronald Thenius
Open-ended on-board Evolutionary Robotics for robot swarms. IEEE Congress on Evolutionary Computation (2009)
Athanasia C. Tzika, Raphaël Helaers, Yves Van de Peer, Michel C. Milinkovitch
MANTIS: a phylogenetic framework for multi-species genome comparisons. Bioinform. 24 (2) (2008)
Yvan Saeys, Huan Liu, Iñaki Inza, Louis Wehenkel, Yves Van de Peer
Preface. FSDM (2008)
Cedric Simillion, Koen Janssens, Lieven Sterck, Yves Van de Peer
i-ADHoRe 2.0: an improved tool to detect degenerated genomic homology using genomic profiles. Bioinform. 24 (1) (2008)
Rubén Armañanzas, Iñaki Inza, Roberto Santana, Yvan Saeys, Jose Luis Flores, José Antonio Lozano, Yves Van de Peer, Rosa Blanco, Víctor Robles, Concha Bielza, Pedro Larrañaga
A review of estimation of distribution algorithms in bioinformatics. BioData Min. 1 (2008)
Yvan Saeys, Thomas Abeel, Yves Van de Peer
Robust Feature Selection Using Ensemble Feature Selection Techniques. ECML/PKDD (2) (2008)
Michiel Van Bel, Yvan Saeys, Yves Van de Peer
FunSiP: a modular and extensible classifier for the prediction of functional sites in DNA. Bioinform. 24 (13) (2008)
Thomas Abeel, Yvan Saeys, Pierre Rouzé, Yves Van de Peer
ProSOM: core promoter prediction based on unsupervised clustering of DNA physical profiles. ISMB (2008)
Anagha Joshi, Yves Van de Peer, Tom Michoel
Analysis of a Gibbs sampler method for model-based clustering of gene expression data. Bioinform. 24 (2) (2008)
Yvan Saeys, Thomas Abeel, Sven Degroeve, Yves Van de Peer
Translation initiation site prediction on a genomic scale: beauty in simplicity. ISMB/ECCB (Supplement of Bioinformatics) (2007)
Tom Michoel, Steven Maere, Eric Bonnet, Anagha Joshi, Yvan Saeys, Tim Van den Bulcke, Koenraad Van Leemput, Piet van Remortel, Martin Kuiper, Kathleen Marchal, Yves Van de Peer
Validating module network learning algorithms using simulated data. BMC Bioinform. 8 (S-2) (2007)
Tineke Casneuf, Yves Van de Peer, Wolfgang Huber
In situ analysis of cross-hybridisation on microarrays and the inference of expression correlation. BMC Bioinform. 8 (2007)
Yvan Saeys, Pierre Rouzé, Yves Van de Peer
In search of the small ones: improved prediction of short exons in vertebrates, plants, fungi and protists. Bioinform. 23 (4) (2007)
Isis Bonet, María M. García, Yvan Saeys, Yves Van de Peer, Ricardo Grau Ábalo
Predicting Human Immunodeficiency Virus (HIV) Drug Resistance Using Recurrent Neural Networks. IWINAC (1) (2007)
Yvan Saeys, Yves Van de Peer
Enhancing Coding Potential Prediction for Short Sequences Using Complementary Sequence Features and Feature Selection. KDECB (2006)
Isis Bonet, Yvan Saeys, Ricardo Grau Ábalo, María M. García, Robersy Sanchez, Yves Van de Peer
Feature Extraction Using Clustering of Protein. CIARP (2006)
Philippe Faes, Bram Minnaert, Mark Christiaens, Eric Bonnet, Yvan Saeys, Dirk Stroobandt, Yves Van de Peer
Scalable hardware accelerator for comparing DNA and protein sequences. Infoscale (2006)
Sven Degroeve, Yvan Saeys, Bernard De Baets, Pierre Rouzé, Yves Van de Peer
SpliceMachine: predicting splice sites from high-dimensional local context representations. Bioinform. 21 (8) (2005)
Jan Wuyts, Guy Perrière, Yves Van de Peer
The European ribosomal RNA database. Nucleic Acids Res. 32 (Database-Issue) (2004)
Yvan Saeys, Sven Degroeve, Dirk Aeyels, Pierre Rouzé, Yves Van de Peer
Feature selection for splice site prediction: A new method using EDA-based feature ranking. BMC Bioinform. 5 (2004)
Eric Bonnet, Jan Wuyts, Pierre Rouzé, Yves Van de Peer
Evidence that microRNA precursors, unlike other non-coding RNAs, have lower folding free energies than random sequences. Bioinform. 20 (17) (2004)
Yvan Saeys, Sven Degroeve, Yves Van de Peer
Digging into Acceptor Splice Site Prediction: An Iterative Feature Selection Approach. PKDD (2004)
Yvan Saeys, Sven Degroeve, Dirk Aeyels, Yves Van de Peer, Pierre Rouzé
Fast feature selection using a simple estimation of distribution algorithm: a case study on splice site prediction. ECCB (2003)
Stephane Rombauts, Yves Van de Peer, Pierre Rouzé
AFLPinSilico, simulating AFLP fingerprints. Bioinform. 19 (6) (2003)
Magali Lescot, Patrice Déhais, Gert Thijs, Kathleen Marchal, Yves Moreau, Yves Van de Peer, Pierre Rouzé, Stephane Rombauts
PlantCARE, a database of plant cis-acting regulatory elements and a portal to tools for in silico analysis of promoter sequences. Nucleic Acids Res. 30 (1) (2002)
Jan Wuyts, Yves Van de Peer, Tina Winkelmans, Rupert De Wachter
The European database on small subunit ribosomal RNA. Nucleic Acids Res. 30 (1) (2002)
Sven Degroeve, Bernard De Baets, Yves Van de Peer, Pierre Rouzé
Feature subset selection for splice site prediction. ECCB (2002)
Yves Van de Peer, John Shawe-Taylor, Jayabalan Joseph, Axel Meyer
Wanda: a database of duplicated fish genes. Nucleic Acids Res. 30 (1) (2002)
Jan Wuyts, Peter De Rijk, Yves Van de Peer, Tina Winkelmans, Rupert De Wachter
The European Large Subunit Ribosomal RNA Database. Nucleic Acids Res. 29 (1) (2001)
Yves Van de Peer, Peter De Rijk, Jan Wuyts, Tina Winkelmans, Rupert De Wachter
The European Small Subunit Ribosomal RNA database. Nucleic Acids Res. 28 (1) (2000)
Peter De Rijk, Jan Wuyts, Yves Van de Peer, Tina Winkelmans, Rupert De Wachter
The European Large Subunit Ribosomal RNA database. Nucleic Acids Res. 28 (1) (2000)
Yves Van de Peer, Elmar Robbrecht, Sybren de Hoog, An Caers, Peter De Rijk, Rupert De Wachter
Database on the structure of small subunit ribosomal RNA. Nucleic Acids Res. 27 (1) (1999)
Peter De Rijk, Elmar Robbrecht, Sybren de Hoog, An Caers, Yves Van de Peer, Rupert De Wachter
Database on the structure of large subunit ribosomal RNA. Nucleic Acids Res. 27 (1) (1999)
Yves Van de Peer, An Caers, Peter De Rijk, Rupert De Wachter
Database on the structure of small ribosomal subunit RNA. Nucleic Acids Res. 26 (1) (1998)
Peter De Rijk, An Caers, Yves Van de Peer, Rupert De Wachter
Database on the structure of large ribosomal subunit RNA. Nucleic Acids Res. 26 (1) (1998)
Peter De Rijk, Yves Van de Peer, Rupert De Wachter
Database on the structure of large ribosomal subunit RNA. Nucleic Acids Res. 25 (1) (1997)
Yves Van de Peer, Jan Jansen, Peter De Rijk, Rupert De Wachter
Database on the structure of small ribosomal subunit RNA. Nucleic Acids Res. 25 (1) (1997)
Yves Van de Peer, Rupert De Wachter
Construction of evolutionary distance trees with TREECON for Windows: accounting for variation in nucleotide substitution rate among sites. Comput. Appl. Biosci. 13 (3) (1997)
Peter De Rijk, Yves Van de Peer, Rupert De Wachter
Database on the structure of large ribosomal subunit RNA. Nucleic Acids Res. 24 (1) (1996)
Yves Van de Peer, Stefan Nicolaï, Peter De Rijk, Rupert De Wachter
Database on the structure of small ribosomal subunit RNA. Nucleic Acids Res. 24 (1) (1996)
Yves Van de Peer, Rupert De Wachter
TREECON for Windows: a software package for the construction and drawing of evolutionary trees for the Microsoft Windows environment. Comput. Appl. Biosci. 10 (5) (1994)
Yves Van de Peer, Rupert De Wachter
TREECON: a software package for the construction and drawing of evolutionary trees. Comput. Appl. Biosci. 9 (2) (1993)
Jean-Marc Neefs, Yves Van de Peer, Peter De Rijk, Sabine Chapelle, Rupert De Wachter
Compilation of small ribosomal subunit RNA structures. Nucleic Acids Res. 21 (13) (1993)