Yves Van de Peer

91 papers A 1B 1C 3Journal 65Unranked 19

Year	Rank	Type	Title / Venue / Authors
2024	J	`jnl`	wgd v2: a suite of tools to uncover and date ancient polyploidy and whole-genome duplication. Bioinform. Hengchi Chen, Arthur Zwaenepoel, Yves Van de Peer
2023	J	`jnl`	syntenet: an R/Bioconductor package for the inference and analysis of synteny networks. Bioinform. Fabricio Almeida-Silva, Tao Zhao, Kristian K. Ullrich, M. Eric Schranz, Yves Van de Peer
2019	J	`jnl`	Illumina error correction near highly repetitive DNA regions improves de novo genome assembly. BMC Bioinform. Mahdi Heydari, Giles Miclotte, Yves Van de Peer, Jan Fostier
2019	J	`jnl`	Mining the Enriched Subgraphs for Specific Vertices in a Biological Graph. IEEE ACM Trans. Comput. Biol. Bioinform. Pieter Meysman, Yvan Saeys, Ehsan Sabaghian, Wout Bittremieux, Yves Van de Peer, Bart Goethals, Kris Laukens
2019	J	`jnl`	Optimising orbit counting of arbitrary order by equation selection. BMC Bioinform. Ine Melckenbeeck, Pieter Audenaert, Thomas Van Parys, Yves Van de Peer, Didier Colle, Mario Pickavet
2019	J	`jnl`	wgd - simple command line tools for the analysis of ancient whole-genome duplications. Bioinform. Arthur Zwaenepoel, Yves Van de Peer
2018	J	`jnl`	BrownieAligner: accurate alignment of Illumina sequencing data to de Bruijn graphs. BMC Bioinform. Mahdi Heydari, Giles Miclotte, Yves Van de Peer, Jan Fostier
2018	J	`jnl`	PLAZA 4.0: an integrative resource for functional, evolutionary and comparative plant genomics. Nucleic Acids Res. Michiel Van Bel, Tim Diels, Emmelien Vancaester, Lukasz Kreft, Alexander Botzki, Yves Van de Peer, Frederik Coppens, Klaas Vandepoele
2017	J	`jnl`	A Cytoscape app for motif enumeration with ISMAGS. Bioinform. Thomas Van Parys, Ine Melckenbeeck, Maarten Houbraken, Pieter Audenaert, Didier Colle, Mario Pickavet, Piet Demeester, Yves Van de Peer
2017	J	`jnl`	Evaluation of the impact of Illumina error correction tools on de novo genome assembly. BMC Bioinform. Mahdi Heydari, Giles Miclotte, Piet Demeester, Yves Van de Peer, Jan Fostier
2017	J	`jnl`	OMSim: a simulator for optical map data. Bioinform. Giles Miclotte, Stéphane Plaisance, Stephane Rombauts, Yves Van de Peer, Pieter Audenaert, Jan Fostier
2017	—	`conf`	Simulating Biological Complexity through Artificial Evolution. CYBCONF Yao Yao, Yves Van de Peer
2016	J	`jnl`	Cell line name recognition in support of the identification of synthetic lethality in cancer from text. Bioinform. Suwisa Kaewphan, Sofie Van Landeghem, Tomoko Ohta, Yves Van de Peer, Filip Ginter, Sampo Pyysalo
2016	J	`jnl`	Diffany: an ontology-driven framework to infer, visualise and analyse differential molecular networks. BMC Bioinform. Sofie Van Landeghem, Thomas Van Parys, Marieke Dubois, Dirk Inzé, Yves Van de Peer
2016	J	`jnl`	Jabba: hybrid error correction for long sequencing reads. Algorithms Mol. Biol. Giles Miclotte, Mahdi Heydari, Piet Demeester, Stephane Rombauts, Yves Van de Peer, Pieter Audenaert, Jan Fostier
2015	J	`jnl`	Application of the EVEX resource to event extraction and network construction: Shared Task entry and result analysis. BMC Bioinform. Kai Hakala, Sofie Van Landeghem, Tapio Salakoski, Yves Van de Peer, Filip Ginter
2015	J	`jnl`	PLAZA 3.0: an access point for plant comparative genomics. Nucleic Acids Res. Sebastian Proost, Michiel Van Bel, Dries Vaneechoutte, Yves Van de Peer, Dirk Inzé, Bernd Mueller-Roeber, Klaas Vandepoele
2015	—	`conf`	The Challenges of Interpreting Phosphoproteomics Data: A Critical View Through the Bioinformatics Lens. CIBB Panayotis Vlastaridis, Stephen G. Oliver, Yves Van de Peer, Grigoris D. Amoutzias
2014	J	`jnl`	ASP-G: an ASP-based method for finding attractors in genetic regulatory networks. Bioinform. Mushthofa Mushthofa, Gustavo Torres, Yves Van de Peer, Kathleen Marchal, Martine De Cock
2013	—	`conf`	EVEX in ST'13: Application of a large-scale text mining resource to event extraction and network construction. BioNLP@ACL (Shared Task) Kai Hakala, Sofie Van Landeghem, Tapio Salakoski, Yves Van de Peer, Filip Ginter
2013	—	`conf`	Evaluating Large-scale Text Mining Applications Beyond the Traditional Numeric Performance Measures. BioNLP@ACL Sofie Van Landeghem, Suwisa Kaewphan, Filip Ginter, Yves Van de Peer
2013	J	`jnl`	The Nat. 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
2013	—	`conf`	Using novel bio-inspired principles to improve adaptability of evolutionary robots in dynamically changing environments. ECAL Yao Yao, Kathleen Marchal, Yves Van de Peer
2012	J	`jnl`	Exploring Biomolecular Literature with EVEX: Connecting Genes through Events, Homology, and Indirect Associations. Adv. Bioinformatics Sofie Van Landeghem, Kai Hakala, Samuel Rönnqvist, Tapio Salakoski, Yves Van de Peer, Filip Ginter
2012	—	`conf`	PubMed-Scale Event Extraction for Post-Translational Modifications, Epigenetics and Protein Structural Relations. BioNLP@HLT-NAACL Jari Björne, Sofie Van Landeghem, Sampo Pyysalo, Tomoko Ohta, Filip Ginter, Yves Van de Peer, Sophia Ananiadou, Tapio Salakoski
2012	J	`jnl`	Semantically linking molecular entities in literature through entity relationships. BMC Bioinform. Sofie Van Landeghem, Jari Björne, Thomas Abeel, Bernard De Baets, Tapio Salakoski, Yves Van de Peer
2011	—	`conf`	A bio-inspired agent-based system for controlling robot behaviour. IEEE IA Yao Yao, Guy Baele, Yves Van de Peer
2011	J	`jnl`	A greedy, graph-based algorithm for the alignment of multiple homologous gene lists. Bioinform. Jan Fostier, Sebastian Proost, Bart Dhoedt, Yvan Saeys, Piet Demeester, Yves Van de Peer, Klaas Vandepoele
2011	J	`jnl`	CyClus3D: a Cytoscape plugin for clustering network motifs in integrated networks. Bioinform. Pieter Audenaert, Thomas Van Parys, Florian Brondel, Mario Pickavet, Piet Demeester, Yves Van de Peer, Tom Michoel
2011	—	`conf`	Detecting Entity Relations as a Supporting Task for Bio-Molecular Event Extraction. BioNLP@ACL (Shared Task) Sofie Van Landeghem, Thomas Abeel, Bernard De Baets, Yves Van de Peer
2011	—	`conf`	EVEX: A PubMed-Scale Resource for Homology-Based Generalization of Text Mining Predictions. BioNLP@ACL Sofie Van Landeghem, Filip Ginter, Yves Van de Peer, Tapio Salakoski
2011	J	`jnl`	High-Precision Bio-molecular Event Extraction from Text Using Parallel Binary Classifiers. Comput. Intell. Sofie Van Landeghem, Bernard De Baets, Yves Van de Peer, Yvan Saeys
2011	J	`jnl`	Peakbin Selection in Mass Spectrometry Data Using a Consensus Approach with Estimation of Distribution Algorithms. IEEE ACM Trans. Comput. Biol. Bioinform. Rubén Armañanzas, Yvan Saeys, Iñaki Inza, Miguel García-Torres, Concha Bielza, Yves Van de Peer, Pedro Larrañaga
2011	J	`jnl`	U-Compare bio-event meta-service: compatible BioNLP event extraction services. BMC Bioinform. 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
2010	J	`jnl`	Discriminative and informative features for biomolecular text mining with ensemble feature selection. Bioinform. Sofie Van Landeghem, Thomas Abeel, Yvan Saeys, Yves Van de Peer
2010	—	`conf`	Event based text mining for integrated network construction. MLSB Yvan Saeys, Sofie Van Landeghem, Yves Van de Peer
2010	J	`jnl`	Highlights of the BioTM 2010 workshop on advances in bio text mining. BMC Bioinform. Thomas Abeel, Sofie Van Landeghem, Roser Morante, Vincent Van Asch, Yves Van de Peer, Walter Daelemans, Yvan Saeys
2010	—	`conf`	Integration of Static Relations to Enhance Event Extraction from Text. BioNLP@ACL Sofie Van Landeghem, Sampo Pyysalo, Tomoko Ohta, Yves Van de Peer
2010	J	`jnl`	Prediction of a gene regulatory network linked to prostate cancer from gene expression, microRNA and clinical data. Bioinform. Eric Bonnet, Tom Michoel, Yves Van de Peer
2010	J	`jnl`	Robust biomarker identification for cancer diagnosis with ensemble feature selection methods. Bioinform. Thomas Abeel, Thibault Helleputte, Yves Van de Peer, Pierre Dupont, Yvan Saeys
2010	J	`jnl`	TAPIR, a web server for the prediction of plant microRNA targets, including target mimics. Bioinform. Eric Bonnet, Ying He, Kenny Billiau, Yves Van de Peer
2009	—	`conf`	Analyzing text in search of bio-molecular events: a high-precision machine learning framework. BioNLP@HLT-NAACL (Shared Task) Sofie Van Landeghem, Yvan Saeys, Bernard De Baets, Yves Van de Peer
2009	J	`jnl`	Comparative analysis of module-based versus direct methods for reverse-engineering transcriptional regulatory networks. BMC Syst. Biol. Tom Michoel, Riet De Smet, Anagha Joshi, Yves Van de Peer, Kathleen Marchal
2009	J	`jnl`	Java-ML: A Machine Learning Library. J. Mach. Learn. Res. Thomas Abeel, Yves Van de Peer, Yvan Saeys
2009	J	`jnl`	Module networks revisited: computational assessment and prioritization of model predictions. Bioinform. Anagha Joshi, Riet De Smet, Kathleen Marchal, Yves Van de Peer, Tom Michoel
2009	B	`conf`	Open-ended on-board Evolutionary Robotics for robot swarms. IEEE Congress on Evolutionary Computation Guy Baele, Nicolas Bredèche, Evert Haasdijk, Steven Maere, Nico K. Michiels, Yves Van de Peer, Thomas Schmickl, Christopher S. F. Schwarzer, Ronald Thenius
2009	J	`jnl`	Toward a gold standard for promoter prediction evaluation. Bioinform. Thomas Abeel, Yves Van de Peer, Yvan Saeys
2008	J	`jnl`	A review of estimation of distribution algorithms in bioinformatics. BioData Min. 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
2008	J	`jnl`	Analysis of a Gibbs sampler method for model-based clustering of gene expression data. Bioinform. Anagha Joshi, Yves Van de Peer, Tom Michoel
2008	J	`jnl`	FunSiP: a modular and extensible classifier for the prediction of functional sites in DNA. Bioinform. Michiel Van Bel, Yvan Saeys, Yves Van de Peer
2008	J	`jnl`	MANTIS: a phylogenetic framework for multi-species genome comparisons. Bioinform. Athanasia C. Tzika, Raphaël Helaers, Yves Van de Peer, Michel C. Milinkovitch
2008	—	`conf`	Preface. FSDM Yvan Saeys, Huan Liu, Iñaki Inza, Louis Wehenkel, Yves Van de Peer
2008	A	`conf`	ProSOM: core promoter prediction based on unsupervised clustering of DNA physical profiles. ISMB Thomas Abeel, Yvan Saeys, Pierre Rouzé, Yves Van de Peer
2008	—	`conf`	Robust Feature Selection Using Ensemble Feature Selection Techniques. ECML/PKDD (2) Yvan Saeys, Thomas Abeel, Yves Van de Peer
2008	—	`ed.`	Third Workshop on New Challenges for Feature Selection in Data Mining and Knowledge Discovery, FSDM 2008, held at ECML-PKDD 2008, Antwerp, Belgium, September 15, 2008 FSDM Yvan Saeys, Huan Liu, Iñaki Inza, Louis Wehenkel, Yves Van de Peer
2008	J	`jnl`	i-ADHoRe 2.0: an improved tool to detect degenerated genomic homology using genomic profiles. Bioinform. Cedric Simillion, Koen Janssens, Lieven Sterck, Yves Van de Peer
2007	J	`jnl`	In search of the small ones: improved prediction of short exons in vertebrates, plants, fungi and protists. Bioinform. Yvan Saeys, Pierre Rouzé, Yves Van de Peer
2007	J	`jnl`	In situ analysis of cross-hybridisation on microarrays and the inference of expression correlation. BMC Bioinform. Tineke Casneuf, Yves Van de Peer, Wolfgang Huber
2007	—	`conf`	Predicting Human Immunodeficiency Virus (HIV) Drug Resistance Using Recurrent Neural Networks. IWINAC (1) Isis Bonet, María M. García, Yvan Saeys, Yves Van de Peer, Ricardo Grau Ábalo
2007	—	`conf`	Translation initiation site prediction on a genomic scale: beauty in simplicity. ISMB/ECCB (Supplement of Bioinformatics) Yvan Saeys, Thomas Abeel, Sven Degroeve, Yves Van de Peer
2007	J	`jnl`	Validating module network learning algorithms using simulated data. BMC Bioinform. 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
2006	—	`conf`	Enhancing Coding Potential Prediction for Short Sequences Using Complementary Sequence Features and Feature Selection. KDECB Yvan Saeys, Yves Van de Peer
2006	C	`conf`	Feature Extraction Using Clustering of Protein. CIARP Isis Bonet, Yvan Saeys, Ricardo Grau Ábalo, María M. García, Robersy Sanchez, Yves Van de Peer
2006	—	`ch.`	Feature Ranking Using an EDA-based Wrapper Approach. Towards a New Evolutionary Computation Yvan Saeys, Sven Degroeve, Yves Van de Peer
2006	—	`conf`	Scalable hardware accelerator for comparing DNA and protein sequences. Infoscale Philippe Faes, Bram Minnaert, Mark Christiaens, Eric Bonnet, Yvan Saeys, Dirk Stroobandt, Yves Van de Peer
2005	J	`jnl`	SpliceMachine: predicting splice sites from high-dimensional local context representations. Bioinform. Sven Degroeve, Yvan Saeys, Bernard De Baets, Pierre Rouzé, Yves Van de Peer
2004	—	`conf`	Digging into Acceptor Splice Site Prediction: An Iterative Feature Selection Approach. PKDD Yvan Saeys, Sven Degroeve, Yves Van de Peer
2004	J	`jnl`	Evidence that microRNA precursors, unlike other non-coding RNAs, have lower folding free energies than random sequences. Bioinform. Eric Bonnet, Jan Wuyts, Pierre Rouzé, Yves Van de Peer
2004	J	`jnl`	Feature selection for splice site prediction: A new method using EDA-based feature ranking. BMC Bioinform. Yvan Saeys, Sven Degroeve, Dirk Aeyels, Pierre Rouzé, Yves Van de Peer
2004	J	`jnl`	The European ribosomal RNA database. Nucleic Acids Res. Jan Wuyts, Guy Perrière, Yves Van de Peer
2003	J	`jnl`	AFLPinSilico, simulating AFLP fingerprints. Bioinform. Stephane Rombauts, Yves Van de Peer, Pierre Rouzé
2003	C	`conf`	Fast feature selection using a simple estimation of distribution algorithm: a case study on splice site prediction. ECCB Yvan Saeys, Sven Degroeve, Dirk Aeyels, Yves Van de Peer, Pierre Rouzé
2002	C	`conf`	Feature subset selection for splice site prediction. ECCB Sven Degroeve, Bernard De Baets, Yves Van de Peer, Pierre Rouzé
2002	J	`jnl`	PlantCARE, a database of plant cis-acting regulatory elements and a portal to tools for in silico analysis of promoter sequences. Nucleic Acids Res. Magali Lescot, Patrice Déhais, Gert Thijs, Kathleen Marchal, Yves Moreau, Yves Van de Peer, Pierre Rouzé, Stephane Rombauts
2002	J	`jnl`	The European database on small subunit ribosomal RNA. Nucleic Acids Res. Jan Wuyts, Yves Van de Peer, Tina Winkelmans, Rupert De Wachter
2002	J	`jnl`	Wanda: a database of duplicated fish genes. Nucleic Acids Res. Yves Van de Peer, John Shawe-Taylor, Jayabalan Joseph, Axel Meyer
2001	J	`jnl`	The European Large Subunit Ribosomal RNA Database. Nucleic Acids Res. Jan Wuyts, Peter De Rijk, Yves Van de Peer, Tina Winkelmans, Rupert De Wachter
2000	J	`jnl`	The European Large Subunit Ribosomal RNA database. Nucleic Acids Res. Peter De Rijk, Jan Wuyts, Yves Van de Peer, Tina Winkelmans, Rupert De Wachter
2000	J	`jnl`	The European Small Subunit Ribosomal RNA database. Nucleic Acids Res. Yves Van de Peer, Peter De Rijk, Jan Wuyts, Tina Winkelmans, Rupert De Wachter
1999	J	`jnl`	Database on the structure of large subunit ribosomal RNA. Nucleic Acids Res. Peter De Rijk, Elmar Robbrecht, Sybren de Hoog, An Caers, Yves Van de Peer, Rupert De Wachter
1999	J	`jnl`	Database on the structure of small subunit ribosomal RNA. Nucleic Acids Res. Yves Van de Peer, Elmar Robbrecht, Sybren de Hoog, An Caers, Peter De Rijk, Rupert De Wachter
1998	J	`jnl`	Database on the structure of large ribosomal subunit RNA. Nucleic Acids Res. Peter De Rijk, An Caers, Yves Van de Peer, Rupert De Wachter
1998	J	`jnl`	Database on the structure of small ribosomal subunit RNA. Nucleic Acids Res. Yves Van de Peer, An Caers, Peter De Rijk, Rupert De Wachter
1997	J	`jnl`	Construction of evolutionary distance trees with TREECON for Windows: accounting for variation in nucleotide substitution rate among sites. Comput. Appl. Biosci. Yves Van de Peer, Rupert De Wachter
1997	J	`jnl`	Database on the structure of large ribosomal subunit RNA. Nucleic Acids Res. Peter De Rijk, Yves Van de Peer, Rupert De Wachter
1997	J	`jnl`	Database on the structure of small ribosomal subunit RNA. Nucleic Acids Res. Yves Van de Peer, Jan Jansen, Peter De Rijk, Rupert De Wachter
1996	J	`jnl`	Database on the structure of large ribosomal subunit RNA. Nucleic Acids Res. Peter De Rijk, Yves Van de Peer, Rupert De Wachter
1996	J	`jnl`	Database on the structure of small ribosomal subunit RNA. Nucleic Acids Res. Yves Van de Peer, Stefan Nicolaï, Peter De Rijk, Rupert De Wachter
1994	J	`jnl`	TREECON for Windows: a software package for the construction and drawing of evolutionary trees for the Microsoft Windows environment. Comput. Appl. Biosci. Yves Van de Peer, Rupert De Wachter
1993	J	`jnl`	Compilation of small ribosomal subunit RNA structures. Nucleic Acids Res. Jean-Marc Neefs, Yves Van de Peer, Peter De Rijk, Sabine Chapelle, Rupert De Wachter
1993	J	`jnl`	TREECON: a software package for the construction and drawing of evolutionary trees. Comput. Appl. Biosci. Yves Van de Peer, Rupert De Wachter