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ORCIDYves Van de Peer
- > Home > Persons > Yves Van de Peer
Publications
- 2019
[j62]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): 27:1-27:13 (2019)- [j61]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): 298:1-298:13 (2019) - [j60]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): 1496-1507 (2019) - 2018
- [j59]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): 311:1-311:10 (2018) - [j58]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): D1190-D1196 (2018) - 2017
- [j57]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): 461-463 (2017) - [j56]Giles Miclotte, Stéphane Plaisance, Stephane Rombauts, Yves Van de Peer, Pieter Audenaert, Jan Fostier:
OMSim: a simulator for optical map data. Bioinform. 33(17): 2740-2742 (2017) - [j55]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): 374:1-374:13 (2017) - [c24]Yao Yao, Yves Van de Peer:
Simulating Biological Complexity through Artificial Evolution. CYBCONF 2017: 1-8 - 2016
- [j54]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: 10 (2016) - [j53]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): 276-282 (2016) - [j52]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: 18 (2016) - 2015
- [j51]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): S3 (2015) - [j50]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): 974-981 (2015) - [c23]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: 196-204 - 2014
- [j49]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): 3086-3092 (2014) - 2013
- [j48]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:
The Mycobacterium tuberculosis regulatory network and hypoxia. Nat. 499(7457): 178-183 (2013) - [c22]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: 26-34 - [c21]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: 63-71 - [c20]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: 1234 - 2012
- [j47]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: 582765:1-582765:12 (2012) - [j46]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): S6 (2012) - [c19]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: 82-90 - 2011
- [j45]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): 749-756 (2011) - [j44]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): 1587-1588 (2011) - [j43]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: 481 (2011) - [j42]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): 645-664 (2011) - [j41]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): 760-774 (2011) - [c18]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: 28-37 - [c17]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: 147-148 - [c16]Yao Yao, Guy Baele, Yves Van de Peer:
A bio-inspired agent-based system for controlling robot behaviour. IEEE IA 2011: 31-38 - 2010
- [j40]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): 392-398 (2010) - [j39]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): 1566-1568 (2010) - [j38]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) - [j37]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) - [j36]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): I1 (2010) - [c15]Sofie Van Landeghem, Sampo Pyysalo, Tomoko Ohta, Yves Van de Peer:
Integration of Static Relations to Enhance Event Extraction from Text. BioNLP@ACL 2010: 144-152 - [c14]Yvan Saeys, Sofie Van Landeghem, Yves Van de Peer:
Event based text mining for integrated network construction. MLSB 2010: 112-121 - 2009
- [j35]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): 490-496 (2009) - [j34]Thomas Abeel, Yves Van de Peer, Yvan Saeys:
Toward a gold standard for promoter prediction evaluation. Bioinform. 25(12) (2009) - [j33]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: 49 (2009) - [j32]Thomas Abeel, Yves Van de Peer, Yvan Saeys:
Java-ML: A Machine Learning Library. J. Mach. Learn. Res. 10: 931-934 (2009) - [c13]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: 128-136 - [c12]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: 1123-1130 - 2008
- [j31]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) - [j30]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): 127-128 (2008) - [j28]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): 176-183 (2008) - [j27]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): 1532-1533 (2008) - [c11]Thomas Abeel, Yvan Saeys, Pierre Rouzé, Yves Van de Peer:
ProSOM: core promoter prediction based on unsupervised clustering of DNA physical profiles. ISMB 2008: 24-31 - [c10]Yvan Saeys, Thomas Abeel, Yves Van de Peer:
Robust Feature Selection Using Ensemble Feature Selection Techniques. ECML/PKDD (2) 2008: 313-325 - [c9]Yvan Saeys, Huan Liu, Iñaki Inza, Louis Wehenkel, Yves Van de Peer:
Preface. FSDM 2008: 1-4 - [e1]Yvan Saeys, Huan Liu, Iñaki Inza, Louis Wehenkel, Yves Van de Peer:
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. JMLR Proceedings 4, JMLR.org 2008 [contents] - 2007
- [j26]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): 414-420 (2007) - [j25]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) - [j24]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) - [c8]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: 418-423 - [c7]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: 234-243 - 2006
- [c6]Isis Bonet, Yvan Saeys, Ricardo Grau Ábalo, María M. García, Robersy Sanchez, Yves Van de Peer:
Feature Extraction Using Clustering of Protein. CIARP 2006: 614-623 - [c5]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: 33 - [c4]Yvan Saeys, Yves Van de Peer:
Enhancing Coding Potential Prediction for Short Sequences Using Complementary Sequence Features and Feature Selection. KDECB 2006: 107-118 - [p1]Yvan Saeys, Sven Degroeve, Yves Van de Peer:
Feature Ranking Using an EDA-based Wrapper Approach. Towards a New Evolutionary Computation 2006: 243-257 - 2005
- [j23]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): 1332-1338 (2005) - 2004
- [j22]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): 2911-2917 (2004) - [j21]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: 64 (2004) - [j20]Jan Wuyts, Guy Perrière, Yves Van de Peer:
The European ribosomal RNA database. Nucleic Acids Res. 32(Database-Issue): 101-103 (2004) - [c3]Yvan Saeys, Sven Degroeve, Yves Van de Peer:
Digging into Acceptor Splice Site Prediction: An Iterative Feature Selection Approach. PKDD 2004: 386-397 - 2003
- [j19]Stephane Rombauts, Yves Van de Peer, Pierre Rouzé:
AFLPinSilico, simulating AFLP fingerprints. Bioinform. 19(6): 776-777 (2003) - [c2]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: 179-188 - 2002
- [j17]Jan Wuyts, Yves Van de Peer, Tina Winkelmans, Rupert De Wachter:
The European database on small subunit ribosomal RNA. Nucleic Acids Res. 30(1): 183-185 (2002) - [j16]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): 325-327 (2002) - [c1]Sven Degroeve, Bernard De Baets, Yves Van de Peer, Pierre Rouzé:
Feature subset selection for splice site prediction. ECCB 2002: 75-83 - 2001
- [j15]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): 175-177 (2001) - 2000
- [j14]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): 175-176 (2000) - [j13]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): 177-178 (2000) - 1999
- [j12]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): 174-178 (1999) - [j11]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): 179-183 (1999) - 1998
- [j10]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): 179-182 (1998) - [j9]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): 183-186 (1998) - 1997
- [j8]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): 227-230 (1997) - [j7]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): 111-116 (1997) - [j6]Peter De Rijk, Yves Van de Peer, Rupert De Wachter:
Database on the structure of large ribosomal subunit RNA. Nucleic Acids Res. 25(1): 117-122 (1997) - 1996
- [j5]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): 86-91 (1996) - [j4]Peter De Rijk, Yves Van de Peer, Rupert De Wachter:
Database on the structure of large ribosomal subunit RNA. Nucleic Acids Res. 24(1): 92-97 (1996) - 1994
- [j3]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): 569-570 (1994) - 1993
- [j2]Yves Van de Peer, Rupert De Wachter:
TREECON: a software package for the construction and drawing of evolutionary trees. Comput. Appl. Biosci. 9(2): 177-182 (1993) - [j1]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): 3025-3049 (1993)
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