Yves Van de Peer

Serge Kernbach, Thomas Schmickl, Guy Baele, 2009, 2009 Computation World: Future Computing, Service Computation, Cognitive, Adaptive, Content, Patterns.

Open-ended on-board Evolutionary Robotics for robot swarms

Thomas Schmickl, Guy Baele, Yves Van de Peer, 2009, 2009 IEEE Congress on Evolutionary Computation.

A review of estimation of distribution algorithms in bioinformatics

Concha Bielza, Pedro Larrañaga, Yvan Saeys, 2008, BioData Mining.

Feature Extraction Using Clustering of Protein

Yvan Saeys, Yves Van de Peer, Ricardo del Corazón Grau-Ábalo, 2006, CIARP.

Database on the structure of large ribosomal subunit RNA

Yves Van de Peer, Rupert De Wachter, Peter De Rijk, 1994, Nucleic Acids Res..

i-ADHoRe 2.0: an improved tool to detect degenerated genomic homology using genomic profiles

Yves Van de Peer, Koen Janssens, Lieven Sterck, 2008, Bioinform..

The European Large Subunit Ribosomal RNA database

Yves Van de Peer, Rupert De Wachter, Peter De Rijk, 2000, Nucleic Acids Res..

EVEX: A PubMed-Scale Resource for Homology-Based Generalization of Text Mining Predictions

Tapio Salakoski, Yves Van de Peer, Filip Ginter, 2011, BioNLP@ACL.

Evaluating Large-scale Text Mining Applications Beyond the Traditional Numeric Performance Measures

Yves Van de Peer, Filip Ginter, Suwisa Kaewphan, 2013, BioNLP@ACL.

Database on the structure of large ribosomal subunit RNA

Yves Van de Peer, Rupert De Wachter, Peter De Rijk, 1997, Nucleic Acids Res..

Scalable hardware accelerator for comparing DNA and protein sequences

Yvan Saeys, Yves Van de Peer, Dirk Stroobandt, 2006, InfoScale '06.

Highlights of the BioTM 2010 workshop on advances in bio text mining

Roser Morante, Walter Daelemans, Yvan Saeys, 2010, BMC Bioinformatics.

Module networks revisited: computational assessment and prioritization of model predictions

Kathleen Marchal, Yves Van de Peer, Anagha Joshi, 2009, Bioinform..

Software regulatory path motifs in integrated networks using perturbational data

Yves Van de Peer, Tom Michoel, Thomas Van Parys, 2010 .

The Mycobacterium tuberculosis regulatory network and hypoxia

Yves Van de Peer, Jonathan M. Dreyfuss, Yang Liu, 2013, Nature.

TAPIR, a web server for the prediction of plant microRNA targets, including target mimics

Yves Van de Peer, Ying He, Eric Bonnet, 2010, Bioinform..

PlantCARE, a database of plant cis-acting regulatory elements and a portal to tools for in silico analysis of promoter sequences

Kathleen Marchal, Stephane Rombauts, Yves Van de Peer, 2002, Nucleic Acids Res..

PLAZA 4.0: an integrative resource for functional, evolutionary and comparative plant genomics

Yves Van de Peer, Frederik Coppens, Michiel Van Bel, 2017, Nucleic Acids Res..

In situ analysis of cross-hybridisation on microarrays and the inference of expression correlation

Yves Van de Peer, Wolfgang Huber, Tineke Casneuf, 2007, BMC Bioinformatics.

ASP-G: an ASP-based method for finding attractors in genetic regulatory networks

Kathleen Marchal, Martine De Cock, Yves Van de Peer, 2014, Bioinform..

Illumina error correction near highly repetitive DNA regions improves de novo genome assembly

Yves Van de Peer, Jan Fostier, Mahdi Heydari, 2019, BMC Bioinformatics.

BrownieAligner: accurate alignment of Illumina sequencing data to de Bruijn graphs

Yves Van de Peer, Mahdi Heydari, Jan Fostier, 2018, BMC Bioinform..

Statistical methods for detecting heterotachy

Yves Van de Peer, Jeroen Raes, Stijn Vansteelandt, 2005 .

Discovery of significantly enriched subgraphs associated with selected vertices in a single graph

Bart Goethals, Wout Bittremieux, Yves Van de Peer, 2015, BIOKDD 2015.

The European Small Subunit Ribosomal RNA database

Yves Van de Peer, Rupert De Wachter, Peter De Rijk, 2000, Nucleic Acids Res..

The European Large Subunit Ribosomal RNA database

Yves Van de Peer, Rupert De Wachter, Peter De Rijk, 2000, Nucleic Acids Res..

Predicting Human Immunodeficiency Virus (HIV) Drug Resistance Using Recurrent Neural Networks

Yvan Saeys, Yves Van de Peer, Ricardo del Corazón Grau-Ábalo, 2006, IWINAC.

Analyzing text in search of bio-molecular events: a high-precision machine learning framework

Yvan Saeys, Bernard De Baets, Yves Van de Peer, 2009, BioNLP@HLT-NAACL.

Jabba: hybrid error correction for long sequencing reads

Piet Demeester, Stephane Rombauts, Yves Van de Peer, 2015, Algorithms for Molecular Biology.

CyClus3D: a Cytoscape plugin for clustering network motifs in integrated networks

Piet Demeester, Mario Pickavet, Yves Van de Peer, 2011, Bioinform..

CHALLENGES OF SYSTEMS BIOLOGY: COMMUNITY EFFORTS TO HARNESS BIOLOGICAL COMPLEXITY

Kathleen Marchal, Yves Van de Peer, Tom Michoel, 2009, CMSB 2009.

Enhancing Coding Potential Prediction for Short Sequences Using Complementary Sequence Features and Feature Selection

Yvan Saeys, Yves Van de Peer, 2006, KDECB.

TREECON for Windows: a software package for the construction and drawing of evolutionary trees for the Microsoft Windows environment

Yves Van de Peer, Rupert De Wachter, Y. Peer, 1994, Comput. Appl. Biosci..

Exploring Biomolecular Literature with EVEX: Connecting Genes through Events, Homology, and Indirect Associations

Tapio Salakoski, Yves Van de Peer, Filip Ginter, 2012, Adv. Bioinformatics.

Optimising orbit counting of arbitrary order by equation selection

Didier Colle, Mario Pickavet, Yves Van de Peer, 2018, BMC Bioinformatics.

Simulating Biological Complexity through Artificial Evolution

Yves Van de Peer, Yao Yao, Y. Peer, 2017, 2017 3rd IEEE International Conference on Cybernetics (CYBCON).

A novel approach to modelling site dependencies: biological realism and computational complexity

Yves Van de Peer, Stijn Vansteelandt, Guy Baele, 2006 .

Evaluation of the impact of Illumina error correction tools on de novo genome assembly

Piet Demeester, Yves Van de Peer, Mahdi Heydari, 2017, BMC Bioinformatics.

Comparative analysis of module-based versus direct methods for reverse-engineering transcriptional regulatory networks

Kathleen Marchal, Yves Van de Peer, Anagha Joshi, 2009, BMC Systems Biology.

Diffany: an ontology-driven framework to infer, visualise and analyse differential molecular networks

Yves Van de Peer, Dirk Inzé, Sofie Van Landeghem, 2016, BMC Bioinformatics.

In search of the small ones: improved prediction of short exons in vertebrates, plants, fungi and protists

Yvan Saeys, Yves Van de Peer, Pierre Rouzé, 2007, Bioinform..

OMSim: a simulator for optical map data

Stephane Rombauts, Yves Van de Peer, Jan Fostier, 2017, Bioinform..

Translation initiation site prediction on a genomic scale: beauty in simplicity

Yvan Saeys, Yves Van de Peer, Sven Degroeve, 2007, ISMB/ECCB.

MANTIS: a phylogenetic framework for multi-species genome comparisons

Yves Van de Peer, Michel C. Milinkovitch, Raphaël Helaers, 2008, Bioinform..

Fast feature selection using a simple estimation of distribution algorithm: a case study on splice site prediction

Yvan Saeys, Yves Van de Peer, Pierre Rouzé, 2003, ECCB.

Database on the structure of large ribosomal subunit RNA

Yves Van de Peer, Rupert De Wachter, An Caers, 1998, Nucleic Acids Res..

ProSOM: core promoter prediction based on unsupervised clustering of DNA physical profiles

Yvan Saeys, Yves Van de Peer, Pierre Rouzé, 2008, ISMB.

An ASP-based simulation method for finding all synchronous and asynchronous attractors in genetic regulatory networks

Kathleen Marchal, Martine De Cock, Yves Van de Peer, 2012 .

Integration of Static Relations to Enhance Event Extraction from Text

Sampo Pyysalo, Yves Van de Peer, Tomoko Ohta, 2010, BioNLP@ACL.

Database on the structure of small ribosomal subunit RNA

Yves Van de Peer, Rupert De Wachter, An Caers, 1998, Nucleic Acids Res..

The Challenges of Interpreting Phosphoproteomics Data: A Critical View Through the Bioinformatics Lens

Yves Van de Peer, Stephen G. Oliver, Grigoris D. Amoutzias, 2015, CIBB.

Benchmarking machine learning techniques for the extraction of protein-protein interactions from text

Yvan Saeys, Bernard De Baets, Yves Van de Peer, 2008 .

Toward a gold standard for promoter prediction evaluation

Yvan Saeys, Yves Van de Peer, Thomas Abeel, 2009, Bioinform..

Digging into Acceptor Splice Site Prediction: An Iterative Feature Selection Approach

Yvan Saeys, Yves Van de Peer, Sven Degroeve, 2004, PKDD.

A Scalable Hardware Accelerator for Comparing Protein Sequences

Yvan Saeys, Yves Van de Peer, Dirk Stroobandt, 2006 .

Robust Feature Selection Using Ensemble Feature Selection Techniques

Yvan Saeys, Yves Van de Peer, Thomas Abeel, 2008, ECML/PKDD.

Database on the structure of large subunit ribosomal RNA

Yves Van de Peer, Rupert De Wachter, Elmar Robbrecht, 1999, Nucleic Acids Res..

The European database on small subunit ribosomal RNA

Yves Van de Peer, Rupert De Wachter, Jan Wuyts, 2002, Nucleic Acids Res..

Size does matter

Yves Van de Peer, 2018, Nature Plants.

Extracting protein-protein interactions from text using rich feature vectors and feature selection

Yvan Saeys, Bernard De Baets, Yves Van de Peer, 2008, SMBM 2008.

Selecting Relevant Features for Splice Site Prediction by Estimation of Distribution Algorithms.

Yvan Saeys, Yves Van de Peer, Pierre Rouzé, 2002 .

Compilation of Pseudomonad Sequences Present in a Database on the Structure of Ribosomal RNA

Yves Van de Peer, Rupert De Wachter, Marc Vancanneyt, 1996 .

Detecting Entity Relations as a Supporting Task for Bio-Molecular Event Extraction

Bernard De Baets, Yves Van de Peer, Thomas Abeel, 2011, BioNLP@ACL.

FunSiP: a modular and extensible classifier for the prediction of functional sites in DNA

Yvan Saeys, Yves Van de Peer, Michiel Van Bel, 2008, Bioinform..

Database on the structure of small ribosomal subunit RNA

Yves Van de Peer, Rupert De Wachter, Peter De Rijk, 1998, Nucleic Acids Res..

Feature selection for splice site prediction: A new method using EDA-based feature ranking

Yvan Saeys, Yves Van de Peer, Pierre Rouzé, 2004, BMC Bioinformatics.

Robust biomarker identification for cancer diagnosis with ensemble feature selection methods

Thibault Helleputte, Yvan Saeys, Yves Van de Peer, 2010, Bioinform..

Selecting relevant features for gene structure prediction

Yvan Saeys, Yves Van de Peer, Pierre Rouzé, 2004 .

The European ribosomal RNA database

Guy Perrière, Yves Van de Peer, Jan Wuyts, 2004, Nucleic Acids Res..

Evidence that microRNA precursors, unlike other non-coding RNAs, have lower folding free energies than random sequences

Yves Van de Peer, Pierre Rouzé, Eric Bonnet, 2004, Bioinform..

A bio-inspired agent-based system for controlling robot behaviour

Guy Baele, Yves Van de Peer, Yao Yao, 2011, 2011 IEEE Symposium on Intelligent Agent (IA).

Database on the structure of small ribosomal subunit RNA

Yves Van de Peer, Rupert De Wachter, Peter De Rijk, 1996, Nucleic Acids Res..

Analysis of a Gibbs sampler method for model-based clustering of gene expression data

Yves Van de Peer, Anagha Joshi, Tom Michoel, 2008, Bioinform..

PLAZA 3.0: an access point for plant comparative genomics

Yves Van de Peer, Dirk Inzé, Sebastian Proost, 2014, Nucleic Acids Res..

Discriminative and informative features for biomolecular text mining with ensemble feature selection

Yvan Saeys, Yves Van de Peer, Thomas Abeel, 2010, Bioinform..

Semantically linking molecular entities in literature through entity relationships

Jari Björne, Tapio Salakoski, Bernard De Baets, 2012, BMC Bioinformatics.

HIGH‐PRECISION BIO‐MOLECULAR EVENT EXTRACTION FROM TEXT USING PARALLEL BINARY CLASSIFIERS

Yvan Saeys, Bernard De Baets, Yves Van de Peer, 2011, Comput. Intell..

Combining signal processing and machine learning techniques for coding potential prediction

Yvan Saeys, Yves Van de Peer, Y. Saeys, 2006 .

Cell line name recognition in support of the identification of synthetic lethality in cancer from text

Sampo Pyysalo, Yves Van de Peer, Filip Ginter, 2015, Bioinform..

Feature subset selection for splice site prediction

Bernard De Baets, Yves Van de Peer, Pierre Rouzé, 2002, ECCB.

Peakbin Selection in Mass Spectrometry Data Using a Consensus Approach with Estimation of Distribution Algorithms

Concha Bielza, Pedro Larrañaga, Yvan Saeys, 2011, IEEE/ACM Transactions on Computational Biology and Bioinformatics.

Using novel bio-inspired principles to improve adaptability of evolutionary robots in dynamically changing environments

Kathleen Marchal, Yves Van de Peer, Yao Yao, 2013, ECAL.

Feature Ranking Using an EDA-based Wrapper Approach

Yvan Saeys, Yves Van de Peer, Sven Degroeve, 2006, Towards a New Evolutionary Computation.

PubMed-Scale Event Extraction for Post-Translational Modifications, Epigenetics and Protein Structural Relations

Jari Björne, Tapio Salakoski, Sampo Pyysalo, 2012, BioNLP@HLT-NAACL.

TREECON: a software package for the construction and drawing of evolutionary trees

Yves Van de Peer, Rupert De Wachter, Y. Peer, 1993, Comput. Appl. Biosci..

EVEX in ST’13: Application of a large-scale text mining resource to event extraction and network construction

Tapio Salakoski, Yves Van de Peer, Filip Ginter, 2013, BioNLP@ACL.

Special issue: Plant synthetic biology

Yves Van de Peer, Dhirendra Kumar, 2020 .

The KnownLeaf literature curation system captures knowledge about Arabidopsis leaf growth and development and facilitates integrated data mining

Yves Van de Peer, Fabio Fiorani, Aalt D. J. van Dijk, 2015 .

A Cytoscape app for motif enumeration with ISMAGS

Didier Colle, Piet Demeester, Mario Pickavet, 2016, Bioinform..

Validating module network learning algorithms using simulated data

Kathleen Marchal, Yvan Saeys, Koenraad Van Leemput, 2007, BMC Bioinformatics.

Genome Annotation in Plants and Fungi: EuGene as a Model Platform

Thomas Schiex, Sylvain Foissac, Stephane Rombauts, 2008 .

zt: A Sofware Tool for Simple and Partial Mantel Tests

Yves Van de Peer, Eric Bonnet, Y. Peer, 2002 .

Gene expression Analysis of a Gibbs sampler method for model-based clustering of gene expression data

Yves Van de Peer, Anagha Joshi, Tom Michoel, 2008 .

Characterizing regulatory path motifs in integrated networks using perturbational data

Yves Van de Peer, Anagha Joshi, Tom Michoel, 2010, Genome Biology.

Phylogenetic relationships among algae based on complete large-subunit rRNA sequences.

Yves Van de Peer, Rupert De Wachter, Y. Peer, 2001 .

Computational approaches to unveiling ancient genome duplications

Yves Van de Peer, Y. Peer, 2004, Nature Reviews Genetics.

Annual Machine Learning Conference of Belgium and The Netherlands

Yvan Saeys, Bernard De Baets, Elena Tsiporkova, 2006 .

The Phaeodactylum genome reveals the evolutionary history of diatom genomes

Leszek Rychlewski, Yves Van de Peer, Jean-Paul Cadoret, 2008, Nature.

Single‐Gene and Whole‐Genome Duplications and the Evolution of Protein–Protein Interaction Networks

Yves Van de Peer, Grigoris D. Amoutzias, Y. Peer, 2010 .

Integrating Large-Scale Text Mining and Co-Expression Networks : Targeting NADP ( H ) Metabolism in E . coli with Event Extraction

Yves Van de Peer, Filip Ginter, Suwisa Kaewphan, 2012 .

2R or not 2R is not the question anymore

Yves Van de Peer, Steven Maere, Axel Meyer, 2010, Nature Reviews Genetics.

Evolutionary Relationships Among the Eukaryotic Crown Taxa Taking into Account Site-to-Site Rate Variation in 18S rRNA

Yves Van de Peer, Rupert De Wachter, Y. Peer, 1997, Journal of Molecular Evolution.

Revisiting recent challenges to the ancient fish-specific genome duplication hypothesis

Yves Van de Peer, Axel Meyer, A. Meyer, 2001, Current Biology.

Genome sequence of the recombinant protein production host Pichia pastoris

Yves Van de Peer, Yao-Cheng Lin, Pierre Rouzé, 2009, Nature Biotechnology.

The genome of the seagrass Zostera marina reveals angiosperm adaptation to the sea

Erich Bornberg-Bauer, Yves Van de Peer, Yao-Cheng Lin, 2016, Nature.

A Snapshot of the Emerging Tomato Genome Sequence

Giorgio Valle, Ying Wang, Vikrant Gupta, 2009 .

Evolution according to large ribosomal subunit RNA

Yves Van de Peer, Rupert De Wachter, Peter De Rijk, 1995, Journal of Molecular Evolution.

Computational approaches to unveiling ancient genome duplications

Yves Van de Peer, Y. Peer, 2009 .

Inferring Transcriptional Networks by Mining 'Omics' Data

Kathleen Marchal, Yves Van de Peer, Tim Van den Bulcke, 2006 .