Jacques van Helden
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Assessing computational tools for the discovery of transcription factor binding sites
M Tompa, N Li, TL Bailey, GM Church, B De Moor, E Eskin, AV Favorov, ...
Nature biotechnology 23 (1), 137-144, 2005
Evaluation of clustering algorithms for protein-protein interaction networks
S Brohee, J van Helden
BMC bioinformatics 7 (1), 488, 2006
Extracting regulatory sites from the upstream region of yeast genes by computational analysis of oligonucleotide frequencies
J van Helden, B André, J Collado-Vides
Journal of molecular biology 281 (5), 827-842, 1998
Discovery of functional elements in 12 Drosophila genomes using evolutionary signatures
A Stark, MF Lin, P Kheradpour, JS Pedersen, L Parts, JW Carlson, ...
Nature 450 (7167), 219, 2007
Regulatory sequence analysis tools
J Van Helden
Nucleic acids research 31 (13), 3593-3596, 2003
Discovering regulatory elements in non-coding sequences by analysis of spaced dyads
J Helden, A Rios, J Collado-Vides
Nucleic acids research 28 (8), 1808-1818, 2000
In vitro screening of a FDA approved chemical library reveals potential inhibitors of SARS-CoV-2 replication
F Touret, M Gilles, K Barral, A Nougairède, J van Helden, E Decroly, ...
Scientific reports 10 (1), 1-8, 2020
CYGD: the comprehensive yeast genome database
U Güldener, M Münsterkötter, G Kastenmüller, N Strack, J van Helden, ...
Nucleic acids research 33 (suppl_1), D364-D368, 2005
RSAT: regulatory sequence analysis tools
M Thomas-Chollier, O Sand, JV Turatsinze, R Janky, M Defrance, ...
Nucleic acids research 36 (suppl_2), W119-W127, 2008
Effect of 21 different nitrogen sources on global gene expression in the yeast Saccharomyces cerevisiae
P Godard, A Urrestarazu, S Vissers, K Kontos, G Bontempi, J van Helden, ...
Molecular and cellular biology 27 (8), 3065-3086, 2007
Using RSAT to scan genome sequences for transcription factor binding sites and cis-regulatory modules
JV Turatsinze, M Thomas-Chollier, M Defrance, J van Helden
Nature protocols 3 (10), 1578-1588, 2008
RSAT 2011: regulatory sequence analysis tools
M Thomas-Chollier, M Defrance, A Medina-Rivera, O Sand, C Herrmann, ...
Nucleic acids research 39 (suppl_2), W86-W91, 2011
RSAT 2015: Regulatory Sequence Analysis Tools
A Medina-Rivera, M Defrance, O Sand, C Herrmann, ...
Nucleic acids research, gkv362, 2015
RSAT peak-motifs: motif analysis in full-size ChIP-seq datasets
M Thomas-Chollier, C Herrmann, M Defrance, O Sand, D Thieffry, ...
Nucleic acids research 40 (4), e31-e31, 2011
Reticulate representation of evolutionary and functional relationships between phage genomes
G Lima-Mendez, J Van Helden, A Toussaint, R Leplae
Molecular biology and evolution 25 (4), 762-777, 2008
Genome-wide characterization of mammalian promoters with distal enhancer functions.
LTM Dao, AO Galindo-Albarrán, JA Castro-Mondragon, C Andrieu-Soler, ...
Nature genetics 49 (7), 1073, 2017
The powerful law of the power law and other myths in network biology
G Lima-Mendez, J van Helden
Molecular BioSystems 5 (12), 1482-1493, 2009
Prophinder: a computational tool for prophage prediction in prokaryotic genomes
G Lima-Mendez, J Van Helden, A Toussaint, R Leplae
Bioinformatics 24 (6), 863-865, 2008
Transcription factor regulation can be accurately predicted from the presence of target gene signatures in microarray gene expression data
A Essaghir, F Toffalini, L Knoops, A Kallin, J van Helden, JB Demoulin
Nucleic acids research 38 (11), e120-e120, 2010
A web site for the computational analysis of yeast regulatory sequences
J van Helden, B André, J Collado‐Vides
Yeast 16 (2), 177-187, 2000
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