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
15012005
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
9611998
Evaluation of clustering algorithms for protein-protein interaction networks
S Brohee, J van Helden
BMC bioinformatics 7 (1), 488, 2006
8912006
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
6622007
Regulatory sequence analysis tools
J Van Helden
Nucleic acids research 31 (13), 3593-3596, 2003
5122003
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
4252000
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
3872005
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
3032008
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
2642011
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
2512008
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
2512007
RSAT 2015: Regulatory Sequence Analysis Tools
A Medina-Rivera, M Defrance, O Sand, C Herrmann, ...
Nucleic acids research, gkv362, 2015
2292015
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
2132011
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
2122000
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
2082008
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
1962009
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
1932008
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
1772010
Statistical analysis of yeast genomic downstream sequences reveals putative polyadenylation signals
J van Helden, M lí del Olmo, JE Pérez-Ortín
Nucleic acids research 28 (4), 1000-1010, 2000
1702000
Molecular evolution of eukaryotic genomes: hemiascomycetous yeast spliceosomal introns
E Bon, S Casaregola, G Blandin, B Llorente, C Neuvéglise, ...
Nucleic acids research 31 (4), 1121-1135, 2003
1582003
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