2016
Contreras-Moreira B, Castro-Mondragon JA, Rioualen C,
Cantalapiedra CP, van Helden J. (2016). RSAT::Plants: Motif
Discovery Within Clusters of Upstream Sequences in Plant
Genomes. Methods Mol Biol. 1482:279-95. doi:
10.1007/978-1-4939-6396-6_18.
[PMID 27557774]
Castro-Mondragon JA, Rioualen C, Contreras-Moreira B, van
Helden J. (2016). RSAT::Plants: Motif Discovery in ChIP-Seq
Peaks of Plant Genomes. Methods Mol Biol. 1482:297-322. doi:
10.1007/978-1-4939-6396-6_19.
[PMID 27557775]
2015
Medina-Rivera A, Defrance M, Sand O, Herrmann C,
Castro-Mondragon J, Delerce J, Jaeger S, Blanchet C, Vincens P,
Caron C, Staines DM, Contreras-Moreira B, Artufel M,
Charbonnier-Khamvongsa L, Hernandez C, Thieffry D,
Thomas-Chollier M, van Helden J (2015) RSAT 2015: Regulatory
Sequence Analysis Tools . Nucleic Acids Res. 2015 (Web
Server issue) in press.
[Full text]
2012
Thomas-Chollier M, Darbo E, Herrmann C, Defrance M, Thieffry
D, van Helden J. (2012). A complete workflow for the analysis
of full-size ChIP-seq (and similar) data sets using
peak-motifs. Nat Protoc 7(8): 1551-1568.
[PMID 22836136]
Thomas-Chollier M, Herrmann C, Defrance M, Sand O, Thieffry D,
van Helden J. (2012). RSAT peak-motifs: motif analysis in
full-size ChIP-seq datasets. Nucleic Acids Res 40(4): e31.
[PMID 22156162]
[Open access]
2011
-
Thomas-Chollier, M., Defrance, M., Medina-Rivera, A., Sand, O.,
Herrmann, C., Thieffry, D. and van Helden, J. (2011). RSAT 2011:
Regulatory Sequence Analysis Tools. Nucleic Acids Research, 2011,
Vol. 39, W86-W91. Web Server issue doi:10.1093/nar/gkr377.
[PMID 21715389]
[Open
access]
-
Brohee, S., Janky, R., Abdel-Sater, F., Vanderstocken, G., Andre,
B. and van Helden, J. (2011). Unraveling networks of co-regulated
genes on the sole basis of genome sequences. Nucleic Acids Res 39,
6340-58.
[PMID
21572103] [Open
access]
2010
-
Medina-Rivera, A., Abreu-Goodger, C., Salgado-Osorio, H.,
Collado-Vides, J. and van Helden, J. (2010). Empirical and
theoretical evaluation of transcription factor binding
motifs. Nucleic Acids Res. 2010 Oct 4. [Epub ahead of print]
[Pubmed
20923783]
[Full
text].
2009
- Sand, O., Thomas-Chollier, M. and van Helden,
J. (2009). Retrieve-ensembl-seq: user-friendly and large-scale
retrieval of single or multi-genome sequences from
Ensembl. Bioinformatics,
2009. DOI:10.1093/bioinformatics/btp519. Pubmed
19720677.
- Defrance, M. and Helden, J. V. (2009). Info-gibbs: a motif
discovery algorithm that directly optimizes information content during
sampling. Bioinformatics. Pubmed
19689955
- Janky, R., Helden, J. V. and Babu, M. M. (2009). Investigating
transcriptional regulation: From analysis of complex networks to
discovery of cis-regulatory
elements. Methods. [Pubmed
19450688] [On line].
- Vingron, M., Brazma, A., Coulson, R., van Helden, J., Manke, T.,
Palin, K., Sand, O. and Ukkonen, E. (2009). Integrating sequence,
evolution and functional genomics in regulatory genomics. Genome Biol 10,
202.
Pubmed
19226437
2008
- Sand, O., Thomas-Chollier, M., Vervisch, E. and van Helden,
J. (2008) Analyzing multiple data sets by interconnecting RSAT
programs via SOAP Web services-an example with ChIP-chip data. Nat
Protoc, 3,
1604-1615. Pubmed 18802441
- Defrance, M., Janky, R., Sand, O. and van Helden, J. (2008)
Using RSAT oligo-analysis and dyad-analysis tools to discover
regulatory signals in nucleic sequences. Nat Protoc, 3,
1589-1603. Pubmed 18802440
- Turatsinze, J.V., Thomas-Chollier, M., Defrance, M. and van
Helden, J. (2008) Using RSAT to scan genome sequences for
transcription factor binding sites and cis-regulatory modules. Nat
Protoc, 3, 1578-1588.
Pubmed
18802439
- Thomas-Chollier, M., Sand, O., Turatsinze, J. V., Janky, R.,
Defrance, M., Vervisch, E., Brohee, S. & van Helden, J. (2008). RSAT:
regulatory sequence analysis tools. Nucleic Acids
Res.
[Pubmed 18495751]
[Full text]
- Janky, R. and van Helden, J. Evaluation of phylogenetic
footprint discovery for the prediction of bacterial cis-regulatory
elements (2008). BMC Bioinformatics 2008, 9:37doi:10.1186/1471-2105-9-37.
[Pubmed 18215291]
[Full text]
- Sand, O., Turatsinze, J. V. and van Helden,
J. (2008). Evaluating the prediction of cis-acting regulatory elements
in genome sequences. In Frishman, D. and Valencia, A. (eds.), Modern
genome annotation: the BioSapiens network. Springer.
- Coulson, R., Manke, T., Palin, K., Roider, H., Sand, O., van
Helden, J., Ukkonen, E., Vingron, M. and Brazma, A. (2008). From
gene expression profiling to gene regulation. In Frishman, D. and
Valencia, A. (eds.), Modern genome annotation: the BioSapiens
network. Springer.
2007
- Aerts, S., van Helden, J., Sand, O. & Hassan,
B. A. (2007). Fine-Tuning Enhancer Models to Predict Transcriptional
Targets across Multiple Genomes. PLoS ONE 2, e1115.
Pubmed
17973026.
- Sand, O. & van Helden, J. (2007). Discovery of motifs in
promoters of co-regulated genes. In Comparative
genomics. Methods in Molecular Biology. ISBN 978-1-58829-693-1
[publisher
site]
- Janky, R. & van Helden, J. (2007). Discovery of conserved
motifs in promoters of orthologous genes or prokaryotes. In Comparative genomics. Methods in Molecular
Biology. ISBN 978-1-58829-693-1 [publisher site]
2005
- Tompa, M., Li, N., Bailey, T. L., Church, G. M., De Moor, B.,
Eskin, E., Favorov, A. V., Frith, M. C., Fu, Y., Kent, W. J., Makeev,
V. J., Mironov, A. A., Noble, W. S., Pavesi, G., Pesole, G., Regnier,
M., Simonis, N., Sinha, S., Thijs, G., van Helden, J., Vandenbogaert,
M., Weng, Z., Workman, C., Ye, C. & Zhu, Z. (2005). Assessing
computational tools for the discovery of transcription factor binding
sites. Nat Biotechnol 23, 137-44. Pubmed
15637633
- Gonze, D., S. Pinloche, O. Gascuel, and J. van
Helden. 2005. Discrimination of yeast genes involved in methionine and
phosphate metabolism on the basis of upstream
motifs. Bioinformatics. Pubmed
15998664.
2004
- van Helden, J. (2004). Metrics for comparing regulatory
sequences on the basis of pattern counts. Bioinformatics, 2004
20(3):399-406. [Pubmed
14764560] [Full
text via OUP]
- Simonis, N., J. Van Helden, G.N. Cohen, and
S.J. Wodak. 2004. Transcriptional regulation of protein complexes in
yeast. Genome Biol 5: R33. [Pubmed
15128447] [Full text]
- Simonis, N., S.J. Wodak, G.N. Cohen, and J. Van
Helden. 2004. Combining pattern discovery and discriminant analysis to
predict gene co-regulation. Bioinformatics. Pubmed
15073004
2003
- van Helden, J. (2003). Prediction of transcriptional regulation
by analysis of the non-coding genome. Current Genomics 4(3), 217-224.
- van Helden, J. (2003). Regulatory sequence analysis
tools. Nucleic Acids Res. 2003 Jul 1;31(13):3593-6. [Pubmed
12824373] [Full
text] [pdf]
2001
- van Helden, J., Gilbert, D., Wernisch, L., Schroeder, M. &
Wodak, S. (2001). Applications of regulatory sequence analysis and
metabolic network analysis to the interpretation of gene expression
data. Lecture Notes in Computer Sciences 2066: 155-172.
Last Century
- van Helden, J., Andr�, B. & Collado-Vides, J. (2000). A web
site for the computational analysis of yeast regulatory
sequences. Yeast 16(2), 177-187. [Pubmed
10641039]
- van Helden, J., Olmo, M. & Perez-Ortin,
J. E. (2000). Statistical analysis of yeast genomic downstream
sequences reveals putative polyadenylation signals. Nucleic Acids Res
28(4), 1000-1010. [Pubmed
10648794] [Full
text]
- van Helden, J., Rios, A. F. & Collado-Vides,
J. (2000). Discovering regulatory elements in intergenic sequences by
analysis of spaced dyads. Nucleic Acids Res. 28(8):1808-18. [Pubmed
10734201] [Full
text].
- van Helden, J., Andr�, B. & Collado-Vides,
J. (1998). Extracting regulatory sites from the upstream region of
yeast genes by computational analysis of oligonucleotide
frequencies. J Mol Biol 281(5), 827-42. [Pubmed
9719638]