-
1
-
-
0032483307
-
Extracting regulatory sites from the upstream region of yeast genes by computational analysis of oligonucleotide frequencies
-
van Helden, J., André, B. and Collado-Vides, J. (1998) Extracting regulatory sites from the upstream region of yeast genes by computational analysis of oligonucleotide frequencies. J. Mol. Biol., 281, 827-842.
-
(1998)
J. Mol. Biol.
, vol.281
, pp. 827-842
-
-
Van Helden, J.1
André, B.2
Collado-Vides, J.3
-
2
-
-
0034731822
-
A web site for the computational analysis of yeast regulatory sequences
-
van Helden, J., Collado-Vides, J., André, B. and Andr, B. (2000) A web site for the computational analysis of yeast regulatory sequences. Yeast, 16, 177-187.
-
(2000)
Yeast
, vol.16
, pp. 177-187
-
-
Van Helden, J.1
Collado-Vides, J.2
André, B.3
Andr, B.4
-
3
-
-
0041620271
-
Regulatory sequence analysis tools
-
van Helden, J. (2003) Regulatory sequence analysis tools. Nucleic Acids Res., 31, 3593-3596.
-
(2003)
Nucleic Acids Res.
, vol.31
, pp. 3593-3596
-
-
Van Helden, J.1
-
4
-
-
48449090922
-
RSAT: Regulatory sequence analysis tools
-
Thomas-Chollier, M., Sand, O., Turatsinze, J.-V., Janky, R., Defrance, M., Vervisch, E., Brohée, S. and van Helden, J. (2008) RSAT: regulatory sequence analysis tools. Nucleic Acids Res., 36, W119-W127.
-
(2008)
Nucleic Acids Res.
, vol.36
, pp. W119-W127
-
-
Thomas-Chollier, M.1
Sand, O.2
Turatsinze, J.-V.3
Janky, R.4
Defrance, M.5
Vervisch, E.6
Brohée, S.7
Van Helden, J.8
-
5
-
-
79959954386
-
RSAT 2011: Regulatory sequence analysis tools
-
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 Res., 39, W86-W91.
-
(2011)
Nucleic Acids Res.
, vol.39
, pp. W86-W91
-
-
Thomas-Chollier, M.1
Defrance, M.2
Medina-Rivera, A.3
Sand, O.4
Herrmann, C.5
Thieffry, D.6
Van Helden, J.7
-
6
-
-
70349989504
-
Retrieve-ensembl-seq: User-friendly and large-scale retrieval of single or multi-genome sequences from Ensembl
-
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, 25, 2739-2740.
-
(2009)
Bioinformatics
, vol.25
, pp. 2739-2740
-
-
Sand, O.1
Thomas-Chollier, M.2
Van Helden, J.3
-
7
-
-
0034656326
-
Discovering regulatory elements in non-coding sequences by analysis of spaced dyads
-
van Helden, J., Rios, A.F. and Collado-Vides, J. (2000) Discovering regulatory elements in non-coding sequences by analysis of spaced dyads. Nucleic Acids Res., 28, 1808-1818.
-
(2000)
Nucleic Acids Res.
, vol.28
, pp. 1808-1818
-
-
Van Helden, J.1
Rios, A.F.2
Collado-Vides, J.3
-
8
-
-
0034651804
-
Statistical analysis of yeast genomic downstream sequences reveals putative polyadenylation signals
-
van Helden, J., del Olmo, M. and Pérez-Ortín, J.E. (2000) Statistical analysis of yeast genomic downstream sequences reveals putative polyadenylation signals. Nucleic Acids Res., 28, 1000-1010.
-
(2000)
Nucleic Acids Res.
, vol.28
, pp. 1000-1010
-
-
Van Helden, J.1
Del Olmo, M.2
Pérez-Ortín, J.E.3
-
9
-
-
84857859359
-
RSAT peak-motifs: Motif analysis in full-size ChIP-seq datasets
-
Thomas-Chollier, M., Herrmann, C., Defrance, M., Sand, O., Thieffry, D. and van Helden, J. (2012) RSAT peak-motifs: motif analysis in full-size ChIP-seq datasets. Nucleic Acids Res., 40, e31.
-
(2012)
Nucleic Acids Res.
, vol.40
, pp. e31
-
-
Thomas-Chollier, M.1
Herrmann, C.2
Defrance, M.3
Sand, O.4
Thieffry, D.5
Van Helden, J.6
-
10
-
-
84864425198
-
A complete workflow for the analysis of full-size ChIP-seq (and similar) data sets using peak-motifs
-
Thomas-Chollier, M., Darbo, E., Herrmann, C., Defrance, M., Thieffry, D. and 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, 1551-1568.
-
(2012)
Nat. Protoc.
, vol.7
, pp. 1551-1568
-
-
Thomas-Chollier, M.1
Darbo, E.2
Herrmann, C.3
Defrance, M.4
Thieffry, D.5
Van Helden, J.6
-
11
-
-
52749097035
-
Using RSAT to scan genome sequences for transcription factor binding sites and cis-regulatory modules
-
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.
-
(2008)
Nat. Protoc.
, vol.3
, pp. 1578-1588
-
-
Turatsinze, J.-V.1
Thomas-Chollier, M.2
Defrance, M.3
Van Helden, J.4
-
12
-
-
79951570672
-
Theoretical and empirical quality assessment of transcription factor-binding motifs
-
Medina-Rivera, A., Abreu-Goodger, C., Thomas-Chollier, M., Salgado, H., Collado-Vides, J. and van Helden, J. (2010) Theoretical and empirical quality assessment of transcription factor-binding motifs. Nucleic Acids Res., 39, 808-824.
-
(2010)
Nucleic Acids Res.
, vol.39
, pp. 808-824
-
-
Medina-Rivera, A.1
Abreu-Goodger, C.2
Thomas-Chollier, M.3
Salgado, H.4
Collado-Vides, J.5
Van Helden, J.6
-
13
-
-
84891808382
-
JASPAR 2014: An extensively expanded and updated open-access database of transcription factor binding profiles
-
Mathelier, A., Zhao, X., Zhang, A.W., Parcy, F., Worsley-Hunt, R., Arenillas, D.J., Buchman, S., Chen, C.-Y., Chou, A., Ienasescu, H. et al. (2013) JASPAR 2014: an extensively expanded and updated open-access database of transcription factor binding profiles. Nucleic Acids Res., 42, D142-D147.
-
(2013)
Nucleic Acids Res.
, vol.42
, pp. D142-D147
-
-
Mathelier, A.1
Zhao, X.2
Zhang, A.W.3
Parcy, F.4
Worsley-Hunt, R.5
Arenillas, D.J.6
Buchman, S.7
Chen, C.-Y.8
Chou, A.9
Ienasescu, H.10
-
14
-
-
84891790401
-
The NHGRI GWAS Catalog, a curated resource of SNP-trait associations
-
Welter, D., MacArthur, J., Morales, J., Burdett, T., Hall, P., Junkins, H., Klemm, A., Flicek, P., Manolio, T., Hindorff, L. et al. (2014) The NHGRI GWAS Catalog, a curated resource of SNP-trait associations. Nucleic Acids Res., 42, D1001-D1006.
-
(2014)
Nucleic Acids Res.
, vol.42
, pp. D1001-D1006
-
-
Welter, D.1
MacArthur, J.2
Morales, J.3
Burdett, T.4
Hall, P.5
Junkins, H.6
Klemm, A.7
Flicek, P.8
Manolio, T.9
Hindorff, L.10
-
15
-
-
84865822182
-
Systematic localization of common disease-associated variation in regulatory DNA
-
Maurano, M.T., Humbert, R., Rynes, E., Thurman, R.E., Haugen, E., Wang, H., Reynolds, A.P., Sandstrom, R., Qu, H., Brody, J. et al. (2012) Systematic localization of common disease-associated variation in regulatory DNA. Science, 337, 1190-1195.
-
(2012)
Science
, vol.337
, pp. 1190-1195
-
-
Maurano, M.T.1
Humbert, R.2
Rynes, E.3
Thurman, R.E.4
Haugen, E.5
Wang, H.6
Reynolds, A.P.7
Sandstrom, R.8
Qu, H.9
Brody, J.10
-
16
-
-
84870495767
-
Genic and nongenic contributions to natural variation of quantitative traits in maize
-
Li, X., Zhu, C., Yeh, C.-T., Wu, W., Takacs, E.M., Petsch, K.A., Tian, F., Bai, G., Buckler, E.S., Muehlbauer, G.J. et al. (2012) Genic and nongenic contributions to natural variation of quantitative traits in maize. Genome Res., 22, 2436-2444.
-
(2012)
Genome Res.
, vol.22
, pp. 2436-2444
-
-
Li, X.1
Zhu, C.2
Yeh, C.-T.3
Wu, W.4
Takacs, E.M.5
Petsch, K.A.6
Tian, F.7
Bai, G.8
Buckler, E.S.9
Muehlbauer, G.J.10
-
17
-
-
39749171239
-
Evaluation of phylogenetic footprint discovery for predicting bacterial cis-regulatory elements and revealing their evolution
-
Janky, R. and van Helden, J. (2008) Evaluation of phylogenetic footprint discovery for predicting bacterial cis-regulatory elements and revealing their evolution. BMC Bioinformatics, 9, 37.
-
(2008)
BMC Bioinformatics
, vol.9
, pp. 37
-
-
Janky, R.1
Van Helden, J.2
-
18
-
-
80055069400
-
Unraveling networks of co-regulated genes on the sole basis of genome sequences
-
Brohée, S., Janky, R., Abdel-Sater, F., Vanderstocken, G., André, B. and van Helden, J. (2011) Unraveling networks of co-regulated genes on the sole basis of genome sequences. Nucleic Acids Res., 39, 6340-6358.
-
(2011)
Nucleic Acids Res.
, vol.39
, pp. 6340-6358
-
-
Brohée, S.1
Janky, R.2
Abdel-Sater, F.3
Vanderstocken, G.4
André, B.5
Van Helden, J.6
-
19
-
-
67849122320
-
MEME SUITE: Tools for motif discovery and searching
-
Bailey, T.L., Boden, M., Buske, F.A., Frith, M., Grant, C.E., Clementi, L., Ren, J., Li, W.W. and Noble, W.S. (2009) MEME SUITE: tools for motif discovery and searching. Nucleic Acids Res., 37, W202-W208.
-
(2009)
Nucleic Acids Res.
, vol.37
, pp. W202-W208
-
-
Bailey, T.L.1
Boden, M.2
Buske, F.A.3
Frith, M.4
Grant, C.E.5
Clementi, L.6
Ren, J.7
Li, W.W.8
Noble, W.S.9
-
20
-
-
84876543942
-
Regulon DB v8.0: Omics data sets, evolutionary conservation, regulatory phrases, cross-validated gold standards and more
-
Salgado, H., Peralta-Gil, M., Gama-Castro, S., Santos-Zavaleta, A., Muñiz-Rascado, L., García-Sotelo, J.S., Weiss, V., Solano-Lira, H., Martínez-Flores, I., Medina-Rivera, A. et al. (2013) Regulon DB v8.0: omics data sets, evolutionary conservation, regulatory phrases, cross-validated gold standards and more. Nucleic Acids Res., 41, D203-D213.
-
(2013)
Nucleic Acids Res.
, vol.41
, pp. D203-D213
-
-
Salgado, H.1
Peralta-Gil, M.2
Gama-Castro, S.3
Santos-Zavaleta, A.4
Muñiz-Rascado, L.5
García-Sotelo, J.S.6
Weiss, V.7
Solano-Lira, H.8
Martínez-Flores, I.9
Medina-Rivera, A.10
-
21
-
-
84892758927
-
Footprint DB: A database of transcription factors with annotated cis elements and binding interfaces
-
Sebastian, A. and Contreras-Moreira, B. (2014) footprint DB: a database of transcription factors with annotated cis elements and binding interfaces. Bioinformatics, 30, 258-265.
-
(2014)
Bioinformatics
, vol.30
, pp. 258-265
-
-
Sebastian, A.1
Contreras-Moreira, B.2
-
22
-
-
84891822189
-
Ensembl genomes 2013: Scaling up access to genome-wide data
-
Kersey, P.J., Allen, J.E., Christensen, M., Davis, P., Falin, L.J., Grabmueller, C., Hughes, D.S.T., Humphrey, J., Kerhornou, A., Khobova, J. et al. (2014) Ensembl Genomes 2013: scaling up access to genome-wide data. Nucleic Acids Res., 42, D546-D552.
-
(2014)
Nucleic Acids Res.
, vol.42
, pp. D546-D552
-
-
Kersey, P.J.1
Allen, J.E.2
Christensen, M.3
Davis, P.4
Falin, L.J.5
Grabmueller, C.6
Hughes, D.S.T.7
Humphrey, J.8
Kerhornou, A.9
Khobova, J.10
-
23
-
-
36548999724
-
Discovery of conserved motifs in promoters of orthologous genes in prokaryotes
-
Janky, R. and van Helden, J. (2007) Discovery of conserved motifs in promoters of orthologous genes in prokaryotes. Methods Mol. Biol., 395, 293-308.
-
(2007)
Methods Mol. Biol.
, vol.395
, pp. 293-308
-
-
Janky, R.1
Van Helden, J.2
-
24
-
-
36549062896
-
Discovery of motifs in promoters of coregulated genes
-
Sand, O. and van Helden, J. (2007) Discovery of motifs in promoters of coregulated genes. Methods Mol. Biol., 395, 329-348.
-
(2007)
Methods Mol. Biol.
, vol.395
, pp. 329-348
-
-
Sand, O.1
Van Helden, J.2
-
25
-
-
52749089913
-
Network analysis tools: From biological networks to clusters and pathways
-
Brohée, S., Faust, K., Lima-Mendez, G., Vanderstocken, G. and van Helden, J. (2008) Network Analysis Tools: from biological networks to clusters and pathways. Nat. Protoc., 3, 1616-1629.
-
(2008)
Nat. Protoc.
, vol.3
, pp. 1616-1629
-
-
Brohée, S.1
Faust, K.2
Lima-Mendez, G.3
Vanderstocken, G.4
Van Helden, J.5
-
26
-
-
52749092937
-
Using RSAT oligo-analysis and dyad-analysis tools to discover regulatory signals in nucleic sequences
-
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.
-
(2008)
Nat. Protoc.
, vol.3
, pp. 1589-1603
-
-
Defrance, M.1
Janky, R.2
Sand, O.3
Van Helden, J.4
-
27
-
-
52749085084
-
Analyzing multiple data sets by interconnecting RSAT programs via SOAPWeb services: An example with ChIP-chip data
-
Sand, O., Thomas-Chollier, M., Vervisch, E. and van Helden, J. (2008) Analyzing multiple data sets by interconnecting RSAT programs via SOAPWeb services: an example with ChIP-chip data. Nat. Protoc., 3, 1604-1615.
-
(2008)
Nat. Protoc.
, vol.3
, pp. 1604-1615
-
-
Sand, O.1
Thomas-Chollier, M.2
Vervisch, E.3
Van Helden, J.4
-
28
-
-
77955801615
-
Galaxy: A comprehensive approach for supporting accessible, reproducible, and transparent computational research in the life sciences
-
Goecks, J., Nekrutenko, A., Taylor, J. and Galaxy Team (2010) Galaxy: a comprehensive approach for supporting accessible, reproducible, and transparent computational research in the life sciences. Genome Biol., 11, R86.
-
(2010)
Genome Biol.
, vol.11
, pp. R86
-
-
Goecks, J.1
Nekrutenko, A.2
Taylor, J.3
Team, G.4
|