-
1
-
-
0028685490
-
Fitting a mixture model by expectation maximization to discover motifs in biopolymers
-
Bailey,T.L. and Elkan,C. (1994) Fitting a mixture model by expectation maximization to discover motifs in biopolymers. Proc. Int. Conf. Intell. Syst. Mol. Biol., 2, 28-36.
-
(1994)
Proc. Int. Conf. Intell. Syst. Mol. Biol.
, vol.2
, pp. 28-36
-
-
Bailey, T.L.1
Elkan, C.2
-
2
-
-
38549096565
-
JASPAR, the open access database of transcription factorbinding profiles: new content and tools in the 2008 update
-
Bryne,J.C. et al. (2008) JASPAR, the open access database of transcription factorbinding profiles: new content and tools in the 2008 update. Nucleic Acids Res., 36, D102-D106.
-
(2008)
Nucleic Acids Res.
, vol.36
-
-
Bryne, J.C.1
-
3
-
-
44649117905
-
Integration of external signaling pathways with the core transcriptional network in embryonic stem cells
-
Chen,X. et al. (2008) Integration of external signaling pathways with the core transcriptional network in embryonic stem cells. Cell, 133, 1106-1117.
-
(2008)
Cell
, vol.133
, pp. 1106-1117
-
-
Chen, X.1
-
4
-
-
33846689706
-
Using GOstats to test gene lists for GO term association
-
Falcon,S. and Gentleman,R. (2007) Using GOstats to test gene lists for GO term association. Bioinformatics, 23, 257-258.
-
(2007)
Bioinformatics
, vol.23
, pp. 257-258
-
-
Falcon, S.1
Gentleman, R.2
-
5
-
-
68949213578
-
Insights from genomic profiling of transcription factors
-
Farnham,P.J. (2009) Insights from genomic profiling of transcription factors. Nat. Rev. Genet., 10, 605-616.
-
(2009)
Nat. Rev. Genet.
, vol.10
, pp. 605-616
-
-
Farnham, P.J.1
-
6
-
-
77955801615
-
Galaxy: a comprehensive approach for supporting accessible, reproducible, and transparent computational research in the life sciences
-
Goecks,J. et al. (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
-
-
Goecks, J.1
-
7
-
-
0032826179
-
Identifying DNA and protein patterns with statistically significant alignments of multiple sequences
-
Hertz,G.Z. and Stormo,G.D. (1999) Identifying DNA and protein patterns with statistically significant alignments of multiple sequences. Bioinformatics, 15, 563-577.
-
(1999)
Bioinformatics
, vol.15
, pp. 563-577
-
-
Hertz, G.Z.1
Stormo, G.D.2
-
8
-
-
77957818564
-
Deep and wide digging for binding motifs in ChIP-Seq data
-
Kulakovskiy,I.V. et al. (2010) Deep and wide digging for binding motifs in ChIP-Seq data. Bioinformatics, 26, 2622-2623.
-
(2010)
Bioinformatics
, vol.26
, pp. 2622-2623
-
-
Kulakovskiy, I.V.1
-
9
-
-
77956339477
-
CUDA-MEME: Accelerating motif discovery in biological sequences using CUDA-enabled graphics processing units
-
Liu,Y. et al. (2010) CUDA-MEME: Accelerating motif discovery in biological sequences using CUDA-enabled graphics processing units. Pattern Recognit. Lett., 31, 2170-2177.
-
(2010)
Pattern Recognit. Lett.
, vol.31
, pp. 2170-2177
-
-
Liu, Y.1
-
10
-
-
34547569191
-
STAMP: a web tool for exploring DNA-binding motif similarities
-
Mahony,S. and Benos,P.V. (2007) STAMP: a web tool for exploring DNA-binding motif similarities. Nucleic Acids Res., 35, W253-W258.
-
(2007)
Nucleic Acids Res.
, vol.35
-
-
Mahony, S.1
Benos, P.V.2
-
11
-
-
0037208166
-
TRANSFAC: transcriptional regulation, from patterns to profiles
-
Matys,V. et al. (2003) TRANSFAC: transcriptional regulation, from patterns to profiles. Nucleic Acids Res., 31, 374-378.
-
(2003)
Nucleic Acids Res.
, vol.31
, pp. 374-378
-
-
Matys, V.1
-
12
-
-
3242884167
-
Weeder Web: discovery of transcription factor binding sites in a set of sequences from co-regulated genes
-
Pavesi,G. et al. (2004) Weeder Web: discovery of transcription factor binding sites in a set of sequences from co-regulated genes. Nucleic Acids Res., 32, W199-W203.
-
(2004)
Nucleic Acids Res.
, vol.32
-
-
Pavesi, G.1
-
13
-
-
0042424602
-
Statistical significance for genomewide studies
-
Storey,J.D. and Tibshirani,R. (2003) Statistical significance for genomewide studies. Proc. Natl Acad. Sci. USA, 100, 9440-9445.
-
(2003)
Proc. Natl Acad. Sci. USA
, vol.100
, pp. 9440-9445
-
-
Storey, J.D.1
Tibshirani, R.2
-
14
-
-
77949505440
-
Tmod: toolbox of motif discovery
-
Sun,H. et al. (2010) Tmod: toolbox of motif discovery. Bioinformatics, 26, 405-407.
-
(2010)
Bioinformatics
, vol.26
, pp. 405-407
-
-
Sun, H.1
-
15
-
-
48449090922
-
RSAT: regulatory sequence analysis tools
-
Thomas-Chollier,M. et al. (2008) RSAT: regulatory sequence analysis tools. Nucleic Acids Res., 36, W119-W127.
-
(2008)
Nucleic Acids Res.
, vol.36
-
-
Thomas-Chollier, M.1
-
16
-
-
21144439147
-
Assessing computational tools for the discovery of transcription factor binding sites
-
Tompa,M. et al. (2005) Assessing computational tools for the discovery of transcription factor binding sites. Nat. Biotechnol., 23, 137-144.
-
(2005)
Nat. Biotechnol.
, vol.23
, pp. 137-144
-
-
Tompa, M.1
-
17
-
-
73449094886
-
Discovery of regulatory elements is improved by a discriminatory approach
-
Valen,E. et al. (2009) Discovery of regulatory elements is improved by a discriminatory approach. PLoS. Comput. Biol., 5, e1000562.
-
(2009)
PLoS. Comput. Biol.
, vol.5
-
-
Valen, E.1
-
18
-
-
79952001349
-
GimmeMotifs: a de novo motif prediction pipeline for ChIP-sequencing experiments
-
[Epub ahead of print, November 15]
-
van Heeringen,S.J. and Veenstra,G.J. (2010) GimmeMotifs: a de novo motif prediction pipeline for ChIP-sequencing experiments. Bioinformatics, [Epub ahead of print, November 15, 2010].
-
(2010)
Bioinformatics
-
-
van Heeringen, S.J.1
Veenstra, G.J.2
-
19
-
-
1842584947
-
Applied bioinformatics for the identification of regulatory elements
-
Wasserman,W.W. and Sandelin,A. (2004) Applied bioinformatics for the identification of regulatory elements. Nat. Rev. Genet., 5, 276-287.
-
(2004)
Nat. Rev. Genet.
, vol.5
, pp. 276-287
-
-
Wasserman, W.W.1
Sandelin, A.2
|