-
1
-
-
1842433988
-
Computational detection of cis-regulatory modules
-
Aerts,S. et al. (2003) Computational detection of cis-regulatory modules. Bioinformatics, 19 (Suppl. 2), ii5-ii14.
-
(2003)
Bioinformatics
, vol.19
, Issue.SUPPL. 2
-
-
Aerts, S.1
-
2
-
-
0016518897
-
Efficient string matching
-
Aho,A. and Corasick,M. (1975) Efficient string matching. CACM, 18, 333-340.
-
(1975)
CACM
, vol.18
, pp. 333-340
-
-
Aho, A.1
Corasick, M.2
-
3
-
-
0030986188
-
The hardwiring of development: Organization and function of genomic regulatory systems
-
Arnone,M. and Davidson,E. (1997) The hardwiring of development: organization and function of genomic regulatory systems. Development 124, 1851-1864.
-
(1997)
Development
, vol.124
, pp. 1851-1864
-
-
Arnone, M.1
Davidson, E.2
-
4
-
-
84972496740
-
Poisson approximation and the Chen-Stein method
-
Arratia,R. et al. (1990) Poisson approximation and the Chen-Stein method. Stat. Sci., 5, 403-434.
-
(1990)
Stat. Sci
, vol.5
, pp. 403-434
-
-
Arratia, R.1
-
5
-
-
4043156577
-
Searching for statistically significant regulatory modules
-
Bailey,T. and Noble,W. (2003) Searching for statistically significant regulatory modules. Bioinformatics, 19, II16-II25.
-
(2003)
Bioinformatics
, vol.19
-
-
Bailey, T.1
Noble, W.2
-
7
-
-
12744263842
-
Computational identification of developmental enhancers: Conservation and function of transcription factor binding-site clusters in Drosophila melanogaster and Drosophila pseudoobscura
-
Berman,B. et al. (2004) Computational identification of developmental enhancers: Conservation and function of transcription factor binding-site clusters in Drosophila melanogaster and Drosophila pseudoobscura. Genome Biol., 5, R61.
-
(2004)
Genome Biol
, vol.5
-
-
Berman, B.1
-
8
-
-
0037154273
-
Exploiting transcription factor binding site clustering to identify cis-regulatory modules involved in pattern formation in the Drosophila genome
-
Berman,B.P. et al. (2002) Exploiting transcription factor binding site clustering to identify cis-regulatory modules involved in pattern formation in the Drosophila genome. Proc. Natl Acad. Sci. USA, 99, 757-762.
-
(2002)
Proc. Natl Acad. Sci. USA
, vol.99
, pp. 757-762
-
-
Berman, B.P.1
-
9
-
-
34548847506
-
A distance difference matrix approach to identifying transcription factors that regulate differential gene expression
-
Bleser,P.D. et al. (2007) A distance difference matrix approach to identifying transcription factors that regulate differential gene expression. Genome Biol., 8, R83.
-
(2007)
Genome Biol
, vol.8
-
-
Bleser, P.D.1
-
10
-
-
37849021289
-
-
Boeva,V. et al. (2007) Exact p-value calculation for heterotypic clusters of regulatory motifs and its application in computational annotation of cis-regulatory modules. Algorithms Mol. Biol., 2 13.
-
Boeva,V. et al. (2007) Exact p-value calculation for heterotypic clusters of regulatory motifs and its application in computational annotation of cis-regulatory modules. Algorithms Mol. Biol., 2 13.
-
-
-
-
11
-
-
0036607144
-
New computational approaches for analysis of cis-regulatory networks
-
Brown,C. et al. (2002) New computational approaches for analysis of cis-regulatory networks. Dev. Biol., 246, 86-102.
-
(2002)
Dev. Biol
, vol.246
, pp. 86-102
-
-
Brown, C.1
-
12
-
-
0001016345
-
The composition of the deoxyribonucleic acid of salmon sperm
-
Chargaff,E. et al. (1951) The composition of the deoxyribonucleic acid of salmon sperm. J. Biol. Chem., 192, 223-230.
-
(1951)
J. Biol. Chem
, vol.192
, pp. 223-230
-
-
Chargaff, E.1
-
13
-
-
0001067389
-
Poisson approximation for dependent trials
-
Chen,L.H.Y. (1975) Poisson approximation for dependent trials. Ann. Probab., 3, 534-545.
-
(1975)
Ann. Probab
, vol.3
, pp. 534-545
-
-
Chen, L.H.Y.1
-
14
-
-
0347987855
-
A self-organizing system of repressor gradients establishes segmental complexity in Drosophila
-
Clyde,D. et al. (2003) A self-organizing system of repressor gradients establishes segmental complexity in Drosophila. Nature, 426, 849-853.
-
(2003)
Nature
, vol.426
, pp. 849-853
-
-
Clyde, D.1
-
15
-
-
2142738304
-
Weblogo: A sequence logo generator
-
Crooks,G.E. et al. (2004) Weblogo: A sequence logo generator. Genome Res., 14, 1188-1190.
-
(2004)
Genome Res
, vol.14
, pp. 1188-1190
-
-
Crooks, G.E.1
-
16
-
-
0031585995
-
A statistical model for locating regulatory regions in genomic DNA
-
Crowley,E. et al. (1997) A statistical model for locating regulatory regions in genomic DNA. J. Mol. Biol., 268, 8-14.
-
(1997)
J. Mol. Biol
, vol.268
, pp. 8-14
-
-
Crowley, E.1
-
17
-
-
0029935832
-
Coordinate positioning of MEF2 and myogenin binding sites
-
Fickett,J.W. (1996) Coordinate positioning of MEF2 and myogenin binding sites. Gene, 172, GC19-GC32.
-
(1996)
Gene
, vol.172
-
-
Fickett, J.W.1
-
18
-
-
0042121118
-
Cluster-buster: Finding dense clusters of motifs in DNA sequences
-
Frith,M. et al. (2003) Cluster-buster: Finding dense clusters of motifs in DNA sequences. Nucleic Acids Res., 31, 3666-3668.
-
(2003)
Nucleic Acids Res
, vol.31
, pp. 3666-3668
-
-
Frith, M.1
-
19
-
-
0034777594
-
Detection of cis-element clusters in higher eukaryotic DNA
-
Frith,M.C. et al. (2001) Detection of cis-element clusters in higher eukaryotic DNA. Bioinformatics, 17, 878-889.
-
(2001)
Bioinformatics
, vol.17
, pp. 878-889
-
-
Frith, M.C.1
-
20
-
-
0037100636
-
Statistical significance of clusters of motifs represented by position specific scoring matrices in nucleotide sequences
-
Frith,M.C. et al. (2002) Statistical significance of clusters of motifs represented by position specific scoring matrices in nucleotide sequences. Nucleic Acids Res., 30, 3214-3224.
-
(2002)
Nucleic Acids Res
, vol.30
, pp. 3214-3224
-
-
Frith, M.C.1
-
21
-
-
2542584654
-
Detection of functional DNA motifs via statistical overrepresentation
-
Frith,M.C. et al. (2004) Detection of functional DNA motifs via statistical overrepresentation. Nucleic Acids Res., 32, 1372-1381.
-
(2004)
Nucleic Acids Res
, vol.32
, pp. 1372-1381
-
-
Frith, M.C.1
-
22
-
-
33746835021
-
Computational identification of transcriptional regulatory elements in DNA sequence
-
GuhaThakurta,D. (2006) Computational identification of transcriptional regulatory elements in DNA sequence. Nucleic Acids Res., 34, 3585-3598.
-
(2006)
Nucleic Acids Res
, vol.34
, pp. 3585-3598
-
-
GuhaThakurta, D.1
-
23
-
-
0034894539
-
Identifying target sites for cooperatively binding factors
-
GuhaThakurta,D. and Stormo,G.D. (2001) Identifying target sites for cooperatively binding factors. Bioinformatics, 17, 608-621.
-
(2001)
Bioinformatics
, vol.17
, pp. 608-621
-
-
GuhaThakurta, D.1
Stormo, G.D.2
-
24
-
-
18844396103
-
De novo cis-regulatory module elicitation for eukaryotic genomes
-
Gupta,M. and Liu,J.S. (2005) De novo cis-regulatory module elicitation for eukaryotic genomes. Proc. Natl Acad. Sci. USA, 102, 7079-7084.
-
(2005)
Proc. Natl Acad. Sci. USA
, vol.102
, pp. 7079-7084
-
-
Gupta, M.1
Liu, J.S.2
-
25
-
-
0036796540
-
Predicting transcription factor synergism
-
Hannenhalli,S. and Levy,S. (2002) Predicting transcription factor synergism. Nucleic Acids Res., 30, 4278-4284.
-
(2002)
Nucleic Acids Res
, vol.30
, pp. 4278-4284
-
-
Hannenhalli, S.1
Levy, S.2
-
26
-
-
4544352942
-
Transcriptional regulatory code of a eukaryotic genome
-
Harbison,C.T. et al. (2004) Transcriptional regulatory code of a eukaryotic genome. Nature, 431, 99-104.
-
(2004)
Nature
, vol.431
, pp. 99-104
-
-
Harbison, C.T.1
-
27
-
-
48549104329
-
Using transcription factor binding site co-occurrence to predict regulatory regions
-
Klein,H. and Vingron,M. (2007) Using transcription factor binding site co-occurrence to predict regulatory regions. Genome Inform., 18 109-118.
-
(2007)
Genome Inform
, vol.18
, pp. 109-118
-
-
Klein, H.1
Vingron, M.2
-
28
-
-
0032948782
-
Functional promoter modules can be detected by formal models independent of overall nucleotide sequence similarity
-
Klingenhoff,A. et al. (1999) Functional promoter modules can be detected by formal models independent of overall nucleotide sequence similarity. Bioinformatics, 15, 180-186.
-
(1999)
Bioinformatics
, vol.15
, pp. 180-186
-
-
Klingenhoff, A.1
-
29
-
-
4043089376
-
Searching for transcription factor binding site clusters: How true are true positives?
-
Krivan,W. (2004) Searching for transcription factor binding site clusters: How true are true positives? J. Bioinform. Comput. Biol. 2, 413-416.
-
(2004)
J. Bioinform. Comput. Biol
, vol.2
, pp. 413-416
-
-
Krivan, W.1
-
30
-
-
0037398319
-
Uniform clusters in Drosophila
-
Lifanov,A. et al. (2003) Uniform clusters in Drosophila. Genome Res., 13, 579-588.
-
(2003)
Genome Res
, vol.13
, pp. 579-588
-
-
Lifanov, A.1
-
31
-
-
26444566379
-
-
Manke,T. et al. (2005) Detecting functional modules of transcription factor binding sites in the human genome. In Lecture Notes in Computer Science. Springer, Berlin/Heidelberg.
-
Manke,T. et al. (2005) Detecting functional modules of transcription factor binding sites in the human genome. In Lecture Notes in Computer Science. Springer, Berlin/Heidelberg.
-
-
-
-
32
-
-
0037154218
-
Genome-wide analysis of clustered dorsal binding sites identifies putative target genes in the Drosophila embryo
-
Markstein,M. et al. (2002) Genome-wide analysis of clustered dorsal binding sites identifies putative target genes in the Drosophila embryo. Proc. Natl Acad. Sci. USA, 99, 763-768.
-
(2002)
Proc. Natl Acad. Sci. USA
, vol.99
, pp. 763-768
-
-
Markstein, M.1
-
33
-
-
0037208166
-
TRANSFAC(R): Transcriptional regulation, from patterns to profiles
-
Matys,V. et al. (2003) TRANSFAC(R): Transcriptional regulation, from patterns to profiles. Nucleic Acids Res., 31, 374-378.
-
(2003)
Nucleic Acids Res
, vol.31
, pp. 374-378
-
-
Matys, V.1
-
34
-
-
33644876958
-
Transfac(r) and its module transcompel(r): Transcriptional gene regulation in eukaryotes
-
Matys,V. et al. (2006) Transfac(r) and its module transcompel(r): transcriptional gene regulation in eukaryotes. Nucleic Acids Res., 34 (Suppl. 1), D108-D110.
-
(2006)
Nucleic Acids Res
, vol.34
, Issue.SUPPL. 1
-
-
Matys, V.1
-
35
-
-
34249676873
-
Clusterdraw web server: A tool to identify and visualize clusters of binding motifs for transcription factors
-
Papatsenko,D. (2007) Clusterdraw web server: A tool to identify and visualize clusters of binding motifs for transcription factors. Bioinformatics, 23, 1032-1034.
-
(2007)
Bioinformatics
, vol.23
, pp. 1032-1034
-
-
Papatsenko, D.1
-
36
-
-
85193596218
-
-
Extraction of functional binding sites from unique regulatory regions: The Drosophila early developmental enhancers, Preliminary version in Drosophila Workshop, Washington
-
Papatsenko,D. et al. (2002) Extraction of functional binding sites from unique regulatory regions: The Drosophila early developmental enhancers. Genome Res., 12, 470-481. [Preliminary version in Drosophila Workshop, Washington 2001].
-
(2001)
Genome Res
, vol.12
, pp. 470-481
-
-
Papatsenko, D.1
-
37
-
-
68549103287
-
-
Ph.D. Thesis, Library of the Free University of Berlin, IMPRS for Computional Biology and Scientific Computing, Max Planck Institute for Molecular Genetics
-
Pape,U.J. (2008) Statistics for Transcription Factor Binding Sites Ph.D. Thesis, Library of the Free University of Berlin, IMPRS for Computional Biology and Scientific Computing, Max Planck Institute for Molecular Genetics.
-
(2008)
Statistics for Transcription Factor Binding Sites
-
-
Pape, U.J.1
-
39
-
-
34447503964
-
A new statistical model to select target sequences bound by transcription factors
-
Pape,U.J. et al. (2006) A new statistical model to select target sequences bound by transcription factors. Genome Inform., 17 134-140.
-
(2006)
Genome Inform
, vol.17
, pp. 134-140
-
-
Pape, U.J.1
-
40
-
-
47549096411
-
Compound Poisson approximation of number of occurrences of a position frequency matrix (PFM) on both strands
-
Pape,U.J. et al. (2008a) Compound Poisson approximation of number of occurrences of a position frequency matrix (PFM) on both strands. J. Comput. Biol., 15, 547-564.
-
(2008)
J. Comput. Biol
, vol.15
, pp. 547-564
-
-
Pape, U.J.1
-
41
-
-
38849122853
-
Natural similarity measures between position frequency matrices with an application to clustering
-
Pape,U.J. et al. (2008b) Natural similarity measures between position frequency matrices with an application to clustering. Bioinformatics, 24, 350-357.
-
(2008)
Bioinformatics
, vol.24
, pp. 350-357
-
-
Pape, U.J.1
-
42
-
-
0034785443
-
Identifying regulatory networks by combinatorial analysis of promoter elements
-
Pilpel,Y. et al. (2001) Identifying regulatory networks by combinatorial analysis of promoter elements. Nat. Genet., 29 153-159.
-
(2001)
Nat. Genet
, vol.29
, pp. 153-159
-
-
Pilpel, Y.1
-
43
-
-
33748690244
-
Dynamic programming algorithms for two statistical problems in computational biology
-
Springer, Heidelberg, pp
-
Rahmann,S. (2003) Dynamic programming algorithms for two statistical problems in computational biology. In Proceedings of the 3rd Workshop of Algorithms in Bioinformatics (WABI). Springer, Heidelberg, pp. 151-164.
-
(2003)
Proceedings of the 3rd Workshop of Algorithms in Bioinformatics (WABI)
, pp. 151-164
-
-
Rahmann, S.1
-
44
-
-
0037162497
-
Score: A computational approach to the identification of cis-regulatory modules and target genes in whole-genome sequence data. site clustering over random expectation
-
Rebeiz,M. et al. (2002) Score: A computational approach to the identification of cis-regulatory modules and target genes in whole-genome sequence data. site clustering over random expectation. Proc. Natl Acad. Sci. USA, 99, 9888-9893.
-
(2002)
Proc. Natl Acad. Sci. USA
, vol.99
, pp. 9888-9893
-
-
Rebeiz, M.1
-
45
-
-
0042121137
-
Target explorer: An automated tool for the identification of new target genes for a specified set of transcription factors
-
Sosinsky,A. et al. (2003) Target explorer: An automated tool for the identification of new target genes for a specified set of transcription factors. Nucleic Acids Res., 31, 3589-3592.
-
(2003)
Nucleic Acids Res
, vol.31
, pp. 3589-3592
-
-
Sosinsky, A.1
-
46
-
-
0034072450
-
DNA binding sites: Representation and discovery
-
Stormo,G.D. (2000) DNA binding sites: Representation and discovery. Bioinformatics, 16, 16-23.
-
(2000)
Bioinformatics
, vol.16
, pp. 16-23
-
-
Stormo, G.D.1
-
47
-
-
0030847502
-
A computational genomics approach to the identification of gene networks
-
Wagner,A. (1997) A computational genomics approach to the identification of gene networks. Nucleic Acids Res., 25, 3594-3604.
-
(1997)
Nucleic Acids Res
, vol.25
, pp. 3594-3604
-
-
Wagner, A.1
-
48
-
-
0033394535
-
Genes regulated cooperatively by one or more transcription factors and their identification in whole eukaryotic genomes
-
Wagner,A. (1999) Genes regulated cooperatively by one or more transcription factors and their identification in whole eukaryotic genomes. Bioinformatics, 15, 776-784.
-
(1999)
Bioinformatics
, vol.15
, pp. 776-784
-
-
Wagner, A.1
-
49
-
-
0032562789
-
Identification of regulatory regions which confer muscle-specific gene expression
-
Wasserman,W. and Fickett,J. (1998) Identification of regulatory regions which confer muscle-specific gene expression. J. Mol. Biol., 278, 167-181.
-
(1998)
J. Mol. Biol
, vol.278
, pp. 167-181
-
-
Wasserman, W.1
Fickett, J.2
-
50
-
-
6744219613
-
Long range interaction of cis-DNA elements mediated by architectural transcription factor bach1
-
Yoshida,C. et al. (1999) Long range interaction of cis-DNA elements mediated by architectural transcription factor bach1. Genes Cells, 4, 643-655.
-
(1999)
Genes Cells
, vol.4
, pp. 643-655
-
-
Yoshida, C.1
-
51
-
-
33750217984
-
Computational analysis of tissue-specific combinatorial gene regulation: Predicting interaction between transcription factors in human tissues
-
Yu,X. et al. (2006) Computational analysis of tissue-specific combinatorial gene regulation: Predicting interaction between transcription factors in human tissues. Nucleic Acids Res., 34 4925-4936.
-
(2006)
Nucleic Acids Res
, vol.34
, pp. 4925-4936
-
-
Yu, X.1
-
52
-
-
0032549745
-
Genomic cis-regulatory logic: Experimental and computational analysis of a sea urchin gene
-
Yuh,C.-H. et al. (1998) Genomic cis-regulatory logic: Experimental and computational analysis of a sea urchin gene. Science, 279 1896-1902.
-
(1998)
Science
, vol.279
, pp. 1896-1902
-
-
Yuh, C.-H.1
-
53
-
-
4344607122
-
CisModule: De novo discovery of cis-regulatory modules by hierarchical mixture modeling
-
Zhou,Q. and Wong,W.H. (2004) CisModule: De novo discovery of cis-regulatory modules by hierarchical mixture modeling. Proc. Natl Acad. Sci., 101, 12114-12119.
-
(2004)
Proc. Natl Acad. Sci
, vol.101
, pp. 12114-12119
-
-
Zhou, Q.1
Wong, W.H.2
|