-
1
-
-
84897531613
-
Reversible and adaptive resistance to BRAF(V600E) inhibition in melanoma
-
Sun, C. et al. Reversible and adaptive resistance to BRAF(V600E) inhibition in melanoma. Nature 508, 118-122 (2014).
-
(2014)
Nature
, vol.508
, pp. 118-122
-
-
Sun, C.1
-
2
-
-
84930541641
-
Tumor heterogeneity and plasticity as elusive drivers for resistance to MAPK pathway inhibition in melanoma
-
Roesch, A. Tumor heterogeneity and plasticity as elusive drivers for resistance to MAPK pathway inhibition in melanoma. Oncogene (2014) doi:10.1038/onc.2014.249.
-
(2014)
Oncogene
-
-
Roesch, A.1
-
3
-
-
84865312905
-
Systematic classification of melanoma cells by phenotype-specific gene expression mapping
-
Widmer, D. S. et al. Systematic classification of melanoma cells by phenotype-specific gene expression mapping. Pigment Cell Melanoma Res. 25, 343-353 (2012).
-
(2012)
Pigment Cell Melanoma Res.
, vol.25
, pp. 343-353
-
-
Widmer, D.S.1
-
4
-
-
38849203228
-
In vivo switching of human melanoma cells between proliferative and invasive states
-
Hoek, K. S. et al. In vivo switching of human melanoma cells between proliferative and invasive states. Cancer Res. 68, 650-656 (2008).
-
(2008)
Cancer Res.
, vol.68
, pp. 650-656
-
-
Hoek, K.S.1
-
5
-
-
84885377160
-
A switch in the expression of embryonic EMT-inducers drives the development of malignant melanoma
-
Caramel, J. et al. A switch in the expression of embryonic EMT-inducers drives the development of malignant melanoma. Cancer Cell 24, 466-480 (2013).
-
(2013)
Cancer Cell
, vol.24
, pp. 466-480
-
-
Caramel, J.1
-
6
-
-
56249119207
-
Novel MITF targets identified using a two-step DNA microarray strategy
-
Hoek, K. S. et al. Novel MITF targets identified using a two-step DNA microarray strategy. Pigment Cell Melanoma Res. 21, 665-676 (2008).
-
(2008)
Pigment Cell Melanoma Res.
, vol.21
, pp. 665-676
-
-
Hoek, K.S.1
-
7
-
-
0035117420
-
PAX3 is expressed in human melanomas and contributes to tumor cell survival
-
Scholl, F. A. et al. PAX3 is expressed in human melanomas and contributes to tumor cell survival. Cancer Res. 61, 823-826 (2001).
-
(2001)
Cancer Res.
, vol.61
, pp. 823-826
-
-
Scholl, F.A.1
-
8
-
-
84864865875
-
Sox10 promotes the formation and maintenance of giant congenital naevi and melanoma
-
Shakhova, O. et al. Sox10 promotes the formation and maintenance of giant congenital naevi and melanoma. Nat. Cell Biol. 14, 882-890 (2012).
-
(2012)
Nat. Cell Biol.
, vol.14
, pp. 882-890
-
-
Shakhova, O.1
-
9
-
-
80051797683
-
Transcriptional activation of ZEB1 by Slug leads to cooperative regulation of the epithelial-mesenchymal transition-like phenotype in melanoma
-
Wels, C., Joshi, S., Koefinger, P., Bergler, H. & Schaider, H. Transcriptional activation of ZEB1 by Slug leads to cooperative regulation of the epithelial-mesenchymal transition-like phenotype in melanoma. J. Invest. Dermatol. 131, 1877-1885 (2011).
-
(2011)
J. Invest. Dermatol.
, vol.131
, pp. 1877-1885
-
-
Wels, C.1
Joshi, S.2
Koefinger, P.3
Bergler, H.4
Schaider, H.5
-
10
-
-
84875537133
-
Epigenetic reprogramming in cancer
-
Suvá, M. L., Riggi, N. & Bernstein, B. E. Epigenetic reprogramming in cancer. Science 339, 1567-1570 (2013).
-
(2013)
Science
, vol.339
, pp. 1567-1570
-
-
Suvá, M.L.1
Riggi, N.2
Bernstein, B.E.3
-
11
-
-
84904070924
-
A melanoma cell state distinction influences sensitivity to MAPK pathway inhibitors
-
Konieczkowski, D. J. et al. A melanoma cell state distinction influences sensitivity to MAPK pathway inhibitors. Cancer Discov. 4, 816-827 (2014).
-
(2014)
Cancer Discov.
, vol.4
, pp. 816-827
-
-
Konieczkowski, D.J.1
-
12
-
-
84880044594
-
Directed phenotype switching as an effective antimelanoma strategy
-
Sáez-Ayala, M. et al. Directed phenotype switching as an effective antimelanoma strategy. Cancer Cell 24, 105-119 (2013).
-
(2013)
Cancer Cell
, vol.24
, pp. 105-119
-
-
Sáez-Ayala, M.1
-
13
-
-
0344464733
-
Gene Expression Dynamics Inspector (GEDI): For integrative analysis of expression profiles
-
Eichler, G. S., Huang, S. & Ingber, D. E. Gene Expression Dynamics Inspector (GEDI): for integrative analysis of expression profiles. Bioinformatics 19, 2321-2322 (2003).
-
(2003)
Bioinformatics
, vol.19
, pp. 2321-2322
-
-
Eichler, G.S.1
Huang, S.2
Ingber, D.E.3
-
14
-
-
84864677524
-
MDM4 is a key therapeutic target in cutaneous melanoma
-
Gembarska, A. et al. MDM4 is a key therapeutic target in cutaneous melanoma. Nat. Med. 18, 1239-1247 (2012).
-
(2012)
Nat. Med.
, vol.18
, pp. 1239-1247
-
-
Gembarska, A.1
-
15
-
-
84891814834
-
Track data hubs enable visualization of user-defined genome-wide annotations on the UCSC Genome Browser
-
Raney, B. J. et al. Track data hubs enable visualization of user-defined genome-wide annotations on the UCSC Genome Browser. Bioinformatics 30, 1003-1005 (2014).
-
(2014)
Bioinformatics
, vol.30
, pp. 1003-1005
-
-
Raney, B.J.1
-
16
-
-
33745753404
-
Metastatic potential of melanomas defined by specific gene expression profiles with no BRAF signature
-
Hoek, K. S. et al. Metastatic potential of melanomas defined by specific gene expression profiles with no BRAF signature. Pigment Cell Res. 19, 290-302 (2006).
-
(2006)
Pigment Cell Res.
, vol.19
, pp. 290-302
-
-
Hoek, K.S.1
-
17
-
-
67649524640
-
Isolation of active regulatory elements from eukaryotic chromatin using FAIRE (formaldehyde assisted isolation of regulatory elements)
-
Giresi, P. G. & Lieb, J. D. Isolation of active regulatory elements from eukaryotic chromatin using FAIRE (formaldehyde assisted isolation of regulatory elements). Methods 48, 233-239 (2009).
-
(2009)
Methods
, vol.48
, pp. 233-239
-
-
Giresi, P.G.1
Lieb, J.D.2
-
18
-
-
84897459814
-
An atlas of active enhancers across human cell types and tissues
-
Andersson, R. et al. An atlas of active enhancers across human cell types and tissues. Nature 507, 455-461 (2014).
-
(2014)
Nature
, vol.507
, pp. 455-461
-
-
Andersson, R.1
-
19
-
-
84855283288
-
Transcription factor Sox10 orchestrates activity of a neural crest-specific enhancer in the vicinity of its gene
-
Wahlbuhl, M., Reiprich, S., Vogl, M. R., Bosl, M. R. & Wegner, M. Transcription factor Sox10 orchestrates activity of a neural crest-specific enhancer in the vicinity of its gene. Nucleic Acids Res. 40, 88-101 (2012).
-
(2012)
Nucleic Acids Res.
, vol.40
, pp. 88-101
-
-
Wahlbuhl, M.1
Reiprich, S.2
Vogl, M.R.3
Bosl, M.R.4
Wegner, M.5
-
20
-
-
0033906468
-
Transcription factor hierarchy in Waardenburg syndrome: Regulation of MITF expression by SOX10 and PAX3
-
Potterf, S. B., Furumura, M., Dunn, K. J., Arnheiter, H. & Pavan, W. J. Transcription factor hierarchy in Waardenburg syndrome: regulation of MITF expression by SOX10 and PAX3. Hum. Genet. 107, 1-6 (2000).
-
(2000)
Hum. Genet.
, vol.107
, pp. 1-6
-
-
Potterf, S.B.1
Furumura, M.2
Dunn, K.J.3
Arnheiter, H.4
Pavan, W.J.5
-
21
-
-
79956120349
-
Essential role of microphthalmia transcription factor for DNA replication, mitosis and genomic stability in melanoma
-
Strub, T. et al. Essential role of microphthalmia transcription factor for DNA replication, mitosis and genomic stability in melanoma. Oncogene 30, 2319-2332 (2011).
-
(2011)
Oncogene
, vol.30
, pp. 2319-2332
-
-
Strub, T.1
-
22
-
-
78650724753
-
Hippo signaling: Growth control and beyond
-
Halder, G. & Johnson, R. L. Hippo signaling: growth control and beyond. Development 138, 9-22 (2011).
-
(2011)
Development
, vol.138
, pp. 9-22
-
-
Halder, G.1
Johnson, R.L.2
-
23
-
-
84899450857
-
Transcriptional enhancers: From properties to genome-wide predictions
-
Shlyueva, D., Stampfel, G. & Stark, A. Transcriptional enhancers: from properties to genome-wide predictions. Nat. Rev. Genet. 15, 272-286 (2014).
-
(2014)
Nat. Rev. Genet.
, vol.15
, pp. 272-286
-
-
Shlyueva, D.1
Stampfel, G.2
Stark, A.3
-
24
-
-
77958570788
-
Inferring regulatory networks from expression data using tree-based methods
-
Huynh-Thu, V. A., Irrthum, A., Wehenkel, L. & Geurts, P. Inferring regulatory networks from expression data using tree-based methods. PLoS ONE 5, e12776 (2010).
-
(2010)
PLoS ONE
, vol.5
, pp. e12776
-
-
Huynh-Thu, V.A.1
Irrthum, A.2
Wehenkel, L.3
Geurts, P.4
-
25
-
-
84255160601
-
The transcriptional coactivator TAZ regulates mesenchymal differentiation in malignant glioma
-
Bhat, K. P. L. et al. The transcriptional coactivator TAZ regulates mesenchymal differentiation in malignant glioma. Genes Dev. 25, 2594-2609 (2011).
-
(2011)
Genes Dev.
, vol.25
, pp. 2594-2609
-
-
Bhat, K.P.L.1
-
26
-
-
84904255200
-
Genome-wide profiling of AP-1-regulated transcription provides insights into the invasiveness of triple-negative breast cancer
-
Zhao, C. et al. Genome-wide profiling of AP-1-regulated transcription provides insights into the invasiveness of triple-negative breast cancer. Cancer Res. 74, 3983-3994 (2014).
-
(2014)
Cancer Res.
, vol.74
, pp. 3983-3994
-
-
Zhao, C.1
-
27
-
-
33750212321
-
Nuclear organization of active and inactive chromatin domains uncovered by chromosome conformation capture-on-chip (4C)
-
Simonis, M. et al. Nuclear organization of active and inactive chromatin domains uncovered by chromosome conformation capture-on-chip (4C). Nat. Genet. 38, 1348-1354 (2006).
-
(2006)
Nat. Genet.
, vol.38
, pp. 1348-1354
-
-
Simonis, M.1
-
28
-
-
0346121540
-
Neural crest development is regulated by the transcription factor Sox9
-
Cheung, M. & Briscoe, J. Neural crest development is regulated by the transcription factor Sox9. Development 130, 5681-5693 (2003).
-
(2003)
Development
, vol.130
, pp. 5681-5693
-
-
Cheung, M.1
Briscoe, J.2
-
29
-
-
40949145618
-
SOX9 is expressed in human fetal prostate epithelium and enhances prostate cancer invasion
-
Wang, H. et al. SOX9 is expressed in human fetal prostate epithelium and enhances prostate cancer invasion. Cancer Res. 68, 1625-1630 (2008).
-
(2008)
Cancer Res.
, vol.68
, pp. 1625-1630
-
-
Wang, H.1
-
30
-
-
84901649822
-
Global view of enhancer-promoter interactome in human cells
-
He, B., Chen, C., Teng, L. & Tan, K. Global view of enhancer-promoter interactome in human cells. Proc. Natl Acad. Sci. USA 111, E2191-E2199 (2014).
-
(2014)
Proc. Natl Acad. Sci. USA
, vol.111
, pp. E2191-E2199
-
-
He, B.1
Chen, C.2
Teng, L.3
Tan, K.4
-
31
-
-
79955583542
-
Mapping and analysis of chromatin state dynamics in nine human cell types
-
Ernst, J. et al. Mapping and analysis of chromatin state dynamics in nine human cell types. Nature 473, 43-49 (2011).
-
(2011)
Nature
, vol.473
, pp. 43-49
-
-
Ernst, J.1
-
32
-
-
81055140859
-
The Hippo transducer TAZ confers cancer stem cell-related traits on breast cancer cells
-
Cordenonsi, M. et al. The Hippo transducer TAZ confers cancer stem cell-related traits on breast cancer cells. Cell 147, 759-772 (2011).
-
(2011)
Cell
, vol.147
, pp. 759-772
-
-
Cordenonsi, M.1
-
33
-
-
84905459985
-
Hippo coactivator YAP1 upregulates SOX9 and endows stem-like properties to esophageal cancer cells
-
Song, S. et al. Hippo coactivator YAP1 upregulates SOX9 and endows stem-like properties to esophageal cancer cells. Cancer Res. 74, 4170-4182 (2014).
-
(2014)
Cancer Res.
, vol.74
, pp. 4170-4182
-
-
Song, S.1
-
34
-
-
84890996895
-
Pro-invasive activity of the Hippo pathway effectors YAP and TAZ in cutaneous melanoma
-
Nallet-Staub, F. et al. Pro-invasive activity of the Hippo pathway effectors YAP and TAZ in cutaneous melanoma. J. Invest. Dermatol. 134, 123-132 (2014).
-
(2014)
J. Invest. Dermatol.
, vol.134
, pp. 123-132
-
-
Nallet-Staub, F.1
-
35
-
-
84904043132
-
YAP/TAZ incorporation in the β-catenin destruction complex orchestrates the Wnt response
-
Azzolin, L. et al. YAP/TAZ incorporation in the β-catenin destruction complex orchestrates the Wnt response. Cell 158, 157-170 (2014).
-
(2014)
Cell
, vol.158
, pp. 157-170
-
-
Azzolin, L.1
-
36
-
-
79959962948
-
Newcomers to the WW domain-mediated network of the hippo tumor suppressor pathway
-
Sudol, M. Newcomers to the WW domain-mediated network of the hippo tumor suppressor pathway. Genes Cancer 1, 1115-1118 (2010).
-
(2010)
Genes Cancer
, vol.1
, pp. 1115-1118
-
-
Sudol, M.1
-
37
-
-
0034858124
-
Antibodies to PAI-1 alter the invasive and migratory properties of human tumour cells in vitro
-
Brooks, T. D. et al. Antibodies to PAI-1 alter the invasive and migratory properties of human tumour cells in vitro . Clin. Exp. Metastasis 18, 445-453 (2000).
-
(2000)
Clin. Exp. Metastasis
, vol.18
, pp. 445-453
-
-
Brooks, T.D.1
-
38
-
-
83555166269
-
EphA2 is a critical oncogene in melanoma
-
Udayakumar, D. et al. EphA2 is a critical oncogene in melanoma. Oncogene 30, 4921-4929 (2011).
-
(2011)
Oncogene
, vol.30
, pp. 4921-4929
-
-
Udayakumar, D.1
-
39
-
-
80855138159
-
Human cutaneous melanomas lacking MITF and melanocyte differentiation antigens express a functional Axl receptor kinase
-
Sensi, M. et al. Human cutaneous melanomas lacking MITF and melanocyte differentiation antigens express a functional Axl receptor kinase. J. Invest. Dermatol. 131, 2448-2457 (2011).
-
(2011)
J. Invest. Dermatol.
, vol.131
, pp. 2448-2457
-
-
Sensi, M.1
-
40
-
-
84923345635
-
Low MITF/AXL ratio predicts early resistance to multiple targeted drugs in melanoma
-
Müller, J. et al. Low MITF/AXL ratio predicts early resistance to multiple targeted drugs in melanoma. Nat. Commun. 5, 5712 (2014).
-
(2014)
Nat. Commun.
, vol.5
, pp. 5712
-
-
Müller, J.1
-
41
-
-
84859169877
-
The Cancer Cell Line Encyclopedia enables predictive modelling of anticancer drug sensitivity
-
Barretina, J. et al. The Cancer Cell Line Encyclopedia enables predictive modelling of anticancer drug sensitivity. Nature 483, 603-607 (2012).
-
(2012)
Nature
, vol.483
, pp. 603-607
-
-
Barretina, J.1
-
42
-
-
78049237405
-
Cancer stem cells versus phenotype-switching in melanoma
-
Hoek, K. S. & Goding, C. R. Cancer stem cells versus phenotype-switching in melanoma. Pigment Cell Melanoma Res. 23, 746-759 (2010).
-
(2010)
Pigment Cell Melanoma Res.
, vol.23
, pp. 746-759
-
-
Hoek, K.S.1
Goding, C.R.2
-
43
-
-
21844478747
-
Integrative genomic analyses identify MITF as a lineage survival oncogene amplified in malignant melanoma
-
Garraway, L. A. et al. Integrative genomic analyses identify MITF as a lineage survival oncogene amplified in malignant melanoma. Nature 436, 117-122 (2005).
-
(2005)
Nature
, vol.436
, pp. 117-122
-
-
Garraway, L.A.1
-
44
-
-
67649412006
-
TEAD transcription factors mediate the function of TAZ in cell growth and epithelial-mesenchymal transition
-
Zhang, H. et al. TEAD transcription factors mediate the function of TAZ in cell growth and epithelial-mesenchymal transition. J. Biol. Chem. 284, 13355-13362 (2009).
-
(2009)
J. Biol. Chem.
, vol.284
, pp. 13355-13362
-
-
Zhang, H.1
-
45
-
-
33644872577
-
-
eds Gentleman, R., Carey, V. J., Huber, W., Irizarry, R. A. &Dudoit, S. Springer
-
Smyth, G. K. in Bioinformatics and Computational Biology Solutions Using R and Bioconductor. (eds Gentleman, R., Carey, V. J., Huber, W., Irizarry, R. A. &Dudoit, S.) 397-420 (Springer, 2005).
-
(2005)
Bioinformatics and Computational Biology Solutions Using R and Bioconductor
, pp. 397-420
-
-
Smyth, G.K.1
-
46
-
-
80755169527
-
inSilicoDb: An R/Bioconductor package for accessing human Affymetrix expert-curated datasets from GEO
-
Taminau, J. et al. inSilicoDb: an R/Bioconductor package for accessing human Affymetrix expert-curated datasets from GEO. Bioinformatics 27, 3204-3205 (2011).
-
(2011)
Bioinformatics
, vol.27
, pp. 3204-3205
-
-
Taminau, J.1
-
47
-
-
0037311919
-
TM4: A free, open-source system for microarray data management and analysis
-
Saeed, A. I. et al. TM4: a free, open-source system for microarray data management and analysis. BioTechniques 34, 374-378 (2003).
-
(2003)
BioTechniques
, vol.34
, pp. 374-378
-
-
Saeed, A.I.1
-
48
-
-
27344435774
-
Gene set enrichment analysis: A knowledge-based approach for interpreting genome-wide expression profiles
-
Subramanian, A. et al. Gene set enrichment analysis: a knowledge-based approach for interpreting genome-wide expression profiles. Proc. Natl Acad. Sci. USA 102, 15545-15550 (2005).
-
(2005)
Proc. Natl Acad. Sci. USA
, vol.102
, pp. 15545-15550
-
-
Subramanian, A.1
-
49
-
-
84874763866
-
Biomolecular events in cancer revealed by attractor metagenes
-
Cheng, W.-Y., Yang, T.-H. O. & Anastassiou, D. Biomolecular events in cancer revealed by attractor metagenes. PLoS Comput. Biol. 9, e1002920 (2013).
-
(2013)
PLoS Comput. Biol.
, vol.9
, pp. e1002920
-
-
Cheng, W.-Y.1
Yang, T.-H.O.2
Anastassiou, D.3
-
50
-
-
84868277668
-
12-Chemokine gene signature identifies lymph node-like structures in melanoma: Potential for patient selection for immunotherapy?
-
Messina, J. L. et al. 12-Chemokine gene signature identifies lymph node-like structures in melanoma: potential for patient selection for immunotherapy? Sci. Rep. 2, 765 (2012).
-
(2012)
Sci. Rep.
, vol.2
, pp. 765
-
-
Messina, J.L.1
-
51
-
-
84924629414
-
Moderated estimation of fold change and dispersion for RNA-Seq data with DESeq2
-
Love, M. I., Huber, W. & Anders, S. Moderated estimation of fold change and dispersion for RNA-Seq data with DESeq2. Genome Biol. 15, 550 (2014).
-
(2014)
Genome Biol.
, vol.15
, pp. 550
-
-
Love, M.I.1
Huber, W.2
Anders, S.3
-
52
-
-
0141993704
-
A gene-coexpression network for global discovery of conserved genetic modules
-
Stuart, J. M., Segal, E., Koller, D. & Kim, S. K. A gene-coexpression network for global discovery of conserved genetic modules. Science 302, 249-255 (2003).
-
(2003)
Science
, vol.302
, pp. 249-255
-
-
Stuart, J.M.1
Segal, E.2
Koller, D.3
Kim, S.K.4
-
53
-
-
33646568805
-
Gene prioritization through genomic data fusion
-
Aerts, S. et al. Gene prioritization through genomic data fusion. Nat. Biotechnol. 24, 537-544 (2006).
-
(2006)
Nat. Biotechnol.
, vol.24
, pp. 537-544
-
-
Aerts, S.1
-
54
-
-
84876996918
-
TopHat2: Accurate alignment of transcriptomes in the presence of insertions, deletions and gene fusions
-
Kim, D. et al. TopHat2: accurate alignment of transcriptomes in the presence of insertions, deletions and gene fusions. Genome Biol. 14, R36 (2013).
-
(2013)
Genome Biol.
, vol.14
, pp. R36
-
-
Kim, D.1
-
55
-
-
84928987900
-
HTSeq - A Python framework to work with high-throughput sequencing data
-
Anders, S., Pyl, P. T. & Huber, W. HTSeq - a Python framework to work with high-throughput sequencing data. Bioinformatics 31, 166-169 (2015).
-
(2015)
Bioinformatics
, vol.31
, pp. 166-169
-
-
Anders, S.1
Pyl, P.T.2
Huber, W.3
-
56
-
-
68549104404
-
The sequence alignment/map format and SAMtools
-
Li, H. et al. The sequence alignment/map format and SAMtools. Bioinformatics 25, 2078-2079 (2009).
-
(2009)
Bioinformatics
, vol.25
, pp. 2078-2079
-
-
Li, H.1
-
57
-
-
77955405475
-
Deriving the consequences of genomic variants with the Ensembl API and SNP Effect Predictor
-
McLaren, W. et al. Deriving the consequences of genomic variants with the Ensembl API and SNP Effect Predictor. Bioinformatics 26, 2069-2070 (2010).
-
(2010)
Bioinformatics
, vol.26
, pp. 2069-2070
-
-
McLaren, W.1
-
58
-
-
84865790047
-
An integrated encyclopedia of DNA elements in the human genome
-
ENCODE Project Consortium. An integrated encyclopedia of DNA elements in the human genome. Nature 489, 57-74 (2012).
-
(2012)
Nature
, vol.489
, pp. 57-74
-
-
-
59
-
-
77950652940
-
Integrating multiple evidence sources to predict transcription factor binding in the human genome
-
Ernst, J., Plasterer, H. L., Simon, I. & Bar-Joseph, Z. Integrating multiple evidence sources to predict transcription factor binding in the human genome. Genome Res. 20, 526-536 (2010).
-
(2010)
Genome Res.
, vol.20
, pp. 526-536
-
-
Ernst, J.1
Plasterer, H.L.2
Simon, I.3
Bar-Joseph, Z.4
-
60
-
-
33644861212
-
ORegAnno: An open access database and curation system for literature-derived promoters, transcription factor binding sites and regulatory variation
-
Montgomery, S. B. et al. ORegAnno: an open access database and curation system for literature-derived promoters, transcription factor binding sites and regulatory variation. Bioinformatics 22, 637-640 (2006).
-
(2006)
Bioinformatics
, vol.22
, pp. 637-640
-
-
Montgomery, S.B.1
-
61
-
-
33751316959
-
In vivo enhancer analysis of human conserved non-coding sequences
-
Pennacchio, L. A. et al. In vivo enhancer analysis of human conserved non-coding sequences. Nature 444, 499-502 (2006).
-
(2006)
Nature
, vol.444
, pp. 499-502
-
-
Pennacchio, L.A.1
-
62
-
-
33846067075
-
PReMod: A database of genome-wide mammalian cis-regulatory module predictions
-
Ferretti, V. et al. PReMod: a database of genome-wide mammalian cis-regulatory module predictions. Nucleic Acids Res. 35, D122-D126 (2007).
-
(2007)
Nucleic Acids Res.
, vol.35
, pp. D122-D126
-
-
Ferretti, V.1
-
63
-
-
84867313376
-
i-cisTarget: An integrative genomics method for the prediction of regulatory features and cis-regulatory modules
-
Herrmann, C., Van de Sande, B., Potier, D. & Aerts, S. i-cisTarget: an integrative genomics method for the prediction of regulatory features and cis-regulatory modules. Nucleic Acids Res. 40, e114 (2012).
-
(2012)
Nucleic Acids Res.
, vol.40
, pp. e114
-
-
Herrmann, C.1
Van De Sande, B.2
Potier, D.3
Aerts, S.4
-
64
-
-
84882738244
-
Transcription factor binding in human cells occurs in dense clusters formed around cohesin anchor sites
-
Yan, J. et al. Transcription factor binding in human cells occurs in dense clusters formed around cohesin anchor sites. Cell 154, 801-813 (2013).
-
(2013)
Cell
, vol.154
, pp. 801-813
-
-
Yan, J.1
-
65
-
-
84905457386
-
iRegulon: From a gene list to a gene regulatory network using large motif and track collections
-
Janky, R. et al. iRegulon: from a gene list to a gene regulatory network using large motif and track collections. PLoS Comput. Biol. 10, e1003731 (2014).
-
(2014)
PLoS Comput. Biol.
, vol.10
, pp. e1003731
-
-
Janky, R.1
-
66
-
-
53849146020
-
Model-based analysis of ChIP-Seq (MACS)
-
Zhang, Y. et al. Model-based analysis of ChIP-Seq (MACS). Genome Biol. 9, R137 (2008).
-
(2008)
Genome Biol.
, vol.9
, pp. R137
-
-
Zhang, Y.1
-
67
-
-
54949147307
-
F-Seq: A feature density estimator for high-throughput sequence tags
-
Boyle, A. P., Guinney, J., Crawford, G. E. & Furey, T. S. F-Seq: a feature density estimator for high-throughput sequence tags. Bioinformatics 24, 2537-2538 (2008).
-
(2008)
Bioinformatics
, vol.24
, pp. 2537-2538
-
-
Boyle, A.P.1
Guinney, J.2
Crawford, G.E.3
Furey, T.S.4
-
68
-
-
84870310006
-
Determining long-range chromatin interactions for selected genomic sites using 4C-seq technology: From fixation to computation
-
Splinter, E., de Wit, E., van de Werken, H. J. G., Klous, P. & de Laat, W. Determining long-range chromatin interactions for selected genomic sites using 4C-seq technology: from fixation to computation. Methods 58, 221-230 (2012).
-
(2012)
Methods
, vol.58
, pp. 221-230
-
-
Splinter, E.1
De Wit, E.2
Van De Werken, H.J.G.3
Klous, P.4
De Laat, W.5
-
69
-
-
84880531963
-
r3Cseq: An R/Bioconductor package for the discovery of long-range genomic interactions from chromosome conformation capture and next-generation sequencing data
-
Thongjuea, S., Stadhouders, R., Grosveld, F. G., Soler, E. & Lenhard, B. r3Cseq: an R/Bioconductor package for the discovery of long-range genomic interactions from chromosome conformation capture and next-generation sequencing data. Nucleic Acids Res. 41, e132 (2013).
-
(2013)
Nucleic Acids Res.
, vol.41
, pp. e132
-
-
Thongjuea, S.1
Stadhouders, R.2
Grosveld, F.G.3
Soler, E.4
Lenhard, B.5
-
70
-
-
0036081355
-
Gene Expression Omnibus: NCBI gene expression and hybridization array data repository
-
Edgar, R., Domrachev, M. & Lash, A. E. Gene Expression Omnibus: NCBI gene expression and hybridization array data repository. Nucleic Acids Res. 30, 207-210 (2002).
-
(2002)
Nucleic Acids Res.
, vol.30
, pp. 207-210
-
-
Edgar, R.1
Domrachev, M.2
Lash, A.E.3
|