-
1
-
-
38649099445
-
High-resolution mapping and characterization of open chromatin across the genome
-
Boyle, A. P. et al. High-resolution mapping and characterization of open chromatin across the genome. Cell 132, 311-322 (2008).
-
(2008)
Cell
, vol.132
, pp. 311-322
-
-
Boyle, A.P.1
-
2
-
-
84865755978
-
The accessible chromatin landscape of the human genome
-
Thurman, R. E. et al. The accessible chromatin landscape of the human genome. Nature 489, 75-82 (2012).
-
(2012)
Nature
, vol.489
, pp. 75-82
-
-
Thurman, R.E.1
-
3
-
-
84877123760
-
Patterns of regulatory activity across diverse human cell types predict tissue identity, transcription factor binding, and long-range interactions
-
Sheffield, N. C. et al. Patterns of regulatory activity across diverse human cell types predict tissue identity, transcription factor binding, and long-range interactions. Genome Res. 23, 777-788 (2013).
-
(2013)
Genome Res.
, vol.23
, pp. 777-788
-
-
Sheffield, N.C.1
-
4
-
-
77956276383
-
DNase-seq: A high-resolution technique for mapping active gene regulatory elements across the genome from mammalian cells
-
Song, L. and Crawford, G. E. DNase-seq: a high-resolution technique for mapping active gene regulatory elements across the genome from mammalian cells. Cold Spring Harb. Protoc. http://dx.doi.org/10.1101/pdb.prot5384 (2010).
-
(2010)
Cold Spring Harb. Protoc.
-
-
Song, L.1
Crawford, G.E.2
-
5
-
-
79952184341
-
Chromatin accessibility pre-determines glucocorticoid receptor binding patterns
-
John, S. et al. Chromatin accessibility pre-determines glucocorticoid receptor binding patterns. Nature Genet. 43, 264-268 (2011).
-
(2011)
Nature Genet.
, vol.43
, pp. 264-268
-
-
John, S.1
-
6
-
-
14644406272
-
Active chromatin domains are defined by acetylation islands revealed by genome-wide mapping
-
Roh, T. Y., Cuddapah, S. and Zhao, K. Active chromatin domains are defined by acetylation islands revealed by genome-wide mapping. Genes Dev. 19, 542-552 (2005).
-
(2005)
Genes Dev.
, vol.19
, pp. 542-552
-
-
Roh, T.Y.1
Cuddapah, S.2
Zhao, K.3
-
7
-
-
0035964869
-
Correlation between histone lysine methylation and developmental changes at the chicken beta-globin locus
-
Litt, M. D., Simpson, M., Gaszner, M., Allis, C. D. and Felsenfeld, G. Correlation between histone lysine methylation and developmental changes at the chicken beta-globin locus. Science 293, 2453-2455 (2001).
-
(2001)
Science
, vol.293
, pp. 2453-2455
-
-
Litt, M.D.1
Simpson, M.2
Gaszner, M.3
Allis, C.D.4
Felsenfeld, G.5
-
8
-
-
33847334699
-
Distinct and predictive chromatin signatures of transcriptional promoters and enhancers in the human genome
-
Heintzman, N. D. et al. Distinct and predictive chromatin signatures of transcriptional promoters and enhancers in the human genome. Nature Genet. 39, 311-318 (2007).
-
(2007)
Nature Genet.
, vol.39
, pp. 311-318
-
-
Heintzman, N.D.1
-
9
-
-
78650758676
-
Histone H3K27ac separates active from poised enhancers and predicts developmental state
-
Creyghton, M. P. et al. Histone H3K27ac separates active from poised enhancers and predicts developmental state. Proc. Natl Acad. Sci. USA 107, 21931-21936 (2010).
-
(2010)
Proc. Natl Acad. Sci. USA
, vol.107
, pp. 21931-21936
-
-
Creyghton, M.P.1
-
10
-
-
79951516056
-
A unique chromatin signature uncovers early developmental enhancers in humans
-
Rada-Iglesias, A. et al. A unique chromatin signature uncovers early developmental enhancers in humans. Nature 470, 279-283 (2011).
-
(2011)
Nature
, vol.470
, pp. 279-283
-
-
Rada-Iglesias, A.1
-
11
-
-
46249112085
-
Combinatorial patterns of histone acetylations and methylations in the human genome
-
Wang, Z. et al. Combinatorial patterns of histone acetylations and methylations in the human genome. Nature Genet. 40, 897-903 (2008).
-
(2008)
Nature Genet.
, vol.40
, pp. 897-903
-
-
Wang, Z.1
-
12
-
-
84903185013
-
Single-cell RNA-seq reveals dynamic paracrine control of cellular variation
-
Shalek, A. K. et al. Single-cell RNA-seq reveals dynamic paracrine control of cellular variation. Nature 510, 363-369 (2014).
-
(2014)
Nature
, vol.510
, pp. 363-369
-
-
Shalek, A.K.1
-
13
-
-
84876085773
-
Quartz-seq: A highly reproducible and sensitive single-cell RNA sequencing method, reveals non-genetic gene-expression heterogeneity
-
Sasagawa, Y. et al. Quartz-seq: a highly reproducible and sensitive single-cell RNA sequencing method, reveals non-genetic gene-expression heterogeneity. Genome Biol. 14, R31 (2013).
-
(2013)
Genome Biol.
, vol.14
, pp. R31
-
-
Sasagawa, Y.1
-
14
-
-
84872605250
-
The RNA Pol II elongation factor Ell3 marks enhancers in ES cells and primes future gene activation
-
Lin, C., Garruss, A. S., Luo, Z., Guo, F. and Shilatifard, A. The RNA Pol II elongation factor Ell3 marks enhancers in ES cells and primes future gene activation. Cell 152, 144-156 (2013).
-
(2013)
Cell
, vol.152
, pp. 144-156
-
-
Lin, C.1
Garruss, A.S.2
Luo, Z.3
Guo, F.4
Shilatifard, A.5
-
15
-
-
84876216563
-
Master transcription factors and mediator establish super-enhancers at key cell identity genes
-
Whyte, W. A. et al. Master transcription factors and mediator establish super-enhancers at key cell identity genes. Cell 153, 307-319 (2013).
-
(2013)
Cell
, vol.153
, pp. 307-319
-
-
Whyte, W.A.1
-
16
-
-
84888015137
-
Super-enhancers in the control of cell identity and disease
-
Hnisz, D. et al. Super-enhancers in the control of cell identity and disease. Cell 155, 934-947 (2013).
-
(2013)
Cell
, vol.155
, pp. 934-947
-
-
Hnisz, D.1
-
17
-
-
84863770814
-
Cancer genetics and epigenetics: Two sides of the same coin?
-
You, J. S. and Jones, P. A. Cancer genetics and epigenetics: two sides of the same coin? Cancer Cell 22, 9-20 (2012).
-
(2012)
Cancer Cell
, vol.22
, pp. 9-20
-
-
You, J.S.1
Jones, P.A.2
-
18
-
-
43049117843
-
HMGA2 mRNA expression correlates with the malignant phenotype in human thyroid neoplasias
-
Chiappetta, G. et al. HMGA2 mRNA expression correlates with the malignant phenotype in human thyroid neoplasias. Eur. J. Cancer 44, 1015-1021 (2008).
-
(2008)
Eur. J. Cancer
, vol.44
, pp. 1015-1021
-
-
Chiappetta, G.1
-
19
-
-
36549087198
-
Upregulation of HMGA2 in thyroid carcinomas: A novel molecular marker to distinguish between benign and malignant follicular neoplasias
-
Belge, G. et al. Upregulation of HMGA2 in thyroid carcinomas: a novel molecular marker to distinguish between benign and malignant follicular neoplasias. Genes Chromosom. Cancer 47, 56-63 (2008).
-
(2008)
Genes Chromosom. Cancer
, vol.47
, pp. 56-63
-
-
Belge, G.1
-
20
-
-
0028225439
-
Identification of an invasion-inducing gene, Tiam-1, that encodes a protein with homology to GDP-GTP exchangers for Rho-like proteins
-
Habets, G. G. et al. Identification of an invasion-inducing gene, Tiam-1, that encodes a protein with homology to GDP-GTP exchangers for Rho-like proteins. Cell 77, 537-549 (1994).
-
(1994)
Cell
, vol.77
, pp. 537-549
-
-
Habets, G.G.1
-
21
-
-
84887933383
-
Depletion of a putatively druggable class of phosphatidylinositol kinases inhibits growth of p53-null tumors
-
Emerling, B. M. et al. Depletion of a putatively druggable class of phosphatidylinositol kinases inhibits growth of p53-null tumors. Cell 155, 844-857 (2013).
-
(2013)
Cell
, vol.155
, pp. 844-857
-
-
Emerling, B.M.1
-
22
-
-
20044391422
-
Expression profiling reveals a distinct transcription signature in follicular thyroid carcinomas with a PAX8-PPAR? Fusion oncogene
-
Lui, W. O. et al. Expression profiling reveals a distinct transcription signature in follicular thyroid carcinomas with a PAX8-PPAR? fusion oncogene. Oncogene 24, 1467-1476 (2005).
-
(2005)
Oncogene
, vol.24
, pp. 1467-1476
-
-
Lui, W.O.1
-
23
-
-
67649359951
-
Thioredoxin Txnl1/TRP32 is a redox-active cofactor of the 26 S proteasome
-
Andersen, K. M. et al. Thioredoxin Txnl1/TRP32 is a redox-active cofactor of the 26 S proteasome. J. Biol. Chem. 284, 15246-15254 (2009).
-
(2009)
J. Biol. Chem.
, vol.284
, pp. 15246-15254
-
-
Andersen, K.M.1
-
24
-
-
80052918984
-
HDAC2 and TXNL1 distinguish aneuploid from diploid colorectal cancers
-
Gemoll, T. et al. HDAC2 and TXNL1 distinguish aneuploid from diploid colorectal cancers. Cell. Mol. Life Sci. 68, 3261-3274 (2011).
-
(2011)
Cell. Mol. Life Sci.
, vol.68
, pp. 3261-3274
-
-
Gemoll, T.1
-
25
-
-
84921914426
-
TXNL1 induces apoptosis in cisplatin resistant human gastric cancer cell lines
-
Ni, P. et al. TXNL1 induces apoptosis in cisplatin resistant human gastric cancer cell lines. Curr. Cancer Drug Targets 14, 850-859 (2015).
-
(2015)
Curr. Cancer Drug Targets
, vol.14
, pp. 850-859
-
-
Ni, P.1
-
26
-
-
84937857359
-
Single-cell chromatin accessibility reveals principles of regulatory variation
-
Buenrostro, J. D. et al. Single-cell chromatin accessibility reveals principles of regulatory variation. Nature 523, 486-490 (2015).
-
(2015)
Nature
, vol.523
, pp. 486-490
-
-
Buenrostro, J.D.1
-
27
-
-
84930006926
-
Multiplex single-cell profiling of chromatin accessibility by combinatorial cellular indexing
-
Cusanovich, D. A. et al. Multiplex single-cell profiling of chromatin accessibility by combinatorial cellular indexing. Science 348, 910-914 (2015).
-
(2015)
Science
, vol.348
, pp. 910-914
-
-
Cusanovich, D.A.1
-
28
-
-
84873581550
-
H2A.Z facilitates access of active and repressive complexes to chromatin in embryonic stem cell self-renewal and differentiation
-
Hu, G. et al. H2A.Z facilitates access of active and repressive complexes to chromatin in embryonic stem cell self-renewal and differentiation. Cell Stem Cell 12, 180-192 (2013).
-
(2013)
Cell Stem Cell
, vol.12
, pp. 180-192
-
-
Hu, G.1
-
29
-
-
84886724189
-
Expression and regulation of intergenic long noncoding RNAs during T cell development and differentiation
-
Hu, G. et al. Expression and regulation of intergenic long noncoding RNAs during T cell development and differentiation. Nature Immunol. 14, 1190-1198 (2013).
-
(2013)
Nature Immunol.
, vol.14
, pp. 1190-1198
-
-
Hu, G.1
-
30
-
-
84886731038
-
Genome-wide incorporation dynamics reveal distinct categories of turnover for the histone variant H3.3
-
Kraushaar, D. C. et al. Genome-wide incorporation dynamics reveal distinct categories of turnover for the histone variant H3.3. Genome Biol. 14, R121 (2013).
-
(2013)
Genome Biol.
, vol.14
, pp. R121
-
-
Kraushaar, D.C.1
-
31
-
-
84865121188
-
Mouse ENCODE Consortium. An encyclopedia of mouse DNA elements (Mouse ENCODE)
-
Stamatoyannopoulos, J. A. et al. Mouse ENCODE Consortium. An encyclopedia of mouse DNA elements (Mouse ENCODE). Genome Biol. 13, 418 (2012).
-
(2012)
Genome Biol.
, vol.13
, pp. 418
-
-
Stamatoyannopoulos, J.A.1
-
32
-
-
84859210032
-
Fast gapped-read alignment with Bowtie 2
-
Langmead, B. and Salzberg, S. L. Fast gapped-read alignment with Bowtie 2. Nature Methods 9, 357-359 (2012).
-
(2012)
Nature Methods
, vol.9
, pp. 357-359
-
-
Langmead, B.1
Salzberg, S.L.2
-
33
-
-
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
-
34
-
-
75249087100
-
EdgeR: A Bioconductor package for differential expression analysis of digital gene expression data
-
Robinson, M. D., McCarthy, D. J. and Smyth, G. K. edgeR: a Bioconductor package for differential expression analysis of digital gene expression data. Bioinformatics 26, 139-140 (2010).
-
(2010)
Bioinformatics
, vol.26
, pp. 139-140
-
-
Robinson, M.D.1
McCarthy, D.J.2
Smyth, G.K.3
-
35
-
-
20144376345
-
Genome-wide midrange transcription profiles reveal expression level relationships in human tissue specification
-
Yanai, I. et al. Genome-wide midrange transcription profiles reveal expression level relationships in human tissue specification. Bioinformatics 21, 650-659 (2005).
-
(2005)
Bioinformatics
, vol.21
, pp. 650-659
-
-
Yanai, I.1
-
36
-
-
67650711619
-
A clustering approach for identification of enriched domains from histone modification ChIP-seq data
-
Zang, C. et al. A clustering approach for identification of enriched domains from histone modification ChIP-seq data. Bioinformatics 25, 1952-1958 (2009).
-
(2009)
Bioinformatics
, vol.25
, pp. 1952-1958
-
-
Zang, C.1
-
37
-
-
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
-
38
-
-
77952214662
-
GREAT improves functional interpretation of cis-regulatory regions
-
McLean, C. Y. et al. GREAT improves functional interpretation of cis-regulatory regions. Nature Biotechnol. 28, 495-501 (2010).
-
(2010)
Nature Biotechnol.
, vol.28
, pp. 495-501
-
-
McLean, C.Y.1
-
39
-
-
68549104404
-
1000 Genome Project Data Processing Subgroup. The Sequence Alignment/Map format and SAMtools
-
Li, H. et al. 1000 Genome Project Data Processing Subgroup. The Sequence Alignment/Map format and SAMtools. Bioinformatics 25, 2078-2079 (2009).
-
(2009)
Bioinformatics
, vol.25
, pp. 2078-2079
-
-
Li, H.1
|