-
1
-
-
0037372003
-
Epigenetic regulation of gene expression: How the genome integrates intrinsic and environmental signals
-
Suppl
-
Jaenisch, R. & Bird, A. Epigenetic regulation of gene expression: How the genome integrates intrinsic and environmental signals. Nat. Genet. 33 Suppl., 245-254 (2003).
-
(2003)
Nat. Genet
, vol.33
, pp. 245-254
-
-
Jaenisch, R.1
Bird, A.2
-
2
-
-
0035839136
-
Translating the histone code
-
Jenuwein, T. & Allis, C.D. Translating the histone code. Science 293, 1074-1080 (2001).
-
(2001)
Science
, vol.293
, pp. 1074-1080
-
-
Jenuwein, T.1
Allis, C.D.2
-
4
-
-
3042760021
-
Global nature of dynamic protein-chromatin interactions in vivo: Three-dimensional genome scanning and dynamic interaction networks of chromatin proteins
-
Phair, R.D. et al. Global nature of dynamic protein-chromatin interactions in vivo: Three-dimensional genome scanning and dynamic interaction networks of chromatin proteins. Mol. Cell Biol. 24, 6393-6402 (2004).
-
(2004)
Mol. Cell Biol
, vol.24
, pp. 6393-6402
-
-
Phair, R.D.1
-
5
-
-
0036024955
-
Identification of unknown target genes of human transcription factors using chromatin immunoprecipitation
-
Weinmann, A.S. & Farnham, P.J. Identification of unknown target genes of human transcription factors using chromatin immunoprecipitation. Methods 26, 37-47 (2002).
-
(2002)
Methods
, vol.26
, pp. 37-47
-
-
Weinmann, A.S.1
Farnham, P.J.2
-
6
-
-
1042276981
-
Analysis of genome-wide histone acety- lation state and enzyme binding using DNA microarrays
-
Robyr, D., Kurdistani, S.K. & Grunstein, M. Analysis of genome-wide histone acety- lation state and enzyme binding using DNA microarrays. Methods Enzymol. 376, 289-304 (2004).
-
(2004)
Methods Enzymol
, vol.376
, pp. 289-304
-
-
Robyr, D.1
Kurdistani, S.K.2
Grunstein, M.3
-
7
-
-
1042288539
-
Use of chromatin immunoprecipitation assays in genome- wide location analysis of mammalian transcription factors
-
Ren, B. & Dynlacht, B.D. Use of chromatin immunoprecipitation assays in genome- wide location analysis of mammalian transcription factors. Methods Enzymol. 376, 304-315 (2004).
-
(2004)
Methods Enzymol
, vol.376
, pp. 304-315
-
-
Ren, B.1
Dynlacht, B.D.2
-
8
-
-
0034007256
-
Identification of in vivo DNA targets of chromatin proteins using tethered dam methyltransferase
-
van Steensel, B. & Henikoff, S. Identification of in vivo DNA targets of chromatin proteins using tethered dam methyltransferase. Nat. Biotechnol. 18, 424-428 (2000).
-
(2000)
Nat. Biotechnol
, vol.18
, pp. 424-428
-
-
Van Steensel, B.1
Henikoff, S.2
-
9
-
-
0035093828
-
Chromatin profiling using targeted DNA adenine methyltransferase
-
van Steensel, B., Delrow, J. & Henikoff, S. Chromatin profiling using targeted DNA adenine methyltransferase. Nat. Genet. 27, 304-308 (2001).
-
(2001)
Nat. Genet
, vol.27
, pp. 304-308
-
-
Van Steensel, B.1
Delrow, J.2
Henikoff, S.3
-
10
-
-
0042736137
-
Epigenomic profiling using microarrays
-
346-350, 352-354
-
van Steensel, B. & Henikoff, S. Epigenomic profiling using microarrays. Biotechniques 35, 346-350, 352-354, 356-357 (2003).
-
(2003)
Biotechniques
, vol.35
, pp. 356-357
-
-
Van Steensel, B.1
Henikoff, S.2
-
11
-
-
84984774255
-
Whole-genome views of chromatin structure
-
(in the press)
-
Lodén, M. & van Steensel, B. Whole-genome views of chromatin structure. Chrom. Res. (in the press).
-
Chrom. Res
-
-
Lodén, M.1
Van Steensel, B.2
-
12
-
-
0041422240
-
Protein-DNA interaction mapping using genomic tiling path microarrays in Drosophila
-
Sun, L.V. et al. Protein-DNA interaction mapping using genomic tiling path microarrays in Drosophila. Proc. Natl. Acad. Sci. USA 100, 9428-9433 (2003).
-
(2003)
Proc. Natl. Acad. Sci. USA
, vol.100
, pp. 9428-9433
-
-
Sun, L.V.1
-
13
-
-
3342927934
-
Role of transposable elements in heterochromatin and epigenetic control
-
Lippman, Z. et al. Role of transposable elements in heterochromatin and epigenetic control. Nature 430, 471-476 (2004).
-
(2004)
Nature
, vol.430
, pp. 471-476
-
-
Lippman, Z.1
-
14
-
-
18444364803
-
A microarray-based method for detecting methylated loci
-
Hatada, I. et al. A microarray-based method for detecting methylated loci. J. Hum. Genet. 47, 448-451 (2002).
-
(2002)
J. Hum. Genet
, vol.47
, pp. 448-451
-
-
Hatada, I.1
-
15
-
-
0037039164
-
Genome-wide profiling of DNA methylation reveals transposon targets of CHROMOMETHYLASE3
-
Tompa, R. et al. Genome-wide profiling of DNA methylation reveals transposon targets of CHROMOMETHYLASE3. Curr. Biol. 12, 65-68 (2002).
-
(2002)
Curr. Biol
, vol.12
, pp. 65-68
-
-
Tompa, R.1
-
16
-
-
0035577862
-
Dissecting complex epigenetic alterations in breast cancer using CpG island microarrays
-
Yan, P.S. et al. Dissecting complex epigenetic alterations in breast cancer using CpG island microarrays. Cancer Res. 61, 8375-8380 (2001).
-
(2001)
Cancer Res
, vol.61
, pp. 8375-8380
-
-
Yan, P.S.1
-
17
-
-
0035992386
-
Methylation microarray analysis of late-stage ovarian carcinomas distinguishes progression-free survival in patients and identifies candidate epigenetic markers
-
Wei, S.H. et al. Methylation microarray analysis of late-stage ovarian carcinomas distinguishes progression-free survival in patients and identifies candidate epigenetic markers. Clin. Cancer Res. 8, 2246-2252 (2002).
-
(2002)
Clin. Cancer Res
, vol.8
, pp. 2246-2252
-
-
Wei, S.H.1
-
18
-
-
0011964662
-
Tumour class prediction and discovery by microarray-based DNA methylation analysis
-
Adorjan, P. et al. Tumour class prediction and discovery by microarray-based DNA methylation analysis. Nucleic Acids Res. 30, e21 (2002).
-
(2002)
Nucleic Acids Res
, vol.e21
, pp. 30
-
-
Adorjan, P.1
-
19
-
-
0036144883
-
Methylation-specific oli- gonucleotide microarray: A new potential for high-throughput methylation analysis
-
Gitan, R.S., Shi, H., Chen, C.M., Yan, P.S. & Huang, T.H. Methylation-specific oli- gonucleotide microarray: A new potential for high-throughput methylation analysis. Genome Res. 12, 158-164 (2002).
-
(2002)
Genome Res
, vol.12
, pp. 158-164
-
-
Gitan, R.S.1
Shi, H.2
Chen, C.M.3
Yan, P.S.4
Huang, T.H.5
-
20
-
-
0034704248
-
Genome-wide location and function of DNA binding proteins
-
Ren, B. et al. Genome-wide location and function of DNA binding proteins. Science 290, 2306-2309 (2000).
-
(2000)
Science
, vol.290
, pp. 2306-2309
-
-
Ren, B.1
-
21
-
-
0034934774
-
Promoter-specific binding of Rap1 revealed by genome-wide maps of protein-DNA association
-
Lieb, J.D., Liu, X., Botstein, D. & Brown, P.O. Promoter-specific binding of Rap1 revealed by genome-wide maps of protein-DNA association. Nat. Genet. 28, 327-334 (2001).
-
(2001)
Nat. Genet
, vol.28
, pp. 327-334
-
-
Lieb, J.D.1
Liu, X.2
Botstein, D.3
Brown, P.O.4
-
22
-
-
0037174671
-
Transcriptional regulatory networks in Saccharomyces cerevisiae
-
Lee, T.I. et al. Transcriptional regulatory networks in Saccharomyces cerevisiae. Science 298, 799-804 (2002).
-
(2002)
Science
, vol.298
, pp. 799-804
-
-
Lee, T.I.1
-
23
-
-
0035945567
-
Genomic binding sites of the yeast cell-cycle transcription factors SBF and MBF
-
Iyer, V.R. et al. Genomic binding sites of the yeast cell-cycle transcription factors SBF and MBF. Nature 409, 533-538 (2001).
-
(2001)
Nature
, vol.409
, pp. 533-538
-
-
Iyer, V.R.1
-
24
-
-
4544352942
-
Transcriptional regulatory code of a eukaryotic genome
-
Harbison, C.T. et al. Transcriptional regulatory code of a eukaryotic genome. Nature 431, 99-104 (2004).
-
(2004)
Nature
, vol.431
, pp. 99-104
-
-
Harbison, C.T.1
-
25
-
-
8644281106
-
A common set of gene regulatory networks links metabolism and growth inhibition
-
Cam, H. et al. A common set of gene regulatory networks links metabolism and growth inhibition. Mol. Cell 16, 399-411 (2004).
-
(2004)
Mol. Cell
, vol.16
, pp. 399-411
-
-
Cam, H.1
-
26
-
-
14644390321
-
An initial blueprint for myogenic differentiation
-
Blais, A. et al. An initial blueprint for myogenic differentiation. Genes Dev. 19, 553569 (2005).
-
(2005)
Genes Dev
, pp. 19
-
-
Blais, A.1
-
27
-
-
0037080483
-
E2F integrates cell cycle progression with DNA repair, replication, and G(2)/M checkpoints
-
Ren, B. et al. E2F integrates cell cycle progression with DNA repair, replication, and G(2)/M checkpoints. Genes Dev. 16, 245-256 (2002).
-
(2002)
Genes Dev
, vol.16
, pp. 245-256
-
-
Ren, B.1
-
28
-
-
10744227070
-
Control of pancreas and liver gene expression by HNF transcription factors
-
Odom, D.T. et al. Control of pancreas and liver gene expression by HNF transcription factors. Science 303, 1378-1381 (2004).
-
(2004)
Science
, vol.303
, pp. 1378-1381
-
-
Odom, D.T.1
-
29
-
-
0038492517
-
A global transcriptional regulatory role for c-Myc in Burkitt’s lymphoma cells
-
Li, Z. et al. A global transcriptional regulatory role for c-Myc in Burkitt’s lymphoma cells. Proc. Natl. Acad. Sci. USA 100, 8164-8169 (2003).
-
(2003)
Proc. Natl. Acad. Sci. USA
, vol.100
, pp. 8164-8169
-
-
Li, Z.1
-
30
-
-
0038185378
-
Genomic targets of the human c-Myc protein
-
Fernandez, P.C. et al. Genomic targets of the human c-Myc protein. Genes Dev. 17, 1115-1129 (2003).
-
(2003)
Genes Dev
, vol.17
, pp. 1115-1129
-
-
Fernandez, P.C.1
-
31
-
-
0038523952
-
Genomic binding by the Drosophila Myc, Max, Mad/Mnt transcription factor network
-
Orian, A. et al. Genomic binding by the Drosophila Myc, Max, Mad/Mnt transcription factor network. Genes Dev. 17, 1101-1114 (2003).
-
(2003)
Genes Dev
, vol.17
, pp. 1101-1114
-
-
Orian, A.1
-
32
-
-
0037418234
-
Genomewide analysis of Drosophila GAGA factor target genes reveals context-dependent DNA binding
-
van Steensel, B., Delrow, J. & Bussemaker, H.J. Genomewide analysis of Drosophila GAGA factor target genes reveals context-dependent DNA binding. Proc. Natl. Acad. Sci. USA 100, 2580-2585 (2003).
-
(2003)
Proc. Natl. Acad. Sci. USA
, vol.100
, pp. 2580-2585
-
-
Van Steensel, B.1
Delrow, J.2
Bussemaker, H.J.3
-
33
-
-
10744226888
-
Unbiased mapping of transcription factor binding sites along human chromosomes 21 and 22 points to widespread regulation of noncoding RNAs
-
Cawley, S. et al. Unbiased mapping of transcription factor binding sites along human chromosomes 21 and 22 points to widespread regulation of noncoding RNAs. Cell 116, 499-509 (2004).
-
(2004)
Cell
, vol.116
, pp. 499-509
-
-
Cawley, S.1
-
34
-
-
11144357294
-
CREB binds to multiple loci on human chromosome 22
-
Euskirchen, G. et al. CREB binds to multiple loci on human chromosome 22. Mol. Cell Biol. 24, 3804-3814 (2004).
-
(2004)
Mol. Cell Biol
, vol.24
, pp. 3804-3814
-
-
Euskirchen, G.1
-
35
-
-
0142027777
-
Distribution of NF-kappaB-binding sites across human chromosome 22
-
Martone, R. et al. Distribution of NF-kappaB-binding sites across human chromosome 22. Proc. Natl. Acad. Sci. USA 100, 12247-12252 (2003).
-
(2003)
Proc. Natl. Acad. Sci. USA
, vol.100
, pp. 12247-12252
-
-
Martone, R.1
-
36
-
-
0037722938
-
Program-specific distribution of a transcription factor dependent on partner transcription factor and MAPK signaling
-
Zeitlinger, J. et al. Program-specific distribution of a transcription factor dependent on partner transcription factor and MAPK signaling. Cell 113, 395-404 (2003).
-
(2003)
Cell
, vol.113
, pp. 395-404
-
-
Zeitlinger, J.1
-
37
-
-
0037435010
-
Identification of novel pRb binding sites using CpG microarrays suggests that E2F recruits pRb to specific genomic sites during S phase
-
Wells, J., Yan, P.S., Cechvala, M., Huang, T. & Farnham, P.J. Identification of novel pRb binding sites using CpG microarrays suggests that E2F recruits pRb to specific genomic sites during S phase. Oncogene 22, 1445-1460 (2003).
-
(2003)
Oncogene
, vol.22
, pp. 1445-1460
-
-
Wells, J.1
Yan, P.S.2
Cechvala, M.3
Huang, T.4
Farnham, P.J.5
-
38
-
-
6344270167
-
Global position and recruitment of HATs and HDACs in the yeast genome
-
Robert, F. et al. Global position and recruitment of HATs and HDACs in the yeast genome. Mol. Cell 16, 199-209 (2004).
-
(2004)
Mol. Cell
, vol.16
, pp. 199-209
-
-
Robert, F.1
-
39
-
-
19344371786
-
Hairy transcriptional repression targets and cofactor recruitment in Drosophila
-
Bianchi-Frias, D. et al. Hairy transcriptional repression targets and cofactor recruitment in Drosophila. PLoS. Biol. 2, E178 (2004).
-
(2004)
Plos. Biol
, vol.2
, pp. E178
-
-
Bianchi-Frias, D.1
-
40
-
-
17944372930
-
Serial regulation of transcriptional regulators in the yeast cell cycle
-
Simon, I. et al. Serial regulation of transcriptional regulators in the yeast cell cycle. Cell 106, 697-708 (2001).
-
(2001)
Cell
, vol.106
, pp. 697-708
-
-
Simon, I.1
-
41
-
-
12544254467
-
DNA methylation profiling identifies CG methylation clusters in Arabidopsis genes
-
Tran, R.K. et al. DNA methylation profiling identifies CG methylation clusters in Arabidopsis genes. Curr. Biol. 15, 154-159 (2005).
-
(2005)
Curr. Biol
, vol.15
, pp. 154-159
-
-
Tran, R.K.1
-
42
-
-
0037728813
-
Triple analysis of the cancer epigenome: An integrated microarray system for assessing gene expression, DNA methylation, and histone acetylation
-
Shi, H. et al. Triple analysis of the cancer epigenome: An integrated microarray system for assessing gene expression, DNA methylation, and histone acetylation. Cancer Res. 63, 2164-2171 (2003).
-
(2003)
Cancer Res
, vol.63
, pp. 2164-2171
-
-
Shi, H.1
-
43
-
-
8544226964
-
Loss of estrogen receptor signaling triggers epigenetic silencing of downstream targets in breast cancer
-
Leu, Y.W. et al. Loss of estrogen receptor signaling triggers epigenetic silencing of downstream targets in breast cancer. Cancer Res. 64, 8184-8192 (2004).
-
(2004)
Cancer Res
, vol.64
, pp. 8184-8192
-
-
Leu, Y.W.1
-
44
-
-
0348134871
-
Methyl-CpG binding proteins identify novel sites of epigenetic inactivation in human cancer
-
Ballestar, E. et al. Methyl-CpG binding proteins identify novel sites of epigenetic inactivation in human cancer. EMBO J. 22, 6335-6345 (2003).
-
(2003)
EMBO J
, vol.22
, pp. 6335-6345
-
-
Ballestar, E.1
-
45
-
-
2642570305
-
The histone modification pattern of active genes revealed through genome-wide chromatin analysis of a higher eukaryote
-
Schübeler, D. et al. The histone modification pattern of active genes revealed through genome-wide chromatin analysis of a higher eukaryote. Genes Dev. 18, 1263-1271 (2004).
-
(2004)
Genes Dev
, vol.18
, pp. 1263-1271
-
-
Schübeler, D.1
-
46
-
-
0037074010
-
Signaling network model of chromatin
-
Schreiber, S.L. & Bernstein, B.E. Signaling network model of chromatin. Cell 111, 771-778 (2002).
-
(2002)
Cell
, vol.111
, pp. 771-778
-
-
Schreiber, S.L.1
Bernstein, B.E.2
-
47
-
-
2942518343
-
Mapping global histone acetylation patterns to gene expression
-
Kurdistani, S.K., Tavazoie, S. & Grunstein, M. Mapping global histone acetylation patterns to gene expression. Cell 117, 721-733 (2004).
-
(2004)
Cell
, vol.117
, pp. 721-733
-
-
Kurdistani, S.K.1
Tavazoie, S.2
Grunstein, M.3
-
48
-
-
0037123767
-
Microarray deacetylation maps determine genome-wide functions for yeast histone deacetylases
-
Robyr, D. et al. Microarray deacetylation maps determine genome-wide functions for yeast histone deacetylases. Cell 109, 437-446 (2002).
-
(2002)
Cell
, vol.109
, pp. 437-446
-
-
Robyr, D.1
-
49
-
-
0036649756
-
Genome-wide binding map of the histone deacetylase Rpd3 in yeast
-
Kurdistani, S.K., Robyr, D., Tavazoie, S. & Grunstein, M. Genome-wide binding map of the histone deacetylase Rpd3 in yeast. Nat. Genet. 31, 248-254 (2002).
-
(2002)
Nat. Genet
, vol.31
, pp. 248-254
-
-
Kurdistani, S.K.1
Robyr, D.2
Tavazoie, S.3
Grunstein, M.4
-
50
-
-
6444241134
-
Rpd3p relocation mediates a transcriptional response to rapamycin in yeast
-
Humphrey, E.L., Shamji, A.F., Bernstein, B.E. & Schreiber, S.L. Rpd3p relocation mediates a transcriptional response to rapamycin in yeast. Chem. Biol. 11, 295-299 (2004).
-
(2004)
Chem. Biol
, vol.11
, pp. 295-299
-
-
Humphrey, E.L.1
Shamji, A.F.2
Bernstein, B.E.3
Schreiber, S.L.4
-
51
-
-
19944430797
-
Genomic maps and comparative analysis of histone modifications in human and mouse
-
Bernstein, B.E. et al. Genomic maps and comparative analysis of histone modifications in human and mouse. Cell 120, 169-181 (2005).
-
(2005)
Cell
, vol.120
, pp. 169-181
-
-
Bernstein, B.E.1
-
52
-
-
2942746179
-
Histone variants, nucleosome assembly and epigenetic inheritance
-
Henikoff, S., Furuyama, T. & Ahmad, K. Histone variants, nucleosome assembly and epigenetic inheritance. Trends Genet. 20, 320-326 (2004).
-
(2004)
Trends Genet
, vol.20
, pp. 320-326
-
-
Henikoff, S.1
Furuyama, T.2
Ahmad, K.3
-
53
-
-
8444245244
-
Global nucleosome occupancy in yeast
-
Bernstein, B.E., Liu, C.L., Humphrey, E.L., Perlstein, E.O. & Schreiber, S.L. Global nucleosome occupancy in yeast. Genome Biol. 5, R62 (2004).
-
(2004)
Genome Biol
, vol.5
, pp. R62
-
-
Bernstein, B.E.1
Liu, C.L.2
Humphrey, E.L.3
Perlstein, E.O.4
Schreiber, S.L.5
-
54
-
-
3543023310
-
Evidence for nucleosome depletion at active regulatory regions genome-wide
-
Lee, C.K., Shibata, Y., Rao, B., Strahl, B.D. & Lieb, J.D. Evidence for nucleosome depletion at active regulatory regions genome-wide. Nat. Genet. 36, 900-905 (2004).
-
(2004)
Nat. Genet
, vol.36
, pp. 900-905
-
-
Lee, C.K.1
Shibata, Y.2
Rao, B.3
Strahl, B.D.4
Lieb, J.D.5
-
55
-
-
0037041422
-
Control of CpNpG DNA meth- ylation by the KRYPTONITE histone H3 methyltransferase
-
Jackson, J.P., Lindroth, A.M., Cao, X. & Jacobsen, S.E. Control of CpNpG DNA meth- ylation by the KRYPTONITE histone H3 methyltransferase. Nature 416, 556-560 (2002).
-
(2002)
Nature
, vol.416
, pp. 556-560
-
-
Jackson, J.P.1
Lindroth, A.M.2
Cao, X.3
Jacobsen, S.E.4
-
56
-
-
0345305758
-
Distinct HP1 and Su(Var)3-9 complexes bind to sets of developmentally coexpressed genes depending on chromosomal location
-
Greil, F. et al. Distinct HP1 and Su(var)3-9 complexes bind to sets of developmentally coexpressed genes depending on chromosomal location. Genes Dev. 17, 2825-2838 (2003).
-
(2003)
Genes Dev
, vol.17
, pp. 2825-2838
-
-
Greil, F.1
-
57
-
-
3042781030
-
Silencing of human polycomb target genes is associated with methylation of histone H3 Lys 27
-
Kirmizis, A. et al. Silencing of human polycomb target genes is associated with methylation of histone H3 Lys 27. Genes Dev. 18, 1592-1605 (2004).
-
(2004)
Genes Dev
, vol.18
, pp. 1592-1605
-
-
Kirmizis, A.1
-
58
-
-
0036852098
-
Gene expression analysis using oligonucleotide arrays produced by maskless photolithography
-
Nuwaysir, E.F. et al. Gene expression analysis using oligonucleotide arrays produced by maskless photolithography. Genome Res. 12, 1749-1755 (2002).
-
(2002)
Genome Res
, vol.12
, pp. 1749-1755
-
-
Nuwaysir, E.F.1
-
59
-
-
20044390368
-
DNA methylation profiling of the human major histocompatibility complex: A pilot study for the human epigenome project
-
Rakyan, V.K. et al. DNA methylation profiling of the human major histocompatibility complex: A pilot study for the human epigenome project. PLoS. Biol. 2, e405 (2004).
-
(2004)
Plos. Biol
, vol.2
, pp. e405
-
-
Rakyan, V.K.1
-
60
-
-
18744380399
-
Mapping DNA-protein interactions in large genomes by sequence tag analysis of genomic enrichment
-
Kim, J., Bhinge, A.A., Morgan, X.C. & Iyer, V.R. Mapping DNA-protein interactions in large genomes by sequence tag analysis of genomic enrichment. Nat. Methods 2, 47 -53 (2005).
-
(2005)
Nat. Methods
, vol.2
-
-
Kim, J.1
Bhinge, A.A.2
Morgan, X.C.3
Iyer, V.R.4
-
61
-
-
7444233156
-
A gene expression map for the euchromatic genome of Drosophila melanogaster
-
Stolc, V. et al. A gene expression map for the euchromatic genome of Drosophila melanogaster. Science 306, 655-660 (2004).
-
(2004)
Science
, vol.306
, pp. 655-660
-
-
Stolc, V.1
-
62
-
-
19944376457
-
Global identification of human transcribed sequences with genome tiling arrays
-
Bertone, P. et al. Global identification of human transcribed sequences with genome tiling arrays. Science 306, 2242-2246 (2004).
-
(2004)
Science
, vol.306
, pp. 2242-2246
-
-
Bertone, P.1
-
63
-
-
4444258534
-
Chromatin architecture of the human genome: Gene-rich domains are enriched in open chromatin fibers
-
Gilbert, N. et al. Chromatin architecture of the human genome: Gene-rich domains are enriched in open chromatin fibers. Cell 118, 555-566 (2004).
-
(2004)
Cell
, vol.118
, pp. 555-566
-
-
Gilbert, N.1
-
64
-
-
2342528298
-
Global survey of chromatin accessibility using DNA microarrays
-
Weil, M.R., Widlak, P., Minna, J.D. & Garner, H.R. Global survey of chromatin accessibility using DNA microarrays. Genome Res. 14, 1374-1381 (2004).
-
(2004)
Genome Res
, vol.14
, pp. 1374-1381
-
-
Weil, M.R.1
Widlak, P.2
Minna, J.D.3
Garner, H.R.4
-
65
-
-
7444260846
-
The ENCODE (ENCyclopedia Of DNA Elements) Project
-
The ENCODE Project Consortium. The ENCODE (ENCyclopedia Of DNA Elements) Project. Science 306, 636-640 (2004).
-
(2004)
Science
, vol.306
, pp. 636-640
-
-
-
66
-
-
0036324753
-
An algorithm for finding protein-DNA binding sites with applications to chromatin-immunoprecipitation microarray experiments
-
Liu, X.S., Brutlag, D.L. & Liu, J.S. An algorithm for finding protein-DNA binding sites with applications to chromatin-immunoprecipitation microarray experiments. Nat. Biotechnol. 20, 835-839 (2002).
-
(2002)
Nat
, vol.20
, pp. 835-839
-
-
Liu, X.S.1
Brutlag, D.L.2
Liu, J.S.3
-
67
-
-
0035135420
-
Regulatory element detection using correlation with expression. Nat
-
Bussemaker, H.J., Li, H. & Siggia, E.D. Regulatory element detection using correlation with expression. Nat. Genet. 27, 167-171 (2001).
-
(2001)
Genet
, vol.27
, pp. 167-171
-
-
Bussemaker, H.J.1
Li, H.2
Siggia, E.D.3
-
68
-
-
0031787969
-
Finding DNA regulatory motifs within unaligned noncoding sequences clustered by whole-genome mRNA quantita- tion
-
Roth, F.P., Hughes, J.D., Estep, P.W. & Church, G.M. Finding DNA regulatory motifs within unaligned noncoding sequences clustered by whole-genome mRNA quantita- tion. Nat. Biotechnol. 16, 939-945 (1998).
-
(1998)
Nat. Biotechnol
, vol.16
, pp. 939-945
-
-
Roth, F.P.1
Hughes, J.D.2
Estep, P.W.3
Church, G.M.4
-
69
-
-
2942606066
-
Structure and evolution of transcriptional regulatory networks
-
Babu, M.M., Luscombe, N.M., Aravind, L., Gerstein, M. & Teichmann, S.A. Structure and evolution of transcriptional regulatory networks. Curr. Opin. Struct. Biol. 14, 283-291 (2004).
-
(2004)
Curr. Opin. Struct. Biol
, vol.14
, pp. 283-291
-
-
Babu, M.M.1
Luscombe, N.M.2
Aravind, L.3
Gerstein, M.4
Teichmann, S.A.5
-
70
-
-
20044396570
-
Integrative analysis of the cancer transcriptome
-
Chinnaiyan, A. Integrative analysis of the cancer transcriptome Nat. Genet. 37, 31-37 (2005).
-
(2005)
Nat. Genet
, vol.37
, pp. 31-37
-
-
Chinnaiyan, A.1
-
71
-
-
20044388557
-
From signatures to models: Understanding cancer using microarrays
-
Koller, D. From signatures to models: Understanding cancer using microarrays. Nat. Genet. 37, 38-45 (2005).
-
(2005)
Nat
, vol.37
, pp. 38-45
-
-
Koller, D.1
-
72
-
-
1942453302
-
Predicting gene expression from sequence
-
Beer, M.A. & Tavazoie, S. Predicting gene expression from sequence. Cell 117, 185198 (2004).
-
(2004)
Cell
, pp. 117
-
-
Beer, M.A.1
Tavazoie, S.2
-
73
-
-
10744226222
-
Computational discovery of gene modules and regulatory networks
-
Bar-Joseph, Z. et al. Computational discovery of gene modules and regulatory networks. Nat. Biotechnol. 21, 1337-1342 (2003).
-
(2003)
Nat. Biotechnol
, vol.21
, pp. 1337-1342
-
-
Bar-Joseph, Z.1
-
74
-
-
2942582468
-
Defining transcriptional networks through integrative modeling of mRNA expression and transcription factor binding data
-
Gao, F., Foat, B.C. & Bussemaker, H.J. Defining transcriptional networks through integrative modeling of mRNA expression and transcription factor binding data. BMC Bioinformatics 5, 31 (2004).
-
(2004)
BMC Bioinformatics
, vol.5
, pp. 31
-
-
Gao, F.1
Foat, B.C.2
Bussemaker, H.J.3
-
75
-
-
0038610819
-
Detailed map of a cis-regulatory input function
-
Setty, Y., Mayo, A.E., Surette, M.G. & Alon, U. Detailed map of a cis-regulatory input function. Proc. Natl. Acad. Sci. USA 100, 7702-7707 (2003).
-
(2003)
Proc. Natl. Acad. Sci. USA
, vol.100
, pp. 7702-7707
-
-
Setty, Y.1
Mayo, A.E.2
Surette, M.G.3
Alon, U.4
|