-
1
-
-
70349267600
-
Mapping accessible chromatin regions using Sono-Seq
-
Auerbach RK, Euskirchen G, Rozowsky J, Lamarre-Vincent N, Moqtaderi Z, Lefraçois P, Struhl K, Gerstein M, Snyder M. 2009. Mapping accessible chromatin regions using Sono-Seq. Proc Natl Acad Sci 106: 14926-14931.
-
(2009)
Proc Natl Acad Sci
, vol.106
, pp. 14926-14931
-
-
Auerbach, R.K.1
Euskirchen, G.2
Rozowsky, J.3
Lamarre-Vincent, N.4
Moqtaderi, Z.5
Lefraçois, P.6
Struhl, K.7
Gerstein, M.8
Snyder, M.9
-
2
-
-
34249026300
-
High-Resolution Profiling of Histone Methylations in the Human Genome
-
DOI 10.1016/j.cell.2007.05.009, PII S0092867407006009
-
Barski A, Cuddapah S, Cui K, Roh T, Schones DE, Wang Z, Wei G, Chepelev I, Zhao K. 2007. High-resolution profiling of histone methylations in the human genome. Cell 129: 823-837. (Pubitemid 46802390)
-
(2007)
Cell
, vol.129
, Issue.4
, pp. 823-837
-
-
Barski, A.1
Cuddapah, S.2
Cui, K.3
Roh, T.-Y.4
Schones, D.E.5
Wang, Z.6
Wei, G.7
Chepelev, I.8
Zhao, K.9
-
3
-
-
67649292737
-
Unlocking the secrets of the genome
-
Celniker SE, Dillon LAL, Gerstein MB, Gunsalus KC, Henikoff S, Karpen GH, Kellis M, Lai EC, Lieb JD, MacAlpine DM, et al. 2009. Unlocking the secrets of the genome. Nature 459: 927-930.
-
(2009)
Nature
, vol.459
, pp. 927-930
-
-
Celniker, S.E.1
Dillon, L.A.L.2
Gerstein, M.B.3
Gunsalus, K.C.4
Henikoff, S.5
Karpen, G.H.6
Kellis, M.7
Lai, E.C.8
Lieb, J.D.9
MacAlpine, D.M.10
-
4
-
-
84862188358
-
ModMine: Flexible access to modENCODE data
-
Contrino S, Smith RN, Butano D, Carr A, Hu F, Lyne R, Rutherford K, Kalderimis A, Sullivan J, Carbon S, et al. 2011. modMine: Flexible access to modENCODE data. Nucleic Acids Res 40: D1082-D1088.
-
(2011)
Nucleic Acids Res
, vol.40
-
-
Contrino, S.1
Smith, R.N.2
Butano, D.3
Carr, A.4
Hu, F.5
Lyne, R.6
Rutherford, K.7
Kalderimis, A.8
Sullivan, J.9
Carbon, S.10
-
5
-
-
0034717335
-
Regulation of B lymphocyte and macrophage development by graded expression of PU.1
-
DeKoter RP, Singh H. 2000. Regulation of B lymphocyte and macrophage development by graded expression of PU.1. Science 288: 1439-1441.
-
(2000)
Science
, vol.288
, pp. 1439-1441
-
-
DeKoter, R.P.1
Singh, H.2
-
6
-
-
52649157765
-
Substantial biases in ultra-short read data sets from high-throughput DNA sequencing
-
doi: 10.1093/nar/gkn425
-
Dohm JC, Lottaz C, Borodina T, Himmelbauer H. 2008. Substantial biases in ultra-short read data sets from high-throughput DNA sequencing. Nucleic Acids Res 36: e105. doi: 10.1093/nar/gkn425.
-
(2008)
Nucleic Acids Res
, vol.36
-
-
Dohm, J.C.1
Lottaz, C.2
Borodina, T.3
Himmelbauer, H.4
-
7
-
-
78650985680
-
An assessment of histone-modification antibody quality
-
Egelhofer TA, Minoda A, Klugman S, Lee K, Kolasinska-Zwierz P, Alekseyenko AA, Cheung M, Day DS, Gadel S, Gorchakov AA, et al. 2011. An assessment of histone-modification antibody quality. Nat Struct Mol Biol 18: 91-93.
-
(2011)
Nat Struct Mol Biol
, vol.18
, pp. 91-93
-
-
Egelhofer, T.A.1
Minoda, A.2
Klugman, S.3
Lee, K.4
Kolasinska-Zwierz, P.5
Alekseyenko, A.A.6
Cheung, M.7
Day, D.S.8
Gadel, S.9
Gorchakov, A.A.10
-
8
-
-
7444260846
-
The ENCODE (ENCyclopedia of DNA Elements) Project
-
The ENCODE Project Consortium
-
The ENCODE Project Consortium. 2004. The ENCODE (ENCyclopedia Of DNA Elements) Project. Science 306: 636-640.
-
(2004)
Science
, vol.306
, pp. 636-640
-
-
-
9
-
-
79955550445
-
A user's guide to the encyclopedia of DNA elements (ENCODE)
-
The ENCODE Project Consortium doi: 10.1371/journal.pbio.1001046
-
The ENCODE Project Consortium. 2011. A user's guide to the encyclopedia of DNA elements (ENCODE). PLoS Biol 9: e1001046. doi: 10.1371/journal.pbio. 1001046.
-
(2011)
PLoS Biol
, vol.9
-
-
-
10
-
-
78650747491
-
Discovery and characterization of chromatin states for systematic annotation of the human genome
-
Ernst J, Kellis M. 2010. Discovery and characterization of chromatin states for systematic annotation of the human genome. Nat Biotechnol 28: 817-825.
-
(2010)
Nat Biotechnol
, vol.28
, pp. 817-825
-
-
Ernst, J.1
Kellis, M.2
-
11
-
-
79955583542
-
Mapping and analysis of chromatin state dynamics in nine human cell types
-
Ernst J, Kheradpour P, Mikkelsen TS, Shoresh N, Ward LD, Epstein CB, Zhang X, Wang L, Issner R, Coyne M, et al. 2011. Mapping and analysis of chromatin state dynamics in nine human cell types. Nature 473: 43-49.
-
(2011)
Nature
, vol.473
, pp. 43-49
-
-
Ernst, J.1
Kheradpour, P.2
Mikkelsen, T.S.3
Shoresh, N.4
Ward, L.D.5
Epstein, C.B.6
Zhang, X.7
Wang, L.8
Issner, R.9
Coyne, M.10
-
12
-
-
0038185378
-
Genomic targets of the human c-Myc protein
-
DOI 10.1101/gad.1067003
-
Fernandez PC, Frank SR, Wang L, Schroeder M, Liu S, Greene J, Cocito A, Amati B. 2003. Genomic targets of the human c-Myc protein. Genes Dev 17: 1115-1129. (Pubitemid 36534986)
-
(2003)
Genes and Development
, vol.17
, Issue.9
, pp. 1115-1129
-
-
Fernandez, P.C.1
Frank, S.R.2
Wang, L.3
Schroeder, M.4
Liu, S.5
Greene, J.6
Cocito, A.7
Amati, B.8
-
13
-
-
78650081714
-
ZNF274 recruits the histone methyltransferase SETDB1 to the 3′ ends of ZNF genes
-
doi: 10.1371/journal.pone.0015082
-
Frietze S, O'Geen H, Blahnik KR, Jin VX, Farnham PJ. 2010. ZNF274 recruits the histone methyltransferase SETDB1 to the 3′ ends of ZNF genes. PLoS ONE 5: e15082. doi: 10.1371/journal.pone.0015082.
-
(2010)
PLoS ONE
, vol.5
-
-
Frietze, S.1
O'Geen, H.2
Blahnik, K.R.3
Jin, V.X.4
Farnham, P.J.5
-
14
-
-
78650410139
-
Integrative analysis of the Caenorhabditis elegans genome by the modENCODE project
-
Gerstein MB, Lu ZJ, Van Nostrand EL, Cheng C, Arshinoff BI, Liu T, Yip KY, Robilotto R, Rechtsteiner A, Ikegami K, et al. 2010. Integrative analysis of the Caenorhabditis elegans genome by the modENCODE project. Science 330: 1775-1787.
-
(2010)
Science
, vol.330
, pp. 1775-1787
-
-
Gerstein, M.B.1
Lu, Z.J.2
Van Nostrand, E.L.3
Cheng, C.4
Arshinoff, B.I.5
Liu, T.6
Yip, K.Y.7
Robilotto, R.8
Rechtsteiner, A.9
Ikegami, K.10
-
15
-
-
77949977555
-
Identification and characterization of enhancers controlling the inflammatory gene expression program in macrophages
-
Ghisletti S, Barozzi I, Mietton F, Polletti S, De Santa F, Venturini E, Gregory L, Lonie L, Chew A, Wei C, et al. 2010. Identification and characterization of enhancers controlling the inflammatory gene expression program in macrophages. Immunity 32: 317-328.
-
(2010)
Immunity
, vol.32
, pp. 317-328
-
-
Ghisletti, S.1
Barozzi, I.2
Mietton, F.3
Polletti, S.4
De Santa, F.5
Venturini, E.6
Gregory, L.7
Lonie, L.8
Chew, A.9
Wei, C.10
-
16
-
-
77952148742
-
Ab initio reconstruction of cell type-specific transcriptomes in mouse reveals the conserved multi-exonic structure of lincRNAs
-
Guttman M, Garber M, Levin JZ, Donaghey J, Robinson J, Adiconis X, Fan L, Koziol MJ, Gnirke A, Nusbaum C, et al. 2010. Ab initio reconstruction of cell type-specific transcriptomes in mouse reveals the conserved multi-exonic structure of lincRNAs. Nat Biotechnol 28: 503-510.
-
(2010)
Nat Biotechnol
, vol.28
, pp. 503-510
-
-
Guttman, M.1
Garber, M.2
Levin, J.Z.3
Donaghey, J.4
Robinson, J.5
Adiconis, X.6
Fan, L.7
Koziol, M.J.8
Gnirke, A.9
Nusbaum, C.10
-
17
-
-
79955027617
-
Co-occupancy by multiple cardiac transcription factors identifies transcriptional enhancers active in heart
-
He A, Kong SW, Ma Q, Pu WT. 2011. Co-occupancy by multiple cardiac transcription factors identifies transcriptional enhancers active in heart. Proc Natl Acad Sci 108: 5632-5637.
-
(2011)
Proc Natl Acad Sci
, vol.108
, pp. 5632-5637
-
-
He, A.1
Kong, S.W.2
Ma, Q.3
Pu, W.T.4
-
18
-
-
79955471381
-
High conservation of transcription factor binding and evidence for combinatorial regulation across six Drosophila species
-
He Q, Bardet AF, Patton B, Purvis J, Johnston J, Paulson A, Gogol M, Stark A, Zeitlinger J. 2011. High conservation of transcription factor binding and evidence for combinatorial regulation across six Drosophila species. Nat Genet 43: 414-420.
-
(2011)
Nat Genet
, vol.43
, pp. 414-420
-
-
He, Q.1
Bardet, A.F.2
Patton, B.3
Purvis, J.4
Johnston, J.5
Paulson, A.6
Gogol, M.7
Stark, A.8
Zeitlinger, J.9
-
19
-
-
77952567987
-
Simple combinations of lineage-determining transcription factors prime cis-regulatory elements required for macrophage and B cell identities
-
Heinz S, Benner C, Spann N, Bertolino E, Lin YC, Laslo P, Cheng JX, Murre C, Singh H, Glass CK. 2010. Simple combinations of lineage-determining transcription factors prime cis-regulatory elements required for macrophage and B cell identities. Mol Cell 38: 576-589.
-
(2010)
Mol Cell
, vol.38
, pp. 576-589
-
-
Heinz, S.1
Benner, C.2
Spann, N.3
Bertolino, E.4
Lin, Y.C.5
Laslo, P.6
Cheng, J.X.7
Murre, C.8
Singh, H.9
Glass, C.K.10
-
20
-
-
0036270889
-
ChIP-chip: A genomic approach for identifying transcription factor binding sites
-
DOI 10.1016/S0076-6879(02)50979-4
-
Horak CE, Snyder M. 2002. ChIP-chip: A genomic approach for identifying transcription factor binding sites. Methods Enzymol 350: 469-483. (Pubitemid 34619507)
-
(2002)
Methods in Enzymology
, vol.350
, pp. 469-483
-
-
Horak, C.E.1
Snyder, M.2
-
21
-
-
67549104319
-
Genomic antagonism between retinoic acid and estrogen signaling in breast cancer
-
Hua S, Kittler R, White KP. 2009. Genomic antagonism between retinoic acid and estrogen signaling in breast cancer. Cell 137: 1259-1271.
-
(2009)
Cell
, vol.137
, pp. 1259-1271
-
-
Hua, S.1
Kittler, R.2
White, K.P.3
-
22
-
-
0035945567
-
Genomic binding sites of the yeast cell-cycle transcription factors SBF and MBF
-
DOI 10.1038/35054095
-
Iyer VR, Horak CE, Scafe CS, Botstein D, Snyder M, Brown PO. 2001. Genomic binding sites of the yeast cell-cycle transcription factors SBF and MBF. Nature 409: 533-538. (Pubitemid 32144361)
-
(2001)
Nature
, vol.409
, Issue.6819
, pp. 533-538
-
-
Iyer, V.R.1
Horak, C.E.2
Scafe, C.S.3
Botstein, D.4
Snyder, M.5
Brown, P.O.6
-
23
-
-
55749094855
-
An integrated software system for analyzing ChIP-chip and ChIP-seq data
-
Ji H, Jiang H, Ma W, Johnson DS, Myers RM, Wong WH. 2008. An integrated software system for analyzing ChIP-chip and ChIP-seq data. Nat Biotechnol 26: 1293-1300.
-
(2008)
Nat Biotechnol
, vol.26
, pp. 1293-1300
-
-
Ji, H.1
Jiang, H.2
Ma, W.3
Johnson, D.S.4
Myers, R.M.5
Wong, W.H.6
-
24
-
-
34250159524
-
Genome-wide mapping of in vivo protein-DNA interactions
-
DOI 10.1126/science.1141319
-
Johnson DS, Mortazavi A, Myers RM, Wold B. 2007. Genome-wide mapping of in vivo protein-DNA interactions. Science 316: 1497-1502. (Pubitemid 46906620)
-
(2007)
Science
, vol.316
, Issue.5830
, pp. 1497-1502
-
-
Johnson, D.S.1
Mortazavi, A.2
Myers, R.M.3
Wold, B.4
-
25
-
-
57449100870
-
Design and analysis of ChIP-seq experiments for DNA-binding proteins
-
Kharchenko PV, Tolstorukov MY, Park PJ. 2008. Design and analysis of ChIP-seq experiments for DNA-binding proteins. Nat Biotechnol 26: 1351-1359.
-
(2008)
Nat Biotechnol
, vol.26
, pp. 1351-1359
-
-
Kharchenko, P.V.1
Tolstorukov, M.Y.2
Park, P.J.3
-
26
-
-
34248198548
-
Identification of genes directly regulated by the oncogene ZNF217 using chromatin immunoprecipitation (ChIP)-chip assays
-
DOI 10.1074/jbc.M611752200
-
Krig SR, Jin VX, Bieda MC, O'Geen H, Yaswen P, Green R, Farnham PJ. 2007. Identification of genes directly regulated by the oncogene ZNF217 using chromatin immunoprecipitation (ChIP)-chip assays. J Biol Chem 282: 9703-9712. (Pubitemid 47104577)
-
(2007)
Journal of Biological Chemistry
, vol.282
, Issue.13
, pp. 9703-9712
-
-
Krig, S.R.1
Jin, V.X.2
Bieda, M.C.3
O'Geen, H.4
Yaswen, P.5
Green, R.6
Farnham, P.J.7
-
27
-
-
77953255983
-
A human B-cell interactome identifies MYB and FOXM1 asmaster regulators of proliferation in germinal centers
-
doi: 10.1038/msb.2010.31
-
Lefebvre C, Rajbhandari P, Alvarez MJ, Bandaru P, Lim WK, Sato M, Wang K, Sumazin P, Kustagi M, Bisikirska BC, et al. 2010. A human B-cell interactome identifies MYB and FOXM1 asmaster regulators of proliferation in germinal centers. Mol Syst Biol 6: 377. doi: 10.1038/msb.2010.31.
-
(2010)
Mol Syst Biol
, vol.6
, pp. 377
-
-
Lefebvre, C.1
Rajbhandari, P.2
Alvarez, M.J.3
Bandaru, P.4
Lim, W.K.5
Sato, M.6
Wang, K.7
Sumazin, P.8
Kustagi, M.9
Bisikirska, B.C.10
-
28
-
-
79955564639
-
Measuring reproducibility of high-throughput experiments
-
Li Q, Brown J, Huang H, Bickel P. 2011. Measuring reproducibility of high-throughput experiments. Ann Appl Stat 5: 1752-1779.
-
(2011)
Ann Appl Stat
, vol.5
, pp. 1752-1779
-
-
Li, Q.1
Brown, J.2
Huang, H.3
Bickel, P.4
-
29
-
-
0034934774
-
Promoter-specific binding of Rap1 revealed by genome-wide maps of protein-DNA association
-
DOI 10.1038/ng569
-
Lieb JD, Liu X, Botstein D, Brown PO. 2001. Promoter-specific binding of Rap1 revealed by genome-wide maps of protein-DNA association. Nat Genet 28: 327-334. (Pubitemid 32702421)
-
(2001)
Nature Genetics
, vol.28
, Issue.4
, pp. 327-334
-
-
Lieb, J.D.1
Liu, X.2
Botstein, D.3
Brown, P.O.4
-
30
-
-
77953763449
-
A global network of transcription factors, involving E2A, EBF1 and Foxo1, that orchestrates B cell fate
-
Lin YC, Jhunjhunwala S, Benner C, Heinz S, Welinder E, Mansson R, Sigvardsson M, Hagman J, Espinoza CA, Dutkowski J, et al. 2010. A global network of transcription factors, involving E2A, EBF1 and Foxo1, that orchestrates B cell fate. Nat Immunol 11: 635-643.
-
(2010)
Nat Immunol
, vol.11
, pp. 635-643
-
-
Lin, Y.C.1
Jhunjhunwala, S.2
Benner, C.3
Heinz, S.4
Welinder, E.5
Mansson, R.6
Sigvardsson, M.7
Hagman, J.8
Espinoza, C.A.9
Dutkowski, J.10
-
31
-
-
34547624303
-
Genome-wide maps of chromatin state in pluripotent and lineage-committed cells
-
DOI 10.1038/nature06008, PII NATURE06008
-
Mikkelsen TS, Ku M, Jaffe DB, Issac B, Lieberman E, Giannoukos G, Alvarez P, Brockman W, Kim T, Koche RP, et al. 2007. Genome-wide maps of chromatin state in pluripotent and lineage-committed cells. Nature 448: 553-560. (Pubitemid 47206934)
-
(2007)
Nature
, vol.448
, Issue.7153
, pp. 553-560
-
-
Mikkelsen, T.S.1
Ku, M.2
Jaffe, D.B.3
Issac, B.4
Lieberman, E.5
Giannoukos, G.6
Alvarez, P.7
Brockman, W.8
Kim, T.-K.9
Koche, R.P.10
Lee, W.11
Mendenhall, E.12
O'Donovan, A.13
Presser, A.14
Russ, C.15
Xie, X.16
Meissner, A.17
Wernig, M.18
Jaenisch, R.19
Nusbaum, C.20
Lander, E.S.21
Bernstein, B.E.22
more..
-
32
-
-
79955550445
-
A user's guide to the encyclopedia of DNA elements (ENCODE)
-
doi: 10.1371/journal.pbio.1001046
-
Myers RM, Stamatoyannopoulos J, Snyder M, Dunham I, Hardison RC, Bernstein BE, Gingeras TR, Kent WJ, Birney E, Wold B, et al. 2011. A user's guide to the encyclopedia of DNA elements (ENCODE). PLoS Biol 9: e1001046. doi: 10.1371/journal.pbio.1001046.
-
(2011)
PLoS Biol
, vol.9
-
-
Myers, R.M.1
Stamatoyannopoulos, J.2
Snyder, M.3
Dunham, I.4
Hardison, R.C.5
Bernstein, B.E.6
Gingeras, T.R.7
Kent, W.J.8
Birney, E.9
Wold, B.10
-
33
-
-
79953311672
-
High resolution mapping of Twist to DNA in Drosophila embryos: Efficient functional analysis and evolutionary conservation
-
Ozdemir A, Fisher-Aylor KI, Pepke S, Samanta M, Dunipace L, McCue K, Zeng L, Ogawa N, Wold BJ, Stathopoulos A. 2011. High resolution mapping of Twist to DNA in Drosophila embryos: Efficient functional analysis and evolutionary conservation. Genome Res 21: 566-577.
-
(2011)
Genome Res
, vol.21
, pp. 566-577
-
-
Ozdemir, A.1
Fisher-Aylor, K.I.2
Pepke, S.3
Samanta, M.4
Dunipace, L.5
McCue, K.6
Zeng, L.7
Ogawa, N.8
Wold, B.J.9
Stathopoulos, A.10
-
34
-
-
70349312354
-
ChIP-seq: Advantages and challenges of a maturing technology
-
Park PJ. 2009. ChIP-seq: Advantages and challenges of a maturing technology. Nat Rev Genet 10: 669-680.
-
(2009)
Nat Rev Genet
, vol.10
, pp. 669-680
-
-
Park, P.J.1
-
35
-
-
70449711243
-
Computation for ChIP-seq and RNA-seq studies
-
Pepke S, Wold B, Mortazavi A. 2009. Computation for ChIP-seq and RNA-seq studies. Nat Methods 6: S22-S32.
-
(2009)
Nat Methods
, vol.6
-
-
Pepke, S.1
Wold, B.2
Mortazavi, A.3
-
36
-
-
42949095911
-
BAC TransgeneOmics: A high-throughput method for exploration of protein function in mammals
-
DOI 10.1038/nmeth.1199, PII NMETH.1199
-
Poser I, Sarov M, Hutchins JRA, Hériché J, Toyoda Y, Pozniakovsky A, Weigl D, Nitzsche A, Hegemann B, Bird AW, et al. 2008. BAC TransgeneOmics: A high-throughput method for exploration of protein function in mammals. Nat Methods 5: 409-415. (Pubitemid 351619099)
-
(2008)
Nature Methods
, vol.5
, Issue.5
, pp. 409-415
-
-
Poser, I.1
Sarov, M.2
Hutchins, J.R.A.3
Heriche, J.-K.4
Toyoda, Y.5
Pozniakovsky, A.6
Weigl, D.7
Nitzsche, A.8
Hegemann, B.9
Bird, A.W.10
Pelletier, L.11
Kittler, R.12
Hua, S.13
Naumann, R.14
Augsburg, M.15
Sykora, M.M.16
Hofemeister, H.17
Zhang, Y.18
Nasmyth, K.19
White, K.P.20
Dietzel, S.21
Mechtler, K.22
Durbin, R.23
Stewart, A.F.24
Peters, J.-M.25
Buchholz, F.26
Hyman, A.A.27
more..
-
37
-
-
77649268269
-
Close association of RNA polymerase II and many transcription factors with Pol III genes
-
Raha D, Wang Z, Moqtaderi Z, Wu L, Zhong G, Gerstein M, Struhl K, Snyder M. 2010. Close association of RNA polymerase II and many transcription factors with Pol III genes. Proc Natl Acad Sci 107: 3639-3644.
-
(2010)
Proc Natl Acad Sci
, vol.107
, pp. 3639-3644
-
-
Raha, D.1
Wang, Z.2
Moqtaderi, Z.3
Wu, L.4
Zhong, G.5
Gerstein, M.6
Struhl, K.7
Snyder, M.8
-
38
-
-
79960614727
-
ZINBA integrates local covariates with DNA-seq data to identify broad and narrow regions of enrichment, even within amplified genomic regions
-
doi: 10.1186/gb-2011-12-7-r67
-
Rashid NU, Giresi PG, Ibrahim JG, Sun W, Lieb JD. 2011. ZINBA integrates local covariates with DNA-seq data to identify broad and narrow regions of enrichment, even within amplified genomic regions. Genome Biol 12: R67. doi: 10.1186/gb-2011-12-7-r67.
-
(2011)
Genome Biol
, vol.12
-
-
Rashid, N.U.1
Giresi, P.G.2
Ibrahim, J.G.3
Sun, W.4
Lieb, J.D.5
-
39
-
-
0034704248
-
Genome-wide location and function of DNA binding proteins
-
DOI 10.1126/science.290.5500.2306
-
Ren B, Robert F, Wyrick JJ, Aparicio O, Jennings EG, Simon I, Zeitlinger J, Schreiber J, Hannett N, Kanin E, et al. 2000. Genome-wide location and function of DNA binding proteins. Science 290: 2306-2309. (Pubitemid 32041573)
-
(2000)
Science
, vol.290
, Issue.5500
, pp. 2306-2309
-
-
Ren, B.1
Robert, F.2
Wyrick, J.J.3
Aparicio, O.4
Jennings, E.G.5
Simon, I.6
Zeitlinger, J.7
Schreiber, J.8
Hannett, N.9
Kanin, E.10
Volkert, T.L.11
Wilson, C.J.12
Bell, S.P.13
Young, R.A.14
-
40
-
-
34547633677
-
Genome-wide profiles of STAT1 DNA association using chromatin immunoprecipitation and massively parallel sequencing
-
DOI 10.1038/nmeth1068, PII NMETH1068
-
Robertson G, Hirst M, Bainbridge M, Bilenky M, Zhao Y, Zeng T, Euskirchen G, Bernier B, Varhol R, Delaney A, et al. 2007. Genome-wide profiles of STAT1 DNA association using chromatin immunoprecipitation and massively parallel sequencing. Nat Methods 4: 651-657. (Pubitemid 47202477)
-
(2007)
Nature Methods
, vol.4
, Issue.8
, pp. 651-657
-
-
Robertson, G.1
Hirst, M.2
Bainbridge, M.3
Bilenky, M.4
Zhao, Y.5
Zeng, T.6
Euskirchen, G.7
Bernier, B.8
Varhol, R.9
Delaney, A.10
Thiessen, N.11
Griffith, O.L.12
He, A.13
Marra, M.14
Snyder, M.15
Jones, S.16
-
41
-
-
84861859517
-
ENCODE wholegenome data in the UCSC Genome Browser: Update 2012
-
Rosenbloom KR, Dreszer TR, Long JC, Malladi VS, Sloan CA, Raney BJ, Cline MS, Karolchik D, Barber GP, Clawson H, et al. 2011. ENCODE wholegenome data in the UCSC Genome Browser: Update 2012. Nucleic Acids Res 40: D912-D917.
-
(2011)
Nucleic Acids Res
, vol.40
-
-
Rosenbloom, K.R.1
Dreszer, T.R.2
Long, J.C.3
Malladi, V.S.4
Sloan, C.A.5
Raney, B.J.6
Cline, M.S.7
Karolchik, D.8
Barber, G.P.9
Clawson, H.10
-
42
-
-
78650331647
-
Identification of functional elements and regulatory circuits by Drosophila modENCODE
-
Roy S, Ernst J, Kharchenko PV, Kheradpour P, Negre N, Eaton ML, Landolin JM, Bristow CA, Ma L, Lin MF, et al. 2010. Identification of functional elements and regulatory circuits by Drosophila modENCODE. Science 330: 1787-1797.
-
(2010)
Science
, vol.330
, pp. 1787-1797
-
-
Roy, S.1
Ernst, J.2
Kharchenko, P.V.3
Kheradpour, P.4
Negre, N.5
Eaton, M.L.6
Landolin, J.M.7
Bristow, C.A.8
Ma, L.9
Lin, M.F.10
-
43
-
-
60149112271
-
PeakSeq enables systematic scoring of ChIP-seq experiments relative to controls
-
Rozowsky J, Euskirchen G, Auerbach RK, Zhang ZD, Gibson T, Bjornson R, Carriero N, Snyder M, Gerstein MB. 2009. PeakSeq enables systematic scoring of ChIP-seq experiments relative to controls. Nat Biotechnol 27: 66-75.
-
(2009)
Nat Biotechnol
, vol.27
, pp. 66-75
-
-
Rozowsky, J.1
Euskirchen, G.2
Auerbach, R.K.3
Zhang, Z.D.4
Gibson, T.5
Bjornson, R.6
Carriero, N.7
Snyder, M.8
Gerstein, M.B.9
-
44
-
-
33745604636
-
Suz12 binds to silenced regions of the genome in a cell-type-specific manner
-
DOI 10.1101/gr.5306606
-
Squazzo SL, O'Geen H, Komashko VM, Krig SR, Jin VX, Jang S, Margueron R, Reinberg D, Green R, Farnham PJ. 2006. Suz12 binds to silenced regions of the genome in a cell-type-specific manner. Genome Res 16: 890-900. (Pubitemid 43992913)
-
(2006)
Genome Research
, vol.16
, Issue.7
, pp. 890-900
-
-
Squazzo, S.L.1
O'Geen, H.2
Komashko, V.M.3
Krig, S.R.4
Jin, V.X.5
Jang, S.-W.6
Margueron, R.7
Reinberg, D.8
Green, R.9
Farnham, P.J.10
-
45
-
-
79955883317
-
Genome-wide analysis of simultaneous GATA1/2, RUNX1, FLI1, and SCL binding in megakaryocytes identifies hematopoietic regulators
-
Tijssen MR, Cvejic A, Joshi A, Hannah RL, Ferreira R, Forrai A, Bellissimo DC, Oram SH, Smethurst PA, Wilson NK, et al. 2011. Genome-wide analysis of simultaneous GATA1/2, RUNX1, FLI1, and SCL binding in megakaryocytes identifies hematopoietic regulators. Dev Cell 20: 597-609.
-
(2011)
Dev Cell
, vol.20
, pp. 597-609
-
-
Tijssen, M.R.1
Cvejic, A.2
Joshi, A.3
Hannah, R.L.4
Ferreira, R.5
Forrai, A.6
Bellissimo, D.C.7
Oram, S.H.8
Smethurst, P.A.9
Wilson, N.K.10
-
46
-
-
50849090969
-
Genome-wide analysis of transcription factor binding sites based on ChIP-Seq data
-
Valouev A, Johnson DS, Sundquist A, Medina C, Anton E, Batzoglou S, Myers RM, Sidow A. 2008. Genome-wide analysis of transcription factor binding sites based on ChIP-Seq data. Nat Methods 5: 829-834.
-
(2008)
Nat Methods
, vol.5
, pp. 829-834
-
-
Valouev, A.1
Johnson, D.S.2
Sundquist, A.3
Medina, C.4
Anton, E.5
Batzoglou, S.6
Myers, R.M.7
Sidow, A.8
-
47
-
-
46249112085
-
Combinatorial patterns of histone acetylations and methylations in the human genome
-
DOI 10.1038/ng.154, PII NG154
-
Wang Z, Zang C, Rosenfeld JA, Schones DE, Barski A, Cuddapah S, Cui K, Roh T, Peng W, Zhang MQ, et al. 2008. Combinatorial patterns of histone acetylations and methylations in the human genome. Nat Genet 40: 897-903. (Pubitemid 351913645)
-
(2008)
Nature Genetics
, vol.40
, Issue.7
, pp. 897-903
-
-
Wang, Z.1
Zang, C.2
Rosenfeld, J.A.3
Schones, D.E.4
Barski, A.5
Cuddapah, S.6
Cui, K.7
Roh, T.-Y.8
Peng, W.9
Zhang, M.Q.10
Zhao, K.11
-
48
-
-
0037080674
-
Isolating human transcription factor targets by coupling chromatin immunoprecipitation and CpG island microarray analysis
-
DOI 10.1101/gad.943102
-
Weinmann AS, Yan PS, Oberley MJ, Huang TH, Farnham PJ. 2002. Isolating human transcription factor targets by coupling chromatin immunoprecipitation and CpG island microarray analysis. Genes Dev 16: 235-244. (Pubitemid 34075815)
-
(2002)
Genes and Development
, vol.16
, Issue.2
, pp. 235-244
-
-
Weinmann, A.S.1
Yan, P.S.2
Oberley, M.J.3
Huang, T.H.-M.4
Farnham, P.J.5
-
49
-
-
77957348625
-
Combinatorial transcriptional control in blood stem/progenitor cells: Genome-wide analysis of tenmajor transcriptional regulators
-
Wilson NK, Foster SD, Wang X, Knezevic K, Schütte J, Kaimakis P, Chilarska PM, Kinston S, Ouwehand WH, Dzierzak E, et al. 2010. Combinatorial transcriptional control in blood stem/progenitor cells: Genome-wide analysis of tenmajor transcriptional regulators. Cell Stem Cell 7: 532-544.
-
(2010)
Cell Stem Cell
, vol.7
, pp. 532-544
-
-
Wilson, N.K.1
Foster, S.D.2
Wang, X.3
Knezevic, K.4
Schütte, J.5
Kaimakis, P.6
Chilarska, P.M.7
Kinston, S.8
Ouwehand, W.H.9
Dzierzak, E.10
-
50
-
-
53849146020
-
Model-based analysis of ChIP-Seq (MACS)
-
doi: 10.1186/gb-2008-9-9-r137
-
Zhang Y, Liu T, Meyer CA, Eeckhoute J, Johnson DS, Bernstein BE, Nusbaum C, Myers RM, Brown M, Li W, et al. 2008. Model-based analysis of ChIP-Seq (MACS). Genome Biol 9: R137. doi: 10.1186/gb-2008-9-9-r137.
-
(2008)
Genome Biol
, vol.9
-
-
Zhang, Y.1
Liu, T.2
Meyer, C.A.3
Eeckhoute, J.4
Johnson, D.S.5
Bernstein, B.E.6
Nusbaum, C.7
Myers, R.M.8
Brown, M.9
Li, W.10
-
51
-
-
77649225979
-
Genome-wide identification of binding sites defines distinct functions for Caenorhabditis elegans PHA-4/FOXA in development and environmental response
-
doi: 10.1371/journal.pgen.1000848
-
Zhong M, Niu W, Lu ZJ, Sarov M, Murray JI, Janette J, Raha D, Sheaffer KL, Lam HYK, Preston E, et al. 2010. Genome-wide identification of binding sites defines distinct functions for Caenorhabditis elegans PHA-4/FOXA in development and environmental response. PLoS Genet 6: e1000848. doi: 10.1371/journal.pgen. 1000848.
-
(2010)
PLoS Genet
, vol.6
-
-
Zhong, M.1
Niu, W.2
Lu, Z.J.3
Sarov, M.4
Murray, J.I.5
Janette, J.6
Raha, D.7
Sheaffer, K.L.8
Lam, H.Y.K.9
Preston, E.10
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