-
2
-
-
68949213578
-
Insights from genomic profiling of transcription factors
-
Farnham PJ: Insights from genomic profiling of transcription factors. Nat Rev Genet 2009, 10(9):605-616.
-
(2009)
Nat Rev Genet
, vol.10
, Issue.9
, pp. 605-616
-
-
Farnham, P.J.1
-
3
-
-
62549128139
-
A census of human transcription factors: Function, expression and evolution
-
Vaquerizas JM, Kummerfeld SK, Teichmann SA, Luscombe NM: A census of human transcription factors: function, expression and evolution. Nat Rev Genet 2009, 10(4):252-263.
-
(2009)
Nat Rev Genet
, vol.10
, Issue.4
, pp. 252-263
-
-
Vaquerizas, J.M.1
Kummerfeld, S.K.2
Teichmann, S.A.3
Luscombe, N.M.4
-
4
-
-
34249299791
-
The complex language of chromatin regulation during transcription
-
Berger SL: The complex language of chromatin regulation during transcription. Nature 2007, 447(7143):407-412.
-
(2007)
Nature
, vol.447
, Issue.7143
, pp. 407-412
-
-
Berger, S.L.1
-
5
-
-
2942518343
-
Mapping global histone acetylation patterns to gene expression
-
Kurdistani SK, Tavazoie S, Grunstein M: Mapping global histone acetylation patterns to gene expression. Cell 2004, 117(6):721-733.
-
(2004)
Cell
, vol.117
, Issue.6
, pp. 721-733
-
-
Kurdistani, S.K.1
Tavazoie, S.2
Grunstein, M.3
-
6
-
-
84878011578
-
Exploring the three-dimensional organization of genomes: Interpreting chromatin interaction data
-
Dekker J, Marti-Renom MA, Mirny LA: Exploring the three-dimensional organization of genomes: interpreting chromatin interaction data. Nat Rev Genet 2013, 14(6):390-403.
-
(2013)
Nat Rev Genet
, vol.14
, Issue.6
, pp. 390-403
-
-
Dekker, J.1
Marti-Renom, M.A.2
Mirny, L.A.3
-
7
-
-
33847070442
-
The role of chromatin during transcription
-
Li B, Carey M, Workman JL: The role of chromatin during transcription. Cell 2007, 128(4):707-719.
-
(2007)
Cell
, vol.128
, Issue.4
, pp. 707-719
-
-
Li, B.1
Carey, M.2
Workman, J.L.3
-
9
-
-
78649270968
-
A unique H3K4me2 profilemarks tissue-specific gene regulation
-
Pekowska A, Benoukraf T, Ferrier P, Spicuglia S: A unique H3K4me2 profilemarks tissue-specific gene regulation. Genome Res 2010, 20(11):1493-1502.
-
(2010)
Genome Res
, vol.20
, Issue.11
, pp. 1493-1502
-
-
Pekowska, A.1
Benoukraf, T.2
Ferrier, P.3
Spicuglia, S.4
-
10
-
-
33847076849
-
Chromatinmodifications and their function
-
Kouzarides T: Chromatinmodifications and their function. Cell 2007, 128(4):693-705.
-
(2007)
Cell
, vol.128
, Issue.4
, pp. 693-705
-
-
Kouzarides, T.1
-
11
-
-
54549083228
-
H3K79methylation profiles definemurine and human MLL-AF4 leukemias
-
Krivtsov AV, Feng Z, Lemieux ME, Faber J, Vempati S, Sinha AU, Xia X, Jesneck J, Bracken AP, Silverman LB, Kutok JL, Kung AL, Armstrong SA: H3K79methylation profiles definemurine and human MLL-AF4 leukemias. Cancer Cell 2008, 14(5):355-368.
-
(2008)
Cancer Cell
, vol.14
, Issue.5
, pp. 355-368
-
-
Krivtsov, A.V.1
Feng, Z.2
Lemieux, M.E.3
Faber, J.4
Vempati, S.5
Sinha, A.U.6
Xia, X.7
Jesneck, J.8
Bracken, A.P.9
Silverman, L.B.10
Kutok, J.L.11
Kung, A.L.12
Armstrong, S.A.13
-
12
-
-
35349006314
-
Histone lysine demethylases: Emerging roles in development, physiology and disease
-
Shi Y: Histone lysine demethylases: emerging roles in development, physiology and disease. Nat Rev Genet 2007, 8(11):829-833.
-
(2007)
Nat Rev Genet
, vol.8
, Issue.11
, pp. 829-833
-
-
Shi, Y.1
-
13
-
-
77957970301
-
Epigenetic modifications and human disease
-
Portela A, Esteller M: Epigenetic modifications and human disease. Nat Biotechnol 2010, 28(10):1057-1068.
-
(2010)
Nat Biotechnol
, vol.28
, Issue.10
, pp. 1057-1068
-
-
Portela, A.1
Esteller, M.2
-
14
-
-
84934981753
-
Predictive modelling of gene expression from transcriptional regulatory elements
-
Budden DM, Hurley DG, Crampin EJ: Predictive modelling of gene expression from transcriptional regulatory elements. Brief Bioinform 2014, bbu034:. doi:10.1093/bib/bbu034.
-
(2014)
Brief Bioinform
, pp. bbu034
-
-
Budden, D.M.1
Hurley, D.G.2
Crampin, E.J.3
-
15
-
-
84868020122
-
Genome-wide in silico prediction of gene expression
-
McLeay RC, Lesluyes T, Partida GC, Bailey TL: Genome-wide in silico prediction of gene expression. Bioinformatics 2012, 28(21):2789-2796.
-
(2012)
Bioinformatics
, vol.28
, Issue.21
, pp. 2789-2796
-
-
McLeay, R.C.1
Lesluyes, T.2
Partida, G.C.3
Bailey, T.L.4
-
16
-
-
84855895602
-
Modeling the relative relationship of transcription factor binding and histone modifications to gene expression levels in mouse embryonic stem cells
-
Cheng C, Gerstein M: Modeling the relative relationship of transcription factor binding and histone modifications to gene expression levels in mouse embryonic stem cells. Nucleic Acids Res 2012, 40(2):553-568.
-
(2012)
Nucleic Acids Res
, vol.40
, Issue.2
, pp. 553-568
-
-
Cheng, C.1
Gerstein, M.2
-
17
-
-
79952696158
-
A statistical framework formodeling gene expression using chromatin features and application tomodENCODE datasets
-
Cheng C, Yan K-K, Yip KY, Rozowsky J, Alexander R, Shou C, Gerstein M: A statistical framework formodeling gene expression using chromatin features and application tomodENCODE datasets. Genome Biol 2011, 12(2):15.
-
(2011)
Genome Biol
, vol.12
, Issue.2
, pp. 15
-
-
Cheng, C.1
Yan, K.-K.2
Yip, K.Y.3
Rozowsky, J.4
Alexander, R.5
Shou, C.6
Gerstein, M.7
-
18
-
-
76049125511
-
ChIP-Seq of transcription factors predicts absolute and differential gene expression in embryonic stem cells
-
Ouyang Z, Zhou Q, Wong WH: ChIP-Seq of transcription factors predicts absolute and differential gene expression in embryonic stem cells. Proc Natl Acad Sci 2009, 106(51):21521-21526.
-
(2009)
Proc Natl Acad Sci
, vol.106
, Issue.51
, pp. 21521-21526
-
-
Ouyang, Z.1
Zhou, Q.2
Wong, W.H.3
-
19
-
-
77649246145
-
Histone modification levels are predictive for gene expression
-
Karlíc R, Chung H-R, Lasserre J, Vlahoviček K, Vingron M: Histone modification levels are predictive for gene expression. Proc Natl Acad Sci 2010, 107(7):2926-2931.
-
(2010)
Proc Natl Acad Sci
, vol.107
, Issue.7
, pp. 2926-2931
-
-
Karlíc, R.1
Chung, H.-R.2
Lasserre, J.3
Vlahoviček, K.4
Vingron, M.5
-
20
-
-
77956649096
-
A survey of cross-validation procedures formodel selection
-
Arlot S, Celisse A: A survey of cross-validation procedures formodel selection. Stat Surv 2010, 4:40-79.
-
(2010)
Stat Surv
, vol.4
, pp. 40-79
-
-
Arlot, S.1
Celisse, A.2
-
21
-
-
44649117905
-
Integration of external signaling pathways with the core transcriptional network in embryonic stem cells
-
Chen X, Xu H, Yuan P, Fang F, Huss M, Vega VB, Wong E, Orlov Y. L, Zhang W, Jiang J, Loh Y-H, Yeo HC, Yeo ZX, Narang V, Govindarajan KR, Leong B, Shahab A, Ruan Y, Bourque G, Sung W-K, Clarke ND, Wei C-L, Ng H-H: Integration of external signaling pathways with the core transcriptional network in embryonic stem cells. Cell 2008, 133(6):1106-1117.
-
(2008)
Cell
, vol.133
, Issue.6
, pp. 1106-1117
-
-
Chen, X.1
Xu, H.2
Yuan, P.3
Fang, F.4
Huss, M.5
Vega, V.B.6
Wong, E.7
Orlov, Y.L.8
Zhang, W.9
Jiang, J.10
Loh, Y.-H.11
Yeo, H.C.12
Yeo, Z.X.13
Narang, V.14
Govindarajan, K.R.15
Leong, B.16
Shahab, A.17
Ruan, Y.18
Bourque, G.19
Sung, W.-K.20
Clarke, N.D.21
Wei, C.-L.22
Ng, H.-H.23
more..
-
22
-
-
77957970498
-
Epigenetic modifications in pluripotent and differentiated cells
-
Meissner A: Epigenetic modifications in pluripotent and differentiated cells. Nat Biotechnol 2010, 28(10):1079-1088.
-
(2010)
Nat Biotechnol
, vol.28
, Issue.10
, pp. 1079-1088
-
-
Meissner, A.1
-
23
-
-
55549145072
-
De novo DNA methylation promoted by G9a prevents reprogramming of embryonically silenced genes
-
Epsztejn-Litman S, Feldman N, Abu-Remaileh M, Shufaro Y, Gerson A, Ueda J, Deplus R, Fuks F, Shinkai Y, Cedar H, Bergman Y: De novo DNA methylation promoted by G9a prevents reprogramming of embryonically silenced genes. Nat Struct Mol Biol 2008, 15(11):1176-1183.
-
(2008)
Nat Struct Mol Biol
, vol.15
, Issue.11
, pp. 1176-1183
-
-
Epsztejn-Litman, S.1
Feldman, N.2
Abu-Remaileh, M.3
Shufaro, Y.4
Gerson, A.5
Ueda, J.6
Deplus, R.7
Fuks, F.8
Shinkai, Y.9
Cedar, H.10
Bergman, Y.11
-
24
-
-
33645132331
-
G9a-mediated irreversible epigenetic inactivation of Oct-3/4 during early embryogenesis
-
Feldman N, Gerson A, Fang J, Li E, Zhang Y, Shinkai Y, Cedar H, Bergman Y: G9a-mediated irreversible epigenetic inactivation of Oct-3/4 during early embryogenesis. Nat Cell Biol 2006, 8(2):188-194.
-
(2006)
Nat Cell Biol
, vol.8
, Issue.2
, pp. 188-194
-
-
Feldman, N.1
Gerson, A.2
Fang, J.3
Li, E.4
Zhang, Y.5
Shinkai, Y.6
Cedar, H.7
Bergman, Y.8
-
25
-
-
46249103973
-
Stem cell transcriptome profiling via massive-scalemRNA sequencing
-
Cloonan N, Forrest AR, Kolle G, Gardiner BB, Faulkner GJ, Brown MK, Taylor DF, Steptoe AL, Wani S, Bethel G, Robertson AJ, Perkins AC, Bruce SJ, Lee CC, Ranade SS, Peckham HE, Manning JM, McKernan KJ, Grimmond SM: Stem cell transcriptome profiling via massive-scalemRNA sequencing. Nat Methods 2008, 5(7):613-619.
-
(2008)
Nat Methods
, vol.5
, Issue.7
, pp. 613-619
-
-
Cloonan, N.1
Forrest, A.R.2
Kolle, G.3
Gardiner, B.B.4
Faulkner, G.J.5
Brown, M.K.6
Taylor, D.F.7
Steptoe, A.L.8
Wani, S.9
Bethel, G.10
Robertson, A.J.11
Perkins, A.C.12
Bruce, S.J.13
Lee, C.C.14
Ranade, S.S.15
Peckham, H.E.16
Manning, J.M.17
McKernan, K.J.18
Grimmond, S.M.19
-
26
-
-
46249106990
-
Mapping and quantifying mammalian transcriptomes by RNA-Seq
-
Mortazavi A, Williams BA, McCue K, Schaeffer L, Wold B: Mapping and quantifying mammalian transcriptomes by RNA-Seq. Nat Methods 2008, 5(7):621-628.
-
(2008)
Nat Methods
, vol.5
, Issue.7
, pp. 621-628
-
-
Mortazavi, A.1
Williams, B.A.2
McCue, K.3
Schaeffer, L.4
Wold, B.5
-
27
-
-
84891768365
-
Ensembl 2014
-
Flicek P, Amode MR, Barrell D, Beal K, Billis K, Brent S, Carvalho-Silva D, Clapham P, Coates G, Fitzgerald S, Gil L, Gironi CG, Gordon L, Hourlier T, Hunt S, Johnson N, Juettemann T, Kahari AK, Keenan S, Kulesha E, Martin FJ, Maurel T, McLaren WM, Murphy DN, Nag R, Overduin B, Pignatelli M, Pritchard B, Pritchard E, Riat HS: Ensembl 2014. Nucleic Acids Res 2014, 42(D1):749-755.
-
(2014)
Nucleic Acids Res
, vol.42
, Issue.D1
, pp. 749-755
-
-
Flicek, P.1
Amode, M.R.2
Barrell, D.3
Beal, K.4
Billis, K.5
Brent, S.6
Carvalho-Silva, D.7
Clapham, P.8
Coates, G.9
Fitzgerald, S.10
Gil, L.11
Gironi, C.G.12
Gordon, L.13
Hourlier, T.14
Hunt, S.15
Johnson, N.16
Juettemann, T.17
Kahari, A.K.18
Keenan, S.19
Kulesha, E.20
Martin, F.J.21
Maurel, T.22
McLaren, W.M.23
Murphy, D.N.24
Nag, R.25
Overduin, B.26
Pignatelli, M.27
Pritchard, B.28
Pritchard, E.29
Riat, H.S.30
more..
-
29
-
-
84988951868
-
-
MIT CHiP-seq data [ftp://ftp.broad.mit.edu/pub/papers/chipseq/]
-
MIT CHiP-seq Data
-
-
-
30
-
-
34547624303
-
Genome-wide maps of chromatin state in pluripotent and lineage-committed cells
-
Mikkelsen TS, Ku M, Jaffe DB, Issac B, Lieberman E, Giannoukos G, Alvarez P, Brockman W, Kim T-K, Koche RP, Lee W, Mendenhall E, O'Donovan A, Presser A, Russ C, Xie X, Meissner A, Wernig M, Jaenisch R, Nusbaum C, Lander ES, Bernstein BE: Genome-wide maps of chromatin state in pluripotent and lineage-committed cells. Nature 2007, 448(7153):553-560.
-
(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..
-
31
-
-
49649125042
-
Genome-scale DNA methylationmaps of pluripotent and differentiated cells
-
Meissner A, Mikkelsen TS, Gu H, Wernig M, Hanna J, Sivachenko A, Zhang X, Bernstein BE, Nusbaum C, Jaffe DB, Gnirke A, Jaenisch R, Lander ES: Genome-scale DNA methylationmaps of pluripotent and differentiated cells. Nature 2008, 454(7205):766-770.
-
(2008)
Nature
, vol.454
, Issue.7205
, pp. 766-770
-
-
Meissner, A.1
Mikkelsen, T.S.2
Gu, H.3
Wernig, M.4
Hanna, J.5
Sivachenko, A.6
Zhang, X.7
Bernstein, B.E.8
Nusbaum, C.9
Jaffe, D.B.10
Gnirke, A.11
Jaenisch, R.12
Lander, E.S.13
-
34
-
-
0034069495
-
Gene ontology: Tool for the unification of biology
-
Ashburner M, Ball CA, Blake JA, Botstein D, Butler H, Cherry JM, Davis AP, Dolinski K, Dwight SS, Eppig JT, Harris MA, Hill DP, Issel-Tarver L, Kasarskis A, Lewis S, Matese JC, Richardson JE, Ringwald M, Rubin GM, Sherlock G: Gene ontology: tool for the unification of biology. Nat Genet 2000, 25(1):25-29.
-
(2000)
Nat Genet
, vol.25
, Issue.1
, pp. 25-29
-
-
Ashburner, M.1
Ball, C.A.2
Blake, J.A.3
Botstein, D.4
Butler, H.5
Cherry, J.M.6
Davis, A.P.7
Dolinski, K.8
Dwight, S.S.9
Eppig, J.T.10
Harris, M.A.11
Hill, D.P.12
Issel-Tarver, L.13
Kasarskis, A.14
Lewis, S.15
Matese, J.C.16
Richardson, J.E.17
Ringwald, M.18
Rubin, G.M.19
Sherlock, G.20
more..
-
36
-
-
84879260661
-
A double take on bivalent promoters
-
Voigt P, Tee W-W, Reinberg D: A double take on bivalent promoters. Genes Dev 2013, 27(12):1318-1338.
-
(2013)
Genes Dev
, vol.27
, Issue.12
, pp. 1318-1338
-
-
Voigt, P.1
Tee, W.-W.2
Reinberg, D.3
-
37
-
-
84873581550
-
H2A.Z facilitates access of active and repressive complexes to chromatin in embryonic stem cell self-renewal and differentiation
-
Hu G, Cui K, Northrup D, Liu C,Wang C, Tang Q, Ge K, Levens D, Crane-Robinson C, Zhao K: H2A.Z facilitates access of active and repressive complexes to chromatin in embryonic stem cell self-renewal and differentiation. Cell Stem Cell 2013, 12(2):180-192.
-
(2013)
Cell Stem Cell
, vol.12
, Issue.2
, pp. 180-192
-
-
Hu, G.1
Cui, K.2
Northrup, D.3
Liu, C.4
Wang, C.5
Tang, Q.6
Ge, K.7
Levens, D.8
Crane-Robinson, C.9
Zhao, K.10
-
38
-
-
84866867319
-
H2A.Z landscapes and dualmodifications in pluripotent and multipotent stem cells underlie complex genome regulatory functions
-
Ku M, Jaffe JD, Koche RP, Rheinbay E, Endoh M, Koseki H, Carr SA, Bernstein BE: H2A.Z landscapes and dualmodifications in pluripotent and multipotent stem cells underlie complex genome regulatory functions. Genome Biol 2012, 13(10):1-13.
-
(2012)
Genome Biol
, vol.13
, Issue.10
, pp. 1-13
-
-
Ku, M.1
Jaffe, J.D.2
Koche, R.P.3
Rheinbay, E.4
Endoh, M.5
Koseki, H.6
Carr, S.A.7
Bernstein, B.E.8
-
39
-
-
34250369235
-
Identification of an OCT4 and SRY regulatory module using integrated computational and experimental genomics approaches
-
Jin VX, O'Geen H, Iyengar S, Green R, Farnham PJ: Identification of an OCT4 and SRY regulatory module using integrated computational and experimental genomics approaches. Genome Res 2007, 17(6):807-817.
-
(2007)
Genome Res
, vol.17
, Issue.6
, pp. 807-817
-
-
Jin, V.X.1
O'Geen, H.2
Iyengar, S.3
Green, R.4
Farnham, P.J.5
-
40
-
-
35949000033
-
A comprehensive ChIP-chip analysis of E2F1, E2F4, and E2F6 in normal and tumor cells reveals interchangeable roles of E2F family members
-
Xu X, Bieda M, Jin VX, Rabinovich A, Oberley MJ, Green R, Farnham PJ: A comprehensive ChIP-chip analysis of E2F1, E2F4, and E2F6 in normal and tumor cells reveals interchangeable roles of E2F family members. Genome Res 2007, 17(11):1550-1561.
-
(2007)
Genome Res
, vol.17
, Issue.11
, pp. 1550-1561
-
-
Xu, X.1
Bieda, M.2
Jin, V.X.3
Rabinovich, A.4
Oberley, M.J.5
Green, R.6
Farnham, P.J.7
-
41
-
-
0037074010
-
Signaling network model of chromatin
-
Schreiber SL, Bernstein BE: Signaling network model of chromatin. Cell 2002, 111(6):771-778.
-
(2002)
Cell
, vol.111
, Issue.6
, pp. 771-778
-
-
Schreiber, S.L.1
Bernstein, B.E.2
-
42
-
-
11844293410
-
Partial correlation and conditional correlation as measures of conditional independence
-
Baba K, Shibata R, Sibuya M: Partial correlation and conditional correlation as measures of conditional independence. Aust N Z J Stat 2004, 46(4):657-664.
-
(2004)
Aust N Z J Stat
, vol.46
, Issue.4
, pp. 657-664
-
-
Baba, K.1
Shibata, R.2
Sibuya, M.3
-
43
-
-
84988964299
-
Controlling the false discovery rate: A practical and powerful approach to multiple testing
-
Benjamini Y, Hochberg Y: Controlling the false discovery rate: a practical and powerful approach to multiple testing. J R Stat Soc Series B (Methodological) 1995, 57:289-300.
-
(1995)
J R Stat Soc Series B (Methodological)
, vol.57
, pp. 289-300
-
-
Benjamini, Y.1
Hochberg, Y.2
-
44
-
-
84870267223
-
The generalization of Student's problem when several different population variances are involved
-
Welch BL: The generalization of Student's problem when several different population variances are involved. Biometrika 1947, 34:28-35.
-
(1947)
Biometrika
, vol.34
, pp. 28-35
-
-
Welch, B.L.1
-
45
-
-
84861095603
-
Topological domains inmammalian genomes identified by analysis of chromatin interactions
-
Dixon JR, Selvaraj S, Yue F, Kim A, Li Y, Shen Y, Hu M, Liu JS, Ren B: Topological domains inmammalian genomes identified by analysis of chromatin interactions. Nature 2012, 485(7398):376-380.
-
(2012)
Nature
, vol.485
, Issue.7398
, pp. 376-380
-
-
Dixon, J.R.1
Selvaraj, S.2
Yue, F.3
Kim, A.4
Li, Y.5
Shen, Y.6
Hu, M.7
Liu, J.S.8
Ren, B.9
-
46
-
-
33745436025
-
Active chromatin hub of themouse α-globin locus forms in a transcription factory of clustered housekeeping genes
-
Zhou G-L, Xin L, Song W, Di L-J, Liu G, Wu X-S, Liu D-P, Liang C-C: Active chromatin hub of themouse α-globin locus forms in a transcription factory of clustered housekeeping genes.Mol Cell Biol 2006, 26(13):5096-5105.
-
(2006)
Mol Cell Biol
, vol.26
, Issue.13
, pp. 5096-5105
-
-
Zhou, G.-L.1
Xin, L.2
Song, W.3
Di, L.-J.4
Liu, G.5
Wu, X.-S.6
Liu, D.-P.7
Liang, C.-C.8
-
47
-
-
67549119096
-
CTCF: Master weaver of the genome
-
Phillips JE, Corces VG: CTCF: Master weaver of the genome. Cell 2009, 137(7):1194-1211.
-
(2009)
Cell
, vol.137
, Issue.7
, pp. 1194-1211
-
-
Phillips, J.E.1
Corces, V.G.2
-
48
-
-
33747453473
-
Insulators: Exploiting transcriptional and epigenetic mechanisms
-
Gaszner M, Felsenfeld G: Insulators: exploiting transcriptional and epigenetic mechanisms. Nat Rev Genet 2006, 7(9):703-713.
-
(2006)
Nat Rev Genet
, vol.7
, Issue.9
, pp. 703-713
-
-
Gaszner, M.1
Felsenfeld, G.2
-
49
-
-
0018581187
-
Involvement of histone H1 in the organization of the nucleosome and of the salt-dependent superstructures of chromatin
-
Thoma F, Koller T, Klug A: Involvement of histone H1 in the organization of the nucleosome and of the salt-dependent superstructures of chromatin. J Cell Biol 1979, 83(2):403-427.
-
(1979)
J Cell Biol
, vol.83
, Issue.2
, pp. 403-427
-
-
Thoma, F.1
Koller, T.2
Klug, A.3
-
50
-
-
0025266610
-
Alternative chromatin structure at CpG islands
-
Tazi J, Bird A: Alternative chromatin structure at CpG islands. Cell 1990, 60(6):909-920.
-
(1990)
Cell
, vol.60
, Issue.6
, pp. 909-920
-
-
Tazi, J.1
Bird, A.2
-
51
-
-
0035859881
-
Kinetic trapping of DNA by transcription factor IIIB
-
Cloutier TE, Librizzi MD, Mollah A, Brenowitz M, Willis IM: Kinetic trapping of DNA by transcription factor IIIB. Proc Natl Acad Sci 2001, 98(17):9581-9586.
-
(2001)
Proc Natl Acad Sci
, vol.98
, Issue.17
, pp. 9581-9586
-
-
Cloutier, T.E.1
Librizzi, M.D.2
Mollah, A.3
Brenowitz, M.4
Willis, I.M.5
-
52
-
-
0031022752
-
RNA polymerase II transcription initiation: A structural view
-
Nikolov D, Burley S: RNA polymerase II transcription initiation: a structural view. Proc Natl Acad Sci 1997, 94(1):15-22.
-
(1997)
Proc Natl Acad Sci
, vol.94
, Issue.1
, pp. 15-22
-
-
Nikolov, D.1
Burley, S.2
-
53
-
-
78049450019
-
Thermodynamics-basedmodels of transcriptional regulation by enhancers: The roles of synergistic activation, cooperative binding and short-range repression
-
He X, Samee MAH, Blatti C, Sinha S: Thermodynamics-basedmodels of transcriptional regulation by enhancers: the roles of synergistic activation, cooperative binding and short-range repression. PLoS Comput Biol 2010, 6(9):1000935.
-
(2010)
PLoS Comput Biol
, vol.6
, Issue.9
, pp. 1000935
-
-
He, X.1
Samee, M.A.H.2
Blatti, C.3
Sinha, S.4
-
54
-
-
3242706926
-
Transcriptional control networks of cell differentiation: Insights from helper T lymphocytes
-
Mariani L, Löhning M, Radbruch A, Höfer T: Transcriptional control networks of cell differentiation: insights from helper T lymphocytes. Progress BiophysMol Biol 2004, 86(1):45-76.
-
(2004)
Progress BiophysMol Biol
, vol.86
, Issue.1
, pp. 45-76
-
-
Mariani, L.1
Löhning, M.2
Radbruch, A.3
Höfer, T.4
-
55
-
-
84870305264
-
Wisdom of crowds for robust gene network inference
-
Marbach D, Costello JC, Küffner R, Vega NM, Prill RJ, Camacho DM, Allison KR, Kellis M, Collins JJ, Stolovitzky G: Wisdom of crowds for robust gene network inference. Nat Methods 2012, 9(8):796-804.
-
(2012)
Nat Methods
, vol.9
, Issue.8
, pp. 796-804
-
-
Marbach, D.1
Costello, J.C.2
Küffner, R.3
Vega, N.M.4
Prill, R.J.5
Camacho, D.M.6
Allison, K.R.7
Kellis, M.8
Collins, J.J.9
Stolovitzky, G.10
-
56
-
-
84892376552
-
Supervised, semi-supervised and unsupervised inference of gene regulatory networks
-
Maetschke SR, Madhamshettiwar PB, Davis MJ, Ragan MA: Supervised, semi-supervised and unsupervised inference of gene regulatory networks. Brief Bioinform 2014, 15(2):195-211.
-
(2014)
Brief Bioinform
, vol.15
, Issue.2
, pp. 195-211
-
-
Maetschke, S.R.1
Madhamshettiwar, P.B.2
Davis, M.J.3
Ragan, M.A.4
-
57
-
-
84893863046
-
Discovery of directional and nondirectional pioneer transcription factors bymodeling DNase profilemagnitude and shape
-
Sherwood RI, Hashimoto T, O'Donnell CW, Lewis S, Barkal AA, van Hoff JP, Karun V, Jaakkola T, Gifford DK: Discovery of directional and nondirectional pioneer transcription factors bymodeling DNase profilemagnitude and shape. Nat Biotechnol 2014, 32(2):171-178.
-
(2014)
Nat Biotechnol
, vol.32
, Issue.2
, pp. 171-178
-
-
Sherwood, R.I.1
Hashimoto, T.2
O'Donnell, C.W.3
Lewis, S.4
Barkal, A.A.5
Van Hoff, J.P.6
Karun, V.7
Jaakkola, T.8
Gifford, D.K.9
-
59
-
-
84865790047
-
An integrated encyclopedia of DNA elements in the human genome
-
The ENCODE Project Consortium: An integrated encyclopedia of DNA elements in the human genome. Nature 2012, 489(7414):57-74.
-
(2012)
Nature
, vol.489
, Issue.7414
, pp. 57-74
-
-
The ENCODE Project Consortium1
-
60
-
-
77952123055
-
Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation
-
Trapnell C, Williams BA, Pertea G, Mortazavi A, Kwan G, van Baren MJ, Salzberg SL, Wold BJ, Pachter L: Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation. Nat Biotechnol 2010, 28(5):511-515.
-
(2010)
Nat Biotechnol
, vol.28
, Issue.5
, pp. 511-515
-
-
Trapnell, C.1
Williams, B.A.2
Pertea, G.3
Mortazavi, A.4
Kwan, G.5
Van Baren, M.J.6
Salzberg, S.L.7
Wold, B.J.8
Pachter, L.9
-
62
-
-
84884416048
-
Human housekeeping genes, revisited
-
Eisenberg E, Levanon EY: Human housekeeping genes, revisited. Trends Genet 2013, 29(10):569-574.
-
(2013)
Trends Genet
, vol.29
, Issue.10
, pp. 569-574
-
-
Eisenberg, E.1
Levanon, E.Y.2
-
63
-
-
0037316303
-
A comparison of normalization methods for high density oligonucleotide array data based on variance and bias
-
Bolstad BM, Irizarry RA, Astrand M, Speed TP: A comparison of normalization methods for high density oligonucleotide array data based on variance and bias. Bioinformatics 2003, 19(2):185-193.
-
(2003)
Bioinformatics
, vol.19
, Issue.2
, pp. 185-193
-
-
Bolstad, B.M.1
Irizarry, R.A.2
Astrand, M.3
Speed, T.P.4
-
65
-
-
69049110853
-
The estimation of R2 and adjusted R2 in incomplete data sets usingmultiple imputation
-
Harel O: The estimation of R2 and adjusted R2 in incomplete data sets usingmultiple imputation. J Appl Stat 2009, 36(10):1109-1118.
-
(2009)
J Appl Stat
, vol.36
, Issue.10
, pp. 1109-1118
-
-
Harel, O.1
-
66
-
-
66349108078
-
Fewer permutations, more accurate p-values
-
Knijnenburg TA, Wessels LF, Reinders MJ, Shmulevich I: Fewer permutations, more accurate p-values. Bioinformatics 2009, 25(12):161-168.
-
(2009)
Bioinformatics
, vol.25
, Issue.12
, pp. 161-168
-
-
Knijnenburg, T.A.1
Wessels, L.F.2
Reinders, M.J.3
Shmulevich, I.4
-
67
-
-
84864929478
-
Computational inference ofmRNA stability from histone modification and transcriptome profiles
-
Wang C, Tian R, Zhao Q, Xu H, Meyer CA, Li C, Zhang Y, Liu XS: Computational inference ofmRNA stability from histone modification and transcriptome profiles. Nucleic Acids Res 2012, 40(14):6414-6423.
-
(2012)
Nucleic Acids Res
, vol.40
, Issue.14
, pp. 6414-6423
-
-
Wang, C.1
Tian, R.2
Zhao, Q.3
Xu, H.4
Meyer, C.A.5
Li, C.6
Zhang, Y.7
Liu, X.S.8
|