-
1
-
-
1842584947
-
Applied bioinformatics for the identification of regulatory elements
-
10.1038/nrg1315, 15131651
-
Wasserman WW, Sandelin A. Applied bioinformatics for the identification of regulatory elements. Nat Rev Genet 2004, 5(4):276-287. 10.1038/nrg1315, 15131651.
-
(2004)
Nat Rev Genet
, vol.5
, Issue.4
, pp. 276-287
-
-
Wasserman, W.W.1
Sandelin, A.2
-
2
-
-
0034819935
-
A predictive model for regulatory sequences directing liver-specific transcription
-
10.1101/gr.180601, 311083, 11544200
-
Krivan W, Wasserman WW. A predictive model for regulatory sequences directing liver-specific transcription. Genome Res 2001, 11:1559-1566. 10.1101/gr.180601, 311083, 11544200.
-
(2001)
Genome Res
, vol.11
, pp. 1559-1566
-
-
Krivan, W.1
Wasserman, W.W.2
-
3
-
-
0032562789
-
Identification of regulatory regions which confer muscle-specific gene expression
-
10.1006/jmbi.1998.1700, 9571041
-
Wasserman WW, Fickett JW. Identification of regulatory regions which confer muscle-specific gene expression. J Mol Biol 1998, 278:167-181. 10.1006/jmbi.1998.1700, 9571041.
-
(1998)
J Mol Biol
, vol.278
, pp. 167-181
-
-
Wasserman, W.W.1
Fickett, J.W.2
-
4
-
-
3242879521
-
CREME: Cis-Regulatory Module Explorer for the human genome
-
10.1093/nar/gkh385, 441523, 15215390
-
Sharan R, Ben-Hur A, Loots GG, Ovcharenko I. CREME: Cis-Regulatory Module Explorer for the human genome. Nucleic Acids Res 2004, 32:W253-256. 10.1093/nar/gkh385, 441523, 15215390.
-
(2004)
Nucleic Acids Res
, vol.32
-
-
Sharan, R.1
Ben-Hur, A.2
Loots, G.G.3
Ovcharenko, I.4
-
5
-
-
48249097859
-
Modeling promoter grammars with evolving hidden Markov models
-
10.1093/bioinformatics/btn254, 18535083
-
Won KJ, Sandelin A, Marstrand TT, Krogh A. Modeling promoter grammars with evolving hidden Markov models. Bioinformatics 2008, 24:1669-1675. 10.1093/bioinformatics/btn254, 18535083.
-
(2008)
Bioinformatics
, vol.24
, pp. 1669-1675
-
-
Won, K.J.1
Sandelin, A.2
Marstrand, T.T.3
Krogh, A.4
-
6
-
-
34250896139
-
Position and distance specificity are important determinants of cis-regulatory motifs in addition to evolutionary conservation
-
10.1093/nar/gkm201, 1904283, 17452354
-
Vardhanabhuti S, Wang J, Hannenhalli S. Position and distance specificity are important determinants of cis-regulatory motifs in addition to evolutionary conservation. Nucleic Acids Res 2007, 35:3203-3213. 10.1093/nar/gkm201, 1904283, 17452354.
-
(2007)
Nucleic Acids Res
, vol.35
, pp. 3203-3213
-
-
Vardhanabhuti, S.1
Wang, J.2
Hannenhalli, S.3
-
7
-
-
70349312354
-
ChIP-seq: advantages and challenges of a maturing technology
-
10.1038/nrg2641, 19736561
-
Park PJ. ChIP-seq: advantages and challenges of a maturing technology. Nat Rev Genet 2009, 10(10):669-680. 10.1038/nrg2641, 19736561.
-
(2009)
Nat Rev Genet
, vol.10
, Issue.10
, pp. 669-680
-
-
Park, P.J.1
-
8
-
-
1242316281
-
ChIP-chip: considerations for the design, analysis, and application of genome-wide chromatin immunoprecipitation experiments
-
10.1016/j.ygeno.2003.11.004, 14986705
-
Buck MJ, Lieb JD. ChIP-chip: considerations for the design, analysis, and application of genome-wide chromatin immunoprecipitation experiments. Genomics 2004, 83(3):349-360. 10.1016/j.ygeno.2003.11.004, 14986705.
-
(2004)
Genomics
, vol.83
, Issue.3
, pp. 349-360
-
-
Buck, M.J.1
Lieb, J.D.2
-
9
-
-
37849044185
-
Graphical models for marked point processes based on local independence
-
Didelez V. Graphical models for marked point processes based on local independence. Journal of the Royal Statistical Society 2008, 70:245-264.
-
(2008)
Journal of the Royal Statistical Society
, vol.70
, pp. 245-264
-
-
Didelez, V.1
-
10
-
-
44649117905
-
Integration of external signaling pathways with the core transcriptional network in embryonic stem cells
-
10.1016/j.cell.2008.04.043, 18555785
-
Chen X, Xu H, Yuan P, Fang F, Huss M, Vega V, Wong E, Orlov Y, Zhang W, Jiang J, Loh Y, Yeo H, Yeo Z, Narang V, Govindarajan K, Leong B, Shahab A, Ruan Y, Bourque G, Sung W, Clarke N, Wei C, Ng H. Integration of external signaling pathways with the core transcriptional network in embryonic stem cells. Cell 2008, 133:1106-1117. 10.1016/j.cell.2008.04.043, 18555785.
-
(2008)
Cell
, vol.133
, pp. 1106-1117
-
-
Chen, X.1
Xu, H.2
Yuan, P.3
Fang, F.4
Huss, M.5
Vega, V.6
Wong, E.7
Orlov, Y.8
Zhang, W.9
Jiang, J.10
Loh, Y.11
Yeo, H.12
Yeo, Z.13
Narang, V.14
Govindarajan, K.15
Leong, B.16
Shahab, A.17
Ruan, Y.18
Bourque, G.19
Sung, W.20
Clarke, N.21
Wei, C.22
Ng, H.23
more..
-
11
-
-
7444260846
-
The ENCODE (ENCyclopedia Of DNA Elements) Project
-
10.1126/science.1105136, 15499007, The ENCODE Project Consortium
-
The ENCODE Project Consortium The ENCODE (ENCyclopedia Of DNA Elements) Project. Science 2004, 306:636-640. 10.1126/science.1105136, 15499007, The ENCODE Project Consortium.
-
(2004)
Science
, vol.306
, pp. 636-640
-
-
-
12
-
-
34250305146
-
Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project
-
10.1038/nature05874, 2212820, 17571346
-
Birney E, Stamatoyannopoulos JA, Dutta A, Guigó R, Gingeras TR, Margulies EH, Weng Z, Snyder M, Dermitzakis ET, Thurman RE, Kuehn MS, Taylor CM, Neph S, Koch CM, Asthana S, Malhotra A, Adzhubei I, Greenbaum JA, Andrews RM, Flicek P, Boyle PJ, Cao H, Carter NP, Clelland GK, Davis S, Day N, Dhami P, Dillon SC, Dorschner MO, Fiegler H, Giresi PG, Goldy J, Hawrylycz M, Haydock A, Humbert R, James KD, Johnson BE, Johnson EM, Frum TT, Rosenzweig ER, Karnani N, Lee K, Lefebvre GC, Navas PA, Neri F, Parker SC, Sabo PJ, Sandstrom R, Shafer A, Vetrie D, Weaver M, Wilcox S, Yu M, Collins FS, Dekker J, Lieb JD, Tullius TD, Crawford GE, Sunyaev S, Noble WS, Dunham I, Denoeud F, Reymond A, Kapranov P, Rozowsky J, Zheng D, Castelo R, Frankish A, Harrow J, Ghosh S, Sandelin A, Hofacker IL, Baertsch R, Keefe D, Dike S, Cheng J, Hirsch HA, Sekinger EA, Lagarde J, Abril JF, Shahab A, Flamm C, Fried C, Hackermüller J, Hertel J, Lindemeyer M, Missal K, Tanzer A, Washietl S, Korbel J, Emanuelsson O, Pedersen JS, Holroyd N, Taylor R, Swarbreck D, Matthews N, Dickson MC, Thomas DJ, Weirauch MT, Gilbert J, Drenkow J, Bell I, Zhao X, Srinivasan KG, Sung WK, Ooi HS, Chiu KP, Foissac S, Alioto T, Brent M, Pachter L, Tress ML, Valencia A, Choo SW, Choo CY, Ucla C, Manzano C, Wyss C, Cheung E, Clark TG, Brown JB, Ganesh M, Patel S, Tammana H, Chrast J, Henrichsen CN, Kai C, Kawai J, Nagalakshmi U, Wu J, Lian Z, Lian J, Newburger P, Zhang X, Bickel P, Mattick JS, Carninci P, Hayashizaki Y, Weissman S, Hubbard T, Myers RM, Rogers J, Stadler PF, Lowe TM, Wei CL, Ruan Y, Struhl K, Gerstein M, Antonarakis SE, Fu Y, Green ED, Karaöz U, Siepel A, Taylor J, Liefer LA, Wetterstrand KA, Good PJ, Feingold EA, Guyer MS, Cooper GM, Asimenos G, Dewey CN, Hou M, Nikolaev S, Montoya-Burgos JI, Löytynoja A, Whelan S, Pardi F, Massingham T, Huang H, Zhang NR, Holmes I, Mullikin JC, Ureta-Vidal A, Paten B, Seringhaus M, Church D, Rosenbloom K, Kent WJ, Stone EA, Batzoglou S, Goldman N, Hardison RC, Haussler D, Miller W, Sidow A, Trinklein ND, Zhang ZD, Barrera L, Stuart R, King DC, Ameur A, Enroth S, Bieda MC, Kim J, Bhinge AA, Jiang N, Liu J, Yao F, Vega VB, Lee CW, Ng P, Shahab A, Yang A, Moqtaderi Z, Zhu Z, Xu X, Squazzo S, Oberley MJ, Inman D, Singer MA, Richmond TA, Munn KJ, Rada-Iglesias A, Wallerman O, Komorowski J, Fowler JC, Couttet P, Bruce AW, Dovey OM, Ellis PD, Langford CF, Nix DA, Euskirchen G, Hartman S, Urban AE, Kraus P, Van Calcar S, Heintzman N, Kim TH, Wang K, Qu C, Hon G, Luna R, Glass CK, Rosenfeld MG, Aldred SF, Cooper SJ, Halees A, Lin JM, Shulha HP, Zhang X, Xu M, Haidar JN, Yu Y, Ruan Y, Iyer VR, Green RD, Wadelius C, Farnham PJ, Ren B, Harte RA, Hinrichs AS, Trumbower H, Clawson H, Hillman-Jackson J, Zweig AS, Smith K, Thakkapallayil A, Barber G, Kuhn RM, Karolchik D, Armengol L, Bird CP, de Bakker PI, Kern AD, Lopez-Bigas N, Martin JD, Stranger BE, Woodroffe A, Davydov E, Dimas A, Eyras E, Hallgrímsdóttir IB, Huppert J, Zody MC, Abecasis GR, Estivill X, Bouffard GG, Guan X, Hansen NF, Idol JR, Maduro VV, Maskeri B, McDowell JC, Park M, Thomas PJ, Young AC, Blakesley RW, Muzny DM, Sodergren E, Wheeler DA, Worley KC, Jiang H, Weinstock GM, Gibbs RA, Graves T, Fulton R, Mardis ER, Wilson RK, Clamp M, Cuff J, Gnerre S, Jaffe DB, Chang JL, Lindblad-Toh K, Lander ES, Koriabine M, Nefedov M, Osoegawa K, Yoshinaga Y, Zhu B, de Jong PJ. Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project. Nature 2007, 447:799-816. 10.1038/nature05874, 2212820, 17571346.
-
(2007)
Nature
, vol.447
, pp. 799-816
-
-
Birney, E.1
Stamatoyannopoulos, J.A.2
Dutta, A.3
Guigó, R.4
Gingeras, T.R.5
Margulies, E.H.6
Weng, Z.7
Snyder, M.8
Dermitzakis, E.T.9
Thurman, R.E.10
Kuehn, M.S.11
Taylor, C.M.12
Neph, S.13
Koch, C.M.14
Asthana, S.15
Malhotra, A.16
Adzhubei, I.17
Greenbaum, J.A.18
Andrews, R.M.19
Flicek, P.20
Boyle, P.J.21
Cao, H.22
Carter, N.P.23
Clelland, G.K.24
Davis, S.25
Day, N.26
Dhami, P.27
Dillon, S.C.28
Dorschner, M.O.29
Fiegler, H.30
Giresi, P.G.31
Goldy, J.32
Hawrylycz, M.33
Haydock, A.34
Humbert, R.35
James, K.D.36
Johnson, B.E.37
Johnson, E.M.38
Frum, T.T.39
Rosenzweig, E.R.40
Karnani, N.41
Lee, K.42
Lefebvre, G.C.43
Navas, P.A.44
Neri, F.45
Parker, S.C.46
Sabo, P.J.47
Sandstrom, R.48
Shafer, A.49
Vetrie, D.50
Weaver, M.51
Wilcox, S.52
Yu, M.53
Collins, F.S.54
Dekker, J.55
Lieb, J.D.56
Tullius, T.D.57
Crawford, G.E.58
Sunyaev, S.59
Noble, W.S.60
Dunham, I.61
Denoeud, F.62
Reymond, A.63
Kapranov, P.64
Rozowsky, J.65
Zheng, D.66
Castelo, R.67
Frankish, A.68
Harrow, J.69
Ghosh, S.70
Sandelin, A.71
Hofacker, I.L.72
Baertsch, R.73
Keefe, D.74
Dike, S.75
Cheng, J.76
Hirsch, H.A.77
Sekinger, E.A.78
Lagarde, J.79
Abril, J.F.80
Shahab, A.81
Flamm, C.82
Fried, C.83
Hackermüller, J.84
Hertel, J.85
Lindemeyer, M.86
Missal, K.87
Tanzer, A.88
Washietl, S.89
Korbel, J.90
Emanuelsson, O.91
Pedersen, J.S.92
Holroyd, N.93
Taylor, R.94
Swarbreck, D.95
Matthews, N.96
Dickson, M.C.97
Thomas, D.J.98
Weirauch, M.T.99
more..
-
13
-
-
34250366235
-
Statistical analysis of the genomic distribution and correlation of regulatory elements in the ENCODE regions
-
10.1101/gr.5573107, 1891338, 17567997
-
Zhang ZD, Paccanaro A, Fu Y, Weissman S, Weng Z, Chang J, Snyder M, Gerstein MB. Statistical analysis of the genomic distribution and correlation of regulatory elements in the ENCODE regions. Genome Res 2007, 17:787-797. 10.1101/gr.5573107, 1891338, 17567997.
-
(2007)
Genome Res
, vol.17
, pp. 787-797
-
-
Zhang, Z.D.1
Paccanaro, A.2
Fu, Y.3
Weissman, S.4
Weng, Z.5
Chang, J.6
Snyder, M.7
Gerstein, M.B.8
-
14
-
-
33745604636
-
Suz12 binds to silenced regions of the genome in a cell-type-specific manner
-
10.1101/gr.5306606, 1484456, 16751344
-
Squazzo SL, O'Geen H, Komashko VM, Krig SR, Jin VX, Jang S, Margueron R, Reinberg D, Green R, Farnham PJ. Suz12 binds to silenced regions of the genome in a cell-type-specific manner. Genome Res 2006, 16:890-900. 10.1101/gr.5306606, 1484456, 16751344.
-
(2006)
Genome Res
, vol.16
, 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.6
Margueron, R.7
Reinberg, D.8
Green, R.9
Farnham, P.J.10
-
15
-
-
34249098071
-
Mammalian RNA polymerase II core promoters: insights from genome-wide studies
-
10.1038/nrg2026, 17486122
-
Sandelin A, Carninci P, Lenhard B, Ponjavic J, Hayashizaki Y, Hume D. Mammalian RNA polymerase II core promoters: insights from genome-wide studies. Nat Rev Genet 2007, 8:424-436. 10.1038/nrg2026, 17486122.
-
(2007)
Nat Rev Genet
, vol.8
, pp. 424-436
-
-
Sandelin, A.1
Carninci, P.2
Lenhard, B.3
Ponjavic, J.4
Hayashizaki, Y.5
Hume, D.6
-
16
-
-
53849146020
-
Model-based analysis of ChIP-Seq (MACS)
-
10.1186/gb-2008-9-9-r137, 2592715, 18798982
-
Zhang Y, Liu T, Meyer CA, Eeckhoute J, Johnson DS, Bernstein BE, Nussbaum C, Myers R, Brown M, Li W, Liu X. Model-based analysis of ChIP-Seq (MACS). Genome Biol 2008, 9(9):R137. 10.1186/gb-2008-9-9-r137, 2592715, 18798982.
-
(2008)
Genome Biol
, vol.9
, Issue.9
-
-
Zhang, Y.1
Liu, T.2
Meyer, C.A.3
Eeckhoute, J.4
Johnson, D.S.5
Bernstein, B.E.6
Nussbaum, C.7
Myers, R.8
Brown, M.9
Li, W.10
Liu, X.11
-
17
-
-
24944525791
-
FADO: a statistical method to detect favored or avoided distances between motif occurrences using the Hawkes' model
-
Gusto G, Schbath S. FADO: a statistical method to detect favored or avoided distances between motif occurrences using the Hawkes' model. Statistical Applications in Genetics and Molecular Biology 2005, 4(1):24.
-
(2005)
Statistical Applications in Genetics and Molecular Biology
, vol.4
, Issue.1
, pp. 24
-
-
Gusto, G.1
Schbath, S.2
-
18
-
-
0037398319
-
Homotypic regulatory clusters in Drosophila
-
10.1101/gr.668403, 430164, 12670999
-
Lifanov AP, Makeev VJ, Nazina AG, Papatsenko DA. Homotypic regulatory clusters in Drosophila. Genome Res 2003, 13:579-588. 10.1101/gr.668403, 430164, 12670999.
-
(2003)
Genome Res
, vol.13
, pp. 579-588
-
-
Lifanov, A.P.1
Makeev, V.J.2
Nazina, A.G.3
Papatsenko, D.A.4
-
19
-
-
77951874066
-
Homotypic clusters of transcription factor binding sites are a key component of human promoters and enhancers
-
10.1101/gr.104471.109, 2860159, 20363979
-
Gotea V, Visel A, Westlund JM, Nobrega MA, Pennacchio LA, Ovcharenko I. Homotypic clusters of transcription factor binding sites are a key component of human promoters and enhancers. Genome Res 2010, 20:565-577. 10.1101/gr.104471.109, 2860159, 20363979.
-
(2010)
Genome Res
, vol.20
, pp. 565-577
-
-
Gotea, V.1
Visel, A.2
Westlund, J.M.3
Nobrega, M.A.4
Pennacchio, L.A.5
Ovcharenko, I.6
-
20
-
-
0037732643
-
Active repression by unliganded retinoid receptors in development: less is sometimes more
-
10.1083/jcb.200211117, 2172895, 12719467
-
Weston AD, Blumberg B, Underhill TM. Active repression by unliganded retinoid receptors in development: less is sometimes more. J Cell Biol 2003, 161:223-228. 10.1083/jcb.200211117, 2172895, 12719467.
-
(2003)
J Cell Biol
, vol.161
, pp. 223-228
-
-
Weston, A.D.1
Blumberg, B.2
Underhill, T.M.3
-
21
-
-
33644943043
-
Histone H3 acetylated at lysine 9 in promoter is associated with low nucleosome density in the vicinity of transcription start site in human cell
-
10.1007/s10577-006-1036-7, 16544193
-
Nishida H, Suzuki T, Kondo S, Miura H, Fujimura Y, Hayashizaki Y. Histone H3 acetylated at lysine 9 in promoter is associated with low nucleosome density in the vicinity of transcription start site in human cell. Chromosome Res 2006, 14:203-211. 10.1007/s10577-006-1036-7, 16544193.
-
(2006)
Chromosome Res
, vol.14
, pp. 203-211
-
-
Nishida, H.1
Suzuki, T.2
Kondo, S.3
Miura, H.4
Fujimura, Y.5
Hayashizaki, Y.6
-
22
-
-
59949085939
-
H3K27me3 forms BLOCs over silent genes and intergenic regions and specifies a histone banding pattern on a mouse autosomal chromosome
-
10.1101/gr.080861.108, 2652204, 19047520
-
Pauler FM, Sloane MA, Huang R, Regha K, Koerner MV, Tamir I, Sommer A, Aszodi A, Jenuwein T, Barlow DP. H3K27me3 forms BLOCs over silent genes and intergenic regions and specifies a histone banding pattern on a mouse autosomal chromosome. Genome Res 2009, 19:221-233. 10.1101/gr.080861.108, 2652204, 19047520.
-
(2009)
Genome Res
, vol.19
, pp. 221-233
-
-
Pauler, F.M.1
Sloane, M.A.2
Huang, R.3
Regha, K.4
Koerner, M.V.5
Tamir, I.6
Sommer, A.7
Aszodi, A.8
Jenuwein, T.9
Barlow, D.P.10
-
23
-
-
77649325496
-
Causal inference in statistics: an overview
-
Pearl J. Causal inference in statistics: an overview. Stat Surv 2009, 3:96-146.
-
(2009)
Stat Surv
, vol.3
, pp. 96-146
-
-
Pearl, J.1
-
27
-
-
0030352915
-
Stability of nonlinear Hawkes processes
-
Brémaud P, Massoulié L. Stability of nonlinear Hawkes processes. Ann Probab 1996, 24(3):1563-1588.
-
(1996)
Ann Probab
, vol.24
, Issue.3
, pp. 1563-1588
-
-
Brémaud, P.1
Massoulié, L.2
-
31
-
-
84944178665
-
Hierarchical Grouping to Optimize an Objective Function
-
Ward JHJ. Hierarchical Grouping to Optimize an Objective Function. Journal of the American Statistical Association 1963, 58(301):236-244.
-
(1963)
Journal of the American Statistical Association
, vol.58
, Issue.301
, pp. 236-244
-
-
Ward, J.H.J.1
|