-
1
-
-
79951792447
-
Signaling networks in RUNX2-dependent bone development
-
10.1002/jcb.22994, 21328448
-
Komori T. Signaling networks in RUNX2-dependent bone development. J Cell Biochem 2011, 112:750-755. 10.1002/jcb.22994, 21328448.
-
(2011)
J Cell Biochem
, vol.112
, pp. 750-755
-
-
Komori, T.1
-
2
-
-
33845987376
-
Networks and hubs for the transcriptional control of osteoblastogenesis
-
Lian JB, Stein GS, Javed A, van Wijnen AJ, Stein JL, Montecino M, Hassan MQ, Gaur T, Lengner CJ, Young DW. Networks and hubs for the transcriptional control of osteoblastogenesis. Rev Endocr Metab Disord 2006, 7:1-16.
-
(2006)
Rev Endocr Metab Disord
, vol.7
, pp. 1-16
-
-
Lian, J.B.1
Stein, G.S.2
Javed, A.3
van Wijnen, A.J.4
Stein, J.L.5
Montecino, M.6
Hassan, M.Q.7
Gaur, T.8
Lengner, C.J.9
Young, D.W.10
-
3
-
-
84255200563
-
Building strong bones: molecular regulation of the osteoblast lineage
-
Long F. Building strong bones: molecular regulation of the osteoblast lineage. Nat Rev Mol Cell Biol 2012, 13:27-38.
-
(2012)
Nat Rev Mol Cell Biol
, vol.13
, pp. 27-38
-
-
Long, F.1
-
4
-
-
0036186852
-
Mutations in the RUNX2 gene in patients with cleidocranial dysplasia
-
10.1002/humu.10043, 11857736
-
Otto F, Kanegane H, Mundlos S. Mutations in the RUNX2 gene in patients with cleidocranial dysplasia. Hum Mutat 2002, 19:209-216. 10.1002/humu.10043, 11857736.
-
(2002)
Hum Mutat
, vol.19
, pp. 209-216
-
-
Otto, F.1
Kanegane, H.2
Mundlos, S.3
-
5
-
-
33750822719
-
Detection of novel skeletogenesis target genes by comprehensive analysis of a Runx2(-/-) mouse model
-
10.1016/j.modgep.2006.05.014, 16829211
-
Hecht J, Seitz V, Urban M, Wagner F, Robinson PN, Stiege A, Dieterich C, Kornak U, Wilkening U, Brieske N, Zwingman C, Kidess A, Stricker S, Mundlos S. Detection of novel skeletogenesis target genes by comprehensive analysis of a Runx2(-/-) mouse model. Gene Expr Patterns 2007, 7:102-112. 10.1016/j.modgep.2006.05.014, 16829211.
-
(2007)
Gene Expr Patterns
, vol.7
, pp. 102-112
-
-
Hecht, J.1
Seitz, V.2
Urban, M.3
Wagner, F.4
Robinson, P.N.5
Stiege, A.6
Dieterich, C.7
Kornak, U.8
Wilkening, U.9
Brieske, N.10
Zwingman, C.11
Kidess, A.12
Stricker, S.13
Mundlos, S.14
-
6
-
-
33748170578
-
Microarray analysis on Runx2-deficient mouse embryos reveals novel Runx2 functions and target genes during intramembranous and endochondral bone formation
-
10.1016/j.bone.2006.04.024, 16774856
-
Vaes BL, Ducy P, Sijbers AM, Hendriks JM, van Someren EP, de Jong NG, van den Heuvel ER, Olijve W, van Zoelen EJ, Dechering KJ. Microarray analysis on Runx2-deficient mouse embryos reveals novel Runx2 functions and target genes during intramembranous and endochondral bone formation. Bone 2006, 39:724-738. 10.1016/j.bone.2006.04.024, 16774856.
-
(2006)
Bone
, vol.39
, pp. 724-738
-
-
Vaes, B.L.1
Ducy, P.2
Sijbers, A.M.3
Hendriks, J.M.4
van Someren, E.P.5
de Jong, N.G.6
van den Heuvel, E.R.7
Olijve, W.8
van Zoelen, E.J.9
Dechering, K.J.10
-
7
-
-
0038607705
-
Activation of peroxisome proliferator-activated receptor-gamma inhibits the Runx2-mediated transcription of osteocalcin in osteoblasts
-
10.1074/jbc.M211610200, 12704187
-
Jeon MJ, Kim JA, Kwon SH, Kim SW, Park KS, Park SW, Kim SY, Shin CS. Activation of peroxisome proliferator-activated receptor-gamma inhibits the Runx2-mediated transcription of osteocalcin in osteoblasts. J Biol Chem 2003, 278:23270-23277. 10.1074/jbc.M211610200, 12704187.
-
(2003)
J Biol Chem
, vol.278
, pp. 23270-23277
-
-
Jeon, M.J.1
Kim, J.A.2
Kwon, S.H.3
Kim, S.W.4
Park, K.S.5
Park, S.W.6
Kim, S.Y.7
Shin, C.S.8
-
8
-
-
84860344707
-
Down-regulation of type I Runx2 mediated by dexamethasone is required for 3T3-L1 adipogenesis
-
10.1210/me.2011-1287, 22422618
-
Zhang YY, Li X, Qian SW, Guo L, Huang HY, He Q, Liu Y, Ma CG, Tang QQ. Down-regulation of type I Runx2 mediated by dexamethasone is required for 3T3-L1 adipogenesis. Mol Endocrinol 2012, 26:798-808. 10.1210/me.2011-1287, 22422618.
-
(2012)
Mol Endocrinol
, vol.26
, pp. 798-808
-
-
Zhang, Y.Y.1
Li, X.2
Qian, S.W.3
Guo, L.4
Huang, H.Y.5
He, Q.6
Liu, Y.7
Ma, C.G.8
Tang, Q.Q.9
-
9
-
-
4744366089
-
Runx2/Cbfa1 stimulates transdifferentiation of primary skeletal myoblasts into a mineralizing osteoblastic phenotype
-
10.1016/j.yexcr.2004.07.031, 15475005
-
Gersbach CA, Byers BA, Pavlath GK, Garcia AJ. Runx2/Cbfa1 stimulates transdifferentiation of primary skeletal myoblasts into a mineralizing osteoblastic phenotype. Exp Cell Res 2004, 300:406-417. 10.1016/j.yexcr.2004.07.031, 15475005.
-
(2004)
Exp Cell Res
, vol.300
, pp. 406-417
-
-
Gersbach, C.A.1
Byers, B.A.2
Pavlath, G.K.3
Garcia, A.J.4
-
10
-
-
26844574658
-
Runx2: a master organizer of gene transcription in developing and maturing osteoblasts
-
10.1002/bdrc.20043, 16187316
-
Schroeder TM, Jensen ED, Westendorf JJ. Runx2: a master organizer of gene transcription in developing and maturing osteoblasts. Birth Defects Res C Embryo Today 2005, 75:213-225. 10.1002/bdrc.20043, 16187316.
-
(2005)
Birth Defects Res C Embryo Today
, vol.75
, pp. 213-225
-
-
Schroeder, T.M.1
Jensen, E.D.2
Westendorf, J.J.3
-
11
-
-
77954757722
-
Mitotic bookmarking of genes: a novel dimension to epigenetic control
-
10.1038/nrg2827, 3033599, 20628351
-
Zaidi SK, Young DW, Montecino MA, Lian JB, van Wijnen AJ, Stein JL, Stein GS. Mitotic bookmarking of genes: a novel dimension to epigenetic control. Nat Rev Genet 2010, 11:583-589. 10.1038/nrg2827, 3033599, 20628351.
-
(2010)
Nat Rev Genet
, vol.11
, pp. 583-589
-
-
Zaidi, S.K.1
Young, D.W.2
Montecino, M.A.3
Lian, J.B.4
van Wijnen, A.J.5
Stein, J.L.6
Stein, G.S.7
-
12
-
-
80755136753
-
Hdac-mediated control of endochondral and intramembranous ossification
-
10.1615/CritRevEukarGeneExpr.v21.i2.10, 3218555, 22077150
-
Bradley EW, McGee-Lawrence ME, Westendorf JJ. Hdac-mediated control of endochondral and intramembranous ossification. Crit Rev Eukaryot Gene Expr 2011, 21:101-113. 10.1615/CritRevEukarGeneExpr.v21.i2.10, 3218555, 22077150.
-
(2011)
Crit Rev Eukaryot Gene Expr
, vol.21
, pp. 101-113
-
-
Bradley, E.W.1
McGee-Lawrence, M.E.2
Westendorf, J.J.3
-
13
-
-
0037129340
-
MOZ and MORF histone acetyltransferases interact with the Runt-domain transcription factor Runx2
-
10.1038/sj.onc.1205367, 11965546
-
Pelletier N, Champagne N, Stifani S, Yang XJ. MOZ and MORF histone acetyltransferases interact with the Runt-domain transcription factor Runx2. Oncogene 2002, 21:2729-2740. 10.1038/sj.onc.1205367, 11965546.
-
(2002)
Oncogene
, vol.21
, pp. 2729-2740
-
-
Pelletier, N.1
Champagne, N.2
Stifani, S.3
Yang, X.J.4
-
14
-
-
33747343713
-
Chromatin remodeling and transcriptional activity of the bone-specific osteocalcin gene require CCAAT/enhancer-binding protein beta-dependent recruitment of SWI/SNF activity
-
10.1074/jbc.M511640200, 16772287
-
Villagra A, Cruzat F, Carvallo L, Paredes R, Olate J, van Wijnen AJ, Stein GS, Lian JB, Stein JL, Imbalzano AN, Montecino M. Chromatin remodeling and transcriptional activity of the bone-specific osteocalcin gene require CCAAT/enhancer-binding protein beta-dependent recruitment of SWI/SNF activity. J Biol Chem 2006, 281:22695-22706. 10.1074/jbc.M511640200, 16772287.
-
(2006)
J Biol Chem
, vol.281
, pp. 22695-22706
-
-
Villagra, A.1
Cruzat, F.2
Carvallo, L.3
Paredes, R.4
Olate, J.5
van Wijnen, A.J.6
Stein, G.S.7
Lian, J.B.8
Stein, J.L.9
Imbalzano, A.N.10
Montecino, M.11
-
15
-
-
2942597448
-
Nomenclature for Runt-related (RUNX) proteins
-
10.1038/sj.onc.1207758, 15156174
-
van Wijnen AJ, Stein GS, Gergen JP, Groner Y, Hiebert SW, Ito Y, Liu P, Neil JC, Ohki M, Speck N. Nomenclature for Runt-related (RUNX) proteins. Oncogene 2004, 23:4209-4210. 10.1038/sj.onc.1207758, 15156174.
-
(2004)
Oncogene
, vol.23
, pp. 4209-4210
-
-
van Wijnen, A.J.1
Stein, G.S.2
Gergen, J.P.3
Groner, Y.4
Hiebert, S.W.5
Ito, Y.6
Liu, P.7
Neil, J.C.8
Ohki, M.9
Speck, N.10
-
16
-
-
77957220857
-
Comparative epigenomic analysis of murine and human adipogenesis
-
10.1016/j.cell.2010.09.006, 2950833, 20887899
-
Mikkelsen TS, Xu Z, Zhang X, Wang L, Gimble JM, Lander ES, Rosen ED. Comparative epigenomic analysis of murine and human adipogenesis. Cell 2010, 143:156-169. 10.1016/j.cell.2010.09.006, 2950833, 20887899.
-
(2010)
Cell
, vol.143
, pp. 156-169
-
-
Mikkelsen, T.S.1
Xu, Z.2
Zhang, X.3
Wang, L.4
Gimble, J.M.5
Lander, E.S.6
Rosen, E.D.7
-
17
-
-
77951935861
-
Genome-wide MyoD binding in skeletal muscle cells: a potential for broad cellular reprogramming
-
10.1016/j.devcel.2010.02.014, 2910615, 20412780
-
Cao Y, Yao Z, Sarkar D, Lawrence M, Sanchez GJ, Parker MH, MacQuarrie KL, Davison J, Morgan MT, Ruzzo WL, Gentleman RC, Tapscott SJ. Genome-wide MyoD binding in skeletal muscle cells: a potential for broad cellular reprogramming. Dev Cell 2010, 18:662-674. 10.1016/j.devcel.2010.02.014, 2910615, 20412780.
-
(2010)
Dev Cell
, vol.18
, pp. 662-674
-
-
Cao, Y.1
Yao, Z.2
Sarkar, D.3
Lawrence, M.4
Sanchez, G.J.5
Parker, M.H.6
MacQuarrie, K.L.7
Davison, J.8
Morgan, M.T.9
Ruzzo, W.L.10
Gentleman, R.C.11
Tapscott, S.J.12
-
18
-
-
84859157183
-
Dynamic transformations of genome-wide epigenetic marking and transcriptional control establish T cell identity
-
10.1016/j.cell.2012.01.056, 3336965, 22500808
-
Zhang JA, Mortazavi A, Williams BA, Wold BJ, Rothenberg EV. Dynamic transformations of genome-wide epigenetic marking and transcriptional control establish T cell identity. Cell 2012, 149:467-482. 10.1016/j.cell.2012.01.056, 3336965, 22500808.
-
(2012)
Cell
, vol.149
, pp. 467-482
-
-
Zhang, J.A.1
Mortazavi, A.2
Williams, B.A.3
Wold, B.J.4
Rothenberg, E.V.5
-
19
-
-
79959699992
-
CTCF-mediated functional chromatin interactome in pluripotent cells
-
10.1038/ng.857, 3436933, 21685913
-
Handoko L, Xu H, Li G, Ngan CY, Chew E, Schnapp M, Lee CW, Ye C, Ping JL, Mulawadi F, Wong E, Sheng J, Zhang Y, Poh T, Chan CS, Kunarso G, Shahab A, Bourque G, Cacheux-Rataboul V, Sung WK, Ruan Y, Wei CL. CTCF-mediated functional chromatin interactome in pluripotent cells. Nat Genet 2011, 43:630-638. 10.1038/ng.857, 3436933, 21685913.
-
(2011)
Nat Genet
, vol.43
, pp. 630-638
-
-
Handoko, L.1
Xu, H.2
Li, G.3
Ngan, C.Y.4
Chew, E.5
Schnapp, M.6
Lee, C.W.7
Ye, C.8
Ping, J.L.9
Mulawadi, F.10
Wong, E.11
Sheng, J.12
Zhang, Y.13
Poh, T.14
Chan, C.S.15
Kunarso, G.16
Shahab, A.17
Bourque, G.18
Cacheux-Rataboul, V.19
Sung, W.K.20
Ruan, Y.21
Wei, C.L.22
more..
-
20
-
-
0032983542
-
Isolation and characterization of MC3T3-E1 preosteoblast subclones with distinct in vitro and in vivo differentiation/mineralization potential
-
10.1359/jbmr.1999.14.6.893, 10352097
-
Wang D, Christensen K, Chawla K, Xiao G, Krebsbach PH, Franceschi RT. Isolation and characterization of MC3T3-E1 preosteoblast subclones with distinct in vitro and in vivo differentiation/mineralization potential. J Bone Miner Res 1999, 14:893-903. 10.1359/jbmr.1999.14.6.893, 10352097.
-
(1999)
J Bone Miner Res
, vol.14
, pp. 893-903
-
-
Wang, D.1
Christensen, K.2
Chawla, K.3
Xiao, G.4
Krebsbach, P.H.5
Franceschi, R.T.6
-
21
-
-
0029984140
-
Expression patterns of bone-related proteins during osteoblastic differentiation in MC3T3-E1 cells
-
10.1002/(SICI)1097-4644(19960616)61:4<609::AID-JCB15>3.0.CO;2-A, 8806085
-
Choi JY, Lee BH, Song KB, Park RW, Kim IS, Sohn KY, Jo JS, Ryoo HM. Expression patterns of bone-related proteins during osteoblastic differentiation in MC3T3-E1 cells. J Cell Biochem 1996, 61:609-618. 10.1002/(SICI)1097-4644(19960616)61:4<609::AID-JCB15>3.0.CO;2-A, 8806085.
-
(1996)
J Cell Biochem
, vol.61
, pp. 609-618
-
-
Choi, J.Y.1
Lee, B.H.2
Song, K.B.3
Park, R.W.4
Kim, I.S.5
Sohn, K.Y.6
Jo, J.S.7
Ryoo, H.M.8
-
22
-
-
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, Nusbaum C, Myers RM, Brown M, Li W, Liu XS. Model-based analysis of ChIP-Seq (MACS). Genome Biol 2008, 9:R137. 10.1186/gb-2008-9-9-r137, 2592715, 18798982.
-
(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
Liu, X.S.11
-
23
-
-
33846057724
-
NCBI reference sequences (RefSeq): a curated non-redundant sequence database of genomes, transcripts and proteins
-
10.1093/nar/gkl842, 1716718, 17130148
-
Pruitt KD, Tatusova T, Maglott DR. NCBI reference sequences (RefSeq): a curated non-redundant sequence database of genomes, transcripts and proteins. Nucleic Acids Res 2007, 35:D61-D65. 10.1093/nar/gkl842, 1716718, 17130148.
-
(2007)
Nucleic Acids Res
, vol.35
-
-
Pruitt, K.D.1
Tatusova, T.2
Maglott, D.R.3
-
24
-
-
67849122320
-
MEME SUITE: tools for motif discovery and searching
-
10.1093/nar/gkp335, 2703892, 19458158
-
Bailey TL, Boden M, Buske FA, Frith M, Grant CE, Clementi L, Ren J, Li WW, Noble WS. MEME SUITE: tools for motif discovery and searching. Nucleic Acids Res 2009, 37:W202-W208. 10.1093/nar/gkp335, 2703892, 19458158.
-
(2009)
Nucleic Acids Res
, vol.37
-
-
Bailey, T.L.1
Boden, M.2
Buske, F.A.3
Frith, M.4
Grant, C.E.5
Clementi, L.6
Ren, J.7
Li, W.W.8
Noble, W.S.9
-
25
-
-
84866108697
-
Genome-wide studies of CCCTC-binding factor (CTCF) and cohesin provide insight into chromatin structure and regulation
-
10.1074/jbc.R111.324962, 3438923, 22952237
-
Lee BK, Iyer VR. Genome-wide studies of CCCTC-binding factor (CTCF) and cohesin provide insight into chromatin structure and regulation. J Biol Chem 2012, 287:30906-30913. 10.1074/jbc.R111.324962, 3438923, 22952237.
-
(2012)
J Biol Chem
, vol.287
, pp. 30906-30913
-
-
Lee, B.K.1
Iyer, V.R.2
-
26
-
-
75549083247
-
JASPAR 2010: the greatly expanded open-access database of transcription factor binding profiles
-
10.1093/nar/gkp950, 2808906, 19906716
-
Portales-Casamar E, Thongjuea S, Kwon AT, Arenillas D, Zhao X, Valen E, Yusuf D, Lenhard B, Wasserman WW, Sandelin A. JASPAR 2010: the greatly expanded open-access database of transcription factor binding profiles. Nucleic Acids Res 2010, 38:D105-D110. 10.1093/nar/gkp950, 2808906, 19906716.
-
(2010)
Nucleic Acids Res
, vol.38
-
-
Portales-Casamar, E.1
Thongjuea, S.2
Kwon, A.T.3
Arenillas, D.4
Zhao, X.5
Valen, E.6
Yusuf, D.7
Lenhard, B.8
Wasserman, W.W.9
Sandelin, A.10
-
27
-
-
78650511231
-
CDK1-dependent phosphorylation of EZH2 suppresses methylation of H3K27 and promotes osteogenic differentiation of human mesenchymal stem cells
-
10.1038/ncb2139, 3076036, 21131960
-
Wei Y, Chen YH, Li LY, Lang J, Yeh SP, Shi B, Yang CC, Yang JY, Lin CY, Lai CC, Hung MC. CDK1-dependent phosphorylation of EZH2 suppresses methylation of H3K27 and promotes osteogenic differentiation of human mesenchymal stem cells. Nat Cell Biol 2011, 13:87-94. 10.1038/ncb2139, 3076036, 21131960.
-
(2011)
Nat Cell Biol
, vol.13
, pp. 87-94
-
-
Wei, Y.1
Chen, Y.H.2
Li, L.Y.3
Lang, J.4
Yeh, S.P.5
Shi, B.6
Yang, C.C.7
Yang, J.Y.8
Lin, C.Y.9
Lai, C.C.10
Hung, M.C.11
-
28
-
-
84883750369
-
Roles of the ubiquitin peptidase USP18 in multiple sclerosis and the response to interferon-beta treatment
-
10.1111/ene.12193, 23700969
-
Malhotra S, Morcillo-Suarez C, Nurtdinov R, Rio J, Sarro E, Moreno M, Castillo J, Navarro A, Montalban X, Comabella M. Roles of the ubiquitin peptidase USP18 in multiple sclerosis and the response to interferon-beta treatment. Eur J Neurol 2013, 20:1390-1397. 10.1111/ene.12193, 23700969.
-
(2013)
Eur J Neurol
, vol.20
, pp. 1390-1397
-
-
Malhotra, S.1
Morcillo-Suarez, C.2
Nurtdinov, R.3
Rio, J.4
Sarro, E.5
Moreno, M.6
Castillo, J.7
Navarro, A.8
Montalban, X.9
Comabella, M.10
-
29
-
-
84899638170
-
PeaksToGenes
-
PeaksToGenes. [https://github.com/peakstogenes/PeaksToGenes].
-
-
-
-
30
-
-
84862963292
-
Discovering transcription factor regulatory targets using gene expression and binding data
-
10.1093/bioinformatics/btr628, 3259433, 22084256
-
Maienschein-Cline M, Zhou J, White KP, Sciammas R, Dinner AR. Discovering transcription factor regulatory targets using gene expression and binding data. Bioinformatics 2012, 28:206-213. 10.1093/bioinformatics/btr628, 3259433, 22084256.
-
(2012)
Bioinformatics
, vol.28
, pp. 206-213
-
-
Maienschein-Cline, M.1
Zhou, J.2
White, K.P.3
Sciammas, R.4
Dinner, A.R.5
-
31
-
-
0038349948
-
Sequencing and comparison of yeast species to identify genes and regulatory elements
-
10.1038/nature01644, 12748633
-
Kellis M, Patterson N, Endrizzi M, Birren B, Lander ES. Sequencing and comparison of yeast species to identify genes and regulatory elements. Nature 2003, 423:241-254. 10.1038/nature01644, 12748633.
-
(2003)
Nature
, vol.423
, pp. 241-254
-
-
Kellis, M.1
Patterson, N.2
Endrizzi, M.3
Birren, B.4
Lander, E.S.5
-
32
-
-
36049018312
-
Discovery of functional elements in 12 Drosophila genomes using evolutionary signatures
-
10.1038/nature06340, 2474711, 17994088
-
Stark A, Lin MF, Kheradpour P, Pedersen JS, Parts L, Carlson JW, Crosby MA, Rasmussen MD, Roy S, Deoras AN, Ruby JG, Brennecke J, Hodges E, Hinrichs AS, Caspi A, Paten B, Park SW, Han MV, Maeder ML, Polansky BJ, Robson BE, Aerts S, van Helden J, Hassan B, Gilbert DG, Eastman DA, Rice M, Weir M, Hahn MW, Park Y, et al. Discovery of functional elements in 12 Drosophila genomes using evolutionary signatures. Nature 2007, 450:219-232. 10.1038/nature06340, 2474711, 17994088.
-
(2007)
Nature
, vol.450
, pp. 219-232
-
-
Stark, A.1
Lin, M.F.2
Kheradpour, P.3
Pedersen, J.S.4
Parts, L.5
Carlson, J.W.6
Crosby, M.A.7
Rasmussen, M.D.8
Roy, S.9
Deoras, A.N.10
Ruby, J.G.11
Brennecke, J.12
Hodges, E.13
Hinrichs, A.S.14
Caspi, A.15
Paten, B.16
Park, S.W.17
Han, M.V.18
Maeder, M.L.19
Polansky, B.J.20
Robson, B.E.21
Aerts, S.22
van Helden, J.23
Hassan, B.24
Gilbert, D.G.25
Eastman, D.A.26
Rice, M.27
Weir, M.28
Hahn, M.W.29
Park, Y.30
more..
-
33
-
-
84865762461
-
Functional analysis of transcription factor binding sites in human promoters
-
10.1186/gb-2012-13-9-r50, 3491394, 22951020
-
Whitfield TW, Wang J, Collins PJ, Partridge EC, Aldred SF, Trinklein ND, Myers RM, Weng Z. Functional analysis of transcription factor binding sites in human promoters. Genome Biol 2012, 13:R50. 10.1186/gb-2012-13-9-r50, 3491394, 22951020.
-
(2012)
Genome Biol
, vol.13
-
-
Whitfield, T.W.1
Wang, J.2
Collins, P.J.3
Partridge, E.C.4
Aldred, S.F.5
Trinklein, N.D.6
Myers, R.M.7
Weng, Z.8
-
34
-
-
33745772571
-
New methods for detecting lineage-specific selection
-
Berlin: Springer-Verlag, Apostolico A, Guerra C, Istrail S, Pevzner P, Waterman M
-
Siepel A, Pollard KS, Haussler D. New methods for detecting lineage-specific selection. Research in Computational Molecular Biology, 10th Annual International Conference, RECOMB 2006; April 2-5, 2006: Venice, Italy 2006, 190-205. Berlin: Springer-Verlag, Apostolico A, Guerra C, Istrail S, Pevzner P, Waterman M.
-
(2006)
Research in Computational Molecular Biology, 10th Annual International Conference, RECOMB 2006; April 2-5, 2006: Venice, Italy
, pp. 190-205
-
-
Siepel, A.1
Pollard, K.S.2
Haussler, D.3
-
35
-
-
77952000649
-
Tumor necrosis factor receptor superfamily member 19 (TNFRSF19) regulates differentiation fate of human mesenchymal (stromal) stem cells through canonical Wnt signaling and C/EBP
-
10.1074/jbc.M109.052001, 2863178, 20223822
-
Qiu W, Hu Y, Andersen TE, Jafari A, Li N, Chen W, Kassem M. Tumor necrosis factor receptor superfamily member 19 (TNFRSF19) regulates differentiation fate of human mesenchymal (stromal) stem cells through canonical Wnt signaling and C/EBP. J Biol Chem 2010, 285:14438-14449. 10.1074/jbc.M109.052001, 2863178, 20223822.
-
(2010)
J Biol Chem
, vol.285
, pp. 14438-14449
-
-
Qiu, W.1
Hu, Y.2
Andersen, T.E.3
Jafari, A.4
Li, N.5
Chen, W.6
Kassem, M.7
-
36
-
-
26244448721
-
Expression of versican and ADAMTS during rat tooth eruption
-
10.1007/s10735-005-5534-2, 16200461
-
Sone S, Nakamura M, Maruya Y, Takahashi I, Mizoguchi I, Mayanagi H, Sasano Y. Expression of versican and ADAMTS during rat tooth eruption. J Mol Histol 2005, 36:281-288. 10.1007/s10735-005-5534-2, 16200461.
-
(2005)
J Mol Histol
, vol.36
, pp. 281-288
-
-
Sone, S.1
Nakamura, M.2
Maruya, Y.3
Takahashi, I.4
Mizoguchi, I.5
Mayanagi, H.6
Sasano, Y.7
-
37
-
-
33745218499
-
Analysis of fracture healing by large-scale transcriptional profile identified temporal relationships between metalloproteinase and ADAMTS mRNA expression
-
10.1016/j.matbio.2006.02.001, 16584876
-
Wang K, Vishwanath P, Eichler GS, Al-Sebaei MO, Edgar CM, Einhorn TA, Smith TF, Gerstenfeld LC. Analysis of fracture healing by large-scale transcriptional profile identified temporal relationships between metalloproteinase and ADAMTS mRNA expression. Matrix Biol 2006, 25:271-281. 10.1016/j.matbio.2006.02.001, 16584876.
-
(2006)
Matrix Biol
, vol.25
, pp. 271-281
-
-
Wang, K.1
Vishwanath, P.2
Eichler, G.S.3
Al-Sebaei, M.O.4
Edgar, C.M.5
Einhorn, T.A.6
Smith, T.F.7
Gerstenfeld, L.C.8
-
38
-
-
33646433471
-
Regulation of the human ADAMTS-4 promoter by transcription factors and cytokines
-
10.1016/j.bbrc.2006.04.023, 16677612
-
Thirunavukkarasu K, Pei Y, Moore TL, Wang H, Yu XP, Geiser AG, Chandrasekhar S. Regulation of the human ADAMTS-4 promoter by transcription factors and cytokines. Biochem Biophys Res Commun 2006, 345:197-204. 10.1016/j.bbrc.2006.04.023, 16677612.
-
(2006)
Biochem Biophys Res Commun
, vol.345
, pp. 197-204
-
-
Thirunavukkarasu, K.1
Pei, Y.2
Moore, T.L.3
Wang, H.4
Yu, X.P.5
Geiser, A.G.6
Chandrasekhar, S.7
-
39
-
-
0035122861
-
Gene array analysis of osteoblast differentiation
-
Beck GR, Zerler B, Moran E. Gene array analysis of osteoblast differentiation. Cell Growth Differ 2001, 12:61-83.
-
(2001)
Cell Growth Differ
, vol.12
, pp. 61-83
-
-
Beck, G.R.1
Zerler, B.2
Moran, E.3
-
40
-
-
77957937697
-
Signaling pathways in human skeletal dysplasias
-
10.1146/annurev-genom-082908-150158, 20690819
-
Baldridge D, Shchelochkov O, Kelley B, Lee B. Signaling pathways in human skeletal dysplasias. Annu Rev Genomics Hum Genet 2010, 11:189-217. 10.1146/annurev-genom-082908-150158, 20690819.
-
(2010)
Annu Rev Genomics Hum Genet
, vol.11
, pp. 189-217
-
-
Baldridge, D.1
Shchelochkov, O.2
Kelley, B.3
Lee, B.4
-
41
-
-
84655173624
-
Cell-type specific and combinatorial usage of diverse transcription factors revealed by genome-wide binding studies in multiple human cells
-
10.1101/gr.127597.111, 3246210, 22090374
-
Lee BK, Bhinge AA, Battenhouse A, McDaniell RM, Liu Z, Song L, Ni Y, Birney E, Lieb JD, Furey TS, Crawford GE, Iyer VR. Cell-type specific and combinatorial usage of diverse transcription factors revealed by genome-wide binding studies in multiple human cells. Genome Res 2012, 22:9-24. 10.1101/gr.127597.111, 3246210, 22090374.
-
(2012)
Genome Res
, vol.22
, pp. 9-24
-
-
Lee, B.K.1
Bhinge, A.A.2
Battenhouse, A.3
McDaniell, R.M.4
Liu, Z.5
Song, L.6
Ni, Y.7
Birney, E.8
Lieb, J.D.9
Furey, T.S.10
Crawford, G.E.11
Iyer, V.R.12
-
42
-
-
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 J, 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 J, Andrews RM, Flicek P, Boyle PJ, Cao H, Carter NP, Clelland GK, Davis S, Day N, Dhami P, Dillon SC, Dorschner MO, Fiegler H, et al. 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.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.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
more..
-
43
-
-
84865708757
-
An expansive human regulatory lexicon encoded in transcription factor footprints
-
10.1038/nature11212, 3736582, 22955618
-
Neph S, Vierstra J, Stergachis AB, Reynolds AP, Haugen E, Vernot B, Thurman RE, John S, Sandstrom R, Johnson AK, Maurano MT, Humbert R, Rynes E, Wang H, Vong S, Lee K, Bates D, Diegel M, Roach V, Dunn D, Neri J, Schafer A, Hansen RS, Kutyavin T, Giste E, Weaver M, Canfield T, Sabo P, Zhang M, Balasundaram G, et al. An expansive human regulatory lexicon encoded in transcription factor footprints. Nature 2012, 489:83-90. 10.1038/nature11212, 3736582, 22955618.
-
(2012)
Nature
, vol.489
, pp. 83-90
-
-
Neph, S.1
Vierstra, J.2
Stergachis, A.B.3
Reynolds, A.P.4
Haugen, E.5
Vernot, B.6
Thurman, R.E.7
John, S.8
Sandstrom, R.9
Johnson, A.K.10
Maurano, M.T.11
Humbert, R.12
Rynes, E.13
Wang, H.14
Vong, S.15
Lee, K.16
Bates, D.17
Diegel, M.18
Roach, V.19
Dunn, D.20
Neri, J.21
Schafer, A.22
Hansen, R.S.23
Kutyavin, T.24
Giste, E.25
Weaver, M.26
Canfield, T.27
Sabo, P.28
Zhang, M.29
Balasundaram, G.30
more..
-
44
-
-
68949213578
-
Insights from genomic profiling of transcription factors
-
10.1038/nrg2636, 2846386, 19668247
-
Farnham PJ. Insights from genomic profiling of transcription factors. Nat Rev Genet 2009, 10:605-616. 10.1038/nrg2636, 2846386, 19668247.
-
(2009)
Nat Rev Genet
, vol.10
, pp. 605-616
-
-
Farnham, P.J.1
-
45
-
-
34547633677
-
Genome-wide profiles of STAT1 DNA association using chromatin immunoprecipitation and massively parallel sequencing
-
10.1038/nmeth1068, 17558387
-
Robertson G, Hirst M, Bainbridge M, Bilenky M, Zhao Y, Zeng T, Euskirchen G, Bernier B, Varhol R, Delaney A, Thiessen N, Griffith OL, He A, Marra M, Snyder M, Jones S. Genome-wide profiles of STAT1 DNA association using chromatin immunoprecipitation and massively parallel sequencing. Nat Methods 2007, 4:651-657. 10.1038/nmeth1068, 17558387.
-
(2007)
Nat Methods
, vol.4
, 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
-
46
-
-
77955629953
-
Genome-wide analysis of estrogen receptor alpha DNA binding and tethering mechanisms identifies Runx1 as a novel tethering factor in receptor-mediated transcriptional activation
-
10.1128/MCB.00118-10, 2916448, 20547749
-
Stender JD, Kim K, Charn TH, Komm B, Chang KC, Kraus WL, Benner C, Glass CK, Katzenellenbogen BS. Genome-wide analysis of estrogen receptor alpha DNA binding and tethering mechanisms identifies Runx1 as a novel tethering factor in receptor-mediated transcriptional activation. Mol Cell Biol 2010, 30:3943-3955. 10.1128/MCB.00118-10, 2916448, 20547749.
-
(2010)
Mol Cell Biol
, vol.30
, pp. 3943-3955
-
-
Stender, J.D.1
Kim, K.2
Charn, T.H.3
Komm, B.4
Chang, K.C.5
Kraus, W.L.6
Benner, C.7
Glass, C.K.8
Katzenellenbogen, B.S.9
-
47
-
-
79955883317
-
Genome-wide analysis of simultaneous GATA1/2, RUNX1, FLI1, and SCL binding in megakaryocytes identifies hematopoietic regulators
-
10.1016/j.devcel.2011.04.008, 3145975, 21571218
-
Tijssen MR, Cvejic A, Joshi A, Hannah RL, Ferreira R, Forrai A, Bellissimo DC, Oram SH, Smethurst PA, Wilson NK, Wang X, Ottersbach K, Stemple DL, Green AR, Ouwehand WH, Gottgens B. Genome-wide analysis of simultaneous GATA1/2, RUNX1, FLI1, and SCL binding in megakaryocytes identifies hematopoietic regulators. Dev Cell 2011, 20:597-609. 10.1016/j.devcel.2011.04.008, 3145975, 21571218.
-
(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
Wang, X.11
Ottersbach, K.12
Stemple, D.L.13
Green, A.R.14
Ouwehand, W.H.15
Gottgens, B.16
-
48
-
-
60149091656
-
ChIP-seq accurately predicts tissue-specific activity of enhancers
-
10.1038/nature07730, 2745234, 19212405
-
Visel A, Blow MJ, Li Z, Zhang T, Akiyama JA, Holt A, Plajzer-Frick I, Shoukry M, Wright C, Chen F, Afzal V, Ren B, Rubin EM, Pennacchio LA. ChIP-seq accurately predicts tissue-specific activity of enhancers. Nature 2009, 457:854-858. 10.1038/nature07730, 2745234, 19212405.
-
(2009)
Nature
, vol.457
, pp. 854-858
-
-
Visel, A.1
Blow, M.J.2
Li, Z.3
Zhang, T.4
Akiyama, J.A.5
Holt, A.6
Plajzer-Frick, I.7
Shoukry, M.8
Wright, C.9
Chen, F.10
Afzal, V.11
Ren, B.12
Rubin, E.M.13
Pennacchio, L.A.14
-
49
-
-
79960876540
-
A high resolution genome-wide scan of HNF4alpha recognition sites infers a regulatory gene network in colon cancer
-
10.1371/journal.pone.0021667, 3145629, 21829439
-
Weltmeier F, Borlak J. A high resolution genome-wide scan of HNF4alpha recognition sites infers a regulatory gene network in colon cancer. PLoS One 2011, 6:e21667. 10.1371/journal.pone.0021667, 3145629, 21829439.
-
(2011)
PLoS One
, vol.6
-
-
Weltmeier, F.1
Borlak, J.2
-
50
-
-
84860354838
-
Genome-wide Runx2 occupancy in prostate cancer cells suggests a role in regulating secretion
-
10.1093/nar/gkr1219, 3333873, 22187159
-
Little GH, Noushmehr H, Baniwal SK, Berman BP, Coetzee GA, Frenkel B. Genome-wide Runx2 occupancy in prostate cancer cells suggests a role in regulating secretion. Nucleic Acids Res 2012, 40:3538-3547. 10.1093/nar/gkr1219, 3333873, 22187159.
-
(2012)
Nucleic Acids Res
, vol.40
, pp. 3538-3547
-
-
Little, G.H.1
Noushmehr, H.2
Baniwal, S.K.3
Berman, B.P.4
Coetzee, G.A.5
Frenkel, B.6
-
51
-
-
0035079804
-
Stein GS: runt homology domain transcription factors (Runx, Cbfa, and AML) mediate repression of the bone sialoprotein promoter: evidence for promoter context-dependent activity of Cbfa proteins
-
10.1128/MCB.21.8.2891-2905.2001, 86918, 11283267
-
Javed A, Barnes GL, Jasanya BO, Stein JL, Gerstenfeld L, Lian JB. Stein GS: runt homology domain transcription factors (Runx, Cbfa, and AML) mediate repression of the bone sialoprotein promoter: evidence for promoter context-dependent activity of Cbfa proteins. Mol Cell Biol 2001, 21:2891-2905. 10.1128/MCB.21.8.2891-2905.2001, 86918, 11283267.
-
(2001)
Mol Cell Biol
, vol.21
, pp. 2891-2905
-
-
Javed, A.1
Barnes, G.L.2
Jasanya, B.O.3
Stein, J.L.4
Gerstenfeld, L.5
Lian, J.B.6
-
52
-
-
4744369224
-
Bone-specific transcription factor Runx2 interacts with the 1alpha,25-dihydroxyvitamin D3 receptor to up-regulate rat osteocalcin gene expression in osteoblastic cells
-
10.1128/MCB.24.20.8847-8861.2004, 517904, 15456860
-
Paredes R, Arriagada G, Cruzat F, Villagra A, Olate J, Zaidi K, van Wijnen A, Lian JB, Stein GS, Stein JL, Montecino M. Bone-specific transcription factor Runx2 interacts with the 1alpha,25-dihydroxyvitamin D3 receptor to up-regulate rat osteocalcin gene expression in osteoblastic cells. Mol Cell Biol 2004, 24:8847-8861. 10.1128/MCB.24.20.8847-8861.2004, 517904, 15456860.
-
(2004)
Mol Cell Biol
, vol.24
, pp. 8847-8861
-
-
Paredes, R.1
Arriagada, G.2
Cruzat, F.3
Villagra, A.4
Olate, J.5
Zaidi, K.6
van Wijnen, A.7
Lian, J.B.8
Stein, G.S.9
Stein, J.L.10
Montecino, M.11
-
53
-
-
22544476244
-
Tissue- and bone cell-specific expression of bone sialoprotein is directed by a 9.0 kb promoter in transgenic mice
-
10.1016/j.matbio.2005.05.009, 15970437
-
Paz J, Wade K, Kiyoshima T, Sodek J, Tang J, Tu Q, Yamauchi M, Chen J. Tissue- and bone cell-specific expression of bone sialoprotein is directed by a 9.0 kb promoter in transgenic mice. Matrix Biol 2005, 24:341-352. 10.1016/j.matbio.2005.05.009, 15970437.
-
(2005)
Matrix Biol
, vol.24
, pp. 341-352
-
-
Paz, J.1
Wade, K.2
Kiyoshima, T.3
Sodek, J.4
Tang, J.5
Tu, Q.6
Yamauchi, M.7
Chen, J.8
-
54
-
-
24744451966
-
Cooperative interactions between RUNX2 and homeodomain protein-binding sites are critical for the osteoblast-specific expression of the bone sialoprotein gene
-
10.1074/jbc.M503942200, 16000302
-
Roca H, Phimphilai M, Gopalakrishnan R, Xiao G, Franceschi RT. Cooperative interactions between RUNX2 and homeodomain protein-binding sites are critical for the osteoblast-specific expression of the bone sialoprotein gene. J Biol Chem 2005, 280:30845-30855. 10.1074/jbc.M503942200, 16000302.
-
(2005)
J Biol Chem
, vol.280
, pp. 30845-30855
-
-
Roca, H.1
Phimphilai, M.2
Gopalakrishnan, R.3
Xiao, G.4
Franceschi, R.T.5
-
55
-
-
84862908850
-
Extensive promoter-centered chromatin interactions provide a topological basis for transcription regulation
-
10.1016/j.cell.2011.12.014, 3339270, 22265404
-
Li G, Ruan X, Auerbach RK, Sandhu KS, Zheng M, Wang P, Poh HM, Goh Y, Lim J, Zhang J, Sim HS, Peh SQ, Mulawadi FH, Ong CT, Orlov YL, Hong S, Zhang Z, Landt S, Raha D, Euskirchen G, Wei CL, Ge W, Wang H, Davis C, Fisher-Aylor KI, Mortazavi A, Gerstein M, Gingeras T, Wold B, Sun Y, et al. Extensive promoter-centered chromatin interactions provide a topological basis for transcription regulation. Cell 2012, 148:84-98. 10.1016/j.cell.2011.12.014, 3339270, 22265404.
-
(2012)
Cell
, vol.148
, pp. 84-98
-
-
Li, G.1
Ruan, X.2
Auerbach, R.K.3
Sandhu, K.S.4
Zheng, M.5
Wang, P.6
Poh, H.M.7
Goh, Y.8
Lim, J.9
Zhang, J.10
Sim, H.S.11
Peh, S.Q.12
Mulawadi, F.H.13
Ong, C.T.14
Orlov, Y.L.15
Hong, S.16
Zhang, Z.17
Landt, S.18
Raha, D.19
Euskirchen, G.20
Wei, C.L.21
Ge, W.22
Wang, H.23
Davis, C.24
Fisher-Aylor, K.I.25
Mortazavi, A.26
Gerstein, M.27
Gingeras, T.28
Wold, B.29
Sun, Y.30
more..
-
56
-
-
84862778066
-
Intragenic enhancers act as alternative promoters
-
10.1016/j.molcel.2011.12.021, 22264824
-
Kowalczyk MS, Hughes JR, Garrick D, Lynch MD, Sharpe JA, Sloane-Stanley JA, McGowan SJ, De Gobbi M, Hosseini M, Vernimmen D, Brown JM, Gray NE, Collavin L, Gibbons RJ, Flint J, Taylor S, Buckle VJ, Milne TA, Wood WG, Higgs DR. Intragenic enhancers act as alternative promoters. Mol Cell 2012, 45:447-458. 10.1016/j.molcel.2011.12.021, 22264824.
-
(2012)
Mol Cell
, vol.45
, pp. 447-458
-
-
Kowalczyk, M.S.1
Hughes, J.R.2
Garrick, D.3
Lynch, M.D.4
Sharpe, J.A.5
Sloane-Stanley, J.A.6
McGowan, S.J.7
De Gobbi, M.8
Hosseini, M.9
Vernimmen, D.10
Brown, J.M.11
Gray, N.E.12
Collavin, L.13
Gibbons, R.J.14
Flint, J.15
Taylor, S.16
Buckle, V.J.17
Milne, T.A.18
Wood, W.G.19
Higgs, D.R.20
more..
-
57
-
-
70349873824
-
Comprehensive mapping of long-range interactions reveals folding principles of the human genome
-
10.1126/science.1181369, 2858594, 19815776
-
Lieberman-Aiden E, van Berkum NL, Williams L, Imakaev M, Ragoczy T, Telling A, Amit I, Lajoie BR, Sabo PJ, Dorschner MO, Sandstrom R, Bernstein B, Bender MA, Groudine M, Gnirke A, Stamatoyannopoulos J, Mirny LA, Lander ES, Dekker J. Comprehensive mapping of long-range interactions reveals folding principles of the human genome. Science 2009, 326:289-293. 10.1126/science.1181369, 2858594, 19815776.
-
(2009)
Science
, vol.326
, pp. 289-293
-
-
Lieberman-Aiden, E.1
van Berkum, N.L.2
Williams, L.3
Imakaev, M.4
Ragoczy, T.5
Telling, A.6
Amit, I.7
Lajoie, B.R.8
Sabo, P.J.9
Dorschner, M.O.10
Sandstrom, R.11
Bernstein, B.12
Bender, M.A.13
Groudine, M.14
Gnirke, A.15
Stamatoyannopoulos, J.16
Mirny, L.A.17
Lander, E.S.18
Dekker, J.19
-
58
-
-
84868193627
-
Gene loops enhance transcriptional directionality
-
10.1126/science.1224350, 3563069, 23019609
-
Tan-Wong SM, Zaugg JB, Camblong J, Xu Z, Zhang DW, Mischo HE, Ansari AZ, Luscombe NM, Steinmetz LM, Proudfoot NJ. Gene loops enhance transcriptional directionality. Science 2012, 338:671-675. 10.1126/science.1224350, 3563069, 23019609.
-
(2012)
Science
, vol.338
, pp. 671-675
-
-
Tan-Wong, S.M.1
Zaugg, J.B.2
Camblong, J.3
Xu, Z.4
Zhang, D.W.5
Mischo, H.E.6
Ansari, A.Z.7
Luscombe, N.M.8
Steinmetz, L.M.9
Proudfoot, N.J.10
-
59
-
-
0034789271
-
A specific targeting signal directs Runx2/Cbfa1 to subnuclear domains and contributes to transactivation of the osteocalcin gene
-
Zaidi SK, Javed A, Choi JY, van Wijnen AJ, Stein JL, Lian JB, Stein GS. A specific targeting signal directs Runx2/Cbfa1 to subnuclear domains and contributes to transactivation of the osteocalcin gene. J Cell Sci 2001, 114:3093-3102.
-
(2001)
J Cell Sci
, vol.114
, pp. 3093-3102
-
-
Zaidi, S.K.1
Javed, A.2
Choi, J.Y.3
van Wijnen, A.J.4
Stein, J.L.5
Lian, J.B.6
Stein, G.S.7
-
60
-
-
33846489816
-
Mitotic occupancy and lineage-specific transcriptional control of rRNA genes by Runx2
-
10.1038/nature05473, 17251981
-
Young DW, Hassan MQ, Pratap J, Galindo M, Zaidi SK, Lee SH, Yang X, Xie R, Javed A, Underwood JM, Furcinitti P, Imbalzano AN, Penman S, Nickerson JA, Montecino MA, Lian JB, Stein JL, van Wijnen AJ, Stein GS. Mitotic occupancy and lineage-specific transcriptional control of rRNA genes by Runx2. Nature 2007, 445:442-446. 10.1038/nature05473, 17251981.
-
(2007)
Nature
, vol.445
, pp. 442-446
-
-
Young, D.W.1
Hassan, M.Q.2
Pratap, J.3
Galindo, M.4
Zaidi, S.K.5
Lee, S.H.6
Yang, X.7
Xie, R.8
Javed, A.9
Underwood, J.M.10
Furcinitti, P.11
Imbalzano, A.N.12
Penman, S.13
Nickerson, J.A.14
Montecino, M.A.15
Lian, J.B.16
Stein, J.L.17
van Wijnen, A.J.18
Stein, G.S.19
-
61
-
-
84899652845
-
FoxPrimer qPCR Primer Design Suite
-
FoxPrimer qPCR Primer Design Suite. [http://www.foxprimer.org].
-
-
-
-
62
-
-
84899626720
-
Nuclear organization in breast cance
-
UMASS Medical School
-
Dobson JR. Nuclear organization in breast cance. PhD thesis 2013, UMASS Medical School.
-
(2013)
PhD thesis
-
-
Dobson, J.R.1
-
63
-
-
54249097017
-
Runx2 transcriptional activation of Indian Hedgehog and a downstream bone metastatic pathway in breast cancer cells
-
10.1158/0008-5472.CAN-08-1078, 2596479, 18829534
-
Pratap J, Wixted JJ, Gaur T, Zaidi SK, Dobson J, Gokul KD, Hussain S, van Wijnen AJ, Stein JL, Stein GS, Lian JB. Runx2 transcriptional activation of Indian Hedgehog and a downstream bone metastatic pathway in breast cancer cells. Cancer Res 2008, 68:7795-7802. 10.1158/0008-5472.CAN-08-1078, 2596479, 18829534.
-
(2008)
Cancer Res
, vol.68
, pp. 7795-7802
-
-
Pratap, J.1
Wixted, J.J.2
Gaur, T.3
Zaidi, S.K.4
Dobson, J.5
Gokul, K.D.6
Hussain, S.7
van Wijnen, A.J.8
Stein, J.L.9
Stein, G.S.10
Lian, J.B.11
-
64
-
-
79951780811
-
R: A Language and Environment for Statistical Computing
-
R: A Language and Environment for Statistical Computing. [http://www.R-project.org].
-
-
-
-
65
-
-
1342288026
-
Affy-analysis of Affymetrix GeneChip data at the probe level
-
10.1093/bioinformatics/btg405, 14960456
-
Gautier L, Cope L, Bolstad BM, Irizarry RA. affy-analysis of Affymetrix GeneChip data at the probe level. Bioinformatics 2004, 20:307-315. 10.1093/bioinformatics/btg405, 14960456.
-
(2004)
Bioinformatics
, vol.20
, pp. 307-315
-
-
Gautier, L.1
Cope, L.2
Bolstad, B.M.3
Irizarry, R.A.4
-
66
-
-
28744458859
-
Bioconductor: open software development for computational biology and bioinformatics
-
10.1186/gb-2004-5-10-r80, 545600, 15461798
-
Gentleman RC, Carey VJ, Bates DM, Bolstad B, Dettling M, Dudoit S, Ellis B, Gautier L, Ge Y, Gentry J, Hornik K, Hothorn T, Huber W, Iacus S, Irizarry R, Leisch F, Li C, Maechler M, Rossini AJ, Sawitzki G, Smith C, Smyth G, Tierney L, Yang JY, Zhang J. Bioconductor: open software development for computational biology and bioinformatics. Genome Biol 2004, 5:R80. 10.1186/gb-2004-5-10-r80, 545600, 15461798.
-
(2004)
Genome Biol
, vol.5
-
-
Gentleman, R.C.1
Carey, V.J.2
Bates, D.M.3
Bolstad, B.4
Dettling, M.5
Dudoit, S.6
Ellis, B.7
Gautier, L.8
Ge, Y.9
Gentry, J.10
Hornik, K.11
Hothorn, T.12
Huber, W.13
Iacus, S.14
Irizarry, R.15
Leisch, F.16
Li, C.17
Maechler, M.18
Rossini, A.J.19
Sawitzki, G.20
Smith, C.21
Smyth, G.22
Tierney, L.23
Yang, J.Y.24
Zhang, J.25
more..
-
67
-
-
33644872577
-
Limma: linear models for microarray data
-
New York: Springer, Gentleman R, Carey VJ, Huber W, Irizarry RA, Dudoit S, [Gail M, Krickeberg K, Samet J, Tsiatis A, Wong W (Series Editors): Statistics for Biology and Health]
-
Smyth GK. Limma: linear models for microarray data. Bioinformatics and Computational Biology Solutions Using R and Bioconductor 2005, 397-420. New York: Springer, Gentleman R, Carey VJ, Huber W, Irizarry RA, Dudoit S, [Gail M, Krickeberg K, Samet J, Tsiatis A, Wong W (Series Editors): Statistics for Biology and Health].
-
(2005)
Bioinformatics and Computational Biology Solutions Using R and Bioconductor
, pp. 397-420
-
-
Smyth, G.K.1
-
68
-
-
0001677717
-
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 Methodol 1995, 57:289-300.
-
(1995)
J R Stat Soc Series B Methodol
, vol.57
, pp. 289-300
-
-
Benjamini, Y.1
Hochberg, Y.2
-
69
-
-
0021100690
-
Accurate transcription initiation by RNA polymerase II in a soluble extract from isolated mammalian nuclei
-
10.1093/nar/11.5.1475, 325809, 6828386
-
Dignam JD, Lebovitz RM, Roeder RG. Accurate transcription initiation by RNA polymerase II in a soluble extract from isolated mammalian nuclei. Nucleic Acids Res 1983, 11:1475-1489. 10.1093/nar/11.5.1475, 325809, 6828386.
-
(1983)
Nucleic Acids Res
, vol.11
, pp. 1475-1489
-
-
Dignam, J.D.1
Lebovitz, R.M.2
Roeder, R.G.3
-
70
-
-
84863139254
-
Genomic promoter occupancy of runt-related transcription factor RUNX2 in Osteosarcoma cells identifies genes involved in cell adhesion and motility
-
10.1074/jbc.M111.287771, 3281617, 22158627
-
van der Deen M, Akech J, Lapointe D, Gupta S, Young DW, Montecino MA, Galindo M, Lian JB, Stein JL, Stein GS, van Wijnen AJ. Genomic promoter occupancy of runt-related transcription factor RUNX2 in Osteosarcoma cells identifies genes involved in cell adhesion and motility. J Biol Chem 2012, 287:4503-4517. 10.1074/jbc.M111.287771, 3281617, 22158627.
-
(2012)
J Biol Chem
, vol.287
, pp. 4503-4517
-
-
van der Deen, M.1
Akech, J.2
Lapointe, D.3
Gupta, S.4
Young, D.W.5
Montecino, M.A.6
Galindo, M.7
Lian, J.B.8
Stein, J.L.9
Stein, G.S.10
van Wijnen, A.J.11
-
71
-
-
62349130698
-
Ultrafast and memory-efficient alignment of short DNA sequences to the human genome
-
10.1186/gb-2009-10-3-r25, 2690996, 19261174
-
Langmead B, Trapnell C, Pop M, Salzberg SL. Ultrafast and memory-efficient alignment of short DNA sequences to the human genome. Genome Biol 2009, 10:R25. 10.1186/gb-2009-10-3-r25, 2690996, 19261174.
-
(2009)
Genome Biol
, vol.10
-
-
Langmead, B.1
Trapnell, C.2
Pop, M.3
Salzberg, S.L.4
-
72
-
-
0036079158
-
The human genome browser at UCSC
-
10.1101/gr.229102. Article published online before print in May 2002, 186604, 12045153
-
Kent WJ, Sugnet CW, Furey TS, Roskin KM, Pringle TH, Zahler AM, Haussler D. The human genome browser at UCSC. Genome Res 2002, 12:996-1006. 10.1101/gr.229102. Article published online before print in May 2002, 186604, 12045153.
-
(2002)
Genome Res
, vol.12
, pp. 996-1006
-
-
Kent, W.J.1
Sugnet, C.W.2
Furey, T.S.3
Roskin, K.M.4
Pringle, T.H.5
Zahler, A.M.6
Haussler, D.7
-
73
-
-
77952214662
-
GREAT improves functional interpretation of cis-regulatory regions
-
10.1038/nbt.1630, 20436461
-
McLean CY, Bristor D, Hiller M, Clarke SL, Schaar BT, Lowe CB, Wenger AM, Bejerano G. GREAT improves functional interpretation of cis-regulatory regions. Nat Biotechnol 2010, 28:495-501. 10.1038/nbt.1630, 20436461.
-
(2010)
Nat Biotechnol
, vol.28
, pp. 495-501
-
-
McLean, C.Y.1
Bristor, D.2
Hiller, M.3
Clarke, S.L.4
Schaar, B.T.5
Lowe, C.B.6
Wenger, A.M.7
Bejerano, G.8
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