-
1
-
-
55749097626
-
Multiple levels of redundant processes inhibit Caenorhabditis elegans vulval cell fates
-
Andersen EC, Saffer AM, Horvitz HR. 2008. Multiple levels of redundant processes inhibit Caenorhabditis elegans vulval cell fates. Genetics 179: 2001–2012.
-
(2008)
Genetics
, vol.179
, pp. 2001-2012
-
-
Andersen, E.C.1
Saffer, A.M.2
Horvitz, H.R.3
-
2
-
-
34249026300
-
High-resolution profiling of histone methylations in the human genome
-
Barski A, Cuddapah S, Cui K, Roh TY, 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.
-
(2007)
Cell
, vol.129
, 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
-
-
36749080303
-
E2F-associated chromatin modifiers and cell cycle control
-
Blais A, Dynlacht BD. 2007. E2F-associated chromatin modifiers and cell cycle control. Curr Opin Cell Biol 19: 658–662.
-
(2007)
Curr Opin Cell Biol
, vol.19
, pp. 658-662
-
-
Blais, A.1
Dynlacht, B.D.2
-
4
-
-
1842583739
-
A new class of C. Elegans synMuv genes implicates a Tip60/NuA4-like HATcomplex as a negative regulator of Ras signaling
-
Ceol CJ, Horvitz HR. 2004. A new class of C. elegans synMuv genes implicates a Tip60/NuA4-like HATcomplex as a negative regulator of Ras signaling. Dev Cell 6: 563–576.
-
(2004)
Dev Cell
, vol.6
, pp. 563-576
-
-
Ceol, C.J.1
Horvitz, H.R.2
-
5
-
-
79251555660
-
VennDiagram: A package for the generation of highly-customizable Venn and Euler diagrams in R
-
Chen H, Boutros PC. 2011. VennDiagram: a package for the generation of highly-customizable Venn and Euler diagrams in R. BMC Bioinformatics 12: 35.
-
(2011)
BMC Bioinformatics
, vol.12
-
-
Chen, H.1
Boutros, P.C.2
-
6
-
-
84879308632
-
The landscape of RNA polymerase II transcription initiation in C. Elegans reveals promoter and enhancer architectures
-
Chen RA, Down TA, Stempor P, Chen QB, Egelhofer TA, Hillier LW, Jeffers TE, Ahringer J. 2013. The landscape of RNA polymerase II transcription initiation in C. elegans reveals promoter and enhancer architectures. Genome Res 23: 1339–1347.
-
(2013)
Genome Res
, vol.23
, pp. 1339-1347
-
-
Chen, R.A.1
Down, T.A.2
Stempor, P.3
Chen, Q.B.4
Egelhofer, T.A.5
Hillier, L.W.6
Jeffers, T.E.7
Ahringer, J.8
-
7
-
-
80052990473
-
Systematic bias in high-throughput sequencing data and its correction by BEADS
-
Cheung MS, Down TA, Latorre I, Ahringer J. 2011. Systematic bias in high-throughput sequencing data and its correction by BEADS. Nucleic Acids Res 39: e103.
-
(2011)
Nucleic Acids Res
, vol.39
-
-
Cheung, M.S.1
Down, T.A.2
Latorre, I.3
Ahringer, J.4
-
8
-
-
33748782233
-
Promotion of oogenesis and embryogenesis in the C. Elegans gonad by EFL-1/DPL-1 (E2F) does not require LIN-35 (pRB)
-
Chi W, Reinke V. 2006. Promotion of oogenesis and embryogenesis in the C. elegans gonad by EFL-1/DPL-1 (E2F) does not require LIN-35 (pRB). Development 133: 3147–3157.
-
(2006)
Development
, vol.133
, pp. 3147-3157
-
-
Chi, W.1
Reinke, V.2
-
9
-
-
84868122260
-
Deposition of histone variant H2A.Z within gene bodies regulates responsive genes
-
Coleman-Derr D, Zilberman D. 2012a. Deposition of histone variant H2A.Z within gene bodies regulates responsive genes. PLoS Genet 8: e1002988.
-
(2012)
Plos Genet
, vol.8
-
-
Coleman-Derr, D.1
Zilberman, D.2
-
10
-
-
84881530204
-
DNA methylation, H2A.Z, and the regulation of constitutive expression
-
Coleman-Derr D, Zilberman D. 2012b. DNA methylation, H2A.Z, and the regulation of constitutive expression. Cold Spring Harb Symp Quant Biol 77: 147–154.
-
(2012)
Cold Spring Harb Symp Quant Biol
, vol.77
, pp. 147-154
-
-
Coleman-Derr, D.1
Zilberman, D.2
-
11
-
-
84876437493
-
The complex containing Drosophila Myb and RB/E2F2 regulates cytokinesis in a histone H2Av-dependent manner
-
DeBruhl H, Wen H, Lipsick JS. 2013. The complex containing Drosophila Myb and RB/E2F2 regulates cytokinesis in a histone H2Av-dependent manner. Mol Cell Biol 33: 1809–1818.
-
(2013)
Mol Cell Biol
, vol.33
, pp. 1809-1818
-
-
Debruhl, H.1
Wen, H.2
Lipsick, J.S.3
-
12
-
-
80052318326
-
RB regulation of developmental transcriptional programs
-
Dimova DK. 2011. RB regulation of developmental transcriptional programs. Fly (Austin) 5: 115–118.
-
(2011)
Fly (Austin)
, vol.5
, pp. 115-118
-
-
Dimova, D.K.1
-
13
-
-
84868014111
-
On the role of retinoblastoma family proteins in the establishment and maintenance of the epigenetic landscape
-
Fiorentino FP, Marchesi I, Giordano A. 2013. On the role of retinoblastoma family proteins in the establishment and maintenance of the epigenetic landscape. J Cell Physiol 228: 276–284.
-
(2013)
J Cell Physiol
, vol.228
, pp. 276-284
-
-
Fiorentino, F.P.1
Marchesi, I.2
Giordano, A.3
-
14
-
-
45849145764
-
Sin3B: An essential regulator of chromatin modifications at E2F target promoters during cell cycle withdrawal
-
Grandinetti KB, David G. 2008. Sin3B: an essential regulator of chromatin modifications at E2F target promoters during cell cycle withdrawal. Cell Cycle 7: 1550–1554.
-
(2008)
Cell Cycle
, vol.7
, pp. 1550-1554
-
-
Grandinetti, K.B.1
David, G.2
-
15
-
-
73349098753
-
The euchromatic and heterochromatic landscapes are shaped by antagonizing effects of transcription on H2A.Z deposition
-
e1000687
-
Hardy S, Jacques PE, Gevry N, Forest A, Fortin ME, Laflamme L, Gaudreau L, Robert F. 2009. The euchromatic and heterochromatic landscapes are shaped by antagonizing effects of transcription on H2A.Z deposition. PLoS Genet 5: e1000687.
-
(2009)
Plos Genet
, vol.5
-
-
Hardy, S.1
Jacques, P.E.2
Gevry, N.3
Forest, A.4
Fortin, M.E.5
Laflamme, L.6
Gaudreau, L.7
Robert, F.8
-
16
-
-
33750963671
-
Some C. Elegans class B synthetic multivulva proteins encode a conserved LIN-35 Rb-containing complex distinct from a NuRD-like complex
-
Harrison MM, Ceol CJ, Lu X, Horvitz HR. 2006. Some C. elegans class B synthetic multivulva proteins encode a conserved LIN-35 Rb-containing complex distinct from a NuRD-like complex. Proc Natl Acad Sci 103: 16782–16787.
-
(2006)
Proc Natl Acad Sci
, vol.103
, pp. 16782-16787
-
-
Harrison, M.M.1
Ceol, C.J.2
Lu, X.3
Horvitz, H.R.4
-
17
-
-
68149150830
-
H3.3/ H2A.Z double variant-containing nucleosomes mark ‘nucleosomefree regions’ of active promoters and other regulatory regions
-
Jin C, Zang C, Wei G, Cui K, Peng W, Zhao K, Felsenfeld G. 2009. H3.3/ H2A.Z double variant-containing nucleosomes mark ‘nucleosomefree regions’ of active promoters and other regulatory regions. Nat Genet 41: 941–945.
-
(2009)
Nat Genet
, vol.41
, pp. 941-945
-
-
Jin, C.1
Zang, C.2
Wei, G.3
Cui, K.4
Peng, W.5
Zhao, K.6
Felsenfeld, G.7
-
18
-
-
77955895425
-
BigWig and BigBed: Enabling browsing of large distributed datasets
-
Kent WJ, Zweig AS, Barber G, Hinrichs AS, Karolchik D. 2010. BigWig and BigBed: enabling browsing of large distributed datasets. Bioinformatics 26: 2204–2207.
-
(2010)
Bioinformatics
, vol.26
, pp. 2204-2207
-
-
Kent, W.J.1
Zweig, A.S.2
Barber, G.3
Hinrichs, A.S.4
Karolchik, D.5
-
19
-
-
34247563433
-
Transcriptome profiling of the C. Elegans Rb ortholog reveals diverse developmental roles
-
Kirienko NV, Fay DS. 2007. Transcriptome profiling of the C. elegans Rb ortholog reveals diverse developmental roles. Dev Biol 305: 674–684.
-
(2007)
Dev Biol
, vol.305
, pp. 674-684
-
-
Kirienko, N.V.1
Fay, D.S.2
-
20
-
-
61349098460
-
Differential chromatin marking of introns and expressed exons by H3K36me3
-
Kolasinska-Zwierz P, Down T, Latorre I, Liu T, Liu XS, Ahringer J. 2009. Differential chromatin marking of introns and expressed exons by H3K36me3. Nat Genet 41: 376–381.
-
(2009)
Nat Genet
, vol.41
, pp. 376-381
-
-
Kolasinska-Zwierz, P.1
Down, T.2
Latorre, I.3
Liu, T.4
Liu, X.S.5
Ahringer, J.6
-
21
-
-
5444237176
-
Native E2F/ RBF complexes contain Myb-interacting proteins and repress transcription of developmentally controlled E2F target genes
-
Korenjak M, Taylor-Harding B, Binne UK, Satterlee JS, Stevaux O, Aasland R, White-Cooper H, Dyson N, Brehm A. 2004. Native E2F/ RBF complexes contain Myb-interacting proteins and repress transcription of developmentally controlled E2F target genes. Cell 119: 181–193.
-
(2004)
Cell
, vol.119
, pp. 181-193
-
-
Korenjak, M.1
Taylor-Harding, B.2
Binne, U.K.3
Satterlee, J.S.4
Stevaux, O.5
Aasland, R.6
White-Cooper, H.7
Dyson, N.8
Brehm, A.9
-
22
-
-
84879288762
-
Condensin controls recruitment of RNA polymerase II to achieve nematode Xchromosome dosage compensation
-
e00808
-
Kruesi WS, Core LJ, Waters CT, Lis JT, Meyer BJ. 2013. Condensin controls recruitment of RNA polymerase II to achieve nematode Xchromosome dosage compensation. eLife 2: e00808.
-
(2013)
Elife
, vol.2
-
-
Kruesi, W.S.1
Core, L.J.2
Waters, C.T.3
Lis, J.T.4
Meyer, B.J.5
-
23
-
-
84872686356
-
Tissue-specific direct targets of Caenorhabditis elegans Rb/ E2F dictate distinct somatic and germline programs
-
R5
-
Kudron M, Niu W, Lu Z, Wang G, Gerstein M, Snyder M, Reinke V. 2013. Tissue-specific direct targets of Caenorhabditis elegans Rb/ E2F dictate distinct somatic and germline programs. Genome Biol 14: R5.
-
(2013)
Genome Biol
, vol.14
-
-
Kudron, M.1
Niu, W.2
Lu, Z.3
Wang, G.4
Gerstein, M.5
Snyder, M.6
Reinke, V.7
-
24
-
-
10044255182
-
Identification of a Drosophila Myb–E2F2/RBF transcriptional repressor complex
-
Lewis PW, Beall EL, Fleischer TC, Georlette D, Link AJ, Botchan MR. 2004. Identification of a Drosophila Myb–E2F2/RBF transcriptional repressor complex. Genes Dev 18: 2929–2940.
-
(2004)
Genes Dev
, vol.18
, pp. 2929-2940
-
-
Lewis, P.W.1
Beall, E.L.2
Fleischer, T.C.3
Georlette, D.4
Link, A.J.5
Botchan, M.R.6
-
25
-
-
67649884743
-
Fast and accurate short read alignment with Burrows-Wheeler transform
-
Li H, Durbin R. 2009. Fast and accurate short read alignment with Burrows-Wheeler transform. Bioinformatics 25: 1754–1760.
-
(2009)
Bioinformatics
, vol.25
, pp. 1754-1760
-
-
Li, H.1
Durbin, R.2
-
26
-
-
34249109173
-
Evolutionarily conserved multisubunit RBL2/p130 and E2F4 protein complex represses human cell cycle-dependent genes in quiescence
-
Litovchick L, Sadasivam S, Florens L, Zhu X, Swanson SK, Velmurugan S, Chen R, Washburn MP, Liu XS, DeCaprio JA. 2007. Evolutionarily conserved multisubunit RBL2/p130 and E2F4 protein complex represses human cell cycle-dependent genes in quiescence. Mol Cell 26: 539–551.
-
(2007)
Mol Cell
, vol.26
, pp. 539-551
-
-
Litovchick, L.1
Sadasivam, S.2
Florens, L.3
Zhu, X.4
Swanson, S.K.5
Velmurugan, S.6
Chen, R.7
Washburn, M.P.8
Liu, X.S.9
Decaprio, J.A.10
-
27
-
-
80052022462
-
Cistrome: An integrative platform for transcriptional regulation studies
-
R83
-
Liu T, Ortiz JA, Taing L, Meyer CA, Lee B, Zhang Y, Shin H, Wong SS, Ma J, Lei Y, et al. 2011. Cistrome: an integrative platform for transcriptional regulation studies. Genome Biol 12: R83.
-
(2011)
Genome Biol
, vol.12
-
-
Liu, T.1
Ortiz, J.A.2
Taing, L.3
Meyer, C.A.4
Lee, B.5
Zhang, Y.6
Shin, H.7
Wong, S.S.8
Ma, J.9
Lei, Y.10
-
28
-
-
84924629414
-
Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2
-
Love MI, Huber W, Anders S. 2014. Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2. Genome Biol 15: 550.
-
(2014)
Genome Biol
, vol.15
-
-
Love, M.I.1
Huber, W.2
Ers, S.3
-
29
-
-
34547201576
-
A genome-wide RNA interference screen identifies putative chromatin regulators essential for E2F repression
-
Lu J, Ruhf ML, Perrimon N, Leder P. 2007. A genome-wide RNA interference screen identifies putative chromatin regulators essential for E2F repression. Proc Natl Acad Sci 104: 9381–9386.
-
(2007)
Proc Natl Acad Sci
, vol.104
, pp. 9381-9386
-
-
Lu, J.1
Ruhf, M.L.2
Perrimon, N.3
Leder, P.4
-
30
-
-
43749099875
-
Nucleosome organization in the Drosophila genome
-
Mavrich TN, Jiang C, Ioshikhes IP, Li X, Venters BJ, Zanton SJ, Tomsho LP, Qi J, Glaser RL, Schuster SC, et al. 2008. Nucleosome organization in the Drosophila genome. Nature 453: 358–362.
-
(2008)
Nature
, vol.453
, pp. 358-362
-
-
Mavrich, T.N.1
Jiang, C.2
Ioshikhes, I.P.3
Li, X.4
Venters, B.J.5
Zanton, S.J.6
Tomsho, L.P.7
Qi, J.8
Glaser, R.L.9
Schuster, S.C.10
-
31
-
-
79955158646
-
SynMuv B proteins antagonize germline fate in the intestine and ensure C. elegans survival
-
Petrella LN, Wang W, Spike CA, Rechtsteiner A, Reinke V, Strome S. 2011. synMuv B proteins antagonize germline fate in the intestine and ensure C. elegans survival. Development 138: 1069–1079.
-
(2011)
Development
, vol.138
, pp. 1069-1079
-
-
Petrella, L.N.1
Wang, W.2
Spike, C.A.3
Rechtsteiner, A.4
Reinke, V.5
-
32
-
-
23044477079
-
Chromatin regulation and sumoylation in the inhibition of Ras-induced vulval development in Caenorhabditis elegans
-
Poulin G, Dong Y, Fraser AG, Hopper NA, Ahringer J. 2005. Chromatin regulation and sumoylation in the inhibition of Ras-induced vulval development in Caenorhabditis elegans. EMBO J 24: 2613–2623.
-
(2005)
EMBO J
, vol.24
, pp. 2613-2623
-
-
Poulin, G.1
Dong, Y.2
Fraser, A.G.3
Hopper, N.A.4
Ahringer, J.5
-
33
-
-
53349161901
-
Imaging individual mRNA molecules using multiple singly labeled probes
-
Raj A, van den Bogaard P, Rifkin SA, van Oudenaarden A, Tyagi S. 2008. Imaging individual mRNA molecules using multiple singly labeled probes. Nat Methods 5: 877–879.
-
(2008)
Nat Methods
, vol.5
, pp. 877-879
-
-
Raj, A.1
Van Den Bogaard, P.2
Rifkin, S.A.3
Van Oudenaarden, A.4
Tyagi, S.5
-
34
-
-
77956308057
-
The histone H3K36 methyltransferase MES-4 acts epigenetically to transmit the memory of germline gene expression to progeny
-
e1001091
-
Rechtsteiner A, Ercan S, Takasaki T, Phippen TM, Egelhofer TA, vWang W, Kimura H, Lieb JD, Strome S. 2010. The histone H3K36 methyltransferase MES-4 acts epigenetically to transmit the memory of germline gene expression to progeny. PLoS Genet 6: e1001091.
-
(2010)
Plos Genet
, vol.6
-
-
Rechtsteiner, A.1
Ercan, S.2
Takasaki, T.3
Phippen, T.M.4
Egelhofer, T.A.5
Vwang, W.6
Kimura, H.7
Lieb, J.D.8
Strome, S.9
-
35
-
-
84881131933
-
The DREAM complex: Master coordinator of cell cycle-dependent gene expression
-
Sadasivam S, DeCaprio JA. 2013. The DREAM complex: master coordinator of cell cycle-dependent gene expression. Nat Rev Cancer 13: 585–595.
-
(2013)
Nat Rev Cancer
, vol.13
, pp. 585-595
-
-
Sadasivam, S.1
Decaprio, J.A.2
-
36
-
-
79957999603
-
Chromosome-biased binding and gene regulation by the Caenorhabditis elegans DRM complex
-
e1002074
-
Tabuchi TM, Deplancke B, Osato N, Zhu LJ, Barrasa MI, Harrison MM, Horvitz HR, Walhout AJ, Hagstrom KA. 2011. Chromosome-biased binding and gene regulation by the Caenorhabditis elegans DRM complex. PLoS Genet 7: e1002074.
-
(2011)
Plos Genet
, vol.7
-
-
Tabuchi, T.M.1
Deplancke, B.2
Osato, N.3
Zhu, L.J.4
Barrasa, M.I.5
Harrison, M.M.6
Horvitz, H.R.7
Walhout, A.J.8
Hagstrom, K.A.9
-
37
-
-
33749400902
-
Temporal regulation of foregut development by HTZ-1/H2A.Z and PHA-4/FoxA
-
e161
-
Updike DL, Mango SE. 2006. Temporal regulation of foregut development by HTZ-1/H2A.Z and PHA-4/FoxA. PLoS Genet 2: e161.
-
(2006)
Plos Genet
, vol.2
-
-
Updike, D.L.1
Mango, S.E.2
-
38
-
-
52949083577
-
The genomic distribution and function of histone variant HTZ-1 during C. Elegans embryogenesis
-
e1000187
-
Whittle CM, McClinic KN, Ercan S, Zhang X, Green RD, Kelly WG, Lieb JD. 2008. The genomic distribution and function of histone variant HTZ-1 during C. elegans embryogenesis. PLoS Genet 4: e1000187.
-
(2008)
Plos Genet
, vol.4
-
-
Whittle, C.M.1
McClinic, K.N.2
Ercan, S.3
Zhang, X.4
Green, R.D.5
Kelly, W.G.6
Lieb, J.D.7
-
39
-
-
53849146020
-
Model-based analysis of ChIP-seq (MACS)
-
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.
-
(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
|