-
1
-
-
0025298495
-
Transient induction of c-jun during hepatic regeneration
-
Alcorn JA, Feitelberg SP, Brenner DA. 1990. Transient induction of c-jun during hepatic regeneration. Hepatology 11: 909-915.
-
(1990)
Hepatology
, vol.11
, pp. 909-915
-
-
Alcorn, J.A.1
Feitelberg, S.P.2
Brenner, D.A.3
-
2
-
-
84897459814
-
An atlas of active enhancers across human cell types and tissues
-
Andersson R, Gebhard C, Miguel-Escalada I, Hoof I, Bornholdt J, Boyd M, Chen Y, Zhao X, Schmidl C, Suzuki T, et al. 2014. An atlas of active enhancers across human cell types and tissues. Nature 507: 455-461.
-
(2014)
Nature
, vol.507
, pp. 455-461
-
-
Andersson, R.1
Gebhard, C.2
Miguel-Escalada, I.3
Hoof, I.4
Bornholdt, J.5
Boyd, M.6
Chen, Y.7
Zhao, X.8
Schmidl, C.9
Suzuki, T.10
-
3
-
-
0026506720
-
Transcription factor loading on the MMTV promoter: A bimodal mechanism for promoter activation
-
Archer TK, Lefebvre P, Wolford RG, Hager GL. 1992. Transcription factor loading on the MMTV promoter: a bimodal mechanism for promoter activation. Science 255: 1573-1576.
-
(1992)
Science
, vol.255
, pp. 1573-1576
-
-
Archer, T.K.1
Lefebvre, P.2
Wolford, R.G.3
Hager, G.L.4
-
4
-
-
84874381107
-
Genome-wide quantitative enhancer activity maps identified by STARR-seq
-
Arnold CD, Gerlach D, Stelzer C, Boryn LM, Rath M, Stark A. 2013. Genome-wide quantitative enhancer activity maps identified by STARR-seq. Science 339: 1074-1077.
-
(2013)
Science
, vol.339
, pp. 1074-1077
-
-
Arnold, C.D.1
Gerlach, D.2
Stelzer, C.3
Boryn, L.M.4
Rath, M.5
Stark, A.6
-
5
-
-
84903640603
-
Quantitative genome-wide enhancer activity maps for five Drosophila species show functional enhancer conservation and turnover during cis-regulatory evolution
-
Arnold CD, Gerlach D, Spies D, Matts JA, Sytnikova YA, Pagani M, Lau NC, Stark A. 2014. Quantitative genome-wide enhancer activity maps for five Drosophila species show functional enhancer conservation and turnover during cis-regulatory evolution. Nat Genet 46: 685-692.
-
(2014)
Nat Genet
, vol.46
, pp. 685-692
-
-
Arnold, C.D.1
Gerlach, D.2
Spies, D.3
Matts, J.A.4
Sytnikova, Y.A.5
Pagani, M.6
Lau, N.C.7
Stark, A.8
-
6
-
-
0019811465
-
Expression of a β-globin gene is enhanced by remote SV40 DNA sequences
-
Banerji J, Rusconi S, Schaffner W. 1981. Expression of a β-globin gene is enhanced by remote SV40 DNA sequences. Cell 27(2 Pt 1): 299-308.
-
(1981)
Cell
, vol.27
, Issue.2
, pp. 299-308
-
-
Banerji, J.1
Rusconi, S.2
Schaffner, W.3
-
7
-
-
0028813664
-
A direct physical association between ETS and AP-1 transcription factors in normal human T cells
-
Bassuk AG, Leiden JM. 1995. A direct physical association between ETS and AP-1 transcription factors in normal human T cells. Immunity 3: 223-237.
-
(1995)
Immunity
, vol.3
, pp. 223-237
-
-
Bassuk, A.G.1
Leiden, J.M.2
-
8
-
-
0035025888
-
A quantitative assay for HIV DNA integration in vivo
-
Butler SL, Hansen MS, Bushman FD. 2001. A quantitative assay for HIV DNA integration in vivo. Nat Med 7: 631-634.
-
(2001)
Nat Med
, vol.7
, pp. 631-634
-
-
Butler, S.L.1
Hansen, M.S.2
Bushman, F.D.3
-
9
-
-
84865790047
-
An integrated encyclopedia of DNA elements in the human genome
-
The ENCODE Project Consortium
-
The ENCODE Project Consortium. 2012. An integrated encyclopedia of DNA elements in the human genome. Nature 489: 57-74.
-
(2012)
Nature
, vol.489
, pp. 57-74
-
-
-
10
-
-
84857707318
-
ChromHMM: Automating chromatin-state discovery and characterization
-
Ernst J, Kellis M. 2012. ChromHMM: automating chromatin-state discovery and characterization. Nat Methods 9: 215-216.
-
(2012)
Nat Methods
, vol.9
, pp. 215-216
-
-
Ernst, J.1
Kellis, M.2
-
11
-
-
84903388630
-
Integrating diverse datasets improves developmental enhancer prediction
-
Erwin GD, Oksenberg N, Truty RM, Kostka D, Murphy KK, Ahituv N, Pollard KS, Capra JA. 2014. Integrating diverse datasets improves developmental enhancer prediction. PLoS Comput Biol 10: e1003677.
-
(2014)
PLoS Comput Biol
, vol.10
, pp. e1003677
-
-
Erwin, G.D.1
Oksenberg, N.2
Truty, R.M.3
Kostka, D.4
Murphy, K.K.5
Ahituv, N.6
Pollard, K.S.7
Capra, J.A.8
-
12
-
-
79953737587
-
Diverse roles and interactions of the SWI/SNF chromatin remodeling complex revealed using global approaches
-
Euskirchen GM, Auerbach RK, Davidov E, Gianoulis TA, Zhong G, Rozowsky J, Bhardwaj N, Gerstein MB, Snyder M. 2011. Diverse roles and interactions of the SWI/SNF chromatin remodeling complex revealed using global approaches. PLoS Genet 7: e1002008.
-
(2011)
PLoS Genet
, vol.7
, pp. e1002008
-
-
Euskirchen, G.M.1
Auerbach, R.K.2
Davidov, E.3
Gianoulis, T.A.4
Zhong, G.5
Rozowsky, J.6
Bhardwaj, N.7
Gerstein, M.B.8
Snyder, M.9
-
13
-
-
84897406127
-
A promoter-level mammalian expression atlas
-
FANTOM Consortium and the RIKEN PMI and CLST (DGT)
-
FANTOM Consortium and the RIKEN PMI and CLST (DGT), Forrest AR, Kawaji H, Rehli M, Baillie JK, de Hoon MJ, Haberle V, Lassmann T, Kulakovskiy IV, Lizio M, et al. 2014. A promoter-level mammalian expression atlas. Nature 507: 462-470.
-
(2014)
Nature
, vol.507
, pp. 462-470
-
-
Forrest, A.R.1
Kawaji, H.2
Rehli, M.3
Baillie, J.K.4
De Hoon, M.J.5
Haberle, V.6
Lassmann, T.7
Kulakovskiy, I.V.8
Lizio, M.9
-
14
-
-
84868325694
-
Cohesin regulates tissue-specific expression by stabilizing highly occupied cis-regulatory modules
-
Faure AJ, Schmidt D, Watt S, Schwalie PC, Wilson MD, Xu H, Ramsay RG, Odom DT, Flicek P. 2012. Cohesin regulates tissue-specific expression by stabilizing highly occupied cis-regulatory modules. Genome Res 22: 2163-2175.
-
(2012)
Genome Res
, vol.22
, pp. 2163-2175
-
-
Faure, A.J.1
Schmidt, D.2
Watt, S.3
Schwalie, P.C.4
Wilson, M.D.5
Xu, H.6
Ramsay, R.G.7
Odom, D.T.8
Flicek, P.9
-
15
-
-
48249141048
-
Viral complementation allows HIV-1 replication without integration
-
Gelderblom HC, Vatakis DN, Burke SA, Lawrie SD, Bristol GC, Levy DN. 2008. Viral complementation allows HIV-1 replication without integration. Retrovirology 5: 60.
-
(2008)
Retrovirology
, vol.5
, pp. 60
-
-
Gelderblom, H.C.1
Vatakis, D.N.2
Burke, S.A.3
Lawrie, S.D.4
Bristol, G.C.5
Levy, D.N.6
-
16
-
-
84905484602
-
Enhanced regulatory sequence prediction using gapped k-mer features
-
Ghandi M, Lee D, Mohammad-Noori M, Beer MA. 2014. Enhanced regulatory sequence prediction using gapped k-mer features. PLoS Comput Biol 10: e1003711.
-
(2014)
PLoS Comput Biol
, vol.10
, pp. e1003711
-
-
Ghandi, M.1
Lee, D.2
Mohammad-Noori, M.3
Beer, M.A.4
-
17
-
-
79959655657
-
DNACLUST: Accurate and efficient clustering of phylogenetic marker genes
-
Ghodsi M, Liu B, Pop M. 2011. DNACLUST: accurate and efficient clustering of phylogenetic marker genes. BMC Bioinformatics 12: 271.
-
(2011)
BMC Bioinformatics
, vol.12
, pp. 271
-
-
Ghodsi, M.1
Liu, B.2
Pop, M.3
-
18
-
-
0025878233
-
Cross-family dimerization of transcription factors Fos/Jun and ATF/CREB alters DNA binding specificity
-
Hai T, Curran T. 1991. Cross-family dimerization of transcription factors Fos/Jun and ATF/CREB alters DNA binding specificity. Proc Natl Acad Sci 88: 3720-3724.
-
(1991)
Proc Natl Acad Sci
, vol.88
, pp. 3720-3724
-
-
Hai, T.1
Curran, T.2
-
19
-
-
34247281521
-
Chromatin-dependent cooperativity between site-specific transcription factors in vivo
-
Hebbar PB, Archer TK. 2007. Chromatin-dependent cooperativity between site-specific transcription factors in vivo. J Biol Chem 282: 8284-8291.
-
(2007)
J Biol Chem
, vol.282
, pp. 8284-8291
-
-
Hebbar, P.B.1
Archer, T.K.2
-
20
-
-
41949083130
-
Altered histone H1 stoichiometry and an absence of nucleosome positioning on transfected DNA
-
Hebbar PB, Archer TK. 2008. Altered histone H1 stoichiometry and an absence of nucleosome positioning on transfected DNA. J Biol Chem 283: 4595-4601.
-
(2008)
J Biol Chem
, vol.283
, pp. 4595-4601
-
-
Hebbar, P.B.1
Archer, T.K.2
-
21
-
-
33847334699
-
Distinct and predictive chromatin signatures of transcriptional promoters and enhancers in the human genome
-
Heintzman ND, Stuart RK, Hon G, Fu Y, Ching CW, Hawkins RD, Barrera LO, Van Calcar S, Qu C, Ching KA, et al. 2007. Distinct and predictive chromatin signatures of transcriptional promoters and enhancers in the human genome. Nat Genet 39: 311-318.
-
(2007)
Nat Genet
, vol.39
, pp. 311-318
-
-
Heintzman, N.D.1
Stuart, R.K.2
Hon, G.3
Fu, Y.4
Ching, C.W.5
Hawkins, R.D.6
Barrera, L.O.7
Van Calcar, S.8
Qu, C.9
Ching, K.A.10
-
22
-
-
12344252237
-
AP-1 subunits: Quarrel and harmony among siblings
-
Hess J, Angel P, Schorpp-Kistner M. 2004. AP-1 subunits: quarrel and harmony among siblings. J Cell Sci 117(Pt 25): 5965-5973.
-
(2004)
J Cell Sci
, vol.117
, pp. 5965-5973
-
-
Hess, J.1
Angel, P.2
Schorpp-Kistner, M.3
-
23
-
-
0027242180
-
C-Jun is essential for normal mouse development and hepatogenesis
-
Hilberg F, Aguzzi A, Howells N, Wagner EF. 1993. c-Jun is essential for normal mouse development and hepatogenesis. Nature 365: 179-181.
-
(1993)
Nature
, vol.365
, pp. 179-181
-
-
Hilberg, F.1
Aguzzi, A.2
Howells, N.3
Wagner, E.F.4
-
24
-
-
84862785201
-
Unsupervised pattern discovery in human chromatin structure through genomic segmentation
-
Hoffman MM, Buske OJ, Wang J, Weng Z, Bilmes JA, Noble WS. 2012. Unsupervised pattern discovery in human chromatin structure through genomic segmentation. Nat Methods 9: 473-476.
-
(2012)
Nat Methods
, vol.9
, pp. 473-476
-
-
Hoffman, M.M.1
Buske, O.J.2
Wang, J.3
Weng, Z.4
Bilmes, J.A.5
Noble, W.S.6
-
25
-
-
0028217604
-
Micrococcal nuclease digestion of nuclei reveals extended nucleosome ladders having anomalous DNA lengths for chromatin assembled on non-replicating plasmids in transfected cells
-
Jeong S, Stein A. 1994. Micrococcal nuclease digestion of nuclei reveals extended nucleosome ladders having anomalous DNA lengths for chromatin assembled on non-replicating plasmids in transfected cells. Nucleic Acids Res 22: 370-375.
-
(1994)
Nucleic Acids Res
, vol.22
, pp. 370-375
-
-
Jeong, S.1
Stein, A.2
-
26
-
-
43449085794
-
UShuffle: A useful tool for shuffling biological sequences while preserving the k-let counts
-
Jiang M, Anderson J, Gillespie J, Mayne M. 2008. uShuffle: a useful tool for shuffling biological sequences while preserving the k-let counts. BMC Bioinformatics 9: 192.
-
(2008)
BMC Bioinformatics
, vol.9
, pp. 192
-
-
Jiang, M.1
Anderson, J.2
Gillespie, J.3
Mayne, M.4
-
27
-
-
84888440095
-
Sin3: Insight into its transcription regulatory functions
-
Kadamb R, Mittal S, Bansal N, Batra H, Saluja D. 2013. Sin3: insight into its transcription regulatory functions. Eur J Cell Biol 92: 237-246.
-
(2013)
Eur J Cell Biol 92
, pp. 237-246
-
-
Kadamb, R.1
Mittal, S.2
Bansal, N.3
Batra, H.4
Saluja, D.5
-
28
-
-
84872796335
-
Enhanced transgene expression from chromatinized plasmid DNA in mouse liver
-
Kamiya H, Miyamoto S, Goto H, Kanda GN, Kobayashi M, Matsuoka I, Harashima H. 2013. Enhanced transgene expression from chromatinized plasmid DNA in mouse liver. Int J Pharm 441: 146-150.
-
(2013)
Int J Pharm
, vol.441
, pp. 146-150
-
-
Kamiya, H.1
Miyamoto, S.2
Goto, H.3
Kanda, G.N.4
Kobayashi, M.5
Matsuoka, I.6
Harashima, H.7
-
29
-
-
73249129445
-
Epigenetic activation of unintegrated HIV-1 genomes by gut-associated short chain fatty acids and its implications for HIV infection
-
Kantor B, Ma H, Webster-Cyriaque J, Monahan PE, Kafri T. 2009. Epigenetic activation of unintegrated HIV-1 genomes by gut-associated short chain fatty acids and its implications for HIV infection. Proc Natl Acad Sci 106: 18786-18791.
-
(2009)
Proc Natl Acad Sci
, vol.106
, pp. 18786-18791
-
-
Kantor, B.1
Ma, H.2
Webster-Cyriaque, J.3
Monahan, P.E.4
Kafri, T.5
-
30
-
-
84877147962
-
Systematic dissection of regulatory motifs in 2000 predicted human enhancers using a massively parallel reporter assay
-
Kheradpour P, Ernst J, Melnikov A, Rogov P, Wang L, Zhang X, Alston J, Mikkelsen TS, Kellis M. 2013. Systematic dissection of regulatory motifs in 2000 predicted human enhancers using a massively parallel reporter assay. Genome Res 23: 800-811.
-
(2013)
Genome Res
, vol.23
, pp. 800-811
-
-
Kheradpour, P.1
Ernst, J.2
Melnikov, A.3
Rogov, P.4
Wang, L.5
Zhang, X.6
Alston, J.7
Mikkelsen, T.S.8
Kellis, M.9
-
31
-
-
77952706498
-
Using deep sequencing to characterize the biophysical mechanism of a transcriptional regulatory sequence
-
Kinney JB, Murugan A, Callan CG Jr, Cox EC. 2010. Using deep sequencing to characterize the biophysical mechanism of a transcriptional regulatory sequence. Proc Natl Acad Sci 107: 9158-9163.
-
(2010)
Proc Natl Acad Sci
, vol.107
, pp. 9158-9163
-
-
Kinney, J.B.1
Murugan, A.2
Callan, C.G.3
Cox, E.C.4
-
32
-
-
84895858942
-
A general framework for estimating the relative pathogenicity of human genetic variants
-
Kircher M, Witten DM, Jain P, O'Roak BJ, Cooper GM, Shendure J. 2014. A general framework for estimating the relative pathogenicity of human genetic variants. Nat Genet 46: 310-315.
-
(2014)
Nat Genet
, vol.46
, pp. 310-315
-
-
Kircher, M.1
Witten, D.M.2
Jain, P.3
O'Roak, B.J.4
Cooper, G.M.5
Shendure, J.6
-
33
-
-
33645395980
-
In vivo RNA interference demonstrates a role for Nramp1 in modifying susceptibility to type 1 diabetes
-
Kissler S, Stern P, Takahashi K, Hunter K, Peterson LB, Wicker LS. 2006. In vivo RNA interference demonstrates a role for Nramp1 in modifying susceptibility to type 1 diabetes. Nat Genet 38: 479-483.
-
(2006)
Nat Genet
, vol.38
, pp. 479-483
-
-
Kissler, S.1
Stern, P.2
Takahashi, K.3
Hunter, K.4
Peterson, L.B.5
Wicker, L.S.6
-
34
-
-
0025869479
-
Scaffold-attached regions from the human interferon β domain can be used to enhance the stable expression of genes under the control of various promoters
-
Klehr D, Maass K, Bode J. 1991. Scaffold-attached regions from the human interferon β domain can be used to enhance the stable expression of genes under the control of various promoters. Biochemistry 30: 1264-1270.
-
(1991)
Biochemistry
, vol.30
, pp. 1264-1270
-
-
Klehr, D.1
Maass, K.2
Bode, J.3
-
35
-
-
84963894167
-
Multiplex pairwise assembly of array-derived DNA oligonucleotides
-
Klein JC, Lajoie MJ, Schwartz JJ, Strauch EM, Nelson J, Baker D, Shendure J. 2016. Multiplex pairwise assembly of array-derived DNA oligonucleotides. Nucleic Acids Res 44: e43.
-
(2016)
Nucleic Acids Res
, vol.44
, pp. e43
-
-
Klein, J.C.1
Lajoie, M.J.2
Schwartz, J.J.3
Strauch, E.M.4
Nelson, J.5
Baker, D.6
Shendure, J.7
-
36
-
-
12444276606
-
Identification of anti-repressor elements that confer high and stable protein production in mammalian cells
-
Kwaks TH, Barnett P, HemrikaW, Siersma T, Sewalt RG, Satijn DP, Brons JF, van Blokland R, Kwakman P, Kruckeberg AL, et al. 2003. Identification of anti-repressor elements that confer high and stable protein production in mammalian cells. Nat Biotechnol 21: 553-558.
-
(2003)
Nat Biotechnol
, vol.21
, pp. 553-558
-
-
Kwaks, T.H.1
Barnett, P.2
Hemrika, W.3
Siersma, T.4
Sewalt, R.G.5
Satijn, D.P.6
Brons, J.F.7
Van Blokland, R.8
Kwakman, P.9
Kruckeberg, A.L.10
-
37
-
-
84869853147
-
Complex effects of nucleotide variants in a mammalian cis-regulatory element
-
Kwasnieski JC, Mogno I, Myers CA, Corbo JC, Cohen BA. 2012. Complex effects of nucleotide variants in a mammalian cis-regulatory element. Proc Natl Acad Sci 109: 19498-19503.
-
(2012)
Proc Natl Acad Sci
, vol.109
, pp. 19498-19503
-
-
Kwasnieski, J.C.1
Mogno, I.2
Myers, C.A.3
Corbo, J.C.4
Cohen, B.A.5
-
38
-
-
0030030041
-
Human immunodeficiency virus type 1 integrase mutants retain in vitro integrase activity yet fail to integrate viral DNA efficiently during infection
-
Leavitt AD, Robles G, Alesandro N, Varmus HE. 1996. Human immunodeficiency virus type 1 integrase mutants retain in vitro integrase activity yet fail to integrate viral DNA efficiently during infection. J Virol 70: 721-728.
-
(1996)
J Virol
, vol.70
, pp. 721-728
-
-
Leavitt, A.D.1
Robles, G.2
Alesandro, N.3
Varmus, H.E.4
-
39
-
-
84992435594
-
LS-GKM: A new gkm-SVM for large-scale datasets
-
Lee D. 2016. LS-GKM: a new gkm-SVM for large-scale datasets. Bioinformatics 32: 2196-2198.
-
(2016)
Bioinformatics
, vol.32
, pp. 2196-2198
-
-
Lee, D.1
-
40
-
-
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
-
41
-
-
40849085514
-
FoxA1 translates epigenetic signatures into enhancer-driven lineage-specific transcription
-
Lupien M, Eeckhoute J, Meyer CA, Wang Q, Zhang Y, Li W, Carroll JS, Liu XS, Brown M. 2008. FoxA1 translates epigenetic signatures into enhancer-driven lineage-specific transcription. Cell 132: 958-970.
-
(2008)
Cell
, vol.132
, pp. 958-970
-
-
Lupien, M.1
Eeckhoute, J.2
Meyer, C.A.3
Wang, Q.4
Zhang, Y.5
Li, W.6
Carroll, J.S.7
Liu, X.S.8
Brown, M.9
-
42
-
-
84863229330
-
Systematic dissection and optimization of inducible enhancers in human cells using a massively parallel reporter assay
-
Melnikov A, Murugan A, Zhang X, Tesileanu T, Wang L, Rogov P, Feizi S, Gnirke A, Callan CG Jr, Kinney JB, et al. 2012. Systematic dissection and optimization of inducible enhancers in human cells using a massively parallel reporter assay. Nat Biotechnol 30: 271-277.
-
(2012)
Nat Biotechnol
, vol.30
, pp. 271-277
-
-
Melnikov, A.1
Murugan, A.2
Zhang, X.3
Tesileanu, T.4
Wang, L.5
Rogov, P.6
Feizi, S.7
Gnirke, A.8
Callan, C.G.9
Kinney, J.B.10
-
43
-
-
0019769520
-
The SV40 72 base repair repeat has a striking effect on gene expression both in SV40 and other chimeric recombinants
-
Moreau P, Hen R, Wasylyk B, Everett R, Gaub MP, Chambon P. 1981. The SV40 72 base repair repeat has a striking effect on gene expression both in SV40 and other chimeric recombinants. Nucleic Acids Res 9: 6047-6068.
-
(1981)
Nucleic Acids Res
, vol.9
, pp. 6047-6068
-
-
Moreau, P.1
Hen, R.2
Wasylyk, B.3
Everett, R.4
Gaub, M.P.5
Chambon, P.6
-
44
-
-
84883541122
-
Quantitative analysis of the time-course of viral DNA forms during the HIV-1 life cycle
-
Munir S, Thierry S, Subra F, Deprez E, Delelis O. 2013. Quantitative analysis of the time-course of viral DNA forms during the HIV-1 life cycle. Retrovirology 10: 87.
-
(2013)
Retrovirology
, vol.10
, pp. 87
-
-
Munir, S.1
Thierry, S.2
Subra, F.3
Deprez, E.4
Delelis, O.5
-
45
-
-
84899670369
-
FIREWACh: High-throughput functional detection of transcriptional regulatory modules in mammalian cells
-
Murtha M, Tokcaer-Keskin Z, Tang Z, Strino F, Chen X, Wang Y, Xi X, Basilico C, Brown S, Bonneau R, et al. 2014. FIREWACh: high-throughput functional detection of transcriptional regulatory modules in mammalian cells. Nat Methods 11: 559-565.
-
(2014)
Nat Methods
, vol.11
, pp. 559-565
-
-
Murtha, M.1
Tokcaer-Keskin, Z.2
Tang, Z.3
Strino, F.4
Chen, X.5
Wang, Y.6
Xi, X.7
Basilico, C.8
Brown, S.9
Bonneau, R.10
-
46
-
-
84865840434
-
Predicting cell-type-specific gene expression from regions of open chromatin
-
Natarajan A, Yardimci GG, Sheffield NC, Crawford GE, Ohler U. 2012. Predicting cell-type-specific gene expression from regions of open chromatin. Genome Res 22: 1711-1722.
-
(2012)
Genome Res
, vol.22
, pp. 1711-1722
-
-
Natarajan, A.1
Yardimci, G.G.2
Sheffield, N.C.3
Crawford, G.E.4
Ohler, U.5
-
47
-
-
33744468295
-
Transient gene expression by nonintegrating lentiviral vectors
-
Nightingale SJ, Hollis RP, Pepper KA, Petersen D, Yu XJ, Yang C, Bahner I, Kohn DB. 2006. Transient gene expression by nonintegrating lentiviral vectors. Mol Ther 13: 1121-1132.
-
(2006)
Mol Ther
, vol.13
, pp. 1121-1132
-
-
Nightingale, S.J.1
Hollis, R.P.2
Pepper, K.A.3
Petersen, D.4
Yu, X.J.5
Yang, C.6
Bahner, I.7
Kohn, D.B.8
-
48
-
-
71849118573
-
Highresolution analysis of DNA regulatory elements by synthetic saturation mutagenesis
-
Patwardhan RP, Lee C, Litvin O, Young DL, Pe'er D, Shendure J. 2009. Highresolution analysis of DNA regulatory elements by synthetic saturation mutagenesis. Nat Biotechnol 27: 1173-1175.
-
(2009)
Nat Biotechnol
, vol.27
, pp. 1173-1175
-
-
Patwardhan, R.P.1
Lee, C.2
Litvin, O.3
Young, D.L.4
Pe'Er, D.5
Shendure, J.6
-
49
-
-
84863230316
-
Massively parallel functional dissection of mammalian enhancers in vivo
-
Patwardhan RP, Hiatt JB, Witten DM, Kim MJ, Smith RP, May D, Lee C, Andrie JM, Lee SI, Cooper GM, et al. 2012. Massively parallel functional dissection of mammalian enhancers in vivo. Nat Biotechnol 30: 265-270.
-
(2012)
Nat Biotechnol
, vol.30
, pp. 265-270
-
-
Patwardhan, R.P.1
Hiatt, J.B.2
Witten, D.M.3
Kim, M.J.4
Smith, R.P.5
May, D.6
Lee, C.7
Andrie, J.M.8
Lee, S.I.9
Cooper, G.M.10
-
50
-
-
79961024414
-
Recognition and suppression of transfected plasmids by protein ZNF511-PRAP1, a potential molecular barrier to transgene expression
-
Qiu GH, Leung CH, Yun T, Xie X, Laban M, Hooi SC. 2011. Recognition and suppression of transfected plasmids by protein ZNF511-PRAP1, a potential molecular barrier to transgene expression. Mol Ther 19: 1478-1486.
-
(2011)
Mol Ther
, vol.19
, pp. 1478-1486
-
-
Qiu, G.H.1
Leung, C.H.2
Yun, T.3
Xie, X.4
Laban, M.5
Hooi, S.C.6
-
51
-
-
77951770756
-
BEDTools: A flexible suite of utilities for comparing genomic features
-
Quinlan AR, Hall IM. 2010. BEDTools: a flexible suite of utilities for comparing genomic features. Bioinformatics 26: 841-842.
-
(2010)
Bioinformatics
, vol.26
, pp. 841-842
-
-
Quinlan, A.R.1
Hall, I.M.2
-
52
-
-
84923362619
-
Integrative analysis of 111 reference human epigenomes
-
Roadmap Epigenomics Consortium
-
Roadmap Epigenomics Consortium, Kundaje A, Meuleman W, Ernst J, Bilenky M, Yen A, Heravi-Moussavi A, Kheradpour P, Zhang Z, Wang J, et al. 2015. Integrative analysis of 111 reference human epigenomes. Nature 518: 317-330.
-
(2015)
Nature
, vol.518
, pp. 317-330
-
-
Kundaje, A.1
Meuleman, W.2
Ernst, J.3
Bilenky, M.4
Yen, A.5
Heravi-Moussavi, A.6
Kheradpour, P.7
Zhang, Z.8
Wang, J.9
-
53
-
-
84956624079
-
Promoter-distal RNA polymerase II binding discriminates active from inactive CCAAT/enhancer-binding protein β binding sites
-
Savic D, Roberts BS, Carleton JB, Partridge EC, White MA, Cohen BA, Cooper GM, Gertz J, Myers RM. 2015. Promoter-distal RNA polymerase II binding discriminates active from inactive CCAAT/enhancer-binding protein β binding sites. Genome Res 25: 1791-1800.
-
(2015)
Genome Res
, vol.25
, pp. 1791-1800
-
-
Savic, D.1
Roberts, B.S.2
Carleton, J.B.3
Partridge, E.C.4
White, M.A.5
Cohen, B.A.6
Cooper, G.M.7
Gertz, J.8
Myers, R.M.9
-
54
-
-
77953062527
-
Five-vertebrate ChIP-seq reveals the evolutionary dynamics of transcription factor binding
-
Schmidt D, Wilson MD, Ballester B, Schwalie PC, Brown GD, Marshall A, Kutter C, Watt S, Martinez-Jimenez CP, Mackay S, et al. 2010. Five-vertebrate ChIP-seq reveals the evolutionary dynamics of transcription factor binding. Science 328: 1036-1040.
-
(2010)
Science
, vol.328
, pp. 1036-1040
-
-
Schmidt, D.1
Wilson, M.D.2
Ballester, B.3
Schwalie, P.C.4
Brown, G.D.5
Marshall, A.6
Kutter, C.7
Watt, S.8
Martinez-Jimenez, C.P.9
Mackay, S.10
-
55
-
-
84907527856
-
Probing the effect of promoters on noise in gene expression using thousands of designed sequences
-
Sharon E, van Dijk D, Kalma Y, Keren L, Manor O, Yakhini Z, Segal E. 2014. Probing the effect of promoters on noise in gene expression using thousands of designed sequences. Genome Res 24: 1698-1706.
-
(2014)
Genome Res
, vol.24
, pp. 1698-1706
-
-
Sharon, E.1
Van Dijk, D.2
Kalma, Y.3
Keren, L.4
Manor, O.5
Yakhini, Z.6
Segal, E.7
-
56
-
-
84956945024
-
Massively parallel cis-regulatory analysis in the mammalian central nervous system
-
Shen SQ, Myers CA, Hughes AE, Byrne LC, Flannery JG, Corbo JC. 2016. Massively parallel cis-regulatory analysis in the mammalian central nervous system. Genome Res 26: 238-255.
-
(2016)
Genome Res
, vol.26
, pp. 238-255
-
-
Shen, S.Q.1
Myers, C.A.2
Hughes, A.E.3
Byrne, L.C.4
Flannery, J.G.5
Corbo, J.C.6
-
57
-
-
84899450857
-
Transcriptional enhancers: From properties to genome-wide predictions
-
Shlyueva D, Stampfel G, Stark A. 2014. Transcriptional enhancers: from properties to genome-wide predictions. Nat Rev Genet 15: 272-286.
-
(2014)
Nat Rev Genet
, vol.15
, pp. 272-286
-
-
Shlyueva, D.1
Stampfel, G.2
Stark, A.3
-
58
-
-
84976872192
-
ENCODE data at the ENCODE portal
-
Sloan CA, Chan ET, Davidson JM, Malladi VS, Strattan JS, Hitz BC, Gabdank I, Narayanan AK, Ho M, Lee BT, et al. 2016. ENCODE data at the ENCODE portal. Nucleic Acids Res 44: D726-D732.
-
(2016)
Nucleic Acids Res
, vol.44
, pp. D726-D732
-
-
Sloan, C.A.1
Chan, E.T.2
Davidson, J.M.3
Malladi, V.S.4
Strattan, J.S.5
Hitz, B.C.6
Gabdank, I.7
Narayanan, A.K.8
Ho, M.9
Lee, B.T.10
-
59
-
-
0030836229
-
Transcriptional regulation of mammalian genes in vivo. A tale of two templates
-
Smith CL, Hager GL. 1997. Transcriptional regulation of mammalian genes in vivo. A tale of two templates. J Biol Chem 272: 27493-27496.
-
(1997)
J Biol Chem
, vol.272
, pp. 27493-27496
-
-
Smith, C.L.1
Hager, G.L.2
-
60
-
-
84883457107
-
Massively parallel decoding of mammalian regulatory sequences supports a flexible organizational model
-
Smith RP, Taher L, Patwardhan RP, Kim MJ, Inoue F, Shendure J, Ovcharenko I, Ahituv N. 2013. Massively parallel decoding of mammalian regulatory sequences supports a flexible organizational model. Nat Genet 45: 1021-1028.
-
(2013)
Nat Genet
, vol.45
, pp. 1021-1028
-
-
Smith, R.P.1
Taher, L.2
Patwardhan, R.P.3
Kim, M.J.4
Inoue, F.5
Shendure, J.6
Ovcharenko, I.7
Ahituv, N.8
-
62
-
-
84968799957
-
Opposite transcriptional regulation of integrated vs unintegrated HIV genomes by the NF-κB pathway
-
Thierry S, Thierry E, Subra F, Deprez E, Leh H, Bury-Moné S, Delelis O. 2016. Opposite transcriptional regulation of integrated vs unintegrated HIV genomes by the NF-κB pathway. Sci Rep 6: 25678.
-
(2016)
Sci Rep
, vol.6
, pp. 25678
-
-
Thierry, S.1
Thierry, E.2
Subra, F.3
Deprez, E.4
Leh, H.5
Bury-Moné, S.6
Delelis, O.7
-
63
-
-
79952073585
-
The CCAAT/enhancer (C/EBP) family of basic-leucine zipper (bZIP) transcription factors is a multifaceted highly-regulated system for gene regulation
-
Tsukada J, Yoshida Y, Kominato Y, Auron PE. 2011. The CCAAT/enhancer (C/EBP) family of basic-leucine zipper (bZIP) transcription factors is a multifaceted highly-regulated system for gene regulation. Cytokine 54: 6-19.
-
(2011)
Cytokine
, vol.54
, pp. 6-19
-
-
Tsukada, J.1
Yoshida, Y.2
Kominato, Y.3
Auron, P.E.4
-
64
-
-
60149091656
-
ChIP-seq accurately predicts tissuespecific activity of enhancers
-
Visel A, Blow MJ, Li Z, Zhang T, Akiyama JA, Holt A, Plajzer-Frick I, Shoukry M, Wright C, Chen F, et al. 2009. ChIP-seq accurately predicts tissuespecific activity of enhancers. Nature 457: 854-858.
-
(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
-
65
-
-
84938876935
-
Massively parallel quantification of the regulatory effects of noncoding genetic variation in a human cohort
-
Vockley CM, Guo C, Majoros WH, Nodzenski M, Scholtens DM, Hayes MG, Lowe WL Jr, Reddy TE. 2015. Massively parallel quantification of the regulatory effects of noncoding genetic variation in a human cohort. Genome Res 25: 1206-1214.
-
(2015)
Genome Res
, vol.25
, pp. 1206-1214
-
-
Vockley, C.M.1
Guo, C.2
Majoros, W.H.3
Nodzenski, M.4
Scholtens, D.M.5
Hayes, M.G.6
Lowe, W.L.7
Reddy, T.E.8
-
66
-
-
80355136115
-
Lentivirus production
-
Wang X, McManus M. 2009. Lentivirus production. J Vis Exp 32: 1499.
-
(2009)
J Vis Exp
, vol.32
, pp. 1499
-
-
Wang, X.1
McManus, M.2
-
67
-
-
0038241793
-
HNF4: A central regulator of hepatocyte differentiation and function
-
Watt AJ, Garrison WD, Duncan SA. 2003. HNF4: a central regulator of hepatocyte differentiation and function. Hepatology 37: 1249-1253.
-
(2003)
Hepatology
, vol.37
, pp. 1249-1253
-
-
Watt, A.J.1
Garrison, W.D.2
Duncan, S.A.3
-
68
-
-
84939265529
-
Understanding how cis-regulatory function is encoded in DNA sequence using massively parallel reporter assays and designed sequences
-
White MA. 2015. Understanding how cis-regulatory function is encoded in DNA sequence using massively parallel reporter assays and designed sequences. Genomics 106: 165-170.
-
(2015)
Genomics
, vol.106
, pp. 165-170
-
-
White, M.A.1
-
69
-
-
84939123947
-
The ensembl regulatory build
-
Zerbino DR, Wilder SP, Johnson N, Juettemann T, Flicek PR. 2015. The Ensembl Regulatory Build. Genome Biol 16: 56.
-
(2015)
Genome Biol
, vol.16
, pp. 56
-
-
Zerbino, D.R.1
Wilder, S.P.2
Johnson, N.3
Juettemann, T.4
Flicek, P.R.5
|