-
1
-
-
77958471357
-
Differential expression analysis for sequence count data
-
Anders S, Huber W. 2010. Differential expression analysis for sequence count data. Genome Biology 11:R106. doi: 10.1186/gb-2010-11-10-r106.
-
(2010)
Genome Biology
, vol.11
-
-
Anders, S.1
Huber, W.2
-
2
-
-
78149417890
-
Analysis of thyroid response element activity during retinal development
-
Billings NA, Emerson MM, Cepko CL. 2010. Analysis of thyroid response element activity during retinal development. PLoS ONE 5:e13739. doi: 10.1371/journal.pone.0013739.
-
(2010)
Plos ONE
, pp. 5
-
-
Billings, N.A.1
Emerson, M.M.2
Cepko, C.L.3
-
3
-
-
83055178312
-
Next-generation sequencing facilitates quantitative analysis of wild-type and Nrl(-/-) retinal transcriptomes
-
Brooks MJ, Rajasimha HK, Roger JE, Swaroop A. 2011. Next-generation sequencing facilitates quantitative analysis of wild-type and Nrl(-/-) retinal transcriptomes. Molecular Vision 17:3034–3054.
-
(2011)
Molecular Vision
, vol.17
, pp. 3034-3054
-
-
Brooks, M.J.1
Rajasimha, H.K.2
Roger, J.E.3
Swaroop, A.4
-
4
-
-
84888877924
-
Transposition of native chromatin for fast and sensitive epigenomic profiling of open chromatin, DNA-binding proteins and nucleosome position
-
Buenrostro JD, Giresi PG, Zaba LC, Chang HY, Greenleaf WJ. 2013. Transposition of native chromatin for fast and sensitive epigenomic profiling of open chromatin, DNA-binding proteins and nucleosome position. Nature Methods 10:1213–1218. doi: 10.1038/nmeth.2688.
-
(2013)
Nature Methods
, vol.10
, pp. 1213-1218
-
-
Buenrostro, J.D.1
Giresi, P.G.2
Zaba, L.C.3
Chang, H.Y.4
Greenleaf, W.J.5
-
6
-
-
0018611506
-
Rods and cones in the mouse retina. I. Structural analysis using light and electron microscopy
-
Carter-Dawson LD, Lavail MM. 1979. Rods and cones in the mouse retina. I. Structural analysis using light and electron microscopy. The Journal of Comparative Neurology 188:245–262. doi: 10.1002/cne.901880204.
-
(1979)
The Journal of Comparative Neurology
, vol.188
, pp. 245-262
-
-
Carter-Dawson, L.D.1
Lavail, M.M.2
-
7
-
-
12144269981
-
The rod photoreceptor-specific nuclear receptor Nr2e3 represses transcription of multiple cone-specific genes
-
Chen J, Rattner A, Nathans J. 2005. The rod photoreceptor-specific nuclear receptor Nr2e3 represses transcription of multiple cone-specific genes. Journal of Neuroscience 25:118–129. doi: 10.1523/JNEUROSCI.3571-04.2005.
-
(2005)
Journal of Neuroscience
, vol.25
, pp. 118-129
-
-
Chen, J.1
Rattner, A.2
Nathans, J.3
-
8
-
-
33144472133
-
A hybrid photoreceptor expressing both rod and cone genes in a mouse model of enhanced S-cone syndrome
-
Corbo JC, Cepko CL. 2005. A hybrid photoreceptor expressing both rod and cone genes in a mouse model of enhanced S-cone syndrome. PLoS Genetics 1:e11. doi: 10.1371/journal.pgen.0010011.
-
(2005)
Plos Genetics
, vol.1
-
-
Corbo, J.C.1
Cepko, C.L.2
-
9
-
-
77956394013
-
CRX ChIP-seq reveals the cis-regulatory architecture of mouse photoreceptors
-
Corbo JC, Lawrence KA, Karlstetter M, Myers CA, Abdelaziz M, Dirkes W, Weigelt K, Seifert M, Benes V, Fritsche LG, Weber BHF, Langmann T. 2010. CRX ChIP-seq reveals the cis-regulatory architecture of mouse photoreceptors. Genome Research 20:1512–1525. doi: 10.1101/gr.109405.110.
-
(2010)
Genome Research
, vol.20
, pp. 1512-1525
-
-
Corbo, J.C.1
Lawrence, K.A.2
Karlstetter, M.3
Myers, C.A.4
Abdelaziz, M.5
Dirkes, W.6
Weigelt, K.7
Seifert, M.8
Benes, V.9
Fritsche, L.G.10
Weber, B.11
Langmann, T.12
-
10
-
-
84880397289
-
Otx2 and Onecut1 promote the fates of cone photoreceptors and horizontal cells and repress rod photoreceptors
-
Emerson MM, Surzenko N, Goetz JJ, Trimarchi J, Cepko CL. 2013. Otx2 and Onecut1 promote the fates of cone photoreceptors and horizontal cells and repress rod photoreceptors. Developmental Cell 26:59–72. doi: 10.1016/j.devcel.2013.06.005.
-
(2013)
Developmental Cell
, vol.26
, pp. 59-72
-
-
Emerson, M.M.1
Surzenko, N.2
Goetz, J.J.3
Trimarchi, J.4
Cepko, C.L.5
-
11
-
-
84899843749
-
A Bayesian hierarchical model to detect differentially methylated loci from single nucleotide resolution sequencing data
-
Feng H, Conneely KN, Wu H. 2014. A Bayesian hierarchical model to detect differentially methylated loci from single nucleotide resolution sequencing data. Nucleic Acids Research 42:e69. doi: 10.1093/nar/gku154.
-
(2014)
Nucleic Acids Research
, vol.42
-
-
Feng, H.1
Conneely, K.N.2
Wu, H.3
-
12
-
-
0032900958
-
Variation of clinical expression in patients with Stargardt dystrophy and sequence variations in the ABCR gene
-
Fishman GA, Stone EM, Grover S, Derlacki DJ, Haines HL, Hockey RR. 1999. Variation of clinical expression in patients with Stargardt dystrophy and sequence variations in the ABCR gene. Archives of Ophthalmology 117: 504–510. doi: 10.1001/archopht.117.4.504.
-
(1999)
Archives of Ophthalmology
, vol.117
, pp. 504-510
-
-
Fishman, G.A.1
Stone, E.M.2
Grover, S.3
Derlacki, D.J.4
Haines, H.L.5
Hockey, R.R.6
-
13
-
-
0030725687
-
Crx, a novel otx-like homeobox gene, shows photoreceptor-specific expression and regulates photoreceptor differentiation
-
Furukawa T, Morrow EM, Cepko CL. 1997. Crx, a novel otx-like homeobox gene, shows photoreceptor-specific expression and regulates photoreceptor differentiation. Cell 91:531–541. doi: 10.1016/S0092-8674(00)80439-0.
-
(1997)
Cell
, vol.91
, pp. 531-541
-
-
Furukawa, T.1
Morrow, E.M.2
Cepko, C.L.3
-
14
-
-
84866303839
-
A high- throughput chromatin immunoprecipitation approach reveals principles of dynamic gene regulation in mammals
-
Garber M, Yosef N, Goren A, Raychowdhury R, Thielke A, Guttman M, Robinson J, Minie B, Chevrier N, Itzhaki Z, Blecher-Gonen R, Bornstein C, Amann-Zalcenstein D, Weiner A, Friedrich D, Meldrim J, Ram O, Cheng C, Gnirke A, Fisher S, Friedman N, Wong B, Bernstein BE, Nusbaum C, Hacohen N, Regev A, Amit I. 2012. A high- throughput chromatin immunoprecipitation approach reveals principles of dynamic gene regulation in mammals. Molecular Cell 47:810–822. doi: 10.1016/j.molcel.2012.07.030.
-
(2012)
Molecular Cell
, vol.47
, pp. 810-822
-
-
Garber, M.1
Yosef, N.2
Goren, A.3
Raychowdhury, R.4
Thielke, A.5
Guttman, M.6
Robinson, J.7
Minie, B.8
Chevrier, N.9
Itzhaki, Z.10
Blecher-Gonen, R.11
Bornstein, C.12
Amann-Zalcenstein, D.13
Weiner, A.14
Friedrich, D.15
Meldrim, J.16
Ram, O.17
Cheng, C.18
Gnirke, A.19
Fisher, S.20
Friedman, N.21
Wong, B.22
Bernstein, B.E.23
Nusbaum, C.24
Hacohen, N.25
Regev, A.26
Amit, I.27
more..
-
16
-
-
84883433950
-
Photoreceptor precursors derived from three-dimensional embryonic stem cell cultures integrate and mature within adult degenerate retina
-
Gonzalez-Cordero A, West EL, Pearson RA, Duran Y, Carvalho LS, Chu CJ, Naeem A, Blackford SJI, Georgiadis A, Lakowski J, Hubank M, Smith AJ, Bainbridge JWB, Sowden JC, Ali RR. 2013. Photoreceptor precursors derived from three-dimensional embryonic stem cell cultures integrate and mature within adult degenerate retina. Nature Biotechnology 31:741–747. doi: 10.1038/nbt.2643.
-
(2013)
Nature Biotechnology
, vol.31
, pp. 741-747
-
-
Gonzalez-Cordero, A.1
West, E.L.2
Pearson, R.A.3
Duran, Y.4
Carvalho, L.S.5
Chu, C.J.6
Naeem, A.7
Blackford, S.8
Georgiadis, A.9
Lakowski, J.10
Hubank, M.11
Smith, A.J.12
Bainbridge, J.13
Sowden, J.C.14
Ali, R.R.15
-
17
-
-
84868318661
-
Integration of ChIP-seq and machine learning reveals enhancers and a predictive regulatory sequence vocabulary in melanocytes
-
Gorkin DU, Lee D, Reed X, Fletez-Brant C, Bessling SL, Loftus SK, Beer MA, Pavan WJ, McCallion AS. 2012. Integration of ChIP-seq and machine learning reveals enhancers and a predictive regulatory sequence vocabulary in melanocytes. Genome Research 22:2290–2301. doi: 10.1101/gr.139360.112.
-
(2012)
Genome Research
, vol.22
, pp. 2290-2301
-
-
Gorkin, D.U.1
Lee, D.2
Reed, X.3
Fletez-Brant, C.4
Bessling, S.L.5
Loftus, S.K.6
Beer, M.A.7
Pavan, W.J.8
McCallion, A.S.9
-
18
-
-
84866086842
-
High resolution genome wide binding event finding and motif discovery reveals transcription factor spatial binding constraints
-
Guo Y, Mahony S, Gifford DK. 2012. High resolution genome wide binding event finding and motif discovery reveals transcription factor spatial binding constraints. PLoS Computational Biology 8:e1002638. doi: 10.1371/journal.pcbi.1002638.
-
(2012)
Plos Computational Biology
, vol.8
-
-
Guo, Y.1
Mahony, S.2
Gifford, D.K.3
-
20
-
-
0033975061
-
Mutation of a nuclear receptor gene, NR2E3, causes enhanced S cone syndrome, a disorder of retinal cell fate
-
Haider NB, Jacobson SG, Cideciyan AV, Swiderski R, Streb LM, Searby C, Beck G, Hockey R, Hanna DB, Gorman S, Duhl D, Carmi R, Bennett J, Weleber RG, Fishman GA, Wright AF, Stone EM, Sheffield VC. 2000. Mutation of a nuclear receptor gene, NR2E3, causes enhanced S cone syndrome, a disorder of retinal cell fate. Nature Genetics 24:127–131. doi: 10.1038/72777.
-
(2000)
Nature Genetics
, vol.24
, pp. 127-131
-
-
Haider, N.B.1
Jacobson, S.G.2
Cideciyan, A.V.3
Swiderski, R.4
Streb, L.M.5
Searby, C.6
Beck, G.7
Hockey, R.8
Hanna, D.B.9
Gorman, S.10
Duhl, D.11
Carmi, R.12
Bennett, J.13
Weleber, R.G.14
Fishman, G.A.15
Wright, A.F.16
Stone, E.M.17
Sheffield, V.C.18
-
21
-
-
0035421442
-
Excess cone cell proliferation due to lack of a functional NR2E3 causes retinal dysplasia and degeneration in rd7/rd7 mice
-
Haider NB, Naggert JK, Nishina PM. 2001. Excess cone cell proliferation due to lack of a functional NR2E3 causes retinal dysplasia and degeneration in rd7/rd7 mice. Human Molecular Genetics 10:1619–1626. doi: 10.1093/hmg/10.16.1619.
-
(2001)
Human Molecular Genetics
, vol.10
, pp. 1619-1626
-
-
Haider, N.B.1
Naggert, J.K.2
Nishina, P.M.3
-
22
-
-
84860572048
-
Transcriptional regulation of rod photoreceptor homeostasis revealed by in vivo NRL targetome analysis
-
Hao H, Kim DS, Klocke B, Johnson KR, Cui K, Gotoh N, Zang C, Gregorski J, Gieser L, Peng W, Fann Y, Seifert M, Zhao K, Swaroop A. 2012. Transcriptional regulation of rod photoreceptor homeostasis revealed by in vivo NRL targetome analysis. PLoS Genetics 8:e1002649. doi: 10.1371/journal.pgen.1002649.
-
(2012)
Plos Genetics
, vol.8
-
-
Hao, H.1
Kim, D.S.2
Klocke, B.3
Johnson, K.R.4
Cui, K.5
Gotoh, N.6
Zang, C.7
Gregorski, J.8
Gieser, L.9
Peng, W.10
Fann, Y.11
Seifert, M.12
Zhao, K.13
Swaroop, A.14
-
23
-
-
84894613651
-
Refined DNase-seq protocol and data analysis reveals intrinsic bias in transcription factor footprint identification
-
He HH, Meyer CA, Hu Sheng’en Shawn, Chen M-W, Zang C, Liu Y, Rao PK, Fei T, Xu H, Long H, Liu XS, Brown M. 2014. Refined DNase-seq protocol and data analysis reveals intrinsic bias in transcription factor footprint identification. Nature Methods 11:73–78. doi: 10.1038/nmeth.2762.
-
(2014)
Nature Methods
, vol.11
, pp. 73-78
-
-
He, H.H.1
Meyer, C.A.2
Sheng’En Shawn, H.3
Chen, M.-W.4
Zang, C.5
Liu, Y.6
Rao, P.K.7
Fei, T.8
Xu, H.9
Long, H.10
Liu, X.S.11
Brown, M.12
-
24
-
-
84885021247
-
Epigenetic memory at embryonic enhancers identified in DNA methylation maps from adult mouse tissues
-
Hon GC, Rajagopal N, Shen Y, McCleary DF, Yue F, Dang MD, Ren B. 2013. Epigenetic memory at embryonic enhancers identified in DNA methylation maps from adult mouse tissues. Nature Genetics 45:1198–1206. doi: 10.1038/ng.2746.
-
(2013)
Nature Genetics
, vol.45
, pp. 1198-1206
-
-
Hon, G.C.1
Rajagopal, N.2
Shen, Y.3
McCleary, D.F.4
Yue, F.5
Dang, M.D.6
Ren, B.7
-
25
-
-
39449091111
-
The cis-regulatory logic of the mammalian photoreceptor transcriptional network
-
Hsiau TH-C, Diaconu C, Myers CA, Lee J, Cepko CL, Corbo JC. 2007. The cis-regulatory logic of the mammalian photoreceptor transcriptional network. PLoS ONE 2:e643. doi: 10.1371/journal.pone.0000643.
-
(2007)
Plos ONE
, vol.2
-
-
Hsiau, T.-C.1
Diaconu, C.2
Myers, C.A.3
Lee, J.4
Cepko, C.L.5
Corbo, J.C.6
-
27
-
-
84949033800
-
Identification of predictive cis-regulatory elements using a discriminative objective function and a dynamic search space
-
Karnik R, Beer MA. 2015. Identification of predictive cis-regulatory elements using a discriminative objective function and a dynamic search space. PLoS ONE 10:e0140557. doi: 10.1371/journal.pone.0140557.
-
(2015)
Plos ONE
, vol.10
-
-
Karnik, R.1
Beer, M.A.2
-
28
-
-
84855837416
-
Rod and cone visual pigments and phototransduction through pharmacological, genetic, and physiological approaches
-
Kefalov VJ. 2012. Rod and cone visual pigments and phototransduction through pharmacological, genetic, and physiological approaches. Journal of Biological Chemistry 287:1635–1641. doi: 10.1074/jbc.R111.303008.
-
(2012)
Journal of Biological Chemistry
, vol.287
, pp. 1635-1641
-
-
Kefalov, V.J.1
-
29
-
-
77956216933
-
In vivo chromatin organization of mouse rod photoreceptors correlates with histone modifications
-
Kizilyaprak C, Spehner D, Devys D, Schultz P. 2010. In vivo chromatin organization of mouse rod photoreceptors correlates with histone modifications. PLoS ONE 5:e11039. doi: 10.1371/journal.pone.0011039.
-
(2010)
Plos ONE
, vol.5
-
-
Kizilyaprak, C.1
Spehner, D.2
Devys, D.3
Schultz, P.4
-
30
-
-
58049200677
-
Transplantation of human embryonic stem cell-derived photoreceptors restores some visual function in Crx-deficient mice
-
Lamba DA, Gust J, Reh TA. 2009. Transplantation of human embryonic stem cell-derived photoreceptors restores some visual function in Crx-deficient mice. Cell Stem Cell 4:73–79. doi: 10.1016/j.stem.2008.10.015.
-
(2009)
Cell Stem Cell
, vol.4
, pp. 73-79
-
-
Lamba, D.A.1
Gust, J.2
Reh, T.A.3
-
31
-
-
62349130698
-
Ultrafast and memory-efficient alignment of short DNA sequences to the human genome
-
Langmead B, Trapnell C, Pop M, Salzberg SL. 2009. Ultrafast and memory-efficient alignment of short DNA sequences to the human genome. Genome Biology 10:R25. doi: 10.1186/gb-2009-10-3-r25.
-
(2009)
Genome Biology
, vol.10
-
-
Langmead, B.1
Trapnell, C.2
Pop, M.3
Salzberg, S.L.4
-
32
-
-
84859210032
-
Fast gapped-read alignment with Bowtie 2
-
Langmead B, Salzberg SL. 2012. Fast gapped-read alignment with Bowtie 2. Nature Methods 9:357–359. doi: 10.1038/nmeth.1923.
-
(2012)
Nature Methods
, vol.9
, pp. 357-359
-
-
Langmead, B.1
Salzberg, S.L.2
-
33
-
-
23844499180
-
Targeted expression of Cre recombinase to cone photoreceptors in transgenic mice
-
Le YZ, Ash JD, Al-Ubaidi MR, Chen Y, Ma JX, Anderson RE. 2004. Targeted expression of Cre recombinase to cone photoreceptors in transgenic mice. Molecular Vision 10:1011–1018.
-
(2004)
Molecular Vision
, vol.10
, pp. 1011-1018
-
-
Le, Y.Z.1
Ash, J.D.2
Al-Ubaidi, M.R.3
Chen, Y.4
Ma, J.X.5
Erson, R.E.6
-
34
-
-
33645831156
-
Mouse opsin promoter-directed Cre recombinase expression in transgenic mice
-
Le YZ, Zheng L, Zheng W, Ash JD, Agbaga MP, Zhu M, Anderson RE. 2006. Mouse opsin promoter-directed Cre recombinase expression in transgenic mice. Molecular Vision 12:389–398.
-
(2006)
Molecular Vision
, vol.12
, pp. 389-398
-
-
Le, Y.Z.1
Zheng, L.2
Zheng, W.3
Ash, J.D.4
Agbaga, M.P.5
Zhu, M.6
Erson, R.E.7
-
35
-
-
84938276507
-
A method to predict the impact of regulatory variants from DNA sequence
-
Lee D, Gorkin DU, Baker M, Strober BJ, Asoni AL, McCallion AS, Beer MA. 2015. A method to predict the impact of regulatory variants from DNA sequence. Nature Genetics 47:955–961. doi: 10.1038/ng.3331.
-
(2015)
Nature Genetics
, vol.47
, pp. 955-961
-
-
Lee, D.1
Gorkin, D.U.2
Baker, M.3
Strober, B.J.4
Asoni, A.L.5
McCallion, A.S.6
Beer, M.A.7
-
36
-
-
84876263777
-
EBSeq: An empirical Bayes hierarchical model for inference in RNA-seq experiments
-
Leng N, Dawson JA, Thomson JA, Ruotti V, Rissman AI, Smits BMG, Haag JD, Gould MN, Stewart RM, Kendziorski C. 2013. EBSeq: an empirical Bayes hierarchical model for inference in RNA-seq experiments. Bioinformatics 29:1035–1043. doi: 10.1093/bioinformatics/btt087.
-
(2013)
Bioinformatics
, vol.29
, pp. 1035-1043
-
-
Leng, N.1
Dawson, J.A.2
Thomson, J.A.3
Ruotti, V.4
Rissman, A.I.5
Smits, B.6
Haag, J.D.7
Gould, M.N.8
Stewart, R.M.9
Kendziorski, C.10
-
37
-
-
79961123152
-
RSEM: Accurate transcript quantification from RNA-seq data with or without a reference genome
-
Li B, Dewey CN. 2011. RSEM: accurate transcript quantification from RNA-seq data with or without a reference genome. BMC Bioinformatics 12:323. doi: 10.1186/1471-2105-12-323.
-
(2011)
BMC Bioinformatics
, vol.12
, pp. 323
-
-
Li, B.1
Dewey, C.N.2
-
38
-
-
42749087226
-
Highly integrated single-base resolution maps of the epigenome in Arabidopsis
-
Lister R, O’Malley RC, Tonti-Filippini J, Gregory BD, Berry CC, Millar AH, Ecker JR. 2008. Highly integrated single-base resolution maps of the epigenome in Arabidopsis. Cell 133:523–536. doi: 10.1016/j.cell.2008.03.
-
(2008)
Cell
, vol.133
, pp. 523-536
-
-
Lister, R.1
O’Malley, R.C.2
Tonti-Filippini, J.3
Gregory, B.D.4
Berry, C.C.5
Millar, A.H.6
Ecker, J.R.7
-
39
-
-
70450217879
-
Human DNA methylomes at base resolution show widespread epigenomic differences
-
Lister R, Pelizzola M, Dowen RH, Hawkins RD, Hon G, Tonti-Filippini J, Nery JR, Lee L, Ye Z, Ngo Q-M, Edsall L, Antosiewicz-Bourget J, Stewart R, Ruotti V, Millar AH, Thomson JA, Ren B, Ecker JR. 2009. Human DNA methylomes at base resolution show widespread epigenomic differences. Nature 462:315–322. doi: 10.1038/nature08514.
-
(2009)
Nature
, vol.462
, pp. 315-322
-
-
Lister, R.1
Pelizzola, M.2
Dowen, R.H.3
Hawkins, R.D.4
Hon, G.5
Tonti-Filippini, J.6
Nery, J.R.7
Lee, L.8
Ye, Z.9
Ngo, Q.-M.10
Edsall, L.11
Antosiewicz-Bourget, J.12
Stewart, R.13
Ruotti, V.14
Millar, A.H.15
Thomson, J.A.16
Ren, B.17
Ecker, J.R.18
-
40
-
-
84879663784
-
Global epigenomic reconfiguration during mammalian brain development
-
Lister R, Mukamel EA, Nery JR, Urich M, Puddifoot CA, Johnson ND, Lucero J, Huang Y, Dwork AJ, Schultz MD, Yu M, Tonti-Filippini J, Heyn H, Hu S, Wu JC, Rao A, Esteller M, He C, Haghighi FG, Sejnowski TJ, Behrens MM, Ecker JR. 2013. Global epigenomic reconfiguration during mammalian brain development. Science 341: 1237905. doi: 10.1126/science.1237905.
-
(2013)
Science
, vol.341
-
-
Lister, R.1
Mukamel, E.A.2
Nery, J.R.3
Urich, M.4
Puddifoot, C.A.5
Johnson, N.D.6
Lucero, J.7
Huang, Y.8
Dwork, A.J.9
Schultz, M.D.10
Yu, M.11
Tonti-Filippini, J.12
Heyn, H.13
Hu, S.14
Wu, J.C.15
Rao, A.16
Esteller, M.17
He, C.18
Haghighi, F.G.19
Sejnowski, T.J.20
Behrens, M.M.21
Ecker, J.R.22
more..
-
41
-
-
0347089037
-
Electroporation and RNA interference in the rodent retina in vivo and in vitro
-
Matsuda T, Cepko CL. 2004. Electroporation and RNA interference in the rodent retina in vivo and in vitro. Proceedings of the National Academy of Sciences 101:16–22. doi: 10.1073/pnas.2235688100.
-
(2004)
Proceedings of the National Academy of Sciences
, vol.101
, pp. 16-22
-
-
Matsuda, T.1
Cepko, C.L.2
-
42
-
-
77952214662
-
GREAT improves functional interpretation of cis-regulatory regions
-
McLean CY, Bristor D, Hiller M, Clarke SL, Schaar BT, Lowe CB, Wenger AM, Bejerano G. 2010. GREAT improves functional interpretation of cis-regulatory regions. Nature Biotechnology 28:495–501. doi: 10.1038/nbt.1630.
-
(2010)
Nature Biotechnology
, 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
-
43
-
-
0035734382
-
Nrl is required for rod photoreceptor development
-
Mears AJ, Kondo M, Swain PK, Takada Y, Bush RA, Saunders TL, Sieving PA, Swaroop A. 2001. Nrl is required for rod photoreceptor development. Nature Genetics 29:447–452. doi: 10.1038/ng774.
-
(2001)
Nature Genetics
, vol.29
, pp. 447-452
-
-
Mears, A.J.1
Kondo, M.2
Swain, P.K.3
Takada, Y.4
Bush, R.A.5
Saunders, T.L.6
Sieving, P.A.7
Swaroop, A.8
-
44
-
-
84863393810
-
Cell-specific DNA methylation patterns of retina-specific genes
-
Merbs SL, Khan MA, Hackler L, Oliver VF, Wan J, Qian J, Zack DJ. 2012. Cell-specific DNA methylation patterns of retina-specific genes. PLoS ONE 7:e32602. doi: 10.1371/journal.pone.0032602.
-
(2012)
Plos ONE
, vol.7
-
-
Merbs, S.L.1
Khan, M.A.2
Hackler, L.3
Oliver, V.F.4
Wan, J.5
Qian, J.6
Zack, D.J.7
-
45
-
-
84931066427
-
Epigenomic signatures of neuronal diversity in the mammalian brain
-
Mo A, Mukamel EA, Davis FP, Luo C, Henry GL, Picard S, Urich MA, Nery JR, Sejnowski TJ, Lister R, Eddy SR, Ecker JR, Nathans J. 2015. Epigenomic signatures of neuronal diversity in the mammalian brain. Neuron 86: 1369–1384. doi: 10.1016/j.neuron.2015.05.018.
-
(2015)
Neuron
, vol.86
, pp. 1369-1384
-
-
Mo, A.1
Mukamel, E.A.2
Davis, F.P.3
Luo, C.4
Henry, G.L.5
Picard, S.6
Urich, M.A.7
Nery, J.R.8
Sejnowski, T.J.9
Lister, R.10
Eddy, S.R.11
Ecker, J.R.12
Nathans, J.13
-
46
-
-
0344442834
-
Otx2 homeobox gene controls retinal photoreceptor cell fate and pineal gland development
-
Nishida A, Furukawa A, Koike C, Tano Y, Aizawa S, Matsuo I, Furukawa T. 2003. Otx2 homeobox gene controls retinal photoreceptor cell fate and pineal gland development. Nature Neuroscience 6:1255–1263. doi: 10.1038/nn1155.
-
(2003)
Nature Neuroscience
, vol.6
, pp. 1255-1263
-
-
Nishida, A.1
Furukawa, A.2
Koike, C.3
Tano, Y.4
Aizawa, S.5
Matsuo, I.6
Furukawa, T.7
-
47
-
-
9644300803
-
Genotype-phenotype correlation in a family with Arg135Leu rhodopsin retinitis pigmentosa
-
Oh KT, Oh DM, Weleber RG, Stone EM, Parikh A, White J, Deboer-Shields KA, Streb L, Vallar C. 2004. Genotype-phenotype correlation in a family with Arg135Leu rhodopsin retinitis pigmentosa. British Journal of Ophthalmology 88:1533–1537. doi: 10.1136/bjo.2004.043653.
-
(2004)
British Journal of Ophthalmology
, vol.88
, pp. 1533-1537
-
-
Oh, K.T.1
Oh, D.M.2
Weleber, R.G.3
Stone, E.M.4
Parikh, A.5
White, J.6
Deboer-Shields, K.A.7
Streb, L.8
Vallar, C.9
-
48
-
-
33846815401
-
Transformation of cone precursors to functional rod photoreceptors by bZIP transcription factor NRL
-
Oh ECT, Khan N, Novelli E, Khanna H, Strettoi E, Swaroop A. 2007. Transformation of cone precursors to functional rod photoreceptors by bZIP transcription factor NRL. Proceedings of the National Academy of Sciences 104:1679–1684. doi: 10.1073/pnas.0605934104.
-
(2007)
Proceedings of the National Academy of Sciences
, vol.104
, pp. 1679-1684
-
-
Oh, E.1
Khan, N.2
Novelli, E.3
Khanna, H.4
Strettoi, E.5
Swaroop, A.6
-
49
-
-
84878623709
-
A novel methyl-binding domain protein enrichment method for identifying genome-wide tissue-specific DNA methylation from nanogram DNA samples
-
Oliver VF, Wan J, Agarwal S, Zack DJ, Qian J, Merbs SL. 2013. A novel methyl-binding domain protein enrichment method for identifying genome-wide tissue-specific DNA methylation from nanogram DNA samples. Epigenetics & Chromatin 6:17–11. doi: 10.1186/1756-8935-6-17.
-
(2013)
Epigenetics & Chromatin
, vol.6
, pp. 11-17
-
-
Oliver, V.F.1
Wan, J.2
Agarwal, S.3
Zack, D.J.4
Qian, J.5
Merbs, S.L.6
-
50
-
-
58549108816
-
Pias3-dependent SUMOylation directs rod photoreceptor development
-
Onishi A, Peng G-H, Hsu C, Alexis U, Chen S, Blackshaw S. 2009. Pias3-dependent SUMOylation directs rod photoreceptor development. Neuron 61:234–246. doi: 10.1016/j.neuron.2008.12.006.
-
(2009)
Neuron
, vol.61
, pp. 234-246
-
-
Onishi, A.1
Peng, G.-H.2
Hsu, C.3
Alexis, U.4
Chen, S.5
Blackshaw, S.6
-
52
-
-
15544371180
-
The photoreceptor-specific nuclear receptor Nr2e3 interacts with Crx and exerts opposing effects on the transcription of rod versus cone genes
-
Peng GH, Ahmad O, Ahmad F, Liu J, Chen S. 2005. The photoreceptor-specific nuclear receptor Nr2e3 interacts with Crx and exerts opposing effects on the transcription of rod versus cone genes. Human Molecular Genetics 14:747–764. doi: 10.1093/hmg/ddi070.
-
(2005)
Human Molecular Genetics
, vol.14
, pp. 747-764
-
-
Peng, G.H.1
Ahmad, O.2
Ahmad, F.3
Liu, J.4
Chen, S.5
-
53
-
-
32544447086
-
Chromatin immunoprecipitation identifies photoreceptor transcription factor targets in mouse models of retinal degeneration: New findings and challenges
-
Peng GH, Chen S. 2005. Chromatin immunoprecipitation identifies photoreceptor transcription factor targets in mouse models of retinal degeneration: new findings and challenges. Visual Neuroscience 22:575–586. doi: 10.1017/S0952523805225063.
-
(2005)
Visual Neuroscience
, vol.22
, pp. 575-586
-
-
Peng, G.H.1
Chen, S.2
-
54
-
-
84897559899
-
Divergent functions of hematopoietic transcription factors in lineage priming and differentiation during erythro-megakaryopoiesis
-
Pimkin M, Kossenkov AV, Mishra T, Morrissey CS, Wu W, Keller CA, Blobel GA, Lee D, Beer MA, Hardison RC, Weiss MJ. 2014. Divergent functions of hematopoietic transcription factors in lineage priming and differentiation during erythro-megakaryopoiesis. Genome Research 24:1932–1944. doi: 10.1101/gr.164178.113.
-
(2014)
Genome Research
, vol.24
, pp. 1932-1944
-
-
Pimkin, M.1
Kossenkov, A.V.2
Mishra, T.3
Morrissey, C.S.4
Wu, W.5
Keller, C.A.6
Blobel, G.A.7
Lee, D.8
Beer, M.A.9
Hardison, R.C.10
Weiss, M.J.11
-
55
-
-
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. doi: 10.1093/bioinformatics/btq033.
-
(2010)
Bioinformatics
, vol.26
, pp. 841-842
-
-
Quinlan, A.R.1
Hall, I.M.2
-
56
-
-
84856008906
-
Differential oestrogen receptor binding is associated with clinical outcome in breast cancer
-
Ross-Innes CS, Stark R, Teschendorff AE, Holmes KA, Ali HR, Dunning MJ, Brown GD, Gojis O, Ellis IO, Green AR, Ali S, Chin S-F, Palmieri C, Caldas C, Carroll JS. 2012. Differential oestrogen receptor binding is associated with clinical outcome in breast cancer. Nature 481:389–393. doi: 10.1038/nature10730.
-
(2012)
Nature
, vol.481
, pp. 389-393
-
-
Ross-Innes, C.S.1
Stark, R.2
Teschendorff, A.E.3
Holmes, K.A.4
Ali, H.R.5
Dunning, M.J.6
Brown, G.D.7
Gojis, O.8
Ellis, I.O.9
Green, A.R.10
Ali, S.11
Chin, S.-F.12
Palmieri, C.13
Caldas, C.14
Carroll, J.S.15
-
57
-
-
84895879439
-
Otx2.ChIP-seq reveals unique and redundant functions in the mature mouse retina
-
Samuel A, Housset M, Fant B, Lamonerie T. 2014. Otx2.ChIP-seq reveals unique and redundant functions in the mature mouse retina. PLoS ONE 9:e89110. doi: 10.1371/journal.pone.0089110.
-
(2014)
Plos ONE
, vol.9
-
-
Samuel, A.1
Housset, M.2
Fant, B.3
Lamonerie, T.4
-
58
-
-
84907584629
-
Onecut1 and Onecut2 redundantly regulate early retinal cell fates during development
-
Sapkota D, Chintala H, Wu F, Fliesler SJ, Hu Z, Mu X. 2014. Onecut1 and Onecut2 redundantly regulate early retinal cell fates during development. Proceedings of the National Academy of Sciences 111:E4086–E4095. doi: 10.1073/pnas.1405354111.
-
(2014)
Proceedings of the National Academy of Sciences
, vol.111
, pp. E4086-E4095
-
-
Sapkota, D.1
Chintala, H.2
Wu, F.3
Fliesler, S.J.4
Hu, Z.5
Mu, X.6
-
59
-
-
84938495948
-
Human body epigenome maps reveal noncanonical DNA methylation variation
-
Schultz MD, He Y, Whitaker JW, Hariharan M, Mukamel EA, Leung D, Rajagopal N, Nery JR, Urich MA, Chen H, Lin S, Lin Y, Jung I, Schmitt AD, Selvaraj S, Ren B, Sejnowski TJ, Wang W, Ecker JR. 2015. Human body epigenome maps reveal noncanonical DNA methylation variation. Nature 523:212–216. doi: 10.1038/nature14465.
-
(2015)
Nature
, vol.523
, pp. 212-216
-
-
Schultz, M.D.1
He, Y.2
Whitaker, J.W.3
Hariharan, M.4
Mukamel, E.A.5
Leung, D.6
Rajagopal, N.7
Nery, J.R.8
Urich, M.A.9
Chen, H.10
Lin, S.11
Lin, Y.12
Jung, I.13
Schmitt, A.D.14
Selvaraj, S.15
Ren, B.16
Sejnowski, T.J.17
Wang, W.18
Ecker, J.R.19
-
60
-
-
0028060401
-
Retinitis pigmentosa and related disorders: Phenotypes of rhodopsin and peripherin/RDS mutations
-
Shastry BS. 1994. Retinitis pigmentosa and related disorders: phenotypes of rhodopsin and peripherin/RDS mutations. American Journal of Medical Genetics 52:467–474. doi: 10.1002/ajmg.1320520413.
-
(1994)
American Journal of Medical Genetics
, vol.52
, pp. 467-474
-
-
Shastry, B.S.1
-
61
-
-
22344446199
-
Histone modifications affect timing of oligodendrocyte progenitor differentiation in the developing rat brain
-
Shen S, Li J, Casaccia-Bonnefil P. 2005. Histone modifications affect timing of oligodendrocyte progenitor differentiation in the developing rat brain. The Journal of Cell Biology 169:577–589. doi: 10.1083/jcb.200412101.
-
(2005)
The Journal of Cell Biology
, vol.169
, pp. 577-589
-
-
Shen, S.1
Li, J.2
Casaccia-Bonnefil, P.3
-
62
-
-
84864462544
-
A map of the cis-regulatory sequences in the mouse genome
-
Shen Y, Yue F, McCleary DF, Ye Z, Edsall L, Kuan S, Wagner U, Dixon J, Lee L, Lobanenkov VV, Ren B. 2012. A map of the cis-regulatory sequences in the mouse genome. Nature 488:116–120. doi: 10.1038/nature11243.
-
(2012)
Nature
, vol.488
, pp. 116-120
-
-
Shen, Y.1
Yue, F.2
McCleary, D.F.3
Ye, Z.4
Edsall, L.5
Kuan, S.6
Wagner, U.7
Dixon, J.8
Lee, L.9
Lobanenkov, V.V.10
Ren, B.11
-
63
-
-
84956945024
-
Massively parallel cis-regulatory analysis in the mammalian central nervous system
-
Shen SQ, Myers CA, Hughes AEO, Byrne LC, Flannery JG, Corbo JC. 2016. Massively parallel cis-regulatory analysis in the mammalian central nervous system. Genome Research 26:238–255. doi: 10.1101/gr.193789.115.
-
(2016)
Genome Research
, vol.26
, pp. 238-255
-
-
Shen, S.Q.1
Myers, C.A.2
Hughes, A.3
Byrne, L.C.4
Flannery, J.G.5
Corbo, J.C.6
-
64
-
-
84857658829
-
Transcriptional code and disease map for adult retinal cell types
-
Siegert S, Cabuy E, Scherf BG, Kohler H, Panda S, Le Y-Z, Fehling HJ, Gaidatzis D, Stadler MB, Roska B. 2012. Transcriptional code and disease map for adult retinal cell types. Nature Neuroscience 15:487–495. doi: 10.1038/nn.3032.
-
(2012)
Nature Neuroscience
, vol.15
, pp. 487-495
-
-
Siegert, S.1
Cabuy, E.2
Scherf, B.G.3
Kohler, H.4
Panda, S.5
Le, Y.-Z.6
Fehling, H.J.7
Gaidatzis, D.8
Stadler, M.B.9
Roska, B.10
-
65
-
-
64249139170
-
Nuclear architecture of rod photoreceptor cells adapts to vision in mammalian evolution
-
Solovei I, Kreysing M, Lanctô t C, Kösem S, Peichl L, Cremer T, Guck J, Joffe B. 2009. Nuclear architecture of rod photoreceptor cells adapts to vision in mammalian evolution. Cell 137:356–368. doi: 10.1016/j.cell.2009.01.052.
-
(2009)
Cell
, vol.137
, pp. 356-368
-
-
Solovei, I.1
Kreysing, M.2
Lanctô T, C.3
Kösem, S.4
Peichl, L.5
Cremer, T.6
Guck, J.7
Joffe, B.8
-
66
-
-
84355163093
-
DNA-binding factors shape the mouse methylome at distal regulatory regions
-
Stadler MB, Murr R, Burger L, Ivanek R, Lienert F, Schöler A, van Nimwegen E, Wirbelauer C, Oakeley EJ, Gaidatzis D, Tiwari VK, Schübeler D. 2011. DNA-binding factors shape the mouse methylome at distal regulatory regions. Nature 480:490–495. doi: 10.1038/nature10716.
-
(2011)
Nature
, vol.480
, pp. 490-495
-
-
Stadler, M.B.1
Murr, R.2
Burger, L.3
Ivanek, R.4
Lienert, F.5
Schöler, A.6
Van Nimwegen, E.7
Wirbelauer, C.8
Oakeley, E.J.9
Gaidatzis, D.10
Tiwari, V.K.11
Schübeler, D.12
-
67
-
-
84865121188
-
An encyclopedia of mouse DNA elements (Mouse ENCODE)
-
Mouse ENCODE Consortium
-
Stamatoyannopoulos JA, Snyder M, Hardison R, Ren B, Gingeras T, Gilbert DM, Groudine M, Bender M, Kaul R, Canfield T, Giste E, Johnson A, Zhang M, Balasundaram G, Byron R, Roach V, Sabo PJ, Sandstrom R, Stehling AS, Thurman RE, Weissman SM, Cayting P, Hariharan M, Lian J, Cheng Y, Landt SG, Ma Z, Wold BJ, Dekker J, Crawford GE, Keller CA, Wu W, Morrissey C, Kumar SA, Mishra T, Jain D, Byrska-Bishop M, Blankenberg D, Lajoie BR, Jain G, Sanyal A, Chen KB, Denas O, Taylor J, Blobel GA, Weiss MJ, Pimkin M, Deng W, Marinov GK, Williams BA, Fisher-Aylor KI, Desalvo G, Kiralusha A, Trout D, Amrhein H, Mortazavi A, Edsall L, McCleary D, Kuan S, Shen Y, Yue F, Ye Z, Davis CA, Zaleski C, Jha S, Xue C, Dobin A, Lin W, Fastuca M, Wang H, Guigo R, Djebali S, Lagarde J, Ryba T, Sasaki T, Malladi VS, Cline MS, Kirkup VM, Learned K, Rosenbloom KR, Kent WJ, Feingold EA, Good PJ, Pazin M, Lowdon RF, Adams LB. Mouse ENCODE Consortium. 2012. An encyclopedia of mouse DNA elements (mouse ENCODE). Genome Biology 13. doi: 10.1186/gb-2012-13-8-418.
-
(2012)
Genome Biology
, pp. 13
-
-
Stamatoyannopoulos, J.A.1
Snyder, M.2
Hardison, R.3
Ren, B.4
Gingeras, T.5
Gilbert, D.M.6
Groudine, M.7
Bender, M.8
Kaul, R.9
Canfield, T.10
Giste, E.11
Johnson, A.12
Zhang, M.13
Balasundaram, G.14
Byron, R.15
Roach, V.16
Sabo, P.J.17
Sandstrom, R.18
Stehling, A.S.19
Thurman, R.E.20
Weissman, S.M.21
Cayting, P.22
Hariharan, M.23
Lian, J.24
Cheng, Y.25
Landt, S.G.26
Ma, Z.27
Wold, B.J.28
Dekker, J.29
Crawford, G.E.30
Keller, C.A.31
Wu, W.32
Morrissey, C.33
Kumar, S.A.34
Mishra, T.35
Jain, D.36
Byrska-Bishop, M.37
Blankenberg, D.38
Lajoie, B.R.39
Jain, G.40
Sanyal, A.41
Chen, K.B.42
Denas, O.43
Taylor, J.44
Blobel, G.A.45
Weiss, M.J.46
Pimkin, M.47
Deng, W.48
Marinov, G.K.49
Williams, B.A.50
Fisher-Aylor, K.I.51
Desalvo, G.52
Kiralusha, A.53
Trout, D.54
Amrhein, H.55
Mortazavi, A.56
Edsall, L.57
McCleary, D.58
Kuan, S.59
Shen, Y.60
Yue, F.61
Ye, Z.62
Davis, C.A.63
Zaleski, C.64
Jha, S.65
Xue, C.66
Dobin, A.67
Lin, W.68
Fastuca, M.69
Wang, H.70
Guigo, R.71
Djebali, S.72
Lagarde, J.73
Ryba, T.74
Sasaki, T.75
Malladi, V.S.76
Cline, M.S.77
Kirkup, V.M.78
Learned, K.79
Rosenbloom, K.R.80
Kent, W.J.81
Feingold, E.A.82
Good, P.J.83
Pazin, M.84
Lowdon, R.F.85
Adams, L.B.86
more..
-
69
-
-
84882766972
-
Developmental fate and cellular maturity encoded in human regulatory DNA landscapes
-
Stergachis AB, Neph S, Reynolds A, Humbert R, Miller B, Paige SL, Vernot B, Cheng JB, Thurman RE, Sandstrom R, Haugen E, Heimfeld S, Murry CE, Akey JM, Stamatoyannopoulos JA. 2013. Developmental fate and cellular maturity encoded in human regulatory DNA landscapes. Cell 154:888–903. doi: 10.1016/j.cell.2013.07.020.
-
(2013)
Cell
, vol.154
, pp. 888-903
-
-
Stergachis, A.B.1
Neph, S.2
Reynolds, A.3
Humbert, R.4
Miller, B.5
Paige, S.L.6
Vernot, B.7
Cheng, J.B.8
Thurman, R.E.9
Sandstrom, R.10
Haugen, E.11
Heimfeld, S.12
Murry, C.E.13
Akey, J.M.14
Stamatoyannopoulos, J.A.15
-
70
-
-
77954879972
-
Transcriptional regulation of photoreceptor development and homeostasis in the mammalian retina
-
Swaroop A, Kim D, Forrest D. 2010. Transcriptional regulation of photoreceptor development and homeostasis in the mammalian retina. Nature Reviews Neuroscience 11:563–576. doi: 10.1038/nrn2880.
-
(2010)
Nature Reviews Neuroscience
, vol.11
, pp. 563-576
-
-
Swaroop, A.1
Kim, D.2
Forrest, D.3
-
71
-
-
84865755978
-
The accessible chromatin landscape of the human genome
-
Thurman RE, Rynes E, Humbert R, Vierstra J, Maurano MT, Haugen E, Sheffield NC, Stergachis AB, Wang H, Vernot B, Garg K, John S, Sandstrom R, Bates D, Boatman L, Canfield TK, Diegel M, Dunn D, Ebersol AK, Frum T, Giste E, Johnson AK, Johnson EM, Kutyavin T, Lajoie B, Lee B-K, Lee K, London D, Lotakis D, Neph S, Neri F, Nguyen ED, Qu H, Reynolds AP, Roach V, Safi A, Sanchez ME, Sanyal A, Shafer A, Simon JM, Song L, Vong S, Weaver M, Yan Y, Zhang Z, Zhang Z, Lenhard B, Tewari M, Dorschner MO, Hansen RS, Navas PA, Stamatoyannopoulos G, Iyer VR, Lieb JD, Sunyaev SR, Akey JM, Sabo PJ, Kaul R, Furey TS, Dekker J, Crawford GE, Stamatoyannopoulos JA. 2012. The accessible chromatin landscape of the human genome. Nature 489: 75–82. doi: 10.1038/nature11232.
-
(2012)
Nature
, vol.489
, pp. 75-82
-
-
Thurman, R.E.1
Rynes, E.2
Humbert, R.3
Vierstra, J.4
Maurano, M.T.5
Haugen, E.6
Sheffield, N.C.7
Stergachis, A.B.8
Wang, H.9
Vernot, B.10
Garg, K.11
John, S.12
Sandstrom, R.13
Bates, D.14
Boatman, L.15
Canfield, T.K.16
Diegel, M.17
Dunn, D.18
Ebersol, A.K.19
Frum, T.20
Giste, E.21
Johnson, A.K.22
Johnson, E.M.23
Kutyavin, T.24
Lajoie, B.25
Lee, B.-K.26
Lee, K.27
London, D.28
Lotakis, D.29
Neph, S.30
Neri, F.31
Nguyen, E.D.32
Qu, H.33
Reynolds, A.P.34
Roach, V.35
Safi, A.36
Sanchez, M.E.37
Sanyal, A.38
Shafer, A.39
Simon, J.M.40
Song, L.41
Vong, S.42
Weaver, M.43
Yan, Y.44
Zhang, Z.45
Zhang, Z.46
Lenhard, B.47
Tewari, M.48
Dorschner, M.O.49
Hansen, R.S.50
Navas, P.A.51
Stamatoyannopoulos, G.52
Iyer, V.R.53
Lieb, J.D.54
Sunyaev, S.R.55
Akey, J.M.56
Sabo, P.J.57
Kaul, R.58
Furey, T.S.59
Dekker, J.60
Crawford, G.E.61
Stamatoyannopoulos, J.A.62
more..
-
72
-
-
65449136284
-
TopHat: Discovering splice junctions with RNA-seq
-
Trapnell C, Pachter L, Salzberg SL. 2009. TopHat: discovering splice junctions with RNA-seq. Bioinformatics 25: 1105–1111. doi: 10.1093/bioinformatics/btp120.
-
(2009)
Bioinformatics
, vol.25
, pp. 1105-1111
-
-
Trapnell, C.1
Pachter, L.2
Salzberg, S.L.3
-
73
-
-
84929154443
-
DNase I hypersensitivity analysis of the mouse brain and retina identifies region-specific regulatory elements
-
Wilken MS, Brzezinski JA, La Torre A, Siebenthall K, Thurman R, Sabo P, Sandstrom RS, Vierstra J, Canfield TK, Hansen R, Bender MA, Stamatoyannopoulos J, Reh TA, Brzezinski JA, La Torre A, Siebenthall K, Thurman R, Sabo P, Sandstrom RS, Vierstra J, Canfield TK, Hansen RS. 2015. DNase I hypersensitivity analysis of the mouse brain and retina identifies region-specific regulatory elements. Epigenetics & Chromatin 8:8. doi: 10.1186/1756-8935-8-8.
-
(2015)
Epigenetics & Chromatin
, vol.8
-
-
Wilken, M.S.1
Brzezinski, J.A.2
La Torre, A.3
Siebenthall, K.4
Thurman, R.5
Sabo, P.6
Sandstrom, R.S.7
Vierstra, J.8
Canfield, T.K.9
Hansen, R.10
Bender, M.A.11
Stamatoyannopoulos, J.12
Reh, T.A.13
Brzezinski, J.A.14
La Torre, A.15
Siebenthall, K.16
Thurman, R.17
Sabo, P.18
Sandstrom, R.S.19
Vierstra, J.20
Canfield, T.K.21
Hansen, R.S.22
more..
-
76
-
-
84857331867
-
Base-resolution analyses of sequence and parent-of-origin dependent DNA methylation in the mouse genome
-
Xie W, Barr CL, Kim A, Yue F, Lee AY, Eubanks J, Dempster EL, Ren B. 2012. Base-resolution analyses of sequence and parent-of-origin dependent DNA methylation in the mouse genome. Cell 148:816–831. doi: 10.1016/j.cell.2011.12.035.
-
(2012)
Cell
, vol.148
, pp. 816-831
-
-
Xie, W.1
Barr, C.L.2
Kim, A.3
Yue, F.4
Lee, A.Y.5
Eubanks, J.6
Dempster, E.L.7
Ren, B.8
-
77
-
-
84878282421
-
Epigenomic analysis of multilineage differentiation of human embryonic stem cells
-
Xie W, Schultz MD, Lister R, Hou Z, Rajagopal N, Ray P, Whitaker JW, Tian S, Hawkins RD, Leung D, Yang H, Wang T, Lee AY, Swanson SA, Zhang J, Zhu Y, Kim A, Nery JR, Urich MA, Kuan S, Yen Chia-an, Klugman S, Yu P, Suknuntha K, Propson NE, Chen H, Edsall LE, Wagner U, Li Y, Ye Z, Kulkarni A, Xuan Z, Chung W-Y, Chi NC, Antosiewicz-Bourget JE, Slukvin I, Stewart R, Zhang MQ, Wang W, Thomson JA, Ecker JR, Ren B. 2013. Epigenomic analysis of multilineage differentiation of human embryonic stem cells. Cell 153:1134–1148. doi: 10.1016/j.cell.2013.04.022.
-
(2013)
Cell
, vol.153
, pp. 1134-1148
-
-
Xie, W.1
Schultz, M.D.2
Lister, R.3
Hou, Z.4
Rajagopal, N.5
Ray, P.6
Whitaker, J.W.7
Tian, S.8
Hawkins, R.D.9
Leung, D.10
Yang, H.11
Wang, T.12
Lee, A.Y.13
Swanson, S.A.14
Zhang, J.15
Zhu, Y.16
Kim, A.17
Nery, J.R.18
Urich, M.A.19
Kuan, S.20
Chia-An, Y.21
Klugman, S.22
Yu, P.23
Suknuntha, K.24
Propson, N.E.25
Chen, H.26
Edsall, L.E.27
Wagner, U.28
Li, Y.29
Ye, Z.30
Kulkarni, A.31
Xuan, Z.32
Chung, W.-Y.33
Chi, N.C.34
Antosiewicz-Bourget, J.E.35
Slukvin, I.36
Stewart, R.37
Zhang, M.Q.38
Wang, W.39
Thomson, J.A.40
Ecker, J.R.41
Ren, B.42
more..
-
78
-
-
84911462077
-
A comparative encyclopedia of DNA elements in the mouse genome
-
Mouse ENCODE Consortium
-
Yue F, Cheng Y, Breschi A, Vierstra J, Wu W, Ryba T, Sandstrom R, Ma Z, Davis C, Pope BD, Shen Y, Pervouchine DD, Djebali S, Thurman RE, Kaul R, Rynes E, Kirilusha A, Marinov GK, Williams BA, Trout D, Amrhein H, Fisher- Aylor K, Antoshechkin I, DeSalvo G, See LH, Fastuca M, Drenkow J, Zaleski C, Dobin A, Prieto P, Lagarde J, Bussotti G, Tanzer A, Denas O, Li K, Bender MA, Zhang M, Byron R, Groudine MT, McCleary D, Pham L, Ye Z, Kuan S, Edsall L, Wu YC, Rasmussen MD, Bansal MS, Kellis M, Keller CA, Morrissey CS, Mishra T, Jain D, Dogan N, Harris RS, Cayting P, Kawli T, Boyle AP, Euskirchen G, Kundaje A, Lin S, Lin Y, Jansen C, Malladi VS, Cline MS, Erickson DT, Kirkup VM, Learned K, Sloan CA, Rosenbloom KR, Lacerda de Sousa B, Beal K, Pignatelli M, Flicek P, Lian J, Kahveci T, Lee D, Kent WJ, Ramalho Santos M, Herrero J, Notredame C, Johnson A, Vong S, Lee K, Bates D, Neri F, Diegel M, Canfield T, Sabo PJ, Wilken MS, Reh TA, Giste E, Shafer A, Kutyavin T, Haugen E, Dunn D, Reynolds AP, Neph S, Humbert R, Hansen RS, De Bruijn M, Selleri L, Rudensky A, Josefowicz S, Samstein R, Eichler EE, Orkin SH, Levasseur D, Papayannopoulou T, Chang KH, Skoultchi A, Gosh S, Disteche C, Treuting P, Wang Y, Weiss MJ, Blobel GA, Cao X, Zhong S, Wang T, Good PJ, Lowdon RF, Adams LB, Zhou XQ, Pazin MJ, Feingold EA, Wold B, Taylor J, Mortazavi A, Weissman SM, Stamatoyannopoulos JA, Snyder MP, Guigo R, Gingeras TR, Gilbert DM, Hardison RC, Beer MA, Ren B.Mouse ENCODE Consortium. 2014. A comparative encyclopedia of DNA elements in the mouse genome. Nature 515: 355–364. doi: 10.1038/nature13992.
-
(2014)
Nature
, vol.515
, pp. 355-364
-
-
Yue, F.1
Cheng, Y.2
Breschi, A.3
Vierstra, J.4
Wu, W.5
Ryba, T.6
Sandstrom, R.7
Ma, Z.8
Davis, C.9
Pope, B.D.10
Shen, Y.11
Pervouchine, D.D.12
Djebali, S.13
Thurman, R.E.14
Kaul, R.15
Rynes, E.16
Kirilusha, A.17
Marinov, G.K.18
Williams, B.A.19
Trout, D.20
Amrhein, H.21
Fisher- Aylor, K.22
Antoshechkin, I.23
Desalvo, G.24
See, L.H.25
Fastuca, M.26
Drenkow, J.27
Zaleski, C.28
Dobin, A.29
Prieto, P.30
Lagarde, J.31
Bussotti, G.32
Tanzer, A.33
Denas, O.34
Li, K.35
Bender, M.A.36
Zhang, M.37
Byron, R.38
Groudine, M.T.39
McCleary, D.40
Pham, L.41
Ye, Z.42
Kuan, S.43
Edsall, L.44
Wu, Y.C.45
Rasmussen, M.D.46
Bansal, M.S.47
Kellis, M.48
Keller, C.A.49
Morrissey, C.S.50
Mishra, T.51
Jain, D.52
Dogan, N.53
Harris, R.S.54
Cayting, P.55
Kawli, T.56
Boyle, A.P.57
Euskirchen, G.58
Kundaje, A.59
Lin, S.60
Lin, Y.61
Jansen, C.62
Malladi, V.S.63
Cline, M.S.64
Erickson, D.T.65
Kirkup, V.M.66
Learned, K.67
Sloan, C.A.68
Rosenbloom, K.R.69
Lacerda De Sousa, B.70
Beal, K.71
Pignatelli, M.72
Flicek, P.73
Lian, J.74
Kahveci, T.75
Lee, D.76
Kent, W.J.77
Ramalho Santos, M.78
Herrero, J.79
Notredame, C.80
Johnson, A.81
Vong, S.82
Lee, K.83
Bates, D.84
Neri, F.85
Diegel, M.86
Canfield, T.87
Sabo, P.J.88
Wilken, M.S.89
Reh, T.A.90
Giste, E.91
Shafer, A.92
Kutyavin, T.93
Haugen, E.94
Dunn, D.95
Reynolds, A.P.96
Neph, S.97
Humbert, R.98
Hansen, R.S.99
De Bruijn, M.100
Selleri, L.101
Rudensky, A.102
Josefowicz, S.103
Samstein, R.104
Eichler, E.E.105
Orkin, S.H.106
Levasseur, D.107
Papayannopoulou, T.108
Chang, K.H.109
Skoultchi, A.110
Gosh, S.111
Disteche, C.112
Treuting, P.113
Wang, Y.114
Weiss, M.J.115
Blobel, G.A.116
Cao, X.117
Zhong, S.118
Wang, T.119
Good, P.J.120
Lowdon, R.F.121
Adams, L.B.122
Zhou, X.Q.123
Pazin, M.J.124
Feingold, E.A.125
Wold, B.126
Taylor, J.127
Mortazavi, A.128
Weissman, S.M.129
Stamatoyannopoulos, J.A.130
Snyder, M.P.131
Guigo, R.132
Gingeras, T.R.133
Gilbert, D.M.134
Hardison, R.C.135
Beer, M.A.136
Ren, B.137
more..
-
79
-
-
67650711619
-
A clustering approach for identification of enriched domains from histone modification ChIP-seq data
-
Zang C, Schones DE, Zeng C, Cui K, Zhao K, Peng W. 2009. A clustering approach for identification of enriched domains from histone modification ChIP-seq data. Bioinformatics 25:1952–1958. doi: 10.1093/bioinformatics/btp340.
-
(2009)
Bioinformatics
, vol.25
, pp. 1952-1958
-
-
Zang, C.1
Schones, D.E.2
Zeng, C.3
Cui, K.4
Zhao, K.5
Peng, W.6
-
80
-
-
53849146020
-
Model-based analysis of ChIP-seq (MACS)
-
Zhang Y, Liu T, Meyer CA, Eeckhoute J, Johnson DS, Bernstein BE, Nussbaum C, Myers RM, Brown M, Li W, Liu XS. 2008. Model-based analysis of ChIP-seq (MACS). Genome Biology 9:R137. doi: 10.1186/gb-2008-9-9-r137.
-
(2008)
Genome Biology
, vol.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.M.8
Brown, M.9
Li, W.10
Liu, X.S.11
-
81
-
-
84882884517
-
Charting a dynamic DNA methylation landscape of the human genome
-
Ziller MJ, Gu H, Müller F, Donaghey J, Tsai LT-Y, Kohlbacher O, De Jager PL, Rosen ED, Bennett DA, Bernstein BE, Gnirke A, Meissner A. 2013. Charting a dynamic DNA methylation landscape of the human genome. Nature 500:477–481. doi: 10.1038/nature12433.
-
(2013)
Nature
, vol.500
, pp. 477-481
-
-
Ziller, M.J.1
Gu, H.2
Müller, F.3
Donaghey, J.4
Tsai, L.-Y.5
Kohlbacher, O.6
De Jager, P.L.7
Rosen, E.D.8
Bennett, D.A.9
Bernstein, B.E.10
Gnirke, A.11
Meissner, A.12
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