-
1
-
-
0037372003
-
Epigenetic regulation of gene expression: How the genome integrates intrinsic and environmental signals
-
Jaenisch, R. & Bird, A. Epigenetic regulation of gene expression: how the genome integrates intrinsic and environmental signals. Nat. Genet. 33 (suppl.), 245-254 (2003).
-
(2003)
Nat. Genet.
, vol.33
, pp. 245-254
-
-
Jaenisch, R.1
Bird, A.2
-
2
-
-
3342989681
-
Epigenetic programming by maternal behavior
-
Weaver, I.C. et al. Epigenetic programming by maternal behavior. Nat. Neurosci. 7, 847-854 (2004).
-
(2004)
Nat. Neurosci.
, vol.7
, pp. 847-854
-
-
Weaver, I.C.1
-
3
-
-
33847614418
-
Covalent modifcation of DNA regulates memory formation
-
Miller, C.A. & Sweatt, J.D. Covalent modifcation of DNA regulates memory formation. Neuron 53, 857-869 (2007).
-
(2007)
Neuron
, vol.53
, pp. 857-869
-
-
Miller, C.A.1
Sweatt, J.D.2
-
4
-
-
60749094831
-
Neuronal activity-induced Gadd45b promotes epigenetic DNA demethylation and adult neurogenesis
-
Ma, D.K. et al. Neuronal activity-induced Gadd45b promotes epigenetic DNA demethylation and adult neurogenesis. Science 323, 1074-1077 (2009).
-
(2009)
Science
, vol.323
, pp. 1074-1077
-
-
Ma, D.K.1
-
5
-
-
77950187447
-
Dnmt1 and Dnmt3a maintain DNA methylation and regulate synaptic function in adult forebrain neurons
-
Feng, J. et al. Dnmt1 and Dnmt3a maintain DNA methylation and regulate synaptic function in adult forebrain neurons. Nat. Neurosci. 13, 423-430 (2010).
-
(2010)
Nat. Neurosci.
, vol.13
, pp. 423-430
-
-
Feng, J.1
-
6
-
-
45449114804
-
The colorful history of active DNA demethylation
-
Ooi, S.K. & Bestor, T.H. The colorful history of active DNA demethylation. Cell 133, 1145-1148 (2008).
-
(2008)
Cell
, vol.133
, pp. 1145-1148
-
-
Ooi, S.K.1
Bestor, T.H.2
-
7
-
-
66149123748
-
The nuclear DNA base 5-hydroxymethylcytosine is present in Purkinje neurons and the brain
-
Kriaucionis, S. & Heintz, N. The nuclear DNA base 5-hydroxymethylcytosine is present in Purkinje neurons and the brain. Science 324, 929-930 (2009).
-
(2009)
Science
, vol.324
, pp. 929-930
-
-
Kriaucionis, S.1
Heintz, N.2
-
8
-
-
66149146320
-
Conversion of 5-methylcytosine to 5-hydroxymethylcytosine in mammalian DNA by MLL partner TET1
-
Tahiliani, M. et al. Conversion of 5-methylcytosine to 5-hydroxymethylcytosine in mammalian DNA by MLL partner TET1. Science 324, 930-935 (2009).
-
(2009)
Science
, vol.324
, pp. 930-935
-
-
Tahiliani, M.1
-
9
-
-
77956189495
-
Role of Tet proteins in 5mC to 5hmC conversion, ES-cell self-renewal and inner cell mass specifcation
-
Ito, S. et al. Role of Tet proteins in 5mC to 5hmC conversion, ES-cell self-renewal and inner cell mass specifcation. Nature 466, 1129-1133 (2010).
-
(2010)
Nature
, vol.466
, pp. 1129-1133
-
-
Ito, S.1
-
10
-
-
78650175023
-
Impaired hydroxylation of 5-methylcytosine in myeloid cancers with mutant TET2
-
Ko, M. et al. Impaired hydroxylation of 5-methylcytosine in myeloid cancers with mutant TET2. Nature 468, 839-843 (2010).
-
(2010)
Nature
, vol.468
, pp. 839-843
-
-
Ko, M.1
-
11
-
-
80052495940
-
Tet-mediated formation of 5-carboxylcytosine and its excision by TDG in mammalian DNA
-
He, Y.F. et al. Tet-mediated formation of 5-carboxylcytosine and its excision by TDG in mammalian DNA. Science 333, 1303-1307 (2011).
-
(2011)
Science
, vol.333
, pp. 1303-1307
-
-
He, Y.F.1
-
12
-
-
80052461558
-
Tet proteins can convert 5-methylcytosine to 5-formylcytosine and 5-carboxylcytosine
-
Ito, S. et al. Tet proteins can convert 5-methylcytosine to 5-formylcytosine and 5-carboxylcytosine. Science 333, 1300-1303 (2011).
-
(2011)
Science
, vol.333
, pp. 1300-1303
-
-
Ito, S.1
-
13
-
-
82955207588
-
Mechanisms and functions of Tet protein-mediated 5-methylcytosine oxidation
-
Wu, H. & Zhang, Y. Mechanisms and functions of Tet protein-mediated 5-methylcytosine oxidation. Genes Dev. 25, 2436-2452 (2011).
-
(2011)
Genes Dev.
, vol.25
, pp. 2436-2452
-
-
Wu, H.1
Zhang, Y.2
-
14
-
-
83855163995
-
Uncovering the role of 5-hydroxymethylcytosine in the epigenome
-
Branco, M.R., Ficz, G. & Reik, W. Uncovering the role of 5-hydroxymethylcytosine in the epigenome. Nat. Rev. Genet. 13, 7-13 (2012).
-
(2012)
Nat. Rev. Genet.
, vol.13
, pp. 7-13
-
-
Branco, M.R.1
Ficz, G.2
Reik, W.3
-
15
-
-
84878260646
-
TETonic shift: Biological roles of TET proteins in DNA demethylation and transcription
-
Pastor, W.A., Aravind, L. & Rao, A. TETonic shift: biological roles of TET proteins in DNA demethylation and transcription. Nat. Rev. Mol. Cell Biol. 14, 341-356 (2013).
-
(2013)
Nat. Rev. Mol. Cell Biol.
, vol.14
, pp. 341-356
-
-
Pastor, W.A.1
Aravind, L.2
Rao, A.3
-
16
-
-
79955538247
-
Hydroxylation of 5-methylcytosine by TET1 promotes active DNA demethylation in the adult brain
-
Guo, J.U., Su, Y., Zhong, C., Ming, G.L. & Song, H. Hydroxylation of 5-methylcytosine by TET1 promotes active DNA demethylation in the adult brain. Cell 145, 423-434 (2011).
-
(2011)
Cell
, vol.145
, pp. 423-434
-
-
Guo, J.U.1
Su, Y.2
Zhong, C.3
Ming, G.L.4
Song, H.5
-
17
-
-
78650826181
-
Tissue distribution of 5-hydroxymethylcytosine and search for active demethylation intermediates
-
Globisch, D. et al. Tissue distribution of 5-hydroxymethylcytosine and search for active demethylation intermediates. PLoS ONE 5, e15367 (2010).
-
(2010)
PLoS ONE
, vol.5
, pp. e15367
-
-
Globisch, D.1
-
18
-
-
78049401678
-
Sensitive enzymatic quantifcation of 5-hydroxymethylcytosine in genomic DNA
-
Szwagierczak, A., Bultmann, S., Schmidt, C.S., Spada, F. & Leonhardt, H. Sensitive enzymatic quantifcation of 5-hydroxymethylcytosine in genomic DNA. Nucleic Acids Res. 38, e181 (2010).
-
(2010)
Nucleic Acids Res.
, vol.38
, pp. e181
-
-
Szwagierczak, A.1
Bultmann, S.2
Schmidt, C.S.3
Spada, F.4
Leonhardt, H.5
-
19
-
-
82255192294
-
5-hmC-mediated epigenetic dynamics during postnatal neurodevelopment and aging
-
Szulwach, K.E. et al. 5-hmC-mediated epigenetic dynamics during postnatal neurodevelopment and aging. Nat. Neurosci. 14, 1607-1616 (2011).
-
(2011)
Nat. Neurosci.
, vol.14
, pp. 1607-1616
-
-
Szulwach, K.E.1
-
20
-
-
84884241288
-
Tet1 is critical for neuronal activity-regulated gene expression and memory extinction
-
Rudenko, A. et al. Tet1 is critical for neuronal activity-regulated gene expression and memory extinction. Neuron 79, 1109-1122 (2013).
-
(2013)
Neuron
, vol.79
, pp. 1109-1122
-
-
Rudenko, A.1
-
21
-
-
84884471932
-
TET1 controls CNS 5-methylcytosine hydroxylation, active DNA Demethylation, gene transcription and memory formation
-
Kaas, G.A. et al. TET1 controls CNS 5-methylcytosine hydroxylation, active DNA Demethylation, gene transcription and memory formation. Neuron 79, 1086-1093 (2013).
-
(2013)
Neuron
, vol.79
, pp. 1086-1093
-
-
Kaas, G.A.1
-
22
-
-
84881178902
-
Tet1 regulates adult hippocampal neurogenesis and cognition
-
Zhang, R.R. et al. Tet1 regulates adult hippocampal neurogenesis and cognition. Cell Stem Cell 13, 237-245 (2013).
-
(2013)
Cell Stem Cell
, vol.13
, pp. 237-245
-
-
Zhang, R.R.1
-
23
-
-
84900513301
-
Neocortical Tet3-mediated accumulation of 5-hydroxymethylcytosine promotes rapid behavioral adaptation
-
Li, X. et al. Neocortical Tet3-mediated accumulation of 5-hydroxymethylcytosine promotes rapid behavioral adaptation. Proc. Natl. Acad. Sci. USA 111, 7120-7125 (2014).
-
(2014)
Proc. Natl. Acad. Sci. USA
, vol.111
, pp. 7120-7125
-
-
Li, X.1
-
24
-
-
0035260641
-
Molecular basis of long-term plasticity underlying addiction
-
Nestler, E.J. Molecular basis of long-term plasticity underlying addiction. Nat. Rev. Neurosci. 2, 119-128 (2001).
-
(2001)
Nat. Rev. Neurosci.
, vol.2
, pp. 119-128
-
-
Nestler, E.J.1
-
25
-
-
84881026418
-
Epigenetic mechanisms of drug addiction
-
Feng, J. & Nestler, E.J. Epigenetic mechanisms of drug addiction. Curr. Opin. Neurobiol. 23, 521-528 (2013).
-
(2013)
Curr. Opin. Neurobiol.
, vol.23
, pp. 521-528
-
-
Feng, J.1
Nestler, E.J.2
-
26
-
-
77956139754
-
Dnmt3a regulates emotional behavior and spine plasticity in the nucleus accumbens
-
LaPlant, Q. et al. Dnmt3a regulates emotional behavior and spine plasticity in the nucleus accumbens. Nat. Neurosci. 13, 1137-1143 (2010).
-
(2010)
Nat. Neurosci.
, vol.13
, pp. 1137-1143
-
-
Laplant, Q.1
-
27
-
-
79953217366
-
A sensitive mass spectrometry method for simultaneous quantifcation of DNA methylation and hydroxymethylation levels in biological samples
-
Le, T., Kim, K.P., Fan, G. & Faull, K.F. A sensitive mass spectrometry method for simultaneous quantifcation of DNA methylation and hydroxymethylation levels in biological samples. Anal. Biochem. 412, 203-209 (2011).
-
(2011)
Anal. Biochem.
, vol.412
, pp. 203-209
-
-
Le, T.1
Kim, K.P.2
Fan, G.3
Faull, K.F.4
-
28
-
-
84876007572
-
RFECS: A random-forest based algorithm for enhancer identifcation from chromatin state
-
Rajagopal, N. et al. RFECS: a random-forest based algorithm for enhancer identifcation from chromatin state. PLOS Comput. Biol. 9, e1002968 (2013).
-
(2013)
PLOS Comput. Biol.
, vol.9
, pp. e1002968
-
-
Rajagopal, N.1
-
29
-
-
84917732422
-
Genome-wide identifcation and characterization of functional neuronal activity-dependent enhancers
-
Malik, A.N. et al. Genome-wide identifcation and characterization of functional neuronal activity-dependent enhancers. Nat. Neurosci. 17, 1330-1339 (2014).
-
(2014)
Nat. Neurosci.
, vol.17
, pp. 1330-1339
-
-
Malik, A.N.1
-
30
-
-
65549104157
-
Histone modifcations at human enhancers refect global cell type-specifc gene expression
-
Heintzman, N.D. et al. Histone modifcations at human enhancers refect global cell type-specifc gene expression. Nature 459, 108-112 (2009).
-
(2009)
Nature
, vol.459
, pp. 108-112
-
-
Heintzman, N.D.1
-
31
-
-
78650758676
-
Histone H3K27ac separates active from poised enhancers and predicts developmental state
-
Creyghton, M.P. et al. Histone H3K27ac separates active from poised enhancers and predicts developmental state. Proc. Natl. Acad. Sci. USA 107, 21931-21936 (2010).
-
(2010)
Proc. Natl. Acad. Sci. USA
, vol.107
, pp. 21931-21936
-
-
Creyghton, M.P.1
-
32
-
-
79955583542
-
Mapping and analysis of chromatin state dynamics in nine human cell types
-
Ernst, J. et al. Mapping and analysis of chromatin state dynamics in nine human cell types. Nature 473, 43-49 (2011).
-
(2011)
Nature
, vol.473
, pp. 43-49
-
-
Ernst, J.1
-
33
-
-
84908499387
-
Chronic cocaine-regulated epigenomic changes in mouse nucleus accumbens
-
Feng, J. et al. Chronic cocaine-regulated epigenomic changes in mouse nucleus accumbens. Genome Biol. 15, R65 (2014).
-
(2014)
Genome Biol.
, vol.15
, pp. R65
-
-
Feng, J.1
-
34
-
-
77956120147
-
Sequence-specifc recognition of methylated DNA by human zinc-fnger proteins
-
Sasai, N., Nakao, M. & Defossez, P.A. Sequence-specifc recognition of methylated DNA by human zinc-fnger proteins. Nucleic Acids Res. 38, 5015-5022 (2010).
-
(2010)
Nucleic Acids Res.
, vol.38
, pp. 5015-5022
-
-
Sasai, N.1
Nakao, M.2
Defossez, P.A.3
-
35
-
-
0034671891
-
Functional requirement for class i MHC in CNS development and plasticity
-
Huh, G.S. et al. Functional requirement for class I MHC in CNS development and plasticity. Science 290, 2155-2159 (2000).
-
(2000)
Science
, vol.290
, pp. 2155-2159
-
-
Huh, G.S.1
-
36
-
-
84876903184
-
The neuron-specifc chromatin regulatory subunit BAF53b is necessary for synaptic plasticity and memory
-
Vogel-Ciernia, A. et al. The neuron-specifc chromatin regulatory subunit BAF53b is necessary for synaptic plasticity and memory. Nat. Neurosci. 16, 552-561 (2013).
-
(2013)
Nat. Neurosci.
, vol.16
, pp. 552-561
-
-
Vogel-Ciernia, A.1
-
37
-
-
84861221693
-
Quantitative sequencing of 5-methylcytosine and 5-hydroxymethylcytosine at single-base resolution
-
Booth, M.J. et al. Quantitative sequencing of 5-methylcytosine and 5-hydroxymethylcytosine at single-base resolution. Science 336, 934-937 (2012).
-
(2012)
Science
, vol.336
, pp. 934-937
-
-
Booth, M.J.1
-
38
-
-
43049181324
-
Distinct roles of adenylyl cyclases 1 and 8 in opiate dependence: Behavioral, electrophysiological and molecular studies
-
Zachariou, V. et al. Distinct roles of adenylyl cyclases 1 and 8 in opiate dependence: behavioral, electrophysiological and molecular studies. Biol. Psychiatry 63, 1013-1021 (2008).
-
(2008)
Biol. Psychiatry
, vol.63
, pp. 1013-1021
-
-
Zachariou, V.1
-
39
-
-
62749141240
-
Tropomyosin-related kinase B in the mesolimbic dopamine system: Region-specifc effects on cocaine reward
-
Graham, D.L. et al. Tropomyosin-related kinase B in the mesolimbic dopamine system: region-specifc effects on cocaine reward. Biol. Psychiatry 65, 696-701 (2009).
-
(2009)
Biol. Psychiatry
, vol.65
, pp. 696-701
-
-
Graham, D.L.1
-
40
-
-
77957938882
-
Cell type-specifc loss of BDNF signaling mimics optogenetic control of cocaine reward
-
Lobo, M.K. et al. Cell type-specifc loss of BDNF signaling mimics optogenetic control of cocaine reward. Science 330, 385-390 (2010).
-
(2010)
Science
, vol.330
, pp. 385-390
-
-
Lobo, M.K.1
-
41
-
-
79956302047
-
TET1 and hydroxymethylcytosine in transcription and DNA methylation fdelity
-
Williams, K. et al. TET1 and hydroxymethylcytosine in transcription and DNA methylation fdelity. Nature 473, 343-348 (2011).
-
(2011)
Nature
, vol.473
, pp. 343-348
-
-
Williams, K.1
-
42
-
-
84867230056
-
5-hmC in the brain is abundant in synaptic genes and shows differences at the exon-intron boundary
-
Khare, T. et al. 5-hmC in the brain is abundant in synaptic genes and shows differences at the exon-intron boundary. Nat. Struct. Mol. Biol. 19, 1037-1043 (2012).
-
(2012)
Nat. Struct. Mol. Biol.
, vol.19
, pp. 1037-1043
-
-
Khare, T.1
-
43
-
-
84901291138
-
The genome in three dimensions: A new frontier in human brain research
-
Mitchell, A.C. et al. The genome in three dimensions: a new frontier in human brain research. Biol. Psychiatry 75, 961-969 (2014).
-
(2014)
Biol. Psychiatry
, vol.75
, pp. 961-969
-
-
Mitchell, A.C.1
-
44
-
-
77952367798
-
Widespread transcription at neuronal activity-regulated enhancers
-
Kim, T.K. et al. Widespread transcription at neuronal activity-regulated enhancers. Nature 465, 182-187 (2010).
-
(2010)
Nature
, vol.465
, pp. 182-187
-
-
Kim, T.K.1
-
45
-
-
84870182699
-
Noncoding transcription at enhancers: General principles and functional models
-
Natoli, G. & Andrau, J.C. Noncoding transcription at enhancers: general principles and functional models. Annu. Rev. Genet. 46, 1-19 (2012).
-
(2012)
Annu. Rev. Genet.
, vol.46
, pp. 1-19
-
-
Natoli, G.1
Andrau, J.C.2
-
46
-
-
33751316959
-
In vivo enhancer analysis of human conserved non-coding sequences
-
Pennacchio, L.A. et al. In vivo enhancer analysis of human conserved non-coding sequences. Nature 444, 499-502 (2006).
-
(2006)
Nature
, vol.444
, pp. 499-502
-
-
Pennacchio, L.A.1
-
47
-
-
84886085321
-
New technologies for examining the role of neuronal ensembles in drug addiction and fear
-
Cruz, F.C. et al. New technologies for examining the role of neuronal ensembles in drug addiction and fear. Nat. Rev. Neurosci. 14, 743-754 (2013).
-
(2013)
Nat. Rev. Neurosci.
, vol.14
, pp. 743-754
-
-
Cruz, F.C.1
-
48
-
-
84871563384
-
MeCP2 binds to 5hmC enriched within active genes and accessible chromatin in the nervous system
-
Mellén, M., Ayata, P., Dewell, S., Kriaucionis, S. & Heintz, N. MeCP2 binds to 5hmC enriched within active genes and accessible chromatin in the nervous system. Cell 151, 1417-1430 (2012).
-
(2012)
Cell
, vol.151
, pp. 1417-1430
-
-
Mellén, M.1
Ayata, P.2
Dewell, S.3
Kriaucionis, S.4
Heintz, N.5
-
49
-
-
33847304609
-
Gene body-specifc methylation on the active X chromosome
-
Hellman, A. & Chess, A. Gene body-specifc methylation on the active X chromosome. Science 315, 1141-1143 (2007).
-
(2007)
Science
, vol.315
, pp. 1141-1143
-
-
Hellman, A.1
Chess, A.2
-
50
-
-
79956292024
-
Dual functions of Tet1 in transcriptional regulation in mouse embryonic stem cells
-
Wu, H. et al. Dual functions of Tet1 in transcriptional regulation in mouse embryonic stem cells. Nature 473, 389-393 (2011).
-
(2011)
Nature
, vol.473
, pp. 389-393
-
-
Wu, H.1
-
51
-
-
84874627808
-
Behavioral and structural responses to chronic cocaine require a feedforward loop involving DeltaFosB and calcium/calmodulin-dependent protein kinase II in the nucleus accumbens shell
-
Robison, A.J. et al. Behavioral and structural responses to chronic cocaine require a feedforward loop involving DeltaFosB and calcium/calmodulin-dependent protein kinase II in the nucleus accumbens shell. J. Neurosci. 33, 4295-4307 (2013).
-
(2013)
J. Neurosci.
, vol.33
, pp. 4295-4307
-
-
Robison, A.J.1
-
52
-
-
77952888646
-
DeltaFosB in brain reward circuits mediates resilience to stress and antidepressant responses
-
Vialou, V. et al. DeltaFosB in brain reward circuits mediates resilience to stress and antidepressant responses. Nat. Neurosci. 13, 745-752 (2010).
-
(2010)
Nat. Neurosci.
, vol.13
, pp. 745-752
-
-
Vialou, V.1
-
53
-
-
77955909841
-
MTOR-dependent synapse formation underlies the rapid antidepressant effects of NMDA antagonists
-
Li, N. et al. mTOR-dependent synapse formation underlies the rapid antidepressant effects of NMDA antagonists. Science 329, 959-964 (2010).
-
(2010)
Science
, vol.329
, pp. 959-964
-
-
Li, N.1
-
54
-
-
78651280460
-
Selective chemical labeling reveals the genome-wide distribution of 5-hydroxymethylcytosine
-
Song, C.X. et al. Selective chemical labeling reveals the genome-wide distribution of 5-hydroxymethylcytosine. Nat. Biotechnol. 29, 68-72 (2011).
-
(2011)
Nat. Biotechnol.
, vol.29
, pp. 68-72
-
-
Song, C.X.1
-
55
-
-
84861600498
-
Serum response factor and cAMP response element binding protein are both required for cocaine induction of DeltaFosB
-
Vialou, V. et al. Serum response factor and cAMP response element binding protein are both required for cocaine induction of DeltaFosB. J. Neurosci. 32, 7577-7584 (2012).
-
(2012)
J. Neurosci.
, vol.32
, pp. 7577-7584
-
-
Vialou, V.1
-
56
-
-
84885012678
-
Oxidative bisulfte sequencing of 5-methylcytosine and 5-hydroxymethylcytosine
-
Booth, M.J. et al. Oxidative bisulfte sequencing of 5-methylcytosine and 5-hydroxymethylcytosine. Nat. Protoc. 8, 1841-1851 (2013).
-
(2013)
Nat. Protoc.
, vol.8
, pp. 1841-1851
-
-
Booth, M.J.1
-
57
-
-
79957868920
-
Bismark: A fexible aligner and methylation caller for Bisulfte-Seq applications
-
Krueger, F. & Andrews, S.R. Bismark: a fexible aligner and methylation caller for Bisulfte-Seq applications. Bioinformatics 27, 1571-1572 (2011).
-
(2011)
Bioinformatics
, vol.27
, pp. 1571-1572
-
-
Krueger, F.1
Andrews, S.R.2
-
58
-
-
62349130698
-
Ultrafast and memory-effcient alignment of short DNA sequences to the human genome
-
Langmead, B., Trapnell, C., Pop, M. & Salzberg, S. Ultrafast and memory-effcient alignment of short DNA sequences to the human genome. Genome Biol. 10, R25 (2009).
-
(2009)
Genome Biol.
, vol.10
, pp. R25
-
-
Langmead, B.1
Trapnell, C.2
Pop, M.3
Salzberg, S.4
-
59
-
-
84878834064
-
DiffReps: Detecting differential chromatin modifcation sites from ChIP-seq data with biological replicates
-
Shen, L. et al. diffReps: detecting differential chromatin modifcation sites from ChIP-seq data with biological replicates. PLoS ONE 8, e65598 (2013).
-
(2013)
PLoS ONE
, vol.8
, pp. e65598
-
-
Shen, L.1
-
60
-
-
84857707318
-
ChromHMM: Automating chromatin-state discovery and characterization
-
Ernst, J. & Kellis, M. ChromHMM: automating chromatin-state discovery and characterization. Nat. Methods 9, 215-216 (2012).
-
(2012)
Nat. Methods
, vol.9
, pp. 215-216
-
-
Ernst, J.1
Kellis, M.2
-
61
-
-
84899493057
-
Ngs.plot: Quick mining and visualization of next-generation sequencing data by integrating genomic databases
-
Shen, L., Shao, N., Liu, X. & Nestler, E. ngs.plot: Quick mining and visualization of next-generation sequencing data by integrating genomic databases. BMC Genomics 15, 284 (2014).
-
(2014)
BMC Genomics
, vol.15
, pp. 284
-
-
Shen, L.1
Shao, N.2
Liu, X.3
Nestler, E.4
-
62
-
-
77952567987
-
Simple combinations of lineage-determining transcription factors prime cis-regulatory elements required for macrophage and B cell identities
-
Heinz, S. et al. Simple combinations of lineage-determining transcription factors prime cis-regulatory elements required for macrophage and B cell identities. Mol. Cell 38, 576-589 (2010).
-
(2010)
Mol. Cell
, vol.38
, pp. 576-589
-
-
Heinz, S.1
-
63
-
-
67849122320
-
MEME SUITE: Tools for motif discovery and searching
-
Bailey, T.L. et al. MEME SUITE: tools for motif discovery and searching. Nucleic Acids Res. 37, W202-W208 (2009).
-
(2009)
Nucleic Acids Res.
, vol.37
, pp. W202-W208
-
-
Bailey, T.L.1
-
64
-
-
61449172037
-
Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources
-
Huang, D.W., Sherman, B.T. & Lempicki, R.A. Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources. Nat. Protoc. 4, 44-57 (2009).
-
(2009)
Nat. Protoc.
, vol.4
, pp. 44-57
-
-
Huang, D.W.1
Sherman, B.T.2
Lempicki, R.A.3
-
65
-
-
84859885816
-
Differential gene and transcript expression analysis of RNA-seq experiments with TopHat and Cuffinks
-
Trapnell, C. et al. Differential gene and transcript expression analysis of RNA-seq experiments with TopHat and Cuffinks. Nat. Protoc. 7, 562-578 (2012).
-
(2012)
Nat. Protoc.
, vol.7
, pp. 562-578
-
-
Trapnell, C.1
-
66
-
-
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. B 57, 289-300 (1995).
-
(1995)
J. R. Stat. Soc. B
, vol.57
, pp. 289-300
-
-
Benjamini, Y.1
Hochberg, Y.2
|