-
1
-
-
21344470923
-
Circadian rhythms from multiple oscillators: Lessons from diverse organisms
-
Bell-Pedersen, D. et al. Circadian rhythms from multiple oscillators: lessons from diverse organisms. Nat. Rev. Genet. 6, 544-556 (2005).
-
(2005)
Nat. Rev. Genet.
, vol.6
, pp. 544-556
-
-
Bell-Pedersen, D.1
-
2
-
-
52149109334
-
The genetics of mammalian circadian order and disorder: Implications for physiology and disease
-
Takahashi, J. S., Hong, H. K., Ko, C. H. &McDearmon, E. L. The genetics of mammalian circadian order and disorder: implications for physiology and disease. Nat. Rev. Genet. 9, 764-775 (2008).
-
(2008)
Nat. Rev. Genet.
, vol.9
, pp. 764-775
-
-
Takahashi, J.S.1
Hong, H.K.2
Ko, C.H.3
McDearmon, E.L.4
-
3
-
-
84859962240
-
The circadian clock and pathology of the ageing brain
-
Kondratova, A. A. &Kondratov, R. V. The circadian clock and pathology of the ageing brain. Nat. Rev. Neurosci. 13, 325-335 (2012).
-
(2012)
Nat. Rev. Neurosci.
, vol.13
, pp. 325-335
-
-
Kondratova, A.A.1
Kondratov, R.V.2
-
4
-
-
80051623066
-
Circadian rhythms, aging, and life span in mammals
-
Froy, O. Circadian rhythms, aging, and life span in mammals. Physiol. (Bethesda) 26, 225-235 (2011).
-
(2011)
Physiol. (Bethesda)
, vol.26
, pp. 225-235
-
-
Froy, O.1
-
5
-
-
33644617485
-
Rhythmic CLOCK-BMAL1 binding to multiple E-box motifs drives circadian Dbp transcription and chromatin transitions
-
Ripperger, J. A. &Schibler, U. Rhythmic CLOCK-BMAL1 binding to multiple E-box motifs drives circadian Dbp transcription and chromatin transitions. Nat. Genet. 38, 369-374 (2006).
-
(2006)
Nat. Genet.
, vol.38
, pp. 369-374
-
-
Ripperger, J.A.1
Schibler, U.2
-
6
-
-
0037194790
-
Coordination of circadian timing in mammals
-
Reppert, S. M. &Weaver, D. R. Coordination of circadian timing in mammals. Nature 418, 935-941 (2002).
-
(2002)
Nature
, vol.418
, pp. 935-941
-
-
Reppert, S.M.1
Weaver, D.R.2
-
7
-
-
84909592563
-
A circadian gene expression atlas in mammals: Implications for biology and medicine
-
Zhang, R., Lahens, N. F., Ballance, H. I., Hughes, M. E. &Hogenesch, J. B. A circadian gene expression atlas in mammals: implications for biology and medicine. Proc. Natl Acad. Sci. USA 111, 16219-16224 (2014).
-
(2014)
Proc. Natl Acad. Sci. USA
, vol.111
, pp. 16219-16224
-
-
Zhang, R.1
Lahens, N.F.2
Ballance, H.I.3
Hughes, M.E.4
Hogenesch, J.B.5
-
8
-
-
84894590704
-
Reprogramming of the circadian clock by nutritional challenge
-
Eckel-Mahan, K. L. et al. Reprogramming of the circadian clock by nutritional challenge. Cell 155, 1464-1478 (2013).
-
(2013)
Cell
, vol.155
, pp. 1464-1478
-
-
Eckel-Mahan, K.L.1
-
9
-
-
79959366611
-
A molecular mechanism for circadian clock negative feedback
-
Duong, H. A., Robles, M. S., Knutti, D. &Weitz, C. J. A molecular mechanism for circadian clock negative feedback. Science 332, 1436-1439 (2011).
-
(2011)
Science
, vol.332
, pp. 1436-1439
-
-
Duong, H.A.1
Robles, M.S.2
Knutti, D.3
Weitz, C.J.4
-
10
-
-
78649886477
-
The histone methyltransferase MLL1 permits the oscillation of circadian gene expression
-
Katada, S. &Sassone-Corsi, P. The histone methyltransferase MLL1 permits the oscillation of circadian gene expression. Nat. Struct. Mol. Biol. 17, 1414-1421 (2010).
-
(2010)
Nat. Struct. Mol. Biol.
, vol.17
, pp. 1414-1421
-
-
Katada, S.1
Sassone-Corsi, P.2
-
11
-
-
84867667011
-
Transcriptional architecture and chromatin landscape of the core circadian clock in mammals
-
Koike, N. et al. Transcriptional architecture and chromatin landscape of the core circadian clock in mammals. Science 338, 349-354 (2012).
-
(2012)
Science
, vol.338
, pp. 349-354
-
-
Koike, N.1
-
12
-
-
84923314840
-
Daily variation in global and local DNA methylation in mouse livers
-
Xia, L. et al. Daily variation in global and local DNA methylation in mouse livers. PLoS ONE 10, e0118101 (2015).
-
(2015)
PLoS ONE
, vol.10
, pp. e0118101
-
-
Xia, L.1
-
13
-
-
84896727522
-
Circadian behavior is light-reprogrammed by plastic DNA methylation
-
Azzi, A. et al. Circadian behavior is light-reprogrammed by plastic DNA methylation. Nat. Neurosci. 17, 377-382 (2014).
-
(2014)
Nat. Neurosci.
, vol.17
, pp. 377-382
-
-
Azzi, A.1
-
14
-
-
84870553909
-
Circadian oscillations of protein-coding and regulatory RNAs in a highly dynamic mammalian liver epigenome
-
Vollmers, C. et al. Circadian oscillations of protein-coding and regulatory RNAs in a highly dynamic mammalian liver epigenome. Cell. Metab. 16, 833-845 (2012).
-
(2012)
Cell. Metab.
, vol.16
, pp. 833-845
-
-
Vollmers, C.1
-
15
-
-
84912078490
-
24-hour rhythms of DNA methylation and their relation with rhythms of RNA expression in the human dorsolateral prefrontal cortex
-
Lim, A. S. et al. 24-hour rhythms of DNA methylation and their relation with rhythms of RNA expression in the human dorsolateral prefrontal cortex. PLoS Genet. 10, e1004792 (2014).
-
(2014)
PLoS Genet.
, vol.10
, pp. e1004792
-
-
Lim, A.S.1
-
16
-
-
84857784165
-
Library-free methylation sequencing with bisulfite padlock probes
-
Diep, D. et al. Library-free methylation sequencing with bisulfite padlock probes. Nat. Methods 9, 270-272 (2012).
-
(2012)
Nat. Methods
, vol.9
, pp. 270-272
-
-
Diep, D.1
-
17
-
-
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
-
18
-
-
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
-
19
-
-
84928980786
-
Circadian rhythm reprogramming during lung inflammation
-
Haspel, J. A. et al. Circadian rhythm reprogramming during lung inflammation. Nat. Commun. 5, 4753 (2014).
-
(2014)
Nat. Commun.
, vol.5
, pp. 4753
-
-
Haspel, J.A.1
-
20
-
-
84875443859
-
Circadian control of the immune system
-
Scheiermann, C., Kunisaki, Y. &Frenette, P. S. Circadian control of the immune system. Nat. Rev. Immunol. 13, 190-198 (2013).
-
(2013)
Nat. Rev. Immunol.
, vol.13
, pp. 190-198
-
-
Scheiermann, C.1
Kunisaki, Y.2
Frenette, P.S.3
-
21
-
-
0038185378
-
Genomic targets of the human c-Myc protein
-
Fernandez, P. C. et al. Genomic targets of the human c-Myc protein. Genes Dev. 17, 1115-1129 (2003).
-
(2003)
Genes Dev.
, vol.17
, pp. 1115-1129
-
-
Fernandez, P.C.1
-
22
-
-
0029864934
-
Discrimination between different Ebox-binding proteins at an endogenous target gene of c-myc
-
Desbarats, L., Gaubatz, S. &Eilers, M. Discrimination between different Ebox-binding proteins at an endogenous target gene of c-myc. Genes Dev. 10, 447-460 (1996).
-
(1996)
Genes Dev.
, vol.10
, pp. 447-460
-
-
Desbarats, L.1
Gaubatz, S.2
Eilers, M.3
-
23
-
-
13444270415
-
Myc represses transcription through recruitment of DNA methyltransferase corepressor
-
Brenner, C. et al. Myc represses transcription through recruitment of DNA methyltransferase corepressor. EMBO J. 24, 336-346 (2005).
-
(2005)
EMBO J.
, vol.24
, pp. 336-346
-
-
Brenner, C.1
-
24
-
-
84884784742
-
Age-associated epigenetic drift: Implications, and a case of epigenetic thrift?
-
Teschendorff, A. E., West, J. &Beck, S. Age-associated epigenetic drift: implications, and a case of epigenetic thrift? Hum. Mol. Genet. 22, R7-R15 (2013).
-
(2013)
Hum. Mol. Genet.
, vol.22
, pp. R7-R15
-
-
Teschendorff, A.E.1
West, J.2
Beck, S.3
-
25
-
-
84964300307
-
Epigenetic assimilation in the aging human brain
-
Oh, G. et al. Epigenetic assimilation in the aging human brain. Genome Biol. 17, 76 (2016).
-
(2016)
Genome Biol.
, vol.17
, pp. 76
-
-
Oh, G.1
-
26
-
-
84919712381
-
Changes in nucleosome occupancy associated with metabolic alterations in aged mammalian liver
-
Bochkis, I. M., Przybylski, D., Chen, J. &Regev, A. Changes in nucleosome occupancy associated with metabolic alterations in aged mammalian liver. Cell Rep. 9, 996-1006 (2014).
-
(2014)
Cell Rep.
, vol.9
, pp. 996-1006
-
-
Bochkis, I.M.1
Przybylski, D.2
Chen, J.3
Regev, A.4
-
27
-
-
36248932675
-
Global expression profiles from C57BL/6J and DBA/2J mouse lungs to determine aging-related genes
-
Misra, V. et al. Global expression profiles from C57BL/6J and DBA/2J mouse lungs to determine aging-related genes. Physiol. Genom. 31, 429-440 (2007).
-
(2007)
Physiol. Genom.
, vol.31
, pp. 429-440
-
-
Misra, V.1
-
28
-
-
84923345958
-
Intermediate DNA methylation is a conserved signature of genome regulation
-
Elliott, G. et al. Intermediate DNA methylation is a conserved signature of genome regulation. Nat. Commun. 6, 6363 (2015).
-
(2015)
Nat. Commun.
, vol.6
, pp. 6363
-
-
Elliott, G.1
-
29
-
-
84878864199
-
The hallmarks of aging
-
Lopez-Otin, C., Blasco, M. A., Partridge, L., Serrano, M. &Kroemer, G. The hallmarks of aging. Cell 153, 1194-1217 (2013).
-
(2013)
Cell
, vol.153
, pp. 1194-1217
-
-
Lopez-Otin, C.1
Blasco, M.A.2
Partridge, L.3
Serrano, M.4
Kroemer, G.5
-
30
-
-
31844443695
-
The environment and disease: Association or causation?
-
Hill, A. B. The environment and disease: association or causation? Proc. R. Soc. Med. 58, 295-300 (1965).
-
(1965)
Proc. R. Soc. Med.
, vol.58
, pp. 295-300
-
-
Hill, A.B.1
-
31
-
-
84886111619
-
DNA methylation age of human tissues and cell types
-
Horvath, S. DNA methylation age of human tissues and cell types. Genome Biol. 14, R115 (2013).
-
(2013)
Genome Biol.
, vol.14
, pp. R115
-
-
Horvath, S.1
-
32
-
-
84991466905
-
DNA methylation-based measures of biological age: Metaanalysis predicting time to death
-
Chen, B. H. et al. DNA methylation-based measures of biological age: metaanalysis predicting time to death. Aging (Albany, NY) 8, 1844-1865 (2016).
-
(2016)
Aging (Albany, NY)
, vol.8
, pp. 1844-1865
-
-
Chen, B.H.1
-
33
-
-
84981165311
-
An epigenetic clock analysis of race/ethnicity, sex, and coronary heart disease
-
Horvath, S. et al. An epigenetic clock analysis of race/ethnicity, sex, and coronary heart disease. Genome Biol. 17, 171 (2016).
-
(2016)
Genome Biol.
, vol.17
, pp. 171
-
-
Horvath, S.1
-
34
-
-
85017019815
-
Huntington's disease accelerates epigenetic aging of human brain and disrupts DNA methylation levels
-
Horvath, S. et al. Huntington's disease accelerates epigenetic aging of human brain and disrupts DNA methylation levels. Aging (Albany, NY) 8, 1485-1512 (2016).
-
(2016)
Aging (Albany, NY)
, vol.8
, pp. 1485-1512
-
-
Horvath, S.1
-
35
-
-
84893397675
-
Senescent cells harbour features of the cancer epigenome
-
Cruickshanks, H. A. et al. Senescent cells harbour features of the cancer epigenome. Nat. Cell. Biol. 15, 1495-1506 (2013).
-
(2013)
Nat. Cell. Biol.
, vol.15
, pp. 1495-1506
-
-
Cruickshanks, H.A.1
-
36
-
-
84997784987
-
Circadian time signatures of fitness and disease
-
Bass, J. &Lazar, M. A. Circadian time signatures of fitness and disease. Science 354, 994-999 (2016).
-
(2016)
Science
, vol.354
, pp. 994-999
-
-
Bass, J.1
Lazar, M.A.2
-
37
-
-
84905049901
-
Trimmomatic: A flexible trimmer for Illumina sequence data
-
Bolger, A. M., Lohse, M. &Usadel, B. Trimmomatic: a flexible trimmer for Illumina sequence data. Bioinformatics 30, 2114-2120 (2014).
-
(2014)
Bioinformatics
, vol.30
, pp. 2114-2120
-
-
Bolger, A.M.1
Lohse, M.2
Usadel, B.3
-
38
-
-
79957868920
-
Bismark: A flexible aligner and methylation caller for Bisulfite-Seq applications
-
Krueger, F. &Andrews, S. R. Bismark: a flexible aligner and methylation caller for Bisulfite-Seq applications. Bioinformatics 27, 1571-1572 (2011).
-
(2011)
Bioinformatics
, vol.27
, pp. 1571-1572
-
-
Krueger, F.1
Andrews, S.R.2
-
39
-
-
84859210032
-
Fast gapped-read alignment with Bowtie 2
-
Langmead, B. &Salzberg, S. L. Fast gapped-read alignment with Bowtie 2. Nat. Methods 9, 357-359 (2012).
-
(2012)
Nat. Methods
, vol.9
, pp. 357-359
-
-
Langmead, B.1
Salzberg, S.L.2
-
40
-
-
11144358198
-
A gene atlas of the mouse and human protein-encoding transcriptomes
-
Su, A. I. et al. A gene atlas of the mouse and human protein-encoding transcriptomes. Proc. Natl Acad. Sci. USA 101, 6062-6067 (2004).
-
(2004)
Proc. Natl Acad. Sci. USA
, vol.101
, pp. 6062-6067
-
-
Su, A.I.1
-
41
-
-
84875498250
-
CircaDB: A database of mammalian circadian gene expression profiles
-
Pizarro, A., Hayer, K., Lahens, N. F. &Hogenesch, J. B. CircaDB: a database of mammalian circadian gene expression profiles. Nucleic Acids Res. 41, D1009-D1013 (2013).
-
(2013)
Nucleic Acids Res.
, vol.41
, pp. D1009-D1013
-
-
Pizarro, A.1
Hayer, K.2
Lahens, N.F.3
Hogenesch, J.B.4
-
42
-
-
85042034368
-
-
R core Team: A language and environment for statistical computing (R Foundation for Statistical Computing, Vienna, Austria, 2016)
-
R core Team: A language and environment for statistical computing (R Foundation for Statistical Computing, Vienna, Austria, 2016).
-
-
-
-
43
-
-
77952214662
-
GREAT improves functional interpretation of cisregulatory regions
-
McLean, C. Y. et al. GREAT improves functional interpretation of cisregulatory regions. Nat. Biotechnol. 28, 495-501 (2010).
-
(2010)
Nat. Biotechnol.
, vol.28
, pp. 495-501
-
-
McLean, C.Y.1
-
44
-
-
79960610118
-
REVIGO summarizes and visualizes long lists of gene ontology terms
-
Supek, F., Bosnjak, M., Skunca, N. &Smuc, T. REVIGO summarizes and visualizes long lists of gene ontology terms. PLoS ONE 6, e21800 (2011).
-
(2011)
PLoS ONE
, vol.6
, pp. e21800
-
-
Supek, F.1
Bosnjak, M.2
Skunca, N.3
Smuc, T.4
-
45
-
-
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
|