-
1
-
-
84864031521
-
Base-pair resolution DNA methylation sequencing reveals profoundly divergent epigenetic landscapes in acute myeloid leukemia
-
Akalin A, Garrett-Bakelman FE, Kormaksson M, Busuttil J, Zhang L, Khrebtukova I et al (2012a). Base-pair resolution DNA methylation sequencing reveals profoundly divergent epigenetic landscapes in acute myeloid leukemia. PLoS Genet 8: e1002781.
-
(2012)
PLoS Genet
, vol.8
, pp. e1002781
-
-
Akalin, A.1
Garrett-Bakelman, F.E.2
Kormaksson, M.3
Busuttil, J.4
Zhang, L.5
Khrebtukova, I.6
-
2
-
-
84866860221
-
MethylKit: A comprehensive R package for the analysis of genome-wide DNA methylation profiles
-
Akalin A, Kormaksson M, Li S, Garrett-Bakelman FE, Figueroa ME, Melnick A et al (2012b). methylKit: a comprehensive R package for the analysis of genome-wide DNA methylation profiles. Genome Biol 13: R87.
-
(2012)
Genome Biol
, vol.13
, pp. R87
-
-
Akalin, A.1
Kormaksson, M.2
Li, S.3
Garrett-Bakelman, F.E.4
Figueroa, M.E.5
Melnick, A.6
-
4
-
-
84859412462
-
Genome-wide DNA methylation differences between late-onset Alzheimer's disease and cognitively normal controls in human frontal cortex
-
Bakulski KM DD, Sartor MA, Paulson HL, Konen JR, Lieberman AP, Albin RL et al (2012). Genome-wide DNA methylation differences between late-onset Alzheimer's disease and cognitively normal controls in human frontal cortex. J Alzheimers Dis 29: 571-588.
-
(2012)
J Alzheimers Dis
, vol.29
, pp. 571-588
-
-
Bakulski, K.M.D.D.1
Sartor, M.A.2
Paulson, H.L.3
Konen, J.R.4
Lieberman, A.P.5
Albin, R.L.6
-
5
-
-
84869496854
-
Epigenetic variation: Origin and transgenerational inheritance
-
Becker C, Weigel D (2012). Epigenetic variation: origin and transgenerational inheritance. Curr Opin Plant Biol 15: 562-567.
-
(2012)
Curr Opin Plant Biol
, vol.15
, pp. 562-567
-
-
Becker, C.1
Weigel, D.2
-
6
-
-
0001677717
-
Controlling the false discovery rate: A practical and powerful approach to multiple testing
-
Benjamini Y, Hochberg Y (1995). Controlling the false discovery rate: a practical and powerful approach to multiple testing. J R Stat Soc B 57: 289-300.
-
(1995)
J R Stat Soc B
, vol.57
, pp. 289-300
-
-
Benjamini, Y.1
Hochberg, Y.2
-
7
-
-
36349011849
-
Genes2Networks: Connecting lists of gene symbols using mammalian protein interactions databases
-
Berger S, Posner J, Ma'ayan A (2007). Genes2Networks: connecting lists of gene symbols using mammalian protein interactions databases. BMC Bioinformatics 8: 372.
-
(2007)
BMC Bioinformatics
, vol.8
, pp. 372
-
-
Berger, S.1
Posner Ma'Ayan J, A.2
-
8
-
-
84871688621
-
Analysing and interpreting DNA methylation data
-
Bock C (2010). Analysing and interpreting DNA methylation data. Nat Rev Genet 13: 705-719.
-
(2010)
Nat Rev Genet
, vol.13
, pp. 705-719
-
-
Bock, C.1
-
9
-
-
79251567720
-
DNA methylation of the first exon is tightly linked to transcriptional silencing
-
Brenet F, Moh M, Funk P, Feierstein E, Viale A, Socci N et al (2011). DNA methylation of the first exon is tightly linked to transcriptional silencing. PLoS One 6: e14524.
-
(2011)
PLoS One
, vol.6
, pp. e14524
-
-
Brenet, F.1
Moh, M.2
Funk, P.3
Feierstein, E.4
Viale, A.5
Socci, N.6
-
10
-
-
67349190247
-
Linking DNA methylation and histone modification: Patterns and paradigms
-
Cedar H, Bergman Y (2009). Linking DNA methylation and histone modification: patterns and paradigms. Nat Rev Genet 10: 295-304.
-
(2009)
Nat Rev Genet
, vol.10
, pp. 295-304
-
-
Cedar, H.1
Bergman, Y.2
-
11
-
-
77953510470
-
DNA methylation in vulnerability to post-traumatic stress in rats: Evidence for the role of the post-synaptic density protein Dlgap2
-
Chertkow-Deutsher Y, Cohen H, Klein E, Ben-Shachar D (2010). DNA methylation in vulnerability to post-traumatic stress in rats: evidence for the role of the post-synaptic density protein Dlgap2. Int J Neuropsychopharmacol 13: 347-359.
-
(2010)
Int J Neuropsychopharmacol
, vol.13
, pp. 347-359
-
-
Chertkow-Deutsher, Y.1
Cohen, H.2
Klein, E.3
Ben-Shachar, D.4
-
12
-
-
84919784465
-
Alzheimer's disease: Early alterations in brain DNA methylation at ANK1, BIN1, RHBDF2 and other loci
-
De Jager PL SG, Lunnon K, Burgess J, Schalkwyk LC, Yu L, Eaton ML et al (2014). Alzheimer's disease: early alterations in brain DNA methylation at ANK1, BIN1, RHBDF2 and other loci. Nat Neurosci 17: 1156-1163.
-
(2014)
Nat Neurosci
, vol.17
, pp. 1156-1163
-
-
De Jager, P.L.S.G.1
Lunnon, K.2
Burgess, J.3
Schalkwyk, L.C.4
Yu, L.5
Eaton, M.L.6
-
13
-
-
79956330964
-
CpG islands and the regulation of transcription
-
Deaton A, Bird A (2011). CpG islands and the regulation of transcription. Genes Dev 25: 1010-1022.
-
(2011)
Genes Dev
, vol.25
, pp. 1010-1022
-
-
Deaton, A.1
Bird, A.2
-
14
-
-
84856356408
-
Rat models of prenatal and adolescent Cannabis exposure
-
Dinieri JA, Hurd YL (2012). Rat models of prenatal and adolescent Cannabis exposure. Methods Mol Biol 829: 231-242.
-
(2012)
Methods Mol Biol
, vol.829
, pp. 231-242
-
-
DiNieri, J.A.1
Hurd, Y.L.2
-
16
-
-
60849139395
-
GOrilla: A tool for discovery and visualization of enriched GO terms in ranked gene lists
-
Eden E, Navon R, Steinfeld I, Lipson D, Yakhini Z (2009). GOrilla: a tool for discovery and visualization of enriched GO terms in ranked gene lists. BMC Bioinformatics 10: 48.
-
(2009)
BMC Bioinformatics
, vol.10
, pp. 48
-
-
Eden, E.1
Navon, R.2
Steinfeld, I.3
Lipson, D.4
Yakhini, Z.5
-
17
-
-
84881026418
-
Epigenetic mechanisms of drug addiction
-
Feng J, Nestler EJ (2013). Epigenetic mechanisms of drug addiction. Curr Opin Neurobiol 23: 521-528.
-
(2013)
Curr Opin Neurobiol
, vol.23
, pp. 521-528
-
-
Feng, J.1
Nestler, E.J.2
-
18
-
-
0023216891
-
CpG islands in vertebrate genomes
-
Gardiner-Garden M, Frommer M (1987). CpG islands in vertebrate genomes. J Mol Biol 196: 261-282.
-
(1987)
J Mol Biol
, vol.196
, pp. 261-282
-
-
Gardiner-Garden, M.1
Frommer, M.2
-
19
-
-
84859519339
-
Global profiling of DNA methylation erasure in mouse primordial germ cells
-
Guibert S, Forne T, Weber M (2012). Global profiling of DNA methylation erasure in mouse primordial germ cells. Genome Res 22: 633-641.
-
(2012)
Genome Res
, vol.22
, pp. 633-641
-
-
Guibert, S.1
Forne, T.2
Weber, M.3
-
20
-
-
84923634571
-
Tissue-specific effects of genetic and epigenetic variation on gene regulation and splicing
-
Gutierrez-Arcelus M, Ongen H, Lappalainen T, Montgomery SB, Buil A, Yurovsky A et al (2015). Tissue-specific effects of genetic and epigenetic variation on gene regulation and splicing. PLoS Genet 11: e1004958.
-
(2015)
PLoS Genet
, vol.11
, pp. e1004958
-
-
Gutierrez-Arcelus, M.1
Ongen, H.2
Lappalainen, T.3
Montgomery, S.B.4
Buil, A.5
Yurovsky, A.6
-
21
-
-
84872770694
-
Germline DNA demethylation dynamics and imprint erasure through 5-hydroxymethylcytosine
-
Hackett JA, Sengupta R, Zylicz JJ, Murakami K, Lee C, Down TA et al (2013). Germline DNA demethylation dynamics and imprint erasure through 5-hydroxymethylcytosine. Science 339: 448-452.
-
(2013)
Science
, vol.339
, pp. 448-452
-
-
Hackett, J.A.1
Sengupta, R.2
Zylicz, J.J.3
Murakami, K.4
Lee, C.5
Down, T.A.6
-
22
-
-
84897139220
-
Transgenerational epigenetic inheritance: Myths and mechanisms
-
Heard E, Martienssen RA (2014). Transgenerational epigenetic inheritance: myths and mechanisms. Cell 157: 95-109.
-
(2014)
Cell
, vol.157
, pp. 95-109
-
-
Heard, E.1
Martienssen, R.A.2
-
23
-
-
55949137722
-
Persistent epigenetic differences associated with prenatal exposure to famine in humans
-
Heijmans BT, Tobi EW, Stein AD, Putter H, Blauw GJ, Susser ES et al (2008). Persistent epigenetic differences associated with prenatal exposure to famine in humans. Proc Natl Acad Sci USA 105: 17046-17049.
-
(2008)
Proc Natl Acad Sci USA
, vol.105
, pp. 17046-17049
-
-
Heijmans, B.T.1
Tobi, E.W.2
Stein, A.D.3
Putter, H.4
Blauw, G.J.5
Susser, E.S.6
-
25
-
-
84884692057
-
DNA methylation presents distinct binding sites for human transcription factors
-
Hu S, Wan J, Su Y, Song Q, Zeng Y, Nguyen HN et al (2013). DNA methylation presents distinct binding sites for human transcription factors. Elife 2: e00726.
-
(2013)
Elife
, vol.2
, pp. e00726
-
-
Hu, S.1
Wan, J.2
Su, Y.3
Song, Q.4
Zeng, Y.5
Nguyen, H.N.6
-
27
-
-
84893765473
-
Epigenome-wide differences in pathology-free regions of multiple sclerosis-affected brains
-
Huynh JL, Garg P, Thin TH, Yoo S, Dutta R, Trapp BD et al (2014). Epigenome-wide differences in pathology-free regions of multiple sclerosis-affected brains. Nat Neurosci 17: 121-130.
-
(2014)
Nat Neurosci
, vol.17
, pp. 121-130
-
-
Huynh, J.L.1
Garg, P.2
Thin, T.H.3
Yoo, S.4
Dutta, R.5
Trapp, B.D.6
-
28
-
-
84885366399
-
-
Institute for Social Research, The University of Michigan: Ann Arbor
-
Johnston LD, O'Malley PM, Miech RA, Bachman JG, Schulenberg JE (2015). Monitoring the Future national survey results on drug use: 1975-2014: Overview, key findings on adolescent drug use. Institute for Social Research, The University of Michigan: Ann Arbor.
-
(2015)
Monitoring the Future National Survey Results on Drug Use 1975-2014: Overview, Key Findings on Adolescent Drug Use
-
-
Johnston, L.D.1
O'Malley, P.M.2
Miech, R.A.3
Bachman, J.G.4
Schulenberg, J.E.5
-
29
-
-
84863986133
-
Functions of DNA methylation: Islands, start sites, gene bodies and beyond
-
Jones P (2012). Functions of DNA methylation: islands, start sites, gene bodies and beyond. Nat Rev Genet 13: 484-492.
-
(2012)
Nat Rev Genet
, vol.13
, pp. 484-492
-
-
Jones, P.1
-
30
-
-
0034284437
-
Repbase Update: A database and an electronic journal of repetitive elements
-
Jurka J (2000). Repbase Update: a database and an electronic journal of repetitive elements. Trends Genet 16: 418-420.
-
(2000)
Trends Genet
, vol.16
, pp. 418-420
-
-
Jurka, J.1
-
31
-
-
0036079158
-
The human genome browser at UCSC
-
Kent WJ SC, Furey TS, Roskin KM, Pringle TH, Zahler AM, Haussler D (2002). The human genome browser at UCSC. Genome Res 12: 996-1006.
-
(2002)
Genome Res
, vol.12
, pp. 996-1006
-
-
Kent, W.J.S.C.1
Furey, T.S.2
Roskin, K.M.3
Pringle, T.H.4
Zahler, A.M.5
Haussler, D.6
-
33
-
-
79957868920
-
Bismark: A flexible aligner and methylation caller for Bisulfite-Seq applications
-
Krueger F, Andrews SR (2011) Bismark: a flexible aligner and methylation caller for Bisulfite-Seq applicationsBioinformatics 27: 1571-1572.
-
(2011)
Bioinformatics
, vol.27
, pp. 1571-1572
-
-
Krueger, F.1
Andrews, S.R.2
-
34
-
-
77949431355
-
Lists2Networks: Integrated analysis of gene/protein lists
-
Lachmann A, Ma'ayan A (2010). Lists2Networks: integrated analysis of gene/protein lists. BMC Bioinformatics 11: 87.
-
(2010)
BMC Bioinformatics
, vol.11
, pp. 87
-
-
Lachmann, A.1
Ma'Ayan, A.2
-
35
-
-
0037298161
-
Resistance of IAPs to methylation reprogramming may provide a mechanism for epigenetic inheritance in the mouse
-
Lane N, Dean W, Erhardt S, Hajkova P, Surani A, Walter J et al (2003). Resistance of IAPs to methylation reprogramming may provide a mechanism for epigenetic inheritance in the mouse. Genesis 35: 88-93.
-
(2003)
Genesis
, vol.35
, pp. 88-93
-
-
Lane, N.1
Dean, W.2
Erhardt, S.3
Hajkova, P.4
Surani, A.5
Walter, J.6
-
36
-
-
77954821594
-
What an epigenome remembers
-
Lange U, Schneider R (2010). What an epigenome remembers. Bioessays 32: 659-668.
-
(2010)
Bioessays
, vol.32
, pp. 659-668
-
-
Lange, U.1
Schneider, R.2
-
37
-
-
0035710746
-
Analysis of relative gene expression data using real-time quantitative PCR and the 2 (-Delta Delta C(T)) Method
-
Livak KJ, Schmittgen TD (2001). Analysis of relative gene expression data using real-time quantitative PCR and the 2 (-Delta Delta C(T)) Method. Methods 25: 402-408.
-
(2001)
Methods
, vol.25
, pp. 402-408
-
-
Livak, K.J.1
Schmittgen, T.D.2
-
38
-
-
84866170442
-
Endocannabinoid-dopamine interactions in striatal synaptic plasticity
-
Mathur BN, Lovinger DM (2012). Endocannabinoid-dopamine interactions in striatal synaptic plasticity. Front Pharmacol 3: 66.
-
(2012)
Front Pharmacol
, vol.3
, pp. 66
-
-
Mathur, B.N.1
Lovinger, D.M.2
-
39
-
-
84924696740
-
Astrocytic abnormalities and global DNA methylation patterns in depression and suicide
-
Nagy C, Suderman M, Yang J, Szyf M, Mechawar N, Ernst C et al (2015). Astrocytic abnormalities and global DNA methylation patterns in depression and suicide. Mol Psychiatry 20: 320-328.
-
(2015)
Mol Psychiatry
, vol.20
, pp. 320-328
-
-
Nagy, C.1
Suderman, M.2
Yang, J.3
Szyf, M.4
Mechawar, N.5
Ernst, C.6
-
40
-
-
84986250451
-
Methylomic profiling of human brain tissue supports a neurodevelopmental origin for schizophrenia
-
Pidsley R, Viana J, Hannon E, Spiers HH, Troakes C, Al-Saraj S et al (2014). Methylomic profiling of human brain tissue supports a neurodevelopmental origin for schizophrenia. Genome Biol 15: 483.
-
(2014)
Genome Biol
, vol.15
, pp. 483
-
-
Pidsley, R.1
Viana, J.2
Hannon, E.3
Spiers, H.H.4
Troakes, C.5
Al-Saraj, S.6
-
41
-
-
84866862172
-
Protection against de novo methylation is instrumental in maintaining parent-of-origin methylation inherited from the gametes
-
Proudhon C, Duffie R, Ajjan S, Cowley M, Iranzo J, Carbajosa G et al (2012). Protection against de novo methylation is instrumental in maintaining parent-of-origin methylation inherited from the gametes. Mol Cell 47: 909-920.
-
(2012)
Mol Cell
, vol.47
, pp. 909-920
-
-
Proudhon, C.1
Duffie, R.2
Ajjan, S.3
Cowley, M.4
Iranzo, J.5
Carbajosa, G.6
-
42
-
-
77951770756
-
BEDTools: A flexible suite of utilities for comparing genomic features
-
Quinlan AR, Hall IM (2011). BEDTools: a flexible suite of utilities for comparing genomic features. Bioinformatics 26: 841-842.
-
(2011)
Bioinformatics
, vol.26
, pp. 841-842
-
-
Quinlan, A.R.1
Hall, I.M.2
-
44
-
-
84898026391
-
The impact of environmental factors in severe psychiatric disorders
-
Schmitt A, Malchow B, Hasan A, Falkai P (2014). The impact of environmental factors in severe psychiatric disorders. Front Neurosci 8: 19.
-
(2014)
Front Neurosci
, vol.8
, pp. 19
-
-
Schmitt, A.1
Malchow, B.2
Hasan, A.3
Falkai, P.4
-
46
-
-
84923928121
-
Methylomic trajectories across human fetal brain development
-
Spiers H, Hannon E, Schalkwyk LC, Smith R, Wong CC, O'Donovan MC et al (2015). Methylomic trajectories across human fetal brain development. Genome Res 25: 338-352.
-
(2015)
Genome Res
, vol.25
, pp. 338-352
-
-
Spiers, H.1
Hannon, E.2
Schalkwyk, L.C.3
Smith, R.4
Wong, C.C.5
O'Donovan, M.C.6
-
47
-
-
84900791580
-
Parental THC exposure leads to compulsive heroin-seeking and altered striatal synaptic plasticity in the subsequent generation
-
Szutorisz H, DiNieri JA, Sweet E, Egervari G, Michaelides M, Carter JM et al (2014). Parental THC exposure leads to compulsive heroin-seeking and altered striatal synaptic plasticity in the subsequent generation. Neuropsychopharmacology 39: 1315-1323.
-
(2014)
Neuropsychopharmacology
, vol.39
, pp. 1315-1323
-
-
Szutorisz, H.1
DiNieri, J.A.2
Sweet, E.3
Egervari, G.4
Michaelides, M.5
Carter, J.M.6
-
48
-
-
84900873681
-
Mechanisms of epigenetic memory and addiction
-
Tuesta LM, Zhang Y (2014). Mechanisms of epigenetic memory and addiction. EMBO J 33: 1091-1103.
-
(2014)
EMBO J
, vol.33
, pp. 1091-1103
-
-
Tuesta, L.M.1
Zhang, Y.2
-
49
-
-
84892169991
-
Mechanisms of transgenerational inheritance of addictive-like behaviors
-
Vassoler FM, Sadri-Vakili G (2014). Mechanisms of transgenerational inheritance of addictive-like behaviors. Neuroscience 264: 198-206.
-
(2014)
Neuroscience
, vol.264
, pp. 198-206
-
-
Vassoler, F.M.1
Sadri-Vakili, G.2
-
50
-
-
84906240612
-
Epigenetic upregulation of PSD-95 contributes to the rewarding behavior by morphine conditioning
-
Wang Z, Yan P, Hui T, Zhang J (2014). Epigenetic upregulation of PSD-95 contributes to the rewarding behavior by morphine conditioning. Eur J Pharmacol 732: 123-129.
-
(2014)
Eur J Pharmacol
, vol.732
, pp. 123-129
-
-
Wang, Z.1
Yan, P.2
Hui, T.3
Zhang, J.4
-
51
-
-
77954269901
-
The GeneMANIA prediction server: Biological network integration for gene prioritization and predicting gene function
-
Warde-Farley D, Donaldson SL, Comes O, Zuberi K, Badrawi R, Chao P et al (2010). The GeneMANIA prediction server: biological network integration for gene prioritization and predicting gene function. Nucleic Acids Res 38: W214-W220.
-
(2010)
Nucleic Acids Res
, vol.38
, pp. W214-W220
-
-
Warde-Farley, D.1
Donaldson, S.L.2
Comes, O.3
Zuberi, K.4
Badrawi, R.5
Chao, P.6
-
52
-
-
84880041591
-
Developmental regulation of neuronal genes by DNA methylation: Environmental influences
-
Wilson ME, Sengoku T (2013). Developmental regulation of neuronal genes by DNA methylation: environmental influences. Int J Dev Neurosci 31: 448-451.
-
(2013)
Int J Dev Neurosci
, vol.31
, pp. 448-451
-
-
Wilson, M.E.1
Sengoku, T.2
-
53
-
-
84881167398
-
RCircos: An R package for Circos 2D track plots
-
Zhang H, Meltzer P, Davis S (2013). RCircos: an R package for Circos 2D track plots. BMC Bioinformatics 14: 244.
-
(2013)
BMC Bioinformatics
, vol.14
, pp. 244
-
-
Zhang, H.1
Meltzer, P.2
Davis, S.3
|