-
1
-
-
84903945993
-
Epigenetic regulation of pluripotency and differentiation
-
10.1161/circresaha.115.301517 4229506 1:CAS:528:DC%2BC2cXhtVOgtLzE 24989490
-
Boland MJ, Nazor KL, Loring JF. Epigenetic regulation of pluripotency and differentiation. Circ Res. 2014;115(2):311-24. doi: 10.1161/circresaha.115.301517.
-
(2014)
Circ Res
, vol.115
, Issue.2
, pp. 311-324
-
-
Boland, M.J.1
Nazor, K.L.2
Loring, J.F.3
-
2
-
-
80053304450
-
High density DNA methylation array with single CpG site resolution
-
10.1016/j.ygeno.2011.07.007 1:CAS:528:DC%2BC3MXht1ClsbfK 21839163
-
Bibikova M, Barnes B, Tsan C, Ho V, Klotzle B, Le JM, et al. High density DNA methylation array with single CpG site resolution. Genomics. 2011;98(4):288-95. doi: 10.1016/j.ygeno.2011.07.007.
-
(2011)
Genomics
, vol.98
, Issue.4
, pp. 288-295
-
-
Bibikova, M.1
Barnes, B.2
Tsan, C.3
Ho, V.4
Klotzle, B.5
Le, J.M.6
-
3
-
-
84884828422
-
Recommendations for the design and analysis of epigenome-wide association studies
-
10.1038/nmeth.2632 1:CAS:528:DC%2BC3sXhsFaks7rN 24076989
-
Michels KB, Binder AM, Dedeurwaerder S, Epstein CB, Greally JM, Gut I, et al. Recommendations for the design and analysis of epigenome-wide association studies. Nat Methods. 2013;10(10):949-55. doi: 10.1038/nmeth.2632.
-
(2013)
Nat Methods
, vol.10
, Issue.10
, pp. 949-955
-
-
Michels, K.B.1
Binder, A.M.2
Dedeurwaerder, S.3
Epstein, C.B.4
Greally, J.M.5
Gut, I.6
-
4
-
-
77952519089
-
DNA methylation as a universal biomarker
-
10.1586/erm.10.17 2933138 1:CAS:528:DC%2BC3cXmtVSnsrg%3D 20465502
-
Levenson VV. DNA methylation as a universal biomarker. Expert review of molecular diagnostics. 2010;10(4):481-8. doi: 10.1586/erm.10.17.
-
(2010)
Expert Review of Molecular Diagnostics.
, vol.10
, Issue.4
, pp. 481-488
-
-
Levenson, V.V.1
-
5
-
-
84927752388
-
Analysis pipelines and packages for Infinium HumanMethylation450 BeadChip (450 k) data
-
10.1016/j.ymeth.2014.08.011
-
Morris TJ, Beck S. Analysis pipelines and packages for Infinium HumanMethylation450 BeadChip (450 k) data. Methods. 2014;. doi: 10.1016/j.ymeth.2014.08.011.
-
(2014)
Methods
-
-
Morris, T.J.1
Beck, S.2
-
6
-
-
84908566266
-
Comprehensive analysis of DNA methylation data with RnBeads
-
Assenov Y, Muller F, Lutsik P, Walter J, Lengauer T, Bock C. Comprehensive analysis of DNA methylation data with RnBeads. Nat Meth. 2014;11(11):1138-40. doi: 10.1038/nmeth.3115. http://www.nature.com/nmeth/journal/v11/n11/abs/nmeth.3115.html#supplementary-information.
-
(2014)
Nat Meth.
, vol.11
, Issue.11
, pp. 1138-1140
-
-
Assenov, Y.1
Muller, F.2
Lutsik, P.3
Walter, J.4
Lengauer, T.5
Bock, C.6
-
7
-
-
84897548625
-
Minfi: A flexible and comprehensive Bioconductor package for the analysis of Infinium DNA methylation microarrays
-
10.1093/bioinformatics/btu049 4016708 1:CAS:528:DC%2BC2cXnslOit78%3D 24478339
-
Aryee MJ, Jaffe AE, Corrada-Bravo H, Ladd-Acosta C, Feinberg AP, Hansen KD, et al. Minfi: A flexible and comprehensive Bioconductor package for the analysis of Infinium DNA methylation microarrays. Bioinformatics. 2014;30(10):1363-9. doi: 10.1093/bioinformatics/btu049.
-
(2014)
Bioinformatics
, vol.30
, Issue.10
, pp. 1363-1369
-
-
Aryee, M.J.1
Jaffe, A.E.2
Corrada-Bravo, H.3
Ladd-Acosta, C.4
Feinberg, A.P.5
Hansen, K.D.6
-
8
-
-
84871688621
-
Analysing and interpreting DNA methylation data
-
10.1038/nrg3273 1:CAS:528:DC%2BC38XhtlGntrrF 22986265
-
Bock C. Analysing and interpreting DNA methylation data. Nat Rev Genet. 2012;13(10):705-19. doi: 10.1038/nrg3273.
-
(2012)
Nat Rev Genet
, vol.13
, Issue.10
, pp. 705-719
-
-
Bock, C.1
-
9
-
-
84869421697
-
Comb-p: Software for combining, analyzing, grouping and correcting spatially correlated P values
-
10.1093/bioinformatics/bts545 3496335 1:CAS:528:DC%2BC38Xhs1Glt7jM 22954632
-
Pedersen BS, Schwartz DA, Yang IV, Kechris KJ. Comb-p: software for combining, analyzing, grouping and correcting spatially correlated P values. Bioinformatics. 2012;28(22):2986-8. doi: 10.1093/bioinformatics/bts545.
-
(2012)
Bioinformatics
, vol.28
, Issue.22
, pp. 2986-2988
-
-
Pedersen, B.S.1
Schwartz, D.A.2
Yang, I.V.3
Kechris, K.J.4
-
10
-
-
84865760395
-
GENCODE: The reference human genome annotation for the ENCODE Project
-
10.1101/gr.135350.111 3431492 1:CAS:528:DC%2BC38XhtlentLvN 22955987
-
Harrow J, Frankish A, Gonzalez JM, Tapanari E, Diekhans M, Kokocinski F, et al. GENCODE: the reference human genome annotation for The ENCODE Project. Genome Res. 2012;22(9):1760-74. doi: 10.1101/gr.135350.111.
-
(2012)
Genome Res
, vol.22
, Issue.9
, pp. 1760-1774
-
-
Harrow, J.1
Frankish, A.2
Gonzalez, J.M.3
Tapanari, E.4
Diekhans, M.5
Kokocinski, F.6
-
11
-
-
84905454459
-
Systems-level regulation of microRNA networks by miR-130/301 promotes pulmonary hypertension
-
10.1172/JCI74773 4109523 1:CAS:528:DC%2BC2cXhtlGkt73L 24960162
-
Bertero T, Lu Y, Annis S, Hale A, Bhat B, Saggar R, et al. Systems-level regulation of microRNA networks by miR-130/301 promotes pulmonary hypertension. J Clin Investig. 2014;124(8):3514-28. doi: 10.1172/JCI74773.
-
(2014)
J Clin Investig
, vol.124
, Issue.8
, pp. 3514-3528
-
-
Bertero, T.1
Lu, Y.2
Annis, S.3
Hale, A.4
Bhat, B.5
Saggar, R.6
-
12
-
-
27344435774
-
Gene set enrichment analysis: A knowledge-based approach for interpreting genome-wide expression profiles
-
10.1073/pnas.0506580102 1239896 1:CAS:528:DC%2BD2MXht1ShtrnO 16199517
-
Subramanian A, Tamayo P, Mootha VK, Mukherjee S, Ebert BL, Gillette MA, et al. Gene set enrichment analysis: A knowledge-based approach for interpreting genome-wide expression profiles. Proc Natl Acad Sci. 2005;102(43):15545-50. doi: 10.1073/pnas.0506580102.
-
(2005)
Proc Natl Acad Sci
, vol.102
, Issue.43
, pp. 15545-15550
-
-
Subramanian, A.1
Tamayo, P.2
Mootha, V.K.3
Mukherjee, S.4
Ebert, B.L.5
Gillette, M.A.6
-
13
-
-
84875634162
-
Integrative Genomics Viewer (IGV): High-performance genomics data visualization and exploration
-
10.1093/bib/bbs017 3603213 1:CAS:528:DC%2BC3sXkvFKrur4%3D 22517427
-
Thorvaldsdottir H, Robinson JT, Mesirov JP. Integrative Genomics Viewer (IGV): high-performance genomics data visualization and exploration. Brief Bioinform. 2013;14(2):178-92. doi: 10.1093/bib/bbs017.
-
(2013)
Brief Bioinform.
, vol.14
, Issue.2
, pp. 178-192
-
-
Thorvaldsdottir, H.1
Robinson, J.T.2
Mesirov, J.P.3
-
14
-
-
0036079158
-
The human genome browser at UCSC
-
10.1101/gr.229102 186604 1:CAS:528:DC%2BD38Xks12hs7s%3D 12045153 (Article published online before print in May 2002)
-
Kent WJ, Sugnet CW, Furey TS, Roskin KM, Pringle TH, Zahler AM, et al. The human genome browser at UCSC. Genome Res. 2002;12(6):996-1006. doi: 10.1101/gr.229102 (Article published online before print in May 2002).
-
(2002)
Genome Res.
, vol.12
, Issue.6
, pp. 996-1006
-
-
Kent, W.J.1
Sugnet, C.W.2
Furey, T.S.3
Roskin, K.M.4
Pringle, T.H.5
Zahler, A.M.6
-
15
-
-
84873576566
-
Epigenome-wide association data implicate DNA methylation as an intermediary of genetic risk in rheumatoid arthritis
-
10.1038/nbt.2487 3598632 1:CAS:528:DC%2BC3sXhtFSgurs%3D 23334450
-
Liu Y, Aryee MJ, Padyukov L, Fallin MD, Hesselberg E, Runarsson A, et al. Epigenome-wide association data implicate DNA methylation as an intermediary of genetic risk in rheumatoid arthritis. Nat Biotechnol. 2013;31(2):142-7. doi: 10.1038/nbt.2487.
-
(2013)
Nat Biotechnol
, vol.31
, Issue.2
, pp. 142-147
-
-
Liu, Y.1
Aryee, M.J.2
Padyukov, L.3
Fallin, M.D.4
Hesselberg, E.5
Runarsson, A.6
-
16
-
-
84908566266
-
Comprehensive analysis of DNA methylation data with RnBeads
-
10.1038/nmeth.3115 4216143 1:CAS:528:DC%2BC2cXhs1yhtrbK 25262207
-
Assenov Y, Muller F, Lutsik P, Walter J, Lengauer T, Bock C. Comprehensive analysis of DNA methylation data with RnBeads. Nat Methods. 2014;11(11):1138-40. doi: 10.1038/nmeth.3115.
-
(2014)
Nat Methods
, vol.11
, Issue.11
, pp. 1138-1140
-
-
Assenov, Y.1
Muller, F.2
Lutsik, P.3
Walter, J.4
Lengauer, T.5
Bock, C.6
-
17
-
-
84922278143
-
The role of transcription factors in atrial fibrillation
-
10.3978/j.issn.2072-1439.2015.01.21 4321073 25713730
-
Zhou M, Liao Y, Tu X. The role of transcription factors in atrial fibrillation. J Thorac Dis. 2015;7(2):152-8. doi: 10.3978/j.issn.2072-1439.2015.01.21.
-
(2015)
J Thorac Dis.
, vol.7
, Issue.2
, pp. 152-158
-
-
Zhou, M.1
Liao, Y.2
Tu, X.3
-
18
-
-
77953095625
-
Pitx2 prevents susceptibility to atrial arrhythmias by inhibiting left-sided pacemaker specification
-
10.1073/pnas.0912585107 2906838 1:CAS:528:DC%2BC3cXntFGqtr8%3D 20457925
-
Wang J, Klysik E, Sood S, Johnson RL, Wehrens XH, Martin JF. Pitx2 prevents susceptibility to atrial arrhythmias by inhibiting left-sided pacemaker specification. Proc Natl Acad Sci USA. 2010;107(21):9753-8. doi: 10.1073/pnas.0912585107.
-
(2010)
Proc Natl Acad Sci USA.
, vol.107
, Issue.21
, pp. 9753-9758
-
-
Wang, J.1
Klysik, E.2
Sood, S.3
Johnson, R.L.4
Wehrens, X.H.5
Martin, J.F.6
-
19
-
-
84903451794
-
Pitx2-microRNA pathway that delimits sinoatrial node development and inhibits predisposition to atrial fibrillation
-
10.1073/pnas.1405411111 4078868 1:CAS:528:DC%2BC2cXpsVKjt7c%3D 24927531
-
Wang J, Bai Y, Li N, Ye W, Zhang M, Greene SB, et al. Pitx2-microRNA pathway that delimits sinoatrial node development and inhibits predisposition to atrial fibrillation. Proc Natl Acad Sci USA. 2014;111(25):9181-6. doi: 10.1073/pnas.1405411111.
-
(2014)
Proc Natl Acad Sci USA.
, vol.111
, Issue.25
, pp. 9181-9186
-
-
Wang, J.1
Bai, Y.2
Li, N.3
Ye, W.4
Zhang, M.5
Greene, S.B.6
-
20
-
-
34248994869
-
Gap junctional complexes: from partners to functions
-
10.1016/j.pbiomolbio.2007.03.010 1:CAS:528:DC%2BD2sXlvVOmu7Y%3D 17507078
-
Herve JC, Bourmeyster N, Sarrouilhe D, Duffy HS. Gap junctional complexes: from partners to functions. Prog Biophys Mol Biol. 2007;94(1-2):29-65. doi: 10.1016/j.pbiomolbio.2007.03.010.
-
(2007)
Prog Biophys Mol Biol
, vol.94
, Issue.1-2
, pp. 29-65
-
-
Herve, J.C.1
Bourmeyster, N.2
Sarrouilhe, D.3
Duffy, H.S.4
-
21
-
-
84878151322
-
SNP rs3825214 in TBX5 is associated with lone atrial fibrillation in Chinese Han population
-
10.1371/journal.pone.0064966 3663751 1:CAS:528:DC%2BC3sXptlSjsr4%3D 23717681
-
Zang X, Zhang S, Xia Y, Li S, Fu F, Li X, et al. SNP rs3825214 in TBX5 is associated with lone atrial fibrillation in Chinese Han population. PLoS One. 2013;8(5):e64966. doi: 10.1371/journal.pone.0064966.
-
(2013)
PLoS One
, vol.8
, Issue.5
, pp. e64966
-
-
Zang, X.1
Zhang, S.2
Xia, Y.3
Li, S.4
Fu, F.5
Li, X.6
-
22
-
-
84899657011
-
Emerging directions in the genetics of atrial fibrillation
-
10.1161/CIRCRESAHA.114.302225 4040146 1:CAS:528:DC%2BC2cXmslygtro%3D 24763465
-
Tucker NR, Ellinor PT. Emerging directions in the genetics of atrial fibrillation. Circ Res. 2014;114(9):1469-82. doi: 10.1161/CIRCRESAHA.114.302225.
-
(2014)
Circ Res
, vol.114
, Issue.9
, pp. 1469-1482
-
-
Tucker, N.R.1
Ellinor, P.T.2
-
23
-
-
34247590280
-
Tbx3 controls the sinoatrial node gene program and imposes pacemaker function on the atria
-
10.1101/gad.416007 1855235 1:CAS:528:DC%2BD2sXltFCns7w%3D 17473172
-
Hoogaars WM, Engel A, Brons JF, Verkerk AO, de Lange FJ, Wong LY, et al. Tbx3 controls the sinoatrial node gene program and imposes pacemaker function on the atria. Genes Dev. 2007;21(9):1098-112. doi: 10.1101/gad.416007.
-
(2007)
Genes Dev
, vol.21
, Issue.9
, pp. 1098-1112
-
-
Hoogaars, W.M.1
Engel, A.2
Brons, J.F.3
Verkerk, A.O.4
De Lange, F.J.5
Wong, L.Y.6
-
24
-
-
79954998151
-
Hox genes define distinct progenitor sub-domains within the second heart field
-
10.1016/j.ydbio.2011.02.029 3115524 1:CAS:528:DC%2BC3MXltFyitLk%3D 21385575
-
Bertrand N, Roux M, Ryckebusch L, Niederreither K, Dolle P, Moon A, et al. Hox genes define distinct progenitor sub-domains within the second heart field. Dev Biol. 2011;353(2):266-74. doi: 10.1016/j.ydbio.2011.02.029.
-
(2011)
Dev Biol
, vol.353
, Issue.2
, pp. 266-274
-
-
Bertrand, N.1
Roux, M.2
Ryckebusch, L.3
Niederreither, K.4
Dolle, P.5
Moon, A.6
-
25
-
-
84893325381
-
ChAMP: 450 k chip analysis methylation pipeline
-
10.1093/bioinformatics/btt684 3904520 1:CAS:528:DC%2BC2cXhs1CjtLo%3D 24336642
-
Morris TJ, Butcher LM, Feber A, Teschendorff AE, Chakravarthy AR, Wojdacz TK, et al. ChAMP: 450 k chip analysis methylation pipeline. Bioinformatics. 2014;30(3):428-30. doi: 10.1093/bioinformatics/btt684.
-
(2014)
Bioinformatics
, vol.30
, Issue.3
, pp. 428-430
-
-
Morris, T.J.1
Butcher, L.M.2
Feber, A.3
Teschendorff, A.E.4
Chakravarthy, A.R.5
Wojdacz, T.K.6
-
26
-
-
84863291989
-
MethLAB: A graphical user interface package for the analysis of array-based DNA methylation data
-
10.4161/epi.7.3.19284
-
Kilaru V, Barfield RT, Schroeder JW, Smith AK, Conneely KN. MethLAB: A graphical user interface package for the analysis of array-based DNA methylation data. Epigenet Off J of the DNA Methyl Soc. 2012;7(3):225-9. doi: 10.4161/epi.7.3.19284.
-
(2012)
Epigenet off J of the DNA Methyl Soc.
, vol.7
, Issue.3
, pp. 225-229
-
-
Kilaru, V.1
Barfield, R.T.2
Schroeder, J.W.3
Smith, A.K.4
Conneely, K.N.5
-
27
-
-
84878866495
-
COHCAP: An integrative genomic pipeline for single-nucleotide resolution DNA methylation analysis
-
10.1093/nar/gkt242 3675470 1:CAS:528:DC%2BC3sXptFCgu7k%3D 23598999
-
Warden CD, Lee H, Tompkins JD, Li X, Wang C, Riggs AD, et al. COHCAP: An integrative genomic pipeline for single-nucleotide resolution DNA methylation analysis. Nucleic Acids Res. 2013;41(11):e117. doi: 10.1093/nar/gkt242.
-
(2013)
Nucleic Acids Res
, vol.41
, Issue.11
, pp. e117
-
-
Warden, C.D.1
Lee, H.2
Tompkins, J.D.3
Li, X.4
Wang, C.5
Riggs, A.D.6
-
28
-
-
84886501367
-
EpiDiff: Entropy-based quantitative identification of differential epigenetic modification regions from epigenomes
-
10.1109/EMBC.2013.6609585 24109772
-
Zhang Y, Su J, Yu D, Wu Q, Yan H. EpiDiff: entropy-based quantitative identification of differential epigenetic modification regions from epigenomes. Conf Proc IEEE Eng Med Biol Soc. 2013;2013:655-8. doi: 10.1109/EMBC.2013.6609585.
-
(2013)
Conf Proc IEEE Eng Med Biol Soc.
, vol.2013
, pp. 655-658
-
-
Zhang, Y.1
Su, J.2
Yu, D.3
Wu, Q.4
Yan, H.5
-
29
-
-
34247884612
-
The function of programmed cell death 1 and its ligands in regulating autoimmunity and infection
-
10.1038/ni1443 1:CAS:528:DC%2BD2sXhslWms78%3D 17304234
-
Sharpe AH, Wherry EJ, Ahmed R, Freeman GJ. The function of programmed cell death 1 and its ligands in regulating autoimmunity and infection. Nat Immunol. 2007;8(3):239-45. doi: 10.1038/ni1443.
-
(2007)
Nat Immunol
, vol.8
, Issue.3
, pp. 239-245
-
-
Sharpe, A.H.1
Wherry, E.J.2
Ahmed, R.3
Freeman, G.J.4
-
30
-
-
77955801615
-
Galaxy: A comprehensive approach for supporting accessible, reproducible, and transparent computational research in the life sciences
-
10.1186/gb-2010-11-8-r86 2945788 20738864
-
Goecks J, Nekrutenko A, Taylor J, Galaxy T. Galaxy: A comprehensive approach for supporting accessible, reproducible, and transparent computational research in the life sciences. Genome Biol. 2010;11(8):R86. doi: 10.1186/gb-2010-11-8-r86.
-
(2010)
Genome Biol
, vol.11
, Issue.8
, pp. R86
-
-
Goecks, J.1
Nekrutenko, A.2
Taylor, J.3
Galaxy, T.4
-
31
-
-
84925554493
-
MIRPIPE: Quantification of microRNAs in niche model organisms
-
10.1093/bioinformatics/btu573 1:CAS:528:DC%2BC2MXisFaltbk%3D 25165094
-
Kuenne C, Preussner J, Herzog M, Braun T, Looso M. MIRPIPE: quantification of microRNAs in niche model organisms. Bioinformatics. 2014;30(23):3412-3. doi: 10.1093/bioinformatics/btu573.
-
(2014)
Bioinformatics
, vol.30
, Issue.23
, pp. 3412-3413
-
-
Kuenne, C.1
Preussner, J.2
Herzog, M.3
Braun, T.4
Looso, M.5
-
32
-
-
60849139395
-
GOrilla: A tool for discovery and visualization of enriched GO terms in ranked gene lists
-
10.1186/1471-2105-10-48
-
Eden E, Navon R, Steinfeld I, Lipson D, Yakhini Z. GOrilla: A tool for discovery and visualization of enriched GO terms in ranked gene lists. BMC Bioinform. 2009;10:48. doi: 10.1186/1471-2105-10-48.
-
(2009)
BMC Bioinform
, vol.10
, pp. 48
-
-
Eden, E.1
Navon, R.2
Steinfeld, I.3
Lipson, D.4
Yakhini, Z.5
|