-
Notifications
You must be signed in to change notification settings - Fork 0
/
paper.bib
103 lines (92 loc) · 3.47 KB
/
paper.bib
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
@Manual{R-DMRcate,
title = {DMRcate: Methylation array and sequencing spatial analysis methods},
author = {Tim Peters and Mike Buckley},
year = {2022},
note = {R package version 2.8.5},
}
@Article{DMRcate2015,
author = {Timothy J Peters and Michael J Buckley and Aaron L Statham and Ruth Pidsley and Katherine Samaras and Reginald V Lord and Susan J Clark and Peter L Molloy},
title = {De novo identification of differentially methylated regions in the human genome},
journal = {Epigenetics & Chromatin},
year = {2015},
volume = {8},
pages = {6},
url = {http://www.epigeneticsandchromatin.com/content/8/1/6},
}
@Article{DMRcate2021,
author = {Timothy J Peters and Michael J Buckley and {Yunshun Chen} and Gordon K Smyth and Christopher C Goodnow and Susan J Clark},
title = {Calling differentially methylated regions from whole genome bisulphite sequencing with DMRcate},
journal = {Nucleic Acids Research},
year = {2021},
volume = {49},
issue = {19},
url = {https://academic.oup.com/nar/article/49/19/e109/6329576},
}
@Article{Mallik2019a,
Author="Mallik, S. and Odom, G. J. and Gao, Z. and Gomez, L. and Chen, X. and Wang, L. ",
Title="{{A}n evaluation of supervised methods for identifying differentially methylated regions in {I}llumina methylation arrays}",
Journal="Brief Bioinform",
Year="2019",
Volume="20",
Number="6",
Pages="2224--2235",
Month="11"
}
@Article{bumphunter,
author = {Andrew E. Jaffe and Peter Murakami and Hwajin Lee and Jeffrey T. Leek and Daniele M. Fallin and Andrew P. Feinberg and Rafael A. Irizarry},
title = {Bump hunting to identify differentially methylated regions in epigenetic epidemiology studies},
journal = {International journal of epidemiology},
year = {2012},
volume = {41},
number = {1},
pages = {200--209},
doi = {10.1093/ije/dyr238},
pubmed = {22422453},
}
@Article{minfi,
title = {Minfi: A flexible and comprehensive Bioconductor package for the analysis of Infinium DNA Methylation microarrays},
author = {Martin J. Aryee and Andrew E. Jaffe and Hector Corrada-Bravo and Christine Ladd-Acosta and Andrew P. Feinberg and Kasper D. Hansen and Rafael A. Irizarry},
year = {2014},
journal = {Bioinformatics},
volume = {30},
number = {10},
pages = {1363--1369},
doi = {10.1093/bioinformatics/btu049},
pubmed = {24478339},
}
@Article{limma,
author = {Matthew E Ritchie and Belinda Phipson and Di Wu and Yifang Hu and Charity W Law and Wei Shi and Gordon K Smyth},
title = {{limma} powers differential expression analyses for {RNA}-sequencing and microarray studies},
journal = {Nucleic Acids Research},
year = {2015},
volume = {43},
number = {7},
pages = {e47},
doi = {10.1093/nar/gkv007},
}
@Article{Sun2019b,
Author="Sun, L. and Namboodiri, S. and Chen, E. and Sun, S. ",
Title="{{P}reliminary {A}nalysis of {W}ithin-{S}ample {C}o-methylation {P}atterns in {N}ormal and {C}ancerous {B}reast {S}amples}",
Journal="Cancer Inform",
Year="2019",
Volume="18",
Pages="1176935119880516"
}
@Article{Sun2019,
Author="Sun, L. and Sun, S. ",
Title="{{W}ithin-sample co-methylation patterns in normal tissues}",
Journal="BioData Min",
Year="2019",
Volume="12",
Pages="9"
}
@Article{sun2022,
Author="Sun, S. and Dammann, J. and Lai, P. and Tian, C. ",
Title="{{T}horough statistical analyses of breast cancer co-methylation patterns}",
Journal="BMC Genom Data",
Year="2022",
Volume="23",
Number="1",
Pages="29",
Month="04"
}