-
Notifications
You must be signed in to change notification settings - Fork 1
/
paper.bib
304 lines (270 loc) · 11.5 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
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
173
174
175
176
177
178
179
180
181
182
183
184
185
186
187
188
189
190
191
192
193
194
195
196
197
198
199
200
201
202
203
204
205
206
207
208
209
210
211
212
213
214
215
216
217
218
219
220
221
222
223
224
225
226
227
228
229
230
231
232
233
234
235
236
237
238
239
240
241
242
243
244
245
246
247
248
249
250
251
252
253
254
255
256
257
258
259
260
261
262
263
264
265
266
267
268
269
270
271
272
273
274
275
276
277
278
279
280
281
282
283
284
285
286
287
288
289
290
291
292
293
294
295
296
297
298
299
300
301
302
303
@article{bulik2015,
author = {Bulik-Sullivan, B. K. and Loh, P.-R. and Finucane, H. K. and Ripke, S. and Yang, J. and Patterson, N. and Daly, M. J. and Price, A. L. and Neale, B. M.},
journal = {Nature Genetics},
pages = {291-295},
title = {LD Score regression distinguishes confounding from polygenicity in genome-wide association studies},
volume = {47},
year = {2015},
}
@article{carter2013,
author = {Carter, H. and Douville, C. and Stenson, P. D. and Cooper, D. N. and Karchin, R.},
journal = {BMC Genomics},
title = {Identifying Mendelian disease genes with the variant effect scoring tool},
volume = {14},
year = {2013},
unidentified = {Suppl 3, S3},
}
@article{fernald2011,
author = {Fernald, G. H. and Capriotti, E. and Daneshjou, R. and Karczewski, K. J. and Altman, R. B.},
journal = {Bioinformatics},
pages = {1741-1748},
title = {Bioinformatics challenges for personalized medicine},
volume = {27},
year = {2011},
}
@article{fernandez2019,
author = {Fernández-Torras, A. and Duran-Frigola, M. and Aloy, P.},
journal = {Genome Medicine},
pages = {17},
title = {Encircling the regions of the pharmacogenomic landscape that determine drug response},
volume = {11},
year = {2019},
}
@unpublished{fuma,
url = {https://fuma.ctglab.nl/},
}
@article{afgan2018,
author = {Afgan, E. and Baker, D. and Batut, B. and van den Beek, M., Bouvier, D., Čech, M., Chilton, J., Clements, D., Coraor, N., Grüning, B., Guerler, A., Hillman-Jackson, J., Hiltemann, S., Jalili, V., Rasche, H., Soranzo, N., Goecks, J., Taylor, J., Nekrutenko},
journal = {Nucleic Acids Research},
pages = {W537-W544},
title = {The Galaxy platform for accessible, reproducible and collaborative biomedical analyses:update},
volume = {46},
year = {2018},
doi = {https://doi.org/10.1093/nar/gky379},
}
@article{hong2020,
author = {Hong, M. and Tao, S. and Zhang, L. and Diao, L.-T. and Huang, X. and Huang, S. and Xie, S.-J. and Xiao, Z.-D. and Zhang, H.},
journal = {J. Hematol. Oncol.J Hematol Oncol},
pages = {166},
title = {RNA sequencing: new technologies and applications in cancer research},
volume = {13},
year = {2020},
}
@article{horak2016,
author = {Horak, P. and Fröhling, S. and Glimm, H.},
journal = {ESMO Open},
title = {Integrating next-generation sequencing into clinical oncology: strategies, promises and pitfalls},
volume = {1},
year = {2016},
}
@article{hormozdiari2014,
author = {Hormozdiari, F. and Kostem, E. and Kang, E. Y. and Pasaniuc, B. and Eskin, E.},
journal = {Genetics},
pages = {497-508},
title = {Identifying Causal Variants at Loci with Multiple Signals of Association},
volume = {198},
year = {2014},
}
@article{hester2019,
author = {Jim Hester},
journal = {R package version},
title = {gmailr: Access the 'Gmail' 'RESTful' API},
volume = {1},
year = {2019},
url = {https://CRAN.R-project.org/package=gmailr},
unidentified = {0.0},
}
@article{karczewski2020,
author = {Karczewski, K. J. and Francioli, L. C. and Tiao, G. and Cummings, B. B. and Alföldi, J. and Wang, Q. and Collins, R. L. and Laricchia, K. M. and Ganna, A. and Birnbaum, D. P. and others},
journal = {Nature},
pages = {434},
title = {The mutational constraint spectrum quantified from variation in 141,456 humans},
volume = {581},
year = {2020},
}
@article{kim2019,
author = {Kim, D. and Paggi, J. M. and Park, C. and Bennett, C. and Salzberg, S. L.},
journal = {Nature Biotechnolology},
pages = {907},
title = {Graph-based genome alignment and genotyping with HISAT2 and HISAT-genotype},
volume = {37},
year = {2019},
unidentified = {–915},
}
@article{liao2014,
author = {Liao, Y. and Smyth, G. K. and Shi, W.},
journal = {Bioinforma. Oxf. Engl.},
pages = {923-930},
title = {featureCounts: an efficient general purpose program for assigning sequence reads to genomic features},
volume = {30},
year = {2014},
}
@article{narrandes2018,
author = {Narrandes, S. and Xu, W.},
journal = {J. Cancer},
pages = {2249-2265},
title = {Gene Expression Detection Assay for Cancer Clinical Use},
volume = {9},
year = {2018},
}
@article{niknafs2013,
author = {Niknafs, N. and Kim, D. and Kim, R. and Diekhans, M. and Ryan, M. and Stenson, P. D. and Cooper, D. N. and Karchin, R.},
journal = {Human Genetics},
pages = {1235-1243},
title = {MuPIT interactive: webserver for mapping variant positions to annotated, interactive 3D structures},
volume = {132},
year = {2013},
}
@article{pagel2020,
author = {Kymberleigh A. Pagel and Rick Kim and Kyle Moad and Ben Busby and Lily Zheng and Collin Tokheim and Michael Ryan and Rachel Karchin},
journal = {JCO Clinical Cancer Informatics},
pages = {310-317},
title = {Integrated Informatics Analysis of Cancer-Related Variants},
volume = {4},
year = {2020},
}
@incollection{pedersen2020,
author = {Pedersen, B. S. and Bhetariya, P. J. and Brown, J. and Kravitz, S. N. and Marth, G. and Jensen, R. L. and Bronner, M. P. and Underhill, H. R. and Quinlan, A. R.},
booktitle = {Genome Medicine},
title = {Somalier: rapid relatedness estimation for cancer and germline studies using efficient genome sketches},
year = {2020},
}
@article{picardi2017,
author = {Picardi, E. and D’Erchia, A. M. and Lo Giudice C., and Pesole, G},
journal = {Nucleic Acids Research},
title = {REDIportal: a comprehensive database of A-to-I RNA editing events in humans},
volume = {45},
year = {2017},
unidentified = {Nucleic Acids Research D750:D757},
}
@unpublished{plink,
author = {Plink Shaun Purcell},
url = {http://zzz.bwh.harvard.edu/plink/},
}
@article{purcell2007,
author = {Purcell, S. and Neale, B. and Todd-Brown, K. and Thomas, L. and Ferreira, M. A. R. and Bender, D. and Maller, J. and Sklar, P. and de Bakker, P. I. W. and Daly, M. J. and others},
journal = {American Journal of Human Genetics},
pages = {559-575},
title = {PLINK: a tool set for whole-genome association and population-based linkage analyses},
volume = {81},
year = {2007},
}
@article{robinson2010,
author = {Robinson, M. D. and McCarthy, D. J. and Smyth, G. K.},
journal = {Bioinforma. Oxf. Engl.},
pages = {139-140},
title = {edgeR: a Bioconductor package for differential expression analysis of digital gene expression data},
volume = {26},
year = {2010},
}
@article{sherry2001,
author = {Sherry, S. T. and Ward, M. H. and Kholodov, M. and Baker, J. and Phan, L. and Smigielski, E. M. and Sirotkin, K.},
journal = {Nucleic Acids Research},
pages = {308-311},
title = {dbSNP: the NCBI database of genetic variation},
volume = {29},
year = {2001},
}
@article{shihab2013,
author = {Shihab, H. A. and Gough, J. and Cooper, D. N. and Stenson, P. D. and Barker, G. L. A. and Edwards, K. J. and Day, I. N. M. and Gaunt, T. R. Predicting the functional},
journal = {Human Mutation},
pages = {57-65},
title = {molecular, and phenotypic consequences of amino acid substitutions using hidden {M}arkov models},
volume = {34},
year = {2013},
}
@book{star2021,
publisher = {January},
title = {STAR Fusion release and CTAT Genome Lib Compatibility Matrix GitHub},
year = {2021},
url = {https://github.com/STAR-Fusion/STAR-Fusion/wiki/STAR-Fusion-release-and-CTAT-Genome-Lib-Compatibility-Matrix},
}
@article{suzuki2019,
author = {Suzuki, A. and Onodera, K. and Matsui, K. and Seki, M. and Esumi, H. and Soga, T. and Sugano, S. and Kohno, T. and Suzuki, Y. and Tsuchihara, K.},
journal = {Scientific Reports},
pages = {19529},
title = {Characterization of cancer omics and drug perturbations in panels of lung cancer cells},
volume = {9},
year = {2019},
url = {https://doi.org/10.1038/s41598-019-55692-9},
}
@article{tate2019,
author = {Tate, J. G. and Bamford, S. and Jubb, H. C. and Sondka, Z. and Beare, D. M. and Bindal, N. and Boutselakis, H. and Cole, C. G. and Creatore, C. and Dawson, E. and others},
journal = {Nucleic Acids Research},
pages = {D941-D947},
title = {COSMIC: the Catalogue Of Somatic Mutations In Cancer},
volume = {47},
year = {2019},
}
@unpublished{kero2021,
month = {January},
title = {The DataBase of Kashiwa Encyclopedia of Researchers of multi-Omics data (DBKERO)},
year = {2021},
url = {https://kero.hgc.jp/},
}
@article{tokheim2019,
author = {Tokheim, C. and Karchin, R.},
journal = {Cell Syst.},
pages = {9-23},
title = {CHASMplus Reveals the Scope of Somatic Missense Mutations Driving Human Cancers},
volume = {9},
year = {2019},
unidentified = {e8},
}
@article{watanabe2017,
author = {Watanabe, K. and Taskesen, E. and van Bochoven, A. and Posthuma, D.},
journal = {Nature Communications},
pages = {1826},
title = {Functional mapping and annotation of genetic associations with FUMA},
volume = {8},
year = {2017},
}
@article{yoshihara2013,
author = {Yoshihara, K. and Shahmoradgoli, M. and Martínez, E. and Vegesna, R. and Kim, H. and Torres-Garcia, W. and Treviño, V. and Shen, H. and Laird, P. W. and Levine, D. A. and others},
journal = {Nature Communications},
pages = {2612},
title = {Inferring tumour purity and stromal and immune cell admixture from expression data},
volume = {4},
year = {2013},
}
@article{zhang2020,
author = {Zhang, J. and Liu, J. and Lee, D. and Feng, J.-J. and Lochovsky, L. and Lou, S. and Rutenberg-Schoenberg, M. and Gerstein, M.},
journal = {Genome Biol},
pages = {151},
title = {RADAR: annotation and prioritization of variants in the post-transcriptional regulome of RNA-binding proteins},
volume = {21},
year = {2020},
}
@article{smith2012,
author = {Smith, Richard N. and Aleksic, Jelena and Butano, Daniela and Carr, Adrian and Contrino, Sergio and Hu, Fengyuan and Lyne, Mike and Lyne, Rachel and Kalderimis, Alex and Rutherford, Kim and Stepan, Radek and Sullivan, Julie and Wakeling, Matthew and Watkins, Xavier and Micklem, Gos},
title = "{InterMine: a flexible data warehouse system for the integration and analysis of heterogeneous biological data}",
journal = {Bioinformatics},
volume = {28},
number = {23},
pages = {3163-3165},
year = {2012},
month = {09},
abstract = "{Summary: InterMine is an open-source data warehouse system that facilitates the building of databases with complex data integration requirements and a need for a fast customizable query facility. Using InterMine, large biological databases can be created from a range of heterogeneous data sources, and the extensible data model allows for easy integration of new data types. The analysis tools include a flexible query builder, genomic region search and a library of ‘widgets’ performing various statistical analyses. The results can be exported in many commonly used formats. InterMine is a fully extensible framework where developers can add new tools and functionality. Additionally, there is a comprehensive set of web services, for which client libraries are provided in five commonly used programming languages.Availability: Freely available from http://www.intermine.org under the LGPL license.Contact:[email protected] information:Supplementary data are available at Bioinformatics online.}",
issn = {1367-4803},
doi = {10.1093/bioinformatics/bts577},
url = {https://doi.org/10.1093/bioinformatics/bts577},
eprint = {https://academic.oup.com/bioinformatics/article-pdf/28/23/3163/18530235/bts577.pdf},
}
@article{fan2020,
author = {Fan, M. and Xia, P. and Clarke, R. and others},
journal = {Nat Commun},
pages = {4861},
title = {Radiogenomic signatures reveal multiscale intratumour heterogeneity associated with biological functions and survival in breast cancer},
volume = {11},
year = {2020},
url = {https://doi.org/10.1038/s41467-020-18703-2},
}
@article{haas2019,
author = {Haas, B. J. and Dobin, A. and Li, B. and others},
journal = {Genome Biol},
pages = {213},
title = {Accuracy assessment of fusion transcript detection via read-mapping and de novo fusion transcript assembly-based methods},
volume = {20},
year = {2019},
url = {https://doi.org/10.1186/s13059-019-1842-9},
}