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2018
J. Saltz
,
Gupta, R.
,
Hou, L.
,
Kurc, T.
,
Singh, P.
,
Nguyen, V.
,
Samaras, D.
,
Shroyer, K. R.
,
Zhao, T.
,
Batiste, R.
, and
,
“
Spatial organization and molecular correlation of tumor-infiltrating lymphocytes using deep learning on pathology images
”
,
Cell reports
, vol. 23, p. 181, 2018.
R. G. Jayasinghe
,
Cao, S.
,
Gao, Q.
,
Wendl, M. C.
,
Vo, N. Sy
,
Reynolds, S. M.
,
Zhao, Y.
,
Climente-González, H.
,
Chai, S.
,
Wang, F.
, and
,
“
Systematic analysis of splice-site-creating mutations in cancer
”
,
Cell reports
, vol. 23, pp. 270–281, 2018.
A. C. Berger
,
Korkut, A.
,
Kanchi, R. S.
,
Hegde, A. M.
,
Lenoir, W.
,
Liu, W.
,
Liu, Y.
,
Fan, H.
,
Shen, H.
,
Ravikumar, V.
, and
,
“
A comprehensive Pan-Cancer molecular study of gynecologic and breast cancers
”
,
Cancer Cell
, vol. 33, pp. 690–705, 2018.
V. Thorsson
,
Gibbs, D. L.
,
Brown, S. D.
,
Wolf, D.
,
Bortone, D. S.
,
Yang, T. - H. Ou
,
Porta-Pardo, E.
,
Gao, G. F.
,
Plaisier, C. L.
,
Eddy, J. A.
, and
,
“
The immune landscape of cancer
”
,
Immunity
, vol. 48, pp. 812–830, 2018.
Z. Wang
,
Yang, B.
,
Zhang, M.
,
Guo, W.
,
Wu, Z.
,
Wang, Y.
,
Jia, L.
,
Li, S.
,
Caesar-Johnson, S. J.
,
Demchok, J. A.
, and
,
“
lncRNA Epigenetic Landscape Analysis Identifies EPIC1 as an Oncogenic lncRNA that Interacts with MYC and Promotes Cell-Cycle Progression in Cancer
”
,
Cancer Cell
, vol. 33, pp. 706–720, 2018.
2017
M. Niepel
,
Hafner, M.
,
Duan, Q.
,
Wang, Z.
,
Paull, E. O.
,
Chung, M.
,
Lu, X.
,
Stuart, J. M.
,
Golub, T. R.
,
Subramanian, A.
, and
,
“
Common and cell-type specific responses to anti-cancer drugs revealed by high throughput transcript profiling
”
,
Nature Communications
, vol. 8, p. 1186, 2017.
M. Gönen
,
Weir, B. A.
,
Cowley, G. S.
,
Vazquez, F.
,
Guan, Y.
,
Jaiswal, A.
,
Karasuyama, M.
,
Uzunangelov, V.
,
Wang, T.
,
Tsherniak, A.
, and
,
“
A Community Challenge for Inferring Genetic Predictors of Gene Essentialities through Analysis of a Functional Screen of Cancer Cell Lines
”
,
Cell systems
, vol. 5, pp. 485–497, 2017.
A. Ally
,
Balasundaram, M.
,
Carlsen, R.
,
Chuah, E.
,
Clarke, A.
,
Dhalla, N.
,
Holt, R. A.
,
Jones, S. J. M.
,
Lee, D.
,
Ma, Y.
, and
,
“
Comprehensive and integrative genomic characterization of hepatocellular carcinoma
”
,
Cell
, vol. 169, pp. 1327–1341, 2017.
L. Fishbein
,
Leshchiner, I.
,
Walter, V.
,
Danilova, L.
,
A Robertson, G.
,
Johnson, A. R.
,
Lichtenberg, T. M.
,
Murray, B. A.
,
Ghayee, H. K.
,
Else, T.
, and
,
“
Comprehensive molecular characterization of pheochromocytoma and paraganglioma
”
,
Cancer Cell
, vol. 31, pp. 181–193, 2017.
E. Rheinbay
,
Nielsen, M. Muhlig
,
Abascal, F.
,
Tiao, G.
,
Hornshøj, H.
,
Hess, J. M.
,
Pedersen, R. Istrup Ist
,
Feuerbach, L.
,
Sabarinathan, R.
,
Madsen, H. Tobias
, and
,
“
Discovery and characterization of coding and non-coding driver mutations in more than 2,500 whole cancer genomes
”
,
BioRxiv
, p. 237313, 2017.
H. Beale
,
Lam, D. Linh
,
Vivian, J.
,
Newton, Y.
,
Shah, A. Tayi
,
Bjork, I.
,
Goldstein, T.
,
Brooks, A. N.
,
Stuart, J.
,
Salama, S.
, and
,
“
Identifying confidently measured genes in single pediatric cancer patient samples using RNA sequencing
”
. American Association for Cancer Research, 2017.
C. Genome Atl Network
and
,
“
Integrated genomic and molecular characterization of cervical cancer
”
,
Nature
, vol. 543, p. 378, 2017.
G. A Robertson
,
Shih, J.
,
Yau, C.
,
Gibb, E. A.
,
Oba, J.
,
Mungall, K. L.
,
Hess, J. M.
,
Uzunangelov, V.
,
Walter, V.
,
Danilova, L.
, and
,
“
Integrative analysis identifies four molecular and clinical subsets in uveal melanoma
”
,
Cancer cell
, vol. 32, pp. 204–220, 2017.
F. Farshidfar
,
Zheng, S.
,
Gingras, M. - C.
,
Newton, Y.
,
Shih, J.
,
A Robertson, G.
,
Hinoue, T.
,
Hoadley, K. A.
,
Gibb, E. A.
,
Roszik, J.
, and
,
“
Integrative genomic analysis of cholangiocarcinoma identifies distinct IDH-mutant molecular profiles
”
,
Cell reports
, vol. 18, pp. 2780–2794, 2017.
J. Guinney
,
Wang, T.
,
Laajala, T. D.
,
Winner, K. Kanigel
,
J Bare, C.
,
Neto, E. Chaibub
,
Khan, S. A.
,
Peddinti, G.
,
Airola, A.
,
Pahikkala, T.
, and
,
“
Prediction of overall survival for patients with metastatic castration-resistant prostate cancer: development of a prognostic model through a crowdsourced challenge with open clinical trial data
”
,
The Lancet Oncology
, vol. 18, pp. 132–142, 2017.
Y. Newton
,
Novak, A. M.
,
Swatloski, T.
,
McColl, D. C.
,
Chopra, S.
,
Graim, K.
,
Weinstein, A. S.
,
Baertsch, R.
,
Salama, S. R.
,
Ellrott, K.
, and
,
“
TumorMap: exploring the molecular similarities of cancer samples in an interactive portal
”
,
Cancer research
, vol. 77, pp. e111–e114, 2017.
O. Morozova
,
Newton, Y.
,
Shah, A. Tayi
,
Beale, H.
,
Lam, D. Linh
,
Vivian, J.
,
Bjork, I.
,
Goldstein, T.
,
Stuart, J.
,
Salama, S.
, and
,
“
A pan-cancer analysis framework for incorporating gene expression information into clinical interpretation of pediatric cancer genomic data
”
. American Association for Cancer Research, 2017.
2016
E. Jay Small
,
Aggarwal, R. Raj
,
Huang, J.
,
Sokolov, A.
,
Zhang, L.
,
Alumkal, J. J.
,
Youngren, J.
,
Ryan, C. J.
,
Foye, A.
,
Reiter, R. Evan
, and
,
“
Clinical and genomic characterization of metastatic small cell/neuroendocrine prostate cancer (SCNC) and intermediate atypical prostate cancer (IAC): Results from the SU2C/PCF/AACRWest Coast Prostate Cancer Dream Team (WCDT).
”
. American Society of Clinical Oncology, 2016.
H. A. Al-Ahmadie
,
Lerner, S.
,
Kim, J.
,
Getz, G.
,
Kwiatkowski, D. J.
,
Weinstein, J.
,
Cherniack, A.
,
Guo, G.
,
Akbani, R.
,
Hoadley, K. A.
, and
,
“
Comprehensive molecular characterization of 412 muscle invasive urothelial carcinomas of the bladder-final analysis of the cancer genome atlas (TCGA) project
”
, in
LABORATORY INVESTIGATION
, 2016, vol. 96, p. 213A–214A.
J. N. Weinstein
,
Lerner, S. P.
,
Kwiatkowski, D. J.
,
Getz, G.
,
Kim, J.
,
Al-ahmadie, H. A.
,
Cherniack, A. D.
,
Guo, G.
,
Akbani, R.
,
Hoadley, K. A.
, and
,
“
Comprehensive molecular characterization of 412 muscle-invasive urothelial bladder carcinomas: final analysis of The Cancer Genome Atlas (TCGA) project
”
. American Association for Cancer Research, 2016.
T. T. Liu
,
Achrol, A. S.
,
Mitchell, L. A.
,
Du, W. A.
,
Loya, J. J.
,
Rodriguez, S. A.
,
Feroze, A.
,
Westbroek, E. M.
,
Yeom, K. W.
,
Stuart, J. M.
, and
,
“
Computational identification of tumor anatomic location associated with survival in 2 large cohorts of human primary glioblastomas
”
,
American Journal of Neuroradiology
, 2016.
W. Kim
,
Ryan, C. J.
,
Zhang, L.
,
Youngren, J.
,
Wilton, J.
,
Alumkal, J. J.
,
Beer, T. M.
,
Baertsch, R.
,
Stuart, J.
,
Chi, K. N.
, and
,
“
Dehydroepiandrosterone (DHEA) in metastatic castration-resistant prostate cancer (mCRPC): Preliminary results from the SU2C/PCF/AACR West Coast Dream Team (WCDT).
”
. American Society of Clinical Oncology, 2016.
W. Kim
,
Ryan, C. J.
,
Zhang, L.
,
Youngren, J.
,
Wilton, J.
,
Alumkal, J. J.
,
Beer, T. M.
,
Baertsch, R.
,
Stuart, J.
,
Chi, K. N.
, and
,
“
Dehydroepiandrosterone in metastatic castration-resistant prostate cancer: Preliminary results from the SU2C-PCF West Coast Dream Team (WCDT).
”
. American Society of Clinical Oncology, 2016.
J. D. Campbell
,
Alexandrov, A.
,
Kim, J.
,
Wala, J.
,
Berger, A. H.
,
Pedamallu, C. Sekhar
,
Shukla, S. A.
,
Guo, G.
,
Brooks, A. N.
,
Murray, B. A.
, and
,
“
Distinct patterns of somatic genome alterations in lung adenocarcinomas and squamous cell carcinomas
”
,
Nature genetics
, vol. 48, p. 607, 2016.
P. H. Waltman
,
Guo, J.
,
Reistetter, E. Nahas
,
Purvine, S.
,
Ansong, C. K.
,
Van Baren, M. J.
,
Wong, C. - H.
,
Wei, C. - L.
,
Smith, R. D.
,
Callister, S. J.
, and
,
“
Identifying aspects of the post-transcriptional program governing the proteome of the green alga Micromonas pusilla
”
,
PloS one
, vol. 11, p. e0155839, 2016.
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