-
1
-
-
84884994218
-
The Cancer Genome Atlas Pan-Cancer analysis project
-
Weinstein JN, Collisson EA, Mills GB, Shaw KR, Ozenberger BA, Ellrott K, et al., Network CGAR: The Cancer Genome Atlas Pan-Cancer analysis project. Nat Genet. 2013;45:1113-20.
-
(2013)
Nat Genet
, vol.45
, pp. 1113-1120
-
-
Weinstein, J.N.1
Collisson, E.A.2
Mills, G.B.3
Shaw, K.R.4
Ozenberger, B.A.5
Ellrott, K.6
-
2
-
-
84908460595
-
Multiplatform analysis of 12 cancer types reveals molecular classification within and across tissues of origin
-
Hoadley KA, Yau C, Wolf DM, Cherniack AD, Tamborero D, Ng S, et al. Multiplatform analysis of 12 cancer types reveals molecular classification within and across tissues of origin. Cell. 2014;158:929-44.
-
(2014)
Cell
, vol.158
, pp. 929-944
-
-
Hoadley, K.A.1
Yau, C.2
Wolf, D.M.3
Cherniack, A.D.4
Tamborero, D.5
Ng, S.6
-
3
-
-
84899836282
-
Neo-antigens predicted by tumor genome meta-analysis correlate with increased patient survival
-
Brown SD, Warren RL, Gibb EA, Martin SD, Spinelli JJ, Nelson BH, Holt RA. Neo-antigens predicted by tumor genome meta-analysis correlate with increased patient survival. Genome Res. 2014;24:743-50.
-
(2014)
Genome Res
, vol.24
, pp. 743-750
-
-
Brown, S.D.1
Warren, R.L.2
Gibb, E.A.3
Martin, S.D.4
Spinelli, J.J.5
Nelson, B.H.6
Holt, R.A.7
-
4
-
-
79961123152
-
RSEM: Accurate transcript quantification from RNA-Seq data with or without a reference genome
-
Li B, Dewey CN: RSEM: accurate transcript quantification from RNA-Seq data with or without a reference genome. BMC Bioinformatics. 2011;12:323.
-
(2011)
BMC Bioinformatics
, vol.12
, pp. 323
-
-
Li, B.1
Dewey, C.N.2
-
5
-
-
84866002291
-
The cBio cancer genomics portal: An open platform for exploring multidimensional cancer genomics data
-
Cerami E, Gao J, Dogrusoz U, Gross BE, Sumer SO, Aksoy BA, et al. The cBio cancer genomics portal: an open platform for exploring multidimensional cancer genomics data. Cancer Discov. 2012;2:401-4.
-
(2012)
Cancer Discov
, vol.2
, pp. 401-404
-
-
Cerami, E.1
Gao, J.2
Dogrusoz, U.3
Gross, B.E.4
Sumer, S.O.5
Aksoy, B.A.6
-
6
-
-
84873922708
-
can-Evolve: A web portal for integrative oncogenomics
-
Samur MK, Yan Z, Wang X, Cao Q, Munshi NC, Li C, Shah PK. can-Evolve: a web portal for integrative oncogenomics. PLoS One 2013, 8:e56228.
-
(2013)
PLoS One
, vol.8
-
-
Samur, M.K.1
Yan, Z.2
Wang, X.3
Cao, Q.4
Munshi, N.C.5
Li, C.6
Shah, P.K.7
-
7
-
-
84924752548
-
PROGgeneV2: Enhancements on the existing database
-
Goswami CP, Nakshatri H. PROGgeneV2: enhancements on the existing database. BMC Cancer. 2014;14:970.
-
(2014)
BMC Cancer
, vol.14
, pp. 970
-
-
Goswami, C.P.1
Nakshatri, H.2
-
8
-
-
63849301203
-
The UCSC Cancer Genomics Browser
-
Zhu J, Sanborn JZ, Benz S, Szeto C, Hsu F, Kuhn RM, et al. The UCSC Cancer Genomics Browser. Nat Methods. 2009;6:239-40.
-
(2009)
Nat Methods
, vol.6
, pp. 239-240
-
-
Zhu, J.1
Sanborn, J.Z.2
Benz, S.3
Szeto, C.4
Hsu, F.5
Kuhn, R.M.6
-
9
-
-
84856535081
-
Mutual exclusivity analysis identifies oncogenic network modules
-
Ciriello G, Cerami E, Sander C, Schultz N. Mutual exclusivity analysis identifies oncogenic network modules. Genome Res. 2012;22:398-406.
-
(2012)
Genome Res
, vol.22
, pp. 398-406
-
-
Ciriello, G.1
Cerami, E.2
Sander, C.3
Schultz, N.4
-
10
-
-
79955166265
-
GISTIC2.0 facilitates sensitive and confident localization of the targets of focal somatic copy-number alteration in human cancers
-
Mermel CH, Schumacher SE, Hill B, Meyerson ML, Beroukhim R, Getz G: GISTIC2.0 facilitates sensitive and confident localization of the targets of focal somatic copy-number alteration in human cancers. Genome Biol. 2011;12:R41.
-
(2011)
Genome Biol
, vol.12
, pp. R41
-
-
Mermel, C.H.1
Schumacher, S.E.2
Hill, B.3
Meyerson, M.L.4
Beroukhim, R.5
Getz, G.6
-
11
-
-
84880507665
-
Mutational heterogeneity in cancer and the search for new cancer-associated genes
-
Lawrence MS, Stojanov P, Polak P, Kryukov GV, Cibulskis K, Sivachenko A, et al. Mutational heterogeneity in cancer and the search for new cancer-associated genes. Nature. 2013;499:214-8.
-
(2013)
Nature
, vol.499
, pp. 214-218
-
-
Lawrence, M.S.1
Stojanov, P.2
Polak, P.3
Kryukov, G.V.4
Cibulskis, K.5
Sivachenko, A.6
-
12
-
-
77954195272
-
Inference of patient-specific pathway activities from multi-dimensional cancer genomics data using PARADIGM
-
Vaske CJ, Benz SC, Sanborn JZ, Earl D, Szeto C, Zhu J, et al. Inference of patient-specific pathway activities from multi-dimensional cancer genomics data using PARADIGM. Bioinformatics. 2010;26:i237-245.
-
(2010)
Bioinformatics
, vol.26
, pp. i237-i245
-
-
Vaske, C.J.1
Benz, S.C.2
Sanborn, J.Z.3
Earl, D.4
Szeto, C.5
Zhu, J.6
-
13
-
-
33947305781
-
ARACNE: An algorithm for the reconstruction of gene regulatory networks in a mammalian cellular context
-
Margolin AA, Nemenman I, Basso K, Wiggins C, Stolovitzky G, Dalla Favera R, Califano A: ARACNE: an algorithm for the reconstruction of gene regulatory networks in a mammalian cellular context. BMC Bioinformatics. 2006;7(Suppl 1):S7.
-
(2006)
BMC Bioinformatics
, vol.7
, pp. S7
-
-
Margolin, A.A.1
Nemenman, I.2
Basso, K.3
Wiggins, C.4
Stolovitzky, G.5
Dalla Favera, R.6
Califano, A.7
-
14
-
-
60549111634
-
WGCNA: An R package for weighted correlation network analysis
-
Langfelder P, Horvath S. WGCNA: an R package for weighted correlation network analysis. BMC Bioinformatics. 2008;9:559.
-
(2008)
BMC Bioinformatics
, vol.9
, pp. 559
-
-
Langfelder, P.1
Horvath, S.2
-
15
-
-
27344435774
-
Gene set enrichment analysis: A knowledge-based approach for interpreting genome-wide expression profiles
-
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 U S A. 2005;102:15545-50.
-
(2005)
Proc Natl Acad Sci U S A
, vol.102
, pp. 15545-15550
-
-
Subramanian, A.1
Tamayo, P.2
Mootha, V.K.3
Mukherjee, S.4
Ebert, B.L.5
Gillette, M.A.6
-
16
-
-
84866929613
-
Integrative analysis of gene and miRNA expression profiles with transcription factor-miRNA feed-forward loops identifies regulators in human cancers
-
Yan Z, Shah PK, Amin SB, Samur MK, Huang N, Wang X, et al. Integrative analysis of gene and miRNA expression profiles with transcription factor-miRNA feed-forward loops identifies regulators in human cancers. Nucleic Acids Res. 2012;40:e135.
-
(2012)
Nucleic Acids Res
, vol.40
, pp. e135
-
-
Yan, Z.1
Shah, P.K.2
Amin, S.B.3
Samur, M.K.4
Huang, N.5
Wang, X.6
-
17
-
-
77949501173
-
DR-Integrator: A new analytic tool for integrating DNA copy number and gene expression data
-
Salari K, Tibshirani R, Pollack JR. DR-Integrator: a new analytic tool for integrating DNA copy number and gene expression data. Bioinformatics. 2010;26:414-6.
-
(2010)
Bioinformatics
, vol.26
, pp. 414-416
-
-
Salari, K.1
Tibshirani, R.2
Pollack, J.R.3
-
18
-
-
25844449770
-
Galaxy: A platform for interactive large-scale genome analysis
-
Giardine B, Riemer C, Hardison RC, Burhans R, Elnitski L, Shah P, et al. Galaxy: a platform for interactive large-scale genome analysis. Genome Res. 2005;15:1451-5.
-
(2005)
Genome Res
, vol.15
, pp. 1451-1455
-
-
Giardine, B.1
Riemer, C.2
Hardison, R.C.3
Burhans, R.4
Elnitski, L.5
Shah, P.6
-
19
-
-
84941092555
-
The UCSC Cancer Genomics Browser: Update 2015
-
Goldman M, Craft B, Swatloski T, Cline M, Morozova O, Diekhans M, et al. The UCSC Cancer Genomics Browser: update 2015. Nucleic Acids Res. 2015;43:D812-817.
-
(2015)
Nucleic Acids Res
, vol.43
, pp. D812-D817
-
-
Goldman, M.1
Craft, B.2
Swatloski, T.3
Cline, M.4
Morozova, O.5
Diekhans, M.6
-
20
-
-
77954238710
-
Human melanoma-initiating cells express neural crest nerve growth factor receptor CD271
-
Boiko AD, Razorenova OV, van de Rijn M, Swetter SM, Johnson DL, Ly DP, et al. Human melanoma-initiating cells express neural crest nerve growth factor receptor CD271. Nature. 2010;466:133-7.
-
(2010)
Nature
, vol.466
, pp. 133-137
-
-
Boiko, A.D.1
Razorenova, O.V.2
Van De Rijn, M.3
Swetter, S.M.4
Johnson, D.L.5
Ly, D.P.6
-
21
-
-
79954617310
-
Human CD271-positive melanoma stem cells associated with metastasis establish tumor heterogeneity and long-term growth
-
Civenni G, Walter A, Kobert N, Mihic-Probst D, Zipser M, Belloni B, et al. Human CD271-positive melanoma stem cells associated with metastasis establish tumor heterogeneity and long-term growth. Cancer Res. 2011;71:3098-09.
-
(2011)
Cancer Res
, vol.71
, pp. 3098-4009
-
-
Civenni, G.1
Walter, A.2
Kobert, N.3
Mihic-Probst, D.4
Zipser, M.5
Belloni, B.6
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