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2014
D. M. Wolf
,
Fan, C.
,
Hoadley, K. A.
,
Yau, C.
,
Sokolov, A.
,
Network, T. C. G. A.
,
Stuart, J.
,
Perou, C.
, and
Veer, Lvan't
,
“
Thousands of published cancer signatures and pathways can be collapsed into a handful of non-redundant gene programs: a TCGA pan-cancer analysis
”
. American Association for Cancer Research, 2014.
P. C. Boutros
,
Margolin, A. A.
,
Stuart, J. M.
,
Califano, A.
, and
Stolovitzky, G.
,
“
Toward better benchmarking: challenge-based methods assessment in cancer genomics
”
,
Genome biology
, vol. 15, p. 462, 2014.
E. Jay Small
,
Youngren, J.
,
Beer, T. M.
,
Ryan, C. J.
,
Thomas, G.
,
Pourmand, N.
,
Reiter, R. Evan
,
Alumkal, J. J.
,
Stuart, J. M.
,
Evans, C. P.
, and
,
“
The molecular and pathway characterization of patients with metastatic castration resistant prostate cancer (mCRPC) refractory to therapy with abiraterone acetate or enzalutamide: Preliminary results from the SU2C/PCF/AACR West Coast Prostate Cancer Dream
”
. American Society of Clinical Oncology, 2014.
2013
L. M. Heiser
,
Shaw, C. A.
,
Wang, N. J.
,
Grasso, C.
,
Anur, P.
,
Ng, S.
,
Goldstein, T.
,
Spellman, P. T.
,
Stuart, J.
,
Osborne, K.
, and
,
“
Acquired therapeutic resistance is mediated by deregulation of multiple pathways.
”
. American Association for Cancer Research, 2013.
A. Gonzalez-Perez
,
Mustonen, V.
,
Reva, B.
,
Ritchie, G. R. S.
,
Creixell, P.
,
Karchin, R.
,
Vazquez, M.
,
J Fink, L.
,
Kassahn, K. S.
,
Pearson, J. V.
, and
,
“
Computational approaches to identify functional genetic variants in cancer genomes
”
,
Nature methods
, vol. 10, p. 723, 2013.
E. O. Paull
,
Carlin, D. E.
,
Niepel, M.
,
Sorger, P. K.
,
Haussler, D.
, and
Stuart, J. M.
,
“
Discovering causal pathways linking genomic events to transcriptional states using Tied Diffusion Through Interacting Events (TieDIE)
”
,
Bioinformatics
, vol. 29, pp. 2757–2764, 2013.
L. Omberg
,
Ellrott, K.
,
Yuan, Y.
,
Kandoth, C.
,
Wong, C.
,
Kellen, M. R.
,
Friend, S. H.
,
Stuart, J.
,
Liang, H.
, and
Margolin, A. A.
,
“
Enabling transparent and collaborative computational analysis of 12 tumor types within The Cancer Genome Atlas
”
,
Nature genetics
, vol. 45, p. 1121, 2013.
C. J. Schulze
,
Bray, W. M.
,
Woerhmann, M. H.
,
Stuart, J.
,
Lokey, S. R.
, and
Linington, R. G.
,
“
"Function-first" lead discovery: mode of action profiling of natural product libraries using image-based screening.
”
,
Chem Biol
, vol. 20, pp. 285–295, 2013.
R. Karchin
,
Ochs, M. F.
,
Stuart, J. M.
,
Ideker, T.
, and
Bader, J. S.
,
“
Identification of aberrant pathway and network activity from high-throughput data
”
, in
Biocomputing 2013
, 2013, pp. 103–110.
P. G. Febbo
,
Goldstein, T. C.
,
Baertsch, R.
,
Youngren, J.
,
Newton, Y.
,
Bivol, A.
,
Small, E. Jay
, and
Stuart, J. M.
,
“
Identification of polo-like kinase 1 (PLK1) in aggressive prostate cancer by paradigm analysis.
”
. American Society of Clinical Oncology, 2013.
D. A. Levine
,
Network, C. Genome Atl
, and
,
“
Integrated genomic characterization of endometrial carcinoma
”
,
Nature
, vol. 497, p. 67, 2013.
M. H. Woehrmann
,
Bray, W. M.
,
Durbin, J. K.
,
Nisam, S. C.
,
Michael, A. K.
,
Glassey, E.
,
Stuart, J. M.
, and
R Lokey, S.
,
“
Large-scale cytological profiling for functional analysis of bioactive compounds
”
,
Molecular BioSystems
, vol. 9, pp. 2604–2617, 2013.
T. Goldstein
,
Paull, E. O.
,
Ellis, M. J.
, and
Stuart, J. M.
,
“
Molecular Pathways: Extracting Medical Knowledge from High Throughput Genomic Data.
”
,
Clin Cancer Res
, 2013.
B. Craft
,
Swatloski, T.
,
Goldman, M.
,
Ellrott, K.
,
Ma, S.
,
Wilks, C.
,
Stuart, J.
,
Haussler, D.
, and
Zhu, J.
,
“
The New UCSC Cancer Genomics Browser
”
,
Nucleic Acids Research
, vol. 41, no. D1, 2013.
M. Goldman
,
Craft, B.
,
Swatloski, T.
,
Ellrott, K.
,
Cline, M.
,
Diekhans, M.
,
Ma, S.
,
Wilks, C.
,
Stuart, J.
,
Haussler, D.
, and
Zhu, J.
,
“
The UCSC Cancer Genomics Browser: update 2013.
”
,
Nucleic Acids Res
, vol. 41, pp. D949–D954, 2013.
C. K. Wong
,
Vaske, C. J.
,
Ng, S.
,
J Sanborn, Z.
,
Benz, S. C.
,
Haussler, D.
, and
Stuart, J. M.
,
“
The UCSC Interaction Browser: multidimensional data views in pathway context
”
,
Nucleic acids research
, vol. 41, pp. W218–W224, 2013.
J. N. Weinstein
,
Collisson, E. A.
,
Mills, G. B.
,
Shaw, K. R. Mills
,
Ozenberger, B. A.
,
Ellrott, K.
,
Shmulevich, I.
,
Sander, C.
,
Stuart, J. M.
,
Network, C. Genome Atl
, and
,
“
The cancer genome atlas pan-cancer analysis project
”
,
Nature genetics
, vol. 45, p. 1113, 2013.
C. W. Brennan
,
Verhaak, R. G. W.
,
McKenna, A.
,
Campos, B.
,
Noushmehr, H.
,
Salama, S. R.
,
Zheng, S.
,
Chakravarty, D.
,
J Sanborn, Z.
,
Berman, S. H.
, and
,
“
The somatic genomic landscape of glioblastoma
”
,
Cell
, vol. 155, pp. 462–477, 2013.
2012
The Cancer Genome Atlas Research Network
,
“
Comprehensive genomic characterization of squamous cell lung cancers
”
,
Nature
, vol. advance online publication, p. –, 2012.
C. Genome Atl Network
and
,
“
Comprehensive genomic characterization of squamous cell lung cancers
”
,
Nature
, vol. 489, p. 519, 2012.
R. Kucherlapati
and
The Cancer Genome Atlas,
“
Comprehensive molecular characterization of human colon and rectal cancer
”
,
Nature
, vol. 487, pp. 330–337, 2012.
C. Genome Atl Network
and
,
“
Comprehensive molecular characterization of human colon and rectal cancer
”
,
Nature
, vol. 487, p. 330, 2012.
TCGA
,
“
Comprehensive molecular portraits of human breast tumours.
”
,
Nature
, vol. 490, pp. 61–70, 2012.
C. Genome Atl Network
and
,
“
Comprehensive molecular portraits of human breast tumours
”
,
Nature
, vol. 490, p. 61, 2012.
R. Karchin
,
Ochs, M. F.
,
Stuart, J. M.
, and
Bader, J. S.
,
“
Identification of Aberrant Pathway and Network Activity from High-Throughput Data
”
, in
Pacific Symposium on Biocomputing
, 2012.
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