Skip to main content
Systems Biology Group
Navigation
Welcome
In The News
People
Resources
Presentations
Publications
Authors
Keywords
Internal Lab Wiki
Contact Us
Biblio
Found 19 results
Filters:
Author
is
Haussler, David
[Clear All Filters]
2014
A. J. Radenbaugh
,
Ma, S.
,
Ewing, A.
,
Stuart, J. M.
,
Collisson, E. A.
,
Zhu, J.
, and
Haussler, D.
,
“
RADIA: RNA and DNA integrated analysis for somatic mutation detection
”
,
PloS one
, vol. 9, p. e111516, 2014.
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.
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.
2012
S. Ng
,
Collisson, E. A.
,
Sokolov, A.
,
Goldstein, T.
,
Gonzalez-Perez, A.
,
Lopez-Bigas, N.
,
Benz, C.
,
Haussler, D.
, and
Stuart, J. M.
,
“
PARADIGM-SHIFT predicts the function of mutations in multiple cancers using pathway impact analysis
”
,
Bioinformatics
, vol. 28, pp. i640-i646, 2012.
S. Ng
,
Collisson, E. A.
,
Sokolov, A.
,
Goldstein, T.
,
Gonzalez-Perez, A.
,
Lopez-Bigas, N.
,
Benz, C.
,
Haussler, D.
, and
Stuart, J. M.
,
“
PARADIGM-SHIFT predicts the function of mutations in multiple cancers using pathway impact analysis
”
,
Bioinformatics
, vol. 28, pp. i640–i646, 2012.
C. J. Vaske
,
Benz, S. C.
,
Stuart, J. M.
, and
Haussler, D.
,
“
Pathway recognition algorithm using data integration on genomic models (PARADIGM)
”
. 2012.
C. J. Vaske
,
Benz, S. C.
,
Stuart, J. M.
, and
Haussler, D.
,
“
Pathway recognition algorithm using data integration on genomic models (PARADIGM)
”
. 2012.
L. M. Heiser
,
Sadanandam, A.
,
Kuo, W. - L.
,
Benz, S. C.
,
Goldstein, T. C.
,
Ng, S.
,
Gibb, W. J.
,
Wang, N. J.
,
Ziyad, S.
,
Tong, F.
,
Bayani, N.
,
Hu, Z.
,
Billig, J. I.
,
Dueregger, A.
,
Lewis, S.
,
Jakkula, L.
,
Korkola, J. E.
,
Durinck, S.
,
Pepin, F.
,
Guan, Y.
,
Purdom, E.
,
Neuvial, P.
,
Bengtsson, H.
,
Wood, K. W.
,
Smith, P. G.
,
Vassilev, L. T.
,
Hennessy, B. T.
,
Greshock, J.
,
Bachman, K. E.
,
Hardwicke, M. A.
,
Park, J. W.
,
Marton, L. J.
,
Wolf, D. M.
,
Collisson, E. A.
,
Neve, R. M.
,
Mills, G. B.
,
Speed, T. P.
,
Feiler, H. S.
,
Wooster, R. F.
,
Haussler, D.
,
Stuart, J. M.
,
Gray, J. W.
, and
Spellman, P. T.
,
“
Subtype and pathway specific responses to anticancer compounds in breast cancer
”
,
Proceedings of the National Academy of Sciences
, vol. 109, pp. 2724-2729, 2012.
M. Goldman
,
Craft, B.
,
Swatloski, T.
,
Ellrott, K.
,
Cline, M.
,
Diekhans, M.
,
Wilks, C.
,
Stuart, J.
,
Haussler, D.
, and
Zhu, J.
,
“
The UCSC cancer genomics browser: update 2013
”
,
Nucleic acids research
, vol. 41, pp. D949–D954, 2012.
2011
B. Craft
,
Ellrott, K.
,
Goldman, M.
,
Wilks, C.
,
Szeto, C.
,
Ma, S.
,
Stuart, J.
,
Zhu, J.
, and
Haussler, D.
,
“
Abstract A39: The UCSC Cancer Genomics Browser
”
. American Association for Cancer Research, 2011.
A. Radenbaugh
,
Sanborn, J. Z.
,
Zerbino, D.
,
Wilks, C.
,
Stuart, J. M.
, and
Haussler, D.
,
“
Identification of RNA editing events in cancer using high-throughput sequencing data
”
. American Association for Cancer Research, 2011.
S. C. Benz
,
Vaske, C.
,
Ng, S.
,
Sanborn, J. Zachary
,
Zhu, J.
,
Haussler, D.
, and
Stuart, J.
,
“
Patient-specific pathway analysis using PARADIGM identifies key activities in multiple cancers
”
. American Association for Cancer Research, 2011.
Z. J. Sanborn
,
Benz, S. C.
,
Craft, B.
,
Szeto, C.
,
Kober, K. M.
,
Meyer, L.
,
Vaske, C. J.
,
Goldman, M.
,
Smith, K. E.
,
Kuhn, R. M.
,
Karolchik, D.
,
Kent, J. W.
,
Stuart, J. M.
,
Haussler, D.
, and
Zhu, J.
,
“
The UCSC cancer genomics browser: update 2011
”
,
Nucleic Acids Research
, vol. 39, pp. D951-D959, 2011.
C. W. Szeto
,
Zhu, J.
,
Durbin, J.
,
Benz, S.
,
Vaske, C.
,
Stuart, J.
, and
Haussler, D.
,
“
Using matrix factorization to discover clinically-relevant molecular signatures across cancers
”
. American Association for Cancer Research, 2011.
2010
C. J. Vaske
,
Benz, S. C.
,
Sanborn, Z. J.
,
Earl, D.
,
Szeto, C.
,
Zhu, J.
,
Haussler, D.
, and
Stuart, J. M.
,
“
Inference of patient-specific pathway activities from multi-dimensional cancer genomics data using PARADIGM
”
,
Bioinformatics
, vol. 26, pp. i237-i245, 2010.
C. J. Vaske
,
Benz, S. C.
,
J Sanborn, Z.
,
Earl, D.
,
Szeto, C.
,
Zhu, J.
,
Haussler, D.
, and
Stuart, J. M.
,
“
Inference of patient-specific pathway activities from multi-dimensional cancer genomics data using PARADIGM
”
,
Bioinformatics
, vol. 26, pp. i237–i245, 2010.
S. Christopher
,
Benz, S.
,
Vaske, C.
,
J Sanborn, Z.
,
Zhu, J.
,
Stuart, J.
, and
Haussler, D.
,
“
Non-negative matrix factorization (NMF) as a clinical classifier: An example with chemotherapy response in ovarian cancer
”
. American Association for Cancer Research, 2010.