-
1
-
-
84880472975
-
Precision oncology: an overview
-
PID: 23589545
-
Garraway, L. A., Verweij, J. and Ballman, K. V. (2013) Precision oncology: an overview. J. Clin. Oncol., 31, 1803–1805
-
(2013)
J. Clin. Oncol.
, vol.31
, pp. 1803-1805
-
-
Garraway, L.A.1
Verweij, J.2
Ballman, K.V.3
-
2
-
-
84895900452
-
Rapid learning for precision oncology
-
PID: 24445514
-
Shrager, J. and Tenenbaum, J. M. (2014) Rapid learning for precision oncology. Nat. Rev. Clin. Oncol., 11, 109–118
-
(2014)
Nat. Rev. Clin. Oncol.
, vol.11
, pp. 109-118
-
-
Shrager, J.1
Tenenbaum, J.M.2
-
3
-
-
84908460595
-
Multiplatform analysis of 12 cancer types reveals molecular classification within and across tissues of origin
-
COI: 1:CAS:528:DC%2BC2cXhtleisrjJ, PID: 25109877
-
Hoadley, K. A., Yau, C.,Wolf, D. M., Cherniack, A. D., Tamborero, D., Ng, S., Leiserson, M. D., Niu, B., McLellan, M. D., Uzunangelov, V., et al. (2014) Multiplatform analysis of 12 cancer types reveals molecular classification within and across tissues of origin. Cell, 158, 929–944
-
(2014)
Cell
, vol.158
, pp. 929-944
-
-
Hoadley, K.A.Y.1
Wolf, D.M.2
Cherniack, A.D.3
Tamborero, D.4
Ng, S.5
Leiserson, M.D.6
Niu, B.7
McLellan, M.D.8
Uzunangelov, V.9
-
4
-
-
84925031191
-
Methods of integrating data to uncover genotype-phenotype interactions
-
COI: 1:CAS:528:DC%2BC2MXmslKrsA%3D%3D, PID: 25582081
-
Ritchie, M. D., Holzinger, E. R., Li, R., Pendergrass, S. A. and Kim, D. (2015) Methods of integrating data to uncover genotype-phenotype interactions. Nat. Rev. Genet., 16, 85–97
-
(2015)
Nat. Rev. Genet.
, vol.16
, pp. 85-97
-
-
Ritchie, M.D.1
Holzinger, E.R.2
Li, R.3
Pendergrass, S.A.4
Kim, D.5
-
5
-
-
84923369732
-
Breast tumor subgroups reveal diverse clinical prognostic power
-
PID: 24499868
-
Liu, Z., Zhang, X. S. and Zhang, S. (2014) Breast tumor subgroups reveal diverse clinical prognostic power. Sci. Rep., 4, 4002
-
(2014)
Sci. Rep.
, vol.4
, pp. 4002
-
-
Liu, Z.1
Zhang, X.S.2
Zhang, S.3
-
6
-
-
84903987099
-
The Pan-Cancer analysis of pseudogene expression reveals biologically and clinically relevant tumour subtypes
-
COI: 1:CAS:528:DC%2BC2cXhvF2mu7zP, PID: 24999802
-
Han, L., Yuan, Y., Zheng, S., Yang, Y., Li, J., Edgerton, M. E., Diao, L., Xu, Y., Verhaak, R. G. and Liang, H. (2014) The Pan-Cancer analysis of pseudogene expression reveals biologically and clinically relevant tumour subtypes. Nat. Commun., 5, 3963
-
(2014)
Nat. Commun.
, vol.5
, pp. 3963
-
-
Han, L.1
Yuan, Y.2
Zheng, S.3
Yang, Y.4
Li, J.5
Edgerton, M.E.6
Diao, L.7
Xu, Y.8
Verhaak, R.G.9
Liang, H.10
-
7
-
-
84861527388
-
The genomic and transcriptomic architecture of 2,000 breast tumours reveals novel subgroups
-
COI: 1:CAS:528:DC%2BC38XlslSnsL8%3D, PID: 22522925
-
Curtis, C., Shah, S. P., Chin, S. F., Turashvili, G., Rueda, O. M., Dunning, M. J., Speed, D., Lynch, A. G., Samarajiwa, S., Yuan, Y., et al. (2012) The genomic and transcriptomic architecture of 2,000 breast tumours reveals novel subgroups. Nature, 486, 346–352
-
(2012)
Nature
, vol.486
, pp. 346-352
-
-
Curtis, C.1
Shah, S.P.2
Chin, S.F.3
Turashvili, G.4
Rueda, O.M.5
Dunning, M.J.6
Speed, D.7
Lynch, A.G.8
Samarajiwa, S.9
Yuan, Y.10
-
8
-
-
84877028141
-
Comprehensive molecular portraits of human breast tumours
-
Cancer Genome Atlas, N. (2012) Comprehensive molecular portraits of human breast tumours. Nature, 490, 61–70
-
(2012)
Nature
, vol.490
, pp. 61-70
-
-
-
9
-
-
14544300998
-
Systematic review of microsatellite instability and colorectal cancer prognosis
-
COI: 1:CAS:528:DC%2BD2MXitVartLY%3D, PID: 15659508
-
Popat, S., Hubner, R. and Houlston, R. S. (2005) Systematic review of microsatellite instability and colorectal cancer prognosis. J. Clin. Oncol., 23, 609–618
-
(2005)
J. Clin. Oncol.
, vol.23
, pp. 609-618
-
-
Popat, S.1
Hubner, R.2
Houlston, R.S.3
-
10
-
-
10344260184
-
CpG island methylator phenotype in cancer
-
COI: 1:CAS:528:DC%2BD2cXhtVarsLjK, PID: 15573120
-
Issa, J. P. (2004) CpG island methylator phenotype in cancer. Nat. Rev. Cancer, 4, 988–993
-
(2004)
Nat. Rev. Cancer
, vol.4
, pp. 988-993
-
-
Issa, J.P.1
-
11
-
-
84899530032
-
Principles and methods of integrative genomic analyses in cancer
-
COI: 1:CAS:528:DC%2BC2cXmslaltbc%3D, PID: 24759209
-
Kristensen, V. N., Lingjærde, O. C., Russnes, H. G., Vollan, H. K., Frigessi, A. and Børresen-Dale, A. L. (2014) Principles and methods of integrative genomic analyses in cancer. Nat. Rev. Cancer, 14, 299–313
-
(2014)
Nat. Rev. Cancer
, vol.14
, pp. 299-313
-
-
Kristensen, V.N.1
Lingjærde, O.C.2
Russnes, H.G.3
Vollan, H.K.4
Frigessi, A.5
Børresen-Dale, A.L.6
-
12
-
-
84881613268
-
Integrating genomic, epigenomic, and transcriptomic features reveals modular signatures underlying poor prognosis in ovarian cancer
-
COI: 1:CAS:528:DC%2BC3sXht1GmurfL, PID: 23933257
-
Zhang, W., Liu, Y., Sun, N., Wang, D., Boyd-Kirkup, J., Dou, X. and Han, J. D. (2013) Integrating genomic, epigenomic, and transcriptomic features reveals modular signatures underlying poor prognosis in ovarian cancer. Cell Reports, 4, 542–553
-
(2013)
Cell Reports
, vol.4
, pp. 542-553
-
-
Zhang, W.1
Liu, Y.2
Sun, N.3
Wang, D.4
Boyd-Kirkup, J.5
Dou, X.6
Han, J.D.7
-
13
-
-
84875016233
-
Pattern discovery and cancer gene identification in integrated cancer genomic data
-
COI: 1:CAS:528:DC%2BC3sXmtVCjtLs%3D, PID: 23431203
-
Mo, Q., Wang, S., Seshan, V. E., Olshen, A. B., Schultz, N., Sander, C., Powers, R. S., Ladanyi, M. and Shen, R. (2013) Pattern discovery and cancer gene identification in integrated cancer genomic data. Proc. Natl. Acad. Sci. USA, 110, 4245–4250
-
(2013)
Proc. Natl. Acad. Sci. USA
, vol.110
, pp. 4245-4250
-
-
Mo, Q.1
Wang, S.2
Seshan, V.E.3
Olshen, A.B.4
Schultz, N.5
Sander, C.6
Powers, R.S.7
Ladanyi, M.8
Shen, R.9
-
14
-
-
84876058478
-
Joint and Individual Variation Explained (Jive) for integrated analysis of multiple data types
-
PID: 23745156
-
Lock, E. F., Hoadley, K. A., Marron, J. S. and Nobel, A. B. (2013) Joint and Individual Variation Explained (Jive) for integrated analysis of multiple data types. Ann. Appl. Stat., 7, 523–542
-
(2013)
Ann. Appl. Stat.
, vol.7
, pp. 523-542
-
-
Lock, E.F.1
Hoadley, K.A.2
Marron, J.S.3
Nobel, A.B.4
-
15
-
-
84949254714
-
Fast dimension reduction and integrative clustering of multi-omics data using low-rank approximation: application to cancer molecular classification
-
PID: 26626453
-
Wu, D., Wang, D., Gu, J. and Zhang, M. Q. (2015) Fast dimension reduction and integrative clustering of multi-omics data using low-rank approximation: application to cancer molecular classification. BMC Genomics, 16, 1022.
-
(2015)
BMC Genomics
, vol.16
, pp. 1022
-
-
Wu, D.1
Wang, D.2
Gu, J.3
Zhang, M.Q.4
-
16
-
-
84868152524
-
Discovery of multi-dimensional modules by integrative analysis of cancer genomic data
-
COI: 1:CAS:528:DC%2BC38XhsFygurbN, PID: 22879375
-
Zhang, S., Liu, C. C., Li, W., Shen, H., Laird, P. W. and Zhou, X. J. (2012) Discovery of multi-dimensional modules by integrative analysis of cancer genomic data. Nucleic Acids Res., 40, 9379–9391
-
(2012)
Nucleic Acids Res.
, vol.40
, pp. 9379-9391
-
-
Zhang, S.1
Liu, C.C.2
Li, W.3
Shen, H.4
Laird, P.W.5
Zhou, X.J.6
-
17
-
-
84876261160
-
Pathway-based personalized analysis of cancer
-
COI: 1:CAS:528:DC%2BC3sXnvVels7w%3D, PID: 23547110
-
Drier, Y., Sheffer, M. and Domany, E. (2013) Pathway-based personalized analysis of cancer. Proc. Natl. Acad. Sci. USA, 110, 6388–6393
-
(2013)
Proc. Natl. Acad. Sci. USA
, vol.110
, pp. 6388-6393
-
-
Drier, Y.1
Sheffer, M.2
Domany, E.3
-
18
-
-
84870796415
-
Bayesian correlated clustering to integrate multiple datasets
-
COI: 1:CAS:528:DC%2BC38XhvVSmsrvF, PID: 23047558
-
Kirk, P., Griffin, J. E., Savage, R. S., Ghahramani, Z. and Wild, D. L. (2012) Bayesian correlated clustering to integrate multiple datasets. Bioinformatics, 28, 3290–3297
-
(2012)
Bioinformatics
, vol.28
, pp. 3290-3297
-
-
Kirk, P.1
Griffin, J.E.2
Savage, R.S.3
Ghahramani, Z.4
Wild, D.L.5
-
19
-
-
84885617335
-
Bayesian consensus clustering
-
COI: 1:CAS:528:DC%2BC3sXhsFOmsbbN, PID: 23990412
-
Lock, E. F. and Dunson, D. B. (2013) Bayesian consensus clustering. Bioinformatics, 29, 2610–2616
-
(2013)
Bioinformatics
, vol.29
, pp. 2610-2616
-
-
Lock, E.F.1
Dunson, D.B.2
-
20
-
-
84895516704
-
Similarity network fusion for aggregating data types on a genomic scale
-
COI: 1:CAS:528:DC%2BC2cXhs1SlsbY%3D, PID: 24464287
-
Wang, B., Mezlini, A. M., Demir, F., Fiume, M., Tu, Z., Brudno, M., Haibe-Kains, B. and Goldenberg, A. (2014) Similarity network fusion for aggregating data types on a genomic scale. Nat. Methods, 11, 333–337
-
(2014)
Nat. Methods
, vol.11
, pp. 333-337
-
-
Wang, B.1
Mezlini, A.M.2
Demir, F.3
Fiume, M.4
Tu, Z.5
Brudno, M.6
Haibe-Kains, B.7
Goldenberg, A.8
-
21
-
-
77954195272
-
Inference of patient-specific pathway activities from multi-dimensional cancer genomics data using PARADIGM
-
COI: 1:CAS:528:DC%2BC3cXnsVOltbk%3D, PID: 20529912
-
Vaske, C. J., Benz, S. C., Sanborn, J. Z., Earl, D., Szeto, C., Zhu, J., Haussler, D. and Stuart, J. M. (2010) Inference of patient-specific pathway activities from multi-dimensional cancer genomics data using PARADIGM. Bioinformatics, 26, i237–i245
-
(2010)
Bioinformatics
, vol.26
, pp. i237
-
-
Vaske, C.J.1
Benz, S.C.2
Sanborn, J.Z.3
Earl, D.4
Szeto, C.5
Zhu, J.6
Haussler, D.7
Stuart, J.M.8
-
22
-
-
70449331456
-
Integrative clustering of multiple genomic data types using a joint latent variable model with application to breast and lung cancer subtype analysis
-
COI: 1:CAS:528:DC%2BD1MXhtl2jt73P, PID: 19759197
-
Shen, R., Olshen, A. B. and Ladanyi, M. (2009) Integrative clustering of multiple genomic data types using a joint latent variable model with application to breast and lung cancer subtype analysis. Bioinformatics, 25, 2906–2912
-
(2009)
Bioinformatics
, vol.25
, pp. 2906-2912
-
-
Shen, R.1
Olshen, A.B.2
Ladanyi, M.3
-
23
-
-
79959448071
-
A novel computational framework for simultaneous integration of multiple types of genomic data to identify microRNA-gene regulatory modules
-
COI: 1:CAS:528:DC%2BC3MXnvVKgurg%3D, PID: 21685098
-
Zhang, S., Li, Q., Liu, J. and Zhou, X. J. (2011) A novel computational framework for simultaneous integration of multiple types of genomic data to identify microRNA-gene regulatory modules. Bioinformatics, 27, i401–i409
-
(2011)
Bioinformatics
, vol.27
, pp. i401
-
-
Zhang, S.1
Li, Q.2
Liu, J.3
Zhou, X.J.4
-
24
-
-
79960675858
-
Robust principal component analysis?
-
Candes, E. J., Li, X. D., Ma, Y. and Wright, J. (2011) Robust principal component analysis? J. ACM, 58
-
(2011)
J. ACM
, vol.58
-
-
Candes, E.J.1
Li, X.D.2
Ma, Y.3
Wright, J.4
-
25
-
-
80051762104
-
Distributed optimization and statistical learning via the alternating direction method of multipliers
-
Boyd, S. Parikh, N. Chu, E. Peleato, A B. Eckstein (2011) Distributed optimization and statistical learning via the alternating direction method of multipliers. Foundations and Trends in Machine Learning, 3, 1–122
-
(2011)
Foundations and Trends in Machine Learning
, vol.3
, pp. 1-122
-
-
Boyd, S.1
Parikh, N.2
Chu, E.3
Peleato, A.4
-
26
-
-
71049116435
-
Exact matrix completion via convex optimization
-
Candès, E. J. and Recht, B. (2009) Exact matrix completion via convex optimization. Found. Comput. Math., 9, 717–772
-
(2009)
Found. Comput. Math.
, vol.9
, pp. 717-772
-
-
Candès, E.J.1
Recht, B.2
-
27
-
-
77951291046
-
A singular value thresholding algorithm for matrix completion
-
Cai, J. F., Candes, E. J. and Shen, Z. W. (2010) A singular value thresholding algorithm for matrix completion. SIAM J. Optim., 20, 1956–1982.
-
(2010)
SIAM J. Optim.
, vol.20
, pp. 1956-1982
-
-
Cai, J.F.1
Candes, E.J.2
Shen, Z.W.3
-
28
-
-
84903977589
-
Piecewise-constant and low-rank approximation for identification of recurrent copy number variations
-
COI: 1:CAS:528:DC%2BC2cXhtFCrtLjP, PID: 24642062
-
Zhou, X., Liu, J., Wan, X. and Yu, W. (2014) Piecewise-constant and low-rank approximation for identification of recurrent copy number variations. Bioinformatics, 30, 1943–1949
-
(2014)
Bioinformatics
, vol.30
, pp. 1943-1949
-
-
Zhou, X.1
Liu, J.2
Wan, X.3
Yu, W.4
-
29
-
-
84928983540
-
Statistical significance of variables driving systematic variation in high-dimensional data
-
PID: 25336500
-
Chung, N. C. and Storey, J. D. (2015) Statistical significance of variables driving systematic variation in high-dimensional data. Bioinformatics, 31, 545–554
-
(2015)
Bioinformatics
, vol.31
, pp. 545-554
-
-
Chung, N.C.1
Storey, J.D.2
-
30
-
-
79959375596
-
Statistical significance of the contribution of variables to the PCA solution: an alternative permutation strategy
-
Linting, M., van Os, B. J. and Meulman, J. J. (2011) Statistical significance of the contribution of variables to the PCA solution: an alternative permutation strategy. Psychometrika, 76, 440–460.
-
(2011)
Psychometrika
, vol.76
, pp. 440-460
-
-
Linting, M.1
van Os, B.J.2
Meulman, J.J.3
-
32
-
-
84893405732
-
Data clustering: a review
-
Jain, A. K., Murty, M. N., and Flynn, P. J. (1999) Data clustering: a review. ACM computing surveys (CSUR), 31, 264–323
-
(1999)
ACM computing surveys (CSUR)
, vol.31
, pp. 264-323
-
-
Jain, A.K.1
Murty, M.N.2
Flynn, P.J.3
-
34
-
-
84903289127
-
Clustering by fast search and find of density peaks
-
COI: 1:CAS:528:DC%2BC2cXhtVaks7%2FL, PID: 24970081
-
Rodriguez, A. and Laio, A. (2014) Clustering by fast search and find of density peaks. Science, 344, 1492–1496
-
(2014)
Science
, vol.344
, pp. 1492-1496
-
-
Rodriguez, A.1
Laio, A.2
-
35
-
-
0141607824
-
Latent dirichlet allocation
-
Blei, D. M., Ng, A. Y., and Jordan, M. I. (2003) Latent dirichlet allocation. J. Mach. Learn. Res., 3, 993–1022
-
(2003)
J. Mach. Learn. Res.
, vol.3
, pp. 993-1022
-
-
Blei, D.M.1
Ng, A.Y.2
Jordan, M.I.3
-
36
-
-
79958266660
-
The Dirichlet labeling process for clustering functional data
-
Nguyen, X. and Gelfand, A. E. (2011) The Dirichlet labeling process for clustering functional data. Stat. Sin., 21, 1249–1289.
-
(2011)
Stat. Sin.
, vol.21
, pp. 1249-1289
-
-
Nguyen, X.1
Gelfand, A.E.2
-
37
-
-
33845756481
-
Model-based clustering for expression data via a Dirichlet process mixture model
-
Cambridge University Press, Cambridge
-
Dahl, D. B. (2006) Model-based clustering for expression data via a Dirichlet process mixture model. In Bayesian inference for gene expression and proteomics, 201–218, Cambridge: Cambridge University Press
-
(2006)
In Bayesian inference for gene expression and proteomics
, pp. 201-218
-
-
Dahl, D.B.1
-
38
-
-
84885597338
-
-
Savage, R. S., Ghahramani, Z., Griffin, J. E., Kirk, P. and Wild, D. L. (2013) Identifying cancer subtypes in glioblastoma by combining genomic, transcriptomic and epigenomic data. arXiv:1304.3577
-
(2013)
Identifying cancer subtypes in glioblastoma by combining genomic, transcriptomic and epigenomic data
-
-
Savage, R.S.1
Ghahramani, Z.2
Griffin, J.E.3
Kirk, P.4
Wild, D.L.5
-
41
-
-
0037062448
-
Community structure in social and biological networks
-
COI: 1:CAS:528:DC%2BD38XkvVGjsL4%3D, PID: 12060727
-
Girvan, M. and Newman, M. E. (2002) Community structure in social and biological networks. Proc. Natl. Acad. Sci. USA, 99, 7821–7826
-
(2002)
Proc. Natl. Acad. Sci. USA
, vol.99
, pp. 7821-7826
-
-
Girvan, M.1
Newman, M.E.2
-
42
-
-
33745012299
-
Modularity and community structure in networks
-
COI: 1:CAS:528:DC%2BD28XlvVCitLw%3D, PID: 16723398
-
Newman, M. E. (2006) Modularity and community structure in networks. Proc. Natl. Acad. Sci. USA, 103, 8577–8582
-
(2006)
Proc. Natl. Acad. Sci. USA
, vol.103
, pp. 8577-8582
-
-
Newman, M.E.1
-
43
-
-
0041875229
-
On spectral clustering: Analysis and an algorithm
-
MIT Press, Cambridge
-
Ng, A. Y., Jordan, M. I. and Weiss, Y. (2001) On spectral clustering: Analysis and an algorithm. In Advances in Neural Information Processing Systems. 849–856, Cambridge: MIT Press
-
(2001)
In Advances in Neural Information Processing Systems
, pp. 849-856
-
-
Ng, A.Y.1
Jordan, M.I.2
Weiss, Y.3
-
44
-
-
34548583274
-
A tutorial on spectral clustering
-
von Luxburg, U. (2007) A tutorial on spectral clustering. Stat. Comput., 17, 395–416.
-
(2007)
Stat. Comput.
, vol.17
, pp. 395-416
-
-
von Luxburg, U.1
-
45
-
-
0036529479
-
An efficient algorithm for large-scale detection of protein families
-
COI: 1:CAS:528:DC%2BD38Xltlajsrk%3D, PID: 11917018
-
Enright, A. J., van Dongen, S. and Ouzounis, C. A. (2002) An efficient algorithm for large-scale detection of protein families. Nucleic Acids Res., 30, 1575–1584
-
(2002)
Nucleic Acids Res.
, vol.30
, pp. 1575-1584
-
-
Enright, A.J.1
van Dongen, S.2
Ouzounis, C.A.3
-
46
-
-
0002727513
-
Distance between sets
-
Levandowsky, M. and Winter, D. (1971) Distance between sets. Nature, 234, 34–35.
-
(1971)
Nature
, vol.234
, pp. 34-35
-
-
Levandowsky, M.1
Winter, D.2
-
47
-
-
0000008146
-
Comparing partitions
-
Hubert, L. and Arabie, P. (1985) Comparing partitions. J. Classif., 2, 193–218.
-
(1985)
J. Classif.
, vol.2
, pp. 193-218
-
-
Hubert, L.1
Arabie, P.2
-
48
-
-
84938799837
-
Toward understanding and exploiting tumor heterogeneity
-
COI: 1:CAS:528:DC%2BC2MXhtlSntrjJ, PID: 26248267
-
Alizadeh, A. A., Aranda, V., Bardelli, A., Blanpain, C., Bock, C., Borowski, C., Caldas, C., Califano, A., Doherty, M., Elsner, M., et al. (2015) Toward understanding and exploiting tumor heterogeneity. Nat. Med., 21, 846–853
-
(2015)
Nat. Med.
, vol.21
, pp. 846-853
-
-
Alizadeh, A.A.1
Aranda, V.2
Bardelli, A.3
Blanpain, C.4
Bock, C.5
Borowski, C.6
Caldas, C.7
Califano, A.8
Doherty, M.9
Elsner, M.10
-
49
-
-
77955660663
-
Diverse somatic mutation patterns and pathway alterations in human cancers
-
COI: 1:CAS:528:DC%2BC3cXptl2rs7s%3D, PID: 20668451
-
Kan, Z., Jaiswal, B. S., Stinson, J., Janakiraman, V., Bhatt, D., Stern, H. M., Yue, P., Haverty, P. M., Bourgon, R., Zheng, J., et al. (2010) Diverse somatic mutation patterns and pathway alterations in human cancers. Nature, 466, 869–873
-
(2010)
Nature
, vol.466
, pp. 869-873
-
-
Kan, Z.1
Jaiswal, B.S.2
Stinson, J.3
Janakiraman, V.4
Bhatt, D.5
Stern, H.M.6
Yue, P.7
Haverty, P.M.8
Bourgon, R.9
Zheng, J.10
-
50
-
-
84857942952
-
Discovery and prioritization of somatic mutations in diffuse large B-cell lymphoma (DLBCL) by whole-exome sequencing
-
COI: 1:CAS:528:DC%2BC38XjvFymt7s%3D, PID: 22343534
-
Lohr, J. G., Stojanov, P., Lawrence, M. S., Auclair, D., Chapuy, B., Sougnez, C., Cruz-Gordillo, P., Knoechel, B., Asmann, Y.W., Slager, S. L., et al. (2012) Discovery and prioritization of somatic mutations in diffuse large B-cell lymphoma (DLBCL) by whole-exome sequencing. Proc. Natl. Acad. Sci. USA, 109, 3879–3884
-
(2012)
Proc. Natl. Acad. Sci. USA
, vol.109
, pp. 3879-3884
-
-
Lohr, J.G.1
Stojanov, P.2
Lawrence, M.S.3
Auclair, D.4
Chapuy, B.5
Sougnez, C.6
Cruz-Gordillo, P.7
Knoechel, B.8
Asmann, Y.W.9
Slager, S.L.10
-
51
-
-
84880507665
-
Mutational heterogeneity in cancer and the search for new cancer-associated genes
-
COI: 1:CAS:528:DC%2BC3sXpsFSgsbo%3D, PID: 23770567
-
Lawrence, M. S., Stojanov, P., Polak, P., Kryukov, G. V., Cibulskis, K., Sivachenko, A., Carter, S. L., Stewart, C., Mermel, C. H., Roberts, S. A., et al. (2013) Mutational heterogeneity in cancer and the search for new cancer-associated genes. Nature, 499, 214–218
-
(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
Carter, S.L.7
Stewart, C.8
Mermel, C.H.9
Roberts, S.A.10
-
52
-
-
84929606441
-
DNA methylation-based prognosis and epidrivers in hepatocellular carcinoma
-
COI: 1:CAS:528:DC%2BC2MXptVSit7c%3D, PID: 25645722
-
Villanueva, A., Portela, A., Sayols, S., Battiston, C., Hoshida, Y., Méndez-González, J., Imbeaud, S., Letouzé, E., Hernandez-Gea, V., Cornella, H., et al. (2015) DNA methylation-based prognosis and epidrivers in hepatocellular carcinoma. Hepatology, 61, 1945–1956
-
(2015)
Hepatology
, vol.61
, pp. 1945-1956
-
-
Villanueva, A.1
Portela, A.2
Sayols, S.3
Battiston, C.4
Hoshida, Y.5
Méndez-González, J.6
Imbeaud, S.7
Letouzé, E.8
Hernandez-Gea, V.9
Cornella, H.10
-
53
-
-
84864326095
-
From cancer genomes to oncogenic drivers, tumour dependencies and therapeutic targets
-
COI: 1:CAS:528:DC%2BC38XpsVWitLg%3D, PID: 22739505
-
Eifert, C. and Powers, R. S. (2012) From cancer genomes to oncogenic drivers, tumour dependencies and therapeutic targets. Nat. Rev. Cancer, 12, 572–578
-
(2012)
Nat. Rev. Cancer
, vol.12
, pp. 572-578
-
-
Eifert, C.1
Powers, R.S.2
-
54
-
-
84925435486
-
Integration of genomic data enables selective discovery of breast cancer drivers
-
COI: 1:CAS:528:DC%2BC2cXhvF2mtLrN, PID: 25433701
-
Sanchez-Garcia, F., Villagrasa, P., Matsui, J., Kotliar, D., Castro, V., Akavia, U. D., Chen, B. J., Saucedo-Cuevas, L., Rodriguez Barrueco, R., Llobet-Navas, D., et al. (2014) Integration of genomic data enables selective discovery of breast cancer drivers. Cell, 159, 1461–1475
-
(2014)
Cell
, vol.159
, pp. 1461-1475
-
-
Sanchez-Garcia, F.1
Villagrasa, P.2
Matsui, J.3
Kotliar, D.4
Castro, V.5
Akavia, U.D.6
Chen, B.J.7
Saucedo-Cuevas, L.R.8
Barrueco, R.9
Llobet-Navas, D.10
-
55
-
-
84892765883
-
Genome-scale CRISPR-Cas9 knockout screening in human cells
-
COI: 1:CAS:528:DC%2BC2cXkslyj, PID: 24336571
-
Shalem, O., Sanjana, N. E., Hartenian, E., Shi, X., Scott, D. A., Mikkelsen, T. S., Heckl, D., Ebert, B. L., Root, D. E., Doench, J. G., et al. (2014) Genome-scale CRISPR-Cas9 knockout screening in human cells. Science, 343, 84–87
-
(2014)
Science
, vol.343
, pp. 84-87
-
-
Shalem, O.1
Sanjana, N.E.2
Hartenian, E.3
Shi, X.4
Scott, D.A.5
Mikkelsen, T.S.6
Heckl, D.7
Ebert, B.L.8
Root, D.E.9
Doench, J.G.10
-
56
-
-
84945567414
-
Network analysis of gene essentiality in functional genomics experiments
-
PID: 26518695
-
Jiang, P., Wang, H., Li, W., Zang, C., Li, B., Wong, Y. J., Meyer, C., Liu, J. S., Aster, J. C. and Liu, X. S. (2015) Network analysis of gene essentiality in functional genomics experiments. Genome Biol., 16, 239
-
(2015)
Genome Biol.
, vol.16
, pp. 239
-
-
Jiang, P.1
Wang, H.2
Li, W.3
Zang, C.4
Li, B.5
Wong, Y.J.6
Meyer, C.7
Liu, J.S.8
Aster, J.C.9
Liu, X.S.10
-
57
-
-
84915815121
-
Identification of causal genetic drivers of human disease through systems-level analysis of regulatory networks
-
COI: 1:CAS:528:DC%2BC2cXhslGjsbnK, PID: 25303533
-
Chen, J. C., Alvarez, M. J., Talos, F., Dhruv, H., Rieckhof, G. E., Iyer, A., Diefes, K. L., Aldape, K., Berens, M., Shen, M. M., et al. (2014) Identification of causal genetic drivers of human disease through systems-level analysis of regulatory networks. Cell, 159, 402–414
-
(2014)
Cell
, vol.159
, pp. 402-414
-
-
Chen, J.C.1
Alvarez, M.J.2
Talos, F.3
Dhruv, H.4
Rieckhof, G.E.5
Iyer, A.6
Diefes, K.L.7
Aldape, K.8
Berens, M.9
Shen, M.M.10
-
58
-
-
84964308876
-
Gene expression analysis identifies global gene dosage sensitivity in cancer
-
COI: 1:CAS:528:DC%2BC2MXmtV2rsw%3D%3D, PID: 25581432
-
Fehrmann, R. S., Karjalainen, J. M., Krajewska, M., Westra, H. J., Maloney, D., Simeonov, A., Pers, T. H., Hirschhorn, J. N., Jansen, R. C., Schultes, E. A., et al. (2015) Gene expression analysis identifies global gene dosage sensitivity in cancer. Nat. Genet., 47, 115–125
-
(2015)
Nat. Genet.
, vol.47
, pp. 115-125
-
-
Fehrmann, R.S.1
Karjalainen, J.M.2
Krajewska, M.3
Westra, H.J.4
Maloney, D.5
Simeonov, A.6
Pers, T.H.7
Hirschhorn, J.N.8
Jansen, R.C.9
Schultes, E.A.10
-
59
-
-
33750204290
-
Genetics of global gene expression
-
COI: 1:CAS:528:DC%2BD28XhtVyktLnP, PID: 17047685
-
Rockman, M. V. and Kruglyak, L. (2006) Genetics of global gene expression. Nat. Rev. Genet., 7, 862–872
-
(2006)
Nat. Rev. Genet.
, vol.7
, pp. 862-872
-
-
Rockman, M.V.1
Kruglyak, L.2
-
60
-
-
78649976005
-
An integrated approach to uncover drivers of cancer
-
COI: 1:CAS:528:DC%2BC3cXhsFGgsrnP, PID: 21129771
-
Akavia, U. D., Litvin, O., Kim, J., Sanchez-Garcia, F., Kotliar, D., Causton, H. C., Pochanard, P., Mozes, E., Garraway, L. A. and Pe’er, D. (2010) An integrated approach to uncover drivers of cancer. Cell, 143, 1005–1017
-
(2010)
Cell
, vol.143
, pp. 1005-1017
-
-
Akavia, U.D.1
Litvin, O.2
Kim, J.3
Sanchez-Garcia, F.4
Kotliar, D.5
Causton, H.C.6
Pochanard, P.7
Mozes, E.8
Garraway, L.A.9
Pe’er, D.10
-
61
-
-
84873288058
-
Integrative eQTL-based analyses reveal the biology of breast cancer risk loci
-
COI: 1:CAS:528:DC%2BC3sXhvFShtb4%3D, PID: 23374354
-
Li, Q., Seo, J. H., Stranger, B., McKenna, A., Pe’er, I., Laframboise, T., Brown, M., Tyekucheva, S. and Freedman, M. L. (2013) Integrative eQTL-based analyses reveal the biology of breast cancer risk loci. Cell, 152, 633–641
-
(2013)
Cell
, vol.152
, pp. 633-641
-
-
Li, Q.1
Seo, J.H.2
Stranger, B.3
McKenna, A.4
Pe’er, I.5
Laframboise, T.6
Brown, M.7
Tyekucheva, S.8
Freedman, M.L.9
-
62
-
-
84908335908
-
Integrated genomic characterization of papillary thyroid carcinoma
-
Cancer Genome Atlas Research Network. (2014) Integrated genomic characterization of papillary thyroid carcinoma. Cell, 159, 676–690
-
(2014)
Cell
, vol.159
, pp. 676-690
-
-
-
63
-
-
77956873627
-
Tackling the widespread and critical impact of batch effects in highthroughput data
-
COI: 1:CAS:528:DC%2BC3cXhtFyju7%2FK, PID: 20838408
-
Leek, J. T., Scharpf, R. B., Bravo, H. C., Simcha, D., Langmead, B., Johnson, W. E., Geman, D., Baggerly, K. and Irizarry, R. A. (2010) Tackling the widespread and critical impact of batch effects in highthroughput data. Nat. Rev. Genet., 11, 733–739
-
(2010)
Nat. Rev. Genet.
, vol.11
, pp. 733-739
-
-
Leek, J.T.1
Scharpf, R.B.2
Bravo, H.C.3
Simcha, D.4
Langmead, B.5
Johnson, W.E.6
Geman, D.7
Baggerly, K.8
Irizarry, R.A.9
-
64
-
-
0038692119
-
Human housekeeping genes are compact
-
COI: 1:CAS:528:DC%2BD3sXlt1eitLc%3D, PID: 12850439
-
Eisenberg, E. and Levanon, E. Y. (2003) Human housekeeping genes are compact. Trends Genet., 19, 362–365
-
(2003)
Trends Genet.
, vol.19
, pp. 362-365
-
-
Eisenberg, E.1
Levanon, E.Y.2
-
66
-
-
84900510076
-
Non-negative matrix factorization with sparseness constraints
-
Hoyer, P. O. (2004) Non-negative matrix factorization with sparseness constraints. J. Mach. Learn. Res., 5, 1457–1469.
-
(2004)
J. Mach. Learn. Res.
, vol.5
, pp. 1457-1469
-
-
Hoyer, P.O.1
-
67
-
-
0033592606
-
Learning the parts of objects by non-negative matrix factorization
-
COI: 1:CAS:528:DyaK1MXntFartrg%3D, PID: 10548103
-
Lee, D. D. and Seung, H. S. (1999) Learning the parts of objects by non-negative matrix factorization. Nature, 401, 788–791
-
(1999)
Nature
, vol.401
, pp. 788-791
-
-
Lee, D.D.1
Seung, H.S.2
-
68
-
-
84858983547
-
KEGG for integration and interpretation of large-scale molecular data sets
-
COI: 1:CAS:528:DC%2BC3MXhs12htbrO, PID: 22080510
-
Kanehisa, M., Goto, S., Sato, Y., Furumichi, M. and Tanabe, M. (2012) KEGG for integration and interpretation of large-scale molecular data sets. Nucleic Acids Res., 40, D109–D114
-
(2012)
Nucleic Acids Res.
, vol.40
, pp. D109
-
-
Kanehisa, M.1
Goto, S.2
Sato, Y.3
Furumichi, M.4
Tanabe, M.5
-
69
-
-
78651275182
-
Reactome: a database of reactions, pathways and biological processes
-
COI: 1:CAS:528:DC%2BC3sXivF2ltLw%3D, PID: 21067998
-
Croft, D., O’Kelly, G., Wu, G., Haw, R., Gillespie, M., Matthews, L., Caudy, M., Garapati, P., Gopinath, G., Jassal, B., et al. (2011) Reactome: a database of reactions, pathways and biological processes. Nucleic Acids Res., 39, D691–D697
-
(2011)
Nucleic Acids Res.
, vol.39
, pp. D691
-
-
Croft, D.1
O’Kelly, G.2
Wu, G.3
Haw, R.4
Gillespie, M.5
Matthews, L.6
Caudy, M.7
Garapati, P.8
Gopinath, G.9
Jassal, B.10
-
70
-
-
84891774001
-
The MetaCyc database of metabolic pathways and enzymes and the BioCyc collection of Pathway/Genome Databases
-
COI: 1:CAS:528:DC%2BC2cXos12h, PID: 24225315
-
Caspi, R., Altman, T., Billington, R., Dreher, K., Foerster, H., Fulcher, C. A., Holland, T. A., Keseler, I. M., Kothari, A., Kubo, A., et al. (2014) The MetaCyc database of metabolic pathways and enzymes and the BioCyc collection of Pathway/Genome Databases. Nucleic Acids Res., 42, D459–D471
-
(2014)
Nucleic Acids Res.
, vol.42
, pp. D459-D471
-
-
Caspi, R.1
Altman, T.2
Billington, R.3
Dreher, K.4
Foerster, H.5
Fulcher, C.A.6
Holland, T.A.7
Keseler, I.M.8
Kothari, A.9
Kubo, A.10
-
71
-
-
84938201089
-
Pathway-based personalized analysis of breast cancer expression data
-
COI: 1:CAS:528:DC%2BC2MXnslOgtbg%3D, PID: 25963740
-
Livshits, A., Git, A., Fuks, G., Caldas, C. and Domany, E. (2015) Pathway-based personalized analysis of breast cancer expression data. Mol. Oncol., 9, 1471–1483
-
(2015)
Mol. Oncol.
, vol.9
, pp. 1471-1483
-
-
Livshits, A.1
Git, A.2
Fuks, G.3
Caldas, C.4
Domany, E.5
-
72
-
-
58049215467
-
A novel signaling pathway impact analysis
-
COI: 1:CAS:528:DC%2BD1MXmvFWr, PID: 18990722
-
Tarca, A. L., Draghici, S., Khatri, P., Hassan, S. S., Mittal, P., Kim, J. S., Kim, C. J., Kusanovic, J. P. and Romero, R. (2009) A novel signaling pathway impact analysis. Bioinformatics, 25, 75–82
-
(2009)
Bioinformatics
, vol.25
, pp. 75-82
-
-
Tarca, A.L.1
Draghici, S.2
Khatri, P.3
Hassan, S.S.4
Mittal, P.5
Kim, J.S.6
Kim, C.J.7
Kusanovic, J.P.8
Romero, R.9
-
73
-
-
84884403849
-
Discovering causal pathways linking genomic events to transcriptional states using Tied Diffusion Through Interacting Events (TieDIE)
-
COI: 1:CAS:528:DC%2BC3sXhs1Cis77F, PID: 23986566
-
Paull, E. O., Carlin, D. E., Niepel, M., Sorger, P. K., Haussler, D. and Stuart, J. M. (2013) Discovering causal pathways linking genomic events to transcriptional states using Tied Diffusion Through Interacting Events (TieDIE). Bioinformatics, 29, 2757–2764
-
(2013)
Bioinformatics
, vol.29
, pp. 2757-2764
-
-
Paull, E.O.1
Carlin, D.E.2
Niepel, M.3
Sorger, P.K.4
Haussler, D.5
Stuart, J.M.6
-
74
-
-
84887084951
-
Network-based stratification of tumor mutations
-
COI: 1:CAS:528:DC%2BC3sXhsVeqsrvM, PID: 24037242
-
Hofree, M., Shen, J. P., Carter, H., Gross, A. and Ideker, T. (2013) Network-based stratification of tumor mutations. Nat. Methods, 10, 1108–1115
-
(2013)
Nat. Methods
, vol.10
, pp. 1108-1115
-
-
Hofree, M.1
Shen, J.P.2
Carter, H.3
Gross, A.4
Ideker, T.5
-
75
-
-
84934753411
-
Tumor characterization and stratification by integrated molecular profiles reveals essential pan-cancer features
-
PID: 26148869
-
Liu, Z. and Zhang, S. (2015) Tumor characterization and stratification by integrated molecular profiles reveals essential pan-cancer features. BMC Genomics, 16, 503
-
(2015)
BMC Genomics
, vol.16
, pp. 503
-
-
Liu, Z.1
Zhang, S.2
-
76
-
-
84884994218
-
The Cancer Genome Atlas Pan-Cancer analysis project
-
Cancer Genome Atlas Research Network, Weinstein, J. N., Collisson, E. A., Mills, G. B., Shaw, K. R., Ozenberger, B. A., Ellrott, K., Shmulevich, I., Sander, C. andStuart, J. M. (2013) The Cancer Genome Atlas Pan-Cancer analysis project. Nat. Genet., 45, 1113–1120
-
(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
Shmulevich, I.7
Sander, C.8
andStuart, J.M.9
-
77
-
-
84907270779
-
Comprehensive molecular characterization of gastric adenocarcinoma
-
Cancer Genome Atlas Research Network. (2014) Comprehensive molecular characterization of gastric adenocarcinoma. Nature, 513, 202–209
-
(2014)
Nature
, vol.513
, pp. 202-209
-
-
-
78
-
-
84903940391
-
Assessing the clinical utility of cancer genomic and proteomic data across tumor types
-
COI: 1:CAS:528:DC%2BC2cXhtVais7rJ, PID: 24952901
-
Yuan, Y., van Allen, E. M., Omberg, L., Wagle, N., Amin-Mansour, A., Sokolov, A., Byers, L. A., Xu, Y., Hess, K. R., Diao, L., et al. (2014) Assessing the clinical utility of cancer genomic and proteomic data across tumor types. Nat. Biotechnol., 32, 644–652
-
(2014)
Nat. Biotechnol.
, vol.32
, pp. 644-652
-
-
Yuan, Y.1
van Allen, E.M.2
Omberg, L.3
Wagle, N.4
Amin-Mansour, A.5
Sokolov, A.6
Byers, L.A.7
Xu, Y.8
Hess, K.R.9
Diao, L.10
-
79
-
-
0002555784
-
The multivariate calibrationproblem in chemistry solved by the Pls Method
-
Wold, S., Martens, H. and Wold, H. (1983) The multivariate calibrationproblem in chemistry solved by the Pls Method. Lect. Notes Math., 973, 286–293.
-
(1983)
Lect. Notes Math.
, vol.973
, pp. 286-293
-
-
Wold, S.1
Martens, H.2
Wold, H.3
-
80
-
-
84929142356
-
Deviance residuals-based sparse PLS and sparse kernel PLS regression for censored data
-
PID: 25286920
-
Bastien, P., Bertrand, F., Meyer, N. and Maumy-Bertrand, M. (2015) Deviance residuals-based sparse PLS and sparse kernel PLS regression for censored data. Bioinformatics, 31, 397–404
-
(2015)
Bioinformatics
, vol.31
, pp. 397-404
-
-
Bastien, P.1
Bertrand, F.2
Meyer, N.3
Maumy-Bertrand, M.4
-
81
-
-
84944345463
-
Building the foundation for genomics in precision medicine
-
COI: 1:CAS:528:DC%2BC2MXhs1KqtLzM, PID: 26469044
-
Aronson, S. J. and Rehm, H. L. (2015) Building the foundation for genomics in precision medicine. Nature, 526, 336–342
-
(2015)
Nature
, vol.526
, pp. 336-342
-
-
Aronson, S.J.1
Rehm, H.L.2
|