-
2
-
-
20044396570
-
Integrative analysis of the cancer transcriptome
-
Rhodes DR, Chinnaiyan AM. Integrative analysis of the cancer transcriptome. Nat Genet. 2005;37:S31-7.
-
(2005)
Nat Genet
, vol.37
, pp. S31-S37
-
-
Rhodes, D.R.1
Chinnaiyan, A.M.2
-
3
-
-
84959433241
-
Now, #xe9 A: Comparison of merging and meta-analysis as alternative approaches for integrative gene expression analysis. ISRN
-
Taminau J, Lazar C, Meganck S. Now, #xe9 A: Comparison of merging and meta-analysis as alternative approaches for integrative gene expression analysis. ISRN. Bioinformatics. 2014;2014:7.
-
(2014)
Bioinformatics
, vol.2014
, pp. 7
-
-
Taminau, J.1
Lazar, C.2
Meganck, S.3
-
4
-
-
27844594381
-
Cross-platform analysis of cancer microarray data improves gene expression based classification of phenotypes
-
Warnat P, Eils R, Brors B. Cross-platform analysis of cancer microarray data improves gene expression based classification of phenotypes. BMC Bioinformatics. 2005;6:265.
-
(2005)
BMC Bioinformatics
, vol.6
, pp. 265
-
-
Warnat, P.1
Eils, R.2
Brors, B.3
-
5
-
-
78951471707
-
Microarray data integration: frameworks and a list of underlying issues
-
Kumar Sarmah C, Samarasinghe S. Microarray data integration: frameworks and a list of underlying issues. Curr Bioinforma. 2010;5(4):280-9.
-
(2010)
Curr Bioinforma
, vol.5
, Issue.4
, pp. 280-289
-
-
Kumar Sarmah, C.1
Samarasinghe, S.2
-
6
-
-
49649105570
-
Systems biology approach to identification of biomarkers for metastatic progression in cancer
-
Ptitsyn AA, Weil MM, Thamm DH: Systems biology approach to identification of biomarkers for metastatic progression in cancer. BMC Bioinformatics 2008;9(Suppl 9):S8.
-
(2008)
BMC Bioinformatics
, vol.9
, pp. S8
-
-
Ptitsyn, A.A.1
Weil, M.M.2
Thamm, D.H.3
-
7
-
-
84907588668
-
A novel model to combine clinical and pathway-based transcriptomic information for the prognosis prediction of breast cancer
-
Huang S, Yee C, Ching T, Yu H, Garmire LX. A novel model to combine clinical and pathway-based transcriptomic information for the prognosis prediction of breast cancer. PLoS Comput Biol. 2014;10(9):e1003851.
-
(2014)
PLoS Comput Biol
, vol.10
, Issue.9
-
-
Huang, S.1
Yee, C.2
Ching, T.3
Yu, H.4
Garmire, L.X.5
-
8
-
-
83755202239
-
Transfer learning of classification rules for biomarker discovery and verification from molecular profiling studies
-
Ganchev P, Malehorn D, Bigbee WL, Gopalakrishnan V. Transfer learning of classification rules for biomarker discovery and verification from molecular profiling studies. J Biomed Inform. 2011;44(Suppl 1):S17-23.
-
(2011)
J Biomed Inform
, vol.44
, pp. S17-23
-
-
Ganchev, P.1
Malehorn, D.2
Bigbee, W.L.3
Gopalakrishnan, V.4
-
9
-
-
77956031473
-
A Survey on Transfer Learning
-
Pan SJ, Yang QA. A Survey on Transfer Learning. Ieee T Knowl Data En. 2010;22(10):1345-59.
-
(2010)
Ieee T Knowl Data En
, vol.22
, Issue.10
, pp. 1345-1359
-
-
Pan, S.J.1
Yang, Q.A.2
-
10
-
-
0002514104
-
Structure mapping in analogy and similarity
-
Gentner D, Markman AB. Structure mapping in analogy and similarity. Am Psychol. 1997;52(1):45.
-
(1997)
Am Psychol
, vol.52
, Issue.1
, pp. 45
-
-
Gentner, D.1
Markman, A.B.2
-
11
-
-
13444282534
-
Outcome signature genes in breast cancer: is there a unique set?
-
Ein-Dor L, Kela I, Getz G, Givol D, Domany E. Outcome signature genes in breast cancer: is there a unique set? Bioinformatics. 2005;21(2):171-8.
-
(2005)
Bioinformatics
, vol.21
, Issue.2
, pp. 171-178
-
-
Ein-Dor, L.1
Kela, I.2
Getz, G.3
Givol, D.4
Domany, E.5
-
12
-
-
33746910265
-
Concordance among gene-expression-based predictors for breast cancer
-
Fan C, Oh DS, Wessels L, Weigelt B, Nuyten DS, Nobel AB, et al. Concordance among gene-expression-based predictors for breast cancer. N Engl J Med. 2006;355(6):560-9.
-
(2006)
N Engl J Med
, vol.355
, Issue.6
, pp. 560-569
-
-
Fan, C.1
Oh, D.S.2
Wessels, L.3
Weigelt, B.4
Nuyten, D.S.5
Nobel, A.B.6
-
13
-
-
1542353401
-
Control of apoptosis by p53
-
Fridman JS, Lowe SW. Control of apoptosis by p53. Oncogene. 2003;22(56):9030-40.
-
(2003)
Oncogene
, vol.22
, Issue.56
, pp. 9030-9040
-
-
Fridman, J.S.1
Lowe, S.W.2
-
14
-
-
0033518234
-
From molecular to modular cell biology
-
Hartwell LH, Hopfield JJ, Leibler S, Murray AW. From molecular to modular cell biology. Nature. 1999;402(6761 Suppl):C47-52.
-
(1999)
Nature
, vol.402
, Issue.6761
, pp. C47-52
-
-
Hartwell, L.H.1
Hopfield, J.J.2
Leibler, S.3
Murray, A.W.4
-
15
-
-
84874613998
-
A survey of discretization techniques: Taxonomy and empirical analysis in supervised learning
-
Garcia S, Luengo J, Sáez JA, López V, Herrera F. A survey of discretization techniques: Taxonomy and empirical analysis in supervised learning. Knowledge and Data Engineering, IEEE Transactions on. 2013;25(4):734-50.
-
(2013)
Knowledge and Data Engineering, IEEE Transactions on
, vol.25
, Issue.4
, pp. 734-750
-
-
Garcia, S.1
Luengo, J.2
Sáez, J.A.3
López, V.4
Herrera, F.5
-
17
-
-
34249966007
-
The CN2 induction algorithm
-
Clark P, Niblett T. The CN2 induction algorithm. Mach Learn. 1989;3(4):261-83.
-
(1989)
Mach Learn
, vol.3
, Issue.4
, pp. 261-283
-
-
Clark, P.1
Niblett, T.2
-
19
-
-
79960654059
-
Application of an efficient Bayesian discretization method to biomedical data
-
Lustgarten J, Visweswaran S, Gopalakrishnan V, Cooper G. Application of an efficient Bayesian discretization method to biomedical data. BMC Bioinformatics. 2011;12(1):309.
-
(2011)
BMC Bioinformatics
, vol.12
, Issue.1
, pp. 309
-
-
Lustgarten, J.1
Visweswaran, S.2
Gopalakrishnan, V.3
Cooper, G.4
-
20
-
-
25444482341
-
Theme discovery from gene lists for identification and viewing of multiple functional groups
-
Pehkonen P, Wong G, Törönen P. Theme discovery from gene lists for identification and viewing of multiple functional groups. BMC bioinformatics. 2005;6(1):162.
-
(2005)
BMC bioinformatics
, vol.6
, Issue.1
, pp. 162
-
-
Pehkonen, P.1
Wong, G.2
Törönen, P.3
-
21
-
-
84896716464
-
A comparison of gene set analysis methods in terms of sensitivity, prioritization and specificity
-
Tarca AL, Bhatti G, Romero R. A comparison of gene set analysis methods in terms of sensitivity, prioritization and specificity. PLoS One. 2013;8(11), e79217.
-
(2013)
PLoS One
, vol.8
, Issue.11
-
-
Tarca, A.L.1
Bhatti, G.2
Romero, R.3
-
23
-
-
58149187893
-
The GOA database in 2009-an integrated Gene Ontology annotation resource
-
Barrell D, Dimmer E, Huntley RP, Binns D, O'Donovan C, Apweiler R. The GOA database in 2009-an integrated Gene Ontology annotation resource. Nucleic Acids Res. 2009;37(Database issue):D396-403.
-
(2009)
Nucleic Acids Res
, vol.37
, Issue.DATABASE ISSUE
, pp. D396-403
-
-
Barrell, D.1
Dimmer, E.2
Huntley, R.P.3
Binns, D.4
O'Donovan, C.5
Apweiler, R.6
-
24
-
-
34447294237
-
A new method to measure the semantic similarity of GO terms
-
Wang JZ, Du Z, Payattakool R, Yu PS, Chen CF. A new method to measure the semantic similarity of GO terms. Bioinformatics. 2007;23(10):1274-81.
-
(2007)
Bioinformatics
, vol.23
, Issue.10
, pp. 1274-1281
-
-
Wang, J.Z.1
Du, Z.2
Payattakool, R.3
Yu, P.S.4
Chen, C.F.5
-
26
-
-
0023453329
-
Silhouettes: a graphical aid to the interpretation and validation of cluster analysis
-
Rousseeuw PJ. Silhouettes: a graphical aid to the interpretation and validation of cluster analysis. J Comput Appl Math. 1987;20:53-65.
-
(1987)
J Comput Appl Math
, vol.20
, pp. 53-65
-
-
Rousseeuw, P.J.1
-
27
-
-
84858766991
-
A Multiplexed Serum Biomarker Immunoassay Panel Discriminates Clinical Lung Cancer Patients from High-Risk Individuals Found to be Cancer-Free by CT Screening
-
Bigbee WL, Gopalakrishnan V, Weissfeld JL, Wilson DO, Dacic S, Lokshin AE, Siegfried JM: A Multiplexed Serum Biomarker Immunoassay Panel Discriminates Clinical Lung Cancer Patients from High-Risk Individuals Found to be Cancer-Free by CT Screening. Journal of Thoracic Oncology 2012, 7(4):698-708 610.1097/JTO.1090b1013e31824ab31826b31820.
-
(2012)
Journal of Thoracic Oncology
, vol.7
, Issue.4
, pp. 698-708
-
-
Bigbee, W.L.1
Gopalakrishnan, V.2
Weissfeld, J.L.3
Wilson, D.O.4
Dacic, S.5
Lokshin, A.E.6
Siegfried, J.M.7
-
29
-
-
28844432511
-
Proteomic profiling of cerebrospinal fluid identifies biomarkers for amyotrophic lateral sclerosis
-
Ranganathan S, Williams E, Ganchev P, Gopalakrishnan V, Lacomis D, Urbinelli L, et al. Proteomic profiling of cerebrospinal fluid identifies biomarkers for amyotrophic lateral sclerosis. J Neurochem. 2005;95(5):1461-71.
-
(2005)
J Neurochem
, vol.95
, Issue.5
, pp. 1461-1471
-
-
Ranganathan, S.1
Williams, E.2
Ganchev, P.3
Gopalakrishnan, V.4
Lacomis, D.5
Urbinelli, L.6
-
30
-
-
77954122515
-
Discovery and verification of amyotrophic lateral sclerosis biomarkers by proteomics
-
Ryberg H, An J, Darko S, Lustgarten JL, Jaffa M, Gopalakrishnan V, et al. Discovery and verification of amyotrophic lateral sclerosis biomarkers by proteomics. Muscle Nerve. 2010;42(1):104-11.
-
(2010)
Muscle Nerve
, vol.42
, Issue.1
, pp. 104-111
-
-
Ryberg, H.1
An, J.2
Darko, S.3
Lustgarten, J.L.4
Jaffa, M.5
Gopalakrishnan, V.6
-
32
-
-
78149315656
-
Using rule sets to maximize ROC performance. In: Data Mining, 2001 ICDM 2001
-
IEEE
-
Fawcett T: Using rule sets to maximize ROC performance. In: Data Mining, 2001 ICDM 2001, Proceedings IEEE International Conference on: 2001. IEEE: 131-138.
-
Proceedings IEEE International Conference on: 2001
, pp. 131-138
-
-
Fawcett, T.1
-
33
-
-
84861414639
-
Comprehensive literature review and statistical considerations for microarray meta-analysis
-
Tseng GC, Ghosh D, Feingold E. Comprehensive literature review and statistical considerations for microarray meta-analysis. Nucleic Acids Res. 2012;40(9):3785-99.
-
(2012)
Nucleic Acids Res
, vol.40
, Issue.9
, pp. 3785-3799
-
-
Tseng, G.C.1
Ghosh, D.2
Feingold, E.3
-
34
-
-
84860491216
-
An adaptively weighted statistic for detecting differential gene expression when combining multiple transcriptomic studies
-
Li J, Tseng GC. An adaptively weighted statistic for detecting differential gene expression when combining multiple transcriptomic studies. The Annals of Applied Statistics. 2011;5(2A):994-1019.
-
(2011)
The Annals of Applied Statistics
, vol.5
, Issue.2
, pp. 994-1019
-
-
Li, J.1
Tseng, G.C.2
-
35
-
-
33845432928
-
Adjusting batch effects in microarray expression data using empirical Bayes methods
-
Johnson WE, Li C, Rabinovic A. Adjusting batch effects in microarray expression data using empirical Bayes methods. Biostatistics. 2007;8(1):118-27.
-
(2007)
Biostatistics
, vol.8
, Issue.1
, pp. 118-127
-
-
Johnson, W.E.1
Li, C.2
Rabinovic, A.3
-
36
-
-
79952284127
-
Hallmarks of cancer: the next generation
-
Hanahan D, Weinberg RA. Hallmarks of cancer: the next generation. Cell. 2011;144(5):646-74.
-
(2011)
Cell
, vol.144
, Issue.5
, pp. 646-674
-
-
Hanahan, D.1
Weinberg, R.A.2
-
37
-
-
28544452631
-
A survey of interestingness measures for knowledge discovery
-
McGarry K. A survey of interestingness measures for knowledge discovery. Knowledge Eng Review. 2005;20(1):39-61.
-
(2005)
Knowledge Eng Review
, vol.20
, Issue.1
, pp. 39-61
-
-
McGarry, K.1
-
38
-
-
73449130242
-
Oncogenic pathway combinations predict clinical prognosis in gastric cancer
-
Ooi CH, Ivanova T, Wu J, Lee M, Tan IB, Tao J, et al. Oncogenic pathway combinations predict clinical prognosis in gastric cancer. PLoS Genet. 2009;5(10):e1000676.
-
(2009)
PLoS Genet
, vol.5
, Issue.10
-
-
Ooi, C.H.1
Ivanova, T.2
Wu, J.3
Lee, M.4
Tan, I.B.5
Tao, J.6
-
39
-
-
13444266370
-
Online Mendelian Inheritance in Man (OMIM), a knowledgebase of human genes and genetic disorders
-
Hamosh A, Scott AF, Amberger JS, Bocchini CA, McKusick VA. Online Mendelian Inheritance in Man (OMIM), a knowledgebase of human genes and genetic disorders. Nucleic Acids Res. 2005;33 suppl 1:D514-7.
-
(2005)
Nucleic Acids Res
, vol.33
, pp. D514-D517
-
-
Hamosh, A.1
Scott, A.F.2
Amberger, J.S.3
Bocchini, C.A.4
McKusick, V.A.5
-
40
-
-
0033982936
-
KEGG: kyoto encyclopedia of genes and genomes
-
Kanehisa M, Goto S. KEGG: kyoto encyclopedia of genes and genomes. Nucleic Acids Res. 2000;28(1):27-30.
-
(2000)
Nucleic Acids Res
, vol.28
, Issue.1
, pp. 27-30
-
-
Kanehisa, M.1
Goto, S.2
-
41
-
-
79958135926
-
Molecular signatures database (MSigDB) 3.0
-
Liberzon A, Subramanian A, Pinchback R, Thorvaldsdóttir H, Tamayo P, Mesirov JP. Molecular signatures database (MSigDB) 3.0. Bioinformatics. 2011;27(12):1739-40.
-
(2011)
Bioinformatics
, vol.27
, Issue.12
, pp. 1739-1740
-
-
Liberzon, A.1
Subramanian, A.2
Pinchback, R.3
Thorvaldsdóttir, H.4
Tamayo, P.5
Mesirov, J.P.6
-
42
-
-
77952833904
-
BioCarta. Biotech Software & Internet Report
-
Nishimura D: BioCarta. Biotech Software & Internet Report: The Computer Software Journal for Scient 2001, 2(3):117-120.
-
(2001)
The Computer Software Journal for Scient
, vol.2
, Issue.3
, pp. 117-120
-
-
Nishimura, D.1
-
43
-
-
13444259844
-
Reactome: a knowledgebase of biological pathways
-
Joshi-Tope G, Gillespie M, Vastrik I, D'Eustachio P, Schmidt E, de Bono B, et al. Reactome: a knowledgebase of biological pathways. Nucleic Acids Res. 2005;33(Suppl 1):D428-32.
-
(2005)
Nucleic Acids Res
, vol.33
, pp. D428-D432
-
-
Joshi-Tope, G.1
Gillespie, M.2
Vastrik, I.3
D'Eustachio, P.4
Schmidt, E.5
de Bono, B.6
-
44
-
-
0036088113
-
PharmGKB: the pharmacogenetics knowledge base
-
Hewett M, Oliver DE, Rubin DL, Easton KL, Stuart JM, Altman RB, et al. PharmGKB: the pharmacogenetics knowledge base. Nucleic Acids Res. 2002;30(1):163-5.
-
(2002)
Nucleic Acids Res
, vol.30
, Issue.1
, pp. 163-165
-
-
Hewett, M.1
Oliver, D.E.2
Rubin, D.L.3
Easton, K.L.4
Stuart, J.M.5
Altman, R.B.6
-
45
-
-
0001677717
-
Controlling the false discovery rate: a practical and powerful approach to multiple testing
-
Benjamini Y, Hochberg Y. Controlling the false discovery rate: a practical and powerful approach to multiple testing. J R Stat Soc Ser B Methodol. 1995;289-300.
-
(1995)
J R Stat Soc Ser B Methodol
, pp. 289-300
-
-
Benjamini, Y.1
Hochberg, Y.2
|