-
1
-
-
33748798478
-
Graph-based methods for analysing networks in cell biology
-
Aittokallio,T. and Schwikowski,B. (2006) Graph-based methods for analysing networks in cell biology. Brief. Bioinform., 7, 243-255.
-
(2006)
Brief. Bioinform
, vol.7
, pp. 243-255
-
-
Aittokallio, T.1
Schwikowski, B.2
-
2
-
-
0001646484
-
Cox's regression model for counting processes: A large sample study
-
Andersen,P. and Gill,R. (1982) Cox's regression model for counting processes: A large sample study. Ann. Stat., 10, 1100-1120.
-
(1982)
Ann. Stat
, vol.10
, pp. 1100-1120
-
-
Andersen, P.1
Gill, R.2
-
3
-
-
46249119591
-
Germinal center B cell-like (GCB) and activated B cell-like (ABC) type of diffuse large B cell lymphoma (DLBCL): Analysis of molecular predictors, signatures, cell cycle state and patient survival
-
Blenk,S. et al. (2007) Germinal center B cell-like (GCB) and activated B cell-like (ABC) type of diffuse large B cell lymphoma (DLBCL): Analysis of molecular predictors, signatures, cell cycle state and patient survival. Cancer Inform., 3, 409-430.
-
(2007)
Cancer Inform
, vol.3
, pp. 409-430
-
-
Blenk, S.1
-
4
-
-
0000732463
-
A limited memory algorithm for bound constrained optimization
-
Byrd,R.H. et al. (1995) A limited memory algorithm for bound constrained optimization. SIAM J. Sci. Comput., 16, 1190-1208.
-
(1995)
SIAM J. Sci. Comput
, vol.16
, pp. 1190-1208
-
-
Byrd, R.H.1
-
5
-
-
20844450402
-
Differential network expression during drug and stress response
-
Cabusora,L. et al. (2005) Differential network expression during drug and stress response. Bioinformatics, 21, 2898-2905.
-
(2005)
Bioinformatics
, vol.21
, pp. 2898-2905
-
-
Cabusora, L.1
-
6
-
-
12744261504
-
Network structures and algorithms in Bioconductor
-
Carey,V.J. et al. (2005) Network structures and algorithms in Bioconductor. Bioinformatics, 21, 135-136.
-
(2005)
Bioinformatics
, vol.21
, pp. 135-136
-
-
Carey, V.J.1
-
7
-
-
38449101120
-
Integration of biological networks and gene expression data using Cytoscape
-
Cline,M.S. et al. (2007) Integration of biological networks and gene expression data using Cytoscape. Nat. Protoc., 2, 2366-2382.
-
(2007)
Nat. Protoc
, vol.2
, pp. 2366-2382
-
-
Cline, M.S.1
-
8
-
-
0002294353
-
Combining independent tests of significance
-
Fisher,R.A. 1948. Combining independent tests of significance. Am. Stat., 2, 30.
-
(1948)
Am. Stat
, vol.2
, pp. 30
-
-
Fisher, R.A.1
-
9
-
-
33748257786
-
Graemlin: General and robust alignment of multiple large interaction networks
-
Flannick,J. et al. (2006) Graemlin: General and robust alignment of multiple large interaction networks. Genome Res., 16, 1169-1181.
-
(2006)
Genome Res
, vol.16
, pp. 1169-1181
-
-
Flannick, J.1
-
10
-
-
0842288337
-
Inferring cellular networks using probabilistic graphical models
-
Friedman,N. (2004) Inferring cellular networks using probabilistic graphical models. Science, 303, 799-805.
-
(2004)
Science
, vol.303
, pp. 799-805
-
-
Friedman, N.1
-
11
-
-
28744458859
-
Bioconductor: Open software development for computational biology and biomformatics
-
Gentleman,R.C. et al. (2004) Bioconductor: Open software development for computational biology and biomformatics. Genome Biol. 5, R80.
-
(2004)
Genome Biol
, vol.5
-
-
Gentleman, R.C.1
-
12
-
-
34548583420
-
Edge-based scoring and searching method for identifying condition-responsive protein-protein interaction sub-network
-
Guo,Z. et al. (2007) Edge-based scoring and searching method for identifying condition-responsive protein-protein interaction sub-network. Bioinformatics, 23, 2121-2128.
-
(2007)
Bioinformatics
, vol.23
, pp. 2121-2128
-
-
Guo, Z.1
-
13
-
-
0000801240
-
Discovering regulatory and signalling circuits in molecular interaction networks
-
Ideker,T. et al. (2002) Discovering regulatory and signalling circuits in molecular interaction networks. Bioinformatics, 18(Suppl. 1), S233-S240.
-
(2002)
Bioinformatics
, vol.18
, Issue.SUPPL. 1
-
-
Ideker, T.1
-
14
-
-
0141593601
-
Conserved pathways within bacteria and yeast as revealed by global protein network alignment
-
Kelley,B.P. et al. (2003) Conserved pathways within bacteria and yeast as revealed by global protein network alignment. Proc. Natl. Acad. Sci. USA, 100, 11394-11399.
-
(2003)
Proc. Natl. Acad. Sci. USA
, vol.100
, pp. 11394-11399
-
-
Kelley, B.P.1
-
16
-
-
29044432227
-
An algorithmic framework for the exact solution of the prize-collecting steiner trec problem
-
Ljubić,I. et al. (2006) An algorithmic framework for the exact solution of the prize-collecting steiner trec problem. Math. Program. Ser. B, 105, 427-449.
-
(2006)
Math. Program. Ser. B
, vol.105
, pp. 427-449
-
-
Ljubić, I.1
-
17
-
-
33644877439
-
-
Mishra,G.R. et al. (2006) Human protein reference database-2006 update. Nucleic Acids Res., 34(Database issue), D411-D414.
-
Mishra,G.R. et al. (2006) Human protein reference database-2006 update. Nucleic Acids Res., 34(Database issue), D411-D414.
-
-
-
-
18
-
-
34248593385
-
Gene expression network analysis and applications to immunology
-
Nacu,S. et al. (2007) Gene expression network analysis and applications to immunology. Bioinformatics, 23, 850-858.
-
(2007)
Bioinformatics
, vol.23
, pp. 850-858
-
-
Nacu, S.1
-
20
-
-
10744224197
-
Development of human protein reference database as an initial platform for approaching systems biology in humans
-
Peri,S. et al. (2003) Development of human protein reference database as an initial platform for approaching systems biology in humans. Genome Res., 13, 2363-2671.
-
(2003)
Genome Res
, vol.13
, pp. 2363-2671
-
-
Peri, S.1
-
21
-
-
0038156106
-
Estimating the occurrence of false positives and false negatives in microarray studies by approximating and partitioning the empirical distribution of p-values
-
Pounds,S. and Morris,S.W. (2003) Estimating the occurrence of false positives and false negatives in microarray studies by approximating and partitioning the empirical distribution of p-values. Bioinformatics 19, 1236-1242.
-
(2003)
Bioinformatics
, vol.19
, pp. 1236-1242
-
-
Pounds, S.1
Morris, S.W.2
-
22
-
-
33748324384
-
-
R Development Core Team , R Foundation for Statistical Computing, Vienna, Austria
-
R Development Core Team (2006) R: A Language and Environment for Statistical Computing. R Foundation for Statistical Computing, Vienna, Austria.
-
(2006)
R: A Language and Environment for Statistical Computing
-
-
-
23
-
-
15944402798
-
Inferring pathways from gene lists using a literature-derived network of biological relationships
-
and AgarwalP
-
Rajagopalan,D. and AgarwalP. (2005) Inferring pathways from gene lists using a literature-derived network of biological relationships. Bioinformatics, 21, 788-793.
-
(2005)
Bioinformatics
, vol.21
, pp. 788-793
-
-
Rajagopalan, D.1
-
24
-
-
0037142053
-
The use of molecular profiling to predict survival after chemotherapy for diffuse large-B-cell lymphoma
-
Rosenwald,A. et al. (2002) The use of molecular profiling to predict survival after chemotherapy for diffuse large-B-cell lymphoma. N. Engl. J. Med., 346, 1937-1947.
-
(2002)
N. Engl. J. Med
, vol.346
, pp. 1937-1947
-
-
Rosenwald, A.1
-
25
-
-
0242490780
-
Cytoscape: A software environment for integrated models of biomolecular interaction networks
-
Shannon,P. et al. (2003) Cytoscape: A software environment for integrated models of biomolecular interaction networks. Genome Res. 13, 2498-2504.
-
(2003)
Genome Res
, vol.13
, pp. 2498-2504
-
-
Shannon, P.1
-
26
-
-
33645732240
-
Modeling cellular machinery through biological network comparison
-
Sharan,R. and Ideker,T. (2006) Modeling cellular machinery through biological network comparison. Nat. Biotechno., 24, 427-433.
-
(2006)
Nat. Biotechno
, vol.24
, pp. 427-433
-
-
Sharan, R.1
Ideker, T.2
-
27
-
-
27544491192
-
ROCR: Visualizing classifier performance in R
-
Sing,T. et al. (2005) ROCR: Visualizing classifier performance in R. Bioinformatics, 21, 3940-3941.
-
(2005)
Bioinformatics
, vol.21
, pp. 3940-3941
-
-
Sing, T.1
-
28
-
-
4544341015
-
Linear models and empirical Bayes methods for assessing differential expression in microarray experiments
-
Article
-
Smyth,G.K. (2004) Linear models and empirical Bayes methods for assessing differential expression in microarray experiments. Stat. Appl. Genet. Mol. Biol., 3, Article 3.
-
(2004)
Stat. Appl. Genet. Mol. Biol
, vol.3
, pp. 3
-
-
Smyth, G.K.1
-
29
-
-
3142706495
-
New methods for joint analysis of biological networks and expression data
-
Sohler,F. et al. (2004) New methods for joint analysis of biological networks and expression data. Bioinformatics, 20, 1517-1521.
-
(2004)
Bioinformatics
, vol.20
, pp. 1517-1521
-
-
Sohler, F.1
-
30
-
-
36348983834
-
Current progress in network research: Toward reference networks for key model organisms
-
Srinivasan,B.S. et al. (2007) Current progress in network research: Toward reference networks for key model organisms. Brief Bioinform., 8, 318-332.
-
(2007)
Brief Bioinform
, vol.8
, pp. 318-332
-
-
Srinivasan, B.S.1
-
31
-
-
77956890008
-
Martingale-based residuals for survival models
-
Themeau,T. et al. (1990) Martingale-based residuals for survival models. Biometrika, 77, 147.
-
(1990)
Biometrika
, vol.77
, pp. 147
-
-
Themeau, T.1
-
32
-
-
33846086800
-
-
STRING 7-recent developments in the integration and prediction of protein interactions, Database issue, D358-D362
-
von Mering,C. et al. (2007) STRING 7-recent developments in the integration and prediction of protein interactions. Nucleic Acids Res., 35(Database issue): D358-D362.
-
(2007)
Nucleic Acids Res
, vol.35
-
-
von Mering, C.1
|