-
1
-
-
0842288337
-
Inferring cellular networks using probabilistic graphical models
-
10.1126/science.1094068, 14764868
-
Friedman N. Inferring cellular networks using probabilistic graphical models. Science 2004, 303(5659):799-805. 10.1126/science.1094068, 14764868.
-
(2004)
Science
, vol.303
, Issue.5659
, pp. 799-805
-
-
Friedman, N.1
-
2
-
-
33748864942
-
A Guide to the Literature on Inferring Genetic Networks by Probabilistic Graphical Models
-
Wiley, New York, Azuaje F, Dopazo J
-
Larrañaga P, Inza I, Flores J. A Guide to the Literature on Inferring Genetic Networks by Probabilistic Graphical Models. Data Analysis and Visualization in Genomics and Proteomics 2005, 215-238. Wiley, New York, Azuaje F, Dopazo J.
-
(2005)
Data Analysis and Visualization in Genomics and Proteomics
, pp. 215-238
-
-
Larrañaga, P.1
Inza, I.2
Flores, J.3
-
4
-
-
84933530882
-
Approximating discrete probability distributions with dependence trees
-
Chow C, Liu C. Approximating discrete probability distributions with dependence trees. Information Theory, IEEE Transactions 1968, 14(3):462-467.
-
(1968)
Information Theory, IEEE Transactions
, vol.14
, Issue.3
, pp. 462-467
-
-
Chow, C.1
Liu, C.2
-
5
-
-
70350674995
-
On the Shortest Spanning Subtree of a Graph and the Traveling Salesman Problem
-
Kruskal J. On the Shortest Spanning Subtree of a Graph and the Traveling Salesman Problem. Proc Am Math Soc 1956, 7:48-50.
-
(1956)
Proc Am Math Soc
, vol.7
, pp. 48-50
-
-
Kruskal, J.1
-
8
-
-
84899032200
-
Thin Junction Trees
-
Cambridge, MA: MIT Press, Dietterich TG, GZ Becker S
-
Bach F, Jordan M. Thin Junction Trees. Advances in Neural Information Processing Systems 2002, 14:569-576. Cambridge, MA: MIT Press, Dietterich TG, GZ Becker S.
-
(2002)
Advances in Neural Information Processing Systems
, vol.14
, pp. 569-576
-
-
Bach, F.1
Jordan, M.2
-
9
-
-
9544257280
-
A formal approach to using data distributions for building causal polytree structures
-
Ouerd M, Oommen B, Matwin S. A formal approach to using data distributions for building causal polytree structures. Information Sciences 2004, 111-132.
-
(2004)
Information Sciences
, pp. 111-132
-
-
Ouerd, M.1
Oommen, B.2
Matwin, S.3
-
10
-
-
0037214793
-
Maximum likelihood bounded tree-width Markov networks
-
Srebro N. Maximum likelihood bounded tree-width Markov networks. Artificial Intelligence 2003, 143:123-138.
-
(2003)
Artificial Intelligence
, vol.143
, pp. 123-138
-
-
Srebro, N.1
-
11
-
-
24044550075
-
Learning with mixtures of trees
-
Meila M, Jordan MI. Learning with mixtures of trees. J Mach Learn Res 2001, 1:1-48.
-
(2001)
J Mach Learn Res
, vol.1
, pp. 1-48
-
-
Meila, M.1
Jordan, M.I.2
-
12
-
-
7544249120
-
Embedded trees: estimation of Gaussian Processes on graphs with cycles
-
Sudderth E, Sudderth E, Wainwright M, Willsky A. Embedded trees: estimation of Gaussian Processes on graphs with cycles. IEEE Transactions on Signal Processing 2004, 52(11):3136-3150.
-
(2004)
IEEE Transactions on Signal Processing
, vol.52
, Issue.11
, pp. 3136-3150
-
-
Sudderth, E.1
Sudderth, E.2
Wainwright, M.3
Willsky, A.4
-
13
-
-
34248668811
-
Conditional Chow-Liu tree structures for modeling discrete-valued vector time series
-
Arlington, Virginia, United States: AUAI Press
-
Kirshner S, Smyth P, Robertson AW. Conditional Chow-Liu tree structures for modeling discrete-valued vector time series. AUAI '04: Proceedings of the 20th conference on Uncertainty in artificial intelligence 2004, 317-324. Arlington, Virginia, United States: AUAI Press.
-
(2004)
AUAI '04: Proceedings of the 20th conference on Uncertainty in artificial intelligence
, pp. 317-324
-
-
Kirshner, S.1
Smyth, P.2
Robertson, A.W.3
-
14
-
-
0008546324
-
Consistency of an estimate of tree-dependent probability distribution
-
IT-19
-
Chou C, Wagner T. Consistency of an estimate of tree-dependent probability distribution. IEEE Transactions on Information Theory 1973, IT-19:369-371.
-
(1973)
IEEE Transactions on Information Theory
, pp. 369-371
-
-
Chou, C.1
Wagner, T.2
-
15
-
-
0000208683
-
Stochastic Complexity
-
Rissanen J. Stochastic Complexity. J Royal Stat Soc B 1987, 49:223-239.
-
(1987)
J Royal Stat Soc B
, vol.49
, pp. 223-239
-
-
Rissanen, J.1
-
16
-
-
0016355478
-
A new look at the statistical identification problem
-
Akaike H. A new look at the statistical identification problem. IEEE Trans Auto Control 1974, 19:716-723.
-
(1974)
IEEE Trans Auto Control
, vol.19
, pp. 716-723
-
-
Akaike, H.1
-
17
-
-
0000120766
-
Estimating the Dimension of a Model
-
Schwarz G. Estimating the Dimension of a Model. Annals of Statistics 1978, 6:461-464.
-
(1978)
Annals of Statistics
, vol.6
, pp. 461-464
-
-
Schwarz, G.1
-
18
-
-
8744307994
-
Multimodel Inference: Understanding AIC and BIC in Model Selection
-
Burnham KP, Anderson DR. Multimodel Inference: Understanding AIC and BIC in Model Selection. Sociological Methods Research 2004, 33:261-304.
-
(2004)
Sociological Methods Research
, vol.33
, pp. 261-304
-
-
Burnham, K.P.1
Anderson, D.R.2
-
19
-
-
60649085930
-
Methods and experiments with bounded tree-width Markov networks
-
MIT
-
Liang P, Srebro N. Methods and experiments with bounded tree-width Markov networks. Tech rep 2004, MIT.
-
(2004)
Tech rep
-
-
Liang, P.1
Srebro, N.2
-
20
-
-
84874655619
-
Estimation of Tree Structure for Variable Selection
-
University of Oxford, to appear.
-
Panayidou K. Estimation of Tree Structure for Variable Selection. PhD thesis University of Oxford, to appear..
-
PhD thesis
-
-
Panayidou, K.1
-
23
-
-
0002480085
-
Graphical models for associations between variables, some of which are qualitative and some quantitative
-
Lauritzen S, Wermuth N. Graphical models for associations between variables, some of which are qualitative and some quantitative. Ann Statist 1989, 17:31-57.
-
(1989)
Ann Statist
, vol.17
, pp. 31-57
-
-
Lauritzen, S.1
Wermuth, N.2
-
24
-
-
0000900644
-
Decomposition of maximum likelihood in mixed graphical interaction models
-
Frydenberg M, Lauritzen S. Decomposition of maximum likelihood in mixed graphical interaction models. Biometrika 1989, 76:539-555.
-
(1989)
Biometrika
, vol.76
, pp. 539-555
-
-
Frydenberg, M.1
Lauritzen, S.2
-
26
-
-
0031477121
-
On the Markov Equivalence of Chain Graphs, Undirected Graphs, and Acyclic Digraphs
-
Andersson SA, Madigan D, Perlman MD. On the Markov Equivalence of Chain Graphs, Undirected Graphs, and Acyclic Digraphs. Scandinavian Journal of Statistics 1997, 24:81-102.
-
(1997)
Scandinavian Journal of Statistics
, vol.24
, pp. 81-102
-
-
Andersson, S.A.1
Madigan, D.2
Perlman, M.D.3
-
28
-
-
34249761849
-
Learning Bayesian Networks: The combination of knowledge and statistical data
-
Heckerman D, Geiger D, Chickering DM. Learning Bayesian Networks: The combination of knowledge and statistical data. Machine Learning 1995, 20:197-243.
-
(1995)
Machine Learning
, vol.20
, pp. 197-243
-
-
Heckerman, D.1
Geiger, D.2
Chickering, D.M.3
-
30
-
-
58049200606
-
Genome-scale reconstruction of the Lrp regulatory network in Escherichia coli
-
10.1073/pnas.0807227105, 2614783, 19052235
-
Cho BK, Barrett CL, Knight EM, Park YS, Palsson B. Genome-scale reconstruction of the Lrp regulatory network in Escherichia coli. Proc Natl Acad Sci USA 2008, 105(49):19462-19467. 10.1073/pnas.0807227105, 2614783, 19052235.
-
(2008)
Proc Natl Acad Sci USA
, vol.105
, Issue.49
, pp. 19462-19467
-
-
Cho, B.K.1
Barrett, C.L.2
Knight, E.M.3
Park, Y.S.4
Palsson, B.5
-
31
-
-
4544341015
-
Linear models and empirical bayes methods for assessing differential expression in microarray experiments
-
Smyth GK. Linear models and empirical bayes methods for assessing differential expression in microarray experiments. Stat Appl Genet Mol Biol 2004, 3:Article3.
-
(2004)
Stat Appl Genet Mol Biol
, vol.3
-
-
Smyth, G.K.1
-
32
-
-
0034973706
-
Activation from a Distance: Roles of Lrp and Integration Host Factor in Transcriptional Activation of gltBDF
-
10.1128/JB.183.13.3910-3918.2001, 95273, 11395454
-
Ligi P, Blumenthal R, Matthews R. Activation from a Distance: Roles of Lrp and Integration Host Factor in Transcriptional Activation of gltBDF. Journal of Bacteriology 2001, 183:3910-3918. 10.1128/JB.183.13.3910-3918.2001, 95273, 11395454.
-
(2001)
Journal of Bacteriology
, vol.183
, pp. 3910-3918
-
-
Ligi, P.1
Blumenthal, R.2
Matthews, R.3
-
33
-
-
26444546442
-
An expression signature for p53 status in human breast cancer predicts mutation status, transcriptional effects, and patient survival
-
10.1073/pnas.0506230102, 1197273,1197273, 16141321
-
Miller LD, Smeds J, George J, Vega VB, Vergara L, Ploner A, Pawitan Y, Hall P, Klaar S, Liu ET, Bergh J. An expression signature for p53 status in human breast cancer predicts mutation status, transcriptional effects, and patient survival. Proc Natl Acad Sci USA 2005, 102(38):13550-13555. 10.1073/pnas.0506230102, 1197273,1197273, 16141321.
-
(2005)
Proc Natl Acad Sci USA
, vol.102
, Issue.38
, pp. 13550-13555
-
-
Miller, L.D.1
Smeds, J.2
George, J.3
Vega, V.B.4
Vergara, L.5
Ploner, A.6
Pawitan, Y.7
Hall, P.8
Klaar, S.9
Liu, E.T.10
Bergh, J.11
-
34
-
-
45849134070
-
Sparse inverse covariance estimation with the graphical lasso
-
10.1093/biostatistics/kxm045, 18079126
-
Friedman J, Hastie T, Tibshirani R. Sparse inverse covariance estimation with the graphical lasso. Biostatistics 2008, 9(3):432-441. 10.1093/biostatistics/kxm045, 18079126.
-
(2008)
Biostatistics
, vol.9
, Issue.3
, pp. 432-441
-
-
Friedman, J.1
Hastie, T.2
Tibshirani, R.3
-
35
-
-
33947524259
-
Estimating High-dimensional Directed Acyclic Graphs with the PC-Algorithm
-
Kalisch M, Buhlmann P. Estimating High-dimensional Directed Acyclic Graphs with the PC-Algorithm. Journal of Machine Learning Research 2007, 8:613-636.
-
(2007)
Journal of Machine Learning Research
, vol.8
, pp. 613-636
-
-
Kalisch, M.1
Buhlmann, P.2
-
36
-
-
59649121280
-
Reverse engineering molecular regulatory networks from microarray data with qp-graphs
-
10.1089/cmb.2008.08TT, 19178140
-
Castelo R, Roverato A. Reverse engineering molecular regulatory networks from microarray data with qp-graphs. J Comput Biol 2009, 16(2):213-227. 10.1089/cmb.2008.08TT, 19178140.
-
(2009)
J Comput Biol
, vol.16
, Issue.2
, pp. 213-227
-
-
Castelo, R.1
Roverato, A.2
-
37
-
-
0017129474
-
Model Search among Multiplicative Models
-
Wermuth N. Model Search among Multiplicative Models. Biometrics 1976, 32(2):253-263.
-
(1976)
Biometrics
, vol.32
, Issue.2
, pp. 253-263
-
-
Wermuth, N.1
-
38
-
-
2442713792
-
Graphical modeling of the joint distribution of alleles at associated loci
-
10.1086/421249, 1182104, 15114533
-
Thomas A, Camp NJ. Graphical modeling of the joint distribution of alleles at associated loci. Am J Hum Genet 2004, 74(6):1088-1101. 10.1086/421249, 1182104, 15114533.
-
(2004)
Am J Hum Genet
, vol.74
, Issue.6
, pp. 1088-1101
-
-
Thomas, A.1
Camp, N.J.2
-
40
-
-
0037174670
-
Network Motifs: Simple Building Blocks of Complex Networks
-
10.1126/science.298.5594.824, 12399590
-
Milo R, Shen-Orr S, Itzkovitz S, Kashtan N, Chkovskii D, Alon U. Network Motifs: Simple Building Blocks of Complex Networks. Science 2002, 298:824-827. 10.1126/science.298.5594.824, 12399590.
-
(2002)
Science
, vol.298
, pp. 824-827
-
-
Milo, R.1
Shen-Orr, S.2
Itzkovitz, S.3
Kashtan, N.4
Chkovskii, D.5
Alon, U.6
-
41
-
-
44349107818
-
A review on models and algorithms for motif discovery in protein-protein interaction networks
-
10.1093/bfgp/eln015, 18443014
-
Ciriello G, Guerra C. A review on models and algorithms for motif discovery in protein-protein interaction networks. Briefings in Functional Genomics and Proteomics 2008, 7(2):147-156. 10.1093/bfgp/eln015, 18443014.
-
(2008)
Briefings in Functional Genomics and Proteomics
, vol.7
, Issue.2
, pp. 147-156
-
-
Ciriello, G.1
Guerra, C.2
-
42
-
-
33947305781
-
ARACNE: an algorithm for the reconstruction of gene regulatory networks in a mammalian cellular context
-
10.1186/1471-2105-7-S1-S7, 1810318, 16723010
-
Margolin AA, Nemenman I, Basso K, Wiggins C, Stolovitzky G, Favera RD, Califano A. ARACNE: an algorithm for the reconstruction of gene regulatory networks in a mammalian cellular context. BMC Bioinformatics 2006, 7(Suppl 1):S7. 10.1186/1471-2105-7-S1-S7, 1810318, 16723010.
-
(2006)
BMC Bioinformatics
, vol.7
, Issue.SUPPL. 1
-
-
Margolin, A.A.1
Nemenman, I.2
Basso, K.3
Wiggins, C.4
Stolovitzky, G.5
Favera, R.D.6
Califano, A.7
-
43
-
-
0042526388
-
The mutual information: detecting and evaluating dependencies between variables
-
Steuer R, Kurths J, Daub CO, Weise J, Selbig J. The mutual information: detecting and evaluating dependencies between variables. Bioinformatics 2002, 18(Suppl 2):S231-S240.
-
(2002)
Bioinformatics
, vol.18
, Issue.SUPPL. 2
-
-
Steuer, R.1
Kurths, J.2
Daub, C.O.3
Weise, J.4
Selbig, J.5
|