-
3
-
-
0033707946
-
Using Bayesian networks to analyze expression data
-
Friedman N, Linial M, Nachman I, Pe'er D, (2000) Using Bayesian networks to analyze expression data. J Comput Biol 7: 601-620.
-
(2000)
J Comput Biol
, vol.7
, pp. 601-620
-
-
Friedman, N.1
Linial, M.2
Nachman, I.3
Pe'er, D.4
-
4
-
-
10244230983
-
Reconstruction of gene networks using Bayesian learning and manipulation experiments
-
Pournara I, Wernisch L, (2004) Reconstruction of gene networks using Bayesian learning and manipulation experiments. Bioinformatics 20 (17) (): 2934-42.
-
(2004)
Bioinformatics
, vol.20
, Issue.17
, pp. 2934-2942
-
-
Pournara, I.1
Wernisch, L.2
-
5
-
-
0037941585
-
Module networks: Identifying regulatory modules and their condition-specific regulators from gene expression data
-
Segal E, Koller D, Friedman N, (2003) Module networks: Identifying regulatory modules and their condition-specific regulators from gene expression data. Nature genetics 34: 166-176.
-
(2003)
Nature Genetics
, vol.34
, pp. 166-176
-
-
Segal, E.1
Koller, D.2
Friedman, N.3
-
6
-
-
35948931439
-
An Arabidopsis gene network based on the graphical Gaussian model
-
Ma S, Gong Q, Bohnert HJ, (2007) An Arabidopsis gene network based on the graphical Gaussian model. Genome Res 17: 1614-1625.
-
(2007)
Genome Res
, vol.17
, pp. 1614-1625
-
-
Ma, S.1
Gong, Q.2
Bohnert, H.J.3
-
7
-
-
15944399178
-
Sparse graphical models for exploring gene expression data
-
Dobra A, West M, (2004) Sparse graphical models for exploring gene expression data. J Multivariate analysis 90: 196-212.
-
(2004)
J Multivariate Analysis
, vol.90
, pp. 196-212
-
-
Dobra, A.1
West, M.2
-
8
-
-
1542357674
-
Revealing modularity and organization in the yeast molecular network by integrated analysis of highly heterogeneous genomewide data
-
Tanay A, Sharan R, Kupiec M, Shamir R, (2004) Revealing modularity and organization in the yeast molecular network by integrated analysis of highly heterogeneous genomewide data. Proc Natl Acad Sci USA 101 (9) (): 2981-6.
-
(2004)
Proc Natl Acad Sci USA
, vol.101
, Issue.9
, pp. 2981-2986
-
-
Tanay, A.1
Sharan, R.2
Kupiec, M.3
Shamir, R.4
-
9
-
-
0038048325
-
Inferring genetic networks and identifying compound mode of action via expression profiling
-
Gardner T, di Bernardo D, Lorenz D, Collins JJ, (2003) Inferring genetic networks and identifying compound mode of action via expression profiling. Science 301: 102-105.
-
(2003)
Science
, vol.301
, pp. 102-105
-
-
Gardner, T.1
di Bernardo, D.2
Lorenz, D.3
Collins, J.J.4
-
10
-
-
16844376909
-
Reverse engineering of regulatory networks in human B cells
-
Basso K, Magolin A, Califano A, (2005) Reverse engineering of regulatory networks in human B cells. Nature Genetics 37: 382-390.
-
(2005)
Nature Genetics
, vol.37
, pp. 382-390
-
-
Basso, K.1
Magolin, A.2
Califano, A.3
-
13
-
-
75149195336
-
The transcriptional network for mesenchymal transformation of brain tumours
-
Carro MS, Califano A, Iavarone A, (2010) The transcriptional network for mesenchymal transformation of brain tumours. Nature 463: 318-325.
-
(2010)
Nature
, vol.463
, pp. 318-325
-
-
Carro, M.S.1
Califano, A.2
Iavarone, A.3
-
14
-
-
70249108504
-
Genome-wide identification of post-translational modulators of transcription factor activity in human B-cells
-
Wang K, Saito M, Califano A, (2009) Genome-wide identification of post-translational modulators of transcription factor activity in human B-cells. Nature Biotechnology 27: 829-839.
-
(2009)
Nature Biotechnology
, vol.27
, pp. 829-839
-
-
Wang, K.1
Saito, M.2
Califano, A.3
-
15
-
-
77954196783
-
SPEX∧2: automated concise extraction of spatial gene expression patterns from fly embryo ISH images
-
Puniyani K, Faloutsos C, Xing E, (2010) SPEX∧2: automated concise extraction of spatial gene expression patterns from fly embryo ISH images. Bioinformatics 26: 47-56.
-
(2010)
Bioinformatics
, vol.26
, pp. 47-56
-
-
Puniyani, K.1
Faloutsos, C.2
Xing, E.3
-
16
-
-
0012252471
-
Systematic determination of patterns of gene expression during Drosophila embryogenesis
-
Tomancak P, Beaton A, Weiszmann R, Kwan E, Shu S, et al. (2002) Systematic determination of patterns of gene expression during Drosophila embryogenesis. Genome Biology 3: research0088.1-research0088.14.
-
(2002)
Genome Biology
, vol.3
, pp. 1-14
-
-
Tomancak, P.1
Beaton, A.2
Weiszmann, R.3
Kwan, E.4
Shu, S.5
-
17
-
-
38349127974
-
Global analysis of patterns of gene expression during drosophila embryogenesis
-
doi: 10.1186/gb-2007-8-7-r145
-
Tomancak P, Berman BP, A B, Weiszmann R, Kwan E, et al. (2007) Global analysis of patterns of gene expression during drosophila embryogenesis. Genome Biology 8doi:10.1186/gb-2007-8-7-r145.
-
(2007)
Genome Biology
, vol.8
-
-
Tomancak, P.1
Berman, B.P.2
Weiszmann, R.3
Kwan, E.4
-
18
-
-
0035755471
-
Systematic analysis of gene expression of the C. elegans genome
-
Yuji K, (2001) Systematic analysis of gene expression of the C. elegans genome. Protein, Nucleic Acid and Enzyme 46: 2425-2431.
-
(2001)
Protein, Nucleic Acid and Enzyme
, vol.46
, pp. 2425-2431
-
-
Yuji, K.1
-
19
-
-
33846252240
-
Genome-wide atlas of gene expression in the adult mouse brain
-
Lein ES, Hawrylycz M, Ao N, Jones AR, (2007) Genome-wide atlas of gene expression in the adult mouse brain. Nature 445: 168-176.
-
(2007)
Nature
, vol.445
, pp. 168-176
-
-
Lein, E.S.1
Hawrylycz, M.2
Ao, N.3
Jones, A.R.4
-
20
-
-
2442497313
-
Genome-wide analysis of spatial gene expression in Arabidopsis owers
-
Wellner F, Meyerowitz EM, (2004) Genome-wide analysis of spatial gene expression in Arabidopsis owers. Plant Cell 16: 1314-1326.
-
(2004)
Plant Cell
, vol.16
, pp. 1314-1326
-
-
Wellner, F.1
Meyerowitz, E.M.2
-
21
-
-
3142779194
-
Embryonic stem cell-like features of testicular carcinoma in situ revealed by genome-wide gene expression profiling
-
Almstrup K, Leffers H, (2004) Embryonic stem cell-like features of testicular carcinoma in situ revealed by genome-wide gene expression profiling. Cancer Research 64: 4736-43.
-
(2004)
Cancer Research
, vol.64
, pp. 4736-4743
-
-
Almstrup, K.1
Leffers, H.2
-
22
-
-
67849135609
-
Tesla: Recovering time-varying networks of dependencies in social and biological studies
-
Ahmed A, Xing EP, (2009) Tesla: Recovering time-varying networks of dependencies in social and biological studies. Proc Natl Acad Sci 106: 11878-11883.
-
(2009)
Proc Natl Acad Sci
, vol.106
, pp. 11878-11883
-
-
Ahmed, A.1
Xing, E.P.2
-
23
-
-
76149094177
-
Systematic image-driven analysis of the spatial Drosophila embryonic expression landscape
-
doi:10.1038/msb.2009.102
-
Frise E, Hammonds A, Celniker S, (2010) Systematic image-driven analysis of the spatial Drosophila embryonic expression landscape. Mol Sys Biology 6doi:10.1038/msb.2009.102.
-
(2010)
Mol Sys Biology
, vol.6
-
-
Frise, E.1
Hammonds, A.2
Celniker, S.3
-
24
-
-
84861332716
-
Learning sparse representations for fruit fly gene expression pattern image annotation and retrieval
-
doi:10.1186/1471-2105-13-107
-
Yuan L, Woodard A, Ji S, Jiang Y, Zhou ZH, et al. (2012) Learning sparse representations for fruit fly gene expression pattern image annotation and retrieval. BMC Bioinformatics 13doi:10.1186/1471-2105-13-107.
-
(2012)
BMC Bioinformatics
, vol.13
-
-
Yuan, L.1
Woodard, A.2
Ji, S.3
Jiang, Y.4
Zhou, Z.H.5
-
25
-
-
77951940746
-
Extraction and comparison of gene expression patterns from 2D RNA in situ hybridization images
-
Mace DL, Ohler U, (2010) Extraction and comparison of gene expression patterns from 2D RNA in situ hybridization images. Bioinformatics 26: 761-769.
-
(2010)
Bioinformatics
, vol.26
, pp. 761-769
-
-
Mace, D.L.1
Ohler, U.2
-
26
-
-
32544434047
-
Automatic annotation techniques for gene expression images of the fruit fly embryo
-
Gargesha M, Yang J, Van Emden B, Panchanathan S, Kumar S (2005) Automatic annotation techniques for gene expression images of the fruit fly embryo. In: Society of Photo-Optical Instrumentation Engineers (SPIE) Conference Series. volume 5960, pp. 576-583.
-
(2005)
Society of Photo-Optical Instrumentation Engineers (SPIE) Conference Series
, vol.5960
, pp. 576-583
-
-
Gargesha, M.1
Yang, J.2
Van Emden, B.3
Panchanathan, S.4
Kumar, S.5
-
27
-
-
1942482010
-
-
In: Becker S, Thrun S, Obermayer K, editors, NIPS
-
Bach F, Jordan M (2002) Learning graphical models with mercer kernels. In: Becker S, Thrun S, Obermayer K, editors, NIPS. volume 15, pp. 1009-1016.
-
(2002)
Learning graphical models with mercer kernels
, vol.15
, pp. 1009-1016
-
-
Bach, F.1
Jordan, M.2
-
28
-
-
84878829769
-
Gene network reconstruction from microarray data
-
Jaffrezic F, Tosser-Klopp G, (2009) Gene network reconstruction from microarray data. BMC Proceedings 3: S12.
-
(2009)
BMC Proceedings
, vol.3
-
-
Jaffrezic, F.1
Tosser-Klopp, G.2
-
29
-
-
38749127589
-
Predicting expression patterns from regulatory sequence in Drosophila segmentation
-
Segal E, Unnerstall U, Gaul U, (2008) Predicting expression patterns from regulatory sequence in Drosophila segmentation. Nature 451: 535-540.
-
(2008)
Nature
, vol.451
, pp. 535-540
-
-
Segal, E.1
Unnerstall, U.2
Gaul, U.3
-
30
-
-
33749137281
-
Quantitative and predictive model of transcriptional control of the Drosophila melanogaster even skipped gene
-
Janssens H, Reinitz J, (2006) Quantitative and predictive model of transcriptional control of the Drosophila melanogaster even skipped gene. Nat Gen 38: 1159-1165.
-
(2006)
Nat Gen
, vol.38
, pp. 1159-1165
-
-
Janssens, H.1
Reinitz, J.2
-
32
-
-
34250698998
-
Convex optimization techniques for fitting sparse Gaussian graphical models
-
Banerjee O, Ghaoui LE, d'Aspremont A, Natsoulis G (2006) Convex optimization techniques for fitting sparse Gaussian graphical models. In: ICML. pp. 89-96. doi:http://doi.acm.org/10.1145/1143844.1143856.
-
(2006)
ICML
, pp. 89-96
-
-
Banerjee, O.1
Ghaoui, L.E.2
d'Aspremont, A.3
Natsoulis, G.4
-
33
-
-
45849134070
-
Sparse inverse covariance estimation with the graphical lasso
-
Friedman J, Hastie T, Tibshirani R, (2007) Sparse inverse covariance estimation with the graphical lasso. Biostatistics 9: 432-441.
-
(2007)
Biostatistics
, vol.9
, pp. 432-441
-
-
Friedman, J.1
Hastie, T.2
Tibshirani, R.3
-
34
-
-
85194972808
-
Regression shrinkage and selection via the lasso
-
Tibshirani R, (1996) Regression shrinkage and selection via the lasso. J R Statist Soc B 58: 267-288.
-
(1996)
J R Statist Soc B
, vol.58
, pp. 267-288
-
-
Tibshirani, R.1
-
39
-
-
80555142374
-
High-dimensional covariance estimation by minimizing L1-penalized log-determinant divergence
-
Ravikumar P, Wainwright M, Raskutti G, Yu B, (2011) High-dimensional covariance estimation by minimizing L1-penalized log-determinant divergence. Electronic Journal of Statistics 5: 935-980.
-
(2011)
Electronic Journal of Statistics
, vol.5
, pp. 935-980
-
-
Ravikumar, P.1
Wainwright, M.2
Raskutti, G.3
Yu, B.4
-
40
-
-
0033284915
-
Object recognition from local scale-invariant features
-
Kerkyra, Greece
-
Lowe DG (1999) Object recognition from local scale-invariant features. In: Seventh International Conference on Computer Vision. Kerkyra, Greece, pp. 1150-1157.
-
(1999)
Seventh International Conference on Computer Vision
, pp. 1150-1157
-
-
Lowe, D.G.1
-
41
-
-
3142698698
-
A simple mesh generator in Matlab
-
Persson P, Strang G, (2004) A simple mesh generator in Matlab. SIAM 46: 329-345.
-
(2004)
SIAM
, vol.46
, pp. 329-345
-
-
Persson, P.1
Strang, G.2
-
42
-
-
33947115409
-
Model selection and estimation in the Gaussian graphical model
-
Yuan M, Lin Y, (2007) Model selection and estimation in the Gaussian graphical model. Biometrika 94: 19-35.
-
(2007)
Biometrika
, vol.94
, pp. 19-35
-
-
Yuan, M.1
Lin, Y.2
-
43
-
-
0042344859
-
Stage-specific regulation of caspase activity in Drosophila oogenesis
-
JS P.,M B.,K M
-
JS P, M B, K M, (2003) Stage-specific regulation of caspase activity in Drosophila oogenesis. Dev Biology 260: 113-123.
-
(2003)
Dev Biology
, vol.260
, pp. 113-123
-
-
-
44
-
-
0345600247
-
A protein interaction map of Drosophila melanogaster
-
Giot L, Bader JS, Brouwer C, et al. (2003) A protein interaction map of Drosophila melanogaster. Science 302: 1727-1736.
-
(2003)
Science
, vol.302
, pp. 1727-1736
-
-
Giot, L.1
Bader, J.S.2
Brouwer, C.3
-
45
-
-
12344269924
-
GO::TermFinder-open source software for accessing gene ontology information and finding significantly enriched gene ontology terms associated with a list of genes
-
Boyle E, Weng S, Sherlock G, (2004) GO::TermFinder-open source software for accessing gene ontology information and finding significantly enriched gene ontology terms associated with a list of genes. Bioinformatics 20: 3710-3715.
-
(2004)
Bioinformatics
, vol.20
, pp. 3710-3715
-
-
Boyle, E.1
Weng, S.2
Sherlock, G.3
-
46
-
-
0036081052
-
The FlyBase database of the Drosophila genome projects and community literature
-
Consortium TF, (2002) The FlyBase database of the Drosophila genome projects and community literature. Nucleic Acids Res 30: 106-108.
-
(2002)
Nucleic Acids Res
, vol.30
, pp. 106-108
-
-
Consortium, T.F.1
-
47
-
-
0037452564
-
A SAGE approach to discovery of genes involved in autophagic cell death
-
Gorski SM, Chittaranjan S, Pleasance ED, Freeman JD, Anderson CL, et al. (2003) A SAGE approach to discovery of genes involved in autophagic cell death. Current Biology 13: 358-363.
-
(2003)
Current Biology
, vol.13
, pp. 358-363
-
-
Gorski, S.M.1
Chittaranjan, S.2
Pleasance, E.D.3
Freeman, J.D.4
Anderson, C.L.5
-
48
-
-
77954889072
-
Interactions between DSIF (DRB sensitivity inducing factor), NELF (negative elongation factor), and the Drosophila RNA polymerase II transcription elongation complex
-
Missra A, Gilmour DS, (2010) Interactions between DSIF (DRB sensitivity inducing factor), NELF (negative elongation factor), and the Drosophila RNA polymerase II transcription elongation complex. Proceedings of the National Academy of Sciences 107: 11301-11306.
-
(2010)
Proceedings of the National Academy of Sciences
, vol.107
, pp. 11301-11306
-
-
Missra, A.1
Gilmour, D.S.2
-
49
-
-
79955682293
-
Genome-wide analysis of self-renewal in Drosophila neural stem cells by transgenic RNAi
-
Neumüller RA, Richter C, Fischer A, Novatchkova M, Neumüller KG, et al. (2011) Genome-wide analysis of self-renewal in Drosophila neural stem cells by transgenic RNAi. Cell Stem Cell 8: 580-593.
-
(2011)
Cell Stem Cell
, vol.8
, pp. 580-593
-
-
Neumüller, R.A.1
Richter, C.2
Fischer, A.3
Novatchkova, M.4
Neumüller, K.G.5
-
50
-
-
0035380711
-
The small subunit of the mammalian mitochondrial ribosome: Identification of the full complement of ribosomal proteins present
-
Koc EC, Burkhart W, Blackburn K, Moseley A, Spremulli LL, (2001) The small subunit of the mammalian mitochondrial ribosome: Identification of the full complement of ribosomal proteins present. Journal of Biological Chemistry 276: 19363-19374.
-
(2001)
Journal of Biological Chemistry
, vol.276
, pp. 19363-19374
-
-
Koc, E.C.1
Burkhart, W.2
Blackburn, K.3
Moseley, A.4
Spremulli, L.L.5
-
53
-
-
84893766307
-
The joint graphical lasso for inverse covariance estimation across multiple classes
-
epub ahead of print. doi10.1111/rssb.12033
-
Danaher P, Wang P, Witten DM, (2013) The joint graphical lasso for inverse covariance estimation across multiple classes. Journal of the Royal Statistical Society, Series B [epub ahead of print. doi: 10.1111/rssb.12033.
-
(2013)
Journal of the Royal Statistical Society, Series B
-
-
Danaher, P.1
Wang, P.2
Witten, D.M.3
|