-
1
-
-
77950803115
-
A Robust Bayesian Two-Sample Test for Detecting Intervals of Differential Gene Expression in Microarray Time Series
-
10.1089/cmb.2009.0175, 20377450
-
Stegle O, Denby KJ, Cooke EJ, Wild DL, Ghahramani Z, Borgwardt KM. A Robust Bayesian Two-Sample Test for Detecting Intervals of Differential Gene Expression in Microarray Time Series. Journal of Computational Biology 2010, 17:355-367. 10.1089/cmb.2009.0175, 20377450.
-
(2010)
Journal of Computational Biology
, vol.17
, pp. 355-367
-
-
Stegle, O.1
Denby, K.J.2
Cooke, E.J.3
Wild, D.L.4
Ghahramani, Z.5
Borgwardt, K.M.6
-
2
-
-
0032441150
-
Cluster Analysis and Display of Genome-wide Expression
-
Eisen M, Spellman P, Brown P, Botstein D. Cluster Analysis and Display of Genome-wide Expression. Proceedings of the National Academy of Sciences 1998, 95:14863-14868.
-
(1998)
Proceedings of the National Academy of Sciences
, vol.95
, pp. 14863-14868
-
-
Eisen, M.1
Spellman, P.2
Brown, P.3
Botstein, D.4
-
3
-
-
0036203115
-
A mixture model-based approach to the clustering of microarray expression data
-
10.1093/bioinformatics/18.3.413, 11934740
-
McLachlan GJ, Bean RW, Peel D. A mixture model-based approach to the clustering of microarray expression data. Bioinformatics 2002, 18:413-422. 10.1093/bioinformatics/18.3.413, 11934740.
-
(2002)
Bioinformatics
, vol.18
, pp. 413-422
-
-
McLachlan, G.J.1
Bean, R.W.2
Peel, D.3
-
4
-
-
27644593731
-
Analyzing Gene Expression Time-Courses
-
10.1109/TCBB.2005.31, 17044182
-
Schliep A, Costa IG, Steinhoff C, Schonhuth A. Analyzing Gene Expression Time-Courses. IEEE/ACM Trans Comput Biol Bioinform 2005, 2:179-193. 10.1109/TCBB.2005.31, 17044182.
-
(2005)
IEEE/ACM Trans Comput Biol Bioinform
, vol.2
, pp. 179-193
-
-
Schliep, A.1
Costa, I.G.2
Steinhoff, C.3
Schonhuth, A.4
-
6
-
-
0041346457
-
Continuous representations of time-series gene expression data
-
10.1089/10665270360688057, 12935332
-
Bar-Joseph Z, Gerber G, Gifford D, Jaakkola T, Simon I. Continuous representations of time-series gene expression data. Journal of Computational Biology 2003, 10(3-4):341-356. 10.1089/10665270360688057, 12935332.
-
(2003)
Journal of Computational Biology
, vol.10
, Issue.3-4
, pp. 341-356
-
-
Bar-Joseph, Z.1
Gerber, G.2
Gifford, D.3
Jaakkola, T.4
Simon, I.5
-
7
-
-
28044449342
-
Bayesian coclustering of Anopheles gene expression time series: Study of immune defense response to multiple experimental challenges
-
Heard NA, Holmes CC, Stephens DA, Hand DJ, Dimopoulos G. Bayesian coclustering of Anopheles gene expression time series: Study of immune defense response to multiple experimental challenges. Proceedings of the National Academy of Sciences 2005, 102(47):16939-16944.
-
(2005)
Proceedings of the National Academy of Sciences
, vol.102
, Issue.47
, pp. 16939-16944
-
-
Heard, N.A.1
Holmes, C.C.2
Stephens, D.A.3
Hand, D.J.4
Dimopoulos, G.5
-
8
-
-
33645507298
-
A Quantitative Study of Gene Regulation Involved in the Immune Response of Anopheline Mosquitoes: An Application of Bayesian Hierarchical Clustering of Curves
-
Heard NA, Holmes CC, Stephens DA. A Quantitative Study of Gene Regulation Involved in the Immune Response of Anopheline Mosquitoes: An Application of Bayesian Hierarchical Clustering of Curves. Journal of the American Statistical Association 2006, 101(473):18.
-
(2006)
Journal of the American Statistical Association
, vol.101
, Issue.473
, pp. 18
-
-
Heard, N.A.1
Holmes, C.C.2
Stephens, D.A.3
-
9
-
-
33644855951
-
A data-driven clustering method for time course gene expression data
-
10.1093/nar/gkl013, 1388097, 16510852
-
Ma P, Castillo-Davis CI, Zhong W, Liu JS. A data-driven clustering method for time course gene expression data. Nucleic Acids Research 2006, 34:1261-1269. 10.1093/nar/gkl013, 1388097, 16510852.
-
(2006)
Nucleic Acids Research
, vol.34
, pp. 1261-1269
-
-
Ma, P.1
Castillo-Davis, C.I.2
Zhong, W.3
Liu, J.S.4
-
10
-
-
77955780874
-
Searching a Multivariate Partition Space Using MAX-SAT
-
Springer, Heidelberg, Masulli F, Peterson L, Tagliaferri R
-
Liverani S, Cussens J, Smith JQ. Searching a Multivariate Partition Space Using MAX-SAT. Computational Intelligence Methods for Bioinformatics and Biostatistics, 6th International Meeting, CIBB 2009 Genova, Italy, Volume 6160 of Lecture Notes in Computer Science 2010, 240-253. Springer, Heidelberg, Masulli F, Peterson L, Tagliaferri R.
-
(2010)
Computational Intelligence Methods for Bioinformatics and Biostatistics, 6th International Meeting, CIBB 2009 Genova, Italy, Volume 6160 of Lecture Notes in Computer Science
, pp. 240-253
-
-
Liverani, S.1
Cussens, J.2
Smith, J.Q.3
-
11
-
-
33747890494
-
A Mixture model with random-effects components for clustering correlated gene-expression profiles
-
10.1093/bioinformatics/btl165, 16675467
-
Ng SK, McLachlan GJ, Wang K, Jones LBT, Ng SW. A Mixture model with random-effects components for clustering correlated gene-expression profiles. Bioinformatics 2006, 22:1745-1752. 10.1093/bioinformatics/btl165, 16675467.
-
(2006)
Bioinformatics
, vol.22
, pp. 1745-1752
-
-
Ng, S.K.1
McLachlan, G.J.2
Wang, K.3
Jones, L.B.T.4
Ng, S.W.5
-
12
-
-
8844277626
-
Analyzing time series gene expression data
-
10.1093/bioinformatics/bth283, 15130923
-
Bar-Joseph Z. Analyzing time series gene expression data. Bioinformatics 2004, 20(16):2493. 10.1093/bioinformatics/bth283, 15130923.
-
(2004)
Bioinformatics
, vol.20
, Issue.16
, pp. 2493
-
-
Bar-Joseph, Z.1
-
14
-
-
69849104854
-
R/BHC: Fast Bayesian Hierarchical Clustering for Microarray Data
-
10.1186/1471-2105-10-242, 2736174, 19660130
-
Savage RS, Heller K, Xu Y, Ghahramani Z, Truman WM, Grant M, Denby KJ, Wild DL. R/BHC: Fast Bayesian Hierarchical Clustering for Microarray Data. BMC Bioinformatics 2009, 10:242. 10.1186/1471-2105-10-242, 2736174, 19660130.
-
(2009)
BMC Bioinformatics
, vol.10
, pp. 242
-
-
Savage, R.S.1
Heller, K.2
Xu, Y.3
Ghahramani, Z.4
Truman, W.M.5
Grant, M.6
Denby, K.J.7
Wild, D.L.8
-
17
-
-
77951941265
-
Estimating replicate time shifts using Gaussian process regression
-
10.1093/bioinformatics/btq022, 2832819, 20147305
-
Liu Q, Lin K, Anderson B, Smyth P, Ihler A. Estimating replicate time shifts using Gaussian process regression. Bioinformatics 2010, 26:770-776. 10.1093/bioinformatics/btq022, 2832819, 20147305.
-
(2010)
Bioinformatics
, vol.26
, pp. 770-776
-
-
Liu, Q.1
Lin, K.2
Anderson, B.3
Smyth, P.4
Ihler, A.5
-
19
-
-
24044488957
-
Biomarker discovery in microarray gene expression data with Gaussian processes
-
Chu W, Ghahramani Z, Falciani F, Wild DL. Biomarker discovery in microarray gene expression data with Gaussian processes. Bioinformatics 2005, 21:3383-3393.
-
(2005)
Bioinformatics
, vol.21
, pp. 3383-3393
-
-
Chu, W.1
Ghahramani, Z.2
Falciani, F.3
Wild, D.L.4
-
20
-
-
65549161909
-
Gaussian process regression bootstrapping: exploring the effect of uncertainty in time course data
-
10.1093/bioinformatics/btp139, 2677737, 19289448
-
Kirk PDW, Stumpf MPH. Gaussian process regression bootstrapping: exploring the effect of uncertainty in time course data. Bioinformatics 2009, 25:1300-1306. 10.1093/bioinformatics/btp139, 2677737, 19289448.
-
(2009)
Bioinformatics
, vol.25
, pp. 1300-1306
-
-
Kirk, P.D.W.1
Stumpf, M.P.H.2
-
21
-
-
66349126734
-
Approximate Inference for Robust Gaussian Process Regression, Technical Report No. 136
-
Kuss M, Pfingsten T, Csato L, Rasmussen CE. Approximate Inference for Robust Gaussian Process Regression, Technical Report No. 136. Max Planck Institute for Biological Cybernetics, Tuübingen 2005,
-
(2005)
Max Planck Institute for Biological Cybernetics, Tuübingen
-
-
Kuss, M.1
Pfingsten, T.2
Csato, L.3
Rasmussen, C.E.4
-
22
-
-
0032112293
-
A Genome-Wide Transcriptional Analysis of the Mitotic Cell Cycle
-
10.1016/S1097-2765(00)80114-8, 9702192
-
Cho R, Campbell M, Steinmetz EWL, Conway A, Wodicka L, Wolfsberg T, Gabrielian A, Landsman D, Lockhart DJ, Davis R. A Genome-Wide Transcriptional Analysis of the Mitotic Cell Cycle. Molecular Cell 1998, 2:65-73. 10.1016/S1097-2765(00)80114-8, 9702192.
-
(1998)
Molecular Cell
, vol.2
, pp. 65-73
-
-
Cho, R.1
Campbell, M.2
Steinmetz, E.W.L.3
Conway, A.4
Wodicka, L.5
Wolfsberg, T.6
Gabrielian, A.7
Landsman, D.8
Lockhart, D.J.9
Davis, R.10
-
23
-
-
77954207953
-
Discovering Transcriptional Modules by Bayesian Data Integration
-
10.1093/bioinformatics/btq210, 2881394, 20529901
-
Savage RS, Ghahramani Z, Griffin JE, de la Cruz BJ, Wild DL. Discovering Transcriptional Modules by Bayesian Data Integration. Bioinformatics 2010, 26:i158-i167. 10.1093/bioinformatics/btq210, 2881394, 20529901.
-
(2010)
Bioinformatics
, vol.26
-
-
Savage, R.S.1
Ghahramani, Z.2
Griffin, J.E.3
de la Cruz, B.J.4
Wild, D.L.5
-
24
-
-
45149097650
-
Global control of cell cycle transcription by coupled CDK and network oscillators
-
Orlando DA, Lin YL, Bernard A, Wang JY, Socolar JES, Iversen ES, Hartemink AJ, Haase SB. Global control of cell cycle transcription by coupled CDK and network oscillators. Nature 2008, 453(7197):994-947.
-
(2008)
Nature
, vol.453
, Issue.7197
, pp. 994-1947
-
-
Orlando, D.A.1
Lin, Y.L.2
Bernard, A.3
Wang, J.Y.4
Socolar, J.E.S.5
Iversen, E.S.6
Hartemink, A.J.7
Haase, S.B.8
-
25
-
-
0031742022
-
Comprehensive Identification of Cell Cycle regulated Genes of the Yeast Saccharomyces cerevisiae by Microarray Hybridization
-
25624, 9843569
-
Spellman P, Sherlock G, Zhang M, Iyer VR, Anders K, Eisen M, Brown P, Botstein D, Futcher B. Comprehensive Identification of Cell Cycle regulated Genes of the Yeast Saccharomyces cerevisiae by Microarray Hybridization. Molecular Biology of the Cell 1998, 9:3273-3297. 25624, 9843569.
-
(1998)
Molecular Biology of the Cell
, vol.9
, pp. 3273-3297
-
-
Spellman, P.1
Sherlock, G.2
Zhang, M.3
Iyer, V.R.4
Anders, K.5
Eisen, M.6
Brown, P.7
Botstein, D.8
Futcher, B.9
-
26
-
-
33747379083
-
The Forkhead transcription factor Hcm1 regulates chromosome segregation genes and fills the S-phase gap in the transcriptional circuitry of the cell cycle
-
10.1101/gad.1450606, 1553209, 16912276
-
Pramila T, Wu W, Miles S, Noble W, Breeden L. The Forkhead transcription factor Hcm1 regulates chromosome segregation genes and fills the S-phase gap in the transcriptional circuitry of the cell cycle. Genes and Development 2006, 20:2266-2278. 10.1101/gad.1450606, 1553209, 16912276.
-
(2006)
Genes and Development
, vol.20
, pp. 2266-2278
-
-
Pramila, T.1
Wu, W.2
Miles, S.3
Noble, W.4
Breeden, L.5
-
27
-
-
3142744689
-
Modeling T-cell activation using gene expression profiling and state-space models
-
10.1093/bioinformatics/bth093, 14962938
-
Rangel C, Angus J, Ghahramani Z, Lioumi M, Sotheran E, Gaiba A, Wild DL, Falciani F. Modeling T-cell activation using gene expression profiling and state-space models. Bioinformatics 2004, 20:1361-1372. 10.1093/bioinformatics/bth093, 14962938.
-
(2004)
Bioinformatics
, vol.20
, pp. 1361-1372
-
-
Rangel, C.1
Angus, J.2
Ghahramani, Z.3
Lioumi, M.4
Sotheran, E.5
Gaiba, A.6
Wild, D.L.7
Falciani, F.8
-
28
-
-
81255214081
-
The analysis of cellular transcriptional response at the genome level: Two case studies with relevance to bacterial pathogenesis
-
Taylor & Francis, Falciani F
-
Carzaniga T, Sarti D, Trevino V, Buckley C, Salmon M, Moobed S, Wild DL, Constantinidou C, Hobman JL, Dehò G, Falciani F. The analysis of cellular transcriptional response at the genome level: Two case studies with relevance to bacterial pathogenesis. Microarray Technology Through Applications 2007, 125-154. Taylor & Francis, Falciani F.
-
(2007)
Microarray Technology Through Applications
, pp. 125-154
-
-
Carzaniga, T.1
Sarti, D.2
Trevino, V.3
Buckley, C.4
Salmon, M.5
Moobed, S.6
Wild, D.L.7
Constantinidou, C.8
Hobman, J.L.9
Dehò, G.10
Falciani, F.11
-
29
-
-
33749428430
-
Methods for evaluating clustering algorithms for gene expression data using a reference set of functional classes
-
10.1186/1471-2105-7-397, 1590054, 16945146
-
Datta S, Datta S. Methods for evaluating clustering algorithms for gene expression data using a reference set of functional classes. BMC Bioinformatics 2006, 7:397. 10.1186/1471-2105-7-397, 1590054, 16945146.
-
(2006)
BMC Bioinformatics
, vol.7
, pp. 397
-
-
Datta, S.1
Datta, S.2
-
30
-
-
46749142532
-
ClValid: An R package for cluster validation
-
Brock G, Pihur V, Datta S, Datta S. clValid: An R package for cluster validation. Journal of Statical Software 2008, 25:1-22.
-
(2008)
Journal of Statical Software
, vol.25
, pp. 1-22
-
-
Brock, G.1
Pihur, V.2
Datta, S.3
Datta, S.4
-
31
-
-
0002344794
-
Bootstrap Methods: Another Look at the Jackknife
-
Efron B. Bootstrap Methods: Another Look at the Jackknife. The Annals of Statistics 1979, 7:1-26.
-
(1979)
The Annals of Statistics
, vol.7
, pp. 1-26
-
-
Efron, B.1
-
33
-
-
0037311919
-
TM4: a free, open-source system for microarray data management and analysis
-
Saeed AI, Sharov V, White J, Li J, Liang W, Bhagabati N, Braisted J, Klapa M, Currier T, Thiagarajan M, Sturn A, Snuffin M, Rezantsev A, Popov D, Rytsov A, Kostukovich E, Borisovsky I, Liu Z, Vinsavich A, Trush V, Quackenbush J. TM4: a free, open-source system for microarray data management and analysis. Biotechniques 2003, 34:374-378.
-
(2003)
Biotechniques
, vol.34
, pp. 374-378
-
-
Saeed, A.I.1
Sharov, V.2
White, J.3
Li, J.4
Liang, W.5
Bhagabati, N.6
Braisted, J.7
Klapa, M.8
Currier, T.9
Thiagarajan, M.10
Sturn, A.11
Snuffin, M.12
Rezantsev, A.13
Popov, D.14
Rytsov, A.15
Kostukovich, E.16
Borisovsky, I.17
Liu, Z.18
Vinsavich, A.19
Trush, V.20
Quackenbush, J.21
more..
-
34
-
-
0034782618
-
Model-based clustering and data transformations for gene expression data
-
10.1093/bioinformatics/17.10.977, 11673243
-
Yeung K, Fraley C, Murua A, Raftery AE, Ruzza WL. Model-based clustering and data transformations for gene expression data. Bioinformatics 2001, 17:977-987. 10.1093/bioinformatics/17.10.977, 11673243.
-
(2001)
Bioinformatics
, vol.17
, pp. 977-987
-
-
Yeung, K.1
Fraley, C.2
Murua, A.3
Raftery, A.E.4
Ruzza, W.L.5
-
35
-
-
33745283400
-
A Bayesian Mixture Model for Paritioning Gene Expression Data
-
10.1111/j.1541-0420.2005.00492.x, 16918916
-
Zhou C, Wakefield J. A Bayesian Mixture Model for Paritioning Gene Expression Data. Biometrics 2006, 62:515-525. 10.1111/j.1541-0420.2005.00492.x, 16918916.
-
(2006)
Biometrics
, vol.62
, pp. 515-525
-
-
Zhou, C.1
Wakefield, J.2
-
36
-
-
10744226486
-
The Molecular Signature of Mantle Cell Lymphoma Reveals Multiple Signals Favoring Cell Survival
-
Martínez N, Camacho FI, Algara P, Rodríguez A, Dopazo A, Ruíz-Ballesteros E, Martín P, Martínez-Climent JA, García-Conde J, Menárguez J, Solano F, Mollejo M, Piris MA. The Molecular Signature of Mantle Cell Lymphoma Reveals Multiple Signals Favoring Cell Survival. Cancer Research 2003, 63:8226-8232.
-
(2003)
Cancer Research
, vol.63
, pp. 8226-8232
-
-
Martínez, N.1
Camacho, F.I.2
Algara, P.3
Rodríguez, A.4
Dopazo, A.5
Ruíz-Ballesteros, E.6
Martín, P.7
Martínez-Climent, J.A.8
García-Conde, J.9
Menárguez, J.10
Solano, F.11
Mollejo, M.12
Piris, M.A.13
-
37
-
-
30444435792
-
Ikaros Increases Normal Apoptosis in Adult Erythroid Cells
-
10.1002/ajh.20507, 16369973
-
Pulte D, Lopez RA, Baker ST, Ward M, Ritchie E, Richardson CA, O'Neill DW, Bank A. Ikaros Increases Normal Apoptosis in Adult Erythroid Cells. American Journal of Hematology 2006, 81:12-18. 10.1002/ajh.20507, 16369973.
-
(2006)
American Journal of Hematology
, vol.81
, pp. 12-18
-
-
Pulte, D.1
Lopez, R.A.2
Baker, S.T.3
Ward, M.4
Ritchie, E.5
Richardson, C.A.6
O'Neill, D.W.7
Bank, A.8
|