-
1
-
-
0032616683
-
Identification of genetic networks from a small number of gene expression patterns under the Boolean network model
-
Akutsu T Miyano S Kuhara S Identification of genetic networks from a small number of gene expression patterns under the Boolean network model Pacific Symposium on Biocomputing 1999, 17-28. 10380182
-
(1999)
Pacific Symposium on Biocomputing
, pp. 17-28
-
-
Akutsu, T.1
Miyano, S.2
Kuhara, S.3
-
2
-
-
0033707946
-
Using Bayesian networks to analyze expression data
-
10.1089/106652700750050961 11108481
-
Friedman N Linial M Nachman I Pe'er D Using Bayesian networks to analyze expression data J Comput Biol 2000, 7 (3-4):601-620. 10.1089/ 106652700750050961 11108481
-
(2000)
J Comput Biol
, vol.7
, Issue.3-4
, pp. 601-620
-
-
Friedman, N.1
Linial, M.2
Nachman, I.3
Pe'er, D.4
-
3
-
-
3042738945
-
Dynamic Bayesian network and nonparametric regression for nonlinear modeling of gene networks from time series gene expression data
-
15245804
-
Kim S Imoto S Miyano S Dynamic Bayesian network and nonparametric regression for nonlinear modeling of gene networks from time series gene expression data Bio Systems 2004, 75(1-3):57-65. 15245804
-
(2004)
Bio Systems
, vol.75
, pp. 57-65
-
-
Kim, S.1
Imoto, S.2
Miyano, S.3
-
4
-
-
0345824737
-
Network component analysis: Reconstruction of regulatory signals in biological systems
-
307600 10.1073/pnas.2136632100
-
Liao JC Boscolo R Yang YL Tran LM Sabatti C Roychowdhury VP Network component analysis: Reconstruction of regulatory signals in biological systems Proceedings of the National Academy of Sciences of the United States of America 2003, 100(26):15522-15527. 307600 14673099 10.1073/ pnas.2136632100
-
(2003)
Proceedings of the National Academy of Sciences of the United States of America
, vol.100
, Issue.26
, pp. 15522-15527
-
-
Liao, J.C.1
Boscolo, R.2
Yang, Y.L.3
Tran, L.M.4
Sabatti, C.5
Roychowdhury, V.P.6
-
5
-
-
0037941585
-
Module networks: Identifying regulatory modules and their condition-specific regulators from gene expression data
-
10.1038/ng1165 12740579
-
Segal E Shapira M Regev A Pe'er D Botstein D Koller D Friedman N Module networks: Identifying regulatory modules and their condition-specific regulators from gene expression data Nature genetics 2003, 34(2):166-176. 10.1038/ng1165 12740579
-
(2003)
Nature Genetics
, vol.34
, Issue.18
, pp. 166-176
-
-
Segal, E.1
Shapira, M.2
Regev, A.3
Pe'er, D.4
Botstein, D.5
Koller, D.6
Friedman, N.7
-
6
-
-
2942582468
-
Defining transcriptional networks through integrative modeling of mRNA expression and transcription factor binding data
-
407845 15113405 10.1186/1471-2105-5-31
-
Gao F Foat BC Bussemaker HJ Defining transcriptional networks through integrative modeling of mRNA expression and transcription factor binding data BMC bioinformatics 2004, 5:31. 407845 15113405 10.1186/ 1471-2105-5-31
-
(2004)
BMC Bioinformatics
, vol.5
, pp. 31
-
-
Gao, F.1
Foat, B.C.2
Bussemaker, H.J.3
-
7
-
-
1942453302
-
Predicting gene expression from sequence
-
10.1016/S0092-8674(04)00304-6 15084257
-
Beer MA Tavazoie S Predicting gene expression from sequence Cell 2004, 117(2):185-198. 10.1016/S0092-8674(04)00304-6 15084257
-
(2004)
Cell
, vol.117
, Issue.2
, pp. 185-198
-
-
Beer, M.A.1
Tavazoie, S.2
-
8
-
-
2442446708
-
Genome-wide discovery of transcriptional modules from DNA sequence and gene expression
-
10.1093/bioinformatics/btg1038 12855470
-
Segal E Yelensky R Koller D Genome-wide discovery of transcriptional modules from DNA sequence and gene expression Bioinformatics (Oxford, England) 2003, 19(Suppl 1):i273-282. 10.1093/bioinformatics/btg1038 12855470
-
(2003)
Bioinformatics (Oxford, England)
, vol.19
, Issue.SUPPL. 1
-
-
Segal, E.1
Yelensky, R.2
Koller, D.3
-
9
-
-
29444455715
-
Cell-cycle control of gene expression in budding and fission yeast
-
10.1146/annurev.genet.39.110304.095808 16285853
-
Bahler J Cell-cycle control of gene expression in budding and fission yeast Annual review of genetics 2005, 39:69-94. 10.1146/ annurev.genet.39.110304.095808 16285853
-
(2005)
Annual Review of Genetics
, vol.39
, pp. 69-94
-
-
Bahler, J.1
-
10
-
-
17944372930
-
Serial regulation of transcriptional regulators in the yeast cell cycle
-
10.1016/S0092-8674(01)00494-9 11572776
-
Simon I Barnett J Hannett N Harbison CT Rinaldi NJ Volkert TL Wyrick JJ Zeitlinger J Gifford DK Jaakkola TS et al Serial regulation of transcriptional regulators in the yeast cell cycle Cell 2001, 106(6):697-708. 10.1016/S0092-8674(01)00494-9 11572776
-
(2001)
Cell
, vol.106
, Issue.6
, pp. 697-708
-
-
Simon, I.1
Barnett, J.2
Hannett, N.3
Harbison, C.T.4
Rinaldi, N.J.5
Volkert, T.L.6
Wyrick, J.J.7
Zeitlinger, J.8
Gifford, D.K.9
Jaakkola, T.S.10
-
11
-
-
33751327438
-
Comparative gene expression analysis by differential clustering approach: Application to the Candida albicans transcription program
-
1239936 10.1371/journal.pgen.0010039
-
Ihmels J Bergmann S Berman J Barkai N Comparative gene expression analysis by differential clustering approach: Application to the Candida albicans transcription program PLoS genetics 2005, 1(3):e39. 1239936 16470937 10.1371/journal.pgen.0010039
-
(2005)
PLoS Genetics
, vol.1
, Issue.3
-
-
Ihmels, J.1
Bergmann, S.2
Berman, J.3
Barkai, N.4
-
12
-
-
3543042493
-
Periodic gene expression program of the fission yeast cell cycle
-
10.1038/ng1377 15195092
-
Rustici G Mata J Kivinen K Lio P Penkett CJ Burns G Hayles J Brazma A Nurse P Bahler J Periodic gene expression program of the fission yeast cell cycle Nature genetics 2004, 36(8):809-817. 10.1038/ng1377 15195092
-
(2004)
Nature Genetics
, vol.36
, Issue.8
, pp. 809-817
-
-
Rustici, G.1
Mata, J.2
Kivinen, K.3
Lio, P.4
Penkett, C.J.5
Burns, G.6
Hayles, J.7
Brazma, A.8
Nurse, P.9
Bahler, J.10
-
13
-
-
20044366888
-
Identification of cell cycle-regulated genes in fission yeast
-
551471 10.1091/mbc.E04-04-0299
-
Peng X Karuturi RK Miller LD Lin K Jia Y Kondu P Wang L Wong LS Liu ET Balasubramanian MK et al Identification of cell cycle-regulated genes in fission yeast Molecular biology of the cell 2005, 16(3):1026-1042. 551471 15616197 10.1091/mbc.E04-04-0299
-
(2005)
Molecular Biology of the Cell
, vol.16
, Issue.3
, pp. 1026-1042
-
-
Peng, X.1
Karuturi, R.K.2
Miller, L.D.3
Lin, K.4
Jia, Y.5
Kondu, P.6
Wang, L.7
Wong, L.S.8
Liu, E.T.9
Balasubramanian, M.K.10
-
14
-
-
22744437234
-
The cell cycle-regulated genes of Schizosaccharomyces pombe
-
1157095 10.1371/journal.pbio.0030225
-
Oliva A Rosebrock A Ferrezuelo F Pyne S Chen H Skiena S Futcher B Leatherwood J The cell cycle-regulated genes of Schizosaccharomyces pombe PLoS biology 2005, 3(7):e225. 1157095 15966770 10.1371/ journal.pbio.0030225
-
(2005)
PLoS Biology
, vol.3
, Issue.7
-
-
Oliva, A.1
Rosebrock, A.2
Ferrezuelo, F.3
Pyne, S.4
Chen, H.5
Skiena, S.6
Futcher, B.7
Leatherwood, J.8
-
15
-
-
14844307159
-
Inferring quantitative models of regulatory networks from expression data
-
10.1093/bioinformatics/bth941 15262806
-
Nachman I Regev A Friedman N Inferring quantitative models of regulatory networks from expression data Bioinformatics (Oxford, England) 2004, 20(Suppl 1):I248-I256. 10.1093/bioinformatics/bth941 15262806
-
(2004)
Bioinformatics (Oxford, England)
, vol.20
-
-
Nachman, I.1
Regev, A.2
Friedman, N.3
-
17
-
-
34250854594
-
Differential regulation of repeated histone genes during the fission yeast cell cycle
-
1904272 17452352 10.1093/nar/gkm213
-
Takayama Y Takahashi K Differential regulation of repeated histone genes during the fission yeast cell cycle Nucleic acids research 2007, 35(10):3223-3237. 1904272 17452352 10.1093/nar/gkm213
-
(2007)
Nucleic Acids Research
, vol.35
, Issue.10
, pp. 3223-3237
-
-
Takayama, Y.1
Takahashi, K.2
-
18
-
-
39449134075
-
Regulation of gene expression during M-G1-phase in fission yeast through Plo1p and forkhead transcription factors
-
10.1242/jcs.019489 18057023
-
Papadopoulou K Ng SS Ohkura H Geymonat M Sedgwick SG McInerny CJ Regulation of gene expression during M-G1-phase in fission yeast through Plo1p and forkhead transcription factors Journal of cell science 2008, 121(Pt 1):38-47. 10.1242/jcs.019489 18057023
-
(2008)
Journal of Cell Science
, vol.121
, Issue.PART 1
, pp. 38-47
-
-
Papadopoulou, K.1
Ng, S.S.2
Ohkura, H.3
Geymonat, M.4
Sedgwick, S.G.5
McInerny, C.J.6
-
19
-
-
34547844132
-
Connecting quantitative regulatory-network models to the genome
-
10.1093/bioinformatics/btm228 17646319
-
Pan Y Durfee T Bockhorst J Craven M Connecting quantitative regulatory-network models to the genome Bioinformatics (Oxford, England) 2007, 23(13):i367-376. 10.1093/bioinformatics/btm228 17646319
-
(2007)
Bioinformatics (Oxford, England)
, vol.23
, Issue.13
-
-
Pan, Y.1
Durfee, T.2
Bockhorst, J.3
Craven, M.4
-
20
-
-
3142550629
-
Multilevel modeling and inference of transcription regulation
-
10.1089/1066527041410364 15285896
-
Tanay A Shamir R Multilevel modeling and inference of transcription regulation J Comput Biol 2004, 11(2-3):357-375. 10.1089/1066527041410364 15285896
-
(2004)
J Comput Biol
, vol.11
, Issue.2-3
, pp. 357-375
-
-
Tanay, A.1
Shamir, R.2
-
21
-
-
0034069495
-
Gene ontology: Tool for the unification of biology. The Gene Ontology Consortium
-
10.1038/75556 10802651
-
Ashburner M Ball CA Blake JA Botstein D Butler H Cherry JM Davis AP Dolinski K Dwight SS Eppig JT et al Gene ontology: Tool for the unification of biology. The Gene Ontology Consortium Nature genetics 2000, 25(1):25-29. 10.1038/75556 10802651
-
(2000)
Nature Genetics
, vol.25
, Issue.1
, pp. 25-29
-
-
Ashburner, M.1
Ball, C.A.2
Blake, J.A.3
Botstein, D.4
Butler, H.5
Cherry, J.M.6
Davis, A.P.7
Dolinski, K.8
Dwight, S.S.9
Eppig, J.T.10
-
22
-
-
34547844121
-
Automatic genome-wide reconstruction of phylogenetic gene trees
-
10.1093/bioinformatics/btm193 17646342
-
Wapinski I Pfeffer A Friedman N Regev A Automatic genome-wide reconstruction of phylogenetic gene trees Bioinformatics (Oxford, England) 2007, 23(13):i549-558. 10.1093/bioinformatics/btm193 17646342
-
(2007)
Bioinformatics (Oxford, England)
, vol.23
, Issue.13
-
-
Wapinski, I.1
Pfeffer, A.2
Friedman, N.3
Regev, A.4
-
23
-
-
0034628901
-
Computational identification of cis-regulatory elements associated with groups of functionally related genes in Saccharomyces cerevisiae
-
10.1006/jmbi.2000.3519 10698627
-
Hughes JD Estep PW Tavazoie S Church GM Computational identification of cis-regulatory elements associated with groups of functionally related genes in Saccharomyces cerevisiae Journal of molecular biology 2000, 296(5):1205-1214. 10.1006/jmbi.2000.3519 10698627
-
(2000)
Journal of Molecular Biology
, vol.296
, Issue.5
, pp. 1205-1214
-
-
Hughes, J.D.1
Estep, P.W.2
Tavazoie, S.3
Church, G.M.4
-
24
-
-
0036324753
-
An algorithm for finding protein-DNA binding sites with applications to chromatin-immunoprecipitation microarray experiments
-
12101404
-
Liu XS Brutlag DL Liu JS An algorithm for finding protein-DNA binding sites with applications to chromatin-immunoprecipitation microarray experiments Nature biotechnology 2002, 20(8):835-839. 12101404
-
(2002)
Nature Biotechnology
, vol.20
, Issue.8
, pp. 835-839
-
-
Liu, X.S.1
Brutlag, D.L.2
Liu, J.S.3
-
26
-
-
25144442704
-
TAMO: A flexible, object-oriented framework for analyzing transcriptional regulation using DNA-sequence motifs
-
10.1093/bioinformatics/bti481 15905282
-
Gordon DB Nekludova L McCallum S Fraenkel E TAMO: A flexible, object-oriented framework for analyzing transcriptional regulation using DNA-sequence motifs Bioinformatics (Oxford, England) 2005, 21(14):3164-3165. 10.1093/bioinformatics/bti481 15905282
-
(2005)
Bioinformatics (Oxford, England)
, vol.21
, Issue.14
, pp. 3164-3165
-
-
Gordon, D.B.1
Nekludova, L.2
McCallum, S.3
Fraenkel, E.4
-
28
-
-
40149105450
-
A Novel Bayesian DNA Motif Comparison Method for Clustering and Retrieval
-
2265534 18463706
-
Habib N Kaplan T Margalit H Friedman N A Novel Bayesian DNA Motif Comparison Method for Clustering and Retrieval PLoS Comput Biol 2008, 4:2. 2265534 18463706
-
(2008)
PLoS Comput Biol
, vol.4
, pp. 2
-
-
Habib, N.1
Kaplan, T.2
Margalit, H.3
Friedman, N.4
|