-
1
-
-
0033736476
-
Genetic network inference: from co-expression clustering to reverse engineering
-
D'haeseleer P., Liang S., and Somogyi R. Genetic network inference: from co-expression clustering to reverse engineering. Bioinformatics 16 (2000) 707-726
-
(2000)
Bioinformatics
, vol.16
, pp. 707-726
-
-
D'haeseleer, P.1
Liang, S.2
Somogyi, R.3
-
2
-
-
0036207347
-
Modeling and simulation of genetic regulatory systems: a literature review
-
de Jong H. Modeling and simulation of genetic regulatory systems: a literature review. J. Comput. Biol. 9 (2002) 67-103
-
(2002)
J. Comput. Biol.
, vol.9
, pp. 67-103
-
-
de Jong, H.1
-
3
-
-
0031616241
-
Reveal, a general reverse engineering algorithm for inference of genetic network architectures
-
Liang S., Fuhrman S., and Somogyi R. Reveal, a general reverse engineering algorithm for inference of genetic network architectures. Pac. Symp. Biocomput. (1998) 18-29
-
(1998)
Pac. Symp. Biocomput.
, pp. 18-29
-
-
Liang, S.1
Fuhrman, S.2
Somogyi, R.3
-
4
-
-
0032616683
-
Identification of genetic networks from a small number of gene expression patterns under the Boolean network model
-
Akutsu T., Miyano S., and Kuhara S. Identification of genetic networks from a small number of gene expression patterns under the Boolean network model. Pac. Symp. Biocomput. (1999) 17-28
-
(1999)
Pac. Symp. Biocomput.
, pp. 17-28
-
-
Akutsu, T.1
Miyano, S.2
Kuhara, S.3
-
5
-
-
0036184629
-
Probabilistic Boolean Networks: a rule-based uncertainty model for gene regulatory networks
-
Shmulevich I., Dougherty E.R., Kim S., and Zhang W. Probabilistic Boolean Networks: a rule-based uncertainty model for gene regulatory networks. Bioinformatics 18 (2002) 261-274
-
(2002)
Bioinformatics
, vol.18
, pp. 261-274
-
-
Shmulevich, I.1
Dougherty, E.R.2
Kim, S.3
Zhang, W.4
-
6
-
-
0032612220
-
Linear modeling of mRNA expression levels during CNS development and injury
-
Big Island of Hawaii, USA
-
D'haeseleer P., Wen X., Fuhrman S., and Somogyi R. Linear modeling of mRNA expression levels during CNS development and injury. Proceedings of the 4th Pacific Symposium on Biocomputing (PSB'99). Big Island of Hawaii, USA (1999) 41-52
-
(1999)
Proceedings of the 4th Pacific Symposium on Biocomputing (PSB'99)
, pp. 41-52
-
-
D'haeseleer, P.1
Wen, X.2
Fuhrman, S.3
Somogyi, R.4
-
7
-
-
0037687416
-
Reverse engineering gene networks: integrating genetic perturbations with dynamical modeling
-
Tegner J., Yeung M.K., Hasty J., and Collins J.J. Reverse engineering gene networks: integrating genetic perturbations with dynamical modeling. Proc. Natl. Acad. Sci. USA 100 (2003) 5944-5949
-
(2003)
Proc. Natl. Acad. Sci. USA
, vol.100
, pp. 5944-5949
-
-
Tegner, J.1
Yeung, M.K.2
Hasty, J.3
Collins, J.J.4
-
10
-
-
4143058645
-
Gene networks inference using dynamic Bayesian networks
-
Perrin B.E., Ralaivola L., Mazurie A., Bottani S., Mallet J., and D'Alche-Buc F. Gene networks inference using dynamic Bayesian networks. Bioinformatics 19 Suppl. 2 (2003) II138-II148
-
(2003)
Bioinformatics
, vol.19
, Issue.SUPPL. 2
-
-
Perrin, B.E.1
Ralaivola, L.2
Mazurie, A.3
Bottani, S.4
Mallet, J.5
D'Alche-Buc, F.6
-
11
-
-
0842288337
-
Inferring cellular networks using probabilistic graphical models
-
Friedman N. Inferring cellular networks using probabilistic graphical models. Science 303 (2004) 799-805
-
(2004)
Science
, vol.303
, pp. 799-805
-
-
Friedman, N.1
-
12
-
-
34547788797
-
Bayesian approaches to reverse engineer cellular systems: a simulation study on nonlinear Gaussian networks
-
Ferrazzi F., Sebastiani P., Ramoni M.F., and Bellazzi R. Bayesian approaches to reverse engineer cellular systems: a simulation study on nonlinear Gaussian networks. BMC Bioinformatics 8 Suppl. 5 (2007) S2
-
(2007)
BMC Bioinformatics
, vol.8
, Issue.SUPPL. 5
-
-
Ferrazzi, F.1
Sebastiani, P.2
Ramoni, M.F.3
Bellazzi, R.4
-
13
-
-
33750353888
-
Reverse engineering cellular networks
-
Margolin A.A., Wang K., Lim W.K., Kustagi M., Nemenman I., and Califano A. Reverse engineering cellular networks. Nat. Protoc. 1 (2006) 662-671
-
(2006)
Nat. Protoc.
, vol.1
, pp. 662-671
-
-
Margolin, A.A.1
Wang, K.2
Lim, W.K.3
Kustagi, M.4
Nemenman, I.5
Califano, A.6
-
14
-
-
0037941585
-
Module networks: identifying regulatory modules and their condition-specific regulators from gene expression data
-
Segal E., Shapira M., Regev A., Pe'er D., Botstein D., Koller D., and Friedman N. Module networks: identifying regulatory modules and their condition-specific regulators from gene expression data. Nat. Genet. 34 (2003) 166-176
-
(2003)
Nat. Genet.
, vol.34
, 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
-
15
-
-
0242490789
-
Importance of input perturbations and stochastic gene expression in the reverse engineering of genetic regulatory networks: insights from an identifiability analysis of an in silico network
-
Zak D.E., Gonye G.E., Schwaber J.S., and Doyle III F.J. Importance of input perturbations and stochastic gene expression in the reverse engineering of genetic regulatory networks: insights from an identifiability analysis of an in silico network. Genome Res. 13 (2003) 2396-2405
-
(2003)
Genome Res.
, vol.13
, pp. 2396-2405
-
-
Zak, D.E.1
Gonye, G.E.2
Schwaber, J.S.3
Doyle III, F.J.4
-
16
-
-
4644301730
-
A benchmark for methods in reverse engineering and model discrimination: problem formulation and solutions
-
Kremling A., Fischer S., Gadkar K., Doyle F.J., Sauter T., Bullinger E., Allgower F., and Gilles E.D. A benchmark for methods in reverse engineering and model discrimination: problem formulation and solutions. Genome Res. 14 (2004) 1773-1785
-
(2004)
Genome Res.
, vol.14
, pp. 1773-1785
-
-
Kremling, A.1
Fischer, S.2
Gadkar, K.3
Doyle, F.J.4
Sauter, T.5
Bullinger, E.6
Allgower, F.7
Gilles, E.D.8
-
17
-
-
0034616930
-
Functional discovery via a compendium of expression profiles
-
Hughes T.R., Marton M.J., Jones A.R., Roberts C.J., Stoughton R., Armour C.D., Bennett H.A., Coffey E., Dai H., He Y.D., Kidd M.J., King A.M., Meyer M.R., Slade D., Lum P.Y., Stepaniants S.B., Shoemaker D.D., Gachotte D., Chakraburtty K., Simon J., Bard M., and Friend S.H. Functional discovery via a compendium of expression profiles. Cell 102 (2000) 109-126
-
(2000)
Cell
, vol.102
, pp. 109-126
-
-
Hughes, T.R.1
Marton, M.J.2
Jones, A.R.3
Roberts, C.J.4
Stoughton, R.5
Armour, C.D.6
Bennett, H.A.7
Coffey, E.8
Dai, H.9
He, Y.D.10
Kidd, M.J.11
King, A.M.12
Meyer, M.R.13
Slade, D.14
Lum, P.Y.15
Stepaniants, S.B.16
Shoemaker, D.D.17
Gachotte, D.18
Chakraburtty, K.19
Simon, J.20
Bard, M.21
Friend, S.H.22
more..
-
18
-
-
0031742022
-
Comprehensive identification of cell cycle-regulated genes of the yeast Saccharomyces cerevisiae by microarray hybridization
-
Spellman P.T., Sherlock G., Zhang M.Q., Iyer V.R., Anders K., Eisen M.B., Brown P.O., Botstein D., and Futcher B. Comprehensive identification of cell cycle-regulated genes of the yeast Saccharomyces cerevisiae by microarray hybridization. Mol. Biol. Cell 9 (1998) 3273-3297
-
(1998)
Mol. Biol. Cell
, vol.9
, pp. 3273-3297
-
-
Spellman, P.T.1
Sherlock, G.2
Zhang, M.Q.3
Iyer, V.R.4
Anders, K.5
Eisen, M.B.6
Brown, P.O.7
Botstein, D.8
Futcher, B.9
-
19
-
-
33646360604
-
Modelling in molecular biology: describing transcription regulatory networks at different scales
-
Schlitt T., and Brazma A. Modelling in molecular biology: describing transcription regulatory networks at different scales. Philos. Trans. R. Soc. Lond. B Biol. Sci. 361 (2006) 483-494
-
(2006)
Philos. Trans. R. Soc. Lond. B Biol. Sci.
, vol.361
, pp. 483-494
-
-
Schlitt, T.1
Brazma, A.2
-
20
-
-
0345928693
-
Building and analysing genome-wide gene disruption networks
-
Rung J., Schlitt T., Brazma A., Freivalds K., and Vilo J. Building and analysing genome-wide gene disruption networks. Bioinformatics 18 Suppl. 2 (2002) S202-S210
-
(2002)
Bioinformatics
, vol.18
, Issue.SUPPL. 2
-
-
Rung, J.1
Schlitt, T.2
Brazma, A.3
Freivalds, K.4
Vilo, J.5
-
21
-
-
0034069495
-
Gene ontology: tool for the unification of biology. The gene ontology consortium
-
Ashburner M., Ball C.A., Blake J.A., Botstein D., Butler H., Cherry J.M., Davis A.P., Dolinski K., Dwight S.S., Eppig J.T., Harris M.A., Hill D.P., Issel-Tarver L., Kasarskis A., Lewis S., Matese J.C., Richardson J.E., Ringwald M., Rubin G.M., and Sherlock G. Gene ontology: tool for the unification of biology. The gene ontology consortium. Nat. Genet. 25 (2000) 25-29
-
(2000)
Nat. Genet.
, vol.25
, 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
Harris, M.A.11
Hill, D.P.12
Issel-Tarver, L.13
Kasarskis, A.14
Lewis, S.15
Matese, J.C.16
Richardson, J.E.17
Ringwald, M.18
Rubin, G.M.19
Sherlock, G.20
more..
-
22
-
-
0032112293
-
A genome-wide transcriptional analysis of the mitotic cell cycle
-
Cho R.J., Campbell M.J., Winzeler E.A., Steinmetz L., Conway A., Wodicka L., Wolfsberg T.G., Gabrielian A.E., Landsman D., Lockhart D.J., and Davis R.W. A genome-wide transcriptional analysis of the mitotic cell cycle. Mol. Cell 2 (1998) 65-73
-
(1998)
Mol. Cell
, vol.2
, pp. 65-73
-
-
Cho, R.J.1
Campbell, M.J.2
Winzeler, E.A.3
Steinmetz, L.4
Conway, A.5
Wodicka, L.6
Wolfsberg, T.G.7
Gabrielian, A.E.8
Landsman, D.9
Lockhart, D.J.10
Davis, R.W.11
-
23
-
-
8744307994
-
Multimodel inference. Understanding AIC and BIC in model selection
-
Burnham K.P., and Anderson D.R. Multimodel inference. Understanding AIC and BIC in model selection. Sociological Methods Res. 33 (2004) 261-304
-
(2004)
Sociological Methods Res.
, vol.33
, pp. 261-304
-
-
Burnham, K.P.1
Anderson, D.R.2
-
27
-
-
0003880161
-
-
Garland Publishing, New York
-
Alberts B., Johnson A., Lewis J., Raff M., Roberts K., and Walter P. Molecular Biology of the Cell. fourth ed. (2002), Garland Publishing, New York
-
(2002)
Molecular Biology of the Cell. fourth ed.
-
-
Alberts, B.1
Johnson, A.2
Lewis, J.3
Raff, M.4
Roberts, K.5
Walter, P.6
-
28
-
-
33847784791
-
Multiple levels of cyclin specificity in cell-cycle control
-
Bloom J., and Cross F.R. Multiple levels of cyclin specificity in cell-cycle control. Nat. Rev. Mol. Cell. Biol. 8 (2007) 149-160
-
(2007)
Nat. Rev. Mol. Cell. Biol.
, vol.8
, pp. 149-160
-
-
Bloom, J.1
Cross, F.R.2
-
29
-
-
3343020085
-
Integrative analysis of cell cycle control in budding yeast
-
Chen K.C., Calzone L., Csikasz-Nagy A., Cross F.R., Novak B., and Tyson J.J. Integrative analysis of cell cycle control in budding yeast. Mol. Biol. Cell 15 (2004) 3841-3862
-
(2004)
Mol. Biol. Cell
, vol.15
, pp. 3841-3862
-
-
Chen, K.C.1
Calzone, L.2
Csikasz-Nagy, A.3
Cross, F.R.4
Novak, B.5
Tyson, J.J.6
-
30
-
-
13244284551
-
Dynamic complex formation during the yeast cell cycle
-
de Lichtenberg U., Jensen L.J., Brunak S., and Bork P. Dynamic complex formation during the yeast cell cycle. Science 307 (2005) 724-727
-
(2005)
Science
, vol.307
, pp. 724-727
-
-
de Lichtenberg, U.1
Jensen, L.J.2
Brunak, S.3
Bork, P.4
-
31
-
-
0037174671
-
Transcriptional regulatory networks in Saccharomyces cerevisiae
-
Lee T.I., Rinaldi N.J., Robert F., Odom D.T., Bar-Joseph Z., Gerber G.K., Hannett N.M., Harbison C.T., Thompson C.M., Simon I., Zeitlinger J., Jennings E.G., Murray H.L., Gordon D.B., Ren B., Wyrick J.J., Tagne J.B., Volkert T.L., Fraenkel E., Gifford D.K., and Young R.A. Transcriptional regulatory networks in Saccharomyces cerevisiae. Science 298 (2002) 799-804
-
(2002)
Science
, vol.298
, pp. 799-804
-
-
Lee, T.I.1
Rinaldi, N.J.2
Robert, F.3
Odom, D.T.4
Bar-Joseph, Z.5
Gerber, G.K.6
Hannett, N.M.7
Harbison, C.T.8
Thompson, C.M.9
Simon, I.10
Zeitlinger, J.11
Jennings, E.G.12
Murray, H.L.13
Gordon, D.B.14
Ren, B.15
Wyrick, J.J.16
Tagne, J.B.17
Volkert, T.L.18
Fraenkel, E.19
Gifford, D.K.20
Young, R.A.21
more..
-
32
-
-
0029082391
-
Cdc6 is an unstable protein whose de novo synthesis in G1 is important for the onset of S phase and for preventing a 'reductional' anaphase in the budding yeast Saccharomyces cerevisiae
-
Piatti S., Lengauer C., and Nasmyth K. Cdc6 is an unstable protein whose de novo synthesis in G1 is important for the onset of S phase and for preventing a 'reductional' anaphase in the budding yeast Saccharomyces cerevisiae. EMBO J. 14 (1995) 3788-3799
-
(1995)
EMBO J.
, vol.14
, pp. 3788-3799
-
-
Piatti, S.1
Lengauer, C.2
Nasmyth, K.3
-
33
-
-
0029791262
-
The transcription factor Swi5 regulates expression of the cyclin kinase inhibitor p40SIC1
-
Knapp D., Bhoite L., Stillman D.J., and Nasmyth K. The transcription factor Swi5 regulates expression of the cyclin kinase inhibitor p40SIC1. Mol. Cell. Biol 16 (1996) 5701-5707
-
(1996)
Mol. Cell. Biol
, vol.16
, pp. 5701-5707
-
-
Knapp, D.1
Bhoite, L.2
Stillman, D.J.3
Nasmyth, K.4
-
34
-
-
0031015401
-
The Swi5 transcription factor of Saccharomyces cerevisiae has a role in exit from mitosis through induction of the cdk-inhibitor Sic1 in telophase
-
Toyn J.H., Johnson A.L., Donovan J.D., Toone W.M., and Johnston L.H. The Swi5 transcription factor of Saccharomyces cerevisiae has a role in exit from mitosis through induction of the cdk-inhibitor Sic1 in telophase. Genetics 145 (1997) 85-96
-
(1997)
Genetics
, vol.145
, pp. 85-96
-
-
Toyn, J.H.1
Johnson, A.L.2
Donovan, J.D.3
Toone, W.M.4
Johnston, L.H.5
-
35
-
-
35448936679
-
-
"KEGG: Kyoto Encyclopedia of Genes and Genomes," http://www.genome.jp/kegg/.
-
-
-
-
36
-
-
0034964368
-
Cdk1 triggers association of RNA polymerase to cell cycle promoters only after recruitment of the mediator by SBF
-
Cosma M.P., Panizza S., and Nasmyth K. Cdk1 triggers association of RNA polymerase to cell cycle promoters only after recruitment of the mediator by SBF. Mol. Cell 7 (2001) 1213-1220
-
(2001)
Mol. Cell
, vol.7
, pp. 1213-1220
-
-
Cosma, M.P.1
Panizza, S.2
Nasmyth, K.3
-
37
-
-
35448965981
-
-
"Saccharomyces Genome Database," http://www.yeastgenome.org/.
-
-
-
-
38
-
-
0036935790
-
KNR4 is a member of the PKC1 signalling pathway and genetically interacts with BCK2, a gene involved in cell cycle progression in Saccharomyces cerevisiae
-
Martin-Yken H., Dagkessamanskaia A., Talibi D., and Francois J. KNR4 is a member of the PKC1 signalling pathway and genetically interacts with BCK2, a gene involved in cell cycle progression in Saccharomyces cerevisiae. Curr. Genet. 41 (2002) 323-332
-
(2002)
Curr. Genet.
, vol.41
, pp. 323-332
-
-
Martin-Yken, H.1
Dagkessamanskaia, A.2
Talibi, D.3
Francois, J.4
-
39
-
-
0037425623
-
Periodic transcription: a cycle within a cycle
-
Breeden L.L. Periodic transcription: a cycle within a cycle. Curr. Biol. 13 (2003) R31-R38
-
(2003)
Curr. Biol.
, vol.13
-
-
Breeden, L.L.1
-
40
-
-
0030977093
-
A novel Mcm1-dependent element in the SWI4, CLN3, CDC6, and CDC47 promoters activates M/G1-specific transcription
-
McInerny C.J., Partridge J.F., Mikesell G.E., Creemer D.P., and Breeden L.L. A novel Mcm1-dependent element in the SWI4, CLN3, CDC6, and CDC47 promoters activates M/G1-specific transcription. Genes Dev. 11 (1997) 1277-1288
-
(1997)
Genes Dev.
, vol.11
, pp. 1277-1288
-
-
McInerny, C.J.1
Partridge, J.F.2
Mikesell, G.E.3
Creemer, D.P.4
Breeden, L.L.5
-
41
-
-
0031737085
-
Regulation of Cdc28 cyclin-dependent protein kinase activity during the cell cycle of the yeast Saccharomyces cerevisiae
-
Mendenhall M.D., and Hodge A.E. Regulation of Cdc28 cyclin-dependent protein kinase activity during the cell cycle of the yeast Saccharomyces cerevisiae. Microbiol. Mol. Biol. Rev. 62 (1998) 1191-1243
-
(1998)
Microbiol. Mol. Biol. Rev.
, vol.62
, pp. 1191-1243
-
-
Mendenhall, M.D.1
Hodge, A.E.2
-
42
-
-
0027527033
-
Mechanisms that help the yeast cell cycle clock tick: G2 cyclins transcriptionally activate G2 cyclins and repress G1 cyclins
-
Amon A., Tyers M., Futcher B., and Nasmyth K. Mechanisms that help the yeast cell cycle clock tick: G2 cyclins transcriptionally activate G2 cyclins and repress G1 cyclins. Cell 74 (1993) 993-1007
-
(1993)
Cell
, vol.74
, pp. 993-1007
-
-
Amon, A.1
Tyers, M.2
Futcher, B.3
Nasmyth, K.4
-
44
-
-
0027220020
-
CLB5 and CLB6, a new pair of B cyclins involved in DNA replication in Saccharomyces cerevisiae
-
Schwob E., and Nasmyth K. CLB5 and CLB6, a new pair of B cyclins involved in DNA replication in Saccharomyces cerevisiae. Genes Dev. 7 (1993) 1160-1175
-
(1993)
Genes Dev.
, vol.7
, pp. 1160-1175
-
-
Schwob, E.1
Nasmyth, K.2
-
45
-
-
33645124786
-
Functional connection between the Clb5 cyclin, the protein kinase C pathway and the Swi4 transcription factor in Saccharomyces cerevisiae
-
Queralt E., and Igual J.C. Functional connection between the Clb5 cyclin, the protein kinase C pathway and the Swi4 transcription factor in Saccharomyces cerevisiae. Genetics 171 (2005) 1485-1498
-
(2005)
Genetics
, vol.171
, pp. 1485-1498
-
-
Queralt, E.1
Igual, J.C.2
-
46
-
-
0033588106
-
Recovery of the yeast cell cycle from heat shock-induced G(1) arrest involves a positive regulation of G(1) cyclin expression by the S phase cyclin Clb5
-
Li X., and Cai M. Recovery of the yeast cell cycle from heat shock-induced G(1) arrest involves a positive regulation of G(1) cyclin expression by the S phase cyclin Clb5. J. Biol. Chem. 274 (1999) 24220-24231
-
(1999)
J. Biol. Chem.
, vol.274
, pp. 24220-24231
-
-
Li, X.1
Cai, M.2
-
48
-
-
27544494569
-
Estimating gene regulatory networks and protein-protein interactions of Saccharomyces cerevisiae from multiple genome-wide data
-
Nariai N., Tamada Y., Imoto S., and Miyano S. Estimating gene regulatory networks and protein-protein interactions of Saccharomyces cerevisiae from multiple genome-wide data. Bioinformatics 21 Suppl. 2 (2005) ii206-ii212
-
(2005)
Bioinformatics
, vol.21
, Issue.SUPPL. 2
-
-
Nariai, N.1
Tamada, Y.2
Imoto, S.3
Miyano, S.4
-
49
-
-
3242891560
-
Estimating gene networks from gene expression data by combining Bayesian network model with promoter element detection
-
Tamada Y., Kim S., Bannai H., Imoto S., Tashiro K., Kuhara S., and Miyano S. Estimating gene networks from gene expression data by combining Bayesian network model with promoter element detection. Bioinformatics 19 Suppl. 2 (2003) II227-II236
-
(2003)
Bioinformatics
, vol.19
, Issue.SUPPL. 2
-
-
Tamada, Y.1
Kim, S.2
Bannai, H.3
Imoto, S.4
Tashiro, K.5
Kuhara, S.6
Miyano, S.7
-
50
-
-
33748669610
-
Constructing biological networks through combined literature mining and microarray analysis: a LMMA approach
-
Li S., Wu L., and Zhang Z. Constructing biological networks through combined literature mining and microarray analysis: a LMMA approach. Bioinformatics 22 (2006) 2143-2150
-
(2006)
Bioinformatics
, vol.22
, pp. 2143-2150
-
-
Li, S.1
Wu, L.2
Zhang, Z.3
|