-
1
-
-
17044424990
-
Gene regulatory networks
-
10.1073/pnas.0502024102, 556010, 15809445
-
Davidson E, Levin M. Gene regulatory networks. Proceedings of the National Academy of Sciences of the United States of America 2005, 102(14):4935. 10.1073/pnas.0502024102, 556010, 15809445.
-
(2005)
Proceedings of the National Academy of Sciences of the United States of America
, vol.102
, Issue.14
, pp. 4935
-
-
Davidson, E.1
Levin, M.2
-
2
-
-
0035319006
-
Computational studies of gene regulatory networks: In numero molecular biology
-
10.1038/35066056, 11283699
-
Hasty J, McMillen D, Isaacs F, Collins JJ. Computational studies of gene regulatory networks: In numero molecular biology. Nature Reviews Genetics 2001, 2:268-279. 10.1038/35066056, 11283699.
-
(2001)
Nature Reviews Genetics
, vol.2
, pp. 268-279
-
-
Hasty, J.1
McMillen, D.2
Isaacs, F.3
Collins, J.J.4
-
3
-
-
0031742022
-
Comprehensive identification of cell cycle-regulated genes of the yeast Saccharomyces cerevisiae by microarray hybridization
-
25624, 9843569
-
Spellman PT, Sherlock G, Zhang MQ, Iyer VR, Anders K, Eisen MB, Brown PO, 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.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
-
4
-
-
0037183901
-
Gene expression during the life cycle of Drosophila melanogaster
-
10.1126/science.1072152, 12351791
-
Arbeitman MN, Furlong EEM, Imam F, Johnson E, Null BH, Baker BS, Krasnow MA, Scott MP, Davis RW, White KP. Gene expression during the life cycle of Drosophila melanogaster. Science 2002, 297(5590):2270-2275. 10.1126/science.1072152, 12351791.
-
(2002)
Science
, vol.297
, Issue.5590
, pp. 2270-2275
-
-
Arbeitman, M.N.1
Furlong, E.E.M.2
Imam, F.3
Johnson, E.4
Null, B.H.5
Baker, B.S.6
Krasnow, M.A.7
Scott, M.P.8
Davis, R.W.9
White, K.P.10
-
5
-
-
33645790960
-
Characterization of peripheral circadian clocks in adipose tissues
-
10.2337/diabetes.55.04.06.db05-0873, 16567517
-
Zvonic S, Ptitsyn AA, Conrad SA, Scott LK, Floyd ZE, Kilroy G, Wu X, Goh BC, Mynatt RL, Gimble JM. Characterization of peripheral circadian clocks in adipose tissues. Diabetes 2006, 55:962-970. 10.2337/diabetes.55.04.06.db05-0873, 16567517.
-
(2006)
Diabetes
, vol.55
, pp. 962-970
-
-
Zvonic, S.1
Ptitsyn, A.A.2
Conrad, S.A.3
Scott, L.K.4
Floyd, Z.E.5
Kilroy, G.6
Wu, X.7
Goh, B.C.8
Mynatt, R.L.9
Gimble, J.M.10
-
6
-
-
0036678794
-
Assigning numbers to the arrows: Parameterizing a gene regulation network by using accurate expression kinetics
-
10.1073/pnas.152046799, 124972, 12145321
-
Ronen M, Rosenberg R, Shraiman BI, Alon U. Assigning numbers to the arrows: Parameterizing a gene regulation network by using accurate expression kinetics. Proceedings of the National Academy of Sciences of the United States of America 2002, 99(16):10555-10560. 10.1073/pnas.152046799, 124972, 12145321.
-
(2002)
Proceedings of the National Academy of Sciences of the United States of America
, vol.99
, Issue.16
, pp. 10555-10560
-
-
Ronen, M.1
Rosenberg, R.2
Shraiman, B.I.3
Alon, U.4
-
7
-
-
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):2493-2503. 10.1093/bioinformatics/bth283, 15130923.
-
(2004)
Bioinformatics
, vol.20
, Issue.16
, pp. 2493-2503
-
-
Bar-Joseph, Z.1
-
10
-
-
0032616683
-
Identification of genetic networks from a small number of gene expression patterns under the Boolean network model
-
Akutsu T. Identification of genetic networks from a small number of gene expression patterns under the Boolean network model. Proceedings of Pacific Symposium Biocomputing 1999, 17-28.
-
(1999)
Proceedings of Pacific Symposium Biocomputing
, pp. 17-28
-
-
Akutsu, T.1
-
11
-
-
4143058645
-
Gene networks inference using dynamic Bayesian networks
-
Perrin BE, Ralaivola L, Mazurie A, Bottani S, Mallet J, d'Alche Buc F. Gene networks inference using dynamic Bayesian networks. Bioinformatics 2003, 19(2):138-148.
-
(2003)
Bioinformatics
, vol.19
, Issue.2
, pp. 138-148
-
-
Perrin, B.E.1
Ralaivola, L.2
Mazurie, A.3
Bottani, S.4
Mallet, J.5
d'Alche Buc, F.6
-
12
-
-
34249740137
-
Reverse engineering of gene regulatory networks
-
10.1049/iet-syb:20060075, 17591174
-
Cho KH, Choo SM, Jung SH, Kim JR, Choi HS, Kim J. Reverse engineering of gene regulatory networks. IET Systems Biology 2007, 1:149-163. 10.1049/iet-syb:20060075, 17591174.
-
(2007)
IET Systems Biology
, vol.1
, pp. 149-163
-
-
Cho, K.H.1
Choo, S.M.2
Jung, S.H.3
Kim, J.R.4
Choi, H.S.5
Kim, J.6
-
13
-
-
3342997427
-
Systems level modeling of gene regulatory networks
-
Springer, Netherlands, Dubitzky W, Azuaje F
-
Stetter M, Schurmann B, Dejori M. Systems level modeling of gene regulatory networks. Artificial intelligence methods and tools for systems biology 2004, 175-194. Springer, Netherlands, Dubitzky W, Azuaje F.
-
(2004)
Artificial intelligence methods and tools for systems biology
, pp. 175-194
-
-
Stetter, M.1
Schurmann, B.2
Dejori, M.3
-
16
-
-
2942694772
-
Artificial gene networks for objective comparison of analysis algorithms
-
90002
-
Mendes P, Sha W, Ye K. Artificial gene networks for objective comparison of analysis algorithms. Bioinformatics 2003, 19(90002):122-129.
-
(2003)
Bioinformatics
, vol.19
, pp. 122-129
-
-
Mendes, P.1
Sha, W.2
Ye, K.3
-
17
-
-
0035375137
-
Computational analysis of microarray data
-
10.1038/35076576, 11389458
-
Quackenbush J. Computational analysis of microarray data. Nature Reviews Genetics 2001, 2(6):418-427. 10.1038/35076576, 11389458.
-
(2001)
Nature Reviews Genetics
, vol.2
, Issue.6
, pp. 418-427
-
-
Quackenbush, J.1
-
18
-
-
77957347866
-
Artificial gene regulation: A data source for validation of reverse bioengineering
-
Schaub H, Detje F, Brggemann U
-
knüpfer C, Dittrich P, Beckstein C. Artificial gene regulation: A data source for validation of reverse bioengineering. Proceedings of the 6th German Workshop on Artificial Life 2004 2004, 66-75. Schaub H, Detje F, Brggemann U.
-
(2004)
Proceedings of the 6th German Workshop on Artificial Life 2004
, pp. 66-75
-
-
knüpfer, C.1
Dittrich, P.2
Beckstein, C.3
-
19
-
-
63049128934
-
A yeast synthetic network for in vivo assessment of reverse-engineering and modeling approaches
-
10.1016/j.cell.2009.01.055, 19327819
-
Cantone I, Marucci L, Iorio F, Ricci MA, Belcastro V, Bansal M, Santini S, di Bernardo M, di Bernardo D, Cosma MP. A yeast synthetic network for in vivo assessment of reverse-engineering and modeling approaches. Cell 2009, 137:172-181. 10.1016/j.cell.2009.01.055, 19327819.
-
(2009)
Cell
, vol.137
, pp. 172-181
-
-
Cantone, I.1
Marucci, L.2
Iorio, F.3
Ricci, M.A.4
Belcastro, V.5
Bansal, M.6
Santini, S.7
di Bernardo, M.8
di Bernardo, D.9
Cosma, M.P.10
-
20
-
-
0032136585
-
Tackling real-coded genetic algorithms: Operators and rools for behavioural analysis
-
Herrera F, Lozano M, Verdegay JL. Tackling real-coded genetic algorithms: Operators and rools for behavioural analysis. Artificial Intelligence Review 1998, 12(4):265-319.
-
(1998)
Artificial Intelligence Review
, vol.12
, Issue.4
, pp. 265-319
-
-
Herrera, F.1
Lozano, M.2
Verdegay, J.L.3
-
21
-
-
0030002954
-
Rules for coupled expression of regulator and effector genes in inducible circuits
-
10.1006/jmbi.1996.0011, 8568860
-
Hlavacek W, Savageau M. Rules for coupled expression of regulator and effector genes in inducible circuits. Journal of Molecular Biology 1996, 255:121-139. 10.1006/jmbi.1996.0011, 8568860.
-
(1996)
Journal of Molecular Biology
, vol.255
, pp. 121-139
-
-
Hlavacek, W.1
Savageau, M.2
-
22
-
-
3142617691
-
Mathematical and computational techniques to deduce complex biochemical reaction mechanisms
-
10.1016/j.pbiomolbio.2004.04.002, 15261526
-
Crampin EJ, Schnell S, McSharry PE. Mathematical and computational techniques to deduce complex biochemical reaction mechanisms. Progress in Biophysics and Molecular Biology 2004, 86:77-112. 10.1016/j.pbiomolbio.2004.04.002, 15261526.
-
(2004)
Progress in Biophysics and Molecular Biology
, vol.86
, pp. 77-112
-
-
Crampin, E.J.1
Schnell, S.2
McSharry, P.E.3
-
23
-
-
4344592548
-
Neural-network-based parameter estimation in S-system models of biological networks
-
Almeida JS, Voit EO. Neural-network-based parameter estimation in S-system models of biological networks. Genome Informatics 2003, 14:114-123.
-
(2003)
Genome Informatics
, vol.14
, pp. 114-123
-
-
Almeida, J.S.1
Voit, E.O.2
-
24
-
-
33746602343
-
Reconstructing gene regulatory networks: From random to scale-free connectivity
-
Wildenhain J, Crampin EJ. Reconstructing gene regulatory networks: From random to scale-free connectivity. IEE Proceedings of Systems Biology 2006, 156(4):247-256.
-
(2006)
IEE Proceedings of Systems Biology
, vol.156
, Issue.4
, pp. 247-256
-
-
Wildenhain, J.1
Crampin, E.J.2
-
25
-
-
0037325058
-
A sigmoidal transcriptional response: cooperativity, synergy and dosage effects
-
10.1017/S1464793102006036, 12620064
-
Veitia R. A sigmoidal transcriptional response: cooperativity, synergy and dosage effects. Biological Reviews 2003, 78(01):149-170. 10.1017/S1464793102006036, 12620064.
-
(2003)
Biological Reviews
, vol.78
, Issue.1
, pp. 149-170
-
-
Veitia, R.1
-
26
-
-
0033736476
-
Genetic network inference: From co-expression clustering to reverse engineering
-
10.1093/bioinformatics/16.8.707, 11099257
-
D'haeseleer P, Liang S, Somogyi R. Genetic network inference: From co-expression clustering to reverse engineering. Bioinformatics 2000, 16(8):707-726. 10.1093/bioinformatics/16.8.707, 11099257.
-
(2000)
Bioinformatics
, vol.16
, Issue.8
, pp. 707-726
-
-
D'haeseleer, P.1
Liang, S.2
Somogyi, R.3
-
30
-
-
36448943921
-
Context-dependent clustering for dynamic cellular state modeling of microarray gene expression
-
10.1093/bioinformatics/btm457, 17846037
-
Yuan S, Li KC. Context-dependent clustering for dynamic cellular state modeling of microarray gene expression. Bioinformatics 2007, 23(22):3039-3047. 10.1093/bioinformatics/btm457, 17846037.
-
(2007)
Bioinformatics
, vol.23
, Issue.22
, pp. 3039-3047
-
-
Yuan, S.1
Li, K.C.2
-
31
-
-
50849128158
-
Finding new pathway-specific regulators by clustering method using threshold standard deviation based on DNA chip data of Streptomyces coelicolor
-
Yang Y, Kim J, Song E, E K, Oh M, BG K. Finding new pathway-specific regulators by clustering method using threshold standard deviation based on DNA chip data of Streptomyces coelicolor. Appl Microbiol Biotechnol 2008, 80:707-717.
-
(2008)
Appl Microbiol Biotechnol
, vol.80
, pp. 707-717
-
-
Yang, Y.1
Kim, J.2
Song, E.3
E, K.4
Oh, M.5
BG, K.6
-
32
-
-
36549040919
-
Ensemble learning of genetic networks from time-series expression data
-
10.1093/bioinformatics/btm514, 17977884
-
Nam D, Yoon SH, Kim JF. Ensemble learning of genetic networks from time-series expression data. Bioinformatics 2007, 23(23):3225-3231. 10.1093/bioinformatics/btm514, 17977884.
-
(2007)
Bioinformatics
, vol.23
, Issue.23
, pp. 3225-3231
-
-
Nam, D.1
Yoon, S.H.2
Kim, J.F.3
-
33
-
-
20144387371
-
Inference of S-system models of genetic networks using a cooperative coevolutionary algorithm
-
10.1093/bioinformatics/bti071, 15514004
-
Kimura S, Ide K, Kashihara A, Kano M, Hatakeyama M, Masui R, Nakagawa N, Yokoyama S, Kuramitsu S, Konagaya A. Inference of S-system models of genetic networks using a cooperative coevolutionary algorithm. Bioinformatics 2005, 21(7):1154-1163. 10.1093/bioinformatics/bti071, 15514004.
-
(2005)
Bioinformatics
, vol.21
, Issue.7
, pp. 1154-1163
-
-
Kimura, S.1
Ide, K.2
Kashihara, A.3
Kano, M.4
Hatakeyama, M.5
Masui, R.6
Nakagawa, N.7
Yokoyama, S.8
Kuramitsu, S.9
Konagaya, A.10
-
34
-
-
17444430052
-
Dynamic network reconstruction from gene expression data applied to immune response during bacterial infection
-
10.1093/bioinformatics/bti226, 15613398
-
Guthke R, Moller U, Hoffmann M, Thies F, Topfer S. Dynamic network reconstruction from gene expression data applied to immune response during bacterial infection. Bioinformatics 2005, 21(8):1626-1634. 10.1093/bioinformatics/bti226, 15613398.
-
(2005)
Bioinformatics
, vol.21
, Issue.8
, pp. 1626-1634
-
-
Guthke, R.1
Moller, U.2
Hoffmann, M.3
Thies, F.4
Topfer, S.5
-
35
-
-
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, Chklovskii 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
Chklovskii, D.5
Alon, U.6
-
36
-
-
0037174671
-
Transcriptional regulatory networks in Saccharomyces cerevisiae
-
10.1126/science.1075090, 12399584
-
Lee TI, Rinaldi NJ, Robert F, Odom DT, Bar-Joseph Z, Gerber GK, Hannett NM, Harbison CT, Thompson CM, Simon I, Zeitlinger J, Jennings EG, Murray HL, Gordon DB, Ren B, Wyrick JJ, Tagne JB, Volkert TL, Fraenkel E, Gifford DK, Young RA. Transcriptional regulatory networks in Saccharomyces cerevisiae. Science 2002, 298(5594):799-804. 10.1126/science.1075090, 12399584.
-
(2002)
Science
, vol.298
, Issue.5594
, 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..
-
37
-
-
33748530630
-
Reverse engineering genetic networks using evolutionary computations
-
Noman N, Iba H. Reverse engineering genetic networks using evolutionary computations. Genome Informatics 2005, 16(2):205-214.
-
(2005)
Genome Informatics
, vol.16
, Issue.2
, pp. 205-214
-
-
Noman, N.1
Iba, H.2
-
38
-
-
0036749274
-
Inference of a gene regulatory network by means of interactive evolutionary computing
-
Iba H, Mimura A. Inference of a gene regulatory network by means of interactive evolutionary computing. Inf Sci Inf Comput Sci 2002, 145(34):225-236.
-
(2002)
Inf Sci Inf Comput Sci
, vol.145
, Issue.34
, pp. 225-236
-
-
Iba, H.1
Mimura, A.2
-
42
-
-
13844301027
-
-
Masters thesis Dept. of Information Technology, Tampere University of Technology, Finland
-
Aho T. Simulation tool for genetic regulatory networks 2003, Masters thesis Dept. of Information Technology, Tampere University of Technology, Finland.
-
(2003)
Simulation tool for genetic regulatory networks
-
-
Aho, T.1
-
43
-
-
33846703173
-
Nonlinear differential equation model for quantification of transcriptional regulation applied to microarray data of Saccharomyces cerevisiae
-
10.1093/nar/gkl1001, 1802551, 17170011
-
Vu TT, Vohradsky J. Nonlinear differential equation model for quantification of transcriptional regulation applied to microarray data of Saccharomyces cerevisiae. Nucleic Acids Research 2007, 35:279-287. 10.1093/nar/gkl1001, 1802551, 17170011.
-
(2007)
Nucleic Acids Research
, vol.35
, pp. 279-287
-
-
Vu, T.T.1
Vohradsky, J.2
-
44
-
-
64149104487
-
Inference of active transcriptional networks by integration of gene expression kinetics modeling and multisource data
-
10.1016/j.ygeno.2009.01.006, 19442636
-
Vu TT, Vohradsky J. Inference of active transcriptional networks by integration of gene expression kinetics modeling and multisource data. Genomics 2009, 93(5):426-433. 10.1016/j.ygeno.2009.01.006, 19442636.
-
(2009)
Genomics
, vol.93
, Issue.5
, pp. 426-433
-
-
Vu, T.T.1
Vohradsky, J.2
-
45
-
-
4344710012
-
Inference of genetic network using the expression profile time course data of mouse P19 cells
-
Maki Y, Ueda T, Okamoto M, Uematsu N, Inamura K, Uchida K, Takahashi Y, Eguchi Y. Inference of genetic network using the expression profile time course data of mouse P19 cells. Genome Informatics 2002, 13:382-383.
-
(2002)
Genome Informatics
, vol.13
, pp. 382-383
-
-
Maki, Y.1
Ueda, T.2
Okamoto, M.3
Uematsu, N.4
Inamura, K.5
Uchida, K.6
Takahashi, Y.7
Eguchi, Y.8
-
46
-
-
84901697990
-
Inference of S-system models of genetic networks using a genetic local search
-
IEEE Press, Sarker R, Reynolds R, Abbass H, Tan KC, McKay B, Essam D, Gedeon T
-
Kimura S, Hatakeyama M, Konagaya A. Inference of S-system models of genetic networks using a genetic local search. Proceedings of the 2003 Congress on Evolutionary Computation 2003, 631-638. IEEE Press, Sarker R, Reynolds R, Abbass H, Tan KC, McKay B, Essam D, Gedeon T.
-
(2003)
Proceedings of the 2003 Congress on Evolutionary Computation
, pp. 631-638
-
-
Kimura, S.1
Hatakeyama, M.2
Konagaya, A.3
-
47
-
-
0000308566
-
Real-coded genetic algorithms and interval schemata
-
Morgan Kaufmann Publishers, Whitley LD
-
Eshelman LJ, Schaffer JD. Real-coded genetic algorithms and interval schemata. Foundations of genetic algorithms 2 1993, Morgan Kaufmann Publishers, Whitley LD.
-
(1993)
Foundations of genetic algorithms 2
-
-
Eshelman, L.J.1
Schaffer, J.D.2
-
48
-
-
33750205459
-
Grid'5000: A large scale and highly reconfigurable experimental grid testbed
-
Bolze R, Cappello F, Caron E, Dayd'e M, Desprez F, Jeannot E, J'egou Y, Lanteri S, Leduc J, Melab N, Mornet G, Namyst R, Primet P, Quetier B, Richard O, Talbi EG, Touche I. Grid'5000: A large scale and highly reconfigurable experimental grid testbed. The International Journal of High Performance Computing Applications 2006, 20(4):481-494.
-
(2006)
The International Journal of High Performance Computing Applications
, vol.20
, Issue.4
, pp. 481-494
-
-
Bolze, R.1
Cappello, F.2
Caron, E.3
Dayd'e, M.4
Desprez, F.5
Jeannot, E.6
J'egou, Y.7
Lanteri, S.8
Leduc, J.9
Melab, N.10
Mornet, G.11
Namyst, R.12
Primet, P.13
Quetier, B.14
Richard, O.15
Talbi, E.G.16
Touche, I.17
-
49
-
-
34147140120
-
Modeling biochemical transformation processes and information processing with Narrator
-
1847530, 17389034
-
Mandel JJ, Fuss H, Palfreyman NM, Dubitzky W. Modeling biochemical transformation processes and information processing with Narrator. BMC Bioinformatics 2007, 8(103). 1847530, 17389034.
-
(2007)
BMC Bioinformatics
, vol.8
, Issue.103
-
-
Mandel, J.J.1
Fuss, H.2
Palfreyman, N.M.3
Dubitzky, W.4
|