-
2
-
-
0032612220
-
'Linear modeling of mRNA expression levels during CNS development and injury'
-
D'haeseleer, P., Wen, X., Fuhrman, S., and Somogyi, R.: 'Linear modeling of mRNA expression levels during CNS development and injury', Pacific Symp. Biocomputing, 1999, p. 41-52
-
(1999)
Pacific Symp. Biocomputing
, pp. 41-52
-
-
D'haeseleer, P.1
Wen, X.2
Fuhrman, S.3
Somogyi, R.4
-
3
-
-
0141925279
-
'Process pathway inference via time series analysis'
-
10.1007/BF02410536 0014-4851
-
Wiggins, C., and Nemenman, I.: 'Process pathway inference via time series analysis', Exp. Mech., 2003, 43, (3), p. 361-370 10.1007/ BF02410536 0014-4851
-
(2003)
Exp. Mech.
, vol.43
, Issue.3
, pp. 361-370
-
-
Wiggins, C.1
Nemenman, I.2
-
4
-
-
33747813561
-
'The inferelator: An algorithm for learning parsimonious regulatory networks from systemsbiology data sets de novo'
-
Bonneau, R., Reiss,AD.J., and Shannon, P.: Et al. 'The inferelator: an algorithm for learning parsimonious regulatory networks from systemsbiology data sets de novo', Genome Biol., 2006, 7, (5), p. R36
-
(2006)
Genome Biol.
, vol.7
, Issue.5
-
-
Bonneau, R.1
Reiss, D.J.2
Shannon, P.3
-
5
-
-
33646360604
-
'Modelling in molecular biology: Describing transcription regulatory networks at different scales'
-
Schlitt, T., and Brazma, A.D 'Modelling in molecular biology: describing transcription regulatory networks at different scales', Philos. Trans. R. Soc. B Biol. Sci., 2006, 361, (1467), p. 483-494
-
(2006)
Philos. Trans. R. Soc. B Biol. Sci.
, vol.361
, Issue.1467
, pp. 483-494
-
-
Schlitt, T.1
Brazma, A.2
-
6
-
-
0030760528
-
'Ethanol production from agricultural biomass substrate'
-
Bothast, R., and Saha, B.: 'Ethanol production from agricultural biomass substrate', Adv. Appl. Microbiol., 1997, 44, p. 261-286
-
(1997)
Adv. Appl. Microbiol.
, vol.44
, pp. 261-286
-
-
Bothast, R.1
Saha, B.2
-
7
-
-
0037623814
-
'Hemicellulose bioconversion'
-
Saha, B.: 'Hemicellulose bioconversion', J. Ind. Microbiol. Biotechnol., 2003, 30, p. 279-291
-
(2003)
J. Ind. Microbiol. Biotechnol.
, vol.30
, pp. 279-291
-
-
Saha, B.1
-
8
-
-
0036008701
-
'Identification of potential fermentation inhibitors in conversion of hybrid poplar hydrolyzate to ethanol'
-
Luo, C., Brink, D., and Blanch, H.: 'Identification of potential fermentation inhibitors in conversion of hybrid poplar hydrolyzate to ethanol', Biomass Bioenergy, 2002, 22, p. 125-138
-
(2002)
Biomass Bioenergy
, vol.22
, pp. 125-138
-
-
Luo, C.1
Brink, D.2
Blanch, H.3
-
9
-
-
0033938545
-
'Physiological effects of 5-Hydroxymethylfurfural on Saccharomyces cerevisiae'
-
Taherzadeh, M., Gustafsson, L., and Niklasson, C.: 'Physiological effects of 5-Hydroxymethylfurfural on Saccharomyces cerevisiae', App Microbiol. Biotechnol., 2000, 53, p. 701-708
-
(2000)
App Microbiol. Biotechnol.
, vol.53
, pp. 701-708
-
-
Taherzadeh, M.1
Gustafsson, L.2
Niklasson, C.3
-
10
-
-
0037416692
-
'Comparison of the resistance of industrial and laboratory strains of Saccharomyces and Zygosaccharomyces to lignocellulose-derived fermentation inhibitors'
-
Martin, C., and Jonsson, L.: 'Comparison of the resistance of industrial and laboratory strains of Saccharomyces and Zygosaccharomyces to lignocellulose-derived fermentation inhibitors', Enzyme Microbial Technol., 2003, 32, p. 386-395
-
(2003)
Enzyme Microbial Technol.
, vol.32
, pp. 386-395
-
-
Martin, C.1
Jonsson, L.2
-
11
-
-
84992281993
-
'Transcriptome dynamics of ethanologenic yeast in response to 5-hydroxymethylfurfural stress related to biomass conversion to ethanol'
-
Liu, Z.L., and Slininger, P.J.: 'Transcriptome dynamics of ethanologenic yeast in response to 5-hydroxymethylfurfural stress related to biomass conversion to ethanol', Recent Research Developments in Multidisciplinary Applied Microbiology: Understanding and Exploiting Microbes and Their Interactions-Biological, Physical, Chemical and Engineering Aspects, 2006, p. 679-684
-
(2006)
Recent Research Developments in Multidisciplinary Applied Microbiology: Understanding and Exploiting Microbes and Their Interactions-Biological, Physical, Chemical and Engineering Aspects
, pp. 679-684
-
-
Liu, Z.L.1
Slininger, P.J.2
-
12
-
-
33750290903
-
'Genomic adaptation of ethanologenic yeast to biomass conversion inhibitors'
-
Liu, Z.L.: 'Genomic adaptation of ethanologenic yeast to biomass conversion inhibitors', Appl. Microbiol. Biotech., 2006, 73, p. 27-36
-
(2006)
Appl. Microbiol. Biotech.
, vol.73
, pp. 27-36
-
-
Liu, Z.L.1
-
13
-
-
0344844807
-
'Modelling regulatory pathways in E. coli from time series expression profiles'
-
Ong, I.M., Glasner, J.D., and Page, D.: 'Modelling regulatory pathways in E. coli from time series expression profiles', Bioinformatics, 2002, 18, p. S241-S248
-
(2002)
Bioinformatics
, vol.18
-
-
Ong, I.M.1
Glasner, J.D.2
Page, D.3
-
14
-
-
3042698613
-
'Bayesian network and nonparametric heteroscedastic regression for nonlinear modeling of genetic network'
-
Imoto, S., Kim, S., and Goto, T.: Et al. 'Bayesian network and nonparametric heteroscedastic regression for nonlinear modeling of genetic network', J. Bioinf. Comput. Biol., 2003, 1, (2), p. 231-252
-
(2003)
J. Bioinf. Comput. Biol.
, vol.1
, Issue.2
, pp. 231-252
-
-
Imoto, S.1
Kim, S.2
Goto, T.3
-
15
-
-
0842288337
-
'Inferring cellular networks using probabilistic graphical models'
-
0036-8075
-
Friedman, N.: 'Inferring cellular networks using probabilistic graphical models', Science, 2004, 303, p. 799-805 0036-8075
-
(2004)
Science
, vol.303
, pp. 799-805
-
-
Friedman, N.1
-
16
-
-
32644431906
-
'Relationships between probabilistic Boolean networks and dynamic Bayesian networks as models of gene regulatory networks'
-
10.1016/j.sigpro.2005.06.008 0165-1684
-
Lähdesmäki, H., Hautaniemi, S., Shmulevich, I., and Yli-Harja, O.: 'Relationships between probabilistic Boolean networks and dynamic Bayesian networks as models of gene regulatory networks', Signal Process., 2006, 86, (4), p. 814-834 10.1016/j.sigpro.2005.06.008 0165-1684
-
(2006)
Signal Process.
, vol.86
, Issue.4
, pp. 814-834
-
-
Lähdesmäki, H.1
Hautaniemi, S.2
Shmulevich, I.3
Yli-Harja, O.4
-
17
-
-
0037108539
-
'Ingeneue: A versatile tool for reconstituting genetic networks, with examples from the segment polarity network'
-
Meir,AE., Munro, E.M., Odell, G.M., and von Dassow, G.: 'Ingeneue: a versatile tool for reconstituting genetic networks, with examples from the segment polarity network', J. Exp. Zool., 2002, 294, p. 216-251
-
(2002)
J. Exp. Zool.
, vol.294
, pp. 216-251
-
-
Meir, E.1
Munro, E.M.2
Odell, G.M.3
von Dassow, G.4
-
18
-
-
17444430052
-
'Dynamic network reconstruction from gene expression data applied to immune response during bacterial infection'
-
Guthke, R., Mller, U., Hoffmann, M., Thies, F., and Tpfer, S.: 'Dynamic network reconstruction from gene expression data applied to immune response during bacterial infection', Bioinformatics, 2005, 21, (8), p. 1626-1634
-
(2005)
Bioinformatics
, vol.21
, Issue.8
, pp. 1626-1634
-
-
Guthke, R.1
Mller, U.2
Hoffmann, M.3
Thies, F.4
Tpfer, S.5
-
20
-
-
0033031386
-
'E-CELL: Software environment for whole-cell simulation'
-
Tomita, M.S Hashimoto, K., and Takahashi, K.: Et al. 'E-CELL: software environment for whole-cell simulation', Bioinformatics, 1999, 15, (1), p. 72-84
-
(1999)
Bioinformatics
, vol.15
, Issue.1
, pp. 72-84
-
-
Tomita, M.1
Hashimoto, K.2
Takahashi, K.3
-
22
-
-
14844321288
-
'Space in systems biology of signaling pathways - Towards intracellular molecular crowding in silico'
-
Takahashi, K., Arjunan, S.N.V., and Tomita, M.: 'Space in systems biology of signaling pathways - Towards intracellular molecular crowding in silico', FEBS Lett., 2005, 579, p. 1783-1788
-
(2005)
FEBS Lett.
, vol.579
, pp. 1783-1788
-
-
Takahashi, K.1
Arjunan, S.N.V.2
Tomita, M.3
-
23
-
-
34547175927
-
'Automated reverse engineering of nonlinear dynamical systems'
-
10.1073/pnas.0609476104 0027-8424
-
Bongard, J., and Lipson, H.: 'Automated reverse engineering of nonlinear dynamical systems', Proc. Natl. Acad. Sci. USA, 2007, 104, (24), p. 9943-9948 10.1073/pnas.0609476104 0027-8424
-
(2007)
Proc. Natl. Acad. Sci. USA
, vol.104
, Issue.24
, pp. 9943-9948
-
-
Bongard, J.1
Lipson, H.2
-
24
-
-
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', Pacific Symp. Biocomput., 1998, 3, p. 18-29
-
(1998)
Pacific Symp. Biocomput.
, vol.3
, pp. 18-29
-
-
Liang, S.1
Fuhrman, S.2
Somogyi, R.3
-
25
-
-
0037418747
-
'Identification of genetic networks by strategic gene disruptions and gene overexpressions under a Boolean model'
-
10.1016/S0304-3975(02)00425-5 0304-3975
-
Akutsu, T., Kuhara, S., Maruyama, O., and Miyano, S.: 'Identification of genetic networks by strategic gene disruptions and gene overexpressions under a Boolean model', Theor. Comput. Sci., 2003, 298, (1), p. 235-251 10.1016/S0304-3975(02)00425-5 0304-3975
-
(2003)
Theor. Comput. Sci.
, vol.298
, Issue.1
, pp. 235-251
-
-
Akutsu, T.1
Kuhara, S.2
Maruyama, O.3
Miyano, S.4
-
26
-
-
27744569877
-
'Generating Boolean networks with a prescribed attractor structure'
-
Pal, R., Ivanov, I., Datta, A., Bittner, M.L., and Dougherty, E.R.: 'Generating Boolean networks with a prescribed attractor structure', Bioinformatics, 2005, 21, p. 4021-4025
-
(2005)
Bioinformatics
, vol.21
, pp. 4021-4025
-
-
Pal, R.1
Ivanov, I.2
Datta, A.3
Bittner, M.L.4
Dougherty, E.R.5
-
27
-
-
33646337667
-
'A methodology for the structural and functional analysis of signaling and regulatory networks'
-
Klamt, S., Saez-Rodriguez, J., Lindquist, J.A., Simeoni, L., and Gilles, E.D.: 'A methodology for the structural and functional analysis of signaling and regulatory networks', BMC Bioinf., 2006, 7, (56)
-
(2006)
BMC Bioinf.
, vol.7
, Issue.56
-
-
Klamt, S.1
Saez-Rodriguez, J.2
Lindquist, J.A.3
Simeoni, L.4
Gilles, E.D.5
-
28
-
-
34547480306
-
'An efficient method for dynamic analysis of gene regulatory networks and in silico gene perturbation experiments'
-
RECOMB, Oakland, CA
-
Garg, A., Xenarios, I., Mendoza, L., and DeMicheli, G.: 'An efficient method for dynamic analysis of gene regulatory networks and in silico gene perturbation experiments', Lecture Notes in Bioinformatics - Proc. RECOMB, Oakland, CA 2007, 4453, p. 62-76
-
(2007)
Lecture Notes in Bioinformatics - Proc.
, vol.4453
, pp. 62-76
-
-
Garg, A.1
Xenarios, I.2
Mendoza, L.3
DeMicheli, G.4
-
29
-
-
32044466073
-
'Markov logical networks'
-
10.1007/s10994-006-5833-1
-
Richardson, M., and Domingos, P.: 'Markov logical networks', Machine Learning, 2006, 62, p. 107-136 10.1007/s10994-006-5833-1
-
(2006)
Machine Learning
, vol.62
, pp. 107-136
-
-
Richardson, M.1
Domingos, P.2
-
30
-
-
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, 2002, 18, p. 261-274
-
(2002)
Bioinformatics
, vol.18
, pp. 261-274
-
-
Shmulevich, I.1
Dougherty, E.R.2
Kim, S.3
Zhang, W.4
-
33
-
-
33847335427
-
'Universal external RNA controls for microbial gene expression analysis using microarray and qRT-PCR'
-
Liu, Z.L., and Slininger, P.J.: 'Universal external RNA controls for microbial gene expression analysis using microarray and qRT-PCR', J Microbiol Methods, 2007, 68, p. 486-496
-
(2007)
J Microbiol Methods
, vol.68
, pp. 486-496
-
-
Liu, Z.L.1
Slininger, P.J.2
-
34
-
-
33748324384
-
-
R Development Core Team. Vienna, Austria ISBN 3-900051-07-0. Available from
-
R Development Core Team. R: A language and environment for statistical computing. Vienna, Austria, 2006, ISBN 3-900051-07-0. Available from http://www.R-project.org
-
(2006)
R: A Language and Environment for Statistical Computing
-
-
-
35
-
-
66249147018
-
-
YEAst Search for Transcriptional Regulators And Consensus Tracking (YEASTRACT) Last Date of Visit: November 22, 2007. Available from:
-
YEAst Search for Transcriptional Regulators And Consensus Tracking (YEASTRACT), 2006. Last Date of Visit: November 22, 2007. Available from: http://www.yeastract.com
-
(2006)
-
-
-
36
-
-
34447279050
-
'Quantitative transcriptome, proteome, and sulfur metabolite profiling of the Saccharomyces cerevisiae response to arsenite'
-
Thorsen, M., Lagniel, G., and Kristiansson, E.: Et al. 'Quantitative transcriptome, proteome, and sulfur metabolite profiling of the Saccharomyces cerevisiae response to arsenite', Phys. Genomics, 2007, 30, (1), p. 35-43
-
(2007)
Phys. Genomics
, vol.30
, Issue.1
, pp. 35-43
-
-
Thorsen, M.1
Lagniel, G.2
Kristiansson, E.3
-
37
-
-
0036000001
-
'Discrimination between paralogs using microarray analysis: Application to the Yap1p and Yap2p transcriptional networks'
-
Cohen, B.A., Pilpel, Y., Mitra, R.D., and Church, G.M.: 'Discrimination between paralogs using microarray analysis: Application to the Yap1p and Yap2p transcriptional networks', Mol. Biol. Cell, 2002, 13, (5), p. 1608-1614
-
(2002)
Mol. Biol. Cell
, vol.13
, Issue.5
, pp. 1608-1614
-
-
Cohen, B.A.1
Pilpel, Y.2
Mitra, R.D.3
Church, G.M.4
-
38
-
-
4644229547
-
'Adaptive response of yeasts to furfural and 5-hydroxymethylfurfural and new chemical evidence for HMF conversion to 2,5-bis-hydroxymethylfuran'
-
Liu, Z.L., Slininger, P.J., Dien, B.S., Berhow, M.A., Kurtzman, C.P., and Gorsich, S.W.: 'Adaptive response of yeasts to furfural and 5-hydroxymethylfurfural and new chemical evidence for HMF conversion to 2,5-bis-hydroxymethylfuran', J. Ind. Microbiol. Biotechnol., 2004, 31, p. 345-352
-
(2004)
J. Ind. Microbiol. Biotechnol.
, vol.31
, pp. 345-352
-
-
Liu, Z.L.1
Slininger, P.J.2
Dien, B.S.3
Berhow, M.A.4
Kurtzman, C.P.5
Gorsich, S.W.6
-
39
-
-
18844392283
-
'Enhanced biotransformation of furfural and 5-hydroxy methylfurfural by newly developed ethanologenic yeast strains'
-
Liu, Z.L., Slininger, P.J., and Gorsich, S.W.: 'Enhanced biotransformation of furfural and 5-hydroxy methylfurfural by newly developed ethanologenic yeast strains', Appl. Biochem. Biotechnol., 2005, 121-124, p. 451-460
-
(2005)
Appl. Biochem. Biotechnol.
, vol.121-124
, pp. 451-460
-
-
Liu, Z.L.1
Slininger, P.J.2
Gorsich, S.W.3
|