-
1
-
-
36549040624
-
Thinking about Bacillus subtilis as a multicellular organism
-
Aguilar C., Vlamakis H., Losick R., Kolter R. Thinking about Bacillus subtilis as a multicellular organism. Current Opinion in Microbiology 2007, 10:638-643.
-
(2007)
Current Opinion in Microbiology
, vol.10
, pp. 638-643
-
-
Aguilar, C.1
Vlamakis, H.2
Losick, R.3
Kolter, R.4
-
2
-
-
71949106492
-
An evaluation of minimal cellular functions to sustain a bacterial cell
-
Azuma Y., Ota M. An evaluation of minimal cellular functions to sustain a bacterial cell. BMC Systems Biology 2009, 3:111.
-
(2009)
BMC Systems Biology
, vol.3
, pp. 111
-
-
Azuma, Y.1
Ota, M.2
-
4
-
-
67749140118
-
Scale-free networks: a decade and beyond
-
Barabasi A.L. Scale-free networks: a decade and beyond. Science 2009, 325:412-413.
-
(2009)
Science
, vol.325
, pp. 412-413
-
-
Barabasi, A.L.1
-
5
-
-
0742305866
-
Network biology: understanding the cell's functional organization
-
Barabasi A.L., Oltvai Z.N. Network biology: understanding the cell's functional organization. Nature Reviews Genetics 2004, 5:101-113.
-
(2004)
Nature Reviews Genetics
, vol.5
, pp. 101-113
-
-
Barabasi, A.L.1
Oltvai, Z.N.2
-
6
-
-
78049507393
-
Rewiring of transcriptional regulatory networks: hierarchy, rather than connectivity, better reflects the importance of regulators
-
Bhardwaj N., Kim P.M., Gerstein M.B. Rewiring of transcriptional regulatory networks: hierarchy, rather than connectivity, better reflects the importance of regulators. Science Signalling 2010, 3:ra79.
-
(2010)
Science Signalling
, vol.3
-
-
Bhardwaj, N.1
Kim, P.M.2
Gerstein, M.B.3
-
8
-
-
80655125440
-
Just-in-time control of Spo0A synthesis in Bacillus subtilis by multiple regulatory mechanisms
-
Chastanet A., Losick R. Just-in-time control of Spo0A synthesis in Bacillus subtilis by multiple regulatory mechanisms. Journal of Bacteriology 2011, 193:6366-6374.
-
(2011)
Journal of Bacteriology
, vol.193
, pp. 6366-6374
-
-
Chastanet, A.1
Losick, R.2
-
9
-
-
77956533047
-
Hierarchical evolution of the bacterial sporulation network
-
de Hoon M.J., Eichenberger P., Vitkup D. Hierarchical evolution of the bacterial sporulation network. Current Biology 2010, 20:R735-R745.
-
(2010)
Current Biology
, vol.20
-
-
de Hoon, M.J.1
Eichenberger, P.2
Vitkup, D.3
-
10
-
-
33846228768
-
Cys303 in the histidine kinase PhoR is crucial for the phosphotransfer reaction in the PhoPR two-component system in Bacillus subtilis
-
Eldakak A., Hulett F.M. Cys303 in the histidine kinase PhoR is crucial for the phosphotransfer reaction in the PhoPR two-component system in Bacillus subtilis. Journal of Bacteriology 2007, 189:410-421.
-
(2007)
Journal of Bacteriology
, vol.189
, pp. 410-421
-
-
Eldakak, A.1
Hulett, F.M.2
-
12
-
-
78651299341
-
RegulonDB version 7.0: transcriptional regulation of Escherichia coli K-12 integrated within genetic sensory response units (Gensor Units)
-
Gama-Castro S., Salgado H., Peralta-Gil M., Santos-Zavaleta A., Muniz-Rascado L., Solano-Lira H., Jimenez-Jacinto V., Weiss V., Garcia-Sotelo J.S., Lopez-Fuentes A., Porron-Sotelo L., Alquicira-Hernandez S., Medina-Rivera A., Martinez-Flores I., Alquicira-Hernandez K., Martinez-Adame R., Bonavides-Martinez C., Miranda-Rios J., Huerta A.M., Mendoza-Vargas A., Collado-Torres L., Taboada B., Vega-Alvarado L., Olvera M., Olvera L., Grande R., Morett E., Collado-Vides J. RegulonDB version 7.0: transcriptional regulation of Escherichia coli K-12 integrated within genetic sensory response units (Gensor Units). Nucleic Acids Research 2010, 39:D98-D105.
-
(2010)
Nucleic Acids Research
, vol.39
-
-
Gama-Castro, S.1
Salgado, H.2
Peralta-Gil, M.3
Santos-Zavaleta, A.4
Muniz-Rascado, L.5
Solano-Lira, H.6
Jimenez-Jacinto, V.7
Weiss, V.8
Garcia-Sotelo, J.S.9
Lopez-Fuentes, A.10
Porron-Sotelo, L.11
Alquicira-Hernandez, S.12
Medina-Rivera, A.13
Martinez-Flores, I.14
Alquicira-Hernandez, K.15
Martinez-Adame, R.16
Bonavides-Martinez, C.17
Miranda-Rios, J.18
Huerta, A.M.19
Mendoza-Vargas, A.20
Collado-Torres, L.21
Taboada, B.22
Vega-Alvarado, L.23
Olvera, M.24
Olvera, L.25
Grande, R.26
Morett, E.27
Collado-Vides, J.28
more..
-
13
-
-
34447096883
-
Regulation of respiratory genes by ResD-ResE signal transduction system in Bacillus subtilis
-
Geng H., Zuber P., Nakano M.M. Regulation of respiratory genes by ResD-ResE signal transduction system in Bacillus subtilis. Methods in Enzymology 2007, 422:448-464.
-
(2007)
Methods in Enzymology
, vol.422
, pp. 448-464
-
-
Geng, H.1
Zuber, P.2
Nakano, M.M.3
-
14
-
-
0021700772
-
Bacterial regulation: global regulatory networks
-
Gottesman S. Bacterial regulation: global regulatory networks. Annual Review of Genetics 1984, 18:415-441.
-
(1984)
Annual Review of Genetics
, vol.18
, pp. 415-441
-
-
Gottesman, S.1
-
15
-
-
28544443425
-
Binding of the Bacillus subtilis LexA protein to the SOS operator
-
Groban E.S., Johnson M.B., Banky P., Burnett P.G., Calderon G.L., Dwyer E.C., Fuller S.N., Gebre B., King L.M., Sheren I.N., Von Mutius L.D., O'Gara T.M., Lovett C.M. Binding of the Bacillus subtilis LexA protein to the SOS operator. Nucleic Acids Research 2005, 33:6287-6295.
-
(2005)
Nucleic Acids Research
, vol.33
, pp. 6287-6295
-
-
Groban, E.S.1
Johnson, M.B.2
Banky, P.3
Burnett, P.G.4
Calderon, G.L.5
Dwyer, E.C.6
Fuller, S.N.7
Gebre, B.8
King, L.M.9
Sheren, I.N.10
Von Mutius, L.D.11
O'Gara, T.M.12
Lovett, C.M.13
-
16
-
-
0028919060
-
The sigma factors of Bacillus subtilis
-
Haldenwang W.G. The sigma factors of Bacillus subtilis. Microbiological Reviews 1995, 59:1-30.
-
(1995)
Microbiological Reviews
, vol.59
, pp. 1-30
-
-
Haldenwang, W.G.1
-
18
-
-
68749092014
-
Plasticity of transcriptional machinery in bacteria is increased by the repertoire of regulatory families
-
Janga S.C., Perez-Rueda E. Plasticity of transcriptional machinery in bacteria is increased by the repertoire of regulatory families. Computational Biology and Chemistry 2009, 33:261-268.
-
(2009)
Computational Biology and Chemistry
, vol.33
, pp. 261-268
-
-
Janga, S.C.1
Perez-Rueda, E.2
-
19
-
-
67649872023
-
Transcriptional regulation shapes the organization of genes on bacterial chromosomes
-
Janga S.C., Salgado H., Martinez-Antonio A. Transcriptional regulation shapes the organization of genes on bacterial chromosomes. Nucleic Acids Research 2009, 37:3680-3688.
-
(2009)
Nucleic Acids Research
, vol.37
, pp. 3680-3688
-
-
Janga, S.C.1
Salgado, H.2
Martinez-Antonio, A.3
-
20
-
-
19544379881
-
Stochasticity in gene expression: from theories to phenotypes
-
Kaern M., Elston T.C., Blake W.J., Collins J.J. Stochasticity in gene expression: from theories to phenotypes. Nature Reviews Genetics 2005, 6:451-464.
-
(2005)
Nature Reviews Genetics
, vol.6
, pp. 451-464
-
-
Kaern, M.1
Elston, T.C.2
Blake, W.J.3
Collins, J.J.4
-
21
-
-
27244436714
-
Expansion of the BioCyc collection of pathway/genome databases to 160 genomes
-
Karp P.D., Ouzounis C.A., Moore-Kochlacs C., Goldovsky L., Kaipa P., Ahren D., Tsoka S., Darzentas N., Kunin V., Lopez-Bigas N. Expansion of the BioCyc collection of pathway/genome databases to 160 genomes. Nucleic Acids Research 2005, 33:6083-6089.
-
(2005)
Nucleic Acids Research
, vol.33
, pp. 6083-6089
-
-
Karp, P.D.1
Ouzounis, C.A.2
Moore-Kochlacs, C.3
Goldovsky, L.4
Kaipa, P.5
Ahren, D.6
Tsoka, S.7
Darzentas, N.8
Kunin, V.9
Lopez-Bigas, N.10
-
22
-
-
73349136300
-
Applications of thiol-disulfide oxidoreductases for optimized in vivo production of functionally active proteins in Bacillus
-
Kouwen T.R., van Dijl J.M. Applications of thiol-disulfide oxidoreductases for optimized in vivo production of functionally active proteins in Bacillus. Applied Microbiology and Biotechnology 2009, 85:45-52.
-
(2009)
Applied Microbiology and Biotechnology
, vol.85
, pp. 45-52
-
-
Kouwen, T.R.1
van Dijl, J.M.2
-
23
-
-
72949090589
-
The powerful law of the power law and other myths in network biology
-
Lima-Mendez G., van Helden J. The powerful law of the power law and other myths in network biology. Molecular BioSystems 2009, 5:1482-1493.
-
(2009)
Molecular BioSystems
, vol.5
, pp. 1482-1493
-
-
Lima-Mendez, G.1
van Helden, J.2
-
24
-
-
43649086589
-
The role of DNA-binding specificity in the evolution of bacterial regulatory networks
-
Lozada-Chavez I., Angarica V.E., Collado-Vides J., Contreras-Moreira B. The role of DNA-binding specificity in the evolution of bacterial regulatory networks. Journal of Molecular Biology 2008, 379:627-643.
-
(2008)
Journal of Molecular Biology
, vol.379
, pp. 627-643
-
-
Lozada-Chavez, I.1
Angarica, V.E.2
Collado-Vides, J.3
Contreras-Moreira, B.4
-
26
-
-
58049208229
-
Ordered cyclic motifs contribute to dynamic stability in biological and engineered networks
-
Ma'ayan A., Cecchi G.A., Wagner J., Rao A.R., Iyengar R., Stolovitzky G. Ordered cyclic motifs contribute to dynamic stability in biological and engineered networks. Proceedings of the National Academy of Sciences of the United States of America 2008, 105:19235-19240.
-
(2008)
Proceedings of the National Academy of Sciences of the United States of America
, vol.105
, pp. 19235-19240
-
-
Ma'ayan, A.1
Cecchi, G.A.2
Wagner, J.3
Rao, A.R.4
Iyengar, R.5
Stolovitzky, G.6
-
27
-
-
13244264814
-
Hierarchical structure and modules in the Escherichia coli transcriptional regulatory network revealed by a new top-down approach
-
Ma H.W., Buer J., Zeng A.P. Hierarchical structure and modules in the Escherichia coli transcriptional regulatory network revealed by a new top-down approach. BMC Bioinformatics 2004, 5:199.
-
(2004)
BMC Bioinformatics
, vol.5
, pp. 199
-
-
Ma, H.W.1
Buer, J.2
Zeng, A.P.3
-
28
-
-
13544269611
-
An extended transcriptional regulatory network of Escherichia coli and analysis of its hierarchical structure and network motifs
-
Ma H.W., Kumar B., Ditges U., Gunzer F., Buer J., Zeng A.P. An extended transcriptional regulatory network of Escherichia coli and analysis of its hierarchical structure and network motifs. Nucleic Acids Research 2004, 32:6643-6649.
-
(2004)
Nucleic Acids Research
, vol.32
, pp. 6643-6649
-
-
Ma, H.W.1
Kumar, B.2
Ditges, U.3
Gunzer, F.4
Buer, J.5
Zeng, A.P.6
-
30
-
-
0242386460
-
Identifying global regulators in transcriptional regulatory networks in bacteria
-
Martinez-Antonio A., Collado-Vides J. Identifying global regulators in transcriptional regulatory networks in bacteria. Current Opinion in Microbiology 2003, 6:482-489.
-
(2003)
Current Opinion in Microbiology
, vol.6
, pp. 482-489
-
-
Martinez-Antonio, A.1
Collado-Vides, J.2
-
31
-
-
0037174670
-
Network motifs: simple building blocks of complex networks
-
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.
-
(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
-
32
-
-
33748679406
-
Identification and analysis of DNA-binding transcription factors in Bacillus subtilis and other Firmicutes-a genomic approach
-
Moreno-Campuzano S., Janga S.C., Perez-Rueda E. Identification and analysis of DNA-binding transcription factors in Bacillus subtilis and other Firmicutes-a genomic approach. BMC Genomics 2006, 7:147.
-
(2006)
BMC Genomics
, vol.7
, pp. 147
-
-
Moreno-Campuzano, S.1
Janga, S.C.2
Perez-Rueda, E.3
-
34
-
-
77956107104
-
Heterologous protein secretion by bacillus species from the cradle to the grave
-
Pohl S., Harwood C.R. Heterologous protein secretion by bacillus species from the cradle to the grave. Advances in Applied Microbiology 2010, 73:1-25.
-
(2010)
Advances in Applied Microbiology
, vol.73
, pp. 1-25
-
-
Pohl, S.1
Harwood, C.R.2
-
35
-
-
34848865681
-
Orthologous transcription factors in bacteria have different functions and regulate different genes
-
Price M.N., Dehal P.S., Arkin A.P. Orthologous transcription factors in bacteria have different functions and regulate different genes. PLoS Computational Biology 2007, 3:1739-1750.
-
(2007)
PLoS Computational Biology
, vol.3
, pp. 1739-1750
-
-
Price, M.N.1
Dehal, P.S.2
Arkin, A.P.3
-
36
-
-
13144283679
-
Modular analysis of the transcriptional regulatory network of E. coli
-
Resendis-Antonio O., Freyre-Gonzalez J.A., Menchaca-Mendez R., Gutierrez-Rios R.M., Martinez-Antonio A., Avila-Sanchez C., Collado-Vides J. Modular analysis of the transcriptional regulatory network of E. coli. Trends in Genetics 2005, 21:16-20.
-
(2005)
Trends in Genetics
, vol.21
, pp. 16-20
-
-
Resendis-Antonio, O.1
Freyre-Gonzalez, J.A.2
Menchaca-Mendez, R.3
Gutierrez-Rios, R.M.4
Martinez-Antonio, A.5
Avila-Sanchez, C.6
Collado-Vides, J.7
-
38
-
-
38549162091
-
DBTBS: a database of transcriptional regulation in Bacillus subtilis containing upstream intergenic conservation information
-
Sierro N., Makita Y., de Hoon M., Nakai K. DBTBS: a database of transcriptional regulation in Bacillus subtilis containing upstream intergenic conservation information. Nucleic Acids Research 2008, 36:D93-D96.
-
(2008)
Nucleic Acids Research
, vol.36
-
-
Sierro, N.1
Makita, Y.2
de Hoon, M.3
Nakai, K.4
-
40
-
-
0003675244
-
Bacillus subtilis: from cells to genes and from genes to cells
-
ASM Press, Washington, DC, A.L. Sonenshein, J.A. Hoch, R. Losick (Eds.)
-
Sonenshein A.L., Hoch J.A., Losick R. Bacillus subtilis: from cells to genes and from genes to cells. Bacillus subtilis and its Closest Relatives: From Genes to Cells 2002, 3-5. ASM Press, Washington, DC. A.L. Sonenshein, J.A. Hoch, R. Losick (Eds.).
-
(2002)
Bacillus subtilis and its Closest Relatives: From Genes to Cells
, pp. 3-5
-
-
Sonenshein, A.L.1
Hoch, J.A.2
Losick, R.3
-
41
-
-
13444263410
-
Self-similarity of complex networks
-
Song C., Havlin S., Makse H.A. Self-similarity of complex networks. Nature 2005, 433:392-395.
-
(2005)
Nature
, vol.433
, pp. 392-395
-
-
Song, C.1
Havlin, S.2
Makse, H.A.3
-
43
-
-
0007712725
-
Multistationarity, the basis of cell differentiation and memory. I. Structural conditions of multistationarity and other nontrivial behavior
-
Thomas R., Kaufman M. Multistationarity, the basis of cell differentiation and memory. I. Structural conditions of multistationarity and other nontrivial behavior. Chaos 2001, 11:170-179.
-
(2001)
Chaos
, vol.11
, pp. 170-179
-
-
Thomas, R.1
Kaufman, M.2
-
44
-
-
70349673425
-
Identification of network topological units coordinating the global expression response to glucose in Bacillus subtilis and its comparison to Escherichia coli
-
Vazquez C.D., Freyre-Gonzalez J.A., Gosset G., Loza J.A., Gutierrez-Rios R.M. Identification of network topological units coordinating the global expression response to glucose in Bacillus subtilis and its comparison to Escherichia coli. BMC Microbiology 2009, 9:176.
-
(2009)
BMC Microbiology
, vol.9
, pp. 176
-
-
Vazquez, C.D.1
Freyre-Gonzalez, J.A.2
Gosset, G.3
Loza, J.A.4
Gutierrez-Rios, R.M.5
-
45
-
-
36749062913
-
One perturbation of the mother cell gene regulatory network suppresses the effects of another during sporulation of Bacillus subtilis
-
Wang L., Perpich J., Driks A., Kroos L. One perturbation of the mother cell gene regulatory network suppresses the effects of another during sporulation of Bacillus subtilis. Journal of Bacteriology 2007, 189:8467-8473.
-
(2007)
Journal of Bacteriology
, vol.189
, pp. 8467-8473
-
-
Wang, L.1
Perpich, J.2
Driks, A.3
Kroos, L.4
-
46
-
-
0026045102
-
Regulation of the SOS response in Bacillus subtilis: evidence for a LexA repressor homolog
-
Wojciechowski M.F., Peterson K.R., Love P.E. Regulation of the SOS response in Bacillus subtilis: evidence for a LexA repressor homolog. Journal of Bacteriology 1991, 173:6489-6498.
-
(1991)
Journal of Bacteriology
, vol.173
, pp. 6489-6498
-
-
Wojciechowski, M.F.1
Peterson, K.R.2
Love, P.E.3
-
47
-
-
77952691738
-
Comparing genomes to computer operating systems in terms of the topology and evolution of their regulatory control networks
-
Yan K.K., Fang G., Bhardwaj N., Alexander R.P., Gerstein M. Comparing genomes to computer operating systems in terms of the topology and evolution of their regulatory control networks. Proceedings of the National Academy of Sciences of the United States of America 2010, 107:9186-9191.
-
(2010)
Proceedings of the National Academy of Sciences of the United States of America
, vol.107
, pp. 9186-9191
-
-
Yan, K.K.1
Fang, G.2
Bhardwaj, N.3
Alexander, R.P.4
Gerstein, M.5
|