-
2
-
-
33846400424
-
Large-scale mapping and validation of Escherichia coli transcriptional regulation from a compendium of expression profiles
-
17214507 10.1371/journal.pbio.0050008 1764438
-
Faith JJ Hayete B Thaden JT Mogno I Wierzbowski J Cottarel G Kasif S Collins JJ Gardner TS Large-scale mapping and validation of Escherichia coli transcriptional regulation from a compendium of expression profiles PLoS Biol 2007, 5:e8. 17214507 10.1371/journal.pbio.0050008 1764438
-
(2007)
PLoS Biol
, vol.5
-
-
Faith, J.J.1
Hayete, B.2
Thaden, J.T.3
Mogno, I.4
Wierzbowski, J.5
Cottarel, G.6
Kasif, S.7
Collins, J.J.8
Gardner, T.S.9
-
3
-
-
0037941585
-
Module networks: Identifying regulatory modules and their condition-specific regulators from gene expression data
-
12740579 10.1038/ng1165
-
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 Nat Genet 2003, 34:166-167. 12740579 10.1038/ng1165
-
(2003)
Nat Genet
, vol.34
, pp. 166-167
-
-
Segal, E.1
Shapira, M.2
Regev, A.3
Pe'er, D.4
Botstein, D.5
Koller, D.6
Friedman, N.7
-
5
-
-
33747813561
-
The Inferelator: An algorithm for learning parsimonious regulatory networks from systems-biology data sets de novo
-
16686963 10.1186/gb-2006-7-5-r36 1779511
-
Bonneau R Reiss DJ Shannon P Facciotti M Hood L Baliga NS Thorsson V The Inferelator: An algorithm for learning parsimonious regulatory networks from systems-biology data sets de novo Genome Biol 2006, 7:R36. 16686963 10.1186/gb-2006-7-5-r36 1779511
-
(2006)
Genome Biol
, vol.7
-
-
Bonneau, R.1
Reiss, D.J.2
Shannon, P.3
Facciotti, M.4
Hood, L.5
Baliga, N.S.6
Thorsson, V.7
-
6
-
-
34547844096
-
Comparing association network algorithms for reverse engineering of large scale gene regulatory networks: Synthetic versus real data
-
17485431 10.1093/bioinformatics/btm163
-
Soranzo N Bianconi G Altafini C Comparing association network algorithms for reverse engineering of large scale gene regulatory networks: synthetic versus real data Bioinformatics 2007, 23:1640-1647. 17485431 10.1093/bioinformatics/btm163
-
(2007)
Bioinformatics
, vol.23
, pp. 1640-1647
-
-
Soranzo, N.1
Bianconi, G.2
Altafini, C.3
-
7
-
-
52149107867
-
Origin of co-expression patterns in E. coli and S. cerevisiae emerging from reverse engineering algorithms
-
18714358 10.1371/journal.pone.0002981 2500178
-
Zampieri M Soranzo N Bianchini D Altafini C Origin of co-expression patterns in E. coli and S. cerevisiae emerging from reverse engineering algorithms PLoS One 2008, 3:e2981. 18714358 10.1371/journal.pone.0002981 2500178
-
(2008)
PLoS One
, vol.3
-
-
Zampieri, M.1
Soranzo, N.2
Bianchini, D.3
Altafini, C.4
-
8
-
-
60149110901
-
Module networks revisited: Computational assessment and prioritization of model predictions
-
19136553 10.1093/bioinformatics/btn658
-
Joshi A De Smet R Marchal K Peer Van de Y Michoel T Module networks revisited: Computational assessment and prioritization of model predictions Bioinformatics 2009, 25:490-496. 19136553 10.1093/ bioinformatics/btn658
-
(2009)
Bioinformatics
, vol.25
, pp. 490-496
-
-
Joshi, A.1
De Smet, R.2
Marchal, K.3
Peer, Y.4
Michoel, T.5
-
9
-
-
38349122751
-
Analysis of a Gibbs sampler for model based clustering of gene expression data
-
18033794 10.1093/bioinformatics/btm562
-
JoshiA Peer Van de Y Michoel T Analysis of a Gibbs sampler for model based clustering of gene expression data Bioinformatics 2008, 24(2):176-183. 18033794 10.1093/bioinformatics/btm562
-
(2008)
Bioinformatics
, vol.24
, Issue.2
, pp. 176-183
-
-
Joshi, A.1
Peer, Y.2
Michoel, T.3
-
10
-
-
0033637153
-
Genomic expression programs in the response of yeast cells to environmental changes
-
15070 11102521
-
Gasch AP Spellman PT Kao CM Carmel-Harel O Eisen MB Storz G Botstein D Brown PO Genomic expression programs in the response of yeast cells to environmental changes Mol Biol Cell 2000, 11:4241-4257. 15070 11102521
-
(2000)
Mol Biol Cell
, vol.11
, pp. 4241-4257
-
-
Gasch, A.P.1
Spellman, P.T.2
Kao, C.M.3
Carmel-Harel, O.4
Eisen, M.B.5
Storz, G.6
Botstein, D.7
Brown, P.O.8
-
11
-
-
33644873438
-
RegulonDB (version 5.0): Escherichia coli K-12 transcriptional regulatory network, operon organization, and growth conditions
-
16381895 10.1093/nar/gkj156 1347518
-
Salgado H Gama-Castro S Peralta-Gil M Diaz-Peredo E Sanchez-Solano F Santos-Zavaleta A Martinez-Flores I Jimenez-Jacinto V Bonavides-Martinez C Segura-Salazar J Martinez-Antonio A Collado-Vides J RegulonDB (version 5.0): Escherichia coli K-12 transcriptional regulatory network, operon organization, and growth conditions Nucleic Acids Res 2006, 34:D394-397. 16381895 10.1093/nar/gkj156 1347518
-
(2006)
Nucleic Acids Res
, vol.34
-
-
Salgado, H.1
Gama-Castro, S.2
Peralta-Gil, M.3
Diaz-Peredo, E.4
Sanchez-Solano, F.5
Santos-Zavaleta, A.6
Martinez-Flores, I.7
Jimenez-Jacinto, V.8
Bonavides-Martinez, C.9
Segura-Salazar, J.10
Martinez-Antonio, A.11
Collado-Vides, J.12
-
12
-
-
33745449162
-
Comprehensive analysis of combinatorial regulation using the transcriptional regulatory network of yeast
-
16762362 10.1016/j.jmb.2006.04.029
-
Balaji S Madan Babu M Iyer LM Luscombe NM Aravind L Comprehensive analysis of combinatorial regulation using the transcriptional regulatory network of yeast J Mol Biol 2006, 360:213-227. 16762362 10.1016/j.jmb.2006.04.029
-
(2006)
J Mol Biol
, vol.360
, pp. 213-227
-
-
Balaji, S.1
Madan Babu, M.2
Iyer, L.M.3
Luscombe, N.M.4
Aravind, L.5
-
13
-
-
46249109755
-
Discerning static and causal interactions in genome-wide reverse engineering problems
-
18467346 10.1093/bioinformatics/btn220
-
Zampieri M Soranzo N Altafini C Discerning static and causal interactions in genome-wide reverse engineering problems Bioinformatics 2008, 24:1510-1515. 18467346 10.1093/bioinformatics/btn220
-
(2008)
Bioinformatics
, vol.24
, pp. 1510-1515
-
-
Zampieri, M.1
Soranzo, N.2
Altafini, C.3
-
14
-
-
0242574985
-
Reconciling gene expression data with known genome-scale regulatory network structures
-
14559784 10.1101/gr.1330003 403761
-
Herrgård MJ Covert MW Palsson Bo Reconciling gene expression data with known genome-scale regulatory network structures Genome Res 2003, 13:2423-2434. 14559784 10.1101/gr.1330003 403761
-
(2003)
Genome Res
, vol.13
, pp. 2423-2434
-
-
Herrgård, M.J.1
Covert, M.W.2
Palsson, Bo.3
-
15
-
-
32044462728
-
The incoherent feed-forward loop accelerates the response-time of the gal system of Escherichia coli
-
16406067 10.1016/j.jmb.2005.12.003
-
Mangan S Itzkovitz S Zaslaver A Alon U The incoherent feed-forward loop accelerates the response-time of the gal system of Escherichia coli J Mol Biol 2006, 356:1073-1081. 16406067 10.1016/j.jmb.2005.12.003
-
(2006)
J Mol Biol
, vol.356
, pp. 1073-1081
-
-
Mangan, S.1
Itzkovitz, S.2
Zaslaver, A.3
Alon, U.4
-
16
-
-
22744444676
-
After 30 years of study, the bacterial SOS response still surprises us
-
16000023 10.1371/journal.pbio.0030255 1174825
-
Michel B After 30 years of study, the bacterial SOS response still surprises us PLoS Biol 2005, 3:e255. 16000023 10.1371/ journal.pbio.0030255 1174825
-
(2005)
PLoS Biol
, vol.3
-
-
Michel, B.1
-
17
-
-
0025647125
-
Identification of hypoxanthine and guanine as the co-repressors for the purine regulon genes of Escherichia coli
-
2089227 10.1111/j.1365-2958.1990.tb00580.x
-
Meng LM Nygaard P Identification of hypoxanthine and guanine as the co-repressors for the purine regulon genes of Escherichia coli Mol Microbiol 1990, 4:2187-2192. 2089227 10.1111/j.1365-2958.1990.tb00580.x
-
(1990)
Mol Microbiol
, vol.4
, pp. 2187-2192
-
-
Meng, L.M.1
Nygaard, P.2
-
18
-
-
13444262374
-
EcoCyc: A comprehensive database resource for Escherichia coli
-
Keseler IM Collado-Vides J Gama-Castro S Ingraham J Paley S Paulsen IT Peralta-Gil M Karp PD EcoCyc: A comprehensive database resource for Escherichia coli Nucleic Acids Res 2005, 33:334-337
-
(2005)
Nucleic Acids Res
, pp. 334-337
-
-
Keseler, I.M.1
Collado-Vides, J.2
Gama-Castro, S.3
Ingraham, J.4
Paley, S.5
Paulsen, I.T.6
Peralta-Gil, M.7
Karp, P.D.8
-
19
-
-
13944254077
-
Chromosome organization is shaped by the transcription regulatory network
-
15734572 10.1016/j.tig.2005.01.003
-
Hershberg R Yeger-Lotem E Margalit H Chromosome organization is shaped by the transcription regulatory network Trends Genet 2005, 21:138-142. 15734572 10.1016/j.tig.2005.01.003
-
(2005)
Trends Genet
, vol.21
, pp. 138-142
-
-
Hershberg, R.1
Yeger-Lotem, E.2
Margalit, H.3
-
20
-
-
40149098889
-
Horizontal gene transfer and the evolution of transcriptional regulation in Escherichia coli
-
18179685 10.1186/gb-2008-9-1-r4 2395238
-
Price MN Dehal PS Arkin AP Horizontal gene transfer and the evolution of transcriptional regulation in Escherichia coli Genome Biol 2008, 9:R4. 18179685 10.1186/gb-2008-9-1-r4 2395238
-
(2008)
Genome Biol
, vol.9
-
-
Price, M.N.1
Dehal, P.S.2
Arkin, A.P.3
-
21
-
-
33644873683
-
The YEASTRACT database: A tool for the analysis of transcription regulatory associations in Saccharomyces cerevisiae
-
16381908 10.1093/nar/gkj013 1347376
-
Teixeira M Monteiro P Jain P Tenreiro S Fernandes A Mira N Alenquer M Freitas A Oliveira A Sà-Correia I The YEASTRACT database: A tool for the analysis of transcription regulatory associations in Saccharomyces cerevisiae Nucleic Acids Res 2006, 34:D446-451. 16381908 10.1093/nar/gkj013 1347376
-
(2006)
Nucleic Acids Res
, vol.34
-
-
Teixeira, M.1
Monteiro, P.2
Jain, P.3
Tenreiro, S.4
Fernandes, A.5
Mira, N.6
Alenquer, M.7
Freitas, A.8
Oliveira, A.9
Sà-Correia, I.10
-
22
-
-
0041673353
-
The rotary motor of bacterial flegella
-
12500982 10.1146/annurev.biochem.72.121801.161737
-
Berg HC The rotary motor of bacterial flegella Annu Rev Biochem 2003, 72:19-54. 12500982 10.1146/annurev.biochem.72.121801.161737
-
(2003)
Annu Rev Biochem
, vol.72
, pp. 19-54
-
-
Berg, H.C.1
-
23
-
-
34147179823
-
Clustering of genes into regulons using integrated modeling-COGRIM
-
17204163 10.1186/gb-2007-8-1-r4 1839128
-
Chen G Jensen S Stoeckert C Clustering of genes into regulons using integrated modeling-COGRIM Genome Biol 2007, 8:R4. 17204163 10.1186/ gb-2007-8-1-r4 1839128
-
(2007)
Genome Biol
, vol.8
-
-
Chen, G.1
Jensen, S.2
Stoeckert, C.3
-
24
-
-
66449112938
-
Expression profile of genes involved in hydrogen sulphide liberation by Saccharomyces cerevisiae grown under different nitrogen concentrations
-
10.1038/npre.2008.2736.1
-
Mendes-Fereira A Barbosa C del Olmo M Mendes-Faia A Leão C Expression profile of genes involved in hydrogen sulphide liberation by Saccharomyces cerevisiae grown under different nitrogen concentrations 2008 10.1038/npre.2008.2736.1
-
(2008)
-
-
Mendes-Fereira, A.1
Barbosa, C.2
del Olmo, M.3
Mendes-Faia, A.4
Leão, C.5
|