-
1
-
-
34548219522
-
Comparative genomic reconstruction of transcriptional regulatory networks in bacteria
-
PMID: 17636889
-
Rodionov D. A. (2007). Comparative genomic reconstruction of transcriptional regulatory networks in bacteria. Chemical reviews, 107(8), 3467-3497. https://doi.org/10.1021/cr068309+ PMID: 17636889
-
(2007)
Chemical Reviews
, vol.107
, Issue.8
, pp. 3467-3497
-
-
Rodionov, D.A.1
-
2
-
-
78649874431
-
Genomic repertoires of DNA-binding transcription factors across the tree of life
-
PMID: 20675356
-
Charoensawan V., Wilson D., &Teichmann S. A. (2010). Genomic repertoires of DNA-binding transcription factors across the tree of life. Nucleic acids research, 38(21), 7364-7377. https://doi.org/10. 1093/nar/gkq617 PMID: 20675356
-
(2010)
Nucleic Acids Research
, vol.38
, Issue.21
, pp. 7364-7377
-
-
Charoensawan, V.1
Wilson, D.2
Teichmann, S.A.3
-
3
-
-
33846400424
-
Large-scale mapping and validation of Escherichia coli transcriptional regulation from a compendium of expression profiles
-
PMID: 17214507
-
Faith J. J., Hayete B., Thaden J. T., Mogno I., Wierzbowski J., Cottarel G. et al., (2007). Large-scale mapping and validation of Escherichia coli transcriptional regulation from a compendium of expression profiles. PLoS biol, 5(1), e8. https://doi.org/10.1371/journal.pbio.0050008 PMID: 17214507
-
(2007)
PLoS Biol
, vol.5
, Issue.1
, pp. e8
-
-
Faith, J.J.1
Hayete, B.2
Thaden, J.T.3
Mogno, I.4
Wierzbowski, J.5
Cottarel, G.6
-
4
-
-
84963800566
-
Transcription profile of Escherichia coli: Genomic SELEX search for regulatory targets of transcription factors
-
Ishihama A., Shimada T., & Yamazaki Y. (2016). Transcription profile of Escherichia coli: genomic SELEX search for regulatory targets of transcription factors. Nucleic acids research, gkw051.
-
(2016)
Nucleic Acids Research
, pp. gkw051
-
-
Ishihama, A.1
Shimada, T.2
Yamazaki, Y.3
-
5
-
-
34447279700
-
Identifying regulatory targets of cell cycle transcription factors using gene expression and ChIP-chip data
-
Wu W., Li W., & Chen B. (2007). Identifying regulatory targets of cell cycle transcription factors using gene expression and ChIP-chip data. BMC bioinformatics, 8(1), 1.
-
(2007)
BMC Bioinformatics
, vol.8
, Issue.1
, pp. 1
-
-
Wu, W.1
Li, W.2
Chen, B.3
-
6
-
-
84895753066
-
COLOMBOS v2.0: An ever expanding collection of bacterial expression compendia
-
Meysman P., Sonego P., Bianco L, Fu Q., Ledezma-Tejeida D., Gama-Castro S. et al., (2013). COLOMBOS v2.0: an ever expanding collection of bacterial expression compendia. Nucleic acids research, gkt1086.
-
(2013)
Nucleic Acids Research
, pp. gkt1086
-
-
Meysman, P.1
Sonego, P.2
Bianco, L.3
Fu, Q.4
Ledezma-Tejeida, D.5
Gama-Castro, S.6
-
7
-
-
0041429503
-
Genome-wide expression analysis in Corynebacterium glutamicum using DNA microarrays
-
Wendisch V. F. (2003). Genome-wide expression analysis in Corynebacterium glutamicum using DNA microarrays. Journal of biotechnology, 104(1), 273-285.
-
(2003)
Journal of Biotechnology
, vol.104
, Issue.1
, pp. 273-285
-
-
Wendisch, V.F.1
-
8
-
-
84874886134
-
ChIP-Seq and the complexity of bacterial transcriptional regulation
-
Galagan J., Lyubetskaya A., & Gomes A. (2012). ChIP-Seq and the complexity of bacterial transcriptional regulation. Systems Biology, 43-68.
-
(2012)
Systems Biology
, pp. 43-68
-
-
Galagan, J.1
Lyubetskaya, A.2
Gomes, A.3
-
9
-
-
80053912671
-
Systematic mapping of two component response regulators to gene targets in a model sulfate reducing bacterium
-
PMID: 21992415
-
Rajeev L, Luning E.G., Dehal P. S., Price M. N., Arkin A. P., & Mukhopadhyay A. (2011). Systematic mapping of two component response regulators to gene targets in a model sulfate reducing bacterium. Genome Biol, 12(10), R99. https://doi.org/10.1186/gb-2011-12-10-r99 PMID: 21992415
-
(2011)
Genome Biol
, vol.12
, Issue.10
, pp. R99
-
-
Rajeev, L.1
Luning, E.G.2
Dehal, P.S.3
Price, M.N.4
Arkin, A.P.5
Mukhopadhyay, A.6
-
12
-
-
14644388890
-
Making connections between novel transcription factors and their DNA motifs
-
PMID: 15653829
-
Tan K., McCue L. A., & Stormo G. D. (2005). Making connections between novel transcription factors and their DNA motifs. Genome research, 15(2), 312-320. https://doi.org/10.1101/gr.3069205 PMID: 15653829
-
(2005)
Genome Research
, vol.15
, Issue.2
, pp. 312-320
-
-
Tan, K.1
McCue, L.A.2
Stormo, G.D.3
-
13
-
-
84886739636
-
RegPrecise 3.0-a resource for genome-scale exploration of transcriptional regulation in bacteria
-
Novichkov P. S., Kazakov A. E., Ravcheev D. A., Leyn S. A., Kovaleva G. Y., Sutormin R. A., et al. (2013). RegPrecise 3.0-a resource for genome-scale exploration of transcriptional regulation in bacteria. BMC genomics, 14(1), 745.
-
(2013)
BMC Genomics
, vol.14
, Issue.1
, pp. 745
-
-
Novichkov, P.S.1
Kazakov, A.E.2
Ravcheev, D.A.3
Leyn, S.A.4
Kovaleva, G.Y.5
Sutormin, R.A.6
-
14
-
-
77954254495
-
RegPredict: An integrated system for regulon inference in prokaryotes by comparative genomics approach
-
Novichkov P. S., Rodionov D. A., Stavrovskaya E. D., Novichkova E. S., Kazakov A. E., Gelfand M. S. et al., (2010). RegPredict: an integrated system for regulon inference in prokaryotes by comparative genomics approach. Nucleic acids research, 38(suppl 2), W299-W307.
-
(2010)
Nucleic Acids Research
, vol.38
, pp. W299-W307
-
-
Novichkov, P.S.1
Rodionov, D.A.2
Stavrovskaya, E.D.3
Novichkova, E.S.4
Kazakov, A.E.5
Gelfand, M.S.6
-
15
-
-
84936929916
-
Rapid quantification of mutant fitness in diverse bacteria by sequencing randomly bar-coded transposons
-
PMID: 25968644
-
Wetmore K. M., Price M. N., Waters R. J., Lamson J. S., He J., Hoover C. A. et al., (2015). Rapid quantification of mutant fitness in diverse bacteria by sequencing randomly bar-coded transposons. MBio, 6 (3), e00306-15. https://doi.org/10.1128/mBio.00306-15 PMID: 25968644
-
(2015)
MBio
, vol.6
, Issue.3
, pp. e00306-e00315
-
-
Wetmore, K.M.1
Price, M.N.2
Waters, R.J.3
Lamson, J.S.4
He, J.5
Hoover, C.A.6
-
16
-
-
85015281028
-
-
bioRxiv
-
Price M. N., Wetmore K.M., Waters R. J., Callaghan M., Ray J., Kuehl J. V., Melnyk R.A., Lamson J. S., Suh Y., Esquivel Z., Sadeeshkumar H., Chakraborty R., Rubin B. E., Bristow J., Blow M. J., Arkin A. P., Deutschbauer A. M. (2016) Deep Annotation of Protein Function across Diverse Bacteria from Mutant Phenotypes. bioRxiv
-
(2016)
Deep Annotation of Protein Function Across Diverse Bacteria from Mutant Phenotypes
-
-
Price, M.N.1
Wetmore, K.M.2
Waters, R.J.3
Callaghan, M.4
Ray, J.5
Kuehl, J.V.6
Melnyk, R.A.7
Lamson, J.S.8
Suh, Y.9
Esquivel, Z.10
Sadeeshkumar, H.11
Chakraborty, R.12
Rubin, B.E.13
Bristow, J.14
Blow, M.J.15
Arkin, A.P.16
Deutschbauer, A.M.17
-
17
-
-
81755163097
-
Evidence-based annotation of gene function in Shewanella oneidensis MR-1 using genome-wide fitness profiling across 121 conditions
-
PMID: 22125499
-
Deutschbauer A., Price M. N., Wetmore K. M., Shao W., Baumohl J. K., Xu Z. et al., (2011). Evidence-based annotation of gene function in Shewanella oneidensis MR-1 using genome-wide fitness profiling across 121 conditions. PLoS Genet, 7(11), e1002385. https://doi.org/10.1371/journal.pgen.1002385 PMID: 22125499
-
(2011)
PLoS Genet
, vol.7
, Issue.11
, pp. e1002385
-
-
Deutschbauer, A.1
Price, M.N.2
Wetmore, K.M.3
Shao, W.4
Baumohl, J.K.5
Xu, Z.6
-
18
-
-
0033047695
-
The role of the trehalose system in regulating the maltose regulon of Escherichia coli
-
Decker Katja, Gerhardt Friederike, and Boos Winfried. "The role of the trehalose system in regulating the maltose regulon of Escherichia coli." Molecular microbiology 32.4 (1999): 777-788.
-
(1999)
Molecular Microbiology
, vol.32
, Issue.4
, pp. 777-788
-
-
Katja, D.1
Friederike, G.2
Winfried, B.3
-
19
-
-
84876543942
-
RegulonDB v8.0: Omics data sets, evolutionary conservation, regulatory phrases, cross-validated gold standards and more
-
Jan 1 Epub 2012 Nov 29
-
Salgado H. et al., (2013). "RegulonDB v8.0: Omics data sets, evolutionary conservation, regulatory phrases, cross-validated gold standards and more". Nucleic Acids Research. 2013 Jan 1; 41(D1): D203-D213. Epub 2012 Nov 29.
-
(2013)
Nucleic Acids Research
, vol.41
, Issue.D1
, pp. D203-D213
-
-
Salgado, H.1
-
20
-
-
84906309533
-
Conservation of transcription start sites within genes across a bacterial genus
-
PMID: 24987095
-
Shao W., Price M. N., Deutschbauer A. M., Romine M. F., & Arkin A. P. (2014). Conservation of transcription start sites within genes across a bacterial genus. MBio, 5(4), e01398-14. https://doi.org/10. 1128/mBio.01398-14 PMID: 24987095
-
(2014)
MBio
, vol.5
, Issue.4
, pp. e01398-e01414
-
-
Shao, W.1
Price, M.N.2
Deutschbauer, A.M.3
Romine, M.F.4
Arkin, A.P.5
-
21
-
-
38549134505
-
Many Microbe Microarrays Database: Uniformly normalized Affymetrix compendia with structured experimental metadata
-
Faith J. J., Driscoll M. E., Fusaro V. A., Cosgrove E. J., Hayete B., Juhn F. S., et al. (2008). Many Microbe Microarrays Database: uniformly normalized Affymetrix compendia with structured experimental metadata. Nucleic acids research, 36(suppl 1), D866-D870.
-
(2008)
Nucleic Acids Research
, vol.36
, pp. D866-D870
-
-
Faith, J.J.1
Driscoll, M.E.2
Fusaro, V.A.3
Cosgrove, E.J.4
Hayete, B.5
Juhn, F.S.6
-
22
-
-
0242386460
-
Identifying global regulators in transcriptional regulatory networks in bacteria
-
PMID: 14572541
-
Martinez-Antonio A., & Collado-Vides J. (2003). Identifying global regulators in transcriptional regulatory networks in bacteria. Current opinion in microbiology, 6(5), 482-489. PMID: 14572541
-
(2003)
Current Opinion in Microbiology
, vol.6
, Issue.5
, pp. 482-489
-
-
Martinez-Antonio, A.1
Collado-Vides, J.2
-
23
-
-
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. (2006). Identification and analysis of DNA-binding transcription factors in Bacillus subtilis and other Firmicutes-a genomic approach. BMC genomics, 7(1), 147.
-
(2006)
BMC Genomics
, vol.7
, Issue.1
, pp. 147
-
-
Moreno-Campuzano, S.1
Janga, S.C.2
Perez-Rueda, E.3
-
24
-
-
77957244650
-
Search and clustering orders of magnitude faster than BLAST
-
PMID: 20709691
-
Edgar R. C. (2010). Search and clustering orders of magnitude faster than BLAST. Bioinformatics, 26 (19), 2460-2461. https://doi.org/10.1093/bioinformatics/btq461 PMID: 20709691
-
(2010)
Bioinformatics
, vol.26
, Issue.19
, pp. 2460-2461
-
-
Edgar, R.C.1
-
25
-
-
85019843250
-
TIGRFAMsand genome properties in 2013
-
Haft D. H., Selengut J. D., Richter R. A., Harkins D., Basu M. K., & Beck E. (2012). TIGRFAMsand genome properties in 2013. Nucleic acids research, gks1234.
-
(2012)
Nucleic Acids Research
, pp. gks1234
-
-
Haft, D.H.1
Selengut, J.D.2
Richter, R.A.3
Harkins, D.4
Basu, M.K.5
Beck, E.6
|