Silva-Rocha R - Search Results

1

Mining novel cis-regulatory elements from the emergent host Rhodosporidium toruloides using transcriptomic data.

Nora LC, Cassiano MHA, Santana ÍP, Guazzaroni ME, Silva-Rocha R, da Silva RR. Nora LC, et al. Front Microbiol. 2023 Jan 6;13:1069443. doi: 10.3389/fmicb.2022.1069443. eCollection 2022. Front Microbiol. 2023. PMID: 36687612 Free PMC article.

2

Quantitative, non-disruptive monitoring of transcription in single cells with a broad-host range GFP-luxCDABE dual reporter system.

Benedetti IM, de Lorenzo V, Silva-Rocha R. Benedetti IM, et al. PLoS One. 2012;7(12):e52000. doi: 10.1371/journal.pone.0052000. Epub 2012 Dec 28. PLoS One. 2012. PMID: 23284849 Free PMC article.

3

Transcription factor levels enable metabolic diversification of single cells of environmental bacteria.

Guantes R, Benedetti I, Silva-Rocha R, de Lorenzo V. Guantes R, et al. ISME J. 2016 May;10(5):1122-33. doi: 10.1038/ismej.2015.193. Epub 2015 Dec 4. ISME J. 2016. PMID: 26636554 Free PMC article.

4

The Standard European Vector Architecture (SEVA): a coherent platform for the analysis and deployment of complex prokaryotic phenotypes.

Silva-Rocha R, Martínez-García E, Calles B, Chavarría M, Arce-Rodríguez A, de Las Heras A, Páez-Espino AD, Durante-Rodríguez G, Kim J, Nikel PI, Platero R, de Lorenzo V. Silva-Rocha R, et al. Nucleic Acids Res. 2013 Jan;41(Database issue):D666-75. doi: 10.1093/nar/gks1119. Epub 2012 Nov 23. Nucleic Acids Res. 2013. PMID: 23180763 Free PMC article.

5

The logic layout of the TOL network of Pseudomonas putida pWW0 plasmid stems from a metabolic amplifier motif (MAM) that optimizes biodegradation of m-xylene.

Silva-Rocha R, de Jong H, Tamames J, de Lorenzo V. Silva-Rocha R, et al. BMC Syst Biol. 2011 Nov 11;5:191. doi: 10.1186/1752-0509-5-191. BMC Syst Biol. 2011. PMID: 22078029 Free PMC article.

6

Linking genes to microbial growth kinetics: an integrated biochemical systems engineering approach.

Koutinas M, Kiparissides A, Silva-Rocha R, Lam MC, Martins Dos Santos VA, de Lorenzo V, Pistikopoulos EN, Mantalaris A. Koutinas M, et al. Metab Eng. 2011 Jul;13(4):401-13. doi: 10.1016/j.ymben.2011.02.001. Epub 2011 Feb 16. Metab Eng. 2011. PMID: 21315172 Free article.

7

Mining logic gates in prokaryotic transcriptional regulation networks.

Silva-Rocha R, de Lorenzo V. Silva-Rocha R, et al. FEBS Lett. 2008 Apr 9;582(8):1237-44. doi: 10.1016/j.febslet.2008.01.060. Epub 2008 Feb 12. FEBS Lett. 2008. PMID: 18275855 Free article. Review.

8

The regulatory logic of m-xylene biodegradation by Pseudomonas putida mt-2 exposed by dynamic modelling of the principal node Ps/Pr of the TOL plasmid.

Koutinas M, Lam MC, Kiparissides A, Silva-Rocha R, Godinho M, Livingston AG, Pistikopoulos EN, de Lorenzo V, Dos Santos VA, Mantalaris A. Koutinas M, et al. Environ Microbiol. 2010 Jun;12(6):1705-18. doi: 10.1111/j.1462-2920.2010.02245.x. Environ Microbiol. 2010. PMID: 20553551

9

Engineering multicellular logic in bacteria with metabolic wires.

Silva-Rocha R, de Lorenzo V. Silva-Rocha R, et al. ACS Synth Biol. 2014 Apr 18;3(4):204-9. doi: 10.1021/sb400064y. Epub 2013 Jul 22. ACS Synth Biol. 2014. PMID: 23863114 Free article.

10

A composite feed-forward loop I4-FFL involving IHF and Crc stabilizes expression of the XylR regulator of Pseudomonas putida mt-2 from growth phase perturbations.

Silva-Rocha R, de Lorenzo V. Silva-Rocha R, et al. Mol Biosyst. 2011 Nov;7(11):2982-90. doi: 10.1039/c1mb05264k. Epub 2011 Aug 18. Mol Biosyst. 2011. PMID: 21853168

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