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Engineering Complexity in Bacterial Regulatory Circuits for Biotechnological Applications.

Westmann CA, Guazzaroni ME, Silva-Rocha R.

mSystems. 2018 Apr 10;3(2). pii: e00151-17. doi: 10.1128/mSystems.00151-17. eCollection 2018 Mar-Apr.


Loving the poison: the methylcitrate cycle and bacterial pathogenesis.

Dolan SK, Wijaya A, Geddis SM, Spring DR, Silva-Rocha R, Welch M.

Microbiology. 2018 Mar;164(3):251-259. doi: 10.1099/mic.0.000604. Epub 2018 Jan 22.


Transcriptome-wide survey of gene expression changes and alternative splicing in Trichophyton rubrum in response to undecanoic acid.

Mendes NS, Bitencourt TA, Sanches PR, Silva-Rocha R, Martinez-Rossi NM, Rossi A.

Sci Rep. 2018 Feb 6;8(1):2520. doi: 10.1038/s41598-018-20738-x.


Galectin-3 impacts Cryptococcus neoformans infection through direct antifungal effects.

Almeida F, Wolf JM, da Silva TA, DeLeon-Rodriguez CM, Rezende CP, Pessoni AM, Fernandes FF, Silva-Rocha R, Martinez R, Rodrigues ML, Roque-Barreira MC, Casadevall A.

Nat Commun. 2017 Dec 6;8(1):1968. doi: 10.1038/s41467-017-02126-7.


Systematic identification of novel regulatory interactions controlling biofilm formation in the bacterium Escherichia coli.

Amores GR, de Las Heras A, Sanches-Medeiros A, Elfick A, Silva-Rocha R.

Sci Rep. 2017 Dec 1;7(1):16768. doi: 10.1038/s41598-017-17114-6.


Emergent Properties in Complex Synthetic Bacterial Promoters.

Monteiro LMO, Arruda LM, Silva-Rocha R.

ACS Synth Biol. 2018 Feb 16;7(2):602-612. doi: 10.1021/acssynbio.7b00344. Epub 2017 Nov 14.


Aspergillus fumigatus protein phosphatase PpzA is involved in iron assimilation, secondary metabolite production, and virulence.

Manfiolli AO, de Castro PA, Dos Reis TF, Dolan S, Doyle S, Jones G, Riaño Pachón DM, Ulaş M, Noble LM, Mattern DJ, Brakhage AA, Valiante V, Silva-Rocha R, Bayram O, Goldman GH.

Cell Microbiol. 2017 Dec;19(12). doi: 10.1111/cmi.12770. Epub 2017 Aug 17.


The Aspergillus fumigatus CrzA Transcription Factor Activates Chitin Synthase Gene Expression during the Caspofungin Paradoxical Effect.

Ries LNA, Rocha MC, de Castro PA, Silva-Rocha R, Silva RN, Freitas FZ, de Assis LJ, Bertolini MC, Malavazi I, Goldman GH.

MBio. 2017 Jun 13;8(3). pii: e00705-17. doi: 10.1128/mBio.00705-17.


Deletion of pH Regulator pac-3 Affects Cellulase and Xylanase Activity during Sugarcane Bagasse Degradation by Neurospora crassa.

Campos Antoniêto AC, Ramos Pedersoli W, Dos Santos Castro L, da Silva Santos R, Cruz AH, Nogueira KM, Silva-Rocha R, Rossi A, Silva RN.

PLoS One. 2017 Jan 20;12(1):e0169796. doi: 10.1371/journal.pone.0169796. eCollection 2017.


The Aspergillus fumigatus SchASCH9 kinase modulates SakAHOG1 MAP kinase activity and it is essential for virulence.

Alves de Castro P, Dos Reis TF, Dolan SK, Oliveira Manfiolli A, Brown NA, Jones GW, Doyle S, Riaño-Pachón DM, Squina FM, Caldana C, Singh A, Del Poeta M, Hagiwara D, Silva-Rocha R, Goldman GH.

Mol Microbiol. 2016 Nov;102(4):642-671. doi: 10.1111/mmi.13484. Epub 2016 Oct 7.


The Post-genomic Era of Trichoderma reesei: What's Next?

Gupta VK, Steindorff AS, de Paula RG, Silva-Rocha R, Mach-Aigner AR, Mach RL, Silva RN.

Trends Biotechnol. 2016 Dec;34(12):970-982. doi: 10.1016/j.tibtech.2016.06.003. Epub 2016 Jul 6. Review.


Pre-mRNA splicing is modulated by antifungal drugs in the filamentous fungus Neurospora crassa.

Mendes NS, Silva PM, Silva-Rocha R, Martinez-Rossi NM, Rossi A.

FEBS Open Bio. 2016 Mar 14;6(4):358-68. doi: 10.1002/2211-5463.12047. eCollection 2016 Apr.


Trichoderma reesei CRE1-mediated Carbon Catabolite Repression in Re-sponse to Sophorose Through RNA Sequencing Analysis.

Antoniêto AC, de Paula RG, Castro Ldos S, Silva-Rocha R, Persinoti GF, Silva RN.

Curr Genomics. 2016 Apr;17(2):119-31. doi: 10.2174/1389202917666151116212901.


Recent Progress on Systems and Synthetic Biology Approaches to Engineer Fungi As Microbial Cell Factories.

Amores GR, Guazzaroni ME, Arruda LM, Silva-Rocha R.

Curr Genomics. 2016 Apr;17(2):85-98. doi: 10.2174/1389202917666151116212255.


Understanding the Role of the Master Regulator XYR1 in Trichoderma reesei by Global Transcriptional Analysis.

Dos Santos Castro L, de Paula RG, Antoniêto AC, Persinoti GF, Silva-Rocha R, Silva RN.

Front Microbiol. 2016 Feb 16;7:175. doi: 10.3389/fmicb.2016.00175. eCollection 2016.


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

Guantes R, Benedetti I, Silva-Rocha R, de Lorenzo V.

ISME J. 2016 May;10(5):1122-33. doi: 10.1038/ismej.2015.193. Epub 2015 Dec 4.


High-resolution analysis of the m-xylene/toluene biodegradation subtranscriptome of Pseudomonas putida mt-2.

Kim J, Pérez-Pantoja D, Silva-Rocha R, Oliveros JC, de Lorenzo V.

Environ Microbiol. 2016 Oct;18(10):3327-3341. doi: 10.1111/1462-2920.13054. Epub 2015 Oct 22.


Engineering Synthetic cis-Regulatory Elements for Simultaneous Recognition of Three Transcriptional Factors in Bacteria.

Amores GR, Guazzaroni ME, Silva-Rocha R.

ACS Synth Biol. 2015 Dec 18;4(12):1287-94. doi: 10.1021/acssynbio.5b00098. Epub 2015 Aug 31.


The impact of chromatin remodelling on cellulase expression in Trichoderma reesei.

Mello-de-Sousa TM, Rassinger A, Pucher ME, dos Santos Castro L, Persinoti GF, Silva-Rocha R, Poças-Fonseca MJ, Mach RL, Nascimento Silva R, Mach-Aigner AR.

BMC Genomics. 2015 Aug 7;16:588. doi: 10.1186/s12864-015-1807-7.


Comparative analyses of downstream signal transduction targets modulated after activation of the AT1 receptor by two β-arrestin-biased agonists.

Santos GA, Duarte DA, Parreiras-E-Silva LT, Teixeira FR, Silva-Rocha R, Oliveira EB, Bouvier M, Costa-Neto CM.

Front Pharmacol. 2015 Jul 1;6:131. doi: 10.3389/fphar.2015.00131. eCollection 2015.


Development of New Modular Genetic Tools for Engineering the Halophilic Archaeon Halobacterium salinarum.

Silva-Rocha R, Pontelli MC, Furtado GP, Zaramela LS, Koide T.

PLoS One. 2015 Jun 10;10(6):e0129215. doi: 10.1371/journal.pone.0129215. eCollection 2015.


The pWW0 plasmid imposes a stochastic expression regime to the chromosomal ortho pathway for benzoate metabolism in Pseudomonas putida.

Silva-Rocha R, de Lorenzo V.

FEMS Microbiol Lett. 2014 Jul;356(2):176-83. doi: 10.1111/1574-6968.12400.


Defining the genome-wide role of CRE1 during carbon catabolite repression in Trichoderma reesei using RNA-Seq analysis.

Antoniêto AC, dos Santos Castro L, Silva-Rocha R, Persinoti GF, Silva RN.

Fungal Genet Biol. 2014 Dec;73:93-103. doi: 10.1016/j.fgb.2014.10.009. Epub 2014 Oct 18.


Synthetic biology approaches to improve biocatalyst identification in metagenomic library screening.

Guazzaroni ME, Silva-Rocha R, Ward RJ.

Microb Biotechnol. 2015 Jan;8(1):52-64. doi: 10.1111/1751-7915.12146. Epub 2014 Aug 13. Review.


Expanding the logic of bacterial promoters using engineered overlapping operators for global regulators.

Guazzaroni ME, Silva-Rocha R.

ACS Synth Biol. 2014 Sep 19;3(9):666-75. doi: 10.1021/sb500084f. Epub 2014 Jul 28.


Deciphering the cis-regulatory elements for XYR1 and CRE1 regulators in Trichoderma reesei.

Silva-Rocha R, Castro Ldos S, Antoniêto AC, Guazzaroni ME, Persinoti GF, Silva RN.

PLoS One. 2014 Jun 18;9(6):e99366. doi: 10.1371/journal.pone.0099366. eCollection 2014.


Chromosomal integration of transcriptional fusions.

Silva-Rocha R, de Lorenzo V.

Methods Mol Biol. 2014;1149:479-89. doi: 10.1007/978-1-4939-0473-0_37.


Comparative metabolism of cellulose, sophorose and glucose in Trichoderma reesei using high-throughput genomic and proteomic analyses.

Dos Santos Castro L, Pedersoli WR, Antoniêto ACC, Steindorff AS, Silva-Rocha R, Martinez-Rossi NM, Rossi A, Brown NA, Goldman GH, Faça VM, Persinoti GF, Silva RN.

Biotechnol Biofuels. 2014 Mar 21;7(1):41. doi: 10.1186/1754-6834-7-41.


The differential response of the Pben promoter of Pseudomonas putida mt-2 to BenR and XylS prevents metabolic conflicts in m-xylene biodegradation.

Pérez-Pantoja D, Kim J, Silva-Rocha R, de Lorenzo V.

Environ Microbiol. 2015 Jan;17(1):64-75. doi: 10.1111/1462-2920.12443. Epub 2014 Apr 2.


Expression pattern of cellulolytic and xylanolytic genes regulated by transcriptional factors XYR1 and CRE1 are affected by carbon source in Trichoderma reesei.

Castro Ldos S, Antoniêto AC, Pedersoli WR, Silva-Rocha R, Persinoti GF, Silva RN.

Gene Expr Patterns. 2014 Mar;14(2):88-95. doi: 10.1016/j.gep.2014.01.003. Epub 2014 Jan 27.


The private life of environmental bacteria: pollutant biodegradation at the single cell level.

Nikel PI, Silva-Rocha R, Benedetti I, de Lorenzo V.

Environ Microbiol. 2014 Mar;16(3):628-42. doi: 10.1111/1462-2920.12360. Epub 2014 Jan 16. Review.


Transcriptomic fingerprinting of Pseudomonas putida under alternative physiological regimes.

Kim J, Oliveros JC, Nikel PI, de Lorenzo V, Silva-Rocha R.

Environ Microbiol Rep. 2013 Dec;5(6):883-91. doi: 10.1111/1758-2229.12090. Epub 2013 Sep 5.


Engineering multicellular logic in bacteria with metabolic wires.

Silva-Rocha R, de Lorenzo V.

ACS Synth Biol. 2014 Apr 18;3(4):204-9. doi: 10.1021/sb400064y. Epub 2013 Jul 22.


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.

PLoS One. 2012;7(12):e52000. doi: 10.1371/journal.pone.0052000. Epub 2012 Dec 28.


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.

Nucleic Acids Res. 2013 Jan;41(Database issue):D666-75. doi: 10.1093/nar/gks1119. Epub 2012 Nov 23.


The TOL network of Pseudomonas putida mt-2 processes multiple environmental inputs into a narrow response space.

Silva-Rocha R, de Lorenzo V.

Environ Microbiol. 2013 Jan;15(1):271-86. doi: 10.1111/1462-2920.12014. Epub 2012 Nov 22.


Decoding the genetic networks of environmental bacteria: regulatory moonlighting of the TOL system of Pseudomonas putida mt-2.

Silva-Rocha R, Pérez-Pantoja D, de Lorenzo V.

ISME J. 2013 Feb;7(2):229-32. doi: 10.1038/ismej.2012.98. Epub 2012 Aug 16. No abstract available.


Stochasticity of TOL plasmid catabolic promoters sets a bimodal expression regime in Pseudomonas putida mt-2 exposed to m-xylene.

Silva-Rocha R, de Lorenzo V.

Mol Microbiol. 2012 Oct;86(1):199-211. doi: 10.1111/j.1365-2958.2012.08184.x. Epub 2012 Aug 16.


Broadening the signal specificity of prokaryotic promoters by modifying cis-regulatory elements associated with a single transcription factor.

Silva-Rocha R, de Lorenzo V.

Mol Biosyst. 2012 Jul 6;8(7):1950-7. doi: 10.1039/c2mb25030f. Epub 2012 May 15.


The IHF regulon of exponentially growing Pseudomonas putida cells.

Silva-Rocha R, Chavarría M, Kleijn RJ, Sauer U, de Lorenzo V.

Environ Microbiol. 2013 Jan;15(1):49-63. doi: 10.1111/j.1462-2920.2012.02750.x. Epub 2012 Apr 18.


A GFP-lacZ bicistronic reporter system for promoter analysis in environmental gram-negative bacteria.

Silva-Rocha R, de Lorenzo V.

PLoS One. 2012;7(4):e34675. doi: 10.1371/journal.pone.0034675. Epub 2012 Apr 6.


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.

BMC Syst Biol. 2011 Nov 11;5:191. doi: 10.1186/1752-0509-5-191.


Functional analysis of the integration host factor site of the σ(54) Pu promoter of Pseudomonas putida by in vivo UV imprinting.

Valls M, Silva-Rocha R, Cases I, Muñoz A, de Lorenzo V.

Mol Microbiol. 2011 Nov;82(3):591-601. doi: 10.1111/j.1365-2958.2011.07835.x. Epub 2011 Sep 30.


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.

Mol Biosyst. 2011 Nov;7(11):2982-90. doi: 10.1039/c1mb05264k. Epub 2011 Aug 18.


Implementing an OR-NOT (ORN) logic gate with components of the SOS regulatory network of Escherichia coli.

Silva-Rocha R, de Lorenzo V.

Mol Biosyst. 2011 Aug;7(8):2389-96. doi: 10.1039/c1mb05094j. Epub 2011 May 17.


A practical teaching course in directed protein evolution using the green fluorescent protein as a model.

Ruller R, Silva-Rocha R, Silva A, Cruz Schneider MP, Ward RJ.

Biochem Mol Biol Educ. 2011 Jan-Feb;39(1):21-7. doi: 10.1002/bmb.20430.


The logicome of environmental bacteria: merging catabolic and regulatory events with Boolean formalisms.

Silva-Rocha R, Tamames J, dos Santos VM, de Lorenzo V.

Environ Microbiol. 2011 Sep;13(9):2389-402. doi: 10.1111/j.1462-2920.2011.02455.x. Epub 2011 Mar 16. Review.


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.

Metab Eng. 2011 Jul;13(4):401-13. doi: 10.1016/j.ymben.2011.02.001. Epub 2011 Feb 16.



Beloqui A, Guazzaroni ME, Pazos F, Vieites JM, Godoy M, Golyshina OV, Chernikova TN, Waliczek A, Silva-Rocha R, Al-Ramahi Y, La Cono V, Mendez C, Salas JA, Solano R, Yakimov MM, Timmis KN, Golyshin PN, Ferrer M.

Science. 2010 Nov 12;330(6006):912. doi: 10.1126/science.330.6006.912-a. No abstract available.


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