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List of works by Rafael Silva-Rocha

A GFP-lacZ Bicistronic Reporter System for Promoter Analysis in Environmental Gram-Negative Bacteria ⬇️

scientific article published on April 6, 2012

A Novel Cys2His2 Zinc Finger Homolog of AZF1 Modulates Holocellulase Expression in Trichoderma reesei

scientific article published on 18 June 2019

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 ⬇️

scientific article published on August 18, 2011

A phylogenetically conserved hnRNP type A/B protein from squid brain

scientific article published on 02 January 2019

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

scientific article

A toolset of constitutive promoters for metabolic engineering of Rhodosporidium toruloides

scientific article published on 29 June 2019

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

scientific article

Benchmarking Bacterial Promoter Prediction Tools: Potentialities and Limitations

scientific article published on 25 August 2020

Boosting Secondary Metabolite Production and Discovery through the Engineering of Novel Microbial Biosensors

scientific article published on 09 July 2018

Boundaries in metagenomic screenings using lacZα-based vectors

scientific article published on 06 March 2020

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

scientific article published on May 15, 2012

CRZ1 regulator and calcium cooperatively modulate holocellulases gene expression in Trichoderma reesei QM6a

scientific article published on 01 January 2020

Calibrating Transcriptional Activity Using Constitutive Synthetic Promoters in Mutants for Global Regulators in Escherichia coli.

scientific article

Chromatin profiling reveals heterogeneity in clinical isolates of the human pathogen Aspergillus fumigatus

scientific article published on 10 January 2022

Chromosomal integration of transcriptional fusions

scientific article published in January 2014

Combining Genetic Circuit and Microbial Growth Kinetic Models: A Challenge for Biological Modelling

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

scientific article published on July 2015

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

scientific article (publication date: 21 March 2014)

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

scientific article

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

scientific article published on 16 August 2012

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

scientific article published on 18 October 2014

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

scientific article

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

scientific article published on 10 June 2015

Emergent Properties in Complex Synthetic Bacterial Promoters

scientific article published in November 2017

Engineering Complexity in Bacterial Regulatory Circuits for Biotechnological Applications

scientific article published in March 2018

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

scientific article published on 25 August 2015

Engineering multicellular logic in bacteria with metabolic wires

scientific article published on 22 July 2013

Expanding the Toolbox of Broad Host-Range Transcriptional Terminators for Proteobacteria through Metagenomics

scientific article published on 09 April 2019

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

scientific article published on 28 July 2014

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

scientific article published on 27 January 2014

Functional Characterization of Clinical Isolates of the Opportunistic Fungal Pathogen Aspergillus nidulans

scientific article published on 08 April 2020

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

scientific article

Galectin-3 impacts Cryptococcus neoformans infection through direct antifungal effects

scientific article published on 6 December 2017

Gene expression of the arsenic resistance operon in Chromobacterium violaceum ATCC 12472

scientific article published on 01 February 2008

Genomic and Postgenomic Approaches to Understand Environmental Microorganisms

scientific article published on 24 October 2018

High Osmolarity Glycerol Mitogen Activated Protein Kinases SakA and MpkC Physically Interact During Osmotic and Cell Wall Stresses

scientific article published on 07 May 2019

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

scientific article published on 16 September 2015

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

scientific article published on May 17, 2011

Improving the prediction of Pseudomonas putida mt-2 growth kinetics with the use of a gene expression regulation model of the TOL plasmid

article

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

scientific article published on 16 February 2011

Loving the poison: the methylcitrate cycle and bacterial pathogenesis

scientific article published on 22 January 2018

Microbial Community Profiling in Intensive Care Units Expose Limitations in Current Sanitary Standards

scientific article published on 28 August 2019

Mining Novel Constitutive Promoter Elements in Soil Metagenomic Libraries in Escherichia coli.

scientific article

Mining logic gates in prokaryotic transcriptional regulation networks

scientific article

Noise and robustness in prokaryotic regulatory networks

scientific article published on January 2010

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

scientific article

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

scientific article

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

scientific article published on April 2016

Recent advances in plasmid-based tools for establishing novel microbial chassis

scientific article published on 19 August 2019

Reverse Engineering of an Aspirin-Responsive Transcriptional Regulator in Escherichia coli

scientific article published on 02 August 2019

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

scientific article published on August 16, 2012

Synthetic and minimalist vectors for Agrobacterium tumefaciens-mediated transformation of fungi

scientific article published on 01 April 2019

Synthetic biology approaches to improve biocatalyst identification in metagenomic library screening

scientific article

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

scientific article published in December 2017

Systems and Synthetic Biology Approaches to Engineer Fungi for Fine Chemical Production

scientific article published on 03 October 2018

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

scientific article published on 13 June 2017

The Aspergillus fumigatus Phosphoproteome Reveals Roles of High-Osmolarity Glycerol Mitogen-Activated Protein Kinases in Promoting Cell Wall Damage and Caspofungin Tolerance

scientific article published on 04 February 2020

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

scientific article published on 19 August 2016

The Cell Wall Integrity Pathway Contributes to the Early Stages of Aspergillus fumigatus Asexual Development

scientific article published on 18 March 2020

The Chromobacterium violaceum ArsR Arsenite Repressor Exerts Tighter Control on Its Cognate Promoter Than the Escherichia coli System.

scientific article

The Duality of the MAPK Signaling Pathway in the Control of Metabolic Processes and Cellulase Production in Trichoderma reesei

scientific article published in Scientific Reports

The IHF regulon of exponentially growing Pseudomonas putida cells

scientific article

The Logic of Decision Making in Environmental Bacteria

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

scientific article

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

scientific article published on 23 November 2012

The art of vector engineering: towards the construction of next-generation genetic tools

scientific article published on 26 September 2018

The differential response of thePbenpromoter ofPseudomonas putida mt-2 to BenR and XylS prevents metabolic conflicts inm-xylene biodegradation

article

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

scientific article published on 7 August 2015

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

scientific article

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

scientific article published on 16 March 2011

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

scientific article published in July 2014

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

scientific article published on 16 January 2014

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.

scientific article published in June 2010

TheTOLnetwork ofPseudomonas putidamt‐2 processes multiple environmental inputs into a narrowresponse space ⬇️

scientific article published on November 22, 2012

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

scientific article published on 04 December 2015

Transcriptional regulation of central carbon metabolism in Pseudomonas aeruginosa

scientific article published on 11 June 2019

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

scientific article

Transcriptomic fingerprinting of Pseudomonas putida under alternative physiological regimes

scientific article published on 5 September 2013

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

scientific article published on April 2016

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

scientific article

Vestigialization of arsenic resistance phenotypes/genotypes inChromobacterium violaceumstrains thriving in pristine Brazilian sites

article

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