Rafael Silva Rocha
CV Lattes
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Universidade de São Paulo (USP). Faculdade de Medicina de Ribeirão Preto (FMRP) (Institutional affiliation for the last research proposal) Birthplace: Brazil
Biologist by the Universidade Federal do Pará, Brazil (Belém, 2007), PhD in Molecular Biology at the Universidad Autónoma de Madrid (Madrid, 2011). Worked as post-doctoral research at the CNB-CSIC (Madrid, 2012) on Systems and Synthetic Biology, and at the FMRP-USP (Riebirão Preto, 2015), working on Systems Biology. From 2015 to 2018 worked as Assistant Professor at the Cell and Molecular Biology Department at FMRP-USP. Since 2018 works as Associate Professor at the Cell and Molecular Biology Department at FMRP-USP, working on Systems and Synthetic Biology, Computational Biology and Bioinformatics. E-mail: silvarochar@gmail.com. HomePage: http://silvarochar.wixsite.com/ssbl. (Source: Lattes Curriculum)
- Loving the poison: molecular basis for metabolism and toxicity of the widely-used food preservative, propionate in Pseudomonas aeruginosa, AP.R
Abstract
We will examine how wild-type PA01 catabolises propionate (in comparison with succinate, a control substrate). This will be done by integrating data obtained from a combination of transcriptomic (RNA-Seq), metabolomic (1N NMR, GC-MS/MS and LC-MS) and proteomic (iTRAQ) analyses. The Welch team has expertise in RNA-Seq, metabolomic and proteomic analyses, whereas the Silva-Rocha team has ...
- Synthetic biology approaches for deciphering the logic of signal integration in complex bacterial promoters, AP.JP
Abstract
The ability to coordinate expression of thousands of genes in response to different stimuli is an essential feature of any live organism. However, current knowledge on this matter is largely inferred from data on extant systems involving just a few regulatory components. In this context, this project propose the adoption of a genetically tractable experimental object (Escherichia coli) ...
- Reconstruction of the gene regulatory network in Pseudomonas aeruginosa, BP.IC
Abstract
Pseudomonas aeruginosa is a bacterium often found in the environment and opportunistic pathogen associated with serious infections. This organism has a genome of more than 6 Mb which is controlled by sophisticated molecular machinery that includes ~25 sigma factors and hundreds of transcription factors. Although many studies have investigated several transcription factors related to the...
- Genome assembly for identification of antibiotic resistance genes in clinical isolates of the Hospital das Clínicas de Ribeirão Preto, BP.IC
Abstract
The problem of antibiotic resistance has become a threat to global health. Increasingly, we are creating an atmosphere of selective pressure that has never been seen before by bacteria, due to either the use or misuse of antibiotics or any environmental contamination due to anthropological action. It is known that genes that confer resistance to antibiotics are both in pathogens and in ...
- Synthetic biology applied to Rhodosporidium toruloides for fine chemical production, BP.DR
Abstract
The oleaginous and carotenogenic yeast Rhodosporidium toruloides is a promising host for the production of bioproducts from lignocellulosic biomass because it is able to efficiently consume C5 and C6 sugars and lignin-derived aromatic compounds. It also presents a high lipid concentration and a potential to store other compounds derived from acetyl-CoA, such as terpenes. Terpenes are a ...
(Only some records are available in English at this moment)
- Standardization of a high-performance expression system for Escherichia coli based on benzoate inducer, BP.TT
- Design of novel synthetic yeast promoters based on in silico approaches, BP.MS
Abstract
Microorganisms of the yeast group are very important for several biotechnological applications. In recent years, several studies have focused on the engineering of synthetic circuits in yeasts aiming to both expand the metabolic and biosynthetic capacities of these organisms and increase their tolerance to aggressive environmental conditions such as those related to different industrial...
- Quantifying the effect of space between -35/-10 boxes in synthetic bacterial promoters, BP.IC
Abstract
In this work, we aim to investigate the effect of space length between the binding regions for RNA Polymerase binding boxes in sigma70 dependent promoters. While most works previous focused on the investigation of the sequences in the recognition boxes of promoters, few have systematically analyzed the effect of box distance. In this work plan, four variants of constitutive synthetic pr...
(Only some records are available in English at this moment)
- Development of an engineered microbe for inflammation sensing in the intestinal environment, BE.EP.MS
Abstract
Synthetic biology directed to biomedical applications aims to develop engineering-driven approaches to the programming of cellular functions that could yield transformative diagnostic tools, as well as unmatched therapeutic strategies for treating significant human pathologies. Our ability to generate bacterial strains with unique and increasingly complex functions has rapidly expanded ...
- Reconstruction of bacterial regulatory networks in environmental terrestrial samples, BE.EP.DR
Abstract
The sharing of genetic information among microbial communities can be represented by a complex network that interconnects the most diverse information, as for example: metabolites, specific genes, enzymes, substrates and also the transcription factors. For instance, the survival and coexistence of a microbial community could be explained or understood through genes expressed by that com...
- Construction of engineered yeast strains for achieving better yields of biomass degradation, BE.EP.MS
Abstract
Plant biomass degradation has been studied for years due to the incredible amount of byproducts generated during this process - ranging from biofuels to other noteworthy chemicals. The candidate current master's project is dedicated on building modular vectors based on synthetic biology for the transformation of fungi, more specifically T. reesei. The interest in this fungus arose becau...
(Only some records are available in English at this moment)
| 2 / 2 | Ongoing research grants |
| 8 / 8 | Ongoing scholarships in Brazil |
| 13 / 12 | Completed scholarships in Brazil |
| 5 / 5 | Completed scholarships abroad |
| 28 / 27 | All research grants and scholarships |
| Associated processes | |
(References retrieved automatically from Web of Science and SciELO through information on FAPESP grants and their corresponding numbers as mentioned in the publications by the authors)
| Publications | 26 |
| Citations | 179 |
| Cit./Article | 6.9 |
| Data from Web of Science | |
OLIVEIRA MONTEIRO, LUMMY MARIA; ARRUDA, LETICIA MAGALHAES; SANCHES-MEDEIROS, ANANDA; MARTINS-SANTANA, LEONARDO; DE FATIMA ALVES, LUANA; DEFELIPE, LUCAS; GUSTAVO TURJANSKI, ADRIAN; GUAZZARONI, MARIA-EUGENIA; DE LORENZO, VICTOR; SILVA-ROCHA, RAFAEL. Reverse Engineering of an Aspirin-Responsive Transcriptional Regulator in Escherichia coli. ACS SYNTHETIC BIOLOGY, v. 8, n. 8, p. 1890-1900, AUG 2019. Web of Science Citations: 1. (16/19179-9, 15/04309-1, 12/22921-8, 17/17924-1, 18/04810-0, 16/06323-4)
ALVES, LUANA DE FATIMA; MELEIRO, LUANA PARRAS; SILVA, ROBERTO N.; WESTMANN, CAUA ANTUNES; GUAZZARONI, MARIA-EUGENIA. Novel Ethanol- and 5-Hydroxymethyl Furfural-Stimulated beta-Glucosidase Retrieved From a Brazilian Secondary Atlantic Forest Soil Metagenome. FRONTIERS IN MICROBIOLOGY, v. 9, OCT 29 2018. Web of Science Citations: 2. (15/04309-1, 16/05472-6, 16/17582-0, 16/06323-4)
DE FRIAS, ULYSSES AMANCIO; BONIFACIO PEREIRA, GREICY KELLY; GUAZZARONI, MARIA-EUGENIA; SILVA-ROCHA, RAFAEL. Boosting Secondary Metabolite Production and Discovery through the Engineering of Novel Microbial Biosensors. BIOMED RESEARCH INTERNATIONAL, 2018. Web of Science Citations: 1. (15/04309-1, 12/22921-8)
WESTMANN, CAUA ANTUNES; GUAZZARONI, MARA-EUGENIA; SILVA-ROCHA, RAFAEL. Engineering Complexity in Bacterial Regulatory Circuits for Biotechnological Applications. MSYSTEMS, v. 3, n. 2, SI, MAR-APR 2018. Web of Science Citations: 1. (15/04309-1, 16/05472-6, 12/22921-8)
AMORES, GERARDO RUIZ; DE LAS HERAS, AITOR; SANCHES-MEDEIROS, ANANDA; ELFICK, ALISTAIR; SILVA-ROCHA, RAFAEL. Systematic identification of novel regulatory interactions controlling biofilm formation in the bacterium Escherichia coli. SCIENTIFIC REPORTS, v. 7, DEC 1 2017. Web of Science Citations: 3. (15/22386-3, 12/22921-8)
OLIVEIRA MONTEIRO, LUMMY MARIA; ARRUDA, LETICIA MAGALHAES; SILVA-ROCHA, RAFAEL. Emergent Properties in Complex Synthetic Bacterial Promoters. ACS SYNTHETIC BIOLOGY, v. 7, n. 2, p. 602-612, FEB 2018. Web of Science Citations: 3. (12/22921-8, 16/19179-9)
ALVES, LUANA DE FATIMA; WESTMANN, CAUA ANTUNES; LOVATE, GABRIEL LENCIONI; VIANA DE SIQUEIRA, GUILHERME MARCELINO; BORELLI, TIAGO CABRAL; GUAZZARONI, MARIA-EUGENIA. Metagenomic Approaches for Understanding New Concepts in Microbial Science. INTERNATIONAL JOURNAL OF GENOMICS, 2018. Web of Science Citations: 4. (15/04309-1, 16/05472-6, 17/20818-9, 16/06323-4)
AMORES, GERARDO RUIZ; GUAZZARONI, MARIA-EUGENIA; ARRUDA, LETICIA MAGALHAES; SILVA-ROCHA, RAFAEL. Recent Progress on Systems and Synthetic Biology Approaches to Engineer Fungi As Microbial Cell Factories. CURRENT GENOMICS, v. 17, n. 2, p. 85-98, 2016. Web of Science Citations: 2. (15/04309-1, 12/22921-8)
GUPTA, VIJAI KUMAR; STEINDORFF, ANDREI STECCA; DE PAULA, RENATO GRACIANO; SILVA-ROCHA, RAFAEL; MACH-AIGNER, ASTRID R.; MACH, ROBERT L.; SILVA, ROBERTO N.. The Post-cenomic Era of Trichoderma reesei: What's Next?. TRENDS IN BIOTECHNOLOGY, v. 34, n. 12, p. 970-982, DEC 2016. Web of Science Citations: 17. (14/23653-2, 12/22921-8)
ARRUDA, LETICIA M.; MONTEIRO, LUMMY M. O.; SILVA-ROCHA, RAFAEL. The Chromobacterium violaceum ArsR Arsenite Repressor Exerts Tighter Control on Its Cognate Promoter Than the Escherichia coil System. FRONTIERS IN MICROBIOLOGY, v. 7, NOV 21 2016. Web of Science Citations: 2. (12/22921-8)
SANCHES-MEDEIROS, ANANDA; OLIVEIRA MONTEIRO, LUMMY MARIA; SILVA-ROCHA, RAFAEL. Calibrating Transcriptional Activity Using Constitutive Synthetic Promoters in Mutants for Global Regulators in Escherichia coli. INTERNATIONAL JOURNAL OF GENOMICS, 2018. Web of Science Citations: 2. (15/22386-3, 12/22921-8, 16/19179-9)
AMARELLE, VANESA; SANCHES-MEDEIROS, ANANDA; SILVA-ROCHA, RAFAEL; GUAZZARONI, MARIA-EUGENIA. Expanding the Toolbox of Broad Host-Range Transcriptional Terminators for Proteobacteria through Metagenomics. ACS SYNTHETIC BIOLOGY, v. 8, n. 4, p. 647-654, APR 2019. Web of Science Citations: 1. (18/04810-0, 15/04309-1)
NORA, LUISA CZAMANSKI; WESTMANN, CAUA ANTUNES; MARTINS-SANTANA, LEONARDO; ALVES, LUANA DE FATIMA; OLIVEIRA MONTEIRO, LUMMY MARIA; GUAZZARONI, MARIA-EUGENIA; SILVA-ROCHA, RAFAEL. The art of vector engineering: towards the construction of next-generation genetic tools. MICROBIAL BIOTECHNOLOGY, v. 12, n. 1, p. 125-147, JAN 2019. Web of Science Citations: 5. (16/03763-3, 16/19179-9, 15/04309-1, 12/22921-8, 17/17924-1, 16/06323-4, 16/05472-6)
CAMPOS ANTONIETO, AMANDA CRISTINA; VIEIRA NOGUEIRA, KAROLINE MARIA; DE PAULA, RENATO GRACIANO; NORA, LUFSA CZAMANSKI; ANZOLINI CASSIANO, MURILO HENRIQUE; GUAZZARONI, MARIA-EUGENIA; ALMEIDA, FAUSTO; DA SILVA, THIAGO APARECIDO; RIES, LAURE NICOLAS ANNICK; DE ASSIS, LEANDRO JOSE; et al. A Novel Cys2His2 Zinc Finger Homolog of AZF1 Modulates Holocellulase Expression in Trichoderma reesei. MSYSTEMS, v. 4, n. 4, JUL-AUG 2019. Web of Science Citations: 1. (16/03322-7, 18/03766-8, 16/23233-9, 16/03763-3, 15/04309-1, 12/22921-8, 17/04217-5, 15/09553-8)
AMORES, GERARDO RUIZ; GUAZZARONI, MARIA-EUGENIA; ARRUDA, LETICIA MAGALHAES; SILVA-ROCHA, RAFAEL. Recent Progress on Systems and Synthetic Biology Approaches to Engineer Fungi As Microbial Cell Factories. CURRENT GENOMICS, v. 17, n. 2, p. 85-98, 2016. Web of Science Citations: 2. (15/04309-1, 12/22921-8)
GUPTA, VIJAI KUMAR; STEINDORFF, ANDREI STECCA; DE PAULA, RENATO GRACIANO; SILVA-ROCHA, RAFAEL; MACH-AIGNER, ASTRID R.; MACH, ROBERT L.; SILVA, ROBERTO N.. The Post-cenomic Era of Trichoderma reesei: What's Next?. TRENDS IN BIOTECHNOLOGY, v. 34, n. 12, p. 970-982, DEC 2016. Web of Science Citations: 17. (14/23653-2, 12/22921-8)
ARRUDA, LETICIA M.; MONTEIRO, LUMMY M. O.; SILVA-ROCHA, RAFAEL. The Chromobacterium violaceum ArsR Arsenite Repressor Exerts Tighter Control on Its Cognate Promoter Than the Escherichia coil System. FRONTIERS IN MICROBIOLOGY, v. 7, NOV 21 2016. Web of Science Citations: 2. (12/22921-8)
OLIVEIRA MONTEIRO, LUMMY MARIA; ARRUDA, LETICIA MAGALHAES; SANCHES-MEDEIROS, ANANDA; MARTINS-SANTANA, LEONARDO; DE FATIMA ALVES, LUANA; DEFELIPE, LUCAS; GUSTAVO TURJANSKI, ADRIAN; GUAZZARONI, MARIA-EUGENIA; DE LORENZO, VICTOR; SILVA-ROCHA, RAFAEL. Reverse Engineering of an Aspirin-Responsive Transcriptional Regulator in Escherichia coli. ACS SYNTHETIC BIOLOGY, v. 8, n. 8, p. 1890-1900, AUG 2019. Web of Science Citations: 1. (16/19179-9, 15/04309-1, 12/22921-8, 17/17924-1, 18/04810-0, 16/06323-4)
ALVES, LUANA DE FATIMA; MELEIRO, LUANA PARRAS; SILVA, ROBERTO N.; WESTMANN, CAUA ANTUNES; GUAZZARONI, MARIA-EUGENIA. Novel Ethanol- and 5-Hydroxymethyl Furfural-Stimulated beta-Glucosidase Retrieved From a Brazilian Secondary Atlantic Forest Soil Metagenome. FRONTIERS IN MICROBIOLOGY, v. 9, OCT 29 2018. Web of Science Citations: 2. (15/04309-1, 16/05472-6, 16/17582-0, 16/06323-4)
AMORES, GERARDO RUIZ; DE LAS HERAS, AITOR; SANCHES-MEDEIROS, ANANDA; ELFICK, ALISTAIR; SILVA-ROCHA, RAFAEL. Systematic identification of novel regulatory interactions controlling biofilm formation in the bacterium Escherichia coli. SCIENTIFIC REPORTS, v. 7, DEC 1 2017. Web of Science Citations: 3. (15/22386-3, 12/22921-8)
OLIVEIRA MONTEIRO, LUMMY MARIA; ARRUDA, LETICIA MAGALHAES; SILVA-ROCHA, RAFAEL. Emergent Properties in Complex Synthetic Bacterial Promoters. ACS SYNTHETIC BIOLOGY, v. 7, n. 2, p. 602-612, FEB 2018. Web of Science Citations: 3. (12/22921-8, 16/19179-9)
ALVES, LUANA DE FATIMA; WESTMANN, CAUA ANTUNES; LOVATE, GABRIEL LENCIONI; VIANA DE SIQUEIRA, GUILHERME MARCELINO; BORELLI, TIAGO CABRAL; GUAZZARONI, MARIA-EUGENIA. Metagenomic Approaches for Understanding New Concepts in Microbial Science. INTERNATIONAL JOURNAL OF GENOMICS, 2018. Web of Science Citations: 4. (15/04309-1, 16/05472-6, 17/20818-9, 16/06323-4)
NORA, LUISA CZAMANSKI; WESTMANN, CAUA ANTUNES; GUAZZARONI, MARIA-EUGENIA; SIDDAIAH, CHANDRANAYAKA; GUPTA, VIJAI KUMAR; SILVA-ROCHA, RAFAEL. Recent advances in plasmid-based tools for establishing novel microbial chassis. BIOTECHNOLOGY ADVANCES, v. 37, n. 8, DEC 2019. Web of Science Citations: 1. (15/04309-1, 16/05472-6, 12/22921-8, 16/03763-3)
DE FRIAS, ULYSSES AMANCIO; BONIFACIO PEREIRA, GREICY KELLY; GUAZZARONI, MARIA-EUGENIA; SILVA-ROCHA, RAFAEL. Boosting Secondary Metabolite Production and Discovery through the Engineering of Novel Microbial Biosensors. BIOMED RESEARCH INTERNATIONAL, 2018. Web of Science Citations: 1. (15/04309-1, 12/22921-8)
NORA, LUISA CZAMANSKI; WEHRS, MAREN; KIM, JOONHOON; CHENG, JAN-FANG; TARVER, ANGELA; SIMMONS, BLAKE A.; MAGNUSON, JON; HARMON-SMITH, MIRANDA; SILVA-ROCHA, RAFAEL; GLADDEN, JOHN M.; et al. A toolset of constitutive promoters for metabolic engineering of Rhodosporidium toruloides. Microbial Cell Factories, v. 18, JUN 29 2019. Web of Science Citations: 0. (12/22921-8, 18/02227-6)
WESTMANN, CAUA ANTUNES; GUAZZARONI, MARA-EUGENIA; SILVA-ROCHA, RAFAEL. Engineering Complexity in Bacterial Regulatory Circuits for Biotechnological Applications. MSYSTEMS, v. 3, n. 2, SI, MAR-APR 2018. Web of Science Citations: 1. (15/04309-1, 16/05472-6, 12/22921-8)