Where Ideas Grow
Filipe Pinto
Associate Researcher

Filipe Pinto (born 1981) has a first degree (2003) and an MSc (2009) in Biochemistry, and a PhD in Biology in the field of Synthetic Biology (2013, Approved with Distinction), all from the University of Porto (UP) in Portugal. He did an Erasmus internship at BRC (Uni. Szeged, HU) in his final college year and since then he was involved in research activities in the fields of molecular microbiology and protein science. He studied phage-triggered bacterial autolysis (2004, Uni. Lisbon, PT), integrated a group of molecular structure of proteins (2005, IBMC/UP, PT) and from 2006 to 2015 he focused his research in the molecular biology of cyanobacteria (IBMC/UP, PT). During this period, he integrated the research team led by Paula Tamagnini and participated in two Synthetic Biology European projects: the pioneer FP6 EU-project “BioModularH2” as a PhD student, and the FP7 EU-project “CyanoFactory” as a Postdoc. He was also involved in the preparation of proposals of funded R&D projects and was part of the research team performing the work; he contributed to the creation of the ideas as well as in writing the proposals. From 2016 to 2021, he was a Postdoctoral Research Associate in the field of Synthetic Biology at the University Edinburgh (UK), accumulating lab manager functions. During this period, his research interests included the design and engineering of new scalable biological circuits by developing and combining libraries of orthogonal split inteins (“protein ligases”), optimized extracytoplasmic function (ECF) sigma factors and orthogonal transcription repressors. Currently, F Pinto is an Assistant Researcher (CEEC- Individual Call – 3rd Edition) at the Bioengineering & Synthetic Microbiology group (i3S/UP, PT), developing his research in the filed of cyanobacterial Synthetic Biology.

With 15+ years of research experience, F Pinto co-authored his first paper while in his degree and, in total, he published 17 papers (4 of which as lead author and 1 as co-first author) in well-established international peer-reviewed scientific journals (with an accumulated IF of over 120), with 560+ citations and h-index 11 (Publons ResearcherID J-9448-2013). Six of the papers were published in the last 5 years and he was lead author in one publication that resulted in granted European patents. The work he developed in this period also resulted in two research articles published in Nature Communications, a highly regarded peer-reviewed journal. He was co-guest editor in a Synthetic Biology special issue in the MDPI journal Life (ISSN 2075-1729). He participated in several national and international meetings where he presented 4 oral communications and 29+ conference posters, including two prestigious Gordon Research Conferences on Synthetic Biology. Regarding F Pinto’s pedagogical role, he co-supervised an undergraduate student within the FP7 EU-project and he was involved in the supervision of several students, including high-school, undergraduate (including 2 Erasmus) and master students. He was also one of the coordinators of the RT-qPCR course, part of the advanced training provided by the Doctoral Program in Molecular and Cell Biology (IBMC, ICBAS, FCUP; UP) in the academic years of 2013-14 and 2014-15. From 2009 to 2015, he gave invited talks in the Environmental Biotechnology syllabus from the Master in Ecology, Environment and Territory (FCUP) and the integrated Master in Bioengineering (FEUP). From 2010 to 2015, F Pinto was part of “Embaixadores da Ciência”, a group of IBMC/INEB researchers engaged in science dissemination in schools. He was awarded a 1st poster prize and 4 conference travel awards, and the prize “Prémio Fundação Eng. António de Almeida” that distinguishes the best FCUP PhD thesis in the areas of Life Sciences, Agricultural Sciences and Landscape Architecture. He is inventor in recently granted patents describing the neutral sites technology in the cyanobacterium Synechocystis (European Patents EP3106521 & EP3461897).

Selected Publications

Pacheco C.C., Pinto F.,
Design and validation of tools for microbial synthetic biology applications. Life11(8):, 2021. [Journal: Editorial] [IF: 3.8 (*)]
DOI: 10.3390/life11080739 SCOPUS: 85111699657.


Pinto F., Thornton E.L., Wang B.,
An expanded library of orthogonal split inteins enables modular multi-peptide assemblies. Nature Communications11(1):, 2020. [Journal: Article] [CI: 10] [IF: 14.9]
DOI: 10.1038/s41467-020-15272-2 SCOPUS: 85082186261.


Wan X., Pinto F., Yu L., Wang B.,
Synthetic protein-binding DNA sponge as a tool to tune gene expression and mitigate protein toxicity. Nature Communications11(1):, 2020. [Journal: Article] [CI: 2] [IF: 14.9]
DOI: 10.1038/s41467-020-19552-9 SCOPUS: 85096522603.


Lindblad P., Fuente D., Borbe F., Cicchi B., Conejero J.A., Couto N., Celešnik H., Diano M.M., Dolinar M., Esposito S., Evans C., Ferreira E.A., Keller J., Khanna N., Kind G., Landels A., Lemus L., Noirel J., Ocklenburg S., Oliveira P., Pacheco C.C., Parker J.L., Pereira J., Pham T.K., Pinto F., Rexroth S., Rögner M., Schmitz H.J., Benavides A.M.S., Siurana M., Tamagnini P., Touloupakis E., Torzillo G., Urchueguía J.F., Wegelius A., Wiegand K., Wright P.C., Wutschel M., Wünschiers R.,
CyanoFactory, a European consortium to develop technologies needed to advance cyanobacteria as chassis for production of chemicals and fuels. Algal Research41:, 2019. [Journal: Review] [CI: 6] [IF: 4]
DOI: 10.1016/j.algal.2019.101510 SCOPUS: 85065805375.


Pacheco C.C., Büttel Z., Pinto F., Rodrigo G., Carrera J., Jaramillo A., Tamagnini P.,
Modulation of Intracellular O2 Concentration in Escherichia coli Strains Using Oxygen Consuming Devices. ACS Synthetic Biology7(7):1742-1752, 2018. [Journal: Article] [CI: 1] [IF: 5,6]
DOI: 10.1021/acssynbio.7b00428 SCOPUS: 85049323685.


Ferreira E.A., Pacheco C.C., Pinto F., Pereira J., Lamosa P., Oliveira P., Kirov B., Jaramillo A., Tamagnini P.,
Expanding the toolbox for Synechocystis sp. PCC 6803: Validation of replicative vectors and characterization of a novel set of promoters. Synthetic Biology3(1):, 2018. [Journal: Article] [CI: 24]
DOI: 10.1093/synbio/ysy014 SCOPUS: 85091655430.


Pinto F., Pacheco C.C., Oliveira P., Montagud A., Landels A., Couto N., Wright P.C., Urchueguía J.F., Tamagnini P.,
Improving a Synechocystis-based photoautotrophic chassis through systematic genome mapping and validation of neutral sites. DNA Research22(6):425-437, 2015. [Journal: Article] [CI: 25] [IF: 5,3]
DOI: 10.1093/dnares/dsv024 SCOPUS: 84950258160.


Pinto F., Pacheco C.C., Ferreira D., Moradas-Ferreira P., Tamagnini P.,
Selection of suitable reference genes for RT-qPCR analyses in cyanobacteria. PLoS ONE7(4):, 2012. [Journal: Article] [CI: 92] [IF: 3,7]
DOI: 10.1371/journal.pone.0034983 SCOPUS: 84859347775.


Pinto F., van Elburg K.A., Pacheco C.C., Lopo M., Noirel J., Montagud A., Urchueguía J.F., Wright P.C., Tamagnini P.,
Construction of a chassis for hydrogen production: Physiological and molecular characterization of a synechocystis sp. PCC 6803 mutant lacking a functional bidirectional hydrogenase. Microbiology158(2):448-464, 2012. [Journal: Article] [CI: 22] [IF: 2,9]
DOI: 10.1099/mic.0.052282-0 SCOPUS: 84856690893.


Tamagnini P., Leitão E., Oliveira P., Ferreira D., Pinto F., Harris D.J., Heidorn T., Lindblad P.,
Cyanobacterial hydrogenases: Diversity, regulation and applications. FEMS Microbiology Reviews31(6):692-720, 2007. [Journal: Review] [CI: 261] [IF: 9,3]
DOI: 10.1111/j.1574-6976.2007.00085.x SCOPUS: 35448935699.