Isabel Rocha



Career

  • 2019 - 2021: Principal Researcher (Non-Tenure Track), Universidade Nova de Lisboa
  • 2011 - 2019: Assistant Professor, Universidade do Minho
  • 2006 - 2011: Invited Assistant Professor, Universidade do Minho
  • 2004 - 2006: Invited Lecturer, Universidade do Minho

Qualifications

  • 2003: PhD Program in Chemical and Biological Engineering, Universidade do Minho

Roles and Responsibilities

  • Since  2013: Member of the Editorial Board of "Frontiers in Bioengineering and Biotechnology - Synthetic Biology"
  • Since  2011: Member of the Scientific Steering Committee of Department, Department of Biological Engineering
  • 2010 - 2013: Program Director, Master Program in Bioinformatics - Biological Sciences
  • 2008 - 2008: APBio
  • Since  2007: Member of Program Studies Steering Committee, PhD Program in Bioengineering

Honors and Awards

  • 2011: Best Poster Award at 5th Annual Workshop on the Business-Government Interface: Systems and Synthetic Biology, Universidade do Minho, Braga. Title: Exploring the gap between dynamic and constraint-based models of metabolism.
  • 2011 - 2019: UMinho Faculty member at Centre of Biological Engineering
  • 1998 - 2003: Model-based strategies for computer-aided operation of recombinant E. coli fermentation

Past Projects

Past Supervision of Researchers


Recent Publications

1
A genome-scale metabolic model for the human pathogen Candida parapsilosis and early identification of putative novel antifungal drug targets
  • Genes, 13(2), 303, 2022
2
  • Pereira, Filipa; Lopes, Hélder; Maia, Paulo; Meyer, Britta; Nocon, Justyna; Jouhten, Paula; Konstantinidis, Dimitrios; Kafkia, Eleni; Rocha, Miguel; Kötter, Peter; Rocha, Isabel; Patil, Kiran R
Model-guided development of an evolutionarily stable yeast chassis
  • Molecular Systems Biology, 17(7), e10253, 2021
3
  • Széliová, Diana; Štor, Jerneja; Thiel, Isabella; Weinguny, Marcus; Hanscho, Michael; Lhota, Gabriele; Borth, Nicole; Zanghellini, Jürgen; Ruckerbauer, David E.; Rocha, Isabel
Inclusion of maintenance energy improves the intracellular flux predictions of CHO
  • PLoS Computational Biology, 17(6), e1009022, 2021
4
  • Alves, Rafael A.; Zetty-Arenas, Ana M.; Demirci, Hüseyin; Dias, Oscar; Rocha, Isabel; Basso, Thiago O.; Freitas, Sindelia
Enhancing acetic acid and 5-hydroxymethyl furfural tolerance of C. saccharoperbutylacetonicum through adaptive laboratory evolution
  • Process Biochemistry, 101, 179-189, 2021
5
  • Viana, Romeu; Dias, Oscar; Lagoa, Davide; Galocha, Mónica; Rocha, Isabel; Teixeira, Miguel Cacho
Genome-scale metabolic model of the human pathogen Candida albicans: a promising platform for drug target prediction
  • Journal of Fungi, 6(3), 171, 2020
6
A review of methods for the reconstruction and analysis of integrated genome-scale models of metabolism and regulation
  • Biochemical Society Transactions, 2020(5), 1889-1903, 2020
7
  • Ferreira, Sofia; Pereira, Rui; Wahl, S. Aljoscha; Rocha, Isabel
Metabolic engineering strategies for butanol production in Escherichia coli
  • Biotechnology and Bioengineering, 117(8), 2571v-2587, 2020
8
Key challenges in designing CHO chassis platforms
  • Processes, 8(6), 643, 2020
9
  • Fernandes, Bruna S.; Dias, Oscar; Costa, Gisela; Kaupert Neto, Antonio A.; Resende, Tiago F.; Oliveira, Juliana V. C.; Riaño-Pachón, Diego M.; Zaiat, Marcelo; Pradella, José G. C.; Rocha, Isabel
Genome-wide sequencing and metabolic annotation of Pythium irregulare CBS 494.86: understanding Eicosapentaenoic acid production
  • BMC Biotechnology, 19(41), 2019
10
  • Ferreira, Sofia; Pereira, Rui; Liu, Filipe; Vilaça, Paulo; Rocha, Isabel
Discovery and implementation of a novel pathway for n-butanol production via 2-oxoglutarate
  • Biotechnology for Biofuels, 12(230), 2019
11
SamPler - a novel method for selecting parameters for gene functional annotation routines
  • BMC Bioinformatics, 20(454), 2019
12
iDS372, a phenotypically reconciled model for the metabolism of Streptococcus pneumoniae strain R6
  • Frontiers in Microbiology, 10(1283), 2019
13
Comparison of pathway analysis and constraint-based methods for cell factory design
  • BMC Bioinformatics, 20(350), 2019
14
Turnover dependent phenotypic simulation: a quantitative constraint-based simulation method that accommodates all main strain design strategies
  • ACS Synthetic Biology, 8(5), 976-988, 2019
15
Mapping Salmonella typhimurium pathways using 13C Metabolic Flux Analysis
  • Metabolic Engineering, 52, 303-314, 2019
16
  • Kallscheuer, Nicolai; Menezes, Regina; Foito, Alexandre; Henriques da Silva, Marcelo D.; Braga, Adelaide; Dekker, Wijbrand; Sevillano, David Méndez; Rosado-Ramos, Rita; Jardim, Carolina; Oliveira, Joana A.; Ferreira, Patrícia; Rocha, Isabel; Silva, Rita M.; Sousa, Márcio; Allwood, James William; Bott, Michael; Faria, Nuno; Stewart, Derek; Ottens, Marcel; Naesby, Michael; Santos, Claudia Nunes dos; Marienhagen, Jan
Identification and microbial production of the raspberry phenol salidroside that is active against Huntington's disease
  • Plant Physiology, 179(3), 969-985, 2019
17
Modulation of the central carbon metabolism of Corynebacterium glutamicum improves malonyl-CoA availability and increases plant polyphenol synthesis
  • Biotechnology and Bioengineering, 116(6), 1380-1391, 2019
18
Production of mannosylglycerate in Saccharomyces cerevisiae by metabolic engineering and bioprocess optimization
  • Microbial Cell Factories, 17(1), 178, 2018
19
Metabolic models and gene essentiality data reveal essential and conserved metabolism in prokaryotes
  • PLoS Computational Biology, 14(11), 1-23, 2018
20
  • Pereira, F.; Lopes, Hélder; Maia, Paulo; Meyer, B.; Konstantinidis, D.; Kafkia, E.; Kötter, P.; Rocha, Isabel; Patil, K.R.
Yeast chassis design for production of dicarboxylic acids
  • New Biotechnology, 44(Suppl.), S8, 2018
Full List