Isabel Rocha
- Research Line: Industrial Biotechnology and Bioengineering
- Research Group: BIOSYSTEMS
- 253 604 414 (office)
- irocha@deb.uminho.pt
- https://www.ceb.uminho.pt/People/Profile/irocha
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
- 2018 - 2021: MIXED-UP - Targeting pathogenesis and engineering cell factories: developing mixed regulatory-metabolic genomic models in yeasts (PI)
- 2017 - 2021: Biodata.pt - Portuguese Biological Data Network (PI)
- 2017 - 2021: BBRI - Biomass and Bioenergy Research Infrastructure (Team Member)
- 2016 - 2020: DD-Decaf - Bioinformatics Services for Data-Driven Design of Cell Factories and Communities (PI)
- 2016 - 2018: SISBI - Intelligent decision support system for Industrial Biotechnology (Team Member)
- 2015 - 2018: DYNAMICS - Analysis and optimization of industrial microorganisms under dynamic process conditions (PI)
- 2014 - 2017: DeYeast Library - Designer yeast strain library optimized for metabolic engineering applications (PI)
- 2012 - 2015: PEM - Platform for Metabolic Engineering (PI)
- 2012 - 2015: Metabolic Circuits - Finding the naturally evolved design principles of prevalent metabolic circuits (PI)
- 2011 - 2014: ToMEGIM - Computational Tools for Metabolic Engineering using Genome-scale Integrated Models (Team Member)
- 2011 - 2012: UM/UVIGO - Desenvolvimento de técnicas de mineração de dados para diagnóstico clínico usando conhecimento biológico (Team Member)
- 2011 - 2012: UM/CSIC - Synthetic biology approaches to metabolic engineering of bacterial catalysts for the valorization of industrial and urban waste (Team Member)
- 2011 - 2012: UM/UFSCAR - Biologia de Sistemas e Engenharia de Bioprocessos e Sistemas: Capacitação de Pessoal nas Fronteiras da Biotecnologia Industrial (Team Member)
- 2011 - 2013: PNEUMONIAE - In silico reconstruction of Streptococcus pneumoniae cellular networks and their impact on virulence (PI)
- 2010 - 2010: FLAD - TEXAS TECH - Metabolic Engineering and Modeling of Recombinant Microorganisms for Cellulosic Biofuels Production (Team Member)
- 2010 - 2013: SYNBIOBACTHER - Synthetic biology approaches to engineer "therapeutic" bacteria (Team Member)
- 2010 - 2013: HeliSysBio - Molecular Systems Biology Helicobacter pylori (PI)
- 2010 - 2013: AshByofactory - Ashbya gossypii: a systems metabolic engineered cell factory (Team Member)
- 2009 - 2012: MPP-SYSBIOL - Bridging Systems and Synthetic Biology for the development of Improved Microbial Cell Factories (Team Member)
- 2008 - 2011: SYSINBIO - Systems Biology as a Driver for Industrial Biotechnology (PI)
- 2008 - 2010: PROPOLIS - Efficacy of propolis in the control of American foul brood: evaluation in controled areas (PI)
- 2008 - 2009: CRUP-UAB - Desenvolvimento de estimadores para monitorização e controlo da taxa específica de crescimento em processos biotecnológicos (Team Member)
- 2007 - 2010: DUPONT - Development of a user-friendly software platform for the rational design of improved microbial strains (PI)
- 2007 - 2009: FLAD - UCIRVINE - Machine Learning Applications in Systems Biology Research (Team Member)
- 2007 - 2008: MABexpress - Desenvolvimento de uma plataforma tecnológica para a produção de anticorpos monoclonais e seus derivados para terapia anticancerígena (Team Member)
- 2006 - 2012: MIT-Portugal Program - Bioengineering Systems (Phase 1) (Team Member)
- 2005 - 2008: recSysBio - A Systems Biology approach for optimization of recombinant fermentation processes (Team Member)
- 2005 - 2008: MOBioPro - Nature-based computation in the modeling and optimization of biotechnological processes (Team Member)
- 2004 - 2007: BIOLIFE - Produção de Ingredientes para Alimentos Funcionais: Galacto-oligossacáridos e Fructo-oligossacáridos (Team Member)
- 1998 - 2001: PROTEXPRESS - Construction of a general bacterial gene expression system, for the production and purification of recombinant human proteins of high commercial and therapeutic value - Cloning of Human Alpha Interferon (Team Member)
Past Supervision of Researchers
- Adelaide Correia Braga - Doctoral Researcher
- Adilson José da Silva - Doctoral Researcher
- Ana Cláudia Fernandes de Carvalho - Research Grant
- Ana Cristina da Silva Esperança Guimarães Pinto Leite - Research Grant
- Ana Margarida Antunes Coelho Alão de Freitas - Master Student
- Ana Margarida Antunes Coelho Alão de Freitas - Research Grant
- Ana Patrícia Moreira Lima - Research Grant
- Ana Rita Castro Carvalho - PhD Student
- Ana Rita Marques da Silva - Collaborator (Non PhD)
- Ana Sofia Araújo Ferreira - PhD Student
- André Charrua de Sousa - Research Grant
- Anis Hamdi - PhD Student
- Bruna Soares Fernandes - Doctoral Researcher
- Bruno Miguel Machado Silva - Master Student
- Bruno Teixeira Pereira - Research Grant
- Carla Andreia Freixo Portela - PhD Student
- Carlos Alberto Galeano Suarez - PhD Student (External)
- Carlos Daniel Moutinho Luz Machado - Doctoral Researcher
- Carlos Daniel Moutinho Luz Machado - PhD Student
- Christopher Borges Costa - Research Grant
- Cíntia Regina Sargo - PhD Student (External)
- Cristiana da Silva Faria - Doctoral Researcher
- Cristiana da Silva Faria - PhD Student
- Daniel Gonçalves Gomes - Research Grant
- Daniela Matilde Marques Correia - PhD Student
- Diana Carolina Tusso Pinzon - PhD Student (External)
- Fábio Soares Ramalho - Research Grant
- Fernando João Pereira da Cruz - Master Student
- Filipe Alexandre Wang Liu - PhD Student
- Filipe Alexandre Wang Liu - Research Grant
- Hélder Moisés Gonçalves Pinheiro Lopes - PhD Student
- Hugo Samuel Oliveira Costa - Research Grant
- Hüseyin Demirci - Doctoral Researcher
- Inti Doraci Cavalcanti Montano - PhD Student (External)
- Joana Filipa Azevedo Oliveira - Collaborator (Non PhD)
- Joana Filipa Azevedo Oliveira - Master Student
- Joana Filipa Azevedo Oliveira - PhD Student
- Joana Rute Calça Xavier - Doctoral Researcher
- Joana Rute Calça Xavier - PhD Student
- João Pedro Leonor Fernandes Saraiva - Research Grant
- José Jorge Sampaio Bastos - Research Grant
- José Miguel Dantas de Sousa - Research Grant
- José Miguel Gonçalves Dias - Master Student
- José Pedro Lopes Faria - PhD Student
- José Roberto Fuzer Neto - PhD Student
- José Vítor de Castro Vieira - Master Student
- José Vítor de Castro Vieira - Research Grant
- Lucinda Janete da Silva Bessa - PhD Student (External)
- Márcio Domingos Moreira de Sousa - Master Student
- Marisa de Lurdes da Rocha e Cunha - Research Grant
- Marta Sofia Costa Sampaio - Research Grant
- Miguel Ângelo Fernandes da Silva - Research Grant
- Oscar Manuel Lima Dias - Doctoral Researcher
- Oscar Manuel Lima Dias - Master Student
- Oscar Manuel Lima Dias - PhD Student
- Oscar Manuel Lima Dias - Research Grant
- Patrícia Marlene Alves Ferreira - Collaborator (PhD)
- Patrícia Raquel Pinheiro Pitrez Pereira - PhD Student
- Patrícia Sofia Sousa Dias - PhD Student
- Paul Drescher - PhD Student
- Paulo Jorge Lopes Maia da Silva - Collaborator (PhD)
- Paulo Jorge Lopes Maia da Silva - PhD Student
- Pedro Santos Barbosa - Collaborator (Non PhD)
- Pedro Tiago Evangelista - Collaborator (PhD)
- Pedro Tiago Evangelista - PhD Student
- Rafael de Castro Carreira - Collaborator (PhD)
- Rafael de Castro Carreira - PhD Student
- Rafael Ferraz Alves - PhD Student (External)
- Rafael Sousa Costa - PhD Student
- Romeu Filipe Nobre Viana - Research Grant
- Rui Manuel dos Santos Nunes - Master Student
- Rui Manuel dos Santos Nunes - Research Grant
- Rui Miguel Pinheiro da Silva Pereira - PhD Student
- Sandra Maria Gomes de Carvalho - Master Student
- Sara Alexandra Gomes Correia - Doctoral Researcher
- Sara Alexandra Gomes Correia - Master Student
- Sara Alexandra Sá Martins Dias - Integrated Master Student
- Sarah Lieder - Research Grant
- Sónia Madalena Azevedo Carneiro - Collaborator (PhD)
- Sónia Madalena Azevedo Carneiro - Doctoral Researcher
- Sónia Madalena Azevedo Carneiro - PhD Student
- Sophia Torres Santos - Master Student
- Sophia Torres Santos - Research Grant
- Steven Sterling Sheridan - Master Student
- Steven Sterling Sheridan - Research Grant
- Sushil Kumar Shakyawar - PhD Student
- Telma Adriana Pereira Afonso - Research Grant
- Tiago Filipe Coelho Resende - Doctoral Researcher
- Tiago Filipe Coelho Resende - Master Student
- Tiago Filipe Coelho Resende - PhD Student
- Tiago Filipe Coelho Resende - Research Grant
- Vítor Damião Baixinho da Silva - Research Grant
- Zita Irene Tany Antoinette Soons - Doctoral Researcher
Recent Publications
| 1 |
A genome-scale metabolic model for the human pathogen Candida parapsilosis and early identification of putative novel antifungal drug targets
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| 2 |
Model-guided development of an evolutionarily stable yeast chassis
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| 3 |
Inclusion of maintenance energy improves the intracellular flux predictions of CHO
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| 4 |
Enhancing acetic acid and 5-hydroxymethyl furfural tolerance of C. saccharoperbutylacetonicum through adaptive laboratory evolution
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| 5 |
Genome-scale metabolic model of the human pathogen Candida albicans: a promising platform for drug target prediction
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| 6 |
A review of methods for the reconstruction and analysis of integrated genome-scale models of metabolism and regulation
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| 7 |
Metabolic engineering strategies for butanol production in Escherichia coli
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| 8 |
Key challenges in designing CHO chassis platforms
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| 9 |
Genome-wide sequencing and metabolic annotation of Pythium irregulare CBS 494.86: understanding Eicosapentaenoic acid production
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| 10 |
Discovery and implementation of a novel pathway for n-butanol production via 2-oxoglutarate
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| 11 |
SamPler - a novel method for selecting parameters for gene functional annotation routines
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| 12 |
iDS372, a phenotypically reconciled model for the metabolism of Streptococcus pneumoniae strain R6
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| 13 |
Comparison of pathway analysis and constraint-based methods for cell factory design
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| 14 |
Turnover dependent phenotypic simulation: a quantitative constraint-based simulation method that accommodates all main strain design strategies
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| 15 |
Mapping Salmonella typhimurium pathways using 13C Metabolic Flux Analysis
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| 16 |
Identification and microbial production of the raspberry phenol salidroside that is active against Huntington's disease
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| 17 |
Modulation of the central carbon metabolism of Corynebacterium glutamicum improves malonyl-CoA availability and increases plant polyphenol synthesis
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| 18 |
Production of mannosylglycerate in Saccharomyces cerevisiae by metabolic engineering and bioprocess optimization
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| 19 |
Metabolic models and gene essentiality data reveal essential and conserved metabolism in prokaryotes
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| 20 |
Yeast chassis design for production of dicarboxylic acids
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CEB is supported by the Portuguese Foundation for Science and Technology (FCT) under the scope of the strategic funding UIDB/04469/2020.
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