Centre of Biological Engineering / Centro de Engenharia Biológica

Isabel Rocha

Principal Investigator

Research Line: Industrial Biotechnology and Bioengineering
Research Group: BIOSYSTEMS
253 604 414 (office)
irocha@deb.uminho.pt
http://ceb.uminho.pt/People/Profile/irocha

Career

Since 2019: Principal Investigator, 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 in Chemical and Biological Engineering, Universidade do Minho

Roles and Responsibilities

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

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.

Since 2019: Systems Biology and Metabolic Engineering
2011 - 2019: UMinho Faculty member at Centre of Biological Engineering
1998 - 2003: Model-based strategies for computer-aided operation of recombinant E. coli fermentation

Projects

Research Students

Anis Hamdi - PhD Student
Hüseyin Demirci - Post-Doc
Joana Filipa Azevedo Oliveira - PhD Student
Marta Sofia Costa Sampaio - Research Grant
Patrícia Sofia Sousa Dias - PhD Student
Paul Drescher - PhD Student
Paulo Jorge Lopes Maia da Silva - Collaborator (PhD)
Rafael de Castro Carreira - Collaborator (PhD)
Simão Pedro de Pinho Soares - Collaborator (Non PhD)
Sophia Torres Santos - PhD Student

Recent Publications

1	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
2	Dias, Oscar; Saraiva, João; Faria, Cristiana; Ramirez, Mario; Pinto, Francisco; Rocha, Isabel iDS372, a phenotypically reconciled model for the metabolism of Streptococcus pneumoniae strain R6 Frontiers in Microbiology, 10(1283), 2019
3	Vieira, Vítor; Maia, Paulo; Rocha, Miguel; Rocha, Isabel Comparison of pathway analysis and constraint-based methods for cell factory design BMC Bioinformatics, 20(350), 2019
4	Pereira, Rui; Vilaça, Paulo; Maia, Paulo; Nielsen, Jens; Rocha, Isabel 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
5	Correia, Daniela M.; Sargo, Cíntia R.; Silva, Adilson J.; Santos, Sophia T.; Giordano, Roberto C.; Ferreira, Eugénio C.; Zangirolami, Teresa C.; Ribeiro, Marcelo P.A.; Rocha, Isabel Mapping Salmonella typhimurium pathways using 13C Metabolic Flux Analysis Metabolic Engineering, 52, 303-314, 2019
6	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, Ana Rita; 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
7	Milke, Lars; Ferreira, Patrícia; Kallscheuer, Nicolai; Braga, Adelaide; Vogt, Michael; Kappelmann, Jannick; Oliveira, Joana A.; Silva, Rita M.; Rocha, Isabel; Bott, Michael; Noack, Stephan; Faria, Nuno; Marienhagen, Jan 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
8	Faria, Cristiana; Borges, Nuno; Rocha, Isabel; Santos, Helena Production of mannosylglycerate in Saccharomyces cerevisiae by metabolic engineering and bioprocess optimization Microbial Cell Factories, 17(1), 178, 2018
9	Xavier, Joana C.; Patil, Kiran Raosaheb; Rocha, Isabel Metabolic models and gene essentiality data reveal essential and conserved metabolism in prokaryotes PLoS Computational Biology, 14(11), 1-23, 2018
10	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
11	Braga, Adelaide; Ferreira, Patrícia; Oliveira, Joana A.; Rocha, Isabel; Faria, Nuno Heterologous production of resveratrol in bacterial hosts: current status and perspectives WORLD JOURNAL OF MICROBIOLOGY & BIOTECHNOLOGY, 34(122), 2018
12	Dudnik, Alexey; Almeida, A. Filipa; Andrade, Ricardo; Avila, Barbara; Bañados, Pilar; Barbay, Diane; Bassard, Jean-Etienne; Benkoulouche, Mounir; Bott, Michael; Braga, Adelaide; Breitel, Dario; Brennan, Rex; Bulteau, Laurent; Chanforan, Celine; Costa, Inês; Costa, Rafael S.; Doostmohammadi, Mahdi; Faria, Nuno; Feng, Chengyong; Fernandes, Armando; Ferreira, Patricia; Ferro, Roberto; Foito, Alexandre; Freitag, Sabine; Garcia, Gonçalo; Gaspar, Paula; Godinho-Pereira, Joana; Hamberger, Björn; Hartmann, András; Heider, Harald; Jardim, Carolina; Julien-Laferriere, Alice; Kallscheuer, Nicolai; Kerbe, Wolfgang; Kuipers, Oscar P.; Li, Shanshan; Love, Nicola; Marchetti-Spaccamela, Alberto; Marienhagen, Jan; Martin, Cathie; Mary, Arnaud; Mazurek, Vincent; Meinhart, Camillo; Sevillano, David Méndez; Menezes, Regina; Naesby, Michael; Nørholm, Morten H. H.; Okkels, Finn T.; Oliveira, Joana; Ottens, Marcel; Parrot, Delphine; Pei, Lei; Rocha, Isabel; Rosado-Ramos, Rita; Rousseau, Caroline; Sagot, Marie-France; dos Santos, Claudia Nunes; Schmidt, Markus; Shelenga, Tatiana; Shepherd, Louise; Silva, Rita M.; da Silva, Marcelo Henriques; Stahlhut, Steen Gustav; Simon, Olivier; Solopova, Ana; Sorokin, Artem; Stewart, Derek; Stougie, Leen; Su, Shang; Thole, Vera; Tikhonova, Olga; Trick, Martin; Vain, Philippe; Veríssimo, André; Vila-Santa, Ana; Vinga, Susana; Vogt, Michael; Wang, Liangsheng; Wang, Lijin; Wei, Wei; Youssef, Sandra; Neves, Ana Rute; Forster, Jochen BacHBerry: BACterial Hosts for production of Bioactive phenolics from bERRY fruits Phytochemistry Reviews, 17(2), 291-326, 2018
13	Faria, José P.; Rocha, Miguel; Rocha, Isabel; Henry, Christopher S. Methods for automated genome-scale metabolic model reconstruction Biochemical Society Transactions, 46(4), 931-936, 2018
14	Braga, Adelaide; Silva, M.; Oliveira, Joana A.; Silva, Rita M.; Ferreira, Patrícia; Ottens, M.; Rocha, Isabel; Faria, Nuno An adsorptive bioprocess for production and recovery of resveratrol with Corynebacterium glutamicum Journal of Chemical Technology and Biotechnology, 93(6), 1661-1668, 2018
15	Pereira, Bruno; Miguel, Joana; Vilaça, Paulo; Simão Soares; Rocha, Isabel; Carneiro, Sónia Reconstruction of a genome-scale metabolic model for Actinobacillus succinogenes 130Z BMC Systems Biology, 12(61), 2018
16	Pinu, Farhana R.; Granucci, Ninna; Daniell, James; Han, Ting-Li; Carneiro, Sónia; Rocha, Isabel; Nielsen, Jens; Villas-Boas, Silas G. Metabolite secretion in microorganisms: the theory of metabolic overflow put to the test Metabolomics, 14(4), 43-43, 2018
17	Dias, Oscar; Basso, Thiago O.; Rocha, Isabel; Ferreira, Eugénio C.; Gombert, Andreas K. Quantitative physiology and elemental composition of Kluyveromyces lactis CBS 2359 during growth on glucose at different specific growth rates Antonie van Leeuwenhoek International Journal of General and Molecular Microbiology, 111(2), 183-195, 2018
18	Braga, Adelaide; Oliveira, Joana A.; Silva, Rita M.; Ferreira, Patrícia; Rocha, Isabel; Kallscheuer, Nicolai; Marienhagen, Jan; Faria, Nuno Impact of the cultivation strategy on resveratrol production from glucose in engineered Corynebacterium glutamicum Journal of Biotechnology, 265, 70-75, 2018
19	Lopes, Hélder; Rocha, Isabel Genome-scale modeling of yeast: chronology, applications and critical perspectives FEMS Yeast Research, 17(5), fox050, 2017
20	Vieira, Vitor; Maia, Paulo; Rocha, Isabel; Rocha, Miguel Development of a framework for metabolic pathway analysis-driven strain optimization methods Interdisciplinary Sciences-Computational Life Sciences, 9(1), 46-55, 2017

Full List

Isabel Rocha

Principal Investigator

Career

Qualifications

Roles and Responsibilities

Honors and Awards

Projects

Past Projects

Research Students

Past Students

Recent Publications

Genome-wide sequencing and metabolic annotation of Pythium irregulare CBS 494.86: understanding Eicosapentaenoic acid production

iDS372, a phenotypically reconciled model for the metabolism of Streptococcus pneumoniae strain R6

Comparison of pathway analysis and constraint-based methods for cell factory design

Turnover dependent phenotypic simulation: a quantitative constraint-based simulation method that accommodates all main strain design strategies

Mapping Salmonella typhimurium pathways using 13C Metabolic Flux Analysis

Identification and microbial production of the raspberry phenol salidroside that is active against Huntington's disease

Modulation of the central carbon metabolism of Corynebacterium glutamicum improves malonyl-CoA availability and increases plant polyphenol synthesis

Production of mannosylglycerate in Saccharomyces cerevisiae by metabolic engineering and bioprocess optimization

Metabolic models and gene essentiality data reveal essential and conserved metabolism in prokaryotes

Yeast chassis design for production of dicarboxylic acids

Heterologous production of resveratrol in bacterial hosts: current status and perspectives

BacHBerry: BACterial Hosts for production of Bioactive phenolics from bERRY fruits

Methods for automated genome-scale metabolic model reconstruction

An adsorptive bioprocess for production and recovery of resveratrol with Corynebacterium glutamicum

Reconstruction of a genome-scale metabolic model for Actinobacillus succinogenes 130Z

Metabolite secretion in microorganisms: the theory of metabolic overflow put to the test

Quantitative physiology and elemental composition of Kluyveromyces lactis CBS 2359 during growth on glucose at different specific growth rates

Impact of the cultivation strategy on resveratrol production from glucose in engineered Corynebacterium glutamicum

Genome-scale modeling of yeast: chronology, applications and critical perspectives

Development of a framework for metabolic pathway analysis-driven strain optimization methods

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BIOSYSTEMS People

Isabel Rocha

Principal Investigator

Career

Qualifications

Roles and Responsibilities

Honors and Awards

Projects

Past Projects

Research Students

Past Students

Recent Publications

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About

Research

Groups

Other Sites

Contact Us

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