BIOSYSTEMS People

Isabel Rocha

Assistant Professor



Career

  • Since  2011: 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.


Projects


Research Students


Recent Publications

1
Development of a framework for metabolic pathway analysis-driven strain optimization methods
  • Interdisciplinary Sciences-Computational Life Sciences, 9(1), 46-55, 2017
2
Integration of biomass formulations of genome-scale metabolic models with experimental data reveals universally essential cofactors in prokaryotes
  • Metabolic Engineering, 39, 200-208, 2017
3
Genome-wide semi-automated annotation of transporter systems
  • IEEE-ACM Transactions on Computational Biology and Bioinformatics, 14(2), 443-456, 2017
4
Rhodococcus opacus B4: a promising bacterium for production of biofuels and biobased chemicals
  • AMB Express, 6(35), 1-11, 2016
5
Improving the flux distributions simulated with genome-scale metabolic models of Saccharomyces cerevisiae
  • Metabolic Engineering Communications, 3, 153-163, 2016
6
Estimation of biomass composition from genomic and transcriptomic information
  • Journal of Integrative Bioinformatics, 13(2), 285, 2016
7
  • Faria, José Pedro; Davis, James J.; Edirisinghe, Janaka N.; Taylor, Ronald C.; Weisenhorn, Pamela; Olson, Robert D.; Stevens, Rick L.; Rocha, Miguel; Rocha, Isabel; Best, Aaron A.; DeJongh, Matthew; Tintle, Nathan L.; Parrello, Bruce; Overbeek, Ross; Henry, Christopher S.
Computing and applying atomic regulons to understand gene expression and regulation
  • Frontiers in Microbiology, 7(1819), 1-14, 2016
8
Stoichiometric representation of gene–protein–reaction associations leverages constraint-based analysis from reaction to gene-level phenotype prediction
  • PLoS Computational Biology, 12(10:e1005140), 1-24, 2016
9
Current state and challenges for dynamic metabolic modeling
  • Current Opinion in Microbiology, 33, 97-104, 2016
10
  • Jouhten, Paula; Boruta, T.; Andrejev, S.; Pereira, Filipa; Rocha, Isabel; Patil, K.R.
Yeast metabolic chassis designs for diverse biotechnological products
  • Scientific Reports, 6(29694), 1-9, 2016
11
In silico constraint-based strain optimization methods: the quest for optimal cell factories
  • Microbiology and Molecular Biology Reviews, 80(1), 45-67, 2016
12
A comparative analysis of dynamic models of the central carbon metabolism of Escherichia coli
  • IFAC-PapersOnLine, 49(26), 270-276, 2016
13
A comparative proteome analysis of Escherichia coli ΔrelA mutant cells
  • Frontiers in Bioengineering and Biotechnology, 4(78), 1-12, 2016
14
Reconstruction of the regulatory network for Bacillus subtilis and reconciliation with gene expression data
  • Frontiers in Microbiology, 7(275), 1-11, 2016
15
Extracting kinetic information from literature with KineticRE
  • Journal of Integrative Bioinformatics, 12(4), 282, 2015
16
Modeling the contribution of allosteric regulation for flux control in the central carbon metabolism of E. coli
  • Frontiers in Bioengineering and Biotechnology, 3(154), 2015
17
Salmonella typhimurium and Escherichia coli dissimilarity: Closely related bacteria with distinct metabolic profiles
  • Biotechnology Progress, 31(5), 1217-1225, 2015
18
Development and application of efficient pathway enumeration algorithms for metabolic engineering applications
  • Computer Methods and Programs in Biomedicine, 118(2), 134-146, 2015
19
Reconstructing genome-scale metabolic models with merlin
  • Nucleic Acids Research, 43(8), 3899-3910, 2015
20
A text mining approach for the extraction of kinetic information from literature
  • Advances in Intelligent Systems and Computing, 375, 89-98, 2015
Full List





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Centro de Engenharia Biológica
Universidade do Minho
Campus de Gualtar
4710-057 Braga Portugal
Phone: (+351) 253 604 400
Fax: (+351) 253 604 429
Email: ceb@ceb.uminho.pt

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