Isabel Rocha

Professor Auxiliar




Carreira

  • Desde  2011: Professor Auxiliar, Universidade do Minho

Qualificações

  • 2003: Tese de Doutoramento em Engenharia Química e Biológica, Universidade do Minho

Cargos e Responsabilidades

  • Desde  2011: Membro da Comissão Coordenadora de Departamento , Departamento de Engenharia Biológica
  • 2010 - 2013: Diretor de Curso, Mestrado em Bioinformática - Ciências Biológicas
  • Desde  2007: Membro da Comissão Diretiva de Curso, Programa Doutoral em Bioengenharia
  • 2008 - 2008: APBio
  • Desde  2013: Member of the Editorial Board of "Frontiers in Bioengineering and Biotechnology - Synthetic Biology"

Honras e Prêmios

  • 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.


Projetos


Alunos de Investigação


Publicações Recentes

1
Integration of biomass formulations of genome-scale metabolic models with experimental data reveals universally essential cofactors in prokaryotes
  • Metabolic Engineering, 39, 200-208, 2017
2
Genome-wide semi-automated annotation of transporter systems
  • IEEE/ACM Transactions on Computational Biology and Bioinformatics, (In Press), 2017
3
Rhodococcus opacus B4: a promising bacterium for production of biofuels and biobased chemicals
  • AMB Express, 6(35), 1-11, 2016
4
Improving the flux distributions simulated with genome-scale metabolic models of Saccharomyces cerevisiae
  • Metabolic Engineering Communications, 3, 153-163, 2016
5
  • 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
6
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
7
Current state and challenges for dynamic metabolic modeling
  • Current Opinion in Microbiology, 33, 97-104, 2016
8
  • 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
9
In silico constraint-based strain optimization methods: the quest for optimal cell factories
  • Microbiology and Molecular Biology Reviews, 80(1), 45-67, 2016
10
A comparative analysis of dynamic models of the central carbon metabolism of Escherichia coli
  • IFAC-PapersOnLine, 49(26), 270-276, 2016
11
A comparative proteome analysis of Escherichia coli ΔrelA mutant cells
  • Frontiers in Bioengineering and Biotechnology, 4(78), 1-12, 2016
12
Reconstruction of the regulatory network for Bacillus subtilis and reconciliation with gene expression data
  • Frontiers in Microbiology, 7(275), 1-11, 2016
13
Extracting kinetic information from literature with KineticRE
  • Journal of Integrative Bioinformatics, 12(4), 282, 2015
14
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
15
Salmonella typhimurium and Escherichia coli dissimilarity: Closely related bacteria with distinct metabolic profiles
  • Biotechnology Progress, 31(5), 1217-1225, 2015
16
Development and application of efficient pathway enumeration algorithms for metabolic engineering applications
  • Computer Methods and Programs in Biomedicine, 118(2), 134-146, 2015
17
Reconstructing genome-scale metabolic models with merlin
  • Nucleic Acids Research, 43(8), 3899-3910, 2015
18
A text mining approach for the extraction of kinetic information from literature
  • Advances in Intelligent Systems and Computing, 375, 89-98, 2015
19
CBFA: phenotype prediction integrating metabolic models with constraints derived from experimental data
  • BMC Systems Biology, 8(123), 2014
20
A kinetic model for curcumin production in Escherichia coli
  • BioSystems, 125, 16-21, 2014
Listagem Completa de Publicações