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IBB - Institute for Biotechnology and Bioengineering
CEB - Centre of Biological Engineering - University of Minho		 Universidade do Minho - Escola de Engenharia
 

 

CEB is part of the Institute for Biotechnology and Bioengineering

 
Sónia Madalena Azevedo Carneiro
Preferred Name:
Sónia Carneiro
E-Mail Address:
soniacarneiro@deb.uminho.pt @deb.uminho.pt
Activity:
Post Doc
Project / Theme:
A systems biology approach to uncover metabolic processes relevant to organ-specific metastasis
Start Date: 10/19/2005
End Date: 12/31/2013
Faculty Supervisor: Isabel Rocha
Telephone: Office:604422
Laboratory: 601966
Laboratory: Laboratório de Bioprocessos
Office: Gabinete Pós Doc Bioinformática EENG2
Birthday: January 1st
Website: http://biopseg.deb.uminho.pt/SoniaCarneiro/
Access after working hours: Yes
Nationality: Portugal
Last Update: 6/13/2011

Selected Publications

1. Lourenço, A.; Carneiro, S.; Pinto, J.P.; Rocha, M.; Ferreira, E.C.; Rocha, I.
  A study of the short and long-term regulation of E. coli metabolic pathways.
  Journal of integrative bioinformatics 8(3), 183-, 2011.
 
2. Carneiro, S.; Ferreira, E.C.; Rocha, I.
  Metabolomics as a tool to understand E. coli metabolic responses in recombinant processes.
  Book of Abstracts of the 11th International Chemical and Biological Engineering Conference (), 4-5, 2011.
 
3. Lourenço, A.; Carneiro, S.; Pinto, J.P.; Rocha, M.; Ferreira, E.C.; Rocha, I.
  Interpreting the regulatory interplay in E. coli metabolic pathways.
  Advances in Intelligent and Soft Computing [5th International Conference on Practical Applications of Computational Biology & Bioinformatics (PACBB 2011)] 93(), 303-312, 2011.
 
4. Carneiro, S.; Ferreira, E.C.; Rocha, I.
  A systematic modeling approach to elucidate the triggering of the stringent response in recombinant E. coli systems.
  Advances in Intelligent and Soft Computing [5th International Conference on Practical Applications of Computational Biology & Bioinformatics (PACBB 2011)] 93(), 313-320, 2011.
 
5. Carneiro, S.
  A systems biology approach for the characterization of metabolic bottlenecks in recombinant protein production processes.
  Doutoramento em Engenharia Química e Biológica (), -, 2010.
 
6. Carneiro, S.; Rocha, I.; Ferreira, E.C.
  Application of a genome-scale metabolic model to the inference of nutritional requirements and metabolic bottlenecks during recombinant protein production in Escherichia coli.
  4th Recombinant Protein Production Meeting – RPP2006 – A Comparative View on Host Physiology Microbial Cell Factories 5 (Suppl 1)(P52), -, 2006.
 
7. Mendes, R.; Lourenço, A.; Carneiro, S.; Ferreira, E.C.; Rocha, I.; Rocha, M.
  A framework for the integrated analysis of metabolic and regulatory networks.
  8th IEEE International Conference on Bioinformatics and Bioengineering. BIBE 2008 (), 1-6, 2008.
 
8. Lourenço, A.; Carreira, R.; Carneiro, S.; Maia, P.; Glez-Peña, D.; Fdez-Riverola, F.; Ferreira, E.C.; Rocha, I.; Rocha, M.
  A framework for the development of biomedical text mining software tools.
  8th IEEE International Conference on Bioinformatics and Bioengineering. BIBE 2008 (), 1-6, 2008.
 
9. Carneiro, S.; Villas-Boas, S.; Ferreira, E.C.; Rocha, I.
  Metabolic footprint analysis of recombinant Escherichia coli strains during fed-batch fermentations.
  Molecular BioSystems 7(3), 899-910, 2011.
 
10. Lourenço, A.; Carneiro, S.; Carreira, R.; Rocha, M.; Rocha, I.; Ferreira, E.C.
  Bringing text miners and biologists closer together.
  3rd International Biocuration Conference (), -, 2009.
 
11. Lourenço, A.; Carneiro, S.; Ferreira, E.C.; Carreira, R.; Rocha, L.M.; Glez-Peña, D.; Méndez, J.R.; Fdez-Riverola, F.; Diaz, F.; Rocha, I.; Rocha, M.
  Biomedical text mining applied to document retrieval and semantic indexing.
  IWANN 2009, Part II, (S. Omatu et al., Eds.) [3rd International Workshop on Practical Applications of Computational Biology & Bioinformatics - IWPACBB'09] Lecture Notes in Computer Science(5518), 954-963, 2009.
 
12. Lourenço, A.; Carneiro, S.; Rocha, M.; Ferreira, E.C.; Rocha, I.
  Challenges in integrating E. coli molecular biology data.
  Briefings in Bioinformatics 12(2), 91-103, 2011.
 
13. Carneiro, S.; Villas-Bôas, S.G.; Rocha, I.; Ferreira, E.C.
  Applying a metabolic footprinting approach to characterize the impact of the recombinant protein production in Escherichia coli.
  Advances in Bioinformatics [4th International Workshop on Practical Applications of Computational Biology & Bioinformatics - IWPACBB 2010. Guimarães, Portugal 16-18 June 2010] Advances in Soft Computing(74), 193-200, 2010.
 
14. Carneiro, S.; Lourenço, A.; Carreira, R.; Rocha, Miguel; Ferreira, E.C.; Rocha, I.
  Digging out evidences on Escherichia coli stringent response from scientific literature.
  Book of Abstracts of MicroBiotec09 (), 30-, 2009.
 
15. Lourenço, A.; Carreira, R.; Glez-Peña, Daniel; Méndez, José R.; Carneiro, S.; Rocha, Luis M.; Díaz, Fernando; Ferreira, E.C.; Rocha, I.; Rocha, Miguel; Fdez-Riverola, Florentino
  BioDR: semantic indexing networks for biomedical document retrieval.
  Expert Systems with Applications 37(4), 3444-3453, 2010.
 
16. Portela, C.; Carneiro, S.; Villas-Bôas, S. G.; Lourenço, A.; Rocha, I.; Ferreira, E.C.
  Metabolic network reconstruction of the pathogen Enterococcus faecalis.
  Jornadas de Bioinformática JB'2009 - Challenges in Bioinformatics: proceedings (), 151-, 2009.
 
17. Carneiro, S.; Lourenço, A.; Mendes, Rui; Rocha, Miguel; Ferreira, E.C.; Rocha, I.
  Network analysis of an integrated metabolic/regulatory model of Escherichia coli.
  Workshop Systems Biology in Medicine (European Science Foundation) (), -, 2008.
 
18. Lourenço, A.; Carreira, R.; Carneiro, S.; Maia, P.; Ferreira, E.C.; Rocha, Miguel; Rocha, I.
  The @Note biomedical text mining workbench.
  Workshop Systems Biology in Medicine (European Science Foundation) (), -, 2008.
 
19. Carneiro, S.; Villas-Bôas, S.; Rocha, I.; Ferreira, E.C.
  Metabolic footprinting of Escherichia coli grown in fed-batch fermentation during recombinant protein production.
  Abstracts of the 14th European Congress on Biotechnology New Biotechtnology 25(S1), S342-, 2009.
 
20. Lourenço, A.; Costa, Hugo; Carneiro, S.; Carreira, R.; Rocha, Miguel; Ferreira, E.C.; Rocha, I.
  Combining syntactic and ontological knowledge to extract biologically relevant relations from scientific papers.
  17th Annual International Conference on Intelligent Systems for Molcular Biology & 8th European Conference on Computational Biology ISBMECCB 2009, Special Interest Group Meeting Program Materials (), 237-240, 2009.
 
21. Carneiro, S.; Lourenço, A.; Carreira, R.; Rocha, Miguel; Ferreira, E.C.; Rocha, I.
  Uncovering mechanisms underlying the Escherichia coli stringent response: application of text mining approaches to identify meaningful relations in text documents.
  International Conference on Microbial Stress: from Molecules to Systems: Book of Abstracts (), -, 2009.
 
22. Lourenço, A.; Carreira, R.; Carneiro, S.; Maia, P.; Glez-Peña, Daniel; Fdez-Riverola, Florentino; Ferreira, E.C.; Rocha, I.; Rocha, Miguel
  @Note: a workbench for biomedical text mining.
  Journal of Biomedical Informatics 42(4), 710-720, 2009.
 
23. Carneiro, S.; Amaral, A.L.; Veloso, A.C.; Dias, T.; Peres, A. M.; Ferreira, E.C.; Rocha, I.
  Assessment of physiological conditions in E. coli fermentations by epifluorescent microscopy and image analysis.
  Biotechnology Progress 25(3), 882-891, 2009.
 
24. Pinto, José P.; Dias, O.; Lourenço, A.; Carneiro, S.; Ferreira, E.C.; Rocha, I.; Rocha, Miguel
  Data integration issues in the reconstruction of the genome-scale metabolic model of Zymomonas mobillis.
  2nd International Workshop on Practical Applications of Computational Biology and Bioinformatics (IWPACBB 2008) Advances in Soft Computing(49), 92-101, 2009.
 
25. Lourenço, A.; Carneiro, S.; Carreira, R.; Rocha, Miguel; Rocha, I.; Ferreira, E.C.
  A tool for the automatic and manual annotation of biomedical documents.
  Proceedings of the Third International Symposium on Semantic Mining in Biomedicine – SMBM 2008 (), 97-104, 2008.
 
26. Carneiro, S.; Lourenço, A.; Mendes, Rui; Rocha, Miguel; Ferreira, E.C.; Rocha, I.
  An integrated analysis of the metabolic and regulatory networks of Escherichia coli K12.
  Abstract Book of the 9th International Conference on Systems Biology – ICSB 2008 (DS2-94), 146-, 2008.
 
27. Rocha, I.; Veloso, A.C.; Carneiro, S.; Costa, R.S.; Ferreira, E.C.
  Implementation of a specific rate controller in a fed-batch E. coli fermentation.
  Proceedings of the 17th IFAC (International Federation of Automatic Control) World Congress (Chung, M.J., Misra, P., Shim, H., Eds.) (), 15565-15570, 2008.
 
28. Costa, R.S.; Carneiro, S.; Rocha, I.; Ferreira, E.C.
  Effect of pH variation on the acetate “switch” and biomass growth in an Escherichia coli aerobic fermentation: global gene expression profiles analysis.
  Livro de Actas do Congresso Micro '07 - Biotec '07 - XXIII JPG (), 176-, 2007.
 
29. Carneiro, S.; Maia, P.; Rocha, Miguel; Ferreira, E.C.; Rocha, I.
  Constraint-based approach for in silico Escherichia coli combined regulatory/metabolic modelling.
  Livro de Actas do Congresso Micro '07 - Biotec '07 - XXIII JPG (), 176-, 2007.
 
30. Carneiro, S.; Ferreira, E.C.; Rocha, I.
  Metabolic modelling of stringent response in recombinant Escherichia coli.
  Conference Foundations of Systems Biology in Engineering: Abstracts (B-30), -, 2007.
 
31. Veloso, A.C.; Rocha, I.; Carvalho, S.; Carneiro, S.; Dias, T.; Peres, A. M.; Ferreira, E.C.
  Escherichia coli expressing a fluorescence protein as a model system for the optimization of environmental and processing conditions.
  Micro’05-Biotec’05: Livro de Actas do Congresso MICROBIOTEC’2005 (), 423-, 2005.
 
32. Rocha, I.; Carneiro, S.; Veloso, A.C.; Ferreira, E.C.
  Application of genome-scale metabolic models to the optimization of recombinant protein production in Escherichia coli.
  Micro’05-Biotec’05: Livro de Actas do Congresso MICROBIOTEC’2005 (), 400-, 2005.
 
33. Carneiro, S.; Veloso, A.C.; Amaral, A.L.; Rocha, I.; Ferreira, E.C.
  Image analysis as a tool for viability and recombinant protein production assessment during E. coli fermentations.
  CHEMPOR 2005 - 9th International Chemical Engineering Conference, Departamento de Engenharia Química da Universidade de Coimbra (), 972-8055, 2005.