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Eugénio C. Ferreira is the Vice-Rector (Research & Innovation) of the University of Minho (since Dec 2019), Chairman of TECMINHO - Associação Universidade Empresa para o Desenvolvimento, and Vice-President of CENTI - Centre for Nanotechnology and Smart Materials. Full Professor at the Department of Biological Engineering and former Director of the PhD program on Bioengineering (MIT Portugal Program). He served as Diretor of the Centre of Biological Engineering (2016-2020), a research unit with more than 400 researchers where he leads the BIOSYSTEMS research group on Bioprocess Engineering and Computational Biosystems. His research expertise relates to Process Systems Engineering in Biotechnological, Chemical and Environmental Applications with particular emphasis in the following areas of activity: Modelling, Monitoring, and Control of Bioprocesses; Systems Biology, Bioinformatics, and Metabolic Engineering; Image Analysis and Chemometrics in (Environmental) Biotechnology. From 2017-2019 he served as Counsellor Member at the General Council of the University Minho. From 2010 to 2013 he served as Associate Dean for Research of the School of Engineering at the University of Minho. From 2004 to 2010 he served as Associate Director of the Department of Biological Engineering and as Director of the Master program on Environmental Management. Professor Ferreira served as Chair of the Chemical & Biological Engineering Section of the Portuguese Engineers Institution (2010-2013), as the General-Secretary of the Portuguese Society of Biotechnology (2004-2019). He was the Portuguese Delegate at the Board of the European Federation of Chemical Engineering (2010-13) and is a member of the IFAC Technical Committee on Biosystems and Bioprocesses and the National Representative to the Technical Committee on Modelling, Monitoring, Measurement, and Control of the European Society of Biochemical Engineering Sciences. In addition, he is Associate Editor of Frontiers in Biotechnology and Bioengineering and Frontiers in Chemical Engineering, member of the Editorial Board of Chemical Product and Process Modeling, Brazilian Journal of Chemical Engineering, and Environmental Engineering and Management Journal and he was the Editor-in-Chief of Engenharia Química journal from 2006 to 2008. He was the Chair of the organization committee of the CHEMPOR2008 - International Chemical Engineering Congress. In addition, he integrated the organizing committees of several conferences (CAC2004, ESCAPE14, ESBES2) and the international program committees of more than 60 Congresses. He acted as Coordinator of the review panel for PhD fellowships in Bioengineering and Biotechnology at the Portuguese Foundation for Science and Technology and he is a coordinator/member of the Assessment Panel for Biotechnology and Bioengineering Academic Programs at the national Agency for the Assessment and accreditation of Higher Education. He also integrated review panels for Agência Nacional de Inovação, European Science Foundation and European Commission. His supervision of students has involved 14 PhD theses, with one of them being awarded the CUF Prize for the Best Chemical and Biological Engineering thesis in Portugal (2003). Professor Ferreira has published 10 books and is the author of more than 200 international refereed papers and book chapters. In addition, more than 325 papers and communications in conferences have been published by him. He graduated (1986) and received his PhD (1995) in Chemical Engineering from the Faculty of Engineering of the University of Porto. He did doctoral research at the Université Catholique de Louvain (Belgium), post-doctorate at the Universitat Autonoma de Barcelona (Spain) and sabbatical at the University of California, San Diego (USA).
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Identification

Personal identification

Full name
Eugénio Campos Ferreira
Gender
Male

Citation names

  • E. C. Ferreira
  • Ferreira, Eugénio C.
  • Ferreira, E.C.

Author identifiers

Ciência ID
CA10-0F06-E2A0
ORCID iD
0000-0002-5400-3333
Google Scholar ID
FXPpP8UAAAAJ
Researcher Id
B-5417-2009
Scopus Author Id
7103157456

Email addresses

  • ecferreira@deb.uminho.pt (Professional)

Addresses

  • Universidade do Minho. Departamento de Engenharia Biológica, Campus de Gualtar, 4710-057, Braga, Braga, Portugal (Professional)

Websites

Knowledge fields

  • Engineering and Technology - Chemical Engineering
  • Engineering and Technology - Environmental Engineering
  • Engineering and Technology - Environmental Biotechnology
  • Engineering and Technology - Industrial Biotechnology
Education
Degree Classification
2022
Ongoing
 Engenharia Química e Biológica (Doutoramento)
Major in Sem especialidade
Universidade do Minho, Portugal
"An approach towards Zero-Waste wastewater technology: Sustainable AGS processes for safe valorization of urban wastewater for irrigation, with minimized ecological and agronomic impacts" (THESIS/DISSERTATION)
2004/07/23
Concluded
 Habilitation (Título de Agregado)
Universidade do Minho, Portugal
"Agregação em Engenharia Química e Biológica " (THESIS/DISSERTATION)
1997 - 1998
Concluded
 Supervision and Control of Biological Wastewater Treatment Plants (Pós-doutoramento)
Universitat Autònoma de Barcelona, Spain
1995/07/11
Concluded
 Doutoramento em Engenharia Química (Doutoramento)
Universidade do Porto, Portugal
"Identificação e Controlo Adaptativo de Processos Biotecnológicos" (THESIS/DISSERTATION)
1981 - 1986/07
Concluded
 Engenharia Química (Licenciatura)
Universidade do Porto, Portugal
Affiliation

Science

Category
Host institution 		Employer
1986/09/01 - 1990/01/31 Researcher (Research) LNETI - Laboratório Nacional de Engenharia e Tecnologia Industrial, Portugal
LNETI - Laboratório Nacional de Engenharia e Tecnologia Industrial, Portugal

Teaching in Higher Education

Category
Host institution 		Employer
2010/11/11 - Current Full Professor (University Teacher) Universidade do Minho Departamento de Engenharia Biológica, Portugal
2004/08 - 2010/11 Associate Professor (University Teacher) Universidade do Minho, Portugal
2001/07 - 2004/07 Associate Professor (University Teacher) Universidade do Minho, Portugal
2000/08 - 2001/06 Assistant Professor (University Teacher) Universidade do Minho, Portugal
1991/03 - 1995/06 Assistant (University Teacher) Universidade do Minho, Portugal

Positions / Appointments

Category
Host institution 		Employer
2022/03 - Current Vice-President Centitvc Centro de Nanotecnologia e Materiais Técnicos Funcionais e Inteligentes, Portugal
Centitvc Centro de Nanotecnologia e Materiais Técnicos Funcionais e Inteligentes, Portugal
2020/01/06 - Current President TecMinho Associação Universidade-Empresa para o Desenvolvimento, Portugal
TecMinho Associação Universidade-Empresa para o Desenvolvimento, Portugal
2019/12/11 - Current Vice-Rector Universidade do Minho, Portugal
Universidade do Minho, Portugal
2011 - 2021 Diretor do Programa Doutoral em Bioengenharia Universidade do Minho, Portugal
Universidade do Minho Escola de Engenharia, Portugal
2020/03 - 2020/12 President Spinpark – Centro de Incubação de Base Tecnológica, Portugal
Spinpark – Centro de Incubação de Base Tecnológica, Portugal
2016/01/26 - 2020/01/26 Organic Unit Director Universidade do Minho Centro de Engenharia Biológica, Portugal
Universidade do Minho Centro de Engenharia Biológica, Portugal
2017/09 - 2019/12/31 Membro da Comissão Diretiva do curso de Mestrado em Bioinformática Universidade do Minho, Portugal
Universidade do Minho Escola de Engenharia, Portugal
2017/04/06 - 2019/12/10 Membro do Conselho Geral Universidade do Minho, Portugal
Universidade do Minho, Portugal
2013/01/01 - 2019/12/10 Conselho Científico Universidade do Minho Escola de Engenharia, Portugal
Universidade do Minho Escola de Engenharia, Portugal
2010/03/03 - 2013/05/03 Organic Unit Vice-President Universidade do Minho Escola de Engenharia, Portugal
Universidade do Minho Escola de Engenharia, Portugal
2004/09 - 2010/10 Diretor do curso de Mestrado em Gestão Ambiental Universidade do Minho, Portugal
Universidade do Minho Escola de Engenharia, Portugal
2001/09 - 2003/09 Diretor de Curso da Licenciatura em Engenharia Biológica Universidade do Minho, Portugal
Universidade do Minho Escola de Engenharia, Portugal
Projects

Contract

Designation Funders
2022/10/01 - 2025/09/30 GIATEX - Intelligent Water Management at ITV
C644943052-00000050
Researcher
Universidade do Minho Centro de Engenharia Biológica, Portugal
 Agência para a Competitividade e Inovação IP
Ongoing
2021/07/01 - 2023/06/30 PortAberta - Portal de Investigação para a Ciência Aberta
POCI-05-5762-FSE-000431
Researcher
Universidade do Minho, Portugal
 AMA - Agência para a Modernização Administrativa
Ongoing
2021/07/01 - 2023/06/30 Portal da Inovação da Universidade do Minho
POCI-01-0246-FEDER-181310
Principal investigator
Universidade do Minho, Portugal
 Agência Nacional de Inovação SA
Ongoing
2021/01/01 - 2022/12/31 MarPlas - Evaluation and valorization of plastics and microplastics in marine environment
NORTE-01-0145-FEDER-000080
Researcher
Universidade do Minho Centro de Engenharia Biológica, Portugal
 Comissao de Coordenacao e Desenvolvimento Regional do Norte
Ongoing
2020/01/01 - 2022/12/31 PAMWater - Predictive and Analytic Models for the Optimization of Multi-municipal Water Systems / Modelos Analíticos e Predictivos para Optimização de Sistemas Multimunicipais de Água
DSAIPA/AI/0099/2019
Researcher
Universidade do Minho, Portugal

Universidade do Minho Centro ALGORITMI, Portugal

Universidade do Minho Centro de Engenharia Biológica, Portugal
Fundação para a Ciência e a Tecnologia
Ongoing
2019/07/01 - 2022/06/30 DEEPBIO - Machine learning and deep learning approaches to industrial biotechnology applications
NORTE-01-0247-FEDER-039831
Researcher
Universidade do Minho Centro de Engenharia Biológica, Portugal

Silicolife Lda., Portugal

Universidade Nova de Lisboa, Portugal
Agência Nacional de Inovação SA
Ongoing
2018/07/01 - 2021/06/30 AGeNT - Aerobic granule technology combined with selected microbial agents for the degradation of toxic wastewater pollutants / Tecnologia de grânulos aeróbios combinada com agentes microbianos selecionados para a degradação de poluentes tóxicos de águas residuais
PTDC/BTA-BTA/31264/2017
Principal investigator
Universidade Católica Portuguesa, Portugal

Universidade do Minho Centro de Engenharia Biológica, Portugal
Fundação para a Ciência e a Tecnologia
Ongoing
2018/07/01 - 2021/06/30 Easy Ride - Experience is Everything
POCI-01-0247-FEDER-039334
Researcher
Universidade do Minho Centro de Engenharia Biológica, Portugal
 Agência para o Investimento e Comércio Externo de Portugal, E.P.E.

Agência Nacional de Inovação SA
Ongoing
2017/01/01 - 2020/12/31 Biomass and Bioenergy Research Infrastructure
PINFRA/22059/2016
Researcher
Universidade do Minho Centro de Engenharia Biológica, Portugal

Laboratório Nacional de Energia e Geologia, Portugal
Fundação para a Ciência e a Tecnologia
Ongoing
2016/10/01 - 2020/09/30 Programa Doutoral em Bioengenharia
NORTE-08-5369-FSE-000053
Principal investigator
Universidade do Minho Centro de Engenharia Biológica, Portugal
 Comissao de Coordenacao e Desenvolvimento Regional do Norte
Ongoing
2016/10/01 - 2020/09/30 Doctoral Program in Chemical and Biological Engineering
NORTE-08-5369-FSE-000052
Principal investigator
Universidade do Minho Centro de Engenharia Biológica, Portugal
 Comissao de Coordenacao e Desenvolvimento Regional do Norte
Ongoing
2017/01/01 - 2020/06/30 MultiBiorefinery - Multi-purpose strategies for broadband agro-forest and fisheries by-products valorisation: a step forward for a truly integrated biorefinery
SAICTPAC/0040/2015
Principal investigator
Universidade de Aveiro, Portugal

Instituto de Biologia Experimental e Tecnológica, Portugal

Universidade Católica Portuguesa, Portugal

Universidade do Minho, Portugal

Universidade de Coimbra, Portugal

Associação para a Inovação e Desenvolvimento da FCT, Portugal
Fundação para a Ciência e a Tecnologia
Ongoing
2016/07/01 - 2020/06/30 BIOTECNORTE - Underpinning Biotechnology to foster the north of Portugal bioeconomy
NORTE-01-0145-FEDER-000004
Principal investigator
Universidade do Minho Centro de Engenharia Biológica, Portugal
 Comissao de Coordenacao e Desenvolvimento Regional do Norte
Ongoing
2017/06/01 - 2020/05/31 Biodata.pt - Portuguese Biological Data Network
POCI-01-0145-FEDER-022231
Researcher
Universidade do Minho Centro de Engenharia Biológica, Portugal
 Fundação para a Ciência e a Tecnologia
Ongoing
2016/03/01 - 2020/02/29 Bioinformatics Services for Data-Driven Design of Cell Factories and Communities
info:eu-repo/grantAgreement/EC/H2020/686070/EU
Researcher
Universidade do Minho Centro de Engenharia Biológica, Portugal
 UK Research and Innovation
Concluded
2019/01/01 - 2019/12/31 Centre of Biological Engineering - University of Minho
UID/BIO/04469/2019
Universidade do Minho, Portugal
 Fundação para a Ciência e a Tecnologia
Concluded
2016/01/01 - 2018/12/31 SISBI - Intelligent decision support system for Industrial Biotechnology
NORTE-01-0247-FEDER-003381
Researcher
Universidade do Minho Centro de Engenharia Biológica, Portugal

Silicolife Lda., Portugal
Agência Nacional de Inovação SA
Concluded
2015/01/01 - 2018/12/31 Centre of Biological Engineering - University of Minho
UID/BIO/04469/2013
Universidade do Minho, Portugal
 Fundação para a Ciência e a Tecnologia
Concluded
2015/04 - 2018/03 DYNAMICS: Analysis and optimization of industrial microorganisms under dynamic process conditions
Provided by PTCRIS: 138757
Researcher
Universidade do Minho Centro de Engenharia Biológica, Portugal
 Fundação para a Ciência e a Tecnologia
2014/03 - 2017/02 DeYeast Library - Designer yeast strain library optimized for metabolic engineering applications
Provided by PTCRIS: 137211
Researcher
Universidade do Minho Centro de Engenharia Biológica, Portugal
 Fundação para a Ciência e a Tecnologia
Concluded
2016/03/01 - 2016/05/31 Genome-scale Constraint-based Modeling of Metabolic and Microbial Community Interactions
SFRH/BSAB/114310/2016
 Fundação para a Ciência e a Tecnologia
Concluded
2012/07/01 - 2015/06/30 PEM - Plataforma tecnológica de suporte à Engenharia Metabólica / Platform for Metabolic Engineering
23060
Researcher
Universidade do Minho Centro de Engenharia Biológica, Portugal

Silicolife Lda., Portugal
Agência Nacional de Inovação SA
Concluded
2010/05 - 2015/04 CamCon - Campylobacter control - novel approaches in primary poultry production
244547
Principal investigator
Universidade do Minho Centro de Engenharia Biológica, Portugal
 European Commission
Concluded
2010/10 - 2014/03 Study of the operation of SBRs for enhanced phosphorous removal and for PHA production by image analysis and multivariable statistical techniques
103147
Provided by PTCRIS: 103147
Principal investigator
Universidade do Minho Centro de Engenharia Biológica, Portugal
 Fundação para a Ciência e a Tecnologia, I.P.
Concluded
2010/05 - 2013/11 SYNBIOBACTHER - Synthetic biology approaches to engineer "therapeutic" bacteria / Construção de bactérias "terapêuticas" usando uma abordagem de biologia sintética
102863
Provided by PTCRIS: 102863
Researcher
Universidade do Minho Centro de Engenharia Biológica, Portugal
 Fundação para a Ciência e a Tecnologia, I.P.
Concluded
2010/04 - 2013/09 AshByofactory - Ashbya gossypii: a systems metabolic engineered cell factory / Ashbya gossypii: uma fábrica celular manipulada por engenharia metabólica de sistemas
Provided by PTCRIS: 101985
101985
Researcher
Universidade do Minho Centro de Engenharia Biológica, Portugal
 Fundação para a Ciência e a Tecnologia, I.P.
Concluded
2010/04 - 2013/09 HeliSysBio - Molecular Systems Biology Helicobacter pylori / Biologia Molecular de Sistemas em Helicobacter pylori
Provided by PTCRIS: 104235
104235
Researcher
Universidade do Minho Centro de Engenharia Biológica, Portugal
 Fundação para a Ciência e a Tecnologia, I.P.
Concluded
2009/04 - 2012/09 Bridging Systems and Synthetic Biology for the development of Improved Microbial Cell Factories
84035
Provided by PTCRIS: 84035
Principal investigator
Universidade do Minho Centro de Engenharia Biológica, Portugal
 Fundação para a Ciência e a Tecnologia, I.P.
Concluded
2008/12 - 2011/11 Systems Biology as a Driver for Industrial Biotechnology
212766
Researcher
Universidade do Minho Centro de Engenharia Biológica, Portugal
 European Commission
Concluded
2007/01 - 2010/01 SuperETAR: Supervision and Intelligent Control of Wastewater Treatment Plants
82686
Provided by PTCRIS: 82686
60141
Provided by PTCRIS: 60141
Principal investigator
Universidade do Minho Centro de Engenharia Biológica, Portugal
 Fundação para a Ciência e a Tecnologia, I.P.
Concluded
2005/05 - 2008/10 PHAGEVET-P - Veterinary phage therapies as alternatives to antibiotics in poultry production
7224
Researcher
Universidade do Minho Centro de Engenharia Biológica, Portugal
 European Commission
Concluded
2005/07 - 2008/06 MOBioPro-Nature-based computation in the modeling and optimization of biotechnological processes / Computação inspirada na natureza para a modelação e optimização de processos biotecnológicos
59899
Provided by PTCRIS: 59899
Researcher
Fundação para a Ciência e a Tecnologia, I.P.
Concluded
2005/05 - 2008/06 recSysBio - A Systems Biology approach for optimization of recombinant fermentation processes
Provided by PTCRIS: 60139
60139
Principal investigator
Universidade do Minho Centro de Engenharia Biológica, Portugal

Universidade de Lisboa Instituto Superior Técnico, Portugal
Fundação para a Ciência e a Tecnologia, I.P.
Concluded
2005/10 - 2008/03 Monitoring of a Wastewater Treatment Plant by Image Analysis Techniques
57069
Provided by PTCRIS: 57069
Principal investigator
Universidade do Minho Centro de Engenharia Biológica, Portugal
 Fundação para a Ciência e a Tecnologia, I.P.
Concluded
2005/01 - 2006/12 Online control of fixed-bed reactors applied to aerobic wastewater treatment
6647
Researcher
Universidade do Minho Centro de Engenharia Biológica, Portugal
 European Commission
1998/07 - 2003/07 Optimal management of wastewater systems
2335
Researcher
Universidade do Minho Centro de Engenharia Biológica, Portugal
 European Commission
Concluded
1997/12 - 2001/11 BioToBio - Biological Removal of Nitrogen: from Biofilms to Bioreactors
FMRX970114
Researcher
Universidade do Minho Centro de Engenharia Biológica, Portugal
 European Commission
Concluded
1998/10/01 - 2001/09/01 Simulação Modular e Optimização Integrada de Processos Industriais
3/3.1/CEG/2641/95
Principal investigator
Universidade do Minho Centro de Engenharia Biológica, Portugal

Universidade do Porto Faculdade de Engenharia, Portugal
JNICT - Junta Nacional de Investigação Científica e Tecnológica
Concluded
Outputs

Publications

Book
  1. Ferreira, Eugénio C.; Sessão Comemorativa "20 anos da Licenciatura em Engenharia Biológica da Universidade do Minho", Braga, 2006. Passado, presente e futuro da Engenharia Biológica. Universidade do Minho. Departamento de Engenharia Biológica (DEB). 2006.
  2. E. C. Ferreira; E. Rodrigues. Fontes de Informação em Ambiente. Famalicão, Portugal: Edições Centro Atlântico. 2002.
    Published
Book chapter
  1. Eugénio Campos Ferreira. "Publicação Científica, Ciência Aberta e Avaliação de Investigação — Breve Análise Crítica". 2023.
    10.21814/uminho.ed.66.6
  2. Quintelas, Cristina; Mesquita, Daniela; Ferreira, Eugénio Campos. "CHAPTER 2. Impact of Industrial Wastewater Discharge on the Environment and Human Health". In Biological Treatment of Industrial Wastewater, 15-39. Royal Society of Chemistry, 2021.
    10.1039/9781839165399-00015
  3. Ferreira, Eugénio C.. "Foreword". Sciendo, 2020.
  4. Dias, O.; Rocha, M.; Ferreira, E.C.; Rocha, I.. "Reconstructing high-quality large-scale metabolic models with merlin". In Molecular and Cell Biology Methods for Fungi, 1-36. Humana Press, 2018.
    Published • 10.1007/978-1-4939-7528-0_1
  5. Veloso, A.C.; Ferreira, E.C.. "Online Analysis for Industrial Bioprocesses". In Current Developments in Biotechnology and Bioengineering, edited by Christian Larroche, Maria Angeles Sanroman, Guocheng Du, Ashok Pandey, 679-704. Elsevier, 2017.
    Published • 10.1016/b978-0-444-63663-8.00023-9
  6. Mesquita, Daniela P.; Selvaggio, Gianluca; Cunha, Jorge R.; Leal, Cristiano S.; Amaral, A. Luís; Ferreira, Eugénio C.. "Image Analysis for Automatic Characterization of Polyhydroxyalcanoates Granules". In Lecture Notes in Computer Science, 790-797. Springer Berlin Heidelberg, 2013.
    10.1007/978-3-642-39094-4_91
  7. Carneiro, Sónia; Ferreira, Eugénio C.; Rocha, Isabel. "A Systematic Modeling Approach to Elucidate the Triggering of the Stringent Response in Recombinant E. coli Systems". In 5th International Conference on Practical Applications of Computational Biology & Bioinformatics (PACBB 2011), 313-320. Springer Berlin Heidelberg, 2011.
    Published • 10.1007/978-3-642-19914-1_41
  8. Lourenço, Anália; Carneiro, Sónia; Pinto, José P.; Rocha, Miguel; Ferreira, Eugénio C.; Rocha, Isabel. "Interpreting the Regulatory Interplay in E. coli Metabolic Pathways". In 5th International Conference on Practical Applications of Computational Biology & Bioinformatics (PACBB 2011), 303-312. Springer Berlin Heidelberg, 2011.
    Published • 10.1007/978-3-642-19914-1_40
  9. Rocha, O.; Nobre, C.; Dominguez, A.; Torres, D.; Faria, N.; Rodrigues, L.; Teixeira, J.A.; Ferreira, E.C.; Rocha, I.. "A Dynamical Model for the Fermentative Production of Fructooligosaccharides". In 10th International Symposium on Process Systems Engineering: Part A, 1827-1832. Elsevier, 2009.
    Published • 10.1016/s1570-7946(09)70695-9
  10. Pinto, José P.; Dias, Oscar; Lourenço, Anália; Carneiro, Sónia; Ferreira, Eugénio C.; Rocha, Isabel; Rocha, Miguel. "Data Integration Issues in the Reconstruction of the Genome-Scale Metabolic Model of Zymomonas Mobillis". In 2nd International Workshop on Practical Applications of Computational Biology and Bioinformatics (IWPACBB 2008), 92-101. Springer Berlin Heidelberg, 2009.
    Published • 10.1007/978-3-540-85861-4_12
  11. Machado, Daniel; Costa, Rafael S.; Rocha, Miguel; Rocha, Isabel; Tidor, Bruce; Ferreira, Eugénio C.. "A Critical Review on Modelling Formalisms and Simulation Tools in Computational Biosystems". In Distributed Computing, Artificial Intelligence, Bioinformatics, Soft Computing, and Ambient Assisted Living, 1063-1070. Springer Berlin Heidelberg, 2009.
    Published • 10.1007/978-3-642-02481-8_161
  12. Evangelista, Pedro; Rocha, Isabel; Ferreira, Eugénio C.; Rocha, Miguel. "A Software Tool for the Simulation and Optimization of Dynamic Metabolic Models". In Distributed Computing, Artificial Intelligence, Bioinformatics, Soft Computing, and Ambient Assisted Living, 1071-1078. Springer Berlin Heidelberg, 2009.
    Published • 10.1007/978-3-642-02481-8_162
  13. Lourenço, Anália; Carneiro, Sónia; Ferreira, Eugénio C.; Carreira, Rafael; Rocha, Luis M.; Glez-Peña, Daniel; Méndez, José R.; et al. "Biomedical Text Mining Applied to Document Retrieval and Semantic Indexing". In Distributed Computing, Artificial Intelligence, Bioinformatics, Soft Computing, and Ambient Assisted Living, 954-963. Springer Berlin Heidelberg, 2009.
    Published • 10.1007/978-3-642-02481-8_146
  14. Dias, Ana M. A.; Ferreira, Eugénio C.. "Computational Intelligence Techniques for Supervision and Diagnosis of Biological Wastewater Treatment Systems". In Computational Intelligence Techniques for Bioprocess Modelling, Supervision and Control, 127-162. Springer Berlin Heidelberg, 2009.
    Published • 10.1007/978-3-642-01888-6_5
  15. Evangelista, Pedro; Rocha, Isabel; Ferreira, Eugénio C.; Rocha, Miguel. "Evolutionary Approaches for Strain Optimization Using Dynamic Models under a Metabolic Engineering Perspective". In Evolutionary Computation, Machine Learning and Data Mining in Bioinformatics, 140-151. Springer Berlin Heidelberg, 2009.
    Published • 10.1007/978-3-642-01184-9_13
  16. Costa, Rafael S.; Machado, Daniel; Rocha, Isabel; Ferreira, Eugénio C.. "Large Scale Dynamic Model Reconstruction for the Central Carbon Metabolism of Escherichia coli". In Distributed Computing, Artificial Intelligence, Bioinformatics, Soft Computing, and Ambient Assisted Living, 1079-1083. Springer Berlin Heidelberg, 2009.
    Published • 10.1007/978-3-642-02481-8_163
  17. Valente, Eduardo; Rocha, Miguel; Ferreira, Eugénio C.; Rocha, Isabel. "Modelling of Biotechnological Processes – An Approach Based on Artificial Neural Networks". In Computational Intelligence Techniques for Bioprocess Modelling, Supervision and Control, 311-332. Springer Berlin Heidelberg, 2009.
    Published • 10.1007/978-3-642-01888-6_11
  18. R. Mendes; I. Rocha; J. P. Pinto; E. C. Ferreira; M. Rocha. "Differential evolution for the offline and online optimization of fed-batch fermentation processes". In Advances in Differential Evolution, 299-317. Vienna, Austria: Springer, 2008.
    Published • 10.1007/978-3-540-68830-3_13
  19. E. Herrera; B. Castillo; J. Ramírez; E. C. Ferreira. "Takagi-Sugeno Fuzzy Controller for a Switching Bioprocess: Sector Nonlinearity Approach". In New Developments in Robotics, Automation and Control, 155-180. Vienna, Austria: In-Tech Education and Publishing, 2008.
    Published
  20. E. C. Ferreira; S. Feyo de Azevedo. "Modelação, monitorização e controlo de reactores biológicos". In Reactores Biológicos - Fundamentos e Aplicações, 193-230. Lisboa, Portugal: Lidel, 2007.
    Published
  21. Rocha, Miguel; Pinto, José P.; Rocha, Isabel; Ferreira, Eugénio C.. "Evaluating Evolutionary Algorithms and Differential Evolution for the Online Optimization of Fermentation Processes". In Evolutionary Computation,Machine Learning and Data Mining in Bioinformatics, 236-246. Germany: Springer Berlin Heidelberg, 2007.
    Published • 10.1007/978-3-540-71783-6_23
  22. Rocha, Miguel; Mendes, Rui; Maia, Paulo; Pinto, José P.; Rocha, Isabel; Ferreira, Eugénio C.. "Evaluating Simulated Annealing Algorithms in the Optimization of Bacterial Strains". In Progress in Artificial Intelligence, 473-484. Germany: Springer Berlin Heidelberg, 2007.
    Published • 10.1007/978-3-540-77002-2_40
  23. Espírito-Santo, I. A. C. P.; Fernandes, Edite M. G. P.; Araújo, M. M.; Ferreira, E. C.. "How Wastewater Processes can be Optimized Using LOQO". In Lecture Notes in Economics and Mathematical Systems, 435-455. Springer-Verlag, 2006.
    Published • 10.1007/3-540-28258-0_26
  24. A. C. Veloso; I. Rocha; E. C. Ferreira. "Identification of yield coefficients in an E. coli model - An optimal experimental design using genetic algorithms". In Computer Applications in Biotechnology, 43-48. London: Elsevier, 2005.
    Published
  25. Rocha, Miguel; Neves, José; Veloso, Ana C.A.; Ferreira, Eugénio C.; Rocha, Isabel. "Evolutionary Algorithms for Static and Dynamic Optimization of Fed-batch Fermentation Processes". In Adaptive and Natural Computing Algorithms, 288-291. Springer-Verlag, 2005.
    10.1007/3-211-27389-1_69
  26. Rocha, Miguel; Neves, José; Rocha, Isabel; Ferreira, Eugénio C.. "Evolutionary Algorithms for Optimal Control in Fed-Batch Fermentation Processes". In Applications of Evolutionary Computing, 84-93. Springer Berlin Heidelberg, 2004.
    Published • 10.1007/978-3-540-24653-4_9
  27. E. C. Ferreira; J. A. Teixeira. "Biorreactores". In Biotecnologia: Fundamentos e Aplicações, 165-194. Lisboa, Portugal: Lidel Edições Técnicas, 2003.
    Published
  28. I. Rocha; E. C. Ferreira. "An integrated system for advanced monitoring and control of fed-batch fermentations of recombinant E. coli". In Computer Applications in Biotechnology, 349-354. Oxford: Pergamon Press, 2002.
    Published
  29. M. da Motta; A. L. Amaral; M. Casellas; M. N. Pons; C. Dagot; N. Roche; E. C. Ferreira; H. Vivier. "Characterisation of Activated Sludge By Automated Image Analysis: Validation on Full-Scale Plants". In Computer Applications in Biotechnology, 427-431. Oxford: Pergamon Press, 2002.
    Published
  30. E. C. Ferreira; M. Mota; M. N. Pons; J. M. S. Cabral; J. Tramper. "Image Analysis and Multiphase Bioreactors". In Multiphase Bioreactor Design, 25-52. London, United Kingdom: Taylor & Francis, 2001.
    Published
  31. S. Feyo de Azevedo; P. Pimenta; F. R. Oliveira; E. C. Ferreira. "Computer-Based Studies on Bioprocess Engineering, II - Tools for Process Operation". In Computer and Information Science Applications in Bioprocess Engineering, 27-49. Dordrecht: Kluwer Academic Publishers, 1996.
    Published
  32. R. Oliveira; E. C. Ferreira; S. Feyo de Azevedo. "Model-based estimation of reaction rates in stirred tank bioreactors". In Computer Applications in Biotechnology, 259-263. Oxford: Elsevier Science Publishers, 1996.
    Published
  33. S. Feyo de Azevedo; P. Pimenta; F. R. Oliveira; E. C. Ferreira; de Azevedo, S.Feyo; Pimenta, P.; Oliveira, F.; Ferreira, E.. "Studies on on-line state and parameter estimation through a real-time process simulator". In Modeling and Control of Biotechnical Processes 1992 (2nd IFAC Symposium) and Computer Applications to Fermentation Technology (5th International Conference), 453-458. Oxford: Pergamon Press, 1992.
    Published
  34. E. C. Ferreira; J. C. Duarte. "Dynamic modelling of complex enzymatic reactions". In Scientific Computing and Automation (Europe) 1990, 211-220. Amsterdam: Elsevier Science Publishers, 1990.
    Published
  35. Ferreira, E.C.; Duarte, J.C.. "Chapter 18 Dynamic Modelling of Complex Enzymatic Reactions". In Data Handling in Science and Technology, 211-220. Amsterdam: Elsevier, 1990.
    Published • 10.1016/S0922-3487(08)70168-0
  36. E. C. Ferreira; L. M. Pereira; S. Feyo de Azevedo; J. C. Duarte. "Parameter estimation of kinetics and modelling in methanogenic fermentation of Methanosarcina barkeri". In Computer Applications in Fermentation Technology: Modelling and Control of Biotechnological Processes, 217-220. London, United Kingdom: Elsevier Applied Science Publishers, 1989.
    Published
Conference abstract
  1. S. Carneiro; P: Maia; M. Rocha; E. C. Ferreira; I. Rocha. "Constraint-based approach for in silico Escherichia coli combined regulatory/metabolic modelling". Paper presented in Congresso Micro '07 - Biotec '07 - XXIII JPG, Lisboa, 2007.
    Published
  2. J. C. Costa; I. Moita; A. A. Abreu; E. C. Ferreira; M. M. Alves. "Use of morphological and physiological information to identify changes in anaerobic granular sludge during organic overloads". Paper presented in Congresso Micro '07 - Biotec '07 - XXIII JPG, Lisboa, 2007.
    Published
  3. R. S. Costa; S. Carneiro; I. Rocha; E. C. Ferreira. "Effect of pH variation on the acetate “switch” and biomass growth in an Escherichia coli aerobic fermentation: global gene expression profiles analysis". Paper presented in Congresso Micro '07 - Biotec '07 - XXIII JPG, Lisboa, 2007.
    Published
  4. A. Lourenço; A. Simões; J. J. Almeida; M. Rocha; I. Rocha; E. C. Ferreira. "Literature mining applied to systems biology information retrieval". Paper presented in Congresso Micro '07 - Biotec '07 - XXIII JPG, Lisboa, 2007.
    Published
  5. D. P. Mesquita; O. Dias; E. C. Ferreira; A. L. Amaral. "Monitoring activated sludge systems from wastewater treatment plants: automated image analysis procedures and their relation with operating parameters". Paper presented in Congresso Micro '07 - Biotec '07 - XXIII JPG, Lisboa, 2007.
    Published
  6. A. Nicolau; S. Santos; C. Carvalho; E. C. Ferreira; J. Azeredo. "Pitfalls and successes in phage therapy: the involvement of the UMinho Team in the European Project Phagevet-P". Paper presented in Congresso Micro '07 - Biotec '07 - XXIII JPG, Lisboa, 2007.
    Published
  7. P. Pimenta; S. Feyo de Azevedo; E. C. Ferreira; F. R. Oliveira. "Model-based identification and control on baker's yeast fed-batch fermentation". Paper presented in 6th European Congress on Biotechnology, Firenze, 1993.
    Published
Conference paper
  1. Forte, Ana Cristina Figueiras; Dourado, Fernando; Gama, F. M.; Ferreira, Eugénio C.. "Economic & environmental assessment of bacterial cellulose production". 2021.
  2. Lima, Diogo Batista; Lagoa, Davide Rafael Santos; Cruz, Fernando João Pereira da; Bastos, José; Capela, João; Ferreira, Eugénio C.; Rocha, Miguel; Dias, Oscar. "merlin v4: an updated platform for reconstructing genome-scale metabolic models". 2020.
  3. Melo, A. R. B.; Padrão, Jorge; Nicolau, Ana; Quintelas, Cristina; Ferreira, Eugénio C.; Mesquita, D. P.. "Toxicity assessment of ibuprofen on activated sludge by respirometric technique". 2019.
  4. Ferreira, Eugénio C.. "Biotecnologia para o desenvolvimento sustentado da bioeconomia do Norte de Portugal". 2019.
  5. Paulo, Ana M. S.; Costa, Joana; Amorim, Catarina L.; Mesquita, Daniela P.; Ferreira, Eugénio C.; Castro, Paula M.L.; Costa, Joana Sofia Gomes; Mesquita, D. P.; Castro, Paula M. L.. "Impact of industrial wastewater on aerobic granules morphology and nitrification process in bioreactors". 2019.
  6. Quintelas, Cristina Maria Catalão; Melo, António Renê Benevides de; Mesquita, D. P.; Ferreira, Eugénio C.; Amaral, António Luís Pereira do. "Rapid method for the quantification and identification of emerging compounds in wastewater based in nir spectroscopy and chemometrics". 2019.
  7. Forte, Ana Cristina Figueiras; Dourado, Fernando; Gama, F. M.; Ferreira, Eugénio C.. "Life cycle assessment (cradle-to-gate) of bacterial cellulose production". 2019.
  8. Soares da Silva, F. A. G.; Dourado, Fernando; Ferreira, Eugénio C.; Poças, F.; Gama, F. M.. "Optimization of bacterial nanocellulose fermentation using lignocellulosic residues and development of novel BNC-starch composites". 2019.
  9. Forte, Ana; Dourado, Fernando; Gama, F. M.; Ferreira, Eugénio C.. "Cradle-to-gate assessment of bacterial cellulose production". 2019.
  10. Silva, Francisco Almeida Garrett Soares; Carvalho, Ricardo Emanuel Silva; Ferreira, Eugénio C.; Dourado, Fernando; Poças, Maria Fátima; Gama, F. M.. "Optimization of bacterial nanocellulose fermentation using lignocellulosic residues and development of novel BNC-starch composites". 2019.
  11. Leal, Cristiano; Val, Angeles; Zlatkova, Anastasiya; Araújo, Bárbara; Mesquita, D. P.; Amaral, A. Luís; Ferreira, Eugénio C.. "Density and sludge volume index estimation in mature aerobic granular sludge by quantitative image analysis and chemometrics tools". 2018.
  12. Lagoa, D.; Liu, Filipe; Ferreira, Eugénio C.; Faria, J.; Henry, C.; Dias, Oscar. "Towards a genome-wide transport systems encoding genes tracker". 2018.
  13. Quintelas, Cristina; Mesquita, D. P.; Ferreira, Eugénio C.; Amaral, A. Luís. "Quantification of pharmaceuticals contaminants in wastewaters by NIR spectroscopy". 2018.
  14. Leal, Cristiano; Val, Angeles; Zlatkova, Anastasiya; Araújo, Bárbara; Mesquita, D. P.; Amaral, A. Luís; Ferreira, Eugénio C.. "Density and sludge volume index estimation in mature aerobic granular sludge by quantitative image analysis and chemometrics tools". 2018.
  15. Lagoa, D.; Liu, Filipe; Ferreira, Eugénio C.; Faria, J.; Henry, C.; Dias, Oscar. "Towards a genome-wide transport systems encoding genes tracker". 2018.
  16. Ferreira, V.; Cortez, Susana; Padrão, Jorge; Mesquita, D. P.; Dias, Nicolina M.; Duarte, Maria Salomé; Ferreira, Eugénio C.; et al. "Impact of professional cleaning agent used in fish-canning industry in wastewater treatment". 2018.
  17. Ferreira, Eugénio C.. "CEB: Centro de Engenharia Biológica [da] Universidade do Minho". 2018.
  18. Santos, Sílvio Roberto Branco; Brandão, Ana Catarina; Oliveira, A.; Melo, Luís Daniel Rodrigues; Pinto, Graça; Oliveira, Hugo Alexandre Mendes; Ferreira, Eugénio C.; Azeredo, Joana. "New bacterial biorecognition elements from phage origin". 2017.
  19. Mesquita, D. P.; Amaral, A. Luís; Ferreira, Eugénio C.. "Quantitative Image Analysis: a monitoring tool in wastewater treatment". 2017.
  20. Oliveira, Ana; Mesquita, D. P.; Amorim, Catarina L.; Amaral, A. Luís; Ferreira, Eugénio C.; Van Loosdrecht, Mark; Castro, Paula M. L.. "Extraction and characterization of extracellular polymeric substances from aerobic granular sludge from a full-scale sequencing batch reactor in Portugal". 2017.
  21. Amaral, A. Luís; Genisheva, Zlatina; Quintelas, Cristina; Mesquita, D. P.; Ferreira, Eugénio C.; Oliveira, José Maria. "Wine chemical characterization by near infrared spectroscopy and chemometric analysis". 2017.
  22. Quintelas, Cristina Maria Catalão; Mesquita, D. P.; Ferreira, Eugénio C.. "Application of near infrared spectroscopy as a process analytical technology". 2017.
  23. Quintelas, Cristina; Mesquita, D. P.; Ferreira, Eugénio C.. "Removal of paracetamol by an activated sludge bioreactor". 2017.
  24. Mesquita, D. P.; Quintelas, Cristina; Ferreira, Eugénio C.. "Characterization of the effects of pharmaceuticals in activated sludge using quantitative image analysis". 2017.
  25. Oliveira, Emanuel; Ferreira, Eugénio C.; Dias, Oscar. "Modelling interspecies interactions of syntrophic communities". 2017.
  26. Oliveira, Ana; Mesquita, Daniela P.; Amorim, Catarina L.; Amaral, A. L.; Ferreira, Eugénio C.; Loosdrecht, Mark V.; Castro, Paula M. L.. "Extraction and characterization of extracellular polymeric substances from aerobic granular sludge from a full-scale sequencing batch reactor in Portugal". 2017.
  27. Oliveira, Ana; Mesquita, D. P.; Amorim, Catarina L.; Amaral, A. Luís; Ferreira, Eugénio C.; Van Loosdrecht, Mark; Castro, Paula M. L.. "Extraction and characterization of extracellular polymeric substances from aerobic granular sludge from a full-scale sequencing batch reactor in Portugal". 2017.
  28. Dias, Oscar; Santos, Sophia Torres; Ferreira, Eugénio C.; Rocha, I.. "Towards an improved version of Kluyveromyces lactis genome-scale metabolic model". 2016.
  29. Quintelas, Cristina; Mesquita, D. P.; Ferreira, Eugénio C.. "Remoção de ibuprofeno por um sistema aeróbio de lamas ativadas". 2016.
  30. Sargo, Cíntia R .; Silva, Adilson J.; Giordano, Roberto C; Ferreira, Eugénio C.; Rocha, I.; Zangirolami, Teresa C.. "Produção e consumo de acetato em cultivos de Salmonella typhimurium em condições aeróbias". 2015.
  31. Amaral, A. L.; Mesquita, D. P.; Braga, Adelaide; Belo, Isabel; Ferreira, Eugénio C.. "Evaluation of dimorphic Yarrowia lipolytica strains growth in different culture media by quantitative image analysis". 2015.
  32. Dias, Oscar; Saraiva, João; Ferreira, Eugénio C.; Rocha, I.. "Towards a genome-scale metabolic model of the Streptococcus pneumoniae R6 avirulent strain". 2015.
  33. Santos, Sílvio Roberto Branco; Martins, Ivone M.; Costa, Ana Rita Martins; Nóbrega, Franklin Luzia; Lavigne, Rob; Ferreira, Eugénio C.; Azeredo, Joana. "Exploiting the proteins encoded in the genome of the broad host range Salmonella phage PVP-SE1". 2015.
  34. Quintelas, C.; Mesquita, D. P.; Lopes, João A.; Ferreira, Eugénio C.; Sousa, Clara Cecília Santana. "Near-infrared spectroscopy for the detection and quantification of bacterial contaminations in pharmaceutical products". 2015.
  35. Silva, A.; Sargo, Cintia Regina; Zangirolami, Teresa Cristina; Giordano, Roberto de Campos; Rocha, Isabel; Ferreira, Eugénio C.. "Metabolic profiling of secreted fermentative byproducts by Salmonella typhimurium". 2014.
  36. Portela, C.; Villas-Bôas, S.; Rocha, I.; Ferreira, E.C.. "Genome scale metabolic network reconstruction of the pathogen Enterococcus faecalis". 2013.
    10.3182/20131216-3-IN-2044.00067
  37. Ferreira, Eugénio C.. "Bio-engineering Systems at MIT Portugal Program". 2013.
  38. Soons, Z.I.T.A.; Ferreira, E.C.; Rocha, I.. "Selection of elementary modes for bioprocess control". 2010.
    10.3182/20100707-3-BE-2012.0019
  39. Machado, D.; Costa, R.S.; Rocha, M.; Rocha, I.; Tidor, B.; Ferreira, E.C.. "Model transformation of metabolic networks using a Petri net based framework". 2010.
  40. Costa, R.S.; Machado, D.; Ferreira, E.C.; Rocha, I.. "Evaluating the integration of proteomic data for the prediction of intracellular fluxes after knockout experiments". 2010.
    10.3182/20100707-3-BE-2012.0108
  41. Dias, O.; Rocha, M.; Ferreira, E.C.; Rocha, I.. "Merlin: Metabolic models reconstruction using genome-scale information". 2010.
    10.3182/20100707-3-BE-2012.0076
  42. Rocha, I.; Dias, Oscar; Rocha, Miguel; Ferreira, Eugénio C.. "Genome-scale metabolic models reconstruction of less characterized organisms with Merlin". 2010.
  43. Rocha, I.; Maia, Paulo; Pinto, José Pedro Basto Gouveia Pereira; Vilaça, Paulo Ricardo Carvalho; Soares, Simão Pedro Pinho; Nielsen, J.; Patil, K. R.; et al. "OptFlux: an open-source software platform for in silico metabolic engineering". 2010.
  44. Nobre, Clarisse; Santos, M.J.; Dominguez, Ana; Torres, Duarte; Peres, António M.; Rocha, Isabel; Ferreira, Eugénio C.; Rodrigues, Lígia R.; Teixeira, José A.. "Adsorption equilibrium of fructose, glucose and sucrose for cationic resins in the sodium and potassium form". 2009.
  45. Ferreira, Eugénio C.. "Systems Biology for the development of microbial cell factories". 2009.
  46. Lourenço, A.; Carneiro, S.; Carreira, R.; Rocha, M.; Rocha, I.; Ferreira, E.. "A tool for the automatic and manual annotation of biomedical documents". 2008.
  47. Loureno, 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". 2008.
    10.1109/BIBE.2008.4696707
  48. Mendes, R.; Lourenço, A.; Carneiro, S.; Rocha, M.; Rocha, I.; Ferreira, E.C.. "A framework for the integrated analysis of metabolic and regulatory networks". 2008.
    10.1109/BIBE.2008.4696727
  49. Maia, P.; Rocha, I.; Ferreira, E.C.; Rocha, M.. "Evaluating evolutionary multiobjective algorithms for the in silico optimization of mutant strains". 2008.
    10.1109/BIBE.2008.4696733
  50. Rocha, I.; Veloso, A.; Carneiro, S.; Ferreira, E.; Costa, R.. "Implementation of a specific rate controller in a fed-batch E. coli fermentation". 2008.
    10.3182/20080706-5-KR-1001.3513
  51. Lourenço, Anália; Carreira, Rafael; Carneiro, Sónia; Maia, Paulo; Ferreira, Eugénio C.; Glez-Peña, D.; Fdez-Riverola, F.; Rocha, Miguel; Rocha, I.. "The @Note biomedical text mining workbench". 2008.
  52. Carneiro, S.; Lourenço, Anália; Mendes, Rui; Rocha, Miguel; Ferreira, Eugénio C.; Rocha, I.. "Network analysis of an integrated metabolic/regulatory model of Escherichia coli". 2008.
  53. A. Lourenço; A. Simões; J. J. Almeida; M. Rocha; I. Rocha; E. C. Ferreira. "An Ontology-Based Approach To Systems Biology Literature Retrieval and Processing". Paper presented in 13th Portuguese Conference in Artificial Intelligence - EPIA 2007, Guimarães, 2007.
    Published
  54. E. Herrera; J. Ramírez; B. Castillo; E. C. Ferreira. "Modelo Exacto Difuso de un Proceso Fermentativo Conmutado". Paper presented in Congreso Nacional de Control Automático, AMCA 2007, Monterrey, Nuevo León, 2007.
    Published
  55. J. C. Costa; M. M. Alves; E. C. Ferreira. "Integration of morphological and physiological data through Principal Component Analysis to identify the effect of organic overloads on anaerobic granular sludge". Paper presented in 11th IWA World Congress on Anaerobic Digestion, Brisbane, 2007.
    Published
  56. J. C. Costa; I. Moita; E. C. Ferreira; M. M. Alves. "Morphology and physiology of anaerobic granular sludge exposed to organic solvents". Paper presented in 11th IWA World Congress on Anaerobic Digestion, Brisbane, 2007.
    Published
  57. I.A.C.P. Espirito-Santo; E. M. G. P. Fernandes; M. A. Araújo; E. C. Ferreira. "Cost Minimization of a WWTP Using an Augmented Lagrangian Pattern Search Based Solver". Paper presented in 10th IWA Specialised Conference on Design, Operation and Economics of Large Wastewater Treatment Plants, Vienna, 2007.
    Published
  58. A. M. A. Dias; M. M. Alves; E. C. Ferreira. "Application of computational intelligence techniques for monitoring and prediction of biological wastewater treatment systems". Paper presented in 3rd International IWA Conference on Automation in Water Quality Monitoring - AutMoNet2007, Gent, 2007.
    Published
  59. A. M. A. Dias; I. Moita; R. Pâscoa; M. M. Alves; J. A. Lopes; E. C. Ferreira; A. L. Amaral. "Activated sludge process monitoring through in-situ NIR spectral analysis". Paper presented in 3rd International IWA Conference on Automation in Water Quality Monitoring - AutMoNet2007, Gent, 2007.
    Published
  60. Y. P. Ginoris; A. L. Amaral; E. C. Ferreira; M. A. Z. Coelho; A. Nicolau. "Aplicação de técnicas de análise de imagem e de estatística multivariável no reconhecimento de protozoários e metazoários típicos de sistemas por lodos ativados". Paper presented in 24º Congresso Brasileiro de Engenharia Sanitária e Ambiental, Belo Horizonte, 2007.
    Published
  61. E. Herrera; B. Castillo; J. Ramírez; E. C. Ferreira. "Exact Fuzzy Observer for a Baker’s Yeast Fed-Batch Fermentation Process". Paper presented in FUZZ-IEEE 2007 - IEEE International Conference on Fuzzy Systems, London, 2007.
    Published • 10.1109/FUZZY.2007.4295502
  62. A. C. Veloso; I. Rocha; E. C. Ferreira; Veloso, A.C.A.; Rocha, I.; Ferreira, E.C.. "Estimation of biomass concentration using interval observers in an E. coli fed-batch fermentation". Paper presented in 10th International IFAC Symposium on Computer Applications on Biotechnology, Cancún, 2007.
    Published
  63. E. Herrera; B. Castillo; J. Ramírez; E. C. Ferreira; Herrera, E.; Castillo, B.; Ramírez, J.; Ferreira, E.C.. "Takagi-Sugeno Multiple-Model controller for a continuous baking yeast fermentation process". Paper presented in 10th International IFAC Symposium on Computer Applications on Biotechnology, Cancún, 2007.
    Published
  64. M. Rocha; J. P. Pinto; I. Rocha; E. C. Ferreira. "Optimization of Bacterial Strains with Variable-Sized Evolutionary Algorithms". Paper presented in 2007 IEEE Symposium on Computational Intelligence in Bioinformatics and Computational Biology (CIBCB 2007), Honolulu, Hawaii, 2007.
    Published
  65. Amaral, A.L.; Mota, M.; Ferreira, E.C.; Crispim, A.; A. L. Amaral; M. Mota; E. C. Ferreira; A. Crispim. "Image analysis methodology to study the evolution of chromium penetration in chromium tannage". Paper presented in Computational Modelling of Objects Represented in Images : Fundamentals, methods and applications, Coimbra, 2007.
    Published
  66. Rocha, M.; Pinto, J.P.; Rocha, I.; Ferreira, E.. "Optimization of bacterial strains with variable-sized evolutionary algorithms". 2007.
  67. I.A.C.P. Espirito-Santo; E. M. G. P. Fernandes; M. A. Araújo; E. C. Ferreira. "Contribution of a Simple Sludge Treatment in a WWTP Optimization Procedure". Paper presented in 5th WSEAS Int. Conf. on System Science and Simulation in Engineering, Tenerife, Canary Islands, 2006.
    Published
  68. A. I. F. Vaz; E. C. Ferreira; A. M. T. Mota. "Optimal trajectory approximation by cubic splines on fed-batch control problems". Paper presented in 5th WSEAS Int. Conf. on System Science and Simulation in Engineering, Tenerife, 2006.
    Published
  69. D. P. Mesquita; M. A. Z. Coelho; E. C. Ferreira. "Efeito do sal no desempenho de um reator batelada sequencial". Paper presented in XVI Congresso Brasileiro de Engenharia Química - COBEQ2006, Santos, 2006.
    Published
  70. I.A.C.P. Espirito-Santo; E. M. G. P. Fernandes; M. A. Araújo; E. C. Ferreira. "Optimization and simulation of secondary settler models". Paper presented in 6th WSEAS International Conference on Simulation, Modelling and Optimization, Lisboa, 2006.
    Published
  71. I. Rocha; E. C. Ferreira. "Specific growth rate regulation in a simulated fed-batch E. coli fermentation". Paper presented in CONTROLO2006 – 7th Portuguese Conference on Automatic Control, Lisboa, 2006.
    Published
  72. R. Mendes; I. Rocha; E. C. Ferreira; M. Rocha. "Comparison of algorithms for the optimization of fermentation processes". Paper presented in 2006 IEEE Congress on Evolutionary Computation, Vancouver, 2006.
    Published
  73. A. I. F. Vaz; E. C. Ferreira. "Optimal control of fed-batch processes with particle swarm optimization". Paper presented in XXIX Congreso Nacional de Estadística e Investigación Operativa, Tenerife, 2006.
    Published
  74. I. Rocha; A. C. Veloso; E. C. Ferreira. "Design of estimators for specific growth rate control in a fed-batch E. coli fermentation". Paper presented in 5th MATHMOD Vienna – 5th Vienna Symposium on Mathematical Modelling, Vienna, 2006.
    Published
  75. Mendes, R.; Rocha, I.; Ferreira, E.C.; Rocha, M.. "A comparison of algorithms for the optimization of fermentation processes". 2006.
  76. I.A.C.P. Espirito-Santo; E. M. G. P. Fernandes; M. M. Araújo; E. C. Ferreira. "Biological process optimal design in a wastewater treatment plant". Paper presented in 6th World Congress on Structural and Multidisciplinary Optimization, Rio de Janeiro, 2005.
    Published
  77. P. Araya-Kroff; A. L. Amaral; M. Mota; E. C. Ferreira; M. M. Alves. "Análisis de imagen para la cuantificación de cambios morfológicos en biomasa granular, inducidos por la presencia de nitrato en reactores EGSB". Paper presented in XVI Congreso de Ingeniería Sanitaria y Ambiental Aidis – Chile, II Simposio Latinoamericano de Lodos y Biosólidos, Viña del Mar, 2005.
    Published
  78. E. Vivanco; A. Puñal; C. Pizarro; E. C. Ferreira; M. M. Alves; R. Chamy. "Effect of addition of an ammonium source in UASB and EGSB reactors when treating low concentrated wastewater: granules morphology". Paper presented in VIII Latin American Workshop and Symposium on Anaerobic Digestion, Montevideo, 2005.
    Published
  79. S. Carneiro; A. C. Veloso; A. L. Amaral; I. Rocha; E. C. Ferreira. "Image analysis as a tool for viability and recombinant protein production assessment during E. coli fermentations". Paper presented in CHEMPOR 2005 - 9th International Chemical Engineering Conference, Coimbra, 2005.
    Published
  80. A. C. Veloso; I. Rocha; E. C. Ferreira. "Design of Interval Observers for an E. coli Fed-Batch Fermentation with Uncertain Inputs". Paper presented in CHEMPOR 2005 - 9th International Chemical Engineering Conference, Coimbra, 2005.
    Published
  81. A. L. Amaral; O. Rocha; C. Gonçalves; A. A. Ferreira; E. C. Ferreira. "Development of Image Analysis Methods to Evaluate Barley / Malt Grain Size". Paper presented in CHEMPOR 2005 - 9th International Chemical Engineering Conference, Coimbra, 2005.
    Published
  82. F. Vidigueira; E. C. Ferreira. "Estratégias de Minimização de Efluentes na Síntese e Integração de Processos". Paper presented in CHEMPOR 2005 - 9th International Chemical Engineering Conference, Coimbra, 2005.
    Published
  83. M. Rocha; I. Rocha; E. C. Ferreira. "A New Representation in Evolutionary Algorithms for the Optimization of Bioprocesses". Paper presented in 2005 IEEE Congress on Evolutionary Computation, Edimburgo, 2005.
    Published
  84. O. C. Pires; C. Palma; I. Moita; J. C. Costa; M. M. Alves; E. C. Ferreira. "A Fuzzy-Logic Based Expert System for Diagnosis and Control of an Integrated Wastewater Treatment". Paper presented in 2nd Mercosur Congress on Chemical Engineering – ENPROMER and 4th Mercosur Congress on Process Systems Engineering, Rio de Janeiro, 2005.
    Published
  85. A. C. Veloso; I. Rocha; E. C. Ferreira. "On-Line Estimation of Biomass in an E. coli Fed-Batch Fermentation". Paper presented in 2nd Mercosur Congress on Chemical Engineering – ENPROMER and 4th Mercosur Congress on Process Systems Engineering, Rio de Janeiro, 2005.
    Published
  86. A. L. Amaral; M. M. Alves; M. Mota; E. C. Ferreira. "Aplicações de Técnicas de Processamento e Análise de Imagem em Processos Biotecnológicos". Paper presented in XV Simpósio Nacional de Bioprocessos – SINAFERM 2005, Recife, 2005.
    Published
  87. R. Pinto; A. L. Amaral; J. Carvalho; E. C. Ferreira; F. M. Gama. "Determinação da Concentração de CBD-FITC Adsorvidos em Fibras por Análise de Imagem". Paper presented in XV Simpósio Nacional de Bioprocessos – SINAFERM 2005, Recife, 2005.
    Published
  88. M. da Motta; M. N. Pons; V. Lins da Silva; A. Clemente de Andrade; A. L. Amaral; E. C. Ferreira. "Utilização do Processamento Digital de Imagens no Monitoramento de Estações de Tratamento de Efluentes". Paper presented in XV Simpósio Nacional de Bioprocessos – SINAFERM 2005, Recife, 2005.
    Published
  89. D.G.P. Pacífico; E. C. Ferreira; B. V. Kilikian. "Influência da velocidade específica de crescimento de Monascus purpureus ATCC36928 na produção de pigmentos vermelhos". Paper presented in XV Simpósio Nacional de Bioprocessos – SINAFERM 2005, Recife, 2005.
    Published
  90. O. C. Pires; C. Palma; J. C. Costa; I. Moita; M. M. Alves; E. C. Ferreira. "Knowledge-based fuzzy system for diagnosis and control of an integrated biological wastewater treatment process". Paper presented in 2nd IWA Conference on Instrumentation, Control and Automation, Busan, 2005.
    Published
  91. Espírito-Santo, I.A.C.P.; Fernandas, E.M.G.P.; Araújo, M.M.; Ferreira, E.C.; E. M. G. P. Fernandes; I.A.C.P. Espirito-Santo; M. M. Araújo; E. C. Ferreira. "NEOS server usage in wastewater treatment cost minimization". 2005.
    Published
  92. Rocha, M.; Rocha, I.; Ferreira, E.. "A new representation in Evolutionary Algorithms for the optimization of bioprocesses". 2005.
  93. Veloso, A.C.A.; Rocha, I.; Ferreira, E.C.; A. C. Veloso; I. Rocha; E. C. Ferreira. "Design of on-line state estimators for a recombinant E. coli FED-batch fermentation". Paper presented in 16th IFAC World Congress, Praha, 2005.
    Published
  94. Carneiro, S.; Rocha, I.; Ferreira, Eugénio C.. "A systems biology approach for the characterization of metabolic bottlenecks in recombinant protein production processes". 2005.
  95. E. M. G. P. Fernandes; I.A.C.P. Espirito-Santo; M. M. Araújo; E. C. Ferreira. "Optimization of wastewater treatment processes". Paper presented in XXVIII Congreso de Estadística e Investigación Operativa, Cádiz, 2004.
    Published
  96. I.A.C.P. Espirito-Santo; E. M. G. P. Fernandes; M. M. Araújo; E. C. Ferreira. "Optimização de um processo biológico de tratamento de águas residuais". Paper presented in 8ª Conferência Nacional de Ambiente, Lisboa, 2004.
    Published
  97. A. I. F. Vaz; E. C. Ferreira. "Air Pollution Control with Semi-Infinite Programming". Paper presented in Congreso XXVIII Congreso Nacional de Estadística e Investigación Operativa (SEIO), Cádiz, 2004.
    Published
  98. A. I. F. Vaz; E. C. Ferreira. "Optimização e Controlo da Poluição Atmosférica". Paper presented in 8ª Conferência Nacional de Ambiente, Lisboa, 2004.
    Published
  99. M. M. Alves; M. A. Pereira; A. L. Amaral; M. N. Pons; M. Mota; E. C. Ferreira. "Image Analysis as a Tool to Predict Washout in Sludge Bed Reactors Through the Quantification of Microbial Filamentous Structures". Paper presented in 10th World Congress on Anaerobic Digestion, Montreal, 2004.
    Published
  100. P. Araya-Kroff; A. L. Amaral; E. C. Ferreira; P. Silva; M. Mota; M. M. Alves. "Monitoring granular stability in an industrial UASB reactor treating brewery wastewater". Paper presented in 10th World Congress on Anaerobic Digestion, Montreal, 2004.
    Published
  101. M. M. Alves; M. A. Pereira; A. L. Amaral; M. N. Pons; M. Mota; E. C. Ferreira; P. Araya-Kroff. "Image analysis to quantify morphological changes in granular sludge induced by nitrate in EGSB reactors". Paper presented in 10th World Congress on Anaerobic Digestion, Montreal, 2004.
    Published
  102. E. C. Ferreira. "Blended Learning in Bioprocess Systems Engineering Education: Issues, Methods, and Applications". Paper presented in ESCAPE-14: European Symposium on Computer Aided Process Engineering, Lisboa, 2004.
    Published
  103. J. A. P. Coutinho; M. A. Z. Coelho; E. C. Ferreira; I. Belo. "Determination and modeling of yeast viability under stress conditions". Paper presented in ESCAPE-14: European Symposium on Computer Aided Process Engineering, Lisboa, 2004.
    Published
  104. I. Rocha; E. C. Ferreira. "Yield and kinetic parameters estimation and model reduction in a recombinant E. coli fermentation". Paper presented in ESCAPE-14: European Symposium on Computer Aided Process Engineering, Lisboa, 2004.
    Published
  105. Amaral, António Luís Pereira do; Neves, L.; Ferreira, Eugénio C.. "Desenvolvimento de métodos de análise de imagem para avaliação do calibre de grãos da cevada/malte". 2004.
  106. Coelho, Maria Alice Z.; Amaral, A. Luís; Belo, Isabel; Mota, Manuel; Coutinho, João A. P.; Ferreira, Eugénio C.. "Use of image analysis technique for the identification and pursuit of ethanol processes". 2004.
  107. V. Lubenova; I. Rocha; E. C. Ferreira. "Estimation of Biomass Concentration and Multiple Specific Growth Rates of Fed-Batch Fermentation of Recombinant E. coli". Paper presented in International Conference Automatics and Informatics’03, Sofia, 2003.
    Published
  108. A. L. Amaral; S. Rodrigues; M. Mota; E. C. Ferreira. "Morphological Characterisation of Biomass in Wastewater Treatment using Partial Least Squares". Paper presented in Second IASTED International Conference on Visualization, Imaging, and Image Processing, Málaga, 2002.
    Published
  109. P. Araya-Kroff; A. L. Amaral; L. Neves; E. C. Ferreira; M. M. Alves; M. Mota. "Image analysis as a tool to recognize anaerobic granulation time". Paper presented in VII Latin American Workshop and Symposium on Anaerobic Digestion, Merida, 2002.
    Published
  110. M. da Motta; A. L. Amaral; L. Neves; P. Araya-Kroff; E. C. Ferreira; M. M. Alves; M. Mota; et al. "Efeito da Diluição na Caracterização da Biomassa de Sistemas de Tratamentos de Efluentes por Análise de Imagem". Paper presented in COBEQ 2002 - XIV Congresso Brasileiro de Engenharia Quimica, Natal, 2002.
    Published
  111. I. Rocha; E. C. Ferreira. "Model-Based Adaptive Control of Acetate Concentration During the Production of Recombinant Proteins with E. coli". Paper presented in 15th IFAC World Congress on Automatic Control, Barcelona, 2002.
    Published
  112. I. Rocha; E. C. Ferreira. "Optimisation Methods for Improving Fed-Batch Cultivation of E. coli Producing Recombinant Proteins". Paper presented in 10th Mediterranean Conference on Control and Automation (MED2002), Lisbon, 2002.
    Published
  113. M. A. Pereira; K. Roest; A. J. M. Stams; A. D. L. Akkermans; A. L. Amaral; M. N. Pons; E. C. Ferreira; M. Mota; M. M. Alves. "Image Analysis, Methanogenic Activity Measurements and Molecular Biological Techniques to Monitor Granular Sludge from an EGSB Reactor Fed With Oleic Acid". Paper presented in International Specialised Conference on Biofilm Monitoring, Porto, 2002.
    Published
  114. Rocha, I.; Ferreira, E.C.. "Model-based adaptive control of acetate concentration during the production of recombinant proteins with E. coli". 2002.
  115. A. L. Amaral; M. da Motta; M. N. Pons; H. Vivier; M. Mota; E. C. Ferreira. "Survey of a Wastewater Treatment Plant Microfauna by Image Analysis". Paper presented in 8th International Chemical Engineering – CHEMPOR’2001, Aveiro, 2001.
    Published
  116. A. L. Amaral; M. A. Pereira; L. Neves; M. da Motta; M. N. Pons; H. Vivier; M. Mota; E. C. Ferreira; M. M. Alves. "Characterisation by image analysis of anaerobic sludge from two EGSB reactors treating oleic acid: automatic detection of granules disintegration". Paper presented in 9th World Congress on Anaerobic Digestion, Antwerpen, 2001.
    Published
  117. M. da Motta; M. N. Pons; H. Vivier; A. L. Amaral; E. C. Ferreira; M. Mota. "Study of Protozoa Population in Wastewater Treatment Plants by Image Analysis". Paper presented in XIX Interamerican Congress of Chemical Engineering/XIV Brazilian Congress of Chemical Engineering, Águas de São Pedro, 2000.
    Published • 10.1590/S0104-66322001000100009
  118. V. Lubenova; E. C. Ferreira. "Adaptive Algorithms for Estimation of Multiple Biomass Growth Rates and Biomass Concentration in a Class of Bioprocesses". Paper presented in CONTROLO'2000: 4th Portuguese Conference on Automatic Control, Guimarães, 2000.
    Published
  119. M. da Motta; M. N. Pons; N. Roche; A. L. Amaral; E. C. Ferreira; M. Mota. "Automated Monitoring of Activated Sludge Using Image Analysis". Paper presented in 1st World Congress of the International Water Association, Paris, 2000.
    Published
  120. J. Baeza; E. C. Ferreira; J. Lafuente. "Knowledge-based supervision and control of WWTP: A real-time implementation". Paper presented in 4th International Symposium on Environmental Biotechnology, Noordwijkerhout, 2000.
    Published
  121. M. da Motta; M. N. Pons; N. Roche; A. L. Amaral; E. C. Ferreira; M. Mota. "Analyse des Flocs Bactériens et de la Microfaune des Boues Activées para Analyse d'Image". Paper presented in GRUTTEE - 3e Congrès Internatonal L'Eau et sa Réutilisation, 3rd International Research Conference Water Reuse - Water Treatment Plants Operation, Toulouse, 1999.
    Published
  122. A. L. Amaral; M. Mota; E. C. Ferreira. "Aplicações de Técnicas de Análise de Imagem em Microbiologia Ambiental". Paper presented in 6º Conferência Nacional sobre a Qualidade do Ambiente, Lisboa, 1999.
    Published
  123. J. Baeza; E. C. Ferreira; J. Lafuente. "Knowledge-Based Distributed System for Supervision and Control of Wastewater Treatment Processes". Paper presented in Water Quality International '98, Vancouver, 1998.
    Published
  124. A. L. Amaral; M. M. Alves; M. Mota; E. C. Ferreira. "Morphological Characterisation of Microbial Aggregates by Image Analysis". Paper presented in RecPad’97 - 9th Portuguese Conference on Pattern Recognition, Coimbra, 1997.
    Published
  125. C. Rocha; E. C. Ferreira. "Identification of yield coefficients in a baker’s yeast model - An optimal design experimental approach". Paper presented in III Congresso Ibérico de Biotecnologia - BIOTEC’96, Valladolid, 1996.
    Published
  126. E. C. Ferreira; S. Feyo de Azevedo. "A New Adaptive Scheme for the Adaptive Linearizing Control of Bioprocesses". Paper presented in 2nd Portuguese Control Conference on Automatic Control - CONTROLO 96, Porto, 1996.
    Published
  127. Ferreira, E.C.; Feyo de Azevedo, S.; E. C. Ferreira; S. Feyo de Azevedo. "Adaptive linearizing control of bioreactors". Paper presented in UKACC International Conference on CONTROL'96, Exete, 1996.
    Published • 10.1049/cp:19960721
  128. Ferreira, Eugénio C.; Mota, Manuel. "Sistema de tratamento por biodiscos". Paper presented in 1ªs Jornadas sobre Tratamento de Efluentes Vinícolas, 1994.
    Published
  129. R. Oliveira; E. C. Ferreira; F. R. Oliveira; S. Feyo de Azevedo. "A Study on the Convergence of Observer-Based Kinetics Estimators in Stirred Tank Bioreactors". Paper presented in 5th International Symposium on Process Systems Engineering, Kyongju, 1994.
    Published
  130. E. C. Ferreira; F. R. Oliveira; S. Feyo de Azevedo. "Requisitos e realização de uma instalação experimental para estudos de modelação e controlo em processos de fermentação". Paper presented in 1º Encontro Português de Controlo Automático - CONTROLO 94, Lisboa, 1994.
    Published
  131. Ferreira, Eugénio C.. "A disciplina de Instrumentação e Controlo na licenciatura em Engenharia Biológica". 1994.
  132. Ferreira, Eugénio C.; Mota, M.. "Lamas activadas - sistema de mistura completa". 1994.
  133. E. C. Ferreira; J. C. Duarte. "Aplicação de Técnicas de Estimativa em Linha em Engenharia de Bioprocessos". Paper presented in CONGRESSO 89 da Ordem dos Engenheiros, Coimbra, 1989.
    Published
Edited book
  1. E. C. Ferreira. BOOK OF ABSTRACTS OF CEB ANNUAL MEETING 2017. Braga, Portugal: Universidade do Minho. 2017.
    Published • 10.21814/cebsam2017 • Editor
  2. E. C. Ferreira. Metabolic Pathway Analysis 2015 - Programme and Abstracts. Braga, Portugal. 2015.
    Published • Editor
  3. E. C. Ferreira. Book of Abstracts of the 2nd Meeting of the Institute for Biotechnology and Bioengineering. Braga, Portugal: Universidade do Minho, Departamento de Engenharia Biológica. 2010.
    Published • Editor
  4. Teixeira, J.A.; Sanches, I.; Ferreira, E.C.; Fonseca, A.; Vicente, A.A.; Venâncio, A.; Oliveira, D.; et al. Book of Abstracts of MICROBIOTEC09. Braga; Vilamoura, Portugal: Universidade do Minho, Departamento de Engenharia Biológica. 2009.
    Published • Editor
  5. Ferreira, E.C.; Mota, M.. Book of Abstracts of the 10th International Chemical and Biological Engineering Conference - CHEMPOR 2008. Braga: Universidade do Minho, Departamento de Engenharia Biológica. 2008.
    Published • Editor
  6. E. C. Ferreira. Proceedings of the 10th International Chemical and Biological Engineering Conference - CHEMPOR 2008 (CD-ROM). Braga, Portugal: Universidade do Minho, Departamento de Engenharia Biológica. 2008.
    Published • Editor
  7. E. C. Ferreira. Engenharia Biológica – 20 Anos (1986-2006). Braga, Portugal: Universidade do Minho, Departamento de Engenharia Biológica. 2006.
    Published
  8. E. C. Ferreira; M. Mota. BIOTEC'98 - Book of Abstracts (IV Iberian Congress on Biotechnology, I Ibero-American Meeting on Biotechnology). Braga, Portugal: Universidade do Minho. Departamento de Engenharia Biológica. 1998.
  9. E. C. Ferreira; S. Feyo de Azevedo; K. Ch. A. M. Luyben; P. Osseweijer. Proceedings of the 2nd European Symposium on Biochemical Engineering Science. Porto, Portugal: Faculdade de Engenharia da Universidade do Porto. 1998.
    Published • Editor
Journal article
  1. Cristina Quintelas; Cláudia Rodrigues; Clara Sousa; Eugénio C. Ferreira; António L. Amaral. "Cookie composition analysis by Fourier transform near infrared spectroscopy coupled to chemometric analysis". Food Chemistry (2024): https://doi.org/10.1016/j.foodchem.2023.137607.
    10.1016/j.foodchem.2023.137607
  2. Fernando Cruz; João Capela; Eugénio C. Ferreira; Miguel Rocha; O. Dias. "BioISO: an objective-oriented application for assisting the curation of genome-scale metabolic models". IEEE/ACM Transactions on Computational Biology and Bioinformatics (2024): http://dx.doi.org/10.1109/tcbb.2023.3339972.
    10.1109/tcbb.2023.3339972
  3. Maria Salomé Duarte; G. Martins; Pedro Oliveira; Bruno Fernandes; Eugénio C. Ferreira; M. Madalena Alves; Frederico Lopes; Pereira MA; Paulo Novais. "A Review of Computational Modeling in Wastewater Treatment Processes". ACS ES&T Water (2023): http://dx.doi.org/10.1021/acsestwater.3c00117.
    10.1021/acsestwater.3c00117
  4. Adelaide Braga; Daniela P. Mesquita; Ana Catarina Cordeiro; Isabel Belo; Eugénio C. Ferreira; A. Luís Amaral. "Monitoring biotechnological processes through quantitative image analysis: Application to 2-phenylethanol production by Yarrowia lipolytica". Process Biochemistry (2023): http://dx.doi.org/10.1016/j.procbio.2023.03.019.
    10.1016/j.procbio.2023.03.019
  5. Daniela P. Mesquita; Cristina Quintelas; Eugénio C. Ferreira. "Fate and occurrence of microplastics in wastewater treatment plants". Environmental Science: Advances (2023): https://doi.org/10.1039/D3VA00167A.
    10.1039/D3VA00167A
  6. Antonio Melo; Joana Costa; Cristina Quintelas; Eugénio C. Ferreira; Daniela P. Mesquita. "Effects of desloratadine on activated sludge: Behaviour of EPS and sludge properties". Journal of Environmental Chemical Engineering (2022): http://dx.doi.org/10.1016/j.jece.2022.108415.
    10.1016/j.jece.2022.108415
  7. João Capela; Davide Lagoa; Ruben Rodrigues; Emanuel Cunha; Fernando Cruz; Ana Barbosa; José Bastos; et al. "merlin, an improved framework for the reconstruction of high-quality genome-scale metabolic models". Nucleic Acids Research (2022): https://doi.org/10.1093/nar/gkac459.
    10.1093/nar/gkac459
  8. Antonio Melo; Cristina Quintelas; Eugénio C. Ferreira; Daniela P. Mesquita. "The Role of Extracellular Polymeric Substances in Micropollutant Removal". Frontiers in Chemical Engineering (2022): http://dx.doi.org/10.3389/fceng.2022.778469.
    10.3389/fceng.2022.778469
  9. Leal, Cristiano; del Río, Angeles Val; Mesquita, Daniela P.; Amaral, António L.; Ferreira, Eugénio C.. "Prediction of sludge settleability, density and suspended solids of aerobic granular sludge in the presence of pharmaceutically active compounds by quantitative image analysis and chemometric tools". Journal of Environmental Chemical Engineering 10 2 (2022): 107136. http://dx.doi.org/10.1016/j.jece.2022.107136.
    Published • 10.1016/j.jece.2022.107136
  10. Cyntia Ely; Irina S. Moreira; João Paulo Bassin; Márcia W.C. Dezotti; Daniela P. Mesquita; Joana Costa; Eugénio C. Ferreira; Paula M.L. Castro. "Treatment of saline wastewater amended with endocrine disruptors by aerobic granular sludge: Assessing performance and microbial community dynamics". Journal of Environmental Chemical Engineering (2022): http://dx.doi.org/10.1016/j.jece.2022.107272.
    10.1016/j.jece.2022.107272
  11. Joana G. Costa; Ana M.S. Paulo; Catarina L. Amorim; A. Luís Amaral; Paula M.L. Castro; Eugénio C. Ferreira; Daniela P. Mesquita. "Quantitative image analysis as a robust tool to assess effluent quality from an aerobic granular sludge system treating industrial wastewater". Chemosphere (2022): 132773-132773. https://doi.org/10.1016/j.chemosphere.2021.132773.
    10.1016/j.chemosphere.2021.132773
  12. C. Quintelas; A. Braga; A. Cordeiro; E.C. Ferreira; I. Belo; R.N.M.J. Páscoa. "FT-NIR spectroscopy analysis for monitoring the microbial production of 2-phenylethanol using crude glycerol as carbon source". LWT 155 (2022): 112951-112951. https://doi.org/10.1016/j.lwt.2021.112951.
    10.1016/j.lwt.2021.112951
  13. Silva, Sérgio A.; Val del Río, Angeles; Amaral, António L.; Ferreira, Eugénio C.; Madalena Alves, M.; Mesquita, Daniela P.. "Monitoring morphological changes from activated sludge to aerobic granular sludge under distinct organic loading rates and increasing minimal imposed sludge settling velocities through quantitative image analysis". Chemosphere 286 (2022): 131637. http://dx.doi.org/10.1016/j.chemosphere.2021.131637.
    10.1016/j.chemosphere.2021.131637
  14. Melo, António; Costa, Joana; Quintelas, Cristina; Ferreira, Eugénio C.; Mesquita, Daniela P.. "Effect of ibuprofen on extracellular polymeric substances (EPS) production and composition, and assessment of microbial structure by quantitative image analysis". Journal of Environmental Management 293 (2021): 112852. http://dx.doi.org/10.1016/j.jenvman.2021.112852.
    10.1016/j.jenvman.2021.112852
  15. Cristiano Leal; Angeles Val del Río; Eugénio C. Ferreira; Daniela Mesquita; António L. Amaral. "Validation of a quantitative image analysis methodology for the assessment of the morphology and structure of aerobic granular sludge in the presence of pharmaceutically active compounds". Environmental Technology & Innovation 23 (2021): 101639-101639. https://doi.org/10.1016/j.eti.2021.101639.
    10.1016/j.eti.2021.101639
  16. Ana Forte; Fernando Dourado; André Mota; Belmira Neto; Miguel Gama; Eugénio Campos Ferreira. "Life cycle assessment of bacterial cellulose production". The International Journal of Life Cycle Assessment (2021): https://doi.org/10.1007/s11367-021-01904-2.
    10.1007/s11367-021-01904-2
  17. Ana S. Oliveira; Catarina L. Amorim; Daniela P. Mesquita; Eugénio C. Ferreira; Mark van Loosdrecht; Paula M.L. Castro. "Increased extracellular polymeric substances production contributes for the robustness of aerobic granular sludge during long-term intermittent exposure to 2-fluorophenol in saline wastewater". Journal of Water Process Engineering 40 (2021): 101977-101977. https://doi.org/10.1016%2Fj.jwpe.2021.101977.
    10.1016/j.jwpe.2021.101977
  18. Jéssica Costa; Eugénio C. Ferreira; Cledir Santos. "COVID-19, Chikungunya, Dengue and Zika Diseases: An Analytical Platform Based on MALDI-TOF MS, IR Spectroscopy and RT-qPCR for Accurate Diagnosis and Accelerate Epidemics Control". Microorganisms 9 4 (2021): 708-708. https://doi.org/10.3390/microorganisms9040708.
    10.3390/microorganisms9040708
  19. Oliveira, Alexandre; Rodrigues, Joana; Ferreira, Eugénio Campos; Rodrigues, Lígia; Dias, Oscar. "A kinetic model of the central carbon metabolism for acrylic acid production in Escherichia coli". PLOS Computational Biology 17 3 (2021): e1008704. http://dx.doi.org/10.1371/journal.pcbi.1008704.
    Open access • Published • 10.1371/journal.pcbi.1008704
  20. Ana M.S. Paulo; Catarina L. Amorim; Joana Costa; Daniela P. Mesquita; Eugénio C. Ferreira; Paula M.L. Castro. "Long-term stability of a non-adapted aerobic granular sludge process treating fish canning wastewater associated to EPS producers in the core microbiome". Science of The Total Environment 756 (2021): 144007-144007. https://doi.org/10.1016%2Fj.scitotenv.2020.144007.
    10.1016/j.scitotenv.2020.144007
  21. C. Quintelas; A. Melo; M. Costa; D.P. Mesquita; E.C. Ferreira; A.L. Amaral. "Environmentally-friendly technology for rapid identification and quantification of emerging pollutants from wastewater using infrared spectroscopy". Environmental Toxicology and Pharmacology 80 (2020): 103458-103458. https://doi.org/10.1016%2Fj.etap.2020.103458.
    10.1016/j.etap.2020.103458
  22. Ana S. Oliveira; Catarina L. Amorim; Miguel A. Ramos; Daniela P. Mesquita; Paulo Inocêncio; Eugénio C. Ferreira; Mark van Loosdrecht; Paula M.L. Castro. "Variability in the composition of extracellular polymeric substances from a full-scale aerobic granular sludge reactor treating urban wastewater". Journal of Environmental Chemical Engineering 8 5 (2020): 104156-104156. https://doi.org/10.1016/j.jece.2020.104156.
    10.1016/j.jece.2020.104156
  23. Beatriz S. Afonso; Ana G. Azevedo; Catarina Gonçalves; Isabel R. Amado; Ferreira, Eugénio C.; Lorenzo M. Pastrana; Miguel Ângelo Cerqueira. "Bio-Based Nanoparticles as a Carrier of ß-Carotene: Production, Characterisation and In Vitro Gastrointestinal Digestion". Molecules (2020): https://www.mdpi.com/1420-3049/25/19/4497.
    10.3390/molecules25194497
  24. Cristiano S. Leal; Daniela P. Mesquita; António Luís Amaral; Almerinda M. Amaral; Eugénio C. Ferreira. "Environmental impact and biological removal processes of pharmaceutically active compounds: The particular case of sulfonamides, anticonvulsants and steroid estrogens". Critical Reviews in Environmental Science and Technology 50 7 (2020): 698-742. https://doi.org/10.1080/10643389.2019.1642831.
    10.1080/10643389.2019.1642831
  25. Leal, Cristiano; Val del Río, Angeles; Mesquita, Daniela P.; Amaral, António L.; Castro, Paula M.L.; Ferreira, Eugénio C.. "Sludge volume index and suspended solids estimation of mature aerobic granular sludge by quantitative image analysis and chemometric tools". Separation and Purification Technology 234 116049 (2020): http://dx.doi.org/10.1016/j.seppur.2019.116049.
    Published • 10.1016/j.seppur.2019.116049
  26. Soares da Silva, Francisco A. G.; Fernandes, Marta; Souto, António Pedro; Ferreira, Eugénio C.; Dourado, Fernando; Gama, Miguel. "Optimization of bacterial nanocellulose fermentation using recycled paper sludge and development of novel composites". Applied Microbiology and Biotechnology 103 21-22 (2019): 9143-9154. http://dx.doi.org/10.1007/s00253-019-10124-6.
    Published • 10.1007/s00253-019-10124-6
  27. Cruz, Fernando; Lagoa, Davide; Mendes, João; Rocha, Isabel; Ferreira, Eugénio C.; Rocha, Miguel; Dias, Oscar. "SamPler – a novel method for selecting parameters for gene functional annotation routines". BMC Bioinformatics 20 454 (2019): http://dx.doi.org/10.1186/s12859-019-3038-4.
    Open access • Published • 10.1186/s12859-019-3038-4
  28. Sousa, Clara; Quintelas, Cristina; Augusto, Catarina; Ferreira, Eugénio C.; Páscoa, Ricardo N.M.J.. "Discrimination of Camellia japonica cultivars and chemometric models: An interlaboratory study". Computers and Electronics in Agriculture 159 (2019): 28-33. http://dx.doi.org/10.1016/j.compag.2019.02.025.
    Published • 10.1016/j.compag.2019.02.025
  29. Quintelas, C.; Mesquita, D.P.; Ferreira, E.C.; Amaral, A.L.. "Quantification of pharmaceutical compounds in wastewater samples by near infrared spectroscopy (NIR)". Talanta 194 (2019): 507-513. http://www.scopus.com/inward/record.url?eid=2-s2.0-85055705375&partnerID=MN8TOARS.
    10.1016/j.talanta.2018.10.076
  30. Correia, D.M.; Sargo, C.R.; Silva, A.J.; Santos, S.T.; Giordano, R.C.; Ferreira, E.C.; Zangirolami, T.C.; Ribeiro, M.P.A.; Rocha, I.. "Mapping Salmonella typhimurium pathways using 13C metabolic flux analysis". Metabolic Engineering 52 (2019): 303-314. http://www.scopus.com/inward/record.url?eid=2-s2.0-85059931870&partnerID=MN8TOARS.
    10.1016/j.ymben.2018.11.011
  31. Quintelas, Cristina; Braga, Adelaide; Mesquita, Daniela P; Amaral, Antonio L; Ferreira, Eugenio C; Belo, Isabel. "NIR spectroscopy applied to the determination of 2-phenylethanol and l -phenylalanine concentrations in culture medium of Yarrowia lipolytica". Journal of Chemical Technology & Biotechnology 94 3 (2018): 812-818. http://dx.doi.org/10.1002/jctb.5827.
    Published • 10.1002/jctb.5827
  32. Quintelas, C.; Ferreira, E.C.; Lopes, J.A.; Sousa, C.. "An Overview of the Evolution of Infrared Spectroscopy Applied to Bacterial Typing". Biotechnology Journal 13 1 (2018): http://www.scopus.com/inward/record.url?eid=2-s2.0-85034076838&partnerID=MN8TOARS.
    10.1002/biot.201700449
  33. Genisheva, Z.; Quintelas, C.; Mesquita, D.P.; Ferreira, E.C.; Oliveira, J.M.; Amaral, A.L.. "New PLS analysis approach to wine volatile compounds characterization by near infrared spectroscopy (NIR)". Food Chemistry 246 (2018): 172-178. http://www.scopus.com/inward/record.url?eid=2-s2.0-85033386173&partnerID=MN8TOARS.
    10.1016/j.foodchem.2017.11.015
  34. Dias, O.; Gomes, D.; Vilaça, P.; Cardoso, J.; Rocha, M.; Ferreira, E.C.; Rocha, I.. "Genome-Wide Semi-Automated Annotation of Transporter Systems". IEEE/ACM Transactions on Computational Biology and Bioinformatics 14 2 (2017): 443-456. http://www.scopus.com/inward/record.url?eid=2-s2.0-85017164643&partnerID=MN8TOARS.
    10.1109/TCBB.2016.2527647
  35. Silva, A.S.; Quintelas, C.; Ferreira, E.C.; Lopes, J.A.; Sousa, C.; Ana Sofia Silva; Cristina Quintelas; et al. "Exploiting intrinsic fluorescence spectroscopy to discriminate between Acinetobacter calcoaceticus-Acinetobacter baumannii complex species". RSC Advances 7 14 (2017): 8581-8588. http://www.scopus.com/inward/record.url?eid=2-s2.0-85011052384&partnerID=MN8TOARS.
    10.1039/c6ra27531a
  36. Dias, O.; Basso, T.O.; Rocha, I.; Ferreira, E.C.; Gombert, A.K.. "Erratum to: 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 (2017): http://www.scopus.com/inward/record.url?eid=2-s2.0-85031425390&partnerID=MN8TOARS.
    10.1007/s10482-017-0948-x
  37. Mesquita, D.P.; Quintelas, C.; Amaral, A.L.; Ferreira, E.C.. "Monitoring biological wastewater treatment processes: recent advances in spectroscopy applications". Reviews in Environmental Science and Biotechnology 16 3 (2017): 395-424. http://www.scopus.com/inward/record.url?eid=2-s2.0-85026806465&partnerID=MN8TOARS.
    10.1007/s11157-017-9439-9
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    10.1007/s10482-017-0940-5
  39. Ramos, C.; Amorim, C.L.; Mesquita, D.P.; Ferreira, E.C.; Carrera, J.; Castro, P.M.L.. "Simultaneous partial nitrification and 2-fluorophenol biodegradation with aerobic granular biomass: Reactor performance and microbial communities". Bioresource Technology 238 (2017): 232-240. http://www.scopus.com/inward/record.url?eid=2-s2.0-85018489586&partnerID=MN8TOARS.
    10.1016/j.biortech.2017.03.173
  40. Amaral, A.L.; Abreu, H.; Leal, C.; Mesquita, D.P.; Castro, L.M.; Ferreira, E.C.. "Quantitative image analysis of polyhydroxyalkanoates inclusions from microbial mixed cultures under different SBR operation strategies". Environmental Science and Pollution Research 24 17 (2017): 15148-15156. http://www.scopus.com/inward/record.url?eid=2-s2.0-85019269121&partnerID=MN8TOARS.
    10.1007/s11356-017-9132-0
  41. Carneiro, Sónia; Villas-Bôas, Silas; Ferreira, Eugénio C.; Rocha, Isabel. "A Comparative Proteome Analysis of Escherichia coli ¿relA Mutant Cells". Frontiers in Bioengineering and Biotechnology 4 (2016): http://dx.doi.org/10.3389/fbioe.2016.00078.
    10.3389/fbioe.2016.00078
  42. Silva, S.; Tobaldini-Valerio, F.; Costa-De-Oliveira, S.; Henriques, M.; Azeredo, J.; Ferreira, E.C.; Lopes, J.A.; Sousa, C.. "Discrimination of clinically relevant: Candida species by Fourier-transform infrared spectroscopy with attenuated total reflectance (FTIR-ATR)". RSC Advances 6 94 (2016): 92065-92072. http://www.scopus.com/inward/record.url?eid=2-s2.0-84989832895&partnerID=MN8TOARS.
    10.1039/c6ra16769a
  43. Mesquita, D.P.; Amaral, A.L.; Ferreira, E.C.. "Estimation of effluent quality parameters from an activated sludge system using quantitative image analysis". Chemical Engineering Journal 285 (2016): 349-357. http://www.scopus.com/inward/record.url?eid=2-s2.0-84944916774&partnerID=MN8TOARS.
    10.1016/j.cej.2015.09.110
  44. Braga, A.; Mesquita, D.P.; Amaral, A.L.; Ferreira, E.C.; Belo, I.. "Quantitative image analysis as a tool for Yarrowia lipolytica dimorphic growth evaluation in different culture media". Journal of Biotechnology 217 (2016): 22-30. http://www.scopus.com/inward/record.url?eid=2-s2.0-84947237883&partnerID=MN8TOARS.
    10.1016/j.jbiotec.2015.10.023
  45. Oscar Dias; Miguel Rocha; Eugénio C. Ferreira; Isabel Rocha. "Reconstructing genome-scale metabolic models with merlin". Nucleic Acids Research 43 8 (2015): 3899-3910. https://doi.org/10.1093/nar/gkv294.
    10.1093/nar/gkv294
  46. Braga, A.; Mesquita, D.P.; Amaral, A.L.; Ferreira, E.C.; Belo, I.. "Aroma production by Yarrowia lipolytica in airlift and stirred tank bioreactors: Differences in yeast metabolism and morphology". Biochemical Engineering Journal 93 (2015): 55-62. http://www.scopus.com/inward/record.url?eid=2-s2.0-84908047008&partnerID=MN8TOARS.
    10.1016/j.bej.2014.09.006
  47. Quintelas, C.; Mesquita, D.P.; Lopes, J.A.; Ferreira, E.C.; Sousa, C.. "Near-infrared spectroscopy for the detection and quantification of bacterial contaminations in pharmaceutical products". International Journal of Pharmaceutics 492 1-2 (2015): 199-206. http://www.scopus.com/inward/record.url?eid=2-s2.0-84937775051&partnerID=MN8TOARS.
    10.1016/j.ijpharm.2015.07.005
  48. Santos, S.B.; Carvalho, C.; Azeredo, J.; Ferreira, E.C.. "Correction: Population dynamics of a salmonella lytic phage and its host: Implications of the host bacterial growth rate in modelling (PlosOne (2015) 10:8 (e0136007))". PLoS ONE 10 8 (2015): http://www.scopus.com/inward/record.url?eid=2-s2.0-84942853201&partnerID=MN8TOARS.
    10.1371/journal.pone.0136007
  49. Mussatto, S.I.; Aguiar, L.M.; Marinha, M.I.; Jorge, R.C.; Ferreira, E.C.. "Economic analysis and environmental impact assessment of three different fermentation processes for fructooligosaccharides production". Bioresource Technology 198 (2015): 673-681. http://www.scopus.com/inward/record.url?eid=2-s2.0-84943145312&partnerID=MN8TOARS.
    10.1016/j.biortech.2015.09.060
  50. Mesquita, D.P.; Amaral, A.L.; Leal, C.; Oehmen, A.; Reis, M.A.M.; Ferreira, E.C.. "Polyhydroxyalkanoate granules quantification in mixed microbial cultures using image analysis: Sudan Black B versus Nile Blue A staining". Analytica Chimica Acta 865 1 (2015): 8-15. http://www.scopus.com/inward/record.url?eid=2-s2.0-84932190726&partnerID=MN8TOARS.
    10.1016/j.aca.2015.01.018
  51. Sargo, C.R.; Campani, G.; Silva, G.G.; Giordano, R.C.; Da Silva, A.J.; Zangirolami, T.C.; Correia, D.M.; Ferreira, E.C.; Rocha, I.. "Salmonella typhimurium and Escherichia coli dissimilarity: Closely related bacteria with distinct metabolic profiles". Biotechnology Progress (2015): http://www.scopus.com/inward/record.url?eid=2-s2.0-84936804684&partnerID=MN8TOARS.
    10.1002/btpr.2128
  52. Gomes, D.; Aguiar, T.Q.; Dias, O.; Ferreira, E.C.; Domingues, L.; Rocha, I.. "Genome-wide metabolic re-annotation of Ashbya gossypii: New insights into its metabolism through a comparative analysis with Saccharomyces cerevisiae and Kluyveromyces lactis". BMC Genomics 15 1 (2014): http://www.scopus.com/inward/record.url?eid=2-s2.0-84908419443&partnerID=MN8TOARS.
    10.1186/1471-2164-15-810
  53. Santos, S.B.; Carvalho, C.; Azeredo, J.; Ferreira, E.C.. "Population dynamics of a Salmonella lytic phage and its host: Implications of the host bacterial growth rate in modelling". PLoS ONE 9 7 (2014): http://www.scopus.com/inward/record.url?eid=2-s2.0-84904651603&partnerID=MN8TOARS.
    10.1371/journal.pone.0102507
  54. Rocha, M.; Mendes, R.; Rocha, O.; Rocha, I.; Ferreira, E.C.. "Optimization of fed-batch fermentation processes with bio-inspired algorithms". Expert Systems with Applications 41 5 (2014): 2186-2195. http://www.scopus.com/inward/record.url?eid=2-s2.0-84890115029&partnerID=MN8TOARS.
    10.1016/j.eswa.2013.09.017
  55. Mesquita, D.P.; Amaral, A.L.; Leal, C.; Carvalheira, M.; Cunha, J.R.; Oehmen, A.; Reis, M.A.M.; Ferreira, E.C.. "Monitoring intracellular polyphosphate accumulation in enhanced biological phosphorus removal systems by quantitative image analysis". Water Science and Technology 69 11 (2014): 2315-2323. http://www.scopus.com/inward/record.url?eid=2-s2.0-84902352343&partnerID=MN8TOARS.
    10.2166/wst.2014.146
  56. Tavares, A.P.M.; Silva, R.P.; Amaral, A.L.; Ferreira, E.C.; Xavier, A.M.R.B.. "Image analysis technique as a tool to identify morphological changes in Trametes versicolor pellets according to exopolysaccharide or laccase production". Applied Biochemistry and Biotechnology 172 4 (2014): 2132-2142. http://www.scopus.com/inward/record.url?eid=2-s2.0-84896316313&partnerID=MN8TOARS.
    10.1007/s12010-013-0675-3
  57. Dias, O.; Pereira, R.; Gombert, A.K.; Ferreira, E.C.; Rocha, I.. "iOD907, the first genome-scale metabolic model for the milk yeast Kluyveromyces lactis". Biotechnology Journal 9 6 (2014): 776-790. http://www.scopus.com/inward/record.url?eid=2-s2.0-84901679540&partnerID=MN8TOARS.
    10.1002/biot.201300242
  58. Pirotta, F.J.C.; Ferreira, E.C.; Bernardo, C.A.. "Energy recovery and impact on land use of Maltese municipal solid waste incineration". Energy 49 1 (2013): 1-11.
    Published • 10.1016/j.energy.2012.10.049
  59. Carneiro, Sónia; Ferreira, Eugénio C.; Rocha, Isabel; Ferreira, Eugénio C. "Metabolic responses to recombinant bioprocesses in Escherichia coli". Journal of Biotechnology 164 3 (2013): 396-408.
    Published • 10.1016/j.jbiotec.2012.08.026
  60. Costa, J. C.; Mesquita, D. P.; Amaral, A. L.; Alves, M. M.; Ferreira, E. C.. "Quantitative image analysis for the characterization of microbial aggregates in biological wastewater treatment: a review". Environmental Science and Pollution Research 20 9 (2013): 5887-5912.
    Published • 10.1007/s11356-013-1824-5
  61. Soons, Zita I. T. A.; Ferreira, Eugénio C; Patil, Kiran R; Rocha, Isabel; Fong, Stephen S.. "Identification of Metabolic Engineering Targets through Analysis of Optimal and Sub-Optimal Routes". PLoS ONE 8 4 (2013): e61648-e61648.
    Published • 10.1371/journal.pone.0061648
  62. Oliveira, H.; Melo, L. D. R.; Santos, S. B.; Nobrega, F. L.; Ferreira, E. C.; Cerca, N.; Azeredo, J.; Kluskens, L. D.. "Molecular Aspects and Comparative Genomics of Bacteriophage Endolysins". Journal of Virology 87 8 (2013): 4558-4570.
    Published • 10.1128/JVI.03277-12
  63. Mesquita, Daniela P; Leal, Cristiano; Cunha, Jorge R.; Oehmen, Adrian; Amaral, A. Luís; Reis, Maria A.M.; Ferreira, Eugénio C. "Prediction of intracellular storage polymers using quantitative image analysis in enhanced biological phosphorus removal systems". Analytica Chimica Acta 770 0 (2013): 36-44.
    Published • 10.1016/j.aca.2013.02.002
  64. Amaral, António L.; Mesquita, Daniela P; Ferreira, Eugénio C. "Automatic identification of activated sludge disturbances and assessment of operational parameters". Chemosphere 91 5 (2013): 705-710.
    Published • 10.1016/j.chemosphere.2012.12.066
  65. Mesquita, D.P.; Amaral, A.L.; Ferreira, E.C.. "Activated sludge characterization through microscopy: A review on quantitative image analysis and chemometric techniques". Analytica Chimica Acta 802 (2013): 14-28. http://www.scopus.com/inward/record.url?eid=2-s2.0-84886747965&partnerID=MN8TOARS.
    10.1016/j.aca.2013.09.016
  66. Dias, Oscar; Gombert, Andreas K; Ferreira, Eugénio C; Rocha, Isabel. "Genome-wide metabolic (re-) annotation of Kluyveromyces lactis". BMC Genomics 13 1 (2012): 517-517.
    Published • 10.1186/1471-2164-13-517
  67. Carneiro, Sónia; Villas-Bôas, Silas; Ferreira, Eugénio; Rocha, Isabel. "Influence of the RelA Activity on E. coli Metabolism by Metabolite Profiling of Glucose-Limited Chemostat Cultures". Metabolites 2 4 (2012): 717-732.
    Published • 10.3390/metabo2040717
  68. Machado, D.; Soons, Z.; Patil, K. R.; Ferreira, E. C.; Rocha, I.. "Random sampling of elementary flux modes in large-scale metabolic networks". Bioinformatics 28 18 (2012): i515-i521.
    Published • 10.1093/bioinformatics/bts401
  69. Machado, Daniel; Costa, Rafael S.; Ferreira, Eugénio C.; Rocha, Isabel; Tidor, Bruce. "Exploring the gap between dynamic and constraint-based models of metabolism". Metabolic Engineering 14 2 (2012): 112-119.
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  70. Barrigón, José M.; Ramon, Ramon; Rocha, Isabel; Valero, Francisco; Ferreira, Eugénio C.; Montesinos, José L.. "State and specific growth estimation in heterologous protein production by Pichia pastoris". AIChE Journal 58 10 (2012): 2966-2979.
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  71. Ordaz, Alberto; Oliveira, Catarina S.; Quijano, Guillermo; Ferreira, Eugenio C.; Alves, Madalena; Thalasso, Frédéric. "Kinetic and stoichiometric characterization of a fixed biofilm reactor by pulse respirometry". Journal of Biotechnology 157 1 (2012): 173-179.
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  72. Carneiro, Sónia; Lourenço, Anália; Ferreira, Eugénio C.; Rocha, Isabel. "Stringent response of Escherichia coli: revisiting the bibliome using literature mining". Microbial Informatics and Experimentation 1 14 (2011): http://dx.doi.org/10.1186/2042-5783-1-14.
    Open access • Published • 10.1186/2042-5783-1-14
  73. Machado, Daniel; Costa, Rafael S; Rocha, Miguel; Ferreira, Eugénio C; Tidor, Bruce; Rocha, Isabel. "Modeling formalisms in Systems Biology". AMB Express 1 1 (2011): 45-45.
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  74. Carreira, Rafael; Carneiro, Sónia; Pereira, Rui; Rocha, Miguel; Rocha, Isabel; Ferreira, Eugénio C; Lourenço, Anália. "Semantic annotation of biological concepts interplaying microbial cellular responses". BMC Bioinformatics 12 1 (2011): 460-460.
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  75. Mesquita, D.P.; Amaral, A.L.; Ferreira, E.C.. "Identifying different types of bulking in an activated sludge system through quantitative image analysis". Chemosphere 85 4 (2011): 643-652.
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  76. Oliveira, Catarina S.; Ordaz, Alberto; Ferreira, Eugénio C.; Alves, Madalena; Thalasso, Frédéric. "In situ pulse respirometric methods for the estimation of kinetic and stoichiometric parameters in aerobic microbial communities". Biochemical Engineering Journal 58-59 - (2011): 12-19.
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  77. Santos, S. B.; Kropinski, A. M.; Ceyssens, P.-J.; Ackermann, H.- W.; Villegas, A.; Lavigne, R.; Krylov, V. N.; et al. "Genomic and Proteomic Characterization of the Broad-Host-Range Salmonella Phage PVP-SE1: Creation of a New Phage Genus". Journal of Virology 85 21 (2011): 11265-11273.
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  78. Soons, Zita I.T.A.; Ferreira, Eugénio C.; Rocha, Isabel. "Identification of minimal metabolic pathway models consistent with phenotypic data". Journal of Process Control 21 10 (2011): 1483-1492.
    Published • 10.1016/j.jprocont.2011.05.012
  79. Mesquita, Daniela P.; Ribeiro, Roberta R.; Amaral, António L.; Ferreira, Eugénio C.; Coelho, Maria Alice Z.. "Image analysis application for the study of activated sludge floc size during the treatment of synthetic and real fishery wastewaters". Environmental Science and Pollution Research 18 8 (2011): 1390-1397.
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  80. Costa, R.S.; Machado, D.; Rocha, I.; Ferreira, E.C.. "Critical perspective on the consequences of the limited availability of kinetic data in metabolic dynamic modelling". IET Systems Biology 5 3 (2011): 157-157.
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  81. Carneiro, Sónia; Villas-Bôas, Silas G.; Ferreira, Eugénio C.; Rocha, Isabel; Carneiro, S.; Villas-Bôas, S.G.; Ferreira, E.C.; Rocha, I.. "Metabolic footprint analysis of recombinant Escherichia coli strains during fed-batch fermentations". Molecular BioSystems 7 3 (2011): 899-910. http://www.scopus.com/inward/record.url?eid=2-s2.0-79951623012&partnerID=MN8TOARS.
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  82. Lourenco, A.; Carneiro, S.; Rocha, M.; Ferreira, E. C.; Rocha, I.. "Challenges in integrating Escherichia coli molecular biology data". Briefings in Bioinformatics 12 2 (2011): 91-103.
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  83. Mesquita, D.P.; Amaral, A.L.; Ferreira, E.C.. "Characterization of activated sludge abnormalities by image analysis and chemometric techniques". Analytica Chimica Acta 705 1-2 (2011): 235-242.
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  84. A. Lourenço; Carneiro, Sónia; J. P. Pinto; E. C. Ferreira; M. Rocha; Rocha, Isabel; Lourenço, A.; et al. "A study of the short and long-term regulation of E. coli metabolic pathways". Journal of Integrative Bioinformatics 8 3 (2011): 183--. http://www.scopus.com/inward/record.url?eid=2-s2.0-84855554919&partnerID=MN8TOARS.
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  85. Domingues, L.; Rocha, I.; Dourado, F.; Alves, M.M.; Ferreira, E.C.. "Virtual laboratories in (bio)chemical engineering education". Education for Chemical Engineers 5 2 (2010): e13-e32.
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  86. Santos, S. B.; Fernandes, E.; Carvalho, C. M.; Sillankorva, S.; Krylov, V. N.; Pleteneva, E. A.; Shaburova, O. V.; et al. "Selection and Characterization of a Multivalent Salmonella Phage and Its Production in a Nonpathogenic Escherichia coli Strain". Applied and Environmental Microbiology 76 21 (2010): 7338-7342.
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  87. Mesquita, D.P.; Dias, O.; Elias, R.A.V.; Amaral, A.L.; Ferreira, E.C.. "Dilution and Magnification Effects on Image Analysis Applications in Activated Sludge Characterization". Microscopy and Microanalysis 16 05 (2010): 561-568.
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  88. Rocha, Isabel; Maia, Paulo; Evangelista, Pedro; Vilaça, Paulo; Soares, Simão; Pinto, José P; Nielsen, Jens; et al. "OptFlux: an open-source software platform for in silico metabolic engineering". BMC Systems Biology 4 1 (2010): 45-45.
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  89. Costa, Rafael S.; Machado, Daniel; Rocha, Isabel; Ferreira, Eugénio C.. "Hybrid dynamic modeling of Escherichia coli central metabolic network combining Michaelis–Menten and approximate kinetic equations". Biosystems 100 2 (2010): 150-157.
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  90. Mesquita, D.P.; Dias, O.; Amaral, A.L.; Ferreira, E.C.. "A Comparison between Bright Field and Phase-Contrast Image Analysis Techniques in Activated Sludge Morphological Characterization". Microscopy and Microanalysis 16 02 (2010): 166-166.
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  91. Costa, J.C.; Alves, M.M.; Ferreira, E.C.. "A chemometric tool to monitor high-rate anaerobic granular sludge reactors during load and toxic disturbances". Biochemical Engineering Journal 53 1 (2010): 38-43.
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  92. Lourenço, Anália; Carreira, Rafael; Glez-Peña, Daniel; Méndez, José R.; Carneiro, Sónia; Rocha, Luis M.; Díaz, Fernando; et al. "BioDR: Semantic indexing networks for biomedical document retrieval". Expert Systems with Applications 37 4 (2010): 3444-3453.
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  93. Morais, S.; Mata, T.M.; Ferreira, E.. "Life cycle assessment of soybean biodiesel and LPG as automotive fuels in Portugal". Chemical Engineering Transactions 19 (2010): 267-272. http://www.scopus.com/inward/record.url?eid=2-s2.0-78650302566&partnerID=MN8TOARS.
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  94. Carneiro, Sonia. "Applying a Metabolic Footprinting Approach to Characterize the Impact of the Recombinant Protein Production in Escherichia coli". Advances in Bioinformatics 74 (2010): 193-200.
    10.1007/978-3-642-13214-8_25
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    10.1016/j.bej.2009.10.004
  96. David F. M. Neri; Victor M. Balcão; Duarte P. M. Torres; Lígia R. M. Rodrigues; Rafael Costa; I. Rocha; E. C. Ferreira; Luiz B. Carvalho Jr.; José A. Teixeira. "Galacto-oligossacharides production during lactose hydrolysis by free Aspergillus oryzae beta-galactosidase and immobilized on magnetic polysiloxane-polyvinyl alcohol". Food Chemistry 115 1 (2009): 92-99. http://hdl.handle.net/1822/8819.
    Published • 10.1016/j.foodchem.2008.11.068
  97. Nobre, C.; Santos, M.J.; Dominguez, A.; Torres, D.; Rocha, O.; Peres, A.M.; Rocha, I.; et al. "Comparison of adsorption equilibrium of fructose, glucose and sucrose on potassium gel-type and macroporous sodium ion-exchange resins". Analytica Chimica Acta 654 1 (2009): 71-76. http://hdl.handle.net/10198/3818.
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  98. Sarraguça, Mafalda C.; Paulo, Ana; Alves, Madalena M.; Dias, Ana M. A.; Lopes, João A.; Ferreira, Eugénio C.. "Quantitative monitoring of an activated sludge reactor using on-line UV-visible and near-infrared spectroscopy". Analytical and Bioanalytical Chemistry 395 4 (2009): 1159-1166.
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  99. Santos, Sílvio B; Carvalho, Carla M; Sillankorva, Sanna; Nicolau, Ana; Ferreira, Eugénio C; Azeredo, Joana. "The use of antibiotics to improve phage detection and enumeration by the double-layer agar technique". BMC Microbiology 9 1 (2009): 148-148.
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  100. Lourenço, Anália; Carreira, Rafael; Carneiro, Sónia; Maia, Paulo; Glez-Peña, Daniel; Fdez-Riverola, Florentino; Ferreira, Eugénio C.; Rocha, Isabel; Rocha, Miguel. "@Note: A workbench for Biomedical Text Mining". Journal of Biomedical Informatics 42 4 (2009): 710-720.
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  101. Mesquita, D.P.; Dias, O.; Dias, A.M.A.; Amaral, A.L.; Ferreira, E.C.. "Correlation between sludge settling ability and image analysis information using partial least squares". Analytica Chimica Acta 642 1-2 (2009): 94-101.
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  102. Oliveira, Catarina S; Ordaz, Alberto; Alba, Joel; Alves, Madalena; Ferreira, Eugénio C; Thalasso, Frederic. "Determination of Kinetic and Stoichiometric Parameters of Pseudomonas putida F1 by Chemostat and In Situ Pulse Respirometry". Chemical Product and Process Modeling 4 2 (2009): ---.
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  103. Costa, J.C.; Moita, I.; Ferreira, E.C.; Alves, M.M.. "Morphology and physiology of anaerobic granular sludge exposed to an organic solvent". Journal of Hazardous Materials 167 1-3 (2009): 393-398.
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  104. Abreu, A.A.; Danko, A.S.; Costa, J.C.; Ferreira, E.C.; Alves, M.M.. "Inoculum type response to different pHs on biohydrogen production from l-arabinose, a component of hemicellulosic biopolymers". International Journal of Hydrogen Energy 34 4 (2009): 1744-1751.
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  105. Carneiro, Sónia; Amaral, António L.; Veloso, Ana C. A.; Dias, Teresa; Peres, António M.; Ferreira, Eugénio C.; Rocha, Isabel. "Assessment of physiological conditions in E. coli fermentations by epifluorescent microscopy and image analysis". Biotechnology Progress 25 3 (2009): 882-891.
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  106. Mesquita, Daniela P; Amaral, Antonio L; Ferreira, Eugenio C; Coelho, Maria AZ. "Study of saline wastewater influence on activated sludge flocs through automated image analysis". Journal of Chemical Technology & Biotechnology 84 4 (2009): 554-560.
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  107. Costa, J.C.; Alves, M.M.; Ferreira, E.C.. "Principal component analysis and quantitative image analysis to predict effects of toxics in anaerobic granular sludge". Bioresource Technology 100 3 (2009): 1180-1185.
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  108. Costa, J.C.; Moita, I.; Abreu, A.A.; Ferreira, E.C.; Alves, M.M.. "Advanced monitoring of high-rate anaerobic reactors through quantitative image analysis of granular sludge and multivariate statistical analysis". Biotechnology and Bioengineering 102 2 (2009): 445-456.
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  109. Veloso, A. C. A.; Rocha, I.; Ferreira, E. C.. "Monitoring of fed-batch E. coli fermentations with software sensors". Bioprocess and Biosystems Engineering 32 3 (2009): 381-388.
    Published • 10.1007/s00449-008-0257-x
  110. Mesquita, D. P.; Dias, O.; Amaral, A. L.; Ferreira, E. C.. "Monitoring of activated sludge settling ability through image analysis: validation on full-scale wastewater treatment plants". Bioprocess and Biosystems Engineering 32 3 (2009): 361-367.
    Published • 10.1007/s00449-008-0255-z
  111. Vaz, A. Ismael F.; Ferreira, Eugénio C.. "Air pollution control with semi-infinite programming". Applied Mathematical Modelling 33 4 (2009): 1957-1969.
    Published • 10.1016/j.apm.2008.05.008
  112. Amaral, António L.; Rocha, Orlando; Gonçalves, Cristina; Ferreira, António A.; Ferreira, Eugénio C. "Application of image analysis to the prediction of EBC barley kernel weight distribution". Industrial Crops and Products 30 3 (2009): 366-371.
    Published • 10.1016/j.indcrop.2009.07.003
  113. Oliveira, C.S.; Ordaz, A.; Alba, J.; Alves, M.; Ferreira, E.C.; Thalasso, F.. "Determination of kinetic and stoichiometric parameters of pseudomonas putida F1 by chemostat and pulse respirometry". Chemical Product and Process Modeling 4 2 (2009): http://www.scopus.com/inward/record.url?eid=2-s2.0-67650477799&partnerID=MN8TOARS.
  114. Ferreira, E.C.; Mota, M.. "Editorial: Special issue contributed by the 10th international chemical and biological engineering conference - CHEMPOR 2008". Chemical Product and Process Modeling 4 4 (2009): http://www.scopus.com/inward/record.url?eid=2-s2.0-68349096077&partnerID=MN8TOARS.
  115. F´erreira, E.C.; Mota, M.. "Selected papers from 10th international chemical and biological engineering conference (chempor 2008): Editorial". International Journal of Chemical Engineering (2009): http://www.scopus.com/inward/record.url?eid=2-s2.0-68149167714&partnerID=MN8TOARS.
    10.1155/2009/294627
  116. Carneiro, S.. "Metabolic footprinting of Escherichia coli grown in fed-batch fermentation during recombinant protein production". New Biotechnology 25 (2009): S342-S342.
    10.1016/j.nbt.2009.06.828
  117. Carneiro, Sónia; Amaral, António L.; Veloso, Ana C.A.; Dias, Teresa; Peres, António M.; Ferreira, Eugénio C.; Rocha, Isabel. "Assessment of physiological conditions in e. Coli fermentations by epifluorescent microscopy and image analysis". (2009): http://hdl.handle.net/10198/3231.
  118. R. Pinto; A. L. Amaral; E. C. Ferreira; M. Mota; M. Vilanova; K. Ruel; F. M. Gama. "Quantification of the CBD-FITC conjugates surface coating on cellulose fibres". BMC Biotechnology 8 2 (2008): 1-7. http://www.biomedcentral.com/1472-6750/8/1.
    Published • 10.1186/1472-6750-8-1
  119. A. Ordaz; C. S. Oliveira; R. Aguilar; M. Carrión; E. C. Ferreira; M. M. Alves; F. Thalasso; et al. "Kinetic and stoichiometric parameters estimation in a nitrifying bubble column through "in-situ" pulse respirometry". Biotechnology and Bioengineering 100 1 (2008): 94-102. http://hdl.handle.net/1822/7799.
    Published • 10.1002/bit.21723
  120. A. L. Amaral; Y. P. Ginoris; A. Nicolau; M. A. Z. Coelho; E. C. Ferreira. "Stalked protozoa identification by image analysis and multivariable statistical techniques". Analytical and Bioanalytical Chemistry 391 4 (2008): 1321-1325. http://hdl.handle.net/1822/7946.
    Published • 10.1007/s00216-008-1845-y
  121. A. M. A. Dias; I. Moita; R. Pâscoa; M. M. Alves; J. A. Lopes; E. C. Ferreira. "Activated sludge process monitoring through in-situ NIR spectral analysis". Water Science & Technology 57 10 (2008): 1643-1650. http://hdl.handle.net/1822/8128.
    Published • 10.2166/wst.2008.147
  122. Rocha, Miguel; Maia, Paulo; Mendes, Rui; Pinto, José P; Ferreira, Eugénio C; Nielsen, Jens; Patil, Kiran; et al. "Natural computation meta-heuristics for the in silico optimization of microbial strains". BMC Bioinformatics 9 1 (2008): 499-499. http://hdl.handle.net/1822/8742.
    Published • 10.1186/1471-2105-9-499
  123. R. Pinto; A. L. Amaral; J. Carvalho; E. C. Ferreira; M. Mota; F. M. Gama. "Development of a method using image analysis and CBD-FITC conjugates for the measurement of CBDs adsorbed onto cellulose fibers". Biotechnology Progress 23 6 (2007): 1492-1497.
    Published • 10.1021/bp070026v
  124. Y. P. Ginoris; A. L. Amaral; A. Nicolau; M. A. Z. Coelho; E. C. Ferreira. "Raw Data Pre-Processing in the Protozoa and Metazoa Identification by Image Analysis and Multivariate Statistical Techniques". Journal of Chemometrics 21 3-4 (2007): 156-164. http://hdl.handle.net/1822/6947.
    Published
  125. Y. P. Ginoris; A. L. Amaral; A. Nicolau; M. A. Z. Coelho; E. C. Ferreira; Ginoris, Y.P.; Amaral, A.L.; et al. "Recognition of protozoa and metazoa using image analysis tools, discriminant analysis, neural networks and decision trees". Analytica Chimica Acta 595 1-2 (2007): 160-169. http://hdl.handle.net/1822/6672.
    Published • 10.1016/j.aca.2006.12.055
  126. Y. P. Ginoris; A. L. Amaral; A. Nicolau; M. A. Z. Coelho; E. C. Ferreira. "Development of an image analysis procedure for identifying protozoa and metazoa typical of activated sludge system". Water Research 42 12 (2007): 2581-2589. http://hdl.handle.net/1822/6665.
    Published
  127. A. A. Abreu; P. Araya-Kroff; J. C. Costa; E. C. Ferreira; M. M. Alves. "Quantitative image analysis as a diagnostic tool for identifying structural changes during a revival process of anaerobic granular sludge". Water Research 41 7 (2007): 1473-1480. http://hdl.handle.net/1822/6308.
    Published
  128. I.A.C.P. Espirito-Santo; E. M. G. P. Fernandes; M. M. Araújo; E. C. Ferreira. "Wasted Sludge Treatment Contributions in the WWTP Total Cost". WSEAS Transactions on Information Science and Applications 4 4 (2007): 655-662. http://hdl.handle.net/1822/6409.
    Published
  129. Espírito Santo, I.A.C.P.; Fernandes, E.M.G.P.; Araújo, M.M.; Ferreira, E.C.. "Wasted sludge treatment contributions in the WWTP total cost". WSEAS Transactions on Information Science and Applications 4 4 (2007): 655-662. http://www.scopus.com/inward/record.url?eid=2-s2.0-34247389165&partnerID=MN8TOARS.
  130. Costa, J.C.; Abreu, A.A.; Ferreira, E.C.; Alves, M.M.. "Quantitative image analysis as a diagnostic tool for monitoring structural changes of anaerobic granular sludge during detergent shock loads". Biotechnology and Bioengineering 98 1 (2007): 60-68. http://www.scopus.com/inward/record.url?eid=2-s2.0-34548228628&partnerID=MN8TOARS.
    10.1002/bit.21381
  131. Ginoris, Y.P.; Amaral, A.L.; Nicolau, A.; Coelho, M.A.Z.; Ferreira, E.C.. "Raw data pre-processing in the protozoa and metazoa identification by image analysis and multivariate statistical techniques". Journal of Chemometrics 21 3-4 (2007): 156-164. http://www.scopus.com/inward/record.url?eid=2-s2.0-34548770024&partnerID=MN8TOARS.
    10.1002/cem.1054
  132. Coelho, M.A.Z.; Coutinho, J.A.P.; Ferreira, E.C.; Mota, M.; Belo, I.; M. A. Z. Coelho; J. A. P. Coutinho; et al. "Analysis of the effects of hyperbaric gases on S. cerevisiae cell cycle through a morphological approach". Process Biochemistry 42 10 (2007): 1378-1383. http://www.scopus.com/inward/record.url?eid=2-s2.0-34548584876&partnerID=MN8TOARS.
    Published • 10.1016/j.procbio.2007.07.003
  133. Ginoris, Y.P.; Amaral, A.L.; Nicolau, A.; Coelho, M.A.Z.; Ferreira, E.C.. "Development of an image analysis procedure for identifying protozoa and metazoa typical of activated sludge system". Water Research 41 12 (2007): 2581-2589. http://www.scopus.com/inward/record.url?eid=2-s2.0-34248997191&partnerID=MN8TOARS.
    10.1016/j.watres.2007.02.006
  134. Abreu, A.A.; Costa, J.C.; Araya-Kroff, P.; Ferreira, E.C.; Alves, M.M.. "Quantitative image analysis as a diagnostic tool for identifying structural changes during a revival process of anaerobic granular sludge". Water Research 41 7 (2007): 1473-1480. http://www.scopus.com/inward/record.url?eid=2-s2.0-33847664282&partnerID=MN8TOARS.
    10.1016/j.watres.2007.01.017
  135. Pires, O.C.; Palma, C.; Costa, J.C.; Moita, I.; Alves, M.M.; Ferreira, E.C.. "Knowledge-based fuzzy system for diagnosis and control of an integrated biological wastewater treatment process". Water Science and Technology 53 4-5 (2006): 313-320. http://dx.doi.org/10.2166/wst.2006.136.
    Published • 10.2166/wst.2006.136
  136. A. I. F. Vaz; E. C. Ferreira; A. M. T. Mota. "Fed-batch trajectory optimal control problems with cubic splines". WSEAS Transactions on Systems and Control 2 1 (2006): 207-213. http://hdl.handle.net/1822/5933.
    Published
  137. I.A.C.P. Espirito-Santo; E. M. G. P. Fernandes; M. M. Araújo; E. C. Ferreira; Espírito Santo, I.A.C.P.; Fernandes, E.M.G.P.; Araújo, M.M.; Ferreira, E.C.. "On the secondary settler models robustness by simulation". WSEAS Transactions on Information Science and Applications 12 3 (2006): 2323-2330. http://hdl.handle.net/1822/5648.
    Published
  138. O. C. Pires; C. Palma; J. C. Costa; I. Moita; E. C. Ferreira; M. M. Alves. "Knowledge-based fuzzy system for diagnosis and control of an integrated biological wastewater treatment process". Water Science and Technology 53 4-5 (2006): 313-320. http://hdl.handle.net/1822/4962.
    Published
  139. A. L. Amaral; E. C. Ferreira. "Activated Sludge Monitoring of a Wastewater Treatment Plant using Image Analysis and Partial Least Squares Regression". Analytica Chimica Acta 544 1-2 (2005): 246-253. http://hdl.handle.net/1822/2622.
    Published
  140. M. A. Araújo; E. C. Ferreira; A. M. Cunha; M. Mota; Araújo, M.A.; Ferreira, E.C.; Cunha, A.M.; Mota, M.. "Determination of diffusion coefficients fo glycerol and glucose from starch based thermoplastic compounds on simulated physiological solution". Journal of Materials Science - Materials in Medicine 16 3 (2005): 239-246. http://hdl.handle.net/1822/2573.
    Published • 10.1007/s10856-005-6685-0
  141. Amaral, A.L.; Ferreira, E.C.. "Activated sludge monitoring of a wastewater treatment plant using image analysis and partial least squares regression". Analytica Chimica Acta 544 1-2 SPEC. (2005): 246-253. http://www.scopus.com/inward/record.url?eid=2-s2.0-20444479883&partnerID=MN8TOARS.
    10.1016/j.aca.2004.12.061
  142. Coutinho, J.A.P.; Belo, I.; Ferreira, E.C.; Coelho, M.A.Z.; J. A. P. Coutinho; I. Belo; E. C. Ferreira; M. A. Z. Coelho. "Assessment of yeast viability under hyperbaric conditions through a modeling approach". Journal of Chemical Technology and Biotechnology 80 8 (2005): 872-877. http://www.scopus.com/inward/record.url?eid=2-s2.0-22744446841&partnerID=MN8TOARS.
    Published • 10.1002/jctb.1248
  143. Veloso, Ana C.A.; Rocha, I.; Ferreira, E.C.. "Identification of Yield Coefficients in an E.coli Model – An Optimal Experimental Design Using Genetic Algorithms". IFAC Proceedings Volumes 37 3 (2004): 43-48. http://dx.doi.org/10.1016/s1474-6670(17)32557-0.
    Published • 10.1016/s1474-6670(17)32557-0
  144. A. L. Amaral; M. A. Pereira; M. da Motta; M. N. Pons; M. Mota; E. C. Ferreira; M. M. Alves; et al. "Development of Image Analysis Techniques as a Tool to Detect and Quantify Morphological Changes in Anaerobic Sludge: II. Application to a Granule Deterioration Process Triggered by Contact With Oleic Acid". Biotechnology and Bioengineering 87 2 (2004): 194-199. http://hdl.handle.net/1822/1419.
    Published • 10.1002/bit.20129
  145. P. Araya-Kroff; A. L. Amaral; L. Neves; E. C. Ferreira; M. N. Pons; M. Mota; M. M. Alves; et al. "Development of Image Analysis Techniques as a Tool to Detect and Quantify Morphological Changes in Anaerobic Sludge: I. Application to a Granulation Process". Biotechnology and Bioengineering 87 2 (2004): 185-193. http://hdl.handle.net/1822/1322.
    Published • 10.1002/bit.20207
  146. M. A. Z. Coelho; I. Belo; R. Pinheiro; A. L. Amaral; M. Mota; J. A. P. Coutinho; E. C. Ferreira; et al. "Effect of hyperbaric stress on yeast morphology: study by automated image analysis". Applied Microbiology and Biotechnology 66 3 (2004): 318-324. http://hdl.handle.net/1822/1405.
    Published • 10.1007/s00253-004-1648-9
  147. E. C. Ferreira; R. Lima; R. Salcedo. "Spreadsheets in Chemical Engineering Education - A Tool in Process Design and Integration". International Journal of Engineering Education 20 6 (2004): 928-938. http://hdl.handle.net/1822/1457.
    Published
  148. Ferreira, E.C.; Lima, R.; Salcedo, R.. "Spreadsheets in chemical engineering education - A tool in process design and process integration". International Journal of Engineering Education 20 6 (2004): 928-938. http://www.scopus.com/inward/record.url?eid=2-s2.0-10044229482&partnerID=MN8TOARS.
  149. Amaral, A.L.; Da Motta, M.; Pons, M.N.; Vivier, H.; Roche, N.; Mota, M.; Ferreira, E.C.; et al. "Survey of Protozoa and Metazoa populations in wastewater treatment plants by image analysis and discriminant analysis". Environmetrics 15 4 (2004): 381-390. http://www.scopus.com/inward/record.url?eid=2-s2.0-2942595894&partnerID=MN8TOARS.
    Published • 10.1002/env.652
  150. V. Lubenova; I. Rocha; E. C. Ferreira. "Estimation of multiple biomass growth rates and biomass concentration in a class of bioprocesses". Bioprocess and Biosystems Engineering 25 6 (2003): 395-406. http://hdl.handle.net/1822/132.
    Published • 10.1007/s00449-003-0325-1
  151. F. M. Kawasse; P. F. Amaral; M. H. M. Rocha-Leão; M. A. Z. Coelho; A. L. Amaral; E. C. Ferreira. "Morphological Analysis of Yarrowia lipolytica under Stress Conditions through Image Processing". Bioprocess and Biosystems Engineering 25 6 (2003): 371-375. http://hdl.handle.net/1822/145.
    Published • 10.1007/s00449-003-0319-z
  152. M. da Motta; M. N. Pons; N. Roche; H. Vivier; A. L. Amaral; E. C. Ferreira; M. Mota. "Estudo do Funcionamento de Estações de Tratamento de Esgotos por Análise de Imagem: Validações e Estudo de Caso". Engenharia Sanitária e Ambiental 8 3 (2003): 170-181. http://hdl.handle.net/1822/126.
    Published
  153. Pereira, M.A.; Roest, K.; Stams, A.J.M.; Akkermans, A.D.L.; Amaral, A.L.; Pons, M.-N.; Ferreira, E.C.; et al. "Image analysis, methanogenic activity measurements, and molecular biological techniques to monitor granular sludge from an EGSB reactor fed with oleic acid". Water Science & Technology 47 5 (2003): 181-188. http://www.scopus.com/inward/record.url?eid=2-s2.0-0242684611&partnerID=MN8TOARS.
    Published
  154. Dias, N.; Amaral, A.L.; Ferreira, E.C.; Lima, N.; N. Dias; A. L. Amaral; E. C. Ferreira; N. Lima. "Automated image analysis to improve bead ingestion toxicity test counts in the protozoan Tetrahymena pyriformis". Letters in Applied Microbiology 37 3 (2003): 230-233. http://www.scopus.com/inward/record.url?eid=2-s2.0-0042880000&partnerID=MN8TOARS.
    Published • 10.1046/j.1472-765X.2003.01382.x
  155. I. Rocha; E. C. Ferreira. "On-line simultaneous monitoring of glucose and acetate with FIA during high cell density fermentation of recombinant E. coli". Analytica Chimica Acta 462 2 (2002): 293-304. http://hdl.handle.net/1822/130.
    Published • 10.1016/S0003-2670(02)00347-1
  156. R. Oliveira; E. C. Ferreira; S. Feyo de Azevedo. "Stability, dynamics of convergence, and tuning of observer-based kinetics estimators". Journal of Process Control 12 2 (2002): 311-323. http://hdl.handle.net/1822/144.
    Published • 10.1016/S0959-1524(01)00031-2
  157. M. da Motta; M. N. Pons; H. Vivier; N. Roche; A. L. Amaral; E. C. Ferreira; M. Mota. "Reconnaissance Semi-Automatique de la Microfaune des Boues Activés des Stations de Traitment d´Eaux Usées: Protorec V2.0". Récents Progrés en Génie des Procédés 15 78 (2001): 167-172. https://repositorium.sdum.uminho.pt/handle/1822/1740.
    Published
  158. N. J. Ribeiro; O. C. Pires; M. Mota; E. C. Ferreira; M. M. Alves. "Influence of up-flow velocity on the performance of an anaerobic filter under oleic acid overloads". Biotechnology Letters 23 22 (2001): 1833-1839. http://hdl.handle.net/1822/149.
    Published • 10.1023/A:1012750507267
  159. E. C. Ferreira; R. Salcedo; Ferreira, E.C.; Salcedo, R.. "A Tool to Optimize VOC Removal During Absorption and Stripping". Chemical Engineering 108 1 (2001): 94-98. http://hdl.handle.net/1822/127.
    Published
  160. E. C. Ferreira; R. Salcedo. "Can Spreadsheet Solvers Solve Demanding Optimization Problems?". Computer Applications in Engineering Education 9 1 (2001): 49-56. http://hdl.handle.net/1822/136.
    Published • 10.1002/cae.1005
  161. M. da Motta; A. L. Amaral; M. N. Pons; E. C. Ferreira; H. Vivier; M. Mota. "Estudo por análise de imagem do comportamento de uma estação de tratamento de efluentes sob condições transientes". Energias Renovables y Medio Ambiente 9 (2001): 49-55. http://hdl.handle.net/1822/131.
    Published
  162. Da Motta, M.; Pons, M.N.; Vivier, H.; Amaral, A.L.; Ferreira, E.C.; Roche, N.; Mota, M.. "The study of protozoa population in wastewater treatment plants by image analysis". Brazilian Journal of Chemical Engineering 18 1 (2001): 103-111. http://www.scopus.com/inward/record.url?eid=2-s2.0-0035275965&partnerID=MN8TOARS.
  163. M. M. Alves; E. C. Ferreira; A. L. Amaral; M. A. Pereira; J. M. Novais; M. Mota. "Staged and Non-Staged Anaerobic Filters: Performance in Relation to Physical and Biological Characteristics of Microbial Aggregates". Journal of Chemical Technology & Biotechnology 75 7 (2000): 601-609. http://hdl.handle.net/1822/142.
    Published
  164. M. M. Alves; A. J. Cavaleiro; E. C. Ferreira; A. L. Amaral; M. Mota; M. da Motta; H. Vivier; M. N. Pons. "Characterization by Image Analysis of Anaerobic Microbial Aggregates under Shock Conditions". Water Science & Technology 41 12 (2000): 207-214. http://hdl.handle.net/1822/1782.
    Published
  165. M. Perrier; S. Feyo de Azevedo; E. C. Ferreira; D. Dochain. "Tuning of Observer-based Estimators: Theory and Application to the On-line Estimation of Kinetic Parameters". Control Engineering Practice 8 4 (2000): 377-388. http://hdl.handle.net/1822/138.
    Published • 10.1016/S0967-0661(99)00164-1
  166. Alves, M.; Ferreira, E.C.; Amaral, A.L.; Pereira, A.; Novais, J.M.; Mota, M.. "Staged and non-staged anaerobic filters: Performance in relation to physical and biological characteristics of microbial aggregates". Journal of Chemical Technology and Biotechnology 75 7 (2000): 601-609. http://www.scopus.com/inward/record.url?eid=2-s2.0-0034235237&partnerID=MN8TOARS.
    10.1002/1097-4660(200007)75:7<601::AID-JCTB255>3.0.CO;2-P
  167. Baeza, J.A.; Ferreira, E.C.; Lafuente, J.; J. Baeza; E. C. Ferreira; J. Lafuente. "Knowledge-based supervision and control of wastewater treatment plant: A real-time implementation". Water Science & Technology 41 12 (2000): 129-137. http://www.scopus.com/inward/record.url?eid=2-s2.0-0033870486&partnerID=MN8TOARS.
    Published
  168. Alves, M.; Cavaleiro, A.J.; Ferreira, E.C.; Amaral, A.L.; Mota, M.; Da Motta, M.; Vivier, H.; Pons, M.-N.. "Characterisation by image analysis of anaerobic sludge under shock conditions". Water Science & Technology 41 12 (2000): 207-214. http://www.scopus.com/inward/record.url?eid=2-s2.0-0033626042&partnerID=MN8TOARS.
    Published
  169. A. L. Amaral; C. Baptiste; M. N. Pons; A. Nicolau; N. Lima; E. C. Ferreira; M. Mota; H. Vivier. "Semi-Automated Recognition of Protozoa by Image Analysis". Biotechnology Techniques 13 2 (1999): 111-118. http://hdl.handle.net/1822/135.
    Published
  170. Amaral, A.L.; Baptiste, C.; Pons, M.N.; Nicolau, A.; Lima, N.; Ferreira, E.C.; Mota, M.; Vivier, H.. "Semi-automated recognition of protozoa by image analysis". Biotechnology Techniques 13 2 (1999): 111-118. http://www.scopus.com/inward/record.url?eid=2-s2.0-0033037374&partnerID=MN8TOARS.
    10.1023/A:1008850701796
  171. A. A. Vicente; M. Dluhý; E. C. Ferreira; J. A. Teixeira; Vicente, A.A.; Dluhý, M.; Ferreira, E.C.; Teixeira, J.A.. "Modelling Diffusion-Reaction Phenomena in Yeast Flocs of Saccharomyces cerevisiae". Bioprocess Engineering 18 5 (1998): 335-342. http://hdl.handle.net/1822/134.
    Published • 10.1007/PL00008993
  172. Vicente, A.A.; Dluhý, M.; Ferreira, E.C.; Mota, M.; Teixeira, J.A.. "Mass transfer properties of glucose and O2in Saccharomyces cerevisiae flocs". Biochemical Engineering Journal 2 1 (1998): 35-43. http://www.scopus.com/inward/record.url?eid=2-s2.0-0041763279&partnerID=MN8TOARS.
    10.1016/S1369-703X(98)00015-1
  173. R. Oliveira; E. C. Ferreira; F. R. Oliveira; S. Feyo de Azevedo. "A Study on the Convergence of Observer-Based Kinetic Estimators in Fed-Batch Fermentations". Journal of Process Control 6 6 (1996): 367-371. http://hdl.handle.net/1822/143.
    Published • 10.1016/0959-1524(95)00037-2
Magazine article
  1. E. C. Ferreira. "Gestão Ambiental na Universidade do Minho", Floresta e Ambiente, 2004, http://hdl.handle.net/1822/3443.
  2. E. C. Ferreira. "Nova Formação em Gestão Ambiental na Universidade do Minho", Ambiente Magazine, 2004, http://hdl.handle.net/1822/3487.
  3. E. C. Ferreira. "A Formação de Ambiente em Portugal", CentroAtlântico.pt Magazine, 2003, http://hdl.handle.net/1822/3441.
  4. E. C. Ferreira. "A Internet como Fonte de Informação para Engenharia", Engenharia e Construção, 1998
  5. E. C. Ferreira. "Fontes de Informação na Internet para Controlo e Automação", Robótica e Automação, 1997, http://hdl.handle.net/1822/3444.
  6. E. C. Ferreira. "A Internet como Fonte de Informação para Engenharia", Ingenium (revista da Ordem dos Engenheiros), 1996, http://hdl.handle.net/1822/3445.
Newspaper article
  1. Ferreira, Eugénio C.. "A Universidade do Minho e os novos laboratórios colaborativos", 2019, http://hdl.handle.net/1822/59870.
Report
  1. Ferreira, Eugénio C.; Araújo, Emília Rodrigues; Ramos, Isabel; Gomes, Manuela E.; Maciel, P.; Jerónimo, Patrícia; Ramada, José António Seara Salgado; Isaías, Margarida. 2021. Proposta de plano para a igualdade de género da Universidade do Minho (IGUM 2022-2024). http://hdl.handle.net/1822/75031.
  2. Reis, R. L.; Rodrigues, Eloy; Ferreira, Eugénio C.; Palha, Joana Almeida; González-Méijome, José Manuel; Gomes, Manuela E.; Gonçalves, Miguel M.; et al. 2017. Estratégia institucional para a gestão dos dados de investigação: estudo e recomendações. http://hdl.handle.net/1822/63930.
Thesis / Dissertation
  1. Fonseca, André Paço da. "A digital image based method to quantify intracellular polyphosphates in microbial aggregates". Master, 2018. http://hdl.handle.net/1822/66151.
  2. Mota, Elisiária Maria Dias da. "Segurança no trabalho: riscos ambientais". Master, 2017. http://hdl.handle.net/1822/54741.
  3. Miragaia, Ricardo Júdice. "Immune tolerance dissected by single-cell transcriptomics". PhD, 2017. http://hdl.handle.net/1822/48631.
  4. Oliveira, Daniel Filipe Braga de. "Plataforma online para caracterizar comunidades microbianas de estações de tratamento de água e efluentes". Master, 2017. http://hdl.handle.net/1822/57384.
  5. Souto, Maria Amélia Moreira. "Implementação do referencial BRC Food Safety versão 7 numa empresa transformadora de carne". Master, 2016. http://hdl.handle.net/1822/47435.

Other

Other output
  1. BioISO: an objective-oriented application for assisting the curation of genome-scale metabolic models. 2021. Fernando Cruz; João Capela; Eugénio C. Ferreira; Miguel Rocha; Oscar Dias. https://doi.org/10.1101/2021.03.07.434259.
    10.1101/2021.03.07.434259
  2. El título de ingeniero químico en el espacio europeo de educación superior. I Workshop de Ingeniería Química. 2013. Ferreira, Eugénio C.. http://hdl.handle.net/1822/59530.
  3. A Comunidade do CEB no RepositóriUM. Intervenção convidada proferida por ocasião do 10º Aniversário do RepositóriUM. 2013. Ferreira, Eugénio C.. http://hdl.handle.net/1822/59528.
  4. A Indústria Química Portuguesa. 12as Jornadas de Engenharia Química da Faculdade de Engenharia da Universidade do Porto. 2012. Ferreira, Eugénio C.; Araújo, Luís. http://hdl.handle.net/1822/59531.
  5. Biologia de Sistemas para o desenvolvimento de fábricas celulares microbianas. Palestra no CTBE Laboratório Nacional de Ciência e Tecnologia do Bioetanol. 2011. Ferreira, Eugénio C.. http://hdl.handle.net/1822/59524.
  6. Biotecnologia. Introdução, Editorial. 2007. E. C. Ferreira.
  7. A alternativa energética. Introdução, Editorial. 2007. E. C. Ferreira.
  8. Potencial da Biotecnologia na Região. Palestra convidada no âmbito do seminário Vale do Ave, região do Conhecimento: Perspectivas e Realidades. 2007. Ferreira, Eugénio C.. http://hdl.handle.net/1822/59548.
  9. Eco-Eficiência e Sustentabilidade Empresarial. Palestra para dirigentes de topo de empresas participantes no Projeto Valor Humano - Qualificação Avançada de Recursos Humanos. 2007. Ferreira, Eugénio C.. http://hdl.handle.net/1822/59552.
  10. The BioProcess Systems Engineering group (BioPSEg) @ The Institute for Biotechnology and Bioengineering. Palestra convidada no Centro de Investigación y Asistencia en Tecnología y Diseño del Estado de Jalisco (CIATEJ). 2007. Ferreira, Eugénio C.. http://hdl.handle.net/1822/59544.
  11. Specific growth rate regulation in a fed-batch E. coli fermentation. Invested Lecture at Automatic Control Unit of Cinvestav - Centro de Investigación y Estudios Avanzados. 2007. Rocha, Isabel; Ferreira, Eugénio C.. http://hdl.handle.net/1822/59534.
  12. Parabéns EQ!. Introdução, Editorial. 2006. E. C. Ferreira.
  13. Propostas de Leitura. Introdução, Editorial. 2006. E. C. Ferreira.
  14. A Pensar nos Leitores. Introdução, Editorial. 2005. E. C. Ferreira.
  15. Tendências Recentes no Ensino da Engenharia Química. 4º Encontro da Associação para o Ensino de Laboratórios de Engenharia Química. 2005. Ferreira, Eugénio C.. http://hdl.handle.net/1822/59554.
  16. Image analysis applications in biological wastewater treatment processes. Palestra na Gheorge Asachi Technical University of Iasi, Faculdade de Química Industrial. 2005. Ferreira, Eugénio C.. http://hdl.handle.net/1822/59532.
  17. Formação em Ambiente no Ensino Superior. 1.º Fórum Nacional de Estudantes de Engenharia do Ambiente. 2004. Ferreira, Eugénio C.. http://hdl.handle.net/1822/59543.
  18. A Engenharia de Sistemas Processuais em Biotecnologia, Química e Ambiente. 2.º Workshop Anual de Engenharia de Processos e Sistemas. 2004. Ferreira, Eugénio C.. http://hdl.handle.net/1822/59545.
  19. Proposta de reformulação do plano de estudos da Licenciatura em Engenharia Biológica da Universidade do Minho. VI Jornadas de Engenharia Biológica e IV Encontro de Jovens Biotecnólogos. 2003. Ferreira, Eugénio C.. http://hdl.handle.net/1822/59458.
  20. Tratamento de efluentes por via anaeróbia. Palestra no Laboratório de Saneamento Ambiental do Departamento de Engenharia Civil da Universidade Federal de Pernambuco. 2003. Ferreira, Eugénio C.. http://hdl.handle.net/1822/59457.
  21. Application of image analysis techniques in environmental biotechnology. IV Curso Internacional de Biotecnologia Industrial Tópicos de Biotecnologia Ambiental. 2003. Ferreira, Eugénio C.. http://hdl.handle.net/1822/58773.
  22. Análise de Imagem e Biotecnologia. Palestra no Departamento de Engenharia Química da Universidade Federal de Pernambuco. 2003. Ferreira, Eugénio C.. http://hdl.handle.net/1822/59460.
  23. Tratamentos biológicos de efluentes e emissões gasosas. Semana Universidade Empresas: Como Valorizar a Inovação, Painel "Novas Oportunidades de Negócio A Bio-Economia. 2002. Ferreira, Eugénio C.. http://hdl.handle.net/1822/58695.
  24. Fontes de informação para ambiente. Acção de Formação em Qualidade e Ambiente no âmbito do Programa Operacional Emprego, Formação e Desenvolvimento Social Região Norte, Medida 3.3.1.4 Especialização Profissional de Quadros Superiores Desempregados. 2001. Ferreira, Eugénio C.. http://hdl.handle.net/1822/59088.
Activities

Supervision

Thesis Title
Role 		Degree Subject (Type)
Institution / Organization
2017/10 - 2022 The role of extracellular polymeric substances during the biodegradation of contaminants.
Co-supervisor of Antônio Renê Benevides de Melo
 Engenharia Química e Biológica (PhD)
Universidade do Minho, Portugal
2013/10/01 - 2017/09/23 Immune Tolerance Dissected by Single-Cell Transcriptomics
Co-supervisor of Ricardo Júdice Miragaia
 Bioengenharia (PhD)
Universidade do Minho Escola de Engenharia, Portugal
2017/01 - 2017/06/12 Segurança no trabalho - Riscos ambientais
Supervisor of Elisiária Maria Dias da Mota
 Engenharia Biológica (Master)
Universidade do Minho, Portugal
2017/01 - 2017/05/31 Desenvolvimentos em engenharia de produto de cremes abrasivos e produtos de detergência
Supervisor of Cristina da Silva Rodriguez
 Engenharia Biológica (Master)
Universidade do Minho, Portugal
2016/10 - 2017/02/27 Plataforma online para caracterizar comunidades microbianas de estações de tratamento de água e efluentes
Supervisor of Daniel Filipe Braga de Oliveira
 Bioinformática (Master)
Universidade do Minho, Portugal
2016/01 - 2016/12/12 Implementação do referencial BRC food safety versão 7 numa empresa transformadora de carne
Supervisor of Maria Amélia Moreira Souto
 Engenharia Biológica (Master)
Universidade do Minho, Portugal
2014/01 - 2014/12/04 Implementação de um Sistema de Gestão da Qualidade e Segurança Alimentar numa adega de vinhos verdes segundo os referenciais ISO 9001:2008, ISO 22000:2005 e BRC Food Issue 6
Supervisor of Mariana Isabel Pimentel Antunes
 Engenharia Biológica (Master)
Universidade do Minho, Portugal
2014 - 2014/11/20 Image analysis of Saccharomyces cerevisiae cells : development of a plugin for IMAGEJ
Supervisor of Vitor Damião Baixinho da Silva
 Bioinformática (Master)
Universidade do Minho, Portugal
2009/01 - 2013/12/11 In vivo metabolic pathway analysis of Enterococcus faecalis for uncovering key pathogenicity factors
Co-supervisor of Carla Andreia Freixo Portela
 Engenharia Química e Biológica (PhD)
Universidade do Minho Escola de Engenharia, Portugal
2009/01 - 2013/06/25 Reconstruction of the Genome-scale Metabolic Network of Kluyveromyces lactis
Supervisor of Óscar Manuel Lima Dias
 Engenharia Química e Biológica (PhD)
Universidade do Minho Escola de Engenharia, Portugal
2008/11 - 2012/01/23 Novel modeling formalisms and simulation tools in Computational Biosystems
Supervisor of Carlos Daniel Moutinho Machado
 Bioengenharia (PhD)
Universidade do Minho Escola de Engenharia, Portugal
2006/01 - 2011/12/21 Systems analysis and metabolic network modeling in Escherichia coli
Supervisor of Rafael Sousa Costa
 Engenharia Química e Biológica (PhD)
Universidade do Minho Escola de Engenharia, Portugal
2006/11 - 2011/03/24 Image analysis and chemometric techniques as monitoring tools to characterize aggregated and filamentous organisms in activated sludge processes
Supervisor of Daniela Patrícia Bernardino Mesquita
 Engenharia Química e Biológica (PhD)
Universidade do Minho Escola de Engenharia, Portugal
2006/01 - 2010/12/30 A Systems Biology approach for the characterization of metabolic bottlenecks in recombinant protein production processes
Supervisor of Sónia Madalena Azevedo Carneiro
 Engenharia Química e Biológica (PhD)
Universidade do Minho Escola de Engenharia, Portugal
2006/11 - 2010/12/10 Characterization of a salmonella phage using omic tools and mathematical models to predict host-phage interaction
Supervisor of Sílvio Roberto Branco dos Santos
 Engenharia Química e Biológica (PhD)
Universidade do Minho, Portugal
2004/04 - 2008/11/07 Supervision of Transient Anaerobic Granular Sludge Process Through Quantitive Image Analysis and Multivariate Statistical Techniques
Supervisor of José Carlos Gomes da Costa
 Engenharia Química e Biológica (PhD)
Universidade do Minho, Portugal
2001/01 - 2008/02/26 Sistemas Inteligentes para Monitorização e Controlo de Processos Integrados de Tratamento Biológico de Efluentes
Supervisor of Olga Cristina Pereira Pires
 Engenharia Química e Biológica (PhD)
Universidade do Minho, Portugal
2001/10 - 2007/02/12 Optimização de Estratégias de Alimentação para a Identificação de Parâmetros de um Modelo de E.coli. Utilização do Modelo em Monitorização e Controlo
Supervisor of Ana Cristina Araújo Veloso
 Engenharia Química e Biológica (PhD)
Universidade do Minho, Portugal
2003 - 2006/07/07 Técnicas de Análise de Imagem no Monitoramento de Sistemas de Tratamento por Lodos Activos
Co-supervisor of Yovanka Pérez Ginoris
 Tecnologia de Processos Químicos e Bioquímicos (PhD)
Universidade Federal do Rio de Janeiro, Brazil
1999/10 - 2003/09/29 Image Analysis in Biotechnological Processes: Applications to Wastewater Treatment
Supervisor of António Luís Pereira do Amaral
 Engenharia Química e Biológica (PhD)
Universidade do Minho, Portugal
1998/04 - 2003/04/17 Model-based Strategies for Computer-Aided Operation of Recombinant E. coli Fermentation
Supervisor of Isabel Cristina de Almeida Pereira da Rocha
 Engenharia Química e Biológica (PhD)
Universidade do Minho, Portugal

Event organisation

Event name
Type of event (Role) 		Institution / Organization
2023 - 2023 CHEMPOR 2023 - 3th International Chemical and Biological Engineering Conference (2023 - 2023)
Congress (Member of the Scientific Committee)
2023 - 2023 CISPEE 2023 - 5th International Conference of the Portuguese Society for Engineering Education (2023 - 2023)
Congress (Member of the Scientific Committee)
2021 - 2021 MicroBiotec 2021 - Portuguese Congress of Microbiology and Biotechnology (2021 - 2021)
Congress (Member of the Scientific Committee)
2021 - 2021 ICEER 2021 - The 8th International Conference on Energy and Environment Research (2021 - 2021)
Congress (Member of the Scientific Committee)
2017/07/06 - 2017/07/06 CEB Scientific Annual Meeting 2017, Braga, Conference Chair (2017/07/06 - 2017/07/06)
Meeting (President of the Organising Committee)
 Universidade do Minho Centro de Engenharia Biológica, Portugal
2017 - 2017 CEB Talk 2017, GNRation, Braga (2017/11/23 - 2017/11/23)
Round table (President of the Organising Committee)
 Universidade do Minho Centro de Engenharia Biológica, Portugal
2016/07/06 - 2016/07/06 Sessão “Biotecnologia para uma Bioeconomia Sustentável” no CIÊNCIA’16 – Encontro com a Ciência e Tecnologia em Portugal, Lisboa (2016/07/06 - 2016/07/06)
Seminar (Co-organisor)
 Fundação para a Ciência e a Tecnologia, Portugal
2016/06/30 - 2016/06/30 2016 MIT Portugal Annual Conference, Braga, Conference Chair (2016/06/30 - 2016/06/30)
Conference (President of the Organising Committee)
 Universidade do Minho, Portugal
2015/06/08 - 2015/06/12 MPA2015 - Metabolic Pathway Analysis, Braga (2015/06/08 - 2015/06/12)
Congress (Member of the Organising Committee)
 Universidade do Minho, Portugal
2012 - 2012 “As Engenharias Química e Biológica - Que Futuro?”, Porto (2012/02/10 - 2012/02/10)
Conference (President of the Organising Committee)
 Ordem dos Engenheiros, Portugal
2011/01/01 - 2011/09/07 CHEMPOR 2011 - 11th International Chemical and Biological Engineering Conference, Caparica (2011/09/05 - 2011/09/07)
Conference (Member of the Organising Committee)
 Universidade Nova de Lisboa, Portugal
2011/01/01 - 2011/06/06 5th Annual Workshop on the Business-Government Interface: Systems and Synthetic Biology, Braga (2011/06/06 - 2011/06/06)
Workshop (Member of the Organising Committee)
 Universidade do Minho Centro de Engenharia Biológica, Portugal
2010/01/01 - 2010/11/06 XVIII Congresso da Ordem dos Engenheiros - “A Engenharia no Século XXI - Qualificação – Inovação – Empreendedorismo”, Aveiro (2010/11/04 - 2010/11/06)
Congress (Member of the Organising Committee)
 Ordem dos Engenheiros, Portugal
2010/01/01 - 2010/10/24 2nd Meeting of the Institute for Biotechnology and Bioengineering. Braga - www.ceb.uminho.pt/2nd_Meeting_IBB (2010/10/23 - 2010/10/24)
Meeting (Co-organisor)
 Universidade do Minho Centro de Engenharia Biológica, Portugal
2008/10/01 - 2009/11/30 MicroBiotec09. Vilamoura, Portugal - www.deb.uminho.pt/microbiotec09 (2009/11/28 - 2009/11/30)
Congress (Co-organisor)
 Sociedade Portuguesa de Biotecnologia, Portugal
2007/01/01 - 2008/12/31 CHEMPOR 2008 - 10 th International Chemical Engineering Conference, Braga, Conference Chair - www.deb.uminho.pt/chempor2008 (2008/09/04 - 2008/09/06)
Conference (President of the Organising Committee)
 Universidade do Minho, Portugal
2008/07/11 - 2008/07/11 Session “Nonlinear Control and Estimation in Bioprocesses” at 17th Triennial World Congress of the International Federation of Automatic Control (IFAC) (2008/07/11 - 2008/07/11)
Seminar (Co-organisor)
 International Federation of Automatic Control, Austria
2008/01/01 - 2008/05/31 Semana da Biotecnologia, Braga: eventos “Encontros para a Competitividade: prioridades para a indústria da biotecnologia”; “BioEmpreenda’08 – Feira de Ideias e Financiamento para o sector das biotecnologias”; “Seminário Caminhos para a Inovação – o bioempreendedorismo”; apresentação do estudo ‘Global Entrepreneurship Monitor Portugal 2007’; Industrial Biotech Forum; Exposição ‘Dispositivos Médicos’; Conferência ’Estratégias de eficiência colectiva no sector agro-alimentar da região do Norte’; Workshop on Medical Devices. (2008/05/26 - 2008/05/31)
Exhibition (Member of the Organising Committee)
 Universidade do Minho, Portugal
2006/09/01 - 2007/07/27 REV 2007 - International Conference Remote Engineering and Virtual Instrumentation, Porto (2007/06/25 - 2007/06/27)
Conference (Member of the Organising Committee)
 Universidade do Porto Faculdade de Engenharia, Portugal
2007 - 2007 Workshop “Introdução ao REACH – Registration, Evaluation, Authorization and Restriction of Chemicals”, Lisboa (2007/12/05 - 2007/12/05)
Workshop (Member of the Organising Committee)
 Ordem dos Engenheiros, Portugal
2006 - 2006 Comemorações dos 20 anos do curso de Engenharia Biológica, Braga, - www.deb.uminho.pt/20anos (2006/10/20 - 2006/10/21)
Other (President of the Organising Committee)
 Universidade do Minho Departamento de Engenharia Biológica, Portugal
2004/09/01 - 2005/09/18 CHEMPOR 2005 - 9th International Chemical Engineering Conference, Coimbra (2005/09/14 - 2005/09/18)
Conference (Member of the Organising Committee)
 Universidade de Coimbra, Portugal

Ordem dos Engenheiros, Portugal
2005 - 2005 Special session "Natural-computing Algorithms to Modeling and Optimization of Bioprocesses" (NAMOB-2005) at 7th International Conference on Adaptive and Natural Computing Algorithms (ICANNGA), Coimbra (2005/03/21 - 2005/03/21)
Seminar (Co-organisor)
 Universidade de Coimbra, Portugal
2003/06/01 - 2004/09/30 CAC-2004 - 9th Chemometrics in Analytical Chemistry Conference, Lisboa (2004/09/20 - 2004/09/23)
Conference (Member of the Organising Committee)
 Universidade de Lisboa Instituto Superior Técnico, Portugal
2003/01/01 - 2004/05/31 ESCAPE-14 - European Symposium on Computer Aided Process Engineering, Lisboa - www.deb.uminho.pt/escape14 (2004/05/16 - 2004/05/19)
Symposium (Member of the Organising Committee)
 Universidade de Lisboa Instituto Superior Técnico, Portugal
1999/06/01 - 2000/10/10 CONTROLO’2000 - 4th Portuguese Conference on Automatic Control, Guimarães - www.deb.uminho.pt/controlo2000 (2000/10/06 - 2000/10/09)
Conference (Member of the Organising Committee)
 Universidade do Minho Escola de Engenharia, Portugal
1997/06/01 - 1998/09/19 ESBES2 - 2nd European Symposium on Biochemical Engineering Science. Porto - www.deb.uminho.pt/esbes2 (1998/09/16 - 1998/09/19)
Symposium (Co-organisor)
 Universidade do Porto Faculdade de Engenharia, Portugal
1997/01/01 - 1998/07/31 BIOTEC'98 - IV Iberian Congress on Biotechnology, I Ibero-American Meeting on Biotechnology Guimarães - www.deb.uminho.pt/biotec98 (1998/07/12 - 1998/07/15)
Congress (Co-organisor)
 Universidade do Minho Centro de Engenharia Biológica, Portugal
1996/03/01 - 1996/09 2nd General Meeting of Network in Chemical Process Control (Human Capital and Mobility Program), Porto (1996/09/27 - 1996/09/28)
Meeting (Co-organisor)
 Universidade do Porto Faculdade de Engenharia, Portugal

Association member

Society Organization name Role
2005/01 - Current ESBES - European Society of Biochemical Engineering Sciences National Delegate to the Technical Committee on Modelling, Monitoring, Measurement, and Control
2004/01 - Current Associação Portuguesa de Engenharia Sanitária e Ambiental
2000/01 - Current IWA - International Water Association
1998/06 - Current Associação Portuguesa de Controlo Automático
1998/01 - Current Federação Europeia de Biotecnologia
1995/01 - Current IFAC - International Federation of Automatic Control National Delegate to the Technical Committee on Biosystems and Bioprocesses
1986/09 - Current Ordem dos Engenheiros
2004/01 - 2019/12 Sociedade Portuguesa de Biotecnologia Secretário-Geral
2010/03 - 2013/04 Ordem dos Engenheiros Presidente do Conselho Nacional do Colégio de Engenharia Química e Biológica
2004/01 - 2010/03 Ordem dos Engenheiros
2002/01 - 2007/12 International Association of Science and Technology for Development
1999/01 - 2004/12 Society for Industrial Microbiology.
2000/01 - 2003/12 Sociedade Portuguesa de Biotecnologia
1993/01 - 2002/12 SCI - Society of Chemical Industry

Committee member

Activity description
Role 		Institution / Organization
2018 - Current Committee on Publication Ethics
Member
 Committee on Publication Ethics, United Kingdom

Conference scientific committee

Conference name Conference host
2020/09/14 - 2020/09/18 CISPEE 2020 - 4th International Conference of the Portuguese Society for Engineering Education Porto
2020/01/01 - 2020/09/18 ICEER 2020 - The 7th International Conference on Energy and Environment Research
2019/12/05 - 2019/12/07 MicroBiotec’19 - Portuguese Congress of Microbiology and Biotechnology Universidade de Coimbra
2019/10/14 - 2019/10/19 FOSBE 2019 - 8th International Conference Foundations of Systems Biology in Engineering Valencia
2019/07/22 - 2019/07/25 ICEER 2019 - The 6th International Conference on Energy and Environment Research Universidade de Aveiro
2018/07/27 - 2018/07/29 CISPEE 2018 - 3rd International Conference of the Portuguese Society for Engineering Education Aveiro
2018/07/23 - 2018/07/27 ICEER 2018 - The 5th International Conference on Energy and Environment Research Praga, Czech Republic
2017/12/07 - 2017/12/09 MicroBiotec’17 - Portuguese Congress of Microbiology and Biotechnology Universidade Católica Portuguesa, Porto
2017/06/17 - 2017/06/20 ICEER 2017 - The 4th International Conference on Energy and Environment Research Porto
2016/10/20 - 2016/10/21 CISPEE 2016 - 2nd International Conference of the Portuguese Society for Engineering Education: Thinking Higher Engineering Education UTAD, Vila Real
2016/06/30 - 2016/06/30 2016 MIT Portugal Annual Conference Universidade do Minho, Braga
2016/06/05 - 2016/06/08 Bio.Iberoamérica 2016 Salamanca, Spain
2015/12/10 - 2015/12/12 MicroBiotec’15 - Portuguese Congress of Microbiology and Biotechnology Évora, Portugal
2015/11/10 - 2015/11/13 AD14 - 14th World Congress on Anaerobic Digestion Viña del Mar, Chile
2015/06/08 - 2015/06/12 MPA2015 - Metabolic Pathway Analysis Braga
2015/06/09 - 2015/06/09 5th MIT Portugal Program Conference - Light: Designed by Nature, Transformed by Science Lisboa
2014/09/10 - 2014/09/12 CHEMPOR 2014 - 12th International Chemical and Biological Engineering Conference Porto
2014/06/27 - 2014/06/27 4th MIT Portugal Program Conference - New Frontiers for a Sustainable Prosperity Coimbra
2014/02/26 - 2014/02/28 REV 2014 - 11th International Conference on Remote Engineering and Virtual Instrumentation Porto, Portugal
2013/12/16 - 2013/12/18 CAB 2013 - 12th International IFAC Symposium on Computer Applications in Biotechnology Mumbai, India
2013/12/06 - 2013/12/08 MicroBiotec’13 - Portuguese Congress of Microbiology and Biotechnology Aveiro
2013/10/31 - 2013/11/01 CISPEE 2013 - 1st International Conference of the Portuguese Society for Engineering Education Porto (ISEP)
2012/09/26 - 2012/09/27 EES 2012 - 1st International Conference on Energy, Environment and Sustainability Porto (ISEP)
2011/12/01 - 2011/12/03 MicroBiotec’11 - Portuguese Congress of Microbiology and Biotechnology Universidade do Minho, Braga

Course / Discipline taught

Academic session Degree Subject (Type) Institution / Organization
2020/03 - 2020/07 Controlo e Instrumentation de Processos / Process Control and Instrumentation Engenharia Biológica (Mestrado integrado) Universidade do Minho, Portugal

Evaluation committee

Activity description
Role 		Institution / Organization Funding entity
2017 - 2020 Coordinator of the review panel for PhD fellowships in Bioengineering and Biotechnology
Evaluator
 Fundação para a Ciência e a Tecnologia, Portugal Fundação para a Ciência e a Tecnologia

Journal scientific committee

Journal title (ISSN) Publisher
2020 - Current Frontiers in Chemical Engineering (2673-2718) Frontiers Media S.A.
2015 - Current Frontiers in Bioengineering and Biotechnology (2296-4185) Frontiers Media S.A.
2014 - Current Procedia Environmental Science, Engineering and Management National Society of Environmental Science and Engineering (Roménia)
2011/09/28 - Current Brazilian Journal of Chemical Engineering Springer
2008/07/01 - Current Chemical Product and Process Modeling De Gruyter
2005/09/01 - Current Engenharia Química - Indústria, Ciência e Tecnologia Publindústria
2004/10/01 - Current Environmental Engineering and Management Journal
2012/01/02 - 2022/03/31 BioMed Research International Hindawi

Other jury / evaluation

Activity description Institution / Organization
2020/05/11 - 2020/05/11 Vogal do Júri do Concurso Documental para para recrutamento de um Professor Associado, de área disciplinar de Biomedicina, Edital n.º 1603/2019, de 27 de dezembro Universidade de Lisboa Faculdade de Ciências, Portugal
2020/05/11 - 2020/05/11 Vogal do Júri do Concurso Documental para para recrutamento de um Professor Associado, de área disciplinar de Bioquímica, Edital n.º 1639-S/2019, de 30 de dezembro Universidade de Lisboa Faculdade de Ciências, Portugal
Distinctions

Title

2017 Membro Conselheiro
Ordem dos Engenheiros, Portugal

Other distinction

2020 Medalha de Mérito Municipal
Câmara Municipal de Esposende, Portugal
2004 Melhor Tese de Doutoramento no país em Engenharia Química e Biológica (Orientador)
Companhia União Fabril Consultadoria e Serviços SA, Portugal