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PT: Professor Associado com Agregação da Universidade do Minho. Leciona no Departamento de Informática principalmente unidades curriculares relacionadas com Bioinformática e Aprendizagem Máquina/ Ciências de Dados, sendo também o DIretor do Curso de Mestrado em Bioinformática, que co-fundou em 2007. É investigador integrado do Centro de Engenharia Biológica, onde lidera o grupo de investigação em Bioinformatics and Systems Biology (mais de 15 membros atualmente), tendo sido/ sendo investigador responsável de 12 projetos de investigação e tendo participado em mais de outros 25 projetos como membro da equipa. É autor de mais de 280 publicações em conferências e revistas internacionais com revisão por pares. Orientou 25 teses de Doutoramento finalizadas (7 atualmente em curso) e mais de 100 dissertações de Mestrado. Foi Diretor do Centro de CIências da Tecnologia da Computação (2010-2013) e membro eleito do Conselho Científico da Escola de Engenharia (2019-2025). Foi ainda (2021-2024), o Presidente eleito do Conselho de Administração da Associação BPI4DAB (BioData.pt) e é membro (representante científico) do Board do ELIXIR. ------------------------------------------------------------------------------------------------------------ EN: He is an Associate Professor with Habilitation from the University of Minho, where he lectures in the Department of Informatics mainly subjects related to Bioinformatics and Machine Learning/ Data Sciences, being also the Director of the MSc in Bioinformatics, a degree he co-founded in 2007. He is a senior researcher at the Centre of Biological Engineering, where he leads the Bioinformatics and Systems Biology group (over 15 members). He is/has been the PI of 12 research projects, and he has also participated in more than 25 projects as a team member. He is the author of over 280 papers in internacional peer-reviewed conferences and journals. He supervised 25 PhD theses (concluded), 7 on-going) and over 100 master theses. He was the Director of the CCTC research centre at U. Minho (2010-2013) and an elected member of the Scientific Council of the School of Engineering (2019-25). He was President of the Board of the BIP4DAB (BioData.pt) Association (2021-2024) and is a member (scientific representative) of the ELIXIR board.
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Identification

Personal identification

Full name
Miguel Rocha

Citation names

  • Rocha, Miguel

Author identifiers

Ciência ID
C71E-042A-53DE
ORCID iD
0000-0001-8439-8172
Google Scholar ID
http://scholar.google.com/citations?user=pT-rwEIAAAAJ&hl=en
Researcher Id
B-9404-2011
Scopus Author Id
7102481188

Email addresses

  • mrocha@di.uminho.pt (Professional)

Telephones

Telephone
  • 253604469 (Professional)

Addresses

  • Campus de Gualtar, Dept. Informática, 4710-057, Braga, Braga, Portugal (Professional)

Websites

Knowledge fields

  • Exact Sciences - Computer and Information Sciences - Bioinformatics
  • Exact Sciences - Computer and Information Sciences - Computer Sciences

Languages

Language Speaking Reading Writing Listening Peer-review
Portuguese (Mother tongue)
English Proficiency (C2) Proficiency (C2) Advanced (C1) Advanced (C1) Advanced (C1)
Spanish; Castilian Elementary (A2) Elementary (A2) Beginner (A1) Elementary (A2) Beginner (A1)
Education
Degree Classification
2017/10/27
Concluded
 Agregação na área científica de Informática (Título de Agregado)
Universidade do Minho, Portugal
2004/04/16
Concluded
 Doutoramento em Informática (Mestrado integrado)
Major in Inteligência Artificial
Universidade do Minho, Portugal
"Optimização de Modelos Conexionistas de Aprendizagem via Computação Genética e Evolucionária" (THESIS/DISSERTATION)
1995/10/01 - 1998/03/15
Concluded
 Mestrado em Informática (Mestrado)
Major in Sistemas Distribídos, Arquitecturas de Computador e Comunicações por Computador
Universidade do Minho, Portugal
"Uma Aproximação à Resolução do Problema do Caixeiro Viajante via Programação Genética" (THESIS/DISSERTATION)
 Muito Bom
1990/10/07 - 1995/09/30
Concluded
 Engenharia de Sistemas e Informática (Licenciatura)
Universidade do Minho, Portugal
 17
Affiliation

Teaching in Higher Education

Category
Host institution 		Employer
2012/08/01 - Current Associate Professor (University Teacher) Universidade do Minho, Portugal
2004/04/16 - 2012/07/31 Assistant Professor (University Teacher) Universidade do Minho, Portugal
1998/04/01 - 2004/04/15 Assistant (University Teacher) Universidade do Minho, Portugal
1996/10/01 - 1997/09/30 Tutor (University Teacher) Universidade do Minho, Portugal

Positions / Appointments

Category
Host institution 		Employer
2021/05/20 - 2024 President Associação BIP4DAB, Portugal

Others

Category
Host institution 		Employer
2021/06 - Current Fundador e CSO OmniumAi , Portugal
Projects

Contract

Designation Funders
2026/01/05 - 2029/01/04 VictuAI – Inteligência Artificial para o ciclo de vida dos suplementos alimentares
NORTE2030-FEDER-02303300
Principal investigator
Universidade do Minho Centro de Engenharia Biológica, Portugal
 Agência Nacional de Inovação SA
Ongoing
2025/10/01 - 2028/09/30 IngredientIA - Ingredientes, microbioma e modelos de digestão para a saúde através da aplicação de Inteligência Artificial
COMPETE2030-FEDER-02307500
Principal investigator
Universidade do Minho Centro de Engenharia Biológica, Portugal
 Agência Nacional de Inovação SA
Ongoing
2025/07/01 - 2028/06/30 CibusAI – Inteligência Artificial para a reformulação de produtos alimentares
NORTE2030-FEDER-01199800
Principal investigator
Universidade do Minho Centro de Engenharia Biológica, Portugal
Ongoing
2021/01/01 - 2025/12/31 Laboratório Associado em Biotecnologia, Bioengenharia e Sistemas microELetromecânicos
LA/P/0029/2020
10.54499/LA/P/0029/2020
Universidade do Minho, Portugal

Universidade do Minho Centro de Engenharia Biológica, Portugal

Universidade do Minho Labbels, Portugal
Fundação para a Ciência e a Tecnologia
Ongoing
2019/01/01 - 2023/02/28 SHIKIFACTORY100 – Modular cell factories for the production of 100 compounds from the shikimate pathway
814408
Principal investigator
Universidade do Minho Centro de Engenharia Biológica, Portugal

SilicoLife, Lda, Portugal

Danmarks Tekniske Universitet - Riso Campus, Denmark

European Molecular Biology Laboratory, Germany

Universidade Nova de Lisboa, Portugal

The University of Manchester, United Kingdom

GalChimia SA, Spain

École Polytechnique Fédérale de Lausanne, Switzerland
EU Framework Programme for Research and Innovation Nanotechnologies Advanced Materials Advanced Manufacturing and Processing and Biotechnology
Ongoing
2019/07/01 - 2022/06/30 DeepBio – Deep and machine learning for industrial biotechnology
NORTE-01-0247-FEDER-039831
Principal investigator
Universidade do Minho, Portugal

SilicoLife, Lda, Portugal
Agência Nacional de Inovação SA
Ongoing
2017/06 - 2020/06 BioData.pt - Portuguese Biological Data Network
POCI-01-0145-FEDER-022231
Principal investigator
Universidade do Minho, Portugal

Instituto Gulbenkian de Ciência, Portugal

Instituto de Engenharia de Sistemas e Computadores Investigação e Desenvolvimento em Lisboa, Portugal

Centro de Biotecnologia Agrícola e Agro-Alimentar do Alentejo, Portugal

Universidade do Porto Instituto de Investigação e Inovação em Saúde, Portugal
Fundação para a Ciência e a Tecnologia
Ongoing
2016/03 - 2020/02 DD-Decaf - Bioinformatics Services for Data-Driven Design of Cell Factories and Communities
H2020-LEIT-BIO-2015-1 686070-1
Researcher
Universidade do Minho, Portugal

Danmarks Tekniske Universitet, Denmark

École Polytechnique Fédérale de Lausanne Bibliothèque, Switzerland

SilicoLife, Lda, Portugal

European Molecular Biology Laboratory, Germany
European Commission
Ongoing
2016/01/01 - 2018/12/31 SISBI – Sistema Inteligente de Suporte à Decisão em Biotecnologia Industrial
NORTE-01-0247-FEDER-003381
Principal investigator
Universidade do Minho Centro de Engenharia Biológica, Portugal

SilicoLife, Lda, Portugal
Agência Nacional de Inovação SA
Concluded
2015/04 - 2018/03 DYNAMICS - Analysis and optimization of industrial microorganisms under dynamic process conditions
ERA-IB-2/0002/2014
Researcher
Universidade do Minho, Portugal
 European Commission
Concluded
2014/03 - 2018/02 An integrated computational platform for knowledge extraction from metabolomics data applied to the analysis of natural products
PVE
Researcher
Universidade Federal de Santa Catarina, Brazil
 Conselho Nacional de Desenvolvimento Científico e Tecnológico
Concluded
2014/01 - 2017/12 Biocontrol: network for studies of systems biology and control methods
N/A
Researcher
Universidade Federal de Santa Catarina, Brazil
 Coordenação de Aperfeiçoamento de Pessoal de Nível Superior
Concluded
2014/03 - 2017/05 DeYeastLibrary: Designer yeast strain library optimized for metabolic engineering applications
N/A
Researcher
Universidade do Minho, Portugal
 European Commission
Concluded
2014/03 - 2017/02 PropMine: Desenvolvimento de ferramentas de descrição e classificação da própolis brasileira via metabolómica e mineração de dados
PropMine
Principal investigator
Universidade do Minho, Portugal

Universidade Federal de Santa Catarina, Brazil
Fundação para a Ciência e a Tecnologia

Conselho Nacional de Desenvolvimento Científico e Tecnológico
Concluded
2012/07 - 2015/06 PEM – Platform for Metabolic Engineering
23060
Researcher
Universidade do Minho, Portugal

SilicoLife, Lda, Portugal
Agência Nacional de Inovação SA

European Regional Development Fund
Concluded
2011/04 - 2014/09 The Transcriptome of the Oncogenic HOXA9 Homeoprotein in Human Glioblastoma: Characterization and Functional Significance
PTDC/SAU-GMG/113795/2009
113795
Provided by PTCRIS: 113795
Researcher
Universidade do Minho, Portugal
 Fundação para a Ciência e a Tecnologia

Universidade de Coimbra
Concluded
2011/03 - 2014/07 ToMEGIM: Computational Tools for Metabolic Engineering using Genome-scale Integrated Models
PTDC/EIA-EIA/115176/2009
115176
Provided by PTCRIS: 115176
Principal investigator
Universidade do Minho, Portugal
 Fundação para a Ciência e a Tecnologia

Universidade de Coimbra
Concluded
2011/01 - 2014/06 In silico reconstruction of Streptococcus pneumoniae cellular networks and their impact on virulence
PTDC/EBB-EBI/113824/2009
Provided by PTCRIS: 113824
113824
Researcher
Universidade do Minho, Portugal

Fundação da Faculdade de Ciências da Universidade de Lisboa, Portugal
Fundação para a Ciência e a Tecnologia

Universidade de Coimbra
Concluded
2011/01/01 - 2013/12/31 Projecto Estratégico - UI 752 - 2011-2012
PEst-OE/EEI/UI0752/2011
Universidade do Minho, Portugal

Universidade do Minho Centro ALGORITMI, Portugal
Fundação para a Ciência e a Tecnologia
Concluded
2010/06 - 2013/12 GAsPar: General-purpose Aspect-Oriented framework for heterogeneous multicore Parallel systems
PTDC/EIA-EIA/108937/2008
108937
Provided by PTCRIS: 108937
Researcher
Universidade do Minho, Portugal
 Fundação para a Ciência e a Tecnologia

Universidade de Coimbra
Concluded
2010/04 - 2013/09 HeliSysBio - Molecular Systems Biology Helicobacter pylori
Provided by PTCRIS: 104235
104235
PTDC/EBB-EBI/104235/2008
Researcher
Universidade do Minho, Portugal
 Universidade de Coimbra

Fundação para a Ciência e a Tecnologia
2008/12 - 2012/11 SYSINBIO- Systems Biology as a Driver for Industrial Biotechnology
212766
Researcher
Universidade do Minho, Portugal

École Polytechnique Fédérale de Lausanne, Switzerland

Chalmers tekniska högskola, Sweden

Danmarks Tekniske Universitet, Denmark

Universität Stuttgart Biologisches Institut, Germany

Universita degli Studi di Milano Facolta di Scienze e Tecnologie, Italy
European Commission
Concluded
2009/04 - 2012/09 Bridging Systems and Synthetic Biology for the development of Improved Microbial Cell Factories
MIT-Pt/BS-BB/0082/2008
84035
Provided by PTCRIS: 84035
Researcher
Universidade do Minho, Portugal
 Fundação para a Ciência e a Tecnologia

Universidade de Coimbra
Concluded
2008/01 - 2010/12 SPAM Telescope Miner: worldwide unsolicited email detection using data mining techniques
PTDC/EIA/64541/2006
64541
Provided by PTCRIS: 64541
Researcher
Universidade do Minho, Portugal
 Fundação para a Ciência e a Tecnologia

Universidade de Coimbra
Concluded
2007/07 - 2010/12 AspectGrid: Pluggable Grid Aspects for Scientific Applications
GRID/GRI/81880/2006
81880
Provided by PTCRIS: 81880
Researcher
Fundação para a Ciência e a Tecnologia

Universidade de Coimbra
Concluded
2007 - 2009 Machine Learning Applications in Systems Biology Research
FLAD-FCT
Researcher
Universidade do Minho, Portugal

University of California Irvine, United States
Fundação Luso-Americana

Fundação para a Ciência e a Tecnologia
Concluded
2007 - 2009 Development of a user-friendly software platform for the rational design of improved microbial strains
N/A
Researcher
Universidade do Minho, Portugal
 Dupont Central Research and Development
Concluded
2007 - 2009 Development of a case-based reasoning tool for cancer diagnosis using microarray datasets
N/A
Researcher
Universidade do Minho, Portugal

Universidade de Vigo - Campus Ourense, Spain
Fundação para a Ciência e a Tecnologia
Concluded
2005/07 - 2008/06 MOBioPro-Nature-based computation in the modeling and optimization of biotechnological processes
59899
Provided by PTCRIS: 59899
Principal investigator
Universidade de Coimbra
2005 - 2007 Neural Network based techniques for Internet Congestion Control
N/A
Researcher
Universidade do Minho, Portugal

University College London, United Kingdom
Conselho de Reitores das Universidades Portuguesas

British Council Portugal
Concluded
2003 - 2006 Intelligent Agents Simulation for the RoboCup
POSI/ROBO/ 43904/2002
Researcher
Universidade do Minho Centro ALGORITMI, Portugal
 Fundação para a Ciência e a Tecnologia
Concluded
Outputs

Publications

Book
  1. Fdez-Riverola, F.; Rocha, M.; Mohamad, M.S.; Caraiman, S.; Gil-González, A.B.. Preface. 2023.
  2. Rocha, M.; Fdez-Riverola, F.; Mohamad, M.S.; Casado-Vara, R.. Preface. 2022.
  3. Panuccio, G.; Fdez-Riverola, F.; Casado-Vara, R.; Rocha, M.; Mohamad, M.S.. Preface. 2021.
  4. Fdez-Riverola, F.; Rocha, M.; Mohamad, M.S.; Zaki, N.; Castellanos-Garzón, J.A.. Preface. 2020.
  5. Mohamad, M.S.; Rocha, M.P.; De Paz, J.F.; Fdez-Riverola, F.; González, P.. Preface. 2019.
  6. Overbeek, R.; Rocha, M.P.; Fdez-Riverola, F.; De Paz, J.F.. 9th International Conference on Practical Applications of Computational Biology and Bioinformatics. 2015.
    10.1007/978-3-319-19776-0
Book chapter
  1. Tiago Sousa; João Correia; Vitor Pereira; Miguel Rocha. "Combining Multi-objective Evolutionary Algorithms with Deep Generative Models Towards Focused Molecular Design". 2021.
    10.1007/978-3-030-72699-7_6
  2. Rocha, Miguel. "Banana (Musa spp.) as a Source of Bioactive Compounds for Health Promotion". In Handbook of Banana Production, Postharvest Science, Processing Technology, and Nutrition, 227-244. Springer, 2020.
    Published
  3. G. Uarrota, Virgílio; de Fatima Moreira de Bairros, Angela; Gindri, Diego; Santini Leolato, Lucieli; Camargo de Andrade, Gisiane; Nerling, Daniele; Stefen, Deivid; et al. "From Neglected and Underutilized Crops to Powerful Sources of Vitamin A: Three Case Studies of Mozambican Cultivated Tacca leontopetaloides, Cowpea, and Cassava". In Vitamin A. IntechOpen, 2019.
    10.5772/intechopen.84829
  4. Bauer, C.M.; Schmitz, C.; Corrêa, R.G.; Herrera, C.M.; Ramlov, F.; Oliveira, E.R.; Pizzato, A.; et al. "In vitro fucoxanthin production by the Phaeodactylum tricornutum diatom". In Studies in Natural Products Chemistry, 211-242. Elsevier, 2019.
    10.1016/b978-0-12-817901-7.00008-3
  5. Ferreira, Jorge; Vieira, Vitor; Rocha, Miguel. "Genome-Scale Metabolic Models". In Reference Module in Biomedical Sciences. Elsevier, 2019.
    10.1016/b978-0-12-801238-3.11514-4
  6. Bauer, C.M.; Schmitz, C.; Corrêa, R.G.; Herrera, C.M.; Ramlov, F.; Oliveira, E.R.; Pizzato, A.; et al. "In vitro fucoxanthin production by the Phaeodactylum tricornutum diatom". 211-242. 2019.
    10.1016/B978-0-12-817901-7.00008-3
  7. Valente, E.; Rocha, M.. "DNA microarrays: Fundamentals, data integration and applications". 349-362. 2019.
  8. Dias, O.; Rocha, M.; Ferreira, E.C.; Rocha, I.. "Reconstructing high-quality large-scale metabolic models with merlin". 1-36. 2018.
    10.1007/978-1-4939-7528-0_1
  9. Vilaça, P.; Maia, P.; Giesteira, H.; Rocha, I.; Rocha, M.. "Analyzing and designing cell factories with OptFlux". 37-76. 2018.
    10.1007/978-1-4939-7528-0_2
  10. Valente, E.; Rocha, M.; Ferreira, E.C.; Rocha, I.. "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.
    10.1007/978-3-642-01888-6_11
  11. Mendes, R.; Rocha, I.; Pinto, J.P.; Ferreira, E.C.; Rocha, M.. "Differential evolution for the offline and online optimization of fed-batch fermentation processes". In Advances in Differential Evolution, 299-317. 2008.
    10.1007/978-3-540-68830-3_13
  12. Cortez, P.; Rocha, M.; Neves, J.. "Time series forecasting by evolutionary neural networks". In Artificial neural networks in real-life applications, 47-70. 2005.
    10.4018/978-1-59140-902-1.ch003
Conference abstract
  1. Azeredo, Joana; Costa e Silva, Elsa; Lino-Neto, Teresa; Ribeiro, Eugénia; Rocha, Miguel; Tereso, Anabela Pereira ; Costa, Manuel João. "A participação em comunidade de prática docente para a inovação pedagógica uma experiência de professores na implementação de TBL (Team-Based Learning)". Paper presented in Congresso Nacional de Práticas Pedagógicas no Ensino Superior (CNaPPES.19), Santarém, 2019.
    Published
  2. Dias, Oscar; Rocha, Miguel; Ferreira, Eugénio C.; Rocha, Isabel; Rocha, I.. "MEtabolic models Reconstruction using genome scaLe INformation (merlin) - assessment and validation". Paper presented in Copenhagen Biosciences Conferences - 7th Conference: Cell Factories and Biosustainability, Copenhagen, 2015.
    Published
  3. Dias, Oscar; Rocha, Miguel; Ferreira, Eugénio C.; Rocha, Isabel; Rocha, I.. "Merlin Latest Developments for Pathways Analysis". Paper presented in MPA2015 - Metabolic Pathway Analysis 2015, Braga, 2015.
    Published
  4. Dias, Oscar; Rocha, Miguel; Rocha, Isabel; Ferreira, Eugénio C.. "Metabolic reconstruction of less characterized microorganisms: a new methodology for reaction identification from genome sequencing data.". Paper presented in JORNADAS DE BIOINFORMÁTICA, Lisboa, 2009.
    Published
Conference paper
  1. Sá, Bruno; Oliveira, Alexandre; Rocha, Miguel. "Evolutionary Algorithms for Metabolic Transformation through Multi-gene Knockout Optimization". Paper presented in GECCO 2025, 2025.
    Published • 10.1145/3712256.3726477
  2. Alves, Nuno; Osório, Nuno S.; Pereira, Vítor; Rocha, Miguel. "Leveraging Large Language Models on Assay Descriptions to Improve the Prediction of Inhibitors for Mycobacterium Tuberculosis.". Paper presented in IWANN 2025, 2025.
    Published • 10.1007/978-3-032-02725-2_9
  3. Sampaio, Marta; Rocha, Miguel; Dias, O.. Corresponding author: Sampaio, Marta. "A multi-omics approach for understanding grape metabolism throughout development". Paper presented in 10th IFAC International Conference on Foundations of Systems Biology in Engineering, 2024.
    Under revision
  4. Oliveira, Alexandre; Rocha, Miguel; Dias, O.. Corresponding author: Dias, O.. "Metabolic modelling reveals key pathways in COVID-19 in an effort to drive drug purposing". Paper presented in 10th IFAC International Conference on Foundations of Systems Biology in Engineering, Corfu, 2024.
    Published • 10.1016/j.ifacol.2024.10.016
  5. Sampaio, Marta; Rocha, Miguel; Dias, O.. Corresponding author: Sampaio, Marta. "iplants: a repository of plant metabolic data". Paper presented in 18th International Conference on Practical Applications of Computational Biology and Bioinformatics, Salamanca, 2024.
    Under revision
  6. João Correia; Vítor Pereira; Miguel Rocha. "Combining Evolutionary Algorithms with Reaction Rules Towards Focused Molecular Design". 2023.
    10.1145/3583131.3590413
  7. Baptista, D.; Correia, J.; Pereira, B.; Rocha, M.. "A Comparison of Different Compound Representations for Drug Sensitivity Prediction". Paper presented in PACBB 2021, Salamanca, 2021.
    Published • 10.1007/978-3-030-86258-9_15
  8. Pereira, V.; Rocha, M.. "Combinatorial Optimization of Succinate Production in Escherichia coli". Paper presented in PACBB 2021, Salamanca, 2021.
    10.1007/978-3-030-86258-9_16
  9. Antunes, D.; Martins, D.; Correia, F.; Rocha, M.; Arrais, J.P.. "Computational Methods for the Identification of Genetic Variants in Complex Diseases". Paper presented in PACBB 2021, Salamanca, 2021.
    Published • 10.1007/978-3-030-86258-9_1
  10. Pereira, B.; Maraschin, M.; Rocha, M.. "Computational Tools for the Analysis of 2D-Nuclear Magnetic Resonance Data". Paper presented in PACBB 2021, Salamanca, 2021.
    10.1007/978-3-030-86258-9_6
  11. Alves, N.; Rodrigues, R.; Rocha, M.. "BioTMPy: A Deep Learning-Based Tool to Classify Biomedical Literature". Paper presented in PACBB 2021, Salamanca, 2021.
    10.1007/978-3-030-86258-9_12
  12. Sequeira, A.M.; Rocha, M.. "Recurrent Deep Neural Networks for Enzyme Functional Annotation". Paper presented in PACBB 2021, Salamanca, 2021.
    10.1007/978-3-030-86258-9_7
  13. Reis, J.; Phan, T.K.; Kheirkhah, M.; Yang, F.; Griffin, D.; Rocha, M.; Rio, M.. "R2L: Routing with Reinforcement Learning". 2021.
    10.1109/IJCNN52387.2021.9533549
  14. Camaz, G.; Pereira, V.; Rocha, M.; Sousa, P.. "Optimizing NFV deployment in Segment Routing,Otimização de implementações NFV em Segment Routing". 2021.
    10.23919/CISTI52073.2021.9476304
  15. Rocha, Miguel; Sequeira, Ana Marta; Lousa, Diana. "A Python Automated Platform for the Classification of Proteins Using Machine Learning". Paper presented in 14th International Conference Practical Applications of Computational Biology & Bioinformatics (PACBB 2020), L'Aquila, 2020.
  16. Rocha, Miguel; Cruz, Fernando; Dias, Oscar. "Reconciliation of Regulatory Data: The Regulatory Networks of Escherichia coli and Bacillus subtilis". Paper presented in 14th International Conference Practical Applications of Computational Biology & Bioinformatics (PACBB 2020), L'Aquila, 2020.
  17. Pereira, Vitor; Rocha, Miguel; Sousa, Pedro. "Hybrid IP/SDN Routing for Inter-Data Center Communications". Paper presented in 2019 IEEE 8th International Conference on Cloud Networking (CloudNet), 2020.
    10.1109/cloudnet47604.2019.9064118
  18. Sequeira, A.M.; Lousa, D.; Rocha, M.. "ProPythia: A Python Automated Platform for the Classification of Proteins Using Machine Learning". Paper presented in 14th International Conference Practical Applications of Computational Biology & Bioinformatics (PACBB 2020), 2020.
    10.1007/978-3-030-54568-0_4
  19. Lima, D.; Cruz, F.; Rocha, M.; Dias, O.. "Reconciliation of Regulatory Data: The Regulatory Networks of Escherichia coli and Bacillus subtilis". Paper presented in 14th International Conference Practical Applications of Computational Biology & Bioinformatics (PACBB 2020), 2020.
    10.1007/978-3-030-54568-0_16
  20. Jorge Ferreira; Vítor Vieira; Jorge Gomes; Sara Correia; Miguel Rocha. "Troppo - A Python Framework for the Reconstruction of Context-Specific Metabolic Models". Paper presented in PACBB 2'019, 2019.
    Published • 10.1007/978-3-030-23873-5_18
  21. Sampaio, M.; Rocha, M.; Oliveira, H.; Dias, O.. "Predicting Promoters in Phage Genomes Using Machine Learning Models". Paper presented in Int. Conf. Practical Applications Bioinformatics and Computational Biology (PACBB 2019), Ávila, 2019.
    Published • 10.1007/978-3-030-23873-5_13
  22. Correia, J.; Resende, T.; Baptista, D.; Rocha, M.. "Artificial Intelligence in Biological Activity Prediction". Paper presented in Int. Conf. on Practical Applications of Bioinformatics and Computational Biology (PACBB 2019), 2019.
    Published • 10.1007/978-3-030-23873-5_20
  23. Cruz, F.; Lima, D.; Faria, J.P.; Rocha, M.; Dias, O.. "Towards the Reconstruction of Integrated Genome-Scale Models of Metabolism and Gene Expression". Paper presented in Int. Conf. Practical Applications Bioinformatics and Computational Biology (PACBB 2019), Ávila, 2019.
    Published • 10.1007/978-3-030-23873-5_21
  24. Rocha, Miguel; Phan, Truong Khoa; Reis, Joao; Griffin, David; Rio, Miguel. "Triptych: Multi-objective Optimisation of Service Deployment Costs, Application Delay and Bandwidth Usage". Paper presented in 2019 IFIP Networking Conference (IFIP Networking), Warsaw, 2019.
    10.23919/ifipnetworking.2019.8816840
  25. Reis, J.; Rocha, M.; Phan, T.K.; Griffin, D.; Le, F.; Rio, M.. "Deep Neural Networks for Network Routing". 2019.
    10.1109/IJCNN.2019.8851733
  26. Pereira, V.; Rocha, M.; Sousa, P.. "Hybrid IP/SDN Routing for Inter-Data Center Communications". 2019.
    10.1109/CloudNet47604.2019.9064118
  27. Rodrigues, R.; Costa, H.; Rocha, M.. "Automating the extraction of essential genes from literature". Paper presented in Industrial Conference on Data Mining, New York, 2018.
    10.1007/978-3-319-95786-9_6
  28. Cardoso, S.; Baptista, D.; Santos, R.; Rocha, M.. "A review on metabolomics data analysis for cancer applications". Paper presented in Int. Conf. Practical Applications Bioinformatics and Computational Biology (PACBB 2018), Toledo, 2018.
    Published • 10.1007/978-3-319-98702-6_19
  29. Bauer, C.M.; Vilaça, P.; Ramlov, F.; de Oliveira, E.R.; Cabral, D.Q.; Schmitz, C.; Corrêa, R.G.; Rocha, M.; Maraschin, M.. "In silico predictions for fucoxanthin production by the diatom phaeodactylum tricornutum". Paper presented in Int. Conf. Practical Applications Bioinformatics and Computational Biology (PACBB 2018), Toledo, 2018.
    Published • 10.1007/978-3-319-98702-6_17
  30. Cabral, D.; Cardoso, S.; Rocco, S.; Sforça, M.; Hengeltraub, S.F.; Bauer, C.; Rocha, M.; Maraschin, M.. "17a-ethinylestradiol analysis of endo- and exometabolome of ulva lactuca (chlorophyta) by 1H-NMR spectroscopy and bioinformatics tools". Paper presented in Practical Applications of Computational Biology and Bioinformatics, 12th International Conference, Toledo, 2018.
    10.1007/978-3-319-98702-6_26
  31. Vieira, V.; Ferreira, J.; Rodrigues, R.; Rocha, M.. "Metabolite integration pipeline for the improvement of human metabolic models". Paper presented in PACBB 2018 - Practical Applications of Computational Biology and Bioinformatics, 12th International Conference, Toledo, 2018.
    10.1007/978-3-319-98702-6_23
  32. Sequeira, J.C.; Rocha, M.; Madalena Alves, M.; Salvador, A.F.. "MOSCA: An automated pipeline for integrated metagenomics and metatranscriptomics data analysis". Paper presented in PACBB 2018, 2018.
    Published • 10.1007/978-3-319-98702-6_22
  33. Pereira, V.; Rocha, M.; Sousa, P.. "Segment routing single link failure congestion optimization". Paper presented in ICETE, 2018.
  34. Pereira, V.; Sousa, P.; Rocha, M.. "Evolutionary computation at work for the optimization of link state routing protocols". Paper presented in Workshops of GECCO 2017, 2017.
    10.1145/3067695.3076110
  35. Maia, P.; Rocha, I.; Rocha, M.. "Identification of robust strain designs via tandem pFBA/LMOMA phenotype prediction". Paper presented in GECCO 2017 Workshops, 2017.
    10.1145/3067695.3082542
  36. Osório, N.; Vilaça, P.; Rocha, M.. "A critical evaluation of automatic atom mapping algorithms and tools". Paper presented in 11th International Conference on Practical Applications of Computational Biology & Bioinformatics, 2017.
    10.1007/978-3-319-60816-7_31
  37. Alves, T.; Rodrigues, R.; Costa, H.; Rocha, M.. "Development of text mining tools for information retrieval from patents". Paper presented in 11th International Conference on Practical Applications of Computational Biology & Bioinformatics, 2017.
    10.1007/978-3-319-60816-7_9
  38. Santiago, A.M.; Rocha, M.; Dourado, A.; Arrais, J.P.. "Mixed-integer programming model for profiling disease biomarkers from gene expression studies". Paper presented in IWBBIO 2017 - International Conference on Bioinformatics and Biomedical Engineering, 2017.
    10.1007/978-3-319-56154-7_6
  39. Lopes, S.; Moresco, L.; Peruch, L.A.M.; Rocha, M.; Maraschin, M.. "UV-vis spectrophotometry and chemometrics as tools for recognition of the biochemical profiles of organic banana peels (Musa sp.) according to the seasonality in southern Brazil". Paper presented in 11th International Conference on Practical Applications of Computational Biology & Bioinformatics, 2017.
    10.1007/978-3-319-60816-7_35
  40. Moresco, R.; Afonso, T.; Uarrota, V.G.; Navarro, B.B.; Nunes, E.C.; Rocha, M.; Maraschin, M.. "Classification tools for carotenoid content estimation in manihot esculenta via metabolomics and machine learning". Paper presented in PACBB 2017 - 11th International Conference on Practical Applications of Computational Biology & Bioinformatics, 2017.
    10.1007/978-3-319-60816-7_34
  41. Oliveira, E.R.; Wickert, E.; Ramlov, F.; Moresco, R.; Simão, L.; Navarro, B.B.; Bauer, C.; et al. "Influence of solar radiation on the production of secondary metabolites in three rice (Oryza sativa) cultivars". Paper presented in PACBB 2017 - 11th International Conference on Practical Applications of Computational Biology & Bioinformatics, 2017.
    10.1007/978-3-319-60816-7_36
  42. Cardoso, S.; Maraschin, M.; Peruch, L.A.M.; Rocha, M.; Pereira, A.. "Characterization of the chemical composition of banana peels from southern brazil across the seasons using nuclear magnetic resonance and chemometrics". Paper presented in International Conference on Practical Applications of Computational Biology & Bioinformatics, 2017.
    10.1007/978-3-319-60816-7_39
  43. Pereira, V.; Rocha, M.; Sousa, P.. "Automated network resilience optimization using computational intelligence methods". Paper presented in Intelligent Distributed Computing IX, 2016.
    10.1007/978-3-319-25017-5_46
  44. Ferreira, J.; Correia, S.; Rocha, M.. "Reconstruction of metabolic models for liver cancer cells". Paper presented in PACBB 2016, 2016.
    10.1007/978-3-319-40126-3_22
  45. Vieira, V.; Maia, P.; Rocha, I.; Rocha, M.. "Development of an integrated framework for minimal cut set enumeration in constraint-based models". Paper presented in PACBB 2016: 10th International Conference on Practical Applications of Computational Biology & Bioinformatics, 2016.
    10.1007/978-3-319-40126-3_20
  46. Rodrigues, R.; Costa, H.; Rocha, M.. "Development of a machine learning framework for biomedical text mining". Paper presented in PACBB 2016 - Practical Applications of Bioinformatics and Computational Biology, 2016.
    10.1007/978-3-319-40126-3_5
  47. Moresco, R.; Uarrota, V.G.; Pereira, A.; Tomazzoli, M.; Nunes, E.C.; Peruch, L.A.M.; Costa, C.; Rocha, M.; Maraschin, M.. "Carotenoid analysis of cassava genotypes roots (Manihot Esculenta Crantz) cultivated in southern Brazil using chemometric tools". Paper presented in PACBB 2016, 2016.
    10.1007/978-3-319-19776-0_2
  48. Pereira, V.; Sousa, P.; Cortez, P.; Rio, M.; Rocha, M.. "Comparison of single and multi-objective evolutionary algorithms for robust link-state routing". Paper presented in EMO 2016, 2016.
    10.1007/978-3-319-15892-1_39
  49. Pereira, R.T.; Costa, H.; Carneiro, S.; Rocha, M.; Mendes, R.. "Reconstructing transcriptional Regulatory Networks using data integration and Text Mining". Paper presented in BIBM 2015, 2015.
    10.1109/BIBM.2015.7359907
  50. Valente, E.; Rocha, M.. "Transcript-based reannotation for microarray probesets". Paper presented in SAC 2015, 2015.
    10.1145/2695664.2695704
  51. Tomazzoli, M.M.; Pai Neto, R.D.; Moresco, R.; Westphal, L.; Zeggio, A.R.S.; Specht, L.; Costa, C.; Rocha, M.; Maraschin, M.. "UV-visible scanning spectrophotometry and chemometric analysis as tools to build descriptive and classification models for propolis from Southern Brazil". Paper presented in PACBB 2015, Salamanca, 2015.
    10.1007/978-3-319-19776-0_3
  52. Correia, S.; Rocha, M.. "A critical evaluation of methods for the reconstruction of tissue-specific models". Paper presented in EPIA 2015, 2015.
    10.1007/978-3-319-23485-4_35
  53. Costa, C.; Maraschin, M.; Rocha, M.. "An integrated computational platform for metabolomics data analysis". Paper presented in PACBB 2015, 2015.
    10.1007/978-3-319-19776-0_5
  54. Valente, E.; Rocha, M.. "Microarray gene expression data integration: An application to brain tumor grade determination". Paper presented in PACBB 2015, 2015.
    10.1007/978-3-319-19776-0_14
  55. Freitas, A.A.; Costa, H.; Rocha, M.; Rocha, I.. "A text mining approach for the extraction of kinetic information from literature". Paper presented in PACBB 2015, 2015.
    10.1007/978-3-319-19776-0_10
  56. Pilatti, F.K.; Costa, C.; Rocha, M.; Maraschin, M.; Viana, A.M.. "UV-visible spectrophotometry-based metabolomic analysis of Cedrela Fissilis Velozzo (Meliaceae) calluses - a screening tool for culture medium composition and cell metabolic profiles". Paper presented in PACBB 2015, 2015.
    10.1007/978-3-319-19776-0_4
  57. Rocha, O.; Vilaça, P.; Rocha, M.; Mendes, R.. "Reg4OptFlux: An OptFlux plug-in that comprises meta-heuristics approaches for Metabolic engineering using integrated models". Paper presented in NABIC 2014, 2014.
    10.1109/NaBIC.2014.6921882
  58. Barbosa, P.; Dias, O.; Arrais, J.P.; Rocha, M.. "Metagenomic analysis of the saliva microbiome with merlin". Paper presented in PACBB 2014, 2014.
    10.1007/978-3-319-07581-5_23
  59. Moresco, R.; Uarrota, V.G.; Nunes, E.C.; Coelho, B.; Amante, E.R.; Gervin, V.M.; Eduardo M Campos, C.; Rocha, M.; Maraschin, M.. "Discrimination of Brazilian Cassava Genotypes (Manihot Esculenta Crantz) According to Their Physicochemical Traits and Functional Properties Through Bioinformatics Tools". Paper presented in 8th International Conference on Practical Applications of Computational Biology & Bioinformatics (PACBB 2014), 2014.
    10.1007/978-3-319-07581-5_7
  60. Liu, F.; Vilaça, P.; Rocha, I.; Rocha, M.. "Evaluating pathway enumeration algorithms in metabolic engineering case studies". Paper presented in PACBB 2014, 2014.
    10.1007/978-3-319-07581-5_26
  61. Evangelista, P.; Rocha, M.; Rocha, I.. "Evolutionary computation for predicting optimal reaction knockouts and enzyme modulation strategies". Paper presented in CEC 2013, 2013.
    10.1109/CEC.2013.6557705
  62. Maia, P.; Rocha, I.; Rocha, M.. "An integrated framework for strain optimization". Paper presented in CEC 2013, 2013.
    10.1109/CEC.2013.6557571
  63. Carreira, R.; Rocha, M.; Villas-Bôas, S.G.; Rocha, I.. "Algorithms to infer metabolic flux ratios from fluxomics data". Paper presented in BIBM, 2013.
    10.1109/BIBM.2013.6732490
  64. Rocha, M.. "Large scale metabolic characterization using flux balance analysis and data mining". Paper presented in ICANNGA 2013, 2013.
    10.1007/978-3-642-37213-1-35
  65. Noronha, A.; Vilaça, P.; Rocha, M.. "Network Visualization Tools to Enhance Metabolic Engineering Platforms". Paper presented in PACBB 2013, 2013.
    10.1007/978-3-319-00578-2_18
  66. Pereira, V.; Sousa, P.; Cortez, P.; Rio, M.; Rocha, M.. "Robust optimization of intradomain routing using Evolutionary Algorithms". Paper presented in DCAI 2013, 2013.
    10.1007/978-3-319-00551-5_25
  67. Pereira, V.; Rocha, M.; Cortez, P.; Rio, M.; Sousa, P.. "A framework for robust traffic engineering using evolutionary computation". Paper presented in IFIP International Conference on Autonomous Infrastructure, Management and Security, 2013.
    10.1007/978-3-642-38998-6_1
  68. Cortez, P.; Vaz, R.; Rocha, M.; Rio, M.; Sousa, P.. "Evolutionary symbiotic feature selection for email spam detection". Paper presented in ICINCO 2012, 2012.
  69. Correia, S.; Rocha, M.. "Computational tools for strain optimization by adding reactions". Paper presented in PACBB 2012, 2012.
    10.1007/978-3-642-28839-5_28
  70. Gonçalves, E.; Rocha, I.; Rocha, M.. "Computational tools for strain optimization by tuning the optimal level of gene expression". Paper presented in 6th International Conference on Practical Applications of Computational Biology & Bioinformatics, Salamanca, 2012.
    10.1007/978-3-642-28839-5_29
  71. Maraschin, M.; Somensi-Zeggio, A.; Oliveira, S.K.; Kuhnen, S.; Tomazzoli, M.M.; Zeri, A.C.M.; Carreira, R.; Rocha, M.. "A machine learning and chemometrics assisted interpretation of spectroscopic data - A NMR-based metabolomics platform for the assessment of Brazilian propolis". Paper presented in PRIB 2012, 2012.
    10.1007/978-3-642-34123-6_12
  72. Cardoso, J.; Vilaça, P.; Soares, S.; Rocha, M.. "An algorithm to assemble gene-protein-reaction associations for genome-scale metabolic model reconstruction". Paper presented in PRIB 2012, 2012.
    10.1007/978-3-642-34123-6_11
  73. Rocha, M.; Sa, T.; Sousa, P.; Cortez, P.; Rio, M.. "Multiobjective evolutionary algorithms for intradomain routing optimization". Paper presented in CEC 2011, 2011.
    10.1109/CEC.2011.5949897
  74. Sousa, P.; Cortez, P.; Rio, M.; Rocha, M.. "Traffic engineering approaches using multicriteria optimization techniques". Paper presented in WWIC, 2011.
    10.1007/978-3-642-21560-5_9
  75. Pinto, J.P.; Rocha, I.; Rocha, M.. "Highlighting metabolic strategies using network analysis over strain optimization results". Paper presented in ACM BCB 2011, 2011.
    10.1007/978-3-642-24855-9_10
  76. Lourenço, A.; Carneiro, S.; Pinto, J.P.; Rocha, M.; Ferreira, E.C.; Rocha, I.. "Interpreting the regulatory interplay in E. Coli metabolic pathways". Paper presented in PACBB 2011, 2011.
    10.1007/978-3-642-19914-1_40
  77. Evangelista, P.; Pinho, J.; Gonçalves, E.; Maia, P.; Sobral, J.L.; Rocha, M.. "A software platform for evolutionary computation with pluggable parallelism and quality assurance". Paper presented in AIAI 2011, 2011.
    10.1007/978-3-642-23960-1_6
  78. Vilaça, P.; Maia, P.; Rocha, M.. "A study on the robustness of strain optimization algorithms". Paper presented in PACBB 2011, 2011.
    10.1007/978-3-642-19914-1_43
  79. 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". Paper presented in PetriNets2010, 2010.
  80. Sousa, P.; Machado, A.; Rocha, M.; Cortez, P.; Rio, M.. "A collaborative approach for spam detection". Paper presented in INTERNET 2010, 2010.
    10.1109/INTERNET.2010.25
  81. Pinto, J.P.; Rocha, I.; Rocha, M.. "A software tool for network topology analysis under a Metabolic Engineering perspective". Paper presented in ACM BCB 2010, 2010.
    10.1145/1854776.1854884
  82. Dias, O.; Rocha, M.; Ferreira, E.C.; Rocha, I.. "Merlin: Metabolic models reconstruction using genome-scale information". Paper presented in IFAC, 2010.
    10.3182/20100707-3-BE-2012.0076
  83. Pinho, J.; Rocha, M.; Sobral, J.L.. "Pluggable parallelization of evolutionary algorithms applied to the optimization of biological processes". Paper presented in PDP 2010, 2010.
    10.1109/PDP.2010.89
  84. Vilaça, P.; Maia, P.; Rocha, I.; Rocha, M.. "Metaheuristics for strain optimization using transcriptional information enriched metabolic models". Paper presented in EvoBio 2010, 2010.
    10.1007/978-3-642-12211-8-18
  85. Cortez, P.; Correia, A.; Sousa, P.; Rocha, M.; Rio, M.. "Spam email filtering using network-level properties". Paper presented in iCDM 2010, 2010.
    10.1007/978-3-642-14400-4_37
  86. Evangelista, P.; Maia, P.; Rocha, M.. "Implementing metaheuristic optimization algorithms with JECoLi". Paper presented in ISDA 2009, 2009.
    10.1109/ISDA.2009.161
  87. Cortez, P.; Lopes, C.; Sousa, P.; Rocha, M.; Rio, M.. "Symbiotic Data Mining for personalized spam filtering". Paper presented in WI-IAT, 2009.
    10.1109/WI-IAT.2009.30
  88. Rocha, O.; Maia, P.; Rocha, I.; Rocha, M.. "Optferm-a computational platform for the optimization of fermentation processes". Paper presented in ESM 2009, 2009.
  89. Evangelista, P.; Rocha, I.; Ferreira, E.C.; Rocha, M.. "Evolutionary approaches for strain optimization using dynamic models under a metabolic engineering perspective". Paper presented in EvoBio 2009, 2009.
    10.1007/978-3-642-01184-9_13
  90. Evangelista, P.; Rocha, I.; Ferreira, E.C.; Rocha, M.. "A software tool for the simulation and optimization of dynamic metabolic models". Paper presented in Practical Applications of Computational Biology and Bioinformatics (PACBB 2009), 2009.
    10.1007/978-3-642-02481-8_162
  91. Lourenço, A.; Carneiro, S.; Ferreira, E.C.; Carreira, R.; Rocha, L.M.; Glez-Peña, D.; Méndez, J.R.; et al. "Biomedical text mining applied to document retrieval and semantic indexing". Paper presented in PACBB 2009 - Practical Applications of Computational Biology and Bioinformatics, 2009.
    10.1007/978-3-642-02481-8_146
  92. Machado, D.; Costa, R.S.; Rocha, M.; Rocha, I.; Tidor, B.; Ferreira, E.C.. "A critical review on modelling formalisms and simulation tools in computational biosystems". Paper presented in Practical Applications of Computational Biology and Bioinformatics 2009, 2009.
    10.1007/978-3-642-02481-8_161
  93. Vilaça, Paulo; Maia, Paulo; Evangelista, Pedro; Ferreira, Eugénio C.; Rocha, Miguel; Rocha, I.. "A study on the effects of using gene-reaction rules on in silico strain optimization". 2009.
  94. Pinto, J.P.; Dias, O.; Lourenço, A.; Carneiro, S.; Ferreira, E.C.; Rocha, I.; Rocha, M.. "Data integration issues in the reconstruction of the genome-scale metabolic model of Zymomonas mobillis". Paper presented in IWPACBB 2008, 2008.
    10.1007/978-3-540-85861-4_12
  95. Valente, E.; Rocha, I.; Rocha, M.. "Modelling fed-batch fermentation processes: An approach based on artificial neural networks". Paper presented in IWPACBB 2008, 2008.
    10.1007/978-3-540-85861-4_4
  96. 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". Paper presented in BIBE 2008, 2008.
    10.1109/BIBE.2008.4696707
  97. Maia, P.; Rocha, I.; Ferreira, E.C.; Rocha, M.. "Evaluating evolutionary multiobjective algorithms for the in silico optimization of mutant strains". Paper presented in BIBE 2008, 2008.
    10.1109/BIBE.2008.4696733
  98. Mendes, R.; Lourenço, A.; Carneiro, S.; Rocha, M.; Rocha, I.; Ferreira, E.C.. "A framework for the integrated analysis of metabolic and regulatory networks". Paper presented in BIBE 2008, 2008.
    10.1109/BIBE.2008.4696727
  99. Cortez, P.; Rio, M.; Sousa, P.; Rocha, M.. "Forecasting internet traffic by neural networks under univariate and multivariate strategies". Paper presented in ANNIIP’2008, 2008.
  100. Lourenço, A.; Carneiro, S.; Carreira, R.; Rocha, M.; Rocha, I.; Ferreira, E.. "A tool for the automatic and manual annotation of biomedical documents". Paper presented in SMBm 2008, 2008.
  101. Rocha, M.; Sousa, P.; Cortez, P.; Rio, M.. "An evolutionary algorithm for unicast/ multicast traffic engineering". Paper presented in ICINCO 2008, 2008.
  102. Machado, D.; Rocha, M.. "getALife - An Artificial Life environment for the evaluation of agent-based systems and evolutionary algorithms for reinforcement learning". Paper presented in IEA AIE 2008, 2008.
    10.1007/978-3-540-79355-7_4
  103. Méndez, J.R.; Cid, I.; Glez-Peña, D.; Rocha, M.; Fdez-Riverola, F.. "A comparative impact study of attribute selection techniques on naïve bayes spam filters". Paper presented in ICDM 2008, 2008.
    10.1007/978-3-540-70720-2_17
  104. Sousa, P.; Rocha, M.; Cortez, P.; Rio, M.. "Multiconstrained optimization of networks with multicast and unicast traffic". Paper presented in MMNS 2008, 2007.
    10.1007/978-3-540-87359-4-13
  105. Rocha, M.; Mendes, R.; Maia, P.; Glez-P¿a, D.; Fdez-Riverola, F.. "A platform for the selection of genes in DNA microarraydata using evolutionary algorithms". Paper presented in GECCO 2007, 2007.
    10.1145/1276958.1277042
  106. Rocha, M.; Sousa, P.; Cortez, P.; Rio, M.. "Evolutionary computation for quality of service internet routing optimization". Paper presented in EvoWorkshops 2007, 2007.
  107. Rocha, M.; Pinto, J.P.; Rocha, I.; Ferreira, E.. "Optimization of bacterial strains with variable-sized evolutionary algorithms". Paper presented in CIBCB 2007, 2007.
  108. Rocha, M.; Mendes, R.; Maia, P.; Pinto, J.P.; Rocha, I.; Ferreira, E.C.. "Evaluating simulated annealing algorithms in the optimization of bacterial strains". Paper presented in Portuguese Conference Artificial Intelligence, 2007.
    10.1007/978-3-540-77002-2_40
  109. Rocha, M.; Pinto, J.P.; Rocha, I.; Ferreira, E.C.. "Evaluating evolutionary algorithms and differential evolution for the online optimization of fermentation processes". Paper presented in Evo Bio 2007, 2007.
    10.1007/978-3-540-71783-6_23
  110. Cortez, P.; Rio, M.; Sousa, P.; Rocha, M.. "Topology aware internet traffic forecasting using neural networks". Paper presented in ICANN 2007, 2007.
    10.1007/978-3-540-74695-9_46
  111. Sousa, P.; Rocha, M.; Rio, M.; Cortez, P.. "Class-based OSPF traffic engineering inspired on evolutionary computation". Paper presented in WWIC 2007, 2007.
    10.1007/978-3-540-72697-5_12
  112. Rocha, M.; Sousa, P.; Rio, M.; Cortez, P.. "QoS constrained internet routing with evolutionary algorithms". Paper presented in CEC 2006, 2006.
  113. Mendes, R.; Rocha, I.; Ferreira, E.C.; Rocha, M.. "A comparison of algorithms for the optimization of fermentation processes". Paper presented in CEC 2006, 2006.
  114. Cortez, P.; Rio, M.; Rocha, M.; Sousa, P.. "Internet traffic forecasting using neural networks". Paper presented in IJCNN 2006, Vancouver, 2006.
  115. Sousa, P.; Rocha, M.; Rio, M.; Cortez, P.. "Efficient OSPF weight allocation for intra-domain QoS optimization". Paper presented in IPOM 2006, 2006.
    10.1007/11908852_4
  116. Rocha, M.; Rocha, I.; Ferreira, E.. "A new representation in Evolutionary Algorithms for the optimization of bioprocesses". Paper presented in CEC 2005, 2005.
  117. Rocha, M.; Cortez, P.; Neves, J.. "Simultaneous evolution of neural network topologies and weights for classification and regression". Paper presented in IWANN 2005, 2005.
  118. Rocha, Miguel; Cortez, Paulo; Neves, José. "Evolutionary Design of Neural Networks for Classification and Regression". Paper presented in ICANNGA 2005, Coimbra, 2005.
  119. Rocha, M.; Neves, J.; Rocha, I.; Ferreira, E.C.. "Evolutionary algorithms for optimal control in fed-batch fermentation processes". Paper presented in EvoWorkshops 2004, 2004.
  120. Tavares Ribeiro, C.; Ribeiro, C.; Dias, P.; Rocha, M.; Neves, J.. "An interdisciplinary E-learning system for the K-6". Paper presented in CATE 2003, 2003.
  121. Rocha, M.; Cortez, P.; Neves, J.. "Evolutionary neural network learning". Paper presented in EPIA 2003, 2003.
  122. Rocha, Miguel; Cortez, Paulo; Neves, José. "Adaptive Learning in Changing Environments". Paper presented in ESANN 2003, Brugges, 2003.
  123. Mendes, R.; Cortez, P.; Rocha, M.; Neves, J.. "Particle swarms for feedforward neural network training". Paper presented in IJCNN 2002, 2002.
  124. Rocha, M.; Mendes, R.; Cortez, P.; Neves, J.. "Sitting guests at a wedding party: Experiments on genetic and evolutionary constrained optimization". Paper presented in CEC 2001, 2001.
  125. Cortez, P.; Rocha, M.; Neves, J.. "Genetic and evolutionary algorithms for time series forecasting". Paper presented in IEA-AIE 2001, 2001.
  126. Rocha, M.; Pereira, F.; Afonso, S.; Neves, J.. "A genetic and evolutionary programming environment with spatially structured populations and Built-In Parallelism". Paper presented in IEA-AIE 2001, 2001.
    10.1007/3-540-45517-5_43
  127. Rocha, Miguel; Paulo Cortez; José Maia Neves. "Lamarkian Training of Feedforward Neural Networks". Paper presented in ESANN 2001, Brugges, 2001.
    Published
  128. Rocha, M.; Vilela, C.; Cortez, P.; Neves, J.. "Viewing scheduling problems through Genetic and Evolutionary Algorithms". Paper presented in IPDPS 2000, 2000.
    10.1007/3-540-45591-4_83
  129. Rocha, M.; Vilela, C.; Neves, J.. "A study of order based genetic and evolutionary algorithms in combinatorial optimization problems". Paper presented in IEA AIE 2000, 2000.
    10.1007/3-540-45049-1_72
  130. Neves, J.; Cortez, P.; Rocha, M.; Abelha, A.; MacHado, J.; Alves, V.; Basto, S.; Botelho, H.. "A unified framework for data modeling on medical information systems". Paper presented in MIE 1999, 1999.
    10.3233/978-1-60750-912-7-68
  131. Rocha, M.; Neves, J.. "Preventing premature convergence to local optima in genetic algorithms via random offspring generation". Paper presented in IEA AIE 1999, 1999.
    10.1007/978-3-540-48765-4_16
  132. José Maia Neves; Rocha, Miguel; H. Rodrigues; M. Biscaia; Victor Alves. "Adaptive Strategies and the Design of Evolutionary Applications". Paper presented in GECOO 1999, 1999.
  133. Cortez, Paulo; Rocha, Miguel; Machado, Jose; Neves, Jose. "Neural network based time series forecasting system". Paper presented in ICNN 95, 1995.
Conference poster
  1. Pereira, Vítor; Barbosa, Carolina; Cruz, Fernando; Rocha, Miguel. "Harnessing computational strain design with MEWpy and SDDB". Paper presented in RECOMB 2023, 2023.
  2. Moreira, Pedro; Parada, Mariana; Vicente, João; Soares, Cláudio M; Rocha, Miguel; Lousa, Diana. "De novo antibody design targeting SARS-CoV-2 BA.5 RBD". Paper presented in V International Conference NOVA health Chronic Disease and Infection, 2022.
  3. Carvalho, Lucas; Pereira, Vítor; Araujo, Guido; Carrazolle, Marcelo; Pereira, Gonçalo; Rocha, Miguel. "Improving xylose-fermenting yeast for 2G ethanol production via constraint-based modeling combined with omics data analysis". Paper presented in ECCB2022 21st European Conference on Computational Biology, 2022.
  4. Rodrigues, Ruben; Costa, Hugo; Rocha, Miguel. "BioTML: a machine learning framework for biomedical text mining". Paper presented in BioCreative Challenge Workshop, 2015.
Edited book
  1. Mohamad, M.S.; Rocha, M.P.; De Paz, J.F.; Fdez-Riverola, F.; González, P., ed. Practical Applications of Computational Biology and Bioinformatics, 12th International Conference. Springer International Publishing. 2018.
    Published • 10.1007/978-3-319-98702-6 • Editor
  2. Fdez-Riverola, F.; De Paz, J.F.; Mohamad, M.S.; Pinto, T.; Rocha, M., ed. 11th International Conference on Practical Applications of Computational Biology & Bioinformatics - Part of the Advances in Intelligent Systems and Computing book series (AISC, volume 616). Springer International Publishing. 2017.
    10.1007/978-3-319-60816-7
  3. Mohamad, M.S.; Rocha, M.P.; Fdez-Riverola, F.; Mayo, F.J.D.; De Paz, J.F., ed. 10th International Conference on Practical Applications of Computational Biology & Bioinformatics - Part of the Advances in Intelligent Systems and Computing book series (AISC). Springer International Publishing. 2016.
    10.1007/978-3-319-40126-3
  4. Overbeek, R.; Rocha, M.P.; Fdez-Riverola, F.; De Paz, J.F., ed. 9th International Conference on Practical Applications of Computational Biology and Bioinformatics - Part of the Advances in Intelligent Systems and Computing book series (AISC). Springer. 2015.
  5. Mohamad, M.S.; Nanni, L.; Rocha, M.P.; Fdez-Riverola, F.; Sáez-Rodríguez, J.; De Paz Santana, J.F., ed. 7th International Conference on Practical Applications of Computational Biology and Bioinformatics. 2013.
    10.1007/978-3-319-00578-2
  6. Rocha, M.P.; Luscombe, N.; Rodríguez, J.M.C.; Fdez-Riverola, F., ed. Advances in Intelligent and Soft Computing - Proc. of the PACBB 2012. 2012.
  7. Omatu, S.; Rocha, M.P.; Bravo, J.; Fernandez, F.; Corchado, E.; Bustillo, A.; Corchado, J.M., ed. Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics): Preface. 2009.
Journal article
  1. Capela, João; Cheixo, João; de Ridder, Dick; Dias, Oscar; Rocha, Miguel. "Predicting precursors of plant specialized metabolites using DeepMol automated machine learning". Journal of Integrative Bioinformatics 22 2 (2025): https://doi.org/10.1515/jib-2024-0050.
    Published • 10.1515/jib-2024-0050
  2. Oliveira, Eva Regina; Ramlov, Fernanda; Schmidt, Éder Carlos; Tomazi, Débora; Bauer, Claudia Marlene; Pilatti, Fernanda K.; Moresco, Rodolfo; et al. "Cellular and biochemical alterations induced by diesel oil in the brown alga Sargassum cymosum var. stenophyllum cultured in vitro". Chemosphere 372 (2025): 144030. https://doi.org/10.1016/j.chemosphere.2024.144030.
    Published • 10.1016/j.chemosphere.2024.144030
  3. Oliveira, Eva Regina; Ramlov, Fernanda; Schmidt, Éder Carlos; Tomazi, Débora; Bauer, Claudia Marlene; Pilatti, Fernanda K.; Moresco, Rodolfo; et al. "Cellular and biochemical alterations induced by diesel oil in the brown alga Sargassum cymosum var. stenophyllum cultured in vitro". Chemosphere 372 (2025): 144030. https://doi.org/10.1016/j.chemosphere.2024.144030.
    Published • 10.1016/j.chemosphere.2024.144030
  4. Capela, João; Zimmermann-Kogadeeva, Maria; Dijk, Aalt D. J. van; de Ridder, Dick; Dias, Oscar; Rocha, Miguel. "Comparative Assessment of Protein Large Language Models for Enzyme Commission Number Prediction". BMC Bioinformatics 26 68 (2025): https://doi.org/10.1186/s12859-025-06081-9.
    Published • 10.1186/s12859-025-06081-9
  5. Oliveira, Alexandre; Ferreira, Jorge; Vieira, Vítor; Sá, Bruno; Rocha, Miguel. "TROPPO: tissue-specific reconstruction and phenotype prediction using omics data". Bioinformatics Advances 5 1 (2025): https://doi.org/10.1093/bioadv/vbaf113.
    Published • 10.1093/bioadv/vbaf113
  6. Sequeira, A.M.; Rocha, M.; Lousa, Diana. "Machine and deep learning to predict viral fusion peptides". Computational and Structural Biotechnology Journal 27 (2025): 692-704. https://doi.org/10.1016/j.csbj.2025.02.011.
    Open access • Published • 10.1016/j.csbj.2025.02.011
  7. Correia, João; Capela, João; Rocha, Miguel. "Deepmol: an automated machine and deep learning framework for computational chemistry". Journal of Cheminformatics 16 1 (2024): 1-17. https://doi.org/10.1186/s13321-024-00937-7.
    Open access • Published • 10.1186/s13321-024-00937-7
  8. Sequeira, A.M.; Ijsselsteijn, M.E.; Rocha, M.; de Miranda, Noel F.C.C.. "PENGUIN: A rapid and efficient image preprocessing tool for multiplexed spatial proteomics". Computational and Structural Biotechnology Journal 23 (2024): 3920-3928. https://doi.org/10.1016/j.csbj.2024.10.048.
    Published • 10.1016/j.csbj.2024.10.048
  9. Sampaio, Marta; Rocha, Miguel; Dias, Oscar. "A diel multi-tissue genome-scale metabolic model of Vitis vinifera". PLOS Computational Biology 20 10 (2024): e1012506. https://doi.org/10.1371/journal.pcbi.1012506.
    Published • 10.1371/journal.pcbi.1012506
  10. Sequeira, João C.; Pereira, Vítor; Alves, M. Madalena; Pereira, M. Alcina; Rocha, Miguel; Salvador, Andreia F.. "MOSCA 2.0: A bioinformatics framework for metagenomics, metatranscriptomics and metaproteomics data analysis and visualization". Molecular Ecology Resources 24 7 (2024): https://doi.org/10.1111/1755-0998.13996.
    Published • 10.1111/1755-0998.13996
  11. Tânia Barata; Vítor Pereira; Ricardo Pires das Neves; Miguel Rocha. "Reconstruction of cell-specific models capturing the influence of metabolism on DNA methylation in cancer". Computers in Biology and Medicine (2024): https://doi.org/10.1016/j.compbiomed.2024.108052.
    10.1016/j.compbiomed.2024.108052
  12. Cruz, F.; Capela, J.; Ferreira, E.C.; Rocha, M.; Dias, O.. "BioISO: an objective-oriented application for assisting the curation of genome-scale metabolic models". IEEE/ACM Transactions on Computational Biology and Bioinformatics (2024): http://www.scopus.com/inward/record.url?eid=2-s2.0-85181554234&partnerID=MN8TOARS.
    10.1109/TCBB.2023.3339972
  13. Delora Baptista; Shihua Zhang; Pedro G. Ferreira; Miguel Rocha. "A systematic evaluation of deep learning methods for the prediction of drug synergy in cancer". PLOS Computational Biology (2023): https://doi.org/10.1371/journal.pcbi.1010200.
    10.1371/journal.pcbi.1010200
  14. Cunha, Emanuel Rodrigues; Silva, Miguel; Chaves, Inês; Demirci, Huseyin; Lagoa, Davide Rafael Santos; Lima, Diogo; Rocha, Miguel; Rocha, Isabel; Dias, Oscar. "The first multi-tissue genome-scale metabolic model of a woody plant highlights suberin biosynthesis pathways in Quercus suber". (2023): https://hdl.handle.net/1822/86827.
    10.1371/journal.pcbi.1011499
  15. Delora Baptista; João Correia; Bruno Pereira; Miguel Rocha. "Evaluating molecular representations in machine learning models for drug response prediction and interpretability". Journal of Integrative Bioinformatics (2022): https://doi.org/10.1515/jib-2022-0006.
    10.1515/jib-2022-0006
  16. 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
  17. Vítor Vieira; Christoph Kaleta; Jorge Ferreira; Miguel Rocha. "A pipeline for the reconstruction and evaluation of context-specific human metabolic models at a large-scale". PLOS Computational Biology 18 6 (2022): e1009294-e1009294. https://doi.org/10.1371/journal.pcbi.1009294.
    10.1371/journal.pcbi.1009294
  18. Barata, T.; Vieira, V.; Rodrigues, R.; Neves, R.P.D.; Rocha, M.. "Reconstruction of tissue-specific genome-scale metabolic models for human cancer stem cells". Computers in Biology and Medicine 142 (2022): http://www.scopus.com/inward/record.url?eid=2-s2.0-85122541665&partnerID=MN8TOARS.
    10.1016/j.compbiomed.2021.105177
  19. Marta Sampaio; Miguel Rocha; Oscar Dias; Sampaio, Marta; Rocha, Miguel; Dias, Oscar. "Exploring synergies between plant metabolic modelling and machine learning". Computational and Structural Biotechnology Journal (2022): https://hdl.handle.net/1822/77194.
    Accepted • 10.1016/j.csbj.2022.04.016
  20. Tiago Sousa; João Correia; Vítor Pereira; Miguel Rocha. "Generative Deep Learning for Targeted Compound Design". Journal of Chemical Information and Modeling (2021): https://doi.org/10.1021/acs.jcim.0c01496.
    10.1021/acs.jcim.0c01496
  21. Elsa Costa e Silva; Teresa Lino-Neto; Eugénia Ribeiro; Miguel Rocha; Manuel João Costa. "Going virtual and going wide: comparing Team-Based Learning in-class versus online and across disciplines". Education and Information Technologies (2021): https://doi.org/10.1007/s10639-021-10683-0.
    10.1007/s10639-021-10683-0
  22. Cardoso, Sara; Cabral, Débora; Maraschin, Marcelo; Rocha, Miguel. "NMRFinder: a novel method for 1D 1H-NMR metabolite annotation". Metabolomics 17 2 (2021): http://dx.doi.org/10.1007/s11306-021-01772-9.
    10.1007/s11306-021-01772-9
  23. Pereira, Vítor; Cruz, Fernando; Rocha, Miguel. "MEWpy: a computational strain optimization workbench in Python". Bioinformatics (2021): http://dx.doi.org/10.1093/bioinformatics/btab013.
    Accepted • 10.1093/bioinformatics/btab013
  24. Dugourd, Aurelien; Kuppe, Christoph; Sciacovelli, Marco; Gjerga, Enio; Gabor, Attila; Emdal, Kristina B.; Vieira, Vitor; et al. "Causal integration of multi-omics data with prior knowledge to generate mechanistic hypotheses". Molecular Systems Biology 17 1 (2021): http://dx.doi.org/10.15252/msb.20209730.
    10.15252/msb.20209730
  25. Pereira, F.; Lopes, H.; Maia, P.; Meyer, B.; Nocon, J.; Jouhten, P.; Konstantinidis, D.; et al. "Model-guided development of an evolutionarily stable yeast chassis". Molecular Systems Biology 17 7 (2021): http://www.scopus.com/inward/record.url?eid=2-s2.0-85111502988&partnerID=MN8TOARS.
    10.15252/msb.202110253
  26. Sequeira, A.M.; Lousa, D.; Rocha, M.. "ProPythia: A Python package for protein classification based on machine and deep learning". Neurocomputing (2021): http://www.scopus.com/inward/record.url?eid=2-s2.0-85119582124&partnerID=MN8TOARS.
    10.1016/j.neucom.2021.07.102
  27. Pereira, Vítor; Sousa, Pedro; Rocha, Miguel. "A comparison of multi-objective optimization algorithms for weight setting problems in traffic engineering". Natural Computing (2020): http://dx.doi.org/10.1007/s11047-020-09807-1.
    10.1007/s11047-020-09807-1
  28. Cruz, Fernando; Faria, José P.; Rocha, Miguel; Rocha, Isabel; Dias, Oscar. "A review of methods for the reconstruction and analysis of integrated genome-scale models of metabolism and regulation". Biochemical Society Transactions 48 5 (2020): 1889-1903. http://dx.doi.org/10.1042/bst20190840.
    10.1042/bst20190840
  29. Pereira, Vitor; Rocha, Miguel; Sousa, Pedro. "Traffic Engineering With Three-Segments Routing". IEEE Transactions on Network and Service Management 17 3 (2020): 1896-1909. http://dx.doi.org/10.1109/tnsm.2020.2993207.
    10.1109/tnsm.2020.2993207
  30. Gavicho Uarrota, Virgílio. "Metabolomic fingerprinting as a powerful diagnostic tool to assess the effects of abiotic stress in plants and seeds.". CAB Reviews: Perspectives in Agriculture, Veterinary Science, Nutrition and Natural Resources 15 041 (2020): http://dx.doi.org/10.1079/pavsnnr202015041.
    10.1079/pavsnnr202015041
  31. Mason, Mike J.; Schinke, Carolina; Eng, Christine L. P.; Towfic, Fadi; Gruber, Fred; Dervan, Andrew; White, Brian S.; et al. "Multiple Myeloma DREAM Challenge reveals epigenetic regulator PHF19 as marker of aggressive disease". Leukemia (2020): http://dx.doi.org/10.1038/s41375-020-0742-z.
    10.1038/s41375-020-0742-z
  32. Baptista, Delora; Ferreira, Pedro G; Rocha, Miguel. "Deep learning for drug response prediction in cancer". Briefings in Bioinformatics (2020): http://dx.doi.org/10.1093/bib/bbz171.
    10.1093/bib/bbz171
  33. Tomazzoli, Maíra Maciel; Zeggio, Amélia Regina Somensi; Pai Neto, Remi Dal; Specht, Leandro; Costa, Christopher; Rocha, Miguel; Yunes, Rosendo Augusto; Maraschin, Marcelo. "Botanical source investigation and evaluation of the effect of seasonality on Brazilian propolis from Apis mellifera L.". Scientia Agricola 77 6 (2020): http://dx.doi.org/10.1590/1678-992x-2018-0258.
    10.1590/1678-992x-2018-0258
  34. Uarrota, V.G.; Garcia, J.; de Andrade, G.C.; de Fátima Moreira de Bairros, Â.; Nerling, D.; Stefen, D.; Rocha, M.; Maraschin, M.. "Metabolomic fingerprinting as a powerful diagnostic tool to assess the effects of abiotic stress in plants and seeds". CAB Reviews: Perspectives in Agriculture, Veterinary Science, Nutrition and Natural Resources 15 41 (2020): http://www.scopus.com/inward/record.url?eid=2-s2.0-85093091233&partnerID=MN8TOARS.
    10.1079/PAVSNNR202015041
  35. Pereira, V.; Rocha, M.; Sousa, P.. "Traffic Engineering with Three-Segments Routing". IEEE Transactions on Network and Service Management 17 3 (2020): 1896-1909. http://www.scopus.com/inward/record.url?eid=2-s2.0-85085154156&partnerID=MN8TOARS.
    10.1109/TNSM.2020.2993207
  36. Cruz, F.; Faria, J.P.; Rocha, M.; Rocha, I.; Dias, O.. "A review of methods for the reconstruction and analysis of integrated genome-scale models of metabolism and regulation". Biochemical Society Transactions 48 5 (2020): 1889-1903. http://www.scopus.com/inward/record.url?eid=2-s2.0-85094982862&partnerID=MN8TOARS.
    10.1042/BST20190840
  37. Marta Sampaio; Miguel Rocha; Hugo Oliveira; Oscar Dias; Alfonso Valencia. "Predicting promoters in phage genomes using PhagePromoter". Bioinformatics 35 24 (2019): 5301-5302. https://doi.org/10.1093/bioinformatics/btz580.
    10.1093/bioinformatics/btz580
  38. Vítor Vieira; Miguel Rocha; Alfonso Valencia. "CoBAMP: a Python framework for metabolic pathway analysis in constraint-based models". Bioinformatics 35 24 (2019): 5361-5362. https://doi.org/10.1093/bioinformatics/btz598.
    10.1093/bioinformatics/btz598
  39. Cardoso, Sara; Afonso, Telma; Maraschin, Marcelo; Rocha, Miguel. "WebSpecmine: A Website for Metabolomics Data Analysis and Mining". Metabolites 9 10 (2019): 237. http://dx.doi.org/10.3390/metabo9100237.
    Published • 10.3390/metabo9100237
  40. Vieira, Vítor; Maia, Paulo; Rocha, Miguel; Rocha, Isabel. "Comparison of pathway analysis and constraint-based methods for cell factory design". BMC Bioinformatics 20 1 (2019): 350. http://dx.doi.org/10.1186/s12859-019-2934-y.
    Open access • Published • 10.1186/s12859-019-2934-y
  41. Menden, Michael P.; Wang, Dennis; Mason, Mike J.; Szalai, Bence; Bulusu, Krishna C.; Guan, Yuanfang; Yu, Thomas; et al. "Community assessment to advance computational prediction of cancer drug combinations in a pharmacogenomic screen". Nature Communications 10 1 (2019): http://dx.doi.org/10.1038/s41467-019-09799-2.
    10.1038/s41467-019-09799-2
  42. Vítor Vieira; Jorge Ferreira; Rúben Rodrigues; Filipe Liu; Miguel Rocha. "A Model Integration Pipeline for the Improvement of Human Genome-Scale Metabolic Reconstructions". Journal of Integrative Bioinformatics 16 1 (2019): https://doi.org/10.1515/jib-2018-0068.
    10.1515/jib-2018-0068
  43. Martins, Joana; Magalhães, Carlos; Rocha, Miguel; Osório, Nuno S. "Machine Learning-Enhanced T Cell Neoepitope Discovery for Immunotherapy Design". Cancer Informatics 18 (2019): 117693511985208. http://dx.doi.org/10.1177/1176935119852081.
    10.1177/1176935119852081
  44. Cruz, F.; Lagoa, D.; Mendes, J.; Rocha, I.; Ferreira, E.C.; Rocha, M.; Dias, O.. "SamPler - a novel method for selecting parameters for gene functional annotation routines". BMC bioinformatics 20 1 (2019): 454-454. http://www.scopus.com/inward/record.url?eid=2-s2.0-85071772242&partnerID=MN8TOARS.
    10.1186/s12859-019-3038-4
  45. Kim, Osvaldo D.; Rocha, Miguel; Maia, Paulo. "A Review of Dynamic Modeling Approaches and Their Application in Computational Strain Optimization for Metabolic Engineering". Frontiers in Microbiology 9 (2018): http://dx.doi.org/10.3389/fmicb.2018.01690.
    10.3389/fmicb.2018.01690
  46. Phan, T.K.; Rocha, M.; Griffin, D.; Rio, M.. "Utilitarian Placement of Composite Services". IEEE Transactions on Network and Service Management 15 2 (2018): 638-649. http://www.scopus.com/inward/record.url?eid=2-s2.0-85040985975&partnerID=MN8TOARS.
    10.1109/TNSM.2018.2798413
  47. Faria, J.P.; Rocha, M.; Rocha, I.; Henry, C.S.. "Methods for automated genome-scale metabolic model reconstruction". Biochemical Society Transactions 46 4 (2018): 931-936. http://www.scopus.com/inward/record.url?eid=2-s2.0-85052068503&partnerID=MN8TOARS.
    10.1042/BST20170246
  48. Alves, T.; Rodrigues, R.; Costa, H.; Rocha, M.. "Development of an information retrieval tool for biomedical patents". Computer Methods and Programs in Biomedicine 159 (2018): 125-134. http://www.scopus.com/inward/record.url?eid=2-s2.0-85044152716&partnerID=MN8TOARS.
    10.1016/j.cmpb.2018.03.012
  49. Xavier-Magalhães, A.; Gonçalves, C.S.; Fogli, A.; Lourenço, T.; Pojo, M.; Pereira, B.; Rocha, M.; et al. "The long non-coding RNA HOTAIR is transcriptionally activated by HOXA9 and is an independent prognostic marker in patients with malignant glioma". Oncotarget 9 21 (2018): 15740-15756. http://www.scopus.com/inward/record.url?eid=2-s2.0-85044210124&partnerID=MN8TOARS.
    10.18632/oncotarget.24597
  50. Gönen, Mehmet; Weir, Barbara A.; Cowley, Glenn S.; Vazquez, Francisca; Guan, Yuanfang; Jaiswal, Alok; Karasuyama, Masayuki; et al. "A Community Challenge for Inferring Genetic Predictors of Gene Essentialities through Analysis of a Functional Screen of Cancer Cell Lines". Cell Systems 5 5 (2017): 485-497.e3. http://dx.doi.org/10.1016/j.cels.2017.09.004.
    10.1016/j.cels.2017.09.004
  51. Seyednasrollah, Fatemeh; Koestler, Devin C.; Wang, Tao; Piccolo, Stephen R.; Vega, Roberto; Greiner, Russell; Fuchs, Christiane; et al. "A DREAM Challenge to Build Prediction Models for Short-Term Discontinuation of Docetaxel in Metastatic Castration-Resistant Prostate Cancer". JCO Clinical Cancer Informatics 1 (2017): 1-15. http://dx.doi.org/10.1200/cci.17.00018.
    10.1200/cci.17.00018
  52. Vitor Vieira; Paulo Maia; Isabel Rocha; Miguel Rocha. "Development of a Framework for Metabolic Pathway Analysis-Driven Strain Optimization Methods". Interdisciplinary Sciences: Computational Life Sciences (2017): https://doi.org/10.1007%2Fs12539-017-0218-7.
    10.1007/s12539-017-0218-7
  53. David Henriques; Kai Tan; Alejandro F. Villaverde; Miguel Rocha; Julio Saez-Rodriguez; Julio R. Banga. "Data-driven reverse engineering of signaling pathways using ensembles of dynamic models". PLOS Computational Biology 13 2 (2017): e1005379-e1005379. https://doi.org/10.1371%2Fjournal.pcbi.1005379.
    10.1371/journal.pcbi.1005379
  54. Uarrota, Virgílio; Rocha, Miguel; Maraschin, Marcelo. "Non-targeted Metabolomic Profiling of Maize Landraces (Zea mays L.) Combined with Chemometric Tools". International Journal of Biochemistry Research & Review 20 1 (2017): 1-9. http://dx.doi.org/10.9734/ijbcrr/2017/35832.
    10.9734/ijbcrr/2017/35832
  55. Guinney, Justin; Wang, Tao; Laajala, Teemu D; Winner, Kimberly Kanigel; Bare, J Christopher; Neto, Elias Chaibub; Khan, Suleiman A; et al. "Prediction of overall survival for patients with metastatic castration-resistant prostate cancer: development of a prognostic model through a crowdsourced challenge with open clinical trial data". The Lancet Oncology 18 1 (2017): 132-142. http://dx.doi.org/10.1016/s1470-2045(16)30560-5.
    10.1016/s1470-2045(16)30560-5
  56. Pereira, Vítor; Rocha, Miguel; Sousa, Pedro. "Optimizing Segment Routing using Evolutionary Computation". Procedia Computer Science 110 (2017): 312-319. http://dx.doi.org/10.1016/j.procs.2017.06.100.
    10.1016/j.procs.2017.06.100
  57. 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
  58. Afonso, T.; Moresco, R.; Uarrota, V.G.; Navarro, B.B.; Nunes, E.D.C.; Maraschin, M.; Rocha, M.. "UV-Vis and CIELAB Based Chemometric Characterization of Manihot esculenta Carotenoid Contents". Journal of integrative bioinformatics 14 4 (2017): http://www.scopus.com/inward/record.url?eid=2-s2.0-85050293226&partnerID=MN8TOARS.
    10.1515/jib-2017-0056
  59. Cardoso, S.; Maraschin, M.; Peruch, L.A.M.; Rocha, M.; Pereira, A.. "A Chemometrics Approach for Nuclear Magnetic Resonance Data to Characterize the Partial Metabolome Banana Peels from Southern Brazil". Journal of integrative bioinformatics 14 4 (2017): http://www.scopus.com/inward/record.url?eid=2-s2.0-85050292179&partnerID=MN8TOARS.
    10.1515/jib-2017-0053
  60. Pilatti, F.K.; Ramlov, F.; Schmidt, E.C.; Costa, C.; Oliveira, E.R.D.; Bauer, C.M.; Rocha, M.; Bouzon, Z.L.; Maraschin, M.. "Metabolomics of Ulva lactuca Linnaeus (Chlorophyta) exposed to oil fuels: Fourier transform infrared spectroscopy and multivariate analysis as tools for metabolic fingerprint". Marine Pollution Bulletin 114 2 (2017): 831-836. http://www.scopus.com/inward/record.url?eid=2-s2.0-85006766690&partnerID=MN8TOARS.
    10.1016/j.marpolbul.2016.11.006
  61. Ferreira, J.; Correia, S.; Rocha, M.. "Analysing Algorithms and Data Sources for the Tissue-Specific Reconstruction of Liver Healthy and Cancer Cells". Interdisciplinary Sciences: Computational Life Sciences 9 1 (2017): 36-45. http://www.scopus.com/inward/record.url?eid=2-s2.0-85016094355&partnerID=MN8TOARS.
    10.1007/s12539-017-0214-y
  62. Faria, J.P.; Overbeek, R.; Taylor, R.C.; Conrad, N.; Vonstein, V.; Goelzer, A.; Fromion, V.; et al. "Reconstruction of the regulatory network for Bacillus subtilis and reconciliation with gene expression data". Frontiers in Microbiology 7 MAR (2016): http://www.scopus.com/inward/record.url?eid=2-s2.0-84964378390&partnerID=MN8TOARS.
    10.3389/fmicb.2016.00275
  63. Uarrota, V.G.; Moresco, R.; Schmidt, E.C.; Bouzon, Z.L.; Da Costa Nunes, E.; De Oliveira Neubert, E.; Peruch, L.A.M.; Rocha, M.; Maraschin, M.. "The role of ascorbate peroxidase, guaiacol peroxidase, and polysaccharides in cassava (Manihot esculenta Crantz) roots under postharvest physiological deterioration". Food Chemistry 197 (2016): 737-746. http://www.scopus.com/inward/record.url?eid=2-s2.0-84946781015&partnerID=MN8TOARS.
    10.1016/j.foodchem.2015.11.025
  64. Pilatti, F.K.; Ramlov, F.; Schmidt, E.C.; Kreusch, M.; Pereira, D.T.; Costa, C.; de Oliveira, E.R.; et al. "In vitro exposure of Ulva lactuca Linnaeus (Chlorophyta) to gasoline - Biochemical and morphological alterations". Chemosphere 156 (2016): 428-437. http://www.scopus.com/inward/record.url?eid=2-s2.0-84966694914&partnerID=MN8TOARS.
    10.1016/j.chemosphere.2016.04.126
  65. Maia, P.; Rocha, M.; Rochaa, I.. "In silico constraint-based strain optimization methods: The quest for optimal cell factories". Microbiology and Molecular Biology Reviews 80 1 (2016): 45-67. http://www.scopus.com/inward/record.url?eid=2-s2.0-84964043843&partnerID=MN8TOARS.
    10.1128/MMBR.00014-15
  66. Maraschin, M.; Somensi-Zeggio, A.; Oliveira, S.K.; Kuhnen, S.; Tomazzoli, M.M.; Raguzzoni, J.C.; Zeri, A.C.M.; et al. "Metabolic Profiling and Classification of Propolis Samples from Southern Brazil: An NMR-Based Platform Coupled with Machine Learning". Journal of Natural Products 79 1 (2016): 13-23. http://www.scopus.com/inward/record.url?eid=2-s2.0-84956752061&partnerID=MN8TOARS.
    10.1021/acs.jnatprod.5b00315
  67. Uarrota, V.G.; Moresco, R.; Schmidt, E.C.; Bouzon, Z.L.; da Costa Nunes, E.; de Oliveira Neubert, E.; Peruch, L.A.M.; Rocha, M.; Maraschin, M.. "Data supporting the role of enzymes and polysaccharides during cassava postharvest physiological deterioration". Data in Brief 6 (2016): 503-506. http://www.scopus.com/inward/record.url?eid=2-s2.0-84953776443&partnerID=MN8TOARS.
    10.1016/j.dib.2015.12.043
  68. Uarrota, V.G.; Nunes, E.C.; Peruch, L.A.M.; Neubert, E.O.; Coelho, B.; Moresco, R.; Domínguez, M.G.; et al. "Toward better understanding of postharvest deterioration: biochemical changes in stored cassava (Manihot esculenta Crantz) roots:". Food Science and Nutrition 4 3 (2016): 409-422. http://www.scopus.com/inward/record.url?eid=2-s2.0-85008466314&partnerID=MN8TOARS.
    10.1002/fsn3.303
  69. Faria, J.P.; Davis, J.J.; Edirisinghe, J.N.; Taylor, R.C.; Weisenhorn, P.; Olson, R.D.; Stevens, R.L.; et al. "Computing and applying atomic regulons to understand gene expression and regulation". Frontiers in Microbiology 7 NOV (2016): http://www.scopus.com/inward/record.url?eid=2-s2.0-85006835839&partnerID=MN8TOARS.
    10.3389/fmicb.2016.01819
  70. Sousa, P.; Pereira, V.; Cortez, P.; Rio, M.; Rocha, M.. "A framework for improving routing configurations using multi-objective optimization mechanisms". Journal of Communications Software and Systems 12 3 (2016): 145-156. http://www.scopus.com/inward/record.url?eid=2-s2.0-85016010009&partnerID=MN8TOARS.
  71. Gonçalves, Céline S.; Xavier-Magalhães, Ana; Pojo, Marta; Oliveira, Ana Isabel; Correia, Sara; Reis, Rui M.; Sousa, Nuno; Rocha, Miguel; Costa, Bruno M.. "Transcriptional profiling of HOXA9-regulated genes in human glioblastoma cell models". Genomics Data 5 (2015): 54-58. http://dx.doi.org/10.1016/j.gdata.2015.05.010.
    10.1016/j.gdata.2015.05.010
  72. Pojo, M.; Gonçalves, C.S.; Xavier-Magalhães, A.; Oliveira, A.I.; Gonçalves, T.; Correia, S.; Rodrigues, A.J.; et al. "A transcriptomic signature mediated by HOXA9 promotes human glioblastoma initiation, aggressiveness and resistance to temozolomide". Oncotarget 6 10 (2015): 7657-7674. http://www.scopus.com/inward/record.url?eid=2-s2.0-84928404326&partnerID=MN8TOARS.
  73. Liu, F.; Vilaça, P.; Rocha, I.; Rocha, M.. "Development and application of efficient pathway enumeration algorithms for metabolic engineering applications". Computer Methods and Programs in Biomedicine 118 2 (2015): 134-146. http://www.scopus.com/inward/record.url?eid=2-s2.0-84922449472&partnerID=MN8TOARS.
    10.1016/j.cmpb.2014.11.010
  74. Gonçalves, C.S.; Xavier-Magalhães, A.; Pojo, M.; Oliveira, A.I.; Correia, S.; Reis, R.M.; Sousa, N.; Rocha, M.; Costa, B.M.. "Transcriptional profiling of HOXA9-regulated genes in human glioblastoma cell models". Genomics Data 5 (2015): 54-58. http://www.scopus.com/inward/record.url?eid=2-s2.0-84930645263&partnerID=MN8TOARS.
    10.1016/j.gdata.2015.05.010
  75. Dias, O.; Rocha, M.; Ferreira, E.C.; Rocha, I.. "Reconstructing genome-scale metabolic models with merlin". Nucleic Acids Research 43 8 (2015): 3899-3910. http://www.scopus.com/inward/record.url?eid=2-s2.0-84930225331&partnerID=MN8TOARS.
    10.1093/nar/gkv294
  76. Costa, C.; Maraschin, M.; Rocha, M.. "An R package for the integrated analysis of metabolomics and spectral data". Computer Methods and Programs in Biomedicine (2015): http://www.scopus.com/inward/record.url?eid=2-s2.0-84957046559&partnerID=MN8TOARS.
    10.1016/j.cmpb.2016.01.008
  77. Tomazzoli, M.M.; Pai Neto, R.D.; Moresco, R.; Westphal, L.; Zeggio, A.R.; Specht, L.; Costa, C.; Rocha, M.; Maraschin, M.. "Discrimination of Brazilian propolis according to the seasoning using chemometrics and machine learning based on UV-Vis scanning data". Journal of integrative bioinformatics 12 4 (2015): http://www.scopus.com/inward/record.url?eid=2-s2.0-84988498670&partnerID=MN8TOARS.
    10.2390/biecoll-jib-2015-279
  78. Moresco, R.; Uarrota, V.G.; Pereira, A.; Tomazzoli, M.M.; Nunes, Ed.aC.; Peruch, L.A.; Gazzola, J.; et al. "UV-visible scanning spectrophotometry and chemometric analysis as tools for carotenoids analysis in cassava genotypes (Manihot esculenta Crantz)". Journal of integrative bioinformatics 12 4 (2015): http://www.scopus.com/inward/record.url?eid=2-s2.0-84988489790&partnerID=MN8TOARS.
    10.2390/biecoll-jib-2015-280
  79. Valente, E.; Rocha, M.. "Integrating data from heterogeneous DNA microarray platforms". Journal of integrative bioinformatics 12 4 (2015): http://www.scopus.com/inward/record.url?eid=2-s2.0-84988487439&partnerID=MN8TOARS.
    10.2390/biecoll-jib-2015-281
  80. Freitas, A.A.; Costa, H.; Rocha, M.; Rocha, I.. "Extracting kinetic information from literature with KineticRE". Journal of integrative bioinformatics 12 4 (2015): http://www.scopus.com/inward/record.url?eid=2-s2.0-84988493253&partnerID=MN8TOARS.
    10.2390/biecoll-jib-2015-282
  81. 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
  82. Uarrota, V.G.; Moresco, R.; Coelho, B.; Nunes, E.D.C.; Peruch, L.A.M.; Neubert, E.D.O.; Rocha, M.; Maraschin, M.. "Metabolomics combined with chemometric tools (PCA, HCA, PLS-DA and SVM) for screening cassava (Manihot esculenta Crantz) roots during postharvest physiological deterioration". Food Chemistry 161 (2014): 67-78. http://www.scopus.com/inward/record.url?eid=2-s2.0-84899064644&partnerID=MN8TOARS.
    10.1016/j.foodchem.2014.03.110
  83. Noronha, A.; Vilaça, P.; Rocha, M.. "An integrated network visualization framework towards metabolic engineering applications". BMC Bioinformatics 15 1 (2014): http://www.scopus.com/inward/record.url?eid=2-s2.0-84924030935&partnerID=MN8TOARS.
    10.1186/s12859-014-0420-0
  84. Henriques, D.; Rocha, M.; Saez-Rodriguez, J.; Banga, J.R.. "Reverse engineering of logic-based differential equation models using a mixed-integer dynamic optimization approach". Bioinformatics 31 18 (2014): 2999-3007. http://www.scopus.com/inward/record.url?eid=2-s2.0-84941769665&partnerID=MN8TOARS.
    10.1093/bioinformatics/btv314
  85. Guimaraes, J.C.; Rocha, M.; Arkin, A.P.. "Transcript level and sequence determinants of protein abundance and noise in Escherichia coli". Nucleic Acids Research 42 8 (2014): 4791-4799. http://www.scopus.com/inward/record.url?eid=2-s2.0-84899881726&partnerID=MN8TOARS.
    10.1093/nar/gku126
  86. Guimaraes, J.C.; Rocha, M.; Arkin, A.P.; Cambray, G.. "D-Tailor: Automated analysis and design of DNA sequences". Bioinformatics 30 8 (2014): 1087-1094. http://www.scopus.com/inward/record.url?eid=2-s2.0-84898903326&partnerID=MN8TOARS.
    10.1093/bioinformatics/btt742
  87. Carreira, R.; Evangelista, P.; Maia, P.; Vilaça, P.; Pont, M.; Tomb, J.-F.; Rocha, I.; Rocha, M.. "CBFA: Phenotype prediction integrating metabolic models with constraints derived from experimental data". BMC Systems Biology (2014): 1-10. http://www.scopus.com/inward/record.url?eid=2-s2.0-84928666526&partnerID=MN8TOARS.
    10.1186/s12918-014-0123-1
  88. Faria, J.P.; Overbeek, R.; Xia, F.; Rocha, M.; Rocha, I.; Henry, C.S.. "Genome-scale bacterial transcriptional regulatory networks: Reconstruction and integrated analysis with metabolic models". Briefings in Bioinformatics 15 4 (2014): 592-611. http://www.scopus.com/inward/record.url?eid=2-s2.0-85047688512&partnerID=MN8TOARS.
    10.1093/bib/bbs071
  89. Gonçalves, E.; Bucher, J.; Ryll, A.; Niklas, J.; Mauch, K.; Klamt, S.; Rocha, M.; Saez-Rodriguez, J.. "Bridging the layers: Towards integration of signal transduction, regulation and metabolism into mathematical models". Molecular BioSystems 9 7 (2013): 1576-1583. http://www.scopus.com/inward/record.url?eid=2-s2.0-84878687687&partnerID=MN8TOARS.
    10.1039/c3mb25489e
  90. Pinho, J.; Sobral, J.L.; Rocha, M.. "Parallel evolutionary computation in bioinformatics applications". Computer Methods and Programs in Biomedicine 110 2 (2013): 183-191. http://www.scopus.com/inward/record.url?eid=2-s2.0-84875901680&partnerID=MN8TOARS.
    10.1016/j.cmpb.2012.10.001
  91. Pinto, J.P.; Pereira, R.; Cardoso, J.; Rocha, I.; Rocha, M.. "TNA4OptFlux - A software tool for the analysis of strain optimization strategies". BMC Research Notes 6 1 (2013): http://www.scopus.com/inward/record.url?eid=2-s2.0-84876956240&partnerID=MN8TOARS.
    10.1186/1756-0500-6-175
  92. Sousa, P.; Cortez, P.; Vaz, R.; Rocha, M.; Rio, M.. "Email spam detection: A symbiotic feature selection approach fostered by evolutionary computation". International Journal of Information Technology and Decision Making 12 4 (2013): 863-884. http://www.scopus.com/inward/record.url?eid=2-s2.0-84882738506&partnerID=MN8TOARS.
    10.1142/S0219622013500326
  93. Resende, T.; Correia, D.M.; Rocha, M.; Rocha, I.. "Re-annotation of the genome sequence of Helicobacter pylori 26695.". Journal of integrative bioinformatics 10 3 (2013): http://www.scopus.com/inward/record.url?eid=2-s2.0-84902927742&partnerID=MN8TOARS.
  94. Maia, P.; Vilaça, P.; Rocha, I.; Pont, M.; Tomb, J.-F.; Rocha, M.. "An integrated computational environment for elementary modes analysis of biochemical networks". International Journal of Data Mining and Bioinformatics 6 4 (2012): 382-395. http://www.scopus.com/inward/record.url?eid=2-s2.0-84867003199&partnerID=MN8TOARS.
    10.1504/IJDMB.2012.049292
  95. Gonçalves, E.; Pereira, R.; Rocha, I.; Rocha, M.. "Optimization approaches for the in silico discovery of optimal targets for gene over/underexpression". Journal of Computational Biology 19 2 (2012): 102-114. http://www.scopus.com/inward/record.url?eid=2-s2.0-84856738987&partnerID=MN8TOARS.
    10.1089/cmb.2011.0265
  96. Correia, S.; Rocha, M.. "In silico strain optimization by adding reactions to metabolic models.". Journal of integrative bioinformatics 9 3 (2012): http://www.scopus.com/inward/record.url?eid=2-s2.0-84875028288&partnerID=MN8TOARS.
  97. Cortez, Paulo; Rio, Miguel; Rocha, Miguel; Sousa, Pedro. "Multi-scale Internet traffic forecasting using neural networks and time series methods". Expert Systems 29 2 (2012): 143-155.
    10.1111/j.1468-0394.2010.00568.x
  98. Machado, D.; Costa, R.S.; Rocha, M.; Ferreira, E.C.; Tidor, B.; Rocha, I.. "Modeling formalisms in systems biology". AMB Express 1 1 (2011): 1-14. http://www.scopus.com/inward/record.url?eid=2-s2.0-84867843623&partnerID=MN8TOARS.
    10.1186/2191-0855-1-45
  99. Rocha, M.; Sousa, P.; Cortez, P.; Rio, M.. "Quality of Service constrained routing optimization using Evolutionary Computation". Applied Soft Computing Journal 11 1 (2011): 356-364. http://www.scopus.com/inward/record.url?eid=2-s2.0-77957906521&partnerID=MN8TOARS.
    10.1016/j.asoc.2009.11.026
  100. Carreira, R.; Carneiro, S.; Pereira, R.; Rocha, M.; Rocha, I.; Ferreira, E.C.; Lourenço, A.. "Semantic annotation of biological concepts interplaying microbial cellular responses". BMC Bioinformatics 12 (2011): http://www.scopus.com/inward/record.url?eid=2-s2.0-82155187091&partnerID=MN8TOARS.
    10.1186/1471-2105-12-460
  101. Lopes, C.; Cortez, P.; Sousa, P.; Rocha, M.; Rio, M.. "Symbiotic filtering for spam email detection". Expert Systems with Applications 38 8 (2011): 9365-9372. http://www.scopus.com/inward/record.url?eid=2-s2.0-79953711706&partnerID=MN8TOARS.
    10.1016/j.eswa.2011.01.174
  102. Lourenço, 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. http://www.scopus.com/inward/record.url?eid=2-s2.0-79953144460&partnerID=MN8TOARS.
    10.1093/bib/bbq067
  103. Vilaça, P.; ocha, I.; Rocha, M.. "A computational tool for the simulation and optimization of microbial strains accounting integrated metabolic/regulatory information". BioSystems 103 3 (2011): 435-441. http://www.scopus.com/inward/record.url?eid=2-s2.0-79751525708&partnerID=MN8TOARS.
    10.1016/j.biosystems.2010.11.012
  104. Lourenço, A.; Carneiro, S.; Pinto, J.P.; Rocha, M.; Ferreira, E.C.; Rocha, I.. "A study of the short and long-term regulation of E. coli metabolic pathways.". Journal of integrative bioinformatics 8 3 (2011): http://www.scopus.com/inward/record.url?eid=2-s2.0-84855554919&partnerID=MN8TOARS.
  105. Rocha, I.; Maia, P.; Evangelista, P.; Vilaça, P.; Soares, S.; Pinto, J.P.; Nielsen, J.; et al. "OptFlux: An open-source software platform for in silico metabolic engineering". BMC Systems Biology 4 (2010): http://www.scopus.com/inward/record.url?eid=2-s2.0-77950960250&partnerID=MN8TOARS.
    10.1186/1752-0509-4-45
  106. Glez-Peña, D.; Reboiro-Jato, M.; Maia, P.; Rocha, M.; Díaz, F.; Fdez-Riverola, F.. "AIBench: A rapid application development framework for translational research in biomedicine". Computer Methods and Programs in Biomedicine 98 2 (2010): 191-203. http://www.scopus.com/inward/record.url?eid=2-s2.0-77952010788&partnerID=MN8TOARS.
    10.1016/j.cmpb.2009.12.003
  107. Lourenço, A.; Carreira, R.; Glez-Peña, D.; Méndez, J.R.; Carneiro, S.; Rocha, L.M.; Díaz, F.; et al. "BioDR: Semantic indexing networks for biomedical document retrieval". Expert Systems with Applications 37 4 (2010): 3444-3453. http://www.scopus.com/inward/record.url?eid=2-s2.0-71349084312&partnerID=MN8TOARS.
    10.1016/j.eswa.2009.10.044
  108. Maia, Paulo; Pont, Marcellinus; Tomb, Jean-Francois; Rocha, Isabel; Rocha, Miguel; Rocha, MP; Riverola, FF; Shatkay, H; Corchado, JM. "Enhancing Elementary Flux Modes Analysis Using Filtering Techniques in an Integrated Environment". Advances in Bioinformatics 74 (2010): 217-224. http://gateway.webofknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcAuth=ORCID&SrcApp=OrcidOrg&DestLinkType=FullRecord&DestApp=WOS_CPL&KeyUT=WOS:000288875100028&KeyUID=WOS:000288875100028.
    10.1007/978-3-642-13214-8_28
  109. Lourenço, A.; Carreira, R.; Carneiro, S.; Maia, P.; Glez-Peña, D.; Fdez-Riverola, F.; Ferreira, E.C.; Rocha, I.; Rocha, M.. "@Note: A workbench for Biomedical Text Mining". Journal of Biomedical Informatics 42 4 (2009): 710-720. http://www.scopus.com/inward/record.url?eid=2-s2.0-67649367551&partnerID=MN8TOARS.
    10.1016/j.jbi.2009.04.002
  110. Rocha, Orlando; Maia, Paulo; Rocha, Isabel; Rocha, Miguel; AlAkaidi, M. "OPTFERM - A COMPUTATIONAL PLATFORM FOR THE OPTIMIZATION OF FERMENTATION PROCESSES". European Simulation and Modelling Conference 2009 (2009): 5-9. http://gateway.webofknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcAuth=ORCID&SrcApp=OrcidOrg&DestLinkType=FullRecord&DestApp=WOS_CPL&KeyUT=WOS:000280117100001&KeyUID=WOS:000280117100001.
  111. Rocha, M.; Maia, P.; Mendes, R.; Pinto, J.P.; Ferreira, E.C.; Nielsen, J.; Patil, K.R.; Rocha, I.. "Natural computation meta-heuristics for the in silico optimization of microbial strains". BMC Bioinformatics 9 (2008): http://www.scopus.com/inward/record.url?eid=2-s2.0-58149307906&partnerID=MN8TOARS.
    10.1186/1471-2105-9-499
  112. Rocha, M.; Cortez, P.; Neves, J.. "Evolution of neural networks for classification and regression". Neurocomputing 70 16-18 (2007): 2809-2816. http://www.scopus.com/inward/record.url?eid=2-s2.0-34548180859&partnerID=MN8TOARS.
    10.1016/j.neucom.2006.05.023
  113. Sousa, P.; Rocha, M.; Rio, M.; Cortez, P.. "Automatic provisioning of QoS aware OSPF configurations". Journal of Networks 2 2 (2007): 1-10. http://www.scopus.com/inward/record.url?eid=2-s2.0-84866842607&partnerID=MN8TOARS.
  114. Cortez, P.; Rocha, M.; Neves, J.. "Evolving time series forecasting ARMA models". Journal of Heuristics 10 4 (2004): 415-429. http://www.scopus.com/inward/record.url?eid=2-s2.0-3142742672&partnerID=MN8TOARS.
    10.1023/B:HEUR.0000034714.09838.1e
  115. Cortez, P.; Rocha, M.; Neves, J.. "A lamarckian approach for neural network training". Neural Processing Letters 15 2 (2002): 105-116. http://www.scopus.com/inward/record.url?eid=2-s2.0-0036529874&partnerID=MN8TOARS.
    10.1023/A:1015259001150
Journal issue
  1. Florentino Fdez-Riverola; Miguel Rocha. "Selected Extended Papers of the 12th International Conference on Practical Applications of Computational Biology and Bioinformatics (PACBB)". Journal of Integrative Bioinformatics 16 1 (2019): https://doi.org/10.1515/jib-2019-0004.
    10.1515/jib-2019-0004
  2. Rocha, M.; Fdez-Riverola, F.. "Advanced practical applications of computational biology & bioinformatics: PACBB’15". Current Bioinformatics 13 6 (2018): http://www.scopus.com/inward/record.url?eid=2-s2.0-85057221728&partnerID=MN8TOARS.
    10.2174/157489361306181107184700
  3. Fdez-Riverola, F.; Rocha, M.. "Selected Extended Papers of the 11th International Conference on Practical Applications of Computational Biology and Bioinformatics (PACBB)". Journal of integrative bioinformatics 14 4 (2017): http://www.scopus.com/inward/record.url?eid=2-s2.0-85060610159&partnerID=MN8TOARS.
    10.1515/jib-2017-0071
  4. Rocha, M.; Fdez-Riverola, F.. "Selected papers from the annual PACBB conference 2014: Special issue". Current Bioinformatics 11 5 (2016): http://www.scopus.com/inward/record.url?eid=2-s2.0-84995902524&partnerID=MN8TOARS.
Online resource
  1. Joana Martins; Carlos Magalhães; Vítor Vieira; Miguel Rocha; Nuno S. Osório. HABIT – a webserver for interactive T cell neoepitope discovery. 2019. https://doi.org/10.1101/535716.
    10.1101/535716
Preprint
  1. Delora Baptista; Pedro G. Ferreira; Miguel Rocha. "A systematic evaluation of deep learning methods for the prediction of drug synergy in cancer". 2022. https://doi.org/10.1101/2022.05.16.492054.
    10.1101/2022.05.16.492054

Intellectual property

Provisional application for patent
  1. 2019. "Method for n-butanol production using heterologous expression of anaerobic pathways".
    Disclosed

Other

Other output
  1. A pipeline for the reconstruction and evaluation of context-specific human metabolic models at a large-scale. 2021. Vítor Vieira; Jorge Ferreira; Miguel Rocha. https://doi.org/10.1101/2021.07.22.453372.
    10.1101/2021.07.22.453372
  2. 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
  3. IEC7871 Quercus suber model: The first multi-tissue diel cycle genome-scale metabolic model of a woody tree. 2021. Cunha, E.; Silva, M.; Chaves, I.; Demirci, H.; Lagoa, D.R.; Lima, D.; Rocha, M.; Rocha, I.; Dias, O.. http://www.scopus.com/inward/record.url?eid=2-s2.0-85105056577&partnerID=MN8TOARS.
    10.1101/2021.03.09.434537
  4. ViralFP: A webserver of viral fusion proteins. 2021. Moreira, P.; Sequeira, A.M.; Pereira, S.; Rodrigues, R.; Rocha, M.; Lousa, D.. http://www.scopus.com/inward/record.url?eid=2-s2.0-85111200512&partnerID=MN8TOARS.
  5. Reconstruction of consensus tissue-specific metabolic models. 2018. Sara Correia; Bruno Costa; Miguel Rocha. https://doi.org/10.1101/327262.
    10.1101/327262
Activities

Supervision

Thesis Title
Role 		Degree Subject (Type)
Institution / Organization
2020/10 - 2025/11 A deep learning framework towards the multidimensional topography of carcinogenesis to guide prevention and therapy
Supervisor
 Programa Doutoral Informática (PhD)
Universidade do Minho Centro de Engenharia Biológica, Portugal
2020/11 - 2025/09 A Systems Biology approach to model COVID19 phenotypes and drive drug discovery
Co-supervisor
 Engenharia Biomédica (PhD)
Universidade do Minho Centro de Engenharia Biológica, Portugal
2025 - 2025 AI2SM: Artificial Intelligence to expose plant Secondary Metabolism
Co-supervisor
 Informática (PhD)
Universidade do Minho, Portugal
2019/10 - 2024/12 DeepRetro: a computational framework for retrosynthesis and pathway design towards optimizing compound bioproduction
Supervisor
 Doutoramento Informática (PhD)
Universidade do Minho, Portugal
2019/10 - 2024/10 Uncovering the role of conductive nanomaterials in anaerobic digestion
Co-supervisor
 Engenharia Química e Biológica (PhD)
Universidade do Minho, Portugal
2019/10 - 2024/07 M3L: Exploring synergies between metabolic modelling and machine learning for studying plants
Co-supervisor
 Informática
Universidade do Minho, Portugal
2024 - 2024 Artificial intelligence approaches to foster the development of novel antibiotics
Supervisor
 Informática (PhD)
Universidade do Minho, Portugal
2018/10 - 2023/07 Blueprint: Documenting the Complexity of Metabolic Regulation by Reconstruction of Integrated Metabolic-Regulatory Models
Co-supervisor
 Engenharia Biomédica (PhD)
Universidade do Minho, Portugal
2018/10 - 2023/05 Systems-level modelling of the cancer and immune metabolome to improve immunotherapeutic outcomes
Supervisor
 Engenharia Biomédica (PhD)
Universidade do Minho, Portugal
2016/10 - 2023/03 Metabolic modelling of cancer stem cells and interplay between cancer metabolism and epigenetics
Supervisor
Universidade de Coimbra, Portugal
2016/10 - 2023/03 Metabolomics-based approaches for Food authentication and Traceability
Supervisor
 Engenharia Química e Biológica (PhD)
Universidade do Minho, Portugal
2023 - 2023 Desenvolvimento de métodos de aprendizagem profunda para a análise de dados de scRNA
Supervisor
 Bioinformática (Master)
Universidade do Minho, Portugal
2023 - 2023 A computational framework towards the study of metabolic interactions of the gut microbiome and the human host in Type 2 Diabetes
Supervisor
 Engenharia Biomédica (PhD)
Universidade do Minho, Portugal
2023 - 2023 Desenvolvimento de uma aplicação baseada em deep learning para prever sensibilidade de linhas celulares de cancro a fármacos
Supervisor
 Engenharia Informática (Master)
Universidade do Minho, Portugal
2023 - 2023 MitoSignatures: Assinaturas de expressão mitocondrial em cancros em órgãos com elevada taxa metabólica
Co-supervisor
 Bioinformática (Master)
Universidade do Minho, Portugal
2023 - 2023 Desenvolvimento de uma arquitetura automática de aprendizagem de máquina para a classificação de proteínas
Supervisor
 Bioinformática (Master)
Universidade do Minho, Portugal
2021 - 2023 Development of Deep Learning Models for scRNA data analysis
Co-supervisor
 Mestrado em Bioinformática (Master)
Universidade do Minho, Portugal
2016 - 2023 Metabolomics- based approaches for food authentication and traceability
Supervisor
 Doutoramento em Engenharia Química e Biológica (PhD)
Universidade do Minho, Portugal
2021/10 - 2022/12 Development of a deep learning-based computational framework for the classification of protein sequences
Supervisor
 Bioinformática (Master)
Universidade do Minho, Portugal
2020/10 - 2022/12 Predicting the impact of psychoactive compounds on human gut bacteria with metabolic modelling
Supervisor
 Bioinformática (Master)
Universidade do Minho, Portugal
2020/10 - 2022/02 Developing deep learning methods to predict phenotypes and clinical outcomes from transcriptomics data
Supervisor
 Bioinformática (Master)
Universidade do Minho, Portugal
2022 - 2022 Desenvolvimento de classificadores de sequências de ADN baseado em deep learning
Supervisor
 Engenharia Informática (Master)
Universidade do Minho, Portugal
2022 - 2022 Integração de modelos cinéticos de metabolismo e baseados em restrições
Co-supervisor
 Bioinformática (Master)
Universidade do Minho, Portugal
2022 - 2022 Transcriptomica monocelular no plexo coroide: implicações para a esclerose multipla
Co-supervisor
 Bioinformática (Master)
Universidade do Minho, Portugal
2022 - 2022 Desenvolvimento de uma ferramenta bioinformática para a identificação de novas enzimas envolvidas na degradação de plásticos
Co-supervisor
 Bioinformática (Master)
Universidade do Minho, Portugal
2022 - 2022 Regulação transcricional da neurogénese pelo fator proneural Ascl1
Co-supervisor
 Bioinformática (Master)
Universidade do Minho, Portugal
2022 - 2022 Modelos generativos de aprendizagem profunda para o desenho de novas enzimas.
Co-supervisor
 Bioinformática (Master)
Universidade do Minho, Portugal
2022 - 2022 Desenvolvimento de métodos de aprendizagem profunda para prever fenótipos e resultados clínicos através de dados transcriptómicos
Supervisor
 Bioinformática (Master)
Universidade do Minho, Portugal
2022 - 2022 Desenvolvimento de uma plataforma computacional para a classificação de sequências proteicas baseada em deep learning.
Supervisor
 Bioinformática (Master)
Universidade do Minho, Portugal
2022 - 2022 Desenvolvimento de técnicas de processamento de linguagem para análise de sequências proteicas.
Supervisor
 Bioinformática (Master)
Universidade do Minho, Portugal
2022 - 2022 Desenvolvimento de um sistema de recomendação para artigos científicos baseado em deep learning.
Supervisor
 Bioinformática (Master)
Universidade do Minho, Portugal
2022 - 2022 Twitter Observatory: desenvolvimento de ferramentas para análise de sentimentos em mensagens da rede social Twitter
Supervisor
 Engenharia Informática (Master)
Universidade do Minho, Portugal
2022 - 2022 Twitter Observatory: desenvolvimento de ferramentas para recolha e classificação de informação da rede social Twitter
Supervisor
 Engenharia Informática (Master)
Universidade do Minho, Portugal
2021 - 2022 Development of DNA sequence classifiers based on deep learning
Supervisor
 Engenharia Informática (Master)
Universidade do Minho, Portugal
2021 - 2022 Twitter Observatory: developing tools to recover and classify information for the social network Twitter
Supervisor
 Engenharia Informática
Universidade do Minho, Portugal
2021 - 2022 Development of tools for sentiment analysis in the Portuguese Language
Supervisor
 Engenharia Informática (Master)
Universidade do Minho, Portugal
2021 - 2022 Development of a recommendation system for scientific literature based on deep learning
Supervisor
 Bioinformática (Master)
Universidade do Minho, Portugal
2021 - 2022 Mining metagenomics datasets for novel plastic degrading enzymes
Co-supervisor
 Bioinformática
Universidade do Minho, Portugal
2021 - 2022 Integrating Kinetic and Constraint-based Models of Metabolism
Co-supervisor
 Bioinformática (Master)
Universidade do Minho, Portugal
2020 - 2022 Transcriptional regulation of neurogenesis by the proneural factor Ascl1
Co-supervisor
 Bioinformática (Master)
Universidade do Minho, Portugal
2019 - 2022 Development of language modelling techniques for protein sequence analysis
Supervisor
 Bioinformática (Master)
Universidade do Minho, Portugal
2017 - 2022 A framework for predicting drug sensitivity and synergy in cancer cells using deep learning
Supervisor
 Doutoramento em Engenharia Biomédica (PhD)
2017 - 2022 Integrative Pathway Analysis Approaches for Cancer Research and Drug Development,
Supervisor
 Doutoramento em Engenharia Biomédica (PhD)
Universidade do Minho, Portugal
2019/09 - 2021/03 Network Anomaly Detection using Adversarial Deep Learning
Supervisor
 Engenharia Informática (Master)
Universidade do Minho, Portugal
2019/10 - 2021/02 Computational methods for the identification of genetic variants in complex diseases
Supervisor
 Bioinformática (Master)
Universidade do Minho, Portugal
2021 - 2021 Implementing a webserver for managing and detecting viral fusion proteins
Supervisor
 Bioinformática (Master)
Universidade do Minho, Portugal
2021 - 2021 Extracting knowledge from documents related with Candida invasive fungal infections in iron overload context
Co-supervisor
 Bioinformática (Master)
Universidade do Minho, Portugal
2021 - 2021 Network anomaly detection using adversarial deep learning
Supervisor
 Engenharia Informática (Master)
Universidade do Minho, Portugal
2021 - 2021 Computacional methods for the identification of genetic variants in complex diseases
Co-supervisor
 Bioinformática (Master)
Universidade do Minho, Portugal
2020 - 2021 A model validation pipeline for healthy tissue genome-scale metabolic models
Supervisor
 Bioinformática (Master)
Universidade do Minho, Portugal
2020 - 2021 Computational approaches for the integration of in vitro chemical and screening data sets
Supervisor
 Bioinformática (Master)
Universidade do Minho, Portugal
2019 - 2021 Transformers for sentiment analysis on social media
Supervisor
 Engenharia Informática (Master)
Universidade do Minho, Portugal
2017 - 2021 In vitro cultivation of Phaeodactylum tricornutum and Chlorella sp. for the production of fucoxanthin and beta-carotene supported in nanomatrices
Co-supervisor
 Biotecnologia e Biociências (PhD)
2019 - 2020 Development of a Tool based on Deep Learning able to classify Biomedical Literature
Supervisor
 Mestrado em Bioinformática (Master)
Universidade do Minho, Portugal
2019 - 2020 Extracting knowledge from documents related with Candida invasive fungal infections in iron overload context
Supervisor
 Bioinformática (Master)
Universidade do Minho, Portugal
2019 - 2020 Development of deep learning-based tools for the design of new compounds with desired biological activities
Supervisor
 Bioinformática (Master)
Universidade do Minho, Portugal
2018 - 2020 Development of Algorithms for the Analysis and Data Mining of Chemical Compound Prices
Supervisor
 Mestrado em Bioinformática (Master)
Universidade do Minho, Portugal
2016 - 2020 In vitro cultivation of Phaeodactylum tricornutum and Chlorella sp. for the production of fucoxanthin and beta-carotene supported in nanomatrices
Co-supervisor
 Programa Doutoral Biotecnologia e Biociências (PhD)
Universidade Federal de Santa Catarina, Brazil
2018 - 2019 Predict immune responses to neoantigens using Machine Learning
Supervisor of Ana Carolina Silva
 Bioinformática (Master)
Universidade do Minho, Portugal
2018 - 2019 Identification and classification of transporter proteins using deep learning models
Supervisor of Andrea Ferreira Meireles Silva
 Bioinformática (Master)
Universidade do Minho, Portugal
2018 - 2019 Development of a Framework for Identification of Candida Species and Detection of Antifungal Resistance
Co-supervisor of Ana Patricia Mota de Oliveira
 Bioinformática (Master)
Universidade do Minho, Portugal
2018 - 2019 Developing deep learning methods to predict cancer and its outcome from transcriptomics data
Supervisor of Óscar Marques Soares
 Bioinformática (Master)
Universidade do Minho, Portugal
2018 - 2019 Building an automated platform for the classification of peptides/proteins using machine learning
Supervisor of Ana Marta Sequeira
 Bioinformática (Master)
Universidade do Minho, Portugal
2018 - 2019 A web server to predict and annotate fungal secretomes or secreted proteins
Co-supervisor of João Pedro Rodrigues Baptista
 Bioinformática (Master)
Universidade do Minho, Portugal
2018 - 2019 In silico investigation of drugs for the treatment of dengue fever disease
Co-supervisor of Daniel Carpinteiro Soares
 Bioinformática (Master)
Universidade do Minho, Portugal
2018 - 2019 In silico objective-driven optimization of microbial communities
Co-supervisor of José Miguel Dantas de Sousa
 Bioinformática (Master)
Universidade do Minho, Portugal
2017 - 2019 Development of a web-based platform for Biomedical Text Mining
Supervisor of Emanuel Queiroga Amorim Fernandes
 Engenharia Informática (Master)
Universidade do Minho, Portugal
2013 - 2019 Robust internet traffic engineering approaches using evolutionary computation
Co-supervisor of Vítor Manuel Sá Pereira
 Informática (PhD)
Universidade do Minho, Portugal
2017 - 2018 Desenvolvimento de uma base de dados e ferramenta web para caracterização in silico de plasmideos
Co-supervisor of Catarina Freitas de Sousa Santos
 Bioinformática (Master)
Universidade do Minho, Portugal
2017 - 2018 Desenvolvimento de ferramentas para análise de sentimentos em redes sociais
Supervisor of Luis Filipe Ferreira Brito
 Mestrado Integrado em Engenharia Informática (Master)
Universidade do Minho, Portugal
2017 - 2018 Implementation and comparison of variant calling in exome sequencing data with clinical applications
Co-supervisor of Marta Carolina Cabral Moreno
 Bioinformática (Master)
Universidade do Minho, Portugal
2017 - 2018 Developing methods for the context-specific reconstruction of metabolic models of cancer cells
Supervisor of Jorge Alexandre Correia Gomes
 Bioinformática (Master)
Universidade do Minho, Portugal
2017 - 2018 HIV-TB-Host Protein Interaction Network
Supervisor of João Filipe Silva Correia
 Bioinformática (Master)
Universidade do Minho, Portugal
2017 - 2018 Building a database of common genetic variation in the Portuguese population using a WES approach
Co-supervisor of Ana Raquel Salgado Ramos
 Bioinformática (Master)
Universidade do Minho, Portugal
2017 - 2018 Development of a tool for partial automated annotation of metabolic reactions
Co-supervisor of Pedro Miguel Teixeira Queirós
 Bioinformática (Master)
Universidade do Minho, Portugal
2017 - 2018 Development of a Scoring System to Assess Potential Biomarkers for Atrial Fibrillation
Co-supervisor of Beatriz Teixeira de Magalha~es
 Bioinformática (Master)
Universidade do Minho, Portugal
2016 - 2018 A text mining based approach for biomarker discovery
Supervisor of André Miguel Portugal Abrantes Cruzeiro Santiago
 Bioinformática (Master)
Universidade do Minho, Portugal
2016 - 2018 Developing deep learning computational tools for câncer using omics data
Supervisor of Luis da Cunha Peixoto
 Bioinformática (Master)
Universidade do Minho, Portugal
2013 - 2018 Evaluation and development of algorithms and computational tools for metabolic pathway optimization
Supervisor of Filipe Alexandre Wang Liu
 Informática (PhD)
Universidade do Minho, Portugal
2016 - 2017 Desenvolvimento de ferramentas baseadas em web para análise e mineração de dados espectrais
Supervisor of Telma Adriana Pereira Afonso
 Bioinformática (Master)
Universidade do Minho, Portugal
2016 - 2017 Desenvolvimento de ferramentas baseadas em web para análise e mineração de dados de metabolómica
Supervisor of Sara Manso de Sousa Cardoso
 Bioinformática (Master)
Universidade do Minho, Portugal
2016 - 2017 Desenvolvimento de uma pipeline automatizada para análise de dados de meta-ómicas
Co-supervisor of João Carlos Sequeira da Costa
 Bioinformática (Master)
Universidade do Minho, Portugal
2016 - 2017 HABIT (HLA binding intelligence) - um servidor web integrado para gerar e interpretar previsões de ligação de péptido HLA
Co-supervisor of Joana dos Santos Martins
 Bioinformática (Master)
Universidade do Minho, Portugal
2016 - 2017 Identificação e caracterização de variação estrutural no genoma do sobreiro
Co-supervisor of Hugo Carvalho Magalhães
 Bioinformática (Master)
Universidade do Minho, Portugal
2015 - 2017 Development of integrated models of hepatocyte cells / Desenvolvimento de modelos integrados para hepatócitos
Supervisor of Jorge Miguel Lourenço Ferreira
 Bioinformática (Master)
Universidade do Minho, Portugal
2014 - 2017 Bioprospecção, metabolômica e caracterização amilácea e de carotenoides em germoplasma biofortificado de mandioca (Manihot esculenta Crantz) via ferramentas de bioinformática
Co-supervisor of Rodolfo Moresco
 Biotecnologia e Biociências (PhD)
Universidade Federal de Santa Catarina, Brazil
2015 - 2016 Development of a data integration pipeline for human metabolic models and databases
Supervisor of Susana Raquel da Silva Barbosa
 Bioinformática (Master)
Universidade do Minho, Portugal
2015 - 2016 Development of text mining tools for information retrieval and extraction from patents
Supervisor of Tiago Alexandre Pinto Alves
 Bioinformática (Master)
Universidade do Minho, Portugal
2015 - 2016 Machine learning approaches for predicting effects of drug combinations in cancer treatment
Supervisor of Delora Soeiro Baptista
 Bioinformática (Master)
Universidade do Minho, Portugal
2015 - 2016 Analise de padrões em dados genómicos multi-plataforma disponiveis pelo TCGA
Co-supervisor of João António Moreira da Silva
 Bioinformática (Master)
Universidade do Minho, Portugal
2015 - 2016 A critical evaluation of automatic atom mapping algorithms and tools
Supervisor of Nuno Manuel Carneiro Osório
 Bioinformática (Master)
Universidade do Minho, Portugal
2015 - 2016 Exploração de paralelismo massivo em algoritmos evolucionários
Co-supervisor of Tiago Augusto Simões Martins
 Engenharia Informática (Master)
Universidade do Minho, Portugal
2012 - 2016 A framework for the reconstruction and analysis of tissue specific genome-scale metabolic models
Supervisor of Sara Alexandra Gomes Correia
 Informática (PhD)
Universidade do Minho, Portugal
2012 - 2016 Network Inference of Logic-Based Ordinary Differential Equations Models
Supervisor of David Saque Henriques
 Informática (PhD)
Universidade do Minho, Portugal
2014 - 2015 Development of a machine learning framework for Biomedical Text Mining
Supervisor of Rúben Rodrigues
 Bioinformática (Master)
Universidade do Minho, Portugal
2014 - 2015 Analysis of transcriptomics data for inference of the function of the ATXN3 gene in neuronal cells
Supervisor of Manuel José Ferreira
 Bioinformática (Master)
Universidade do Minho, Portugal
2010 - 2015 Modeling microbes: New methods for integrated metabolic and regulatory network reconstruction
Co-supervisor of José Pedro Lopes Faria
 Bioengenharia (PhD)
Universidade do Minho, Portugal
2009 - 2015 Algorithms and computational tools for metabolic flux analysis
Supervisor of Rafael de Castro Carreira
 Engenharia Biomédica (PhD)
Universidade do Minho, Portugal
2009 - 2015 Algorithms and Tools for in silico Design of Cell Factories
Co-supervisor of Paulo Jorge Maia Silva
 Bioengenharia (PhD)
Universidade do Minho, Portugal
2009 - 2015 Development of computational tools for the integrated analysis of DNA microarray data with applications in cancer research
Supervisor of Eduardo Sabina dos Santos Valente
 Informática (PhD)
Universidade do Minho, Portugal
2009 - 2015 Novel approaches for dynamic modeling of E. coli and their application in Metabolic Engineering
Co-supervisor of Pedro Tiago Evangelista
 Bioengenharia (PhD)
Universidade do Minho, Portugal
2013 - 2014 Development of an integrated platform for the in silico phenotype simulation of microbial strains
Supervisor of Hugo Miguel Melo Giesteira
 Bioinformática (Master)
Universidade do Minho, Portugal
2013 - 2014 Computational tools for pathway optimization towards metabolic engineering applications
Supervisor
 Engenharia Informática (Master)
Universidade do Minho, Portugal
2013 - 2014 Development of an integrated computational platform for metabolomics data analysis and knowledge extraction
Supervisor of Christopher Costa
 Bioinformática (Master)
Universidade do Minho, Portugal
2013 - 2014 Extraction of kinetic information from literature
Supervisor of Ana Alão Freitas
 Bioinformática (Master)
Universidade do Minho, Portugal
2012 - 2013 Taxonomic and functional analysis of metagenomes
Co-supervisor of Pedro Santos Barbosa
 Bioinformática (Master)
Universidade do Minho, Portugal
2012 - 2013 Development of a computational platform for the visualization of metabolic models
Supervisor of Alberto Miguel Silva de Noronha
 Bioinformática (Master)
Universidade do Minho, Portugal
2012 - 2013 Desenvolvimento de um sistema integrado para o tratamento de dados de sequenciação de próxima geração
Supervisor of Marco André Ferreira Reis
 Bioinformática (Master)
Universidade do Minho, Portugal
2012 - 2013 Computational tools for pathway optimization towards metabolic engineering applications
Supervisor of Filipe Alexandre Wang Liu
 Engenharia Informática (Master)
Universidade do Minho, Portugal
2012 - 2013 Enhancing Machine Learning Methods for the Prediction of Cancer Cell Sensitivity to Drugs
Supervisor of Vi´tor Daniel Costa
 Bioinformática (Master)
Universidade do Minho, Portugal
2011 - 2012 Engenharia de Tráfego Robusta Usando Computação Evolucionária
Co-supervisor of Vítor Manuel Pereira
 Engenharia de Redes e Serviços de Comunicações (Master)
Universidade do Minho, Portugal
2011 - 2012 Development of an integrated computational workflow for the reconstruction of genome-scale models
Supervisor of João Cardoso
 Bioinformática (Master)
Universidade do Minho, Portugal
2011 - 2012 Estudo de um modelo de automatização de análises de diversidade genética em populações humanas
Co-supervisor of Sara Fonseca
 Bioinformática (Master)
Universidade do Minho, Portugal
2011 - 2012 Integration of Logic Modelling and Network Visualization Tools
Supervisor of Emanuel Gonçalves
 Bioinformática (Master)
Universidade do Minho, Portugal
2008 - 2012 Design principles for controlling gene expression
Co-supervisor of João Carlos Azevedo Salgado Guimarães
 Informática (PhD)
Universidade do Minho, Portugal
2008 - 2012 Computational Tools for large-scale biological network analysis
Supervisor of José Pedro Basto Gouveia Pereira Pinto
 Informática (PhD)
Universidade do Minho, Portugal
2010 - 2011 Calibration of Logic Based Ordinary Differential Equation Models
Supervisor of David Saque Henriques
 Bioinformática (Master)
Universidade do Minho, Portugal
2010 - 2011 Desenvolvimento de ferramentas computacionais para optimização de estirpes por adição de reações ao modelo metabólico
Supervisor of Sara Correia
 Bioinformática (Master)
Universidade do Minho, Portugal
2009 - 2010 Studying the effect of regulatory and thermodynamic constraints on genome-scale model predictions
Supervisor of José Pedro Faria
 Bioinformática (Master)
Universidade do Minho, Portugal
2008 - 2009 Desenvolvimento de ferramentas computacionais para a simulação e análise de redes de regulação genética com base em modelos booleanos
Supervisor of Paulo Vilaça
 Bioinformática (Master)
Universidade do Minho, Portugal
2008 - 2009 Implementação de um ambiente integrado baseado em componentes para a análise de dados de expressão genética
Supervisor of Danilo Santos
 Bioinformática (Master)
Universidade do Minho, Portugal
2008 - 2009 Desenvolvimento de algoritmos evolucionários para ambientes Grid com aplicações à optimização de sistemas biológicos
Supervisor of Jorge Pinho
 Bioinformática (Master)
Universidade do Minho, Portugal
2008 - 2009 Multi-objective Evolutionary Algorithms for in the silico Optimization of Mutant Strains
Supervisor of Paulo Jorge Maia Silva
 Bioinformática (Master)
Universidade do Minho, Portugal
2008 - 2009 Computational Tools for the Simulation and Optimization of Biological Processes with Dynamical Models
Supervisor of Pedro Tiago Evangelista
 Bioinformática (Master)
Universidade do Minho, Portugal
2007 - 2009 Desenvolvimento de ferramentas computacionais para a optimização de processos de fermentação em Biotecnologia
Supervisor of Orlando Rocha
 Engenharia Informática (Master)
Universidade do Minho, Portugal
2007 - 2009 Um Estudo sobre a Emergência de Linguagens para a Comunicação de Agentes em Ambientes de Vida Artificial
Supervisor of Carlos Manuel Silva
 Informática (Master)
Universidade do Minho, Portugal
2007 - 2008 Computational Tools for the Reconstruction of Genome-scale Metabolic Models
Supervisor of Óscar Manuel Dias
 Informática (Master)
Universidade do Minho, Portugal
2006 - 2007 Ferramentas computacionais para a Modelação e controlo de processos biotecnológicos
Supervisor of Eduardo Valente
 Informática (Master)
Universidade do Minho, Portugal
2006 - 2007 Utilização de técnicas de Bioinformática para a Optimização de um processo de Biotecnologia Industrial
Supervisor
 Engenharia Biológica (Master)
Universidade do Minho, Portugal