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Francisco Rodrigues Pinto is an Assistant Professor of Biochemistry at the Faculty of Sciences, University of Lisbon and a researcher at the RNA Systems Biology group within the Biosystems and Integrated Sciences Institute (BioISI). His research interests focus on networks of biological molecules that regulate cellular processes. To understand the structure and function of these networks, in health and disease states, he uses and develops mathematical and computational methods.
Identification

Personal identification

Full name
Francisco Rodrigues Pinto

Citation names

  • Pinto, Francisco
  • Francisco R. Pinto

Author identifiers

Ciência ID
C911-208F-9F71
ORCID iD
0000-0002-4217-0054
Google Scholar ID
HnLOaZcAAAAJ
Researcher Id
A-7443-2008
Scopus Author Id
8060679500

Knowledge fields

  • Exact Sciences - Computer and Information Sciences - Bioinformatics
  • Exact Sciences - Mathematics - Applied Mathematics
  • Natural sciences - Biological Sciences

Languages

Language Speaking Reading Writing Listening Peer-review
English Advanced (C1) Advanced (C1) Advanced (C1) Advanced (C1) Advanced (C1)
Education
Degree Classification
2002/01/01 - 2005/12/05
Concluded
 Bioquímica (Doutoramento)
Major in Bioquímica
Universidade Nova de Lisboa Instituto de Tecnologia Química e Biológica, Portugal
"Gene regulatory networks: tools for an enhanced understanding" (THESIS/DISSERTATION)
1996/09/15 - 2001/06/21
Concluded
 Bioquímica (Licenciatura)
Universidade de Lisboa Faculdade de Ciências, Portugal
 18
Affiliation

Science

Category
Host institution 		Employer
2015/01/01 - Current Researcher (Research) Universidade de Lisboa Instituto de Biossistemas e Ciências Integrativas, Portugal
2017/08/21 - 2017/09/22 Visiting Researcher (Research) Memorial Sloan Kettering Cancer Center, United States
2008/03/01 - 2008/09/30 Contracted Researcher (Research) Instituto de Medicina Molecular, Portugal
2006/01/01 - 2008/02/29 Postdoc (Research) Instituto de Medicina Molecular, Portugal
2001/07/01 - 2005/12/31 Research Trainee (Research) Universidade Nova de Lisboa Instituto de Tecnologia Química e Biológica, Portugal
2002/02/01 - 2004/12/20 Research Trainee (Research) Medical University of South Carolina Biostatistics & Bioinformatics Research, United States
2000/11/01 - 2001/06/30 Research Trainee (Research) REQUIMTE, Portugal
2000/07/25 - 2000/10/28 Research Trainee (Research) Mayo Clinic Department of Immunology, United States

Teaching in Higher Education

Category
Host institution 		Employer
2008/10/01 - Current Assistant Professor (University Teacher) Universidade de Lisboa, Portugal
2007/03/01 - 2008/09/30 Invited Assistant Professor (University Teacher) Universidade Nova de Lisboa Faculdade de Ciências e Tecnologia, Portugal
Projects

Grant

Designation Funders
2023 - 2024 Exploring the cellular pathways to promote rescue of mutant CFTR protein in cystic fibrosis
FFC#2/2023
Researcher
Universidade de Lisboa Instituto de Biossistemas e Ciências Integrativas, Portugal
 Fondazione per La Ricerca sulla Fibrosi Cistica
Ongoing

Contract

Designation Funders
2022/01/01 - 2024/12/31 Exploring respiratory proteins from human bacterial pathogens
PTDC/BIA-BQM/2599/2021
Co-Principal Investigator (Co-PI)
Universidade de Lisboa Instituto de Biossistemas e Ciências Integrativas, Portugal
 Fundação para a Ciência e a Tecnologia
Ongoing
2018/10 - 2021/09 Fire4CAST: Fitting Immunocytometry and RNA-technologies for Epidemiological Modeling of Fire Blight
PTDC/ASP-PLA/28305/2017
Researcher
Fundação para a Ciência e a Tecnologia
Ongoing
2018/10 - 2021/09 Novel signaling pathways regulating cell-surface retention of epithelial chloride transport proteins
PTDC/BIA-CEL/28408/2017
Researcher
Fundação para a Ciência e a Tecnologia
2017 - 2020 LUNGCARD - Blood test for clinical therapy guidance of non-small cell lung cancer patients
734790
Researcher
European Commission
2019/01/01 - 2019/12/31 Instituto de Biosistemas & Ciências Integrativas
UID/Multi/04046/2019
Instituto Nacional de Saúde Doutor Ricardo Jorge, Portugal

Universidade do Minho, Portugal

Universidade do Porto Faculdade de Ciências, Portugal

Fundação da Faculdade de Ciências da Universidade de Lisboa, Portugal

FCiênciasID Associação para a Investigação e Desenvolvimento de Ciências, Portugal

Universidade de Lisboa Faculdade de Ciências, Portugal

Universidade de Lisboa Instituto de Biossistemas e Ciências Integrativas, Portugal
Fundação para a Ciência e a Tecnologia
Concluded
2015 - 2018 Fly-SMALS - Common RNA-dependent pathways for motor-neuron degeneration in spinocerebellar muscular atrophy and amyotrophic lateral sclerosis
JPND-CD/0002/2013
Researcher
Fundação para a Ciência e a Tecnologia
2017/01 - 2017/12 Protein complexes stabilizing CFTR at the plasma membrane: functional validation and construction of an integrated interaction network
BioISI/6202 P0 2.B
Principal investigator
Universidade de Lisboa Instituto de Biossistemas e Ciências Integrativas, Portugal
 Universidade de Lisboa Instituto de Biossistemas e Ciências Integrativas
Concluded
2011/01 - 2014/06 In silico reconstruction of Streptococcus pneumoniae cellular networks and their impact on virulence
Provided by PTCRIS: 113824
113824
Principal investigator
Fundação para a Ciência e a Tecnologia
2010/01 - 2013/06 Metabolic circuits in inflicted bacterial cell death
101375
Provided by PTCRIS: 101375
Co-Principal Investigator (Co-PI)
Fundação para a Ciência e a Tecnologia
2011/01/01 - 2012/12/31 Strategic Project - UI 612 - 2011-2012
PEst-OE/QUI/UI0612/2011
Fundação da Faculdade de Ciências da Universidade de Lisboa, Portugal
 Fundação para a Ciência e a Tecnologia
Concluded
2009/02 - 2012/12 Implications for therapy and disease presentation of the changes triggered by the use of the pneumococcal 7-valent conjugate vaccine
Provided by PTCRIS: 83065
83065
Researcher
Fundação para a Ciência e a Tecnologia
2008/10 - 2012/05 Population and genomic consequences of vaccination against Streptococcus pneumoniae
64888
Provided by PTCRIS: 64888
Researcher
Fundação para a Ciência e a Tecnologia
2008/10 - 2011/09 A computational biology approach using Streptococcus pneumoniae as a model towards an integrative view of bacteria/host interactions and evolution
71499
Provided by PTCRIS: 71499
Researcher
Fundação para a Ciência e a Tecnologia
2006/01 - 2009/12 Population based identification of pneumococcal virulence and colonization factors
GENREQ-195
Principal investigator
National Institute of Allergy and Infectious Diseases
2004 - 2007 PREVIS: Pneumococcal Resistance Epidemicity and Virulence - An International Study. Molecular Mechanisms of resistance, virulence and epidemicity in Streptococcus pneumoniae
LSHM-CT-2003-503413
Researcher
European Commission
2001/01 - 2003/12 Dynamic Invariance in Biological Systems
POCTI/BSE/34794/2000
Researcher
Fundação para a Ciência e a Tecnologia
Outputs

Publications

Book chapter
  1. Pinto, Francisco. "The System of Cystic Fibrosis". 2019.
    10.1016/b978-0-12-801238-3.11511-9
  2. Fernandes, R.; Nogueira, G.; da Costa, P.J.; Pinto, F.; Romão, L.. "Nonsense-Mediated mRNA Decay in Development, Stress and Cancer". 41-83. 2019.
    10.1007/978-3-030-19966-1_3
Conference abstract
  1. CARROLO, Margarida; Guilherme Vilhais; Miranda, João A. I.; Francisco R. Pinto; António Quintela. "Cavitating pulmonary metastases associated with improved survival in pancreatic ductal adenocarcinoma cancer patients". Paper presented in 20º Congresso Nacional de Oncologia, Estoril, 2023.
    Published
  2. Filipa V.M.A. Pereira; Miranda, João A. I.; Alexandre F.R. Coelho; Fiviano L. Santos; Paulo R.C. Lopes; CARROLO, Margarida; Francisco R. Pinto. Corresponding author: Francisco R. Pinto. "Exploring cancer tissue specificities through protein physical interaction networks". Paper presented in 8th International Iberian Biophysics Congress, Bilbao, 2022.
    Published
Conference paper
  1. Francisco R. Pinto. "Cross Disease Network Analysis". 2019.
    10.1109/enbeng.2019.8692469
  2. Grego, T.; Pinto, F.; Couto, F.M.. "LASIGE: using Conditional Random Fields and ChEBI ontology". 2013.
Conference poster
  1. Miranda, João A. I.; Francisco R. Pinto. "Understanding Metastasis Organotropism Patterns Through Within-cell and Between-cells Molecular Interaction Networks". Paper presented in 13th EMBO Young Scientists’ Forum, 2023.
  2. CARROLO, Margarida; MIRANDA, João André Isidoro; Coelho, Alexandre; Quintela, António; Pinto, Francisco. "Metastasis organotropism: unveiling associated proteins using network biology". Paper presented in ESMO Congress 2023, 2023.
  3. Peralta, Pedro; Murtinheira, Fernanda; Vukosava Milic Torres; Francisco R. Pinto; Mario S Rodrigues; Herrera, Federico. "SPAX8-related mutations disrupt the subcellular distribution of NKX6-2 transcription factor.". Paper presented in Jornadas Científicas da ULisboa 2023, 2023.
  4. Matos, Ana Margarida; Pinto, Francisco; Barros, Patrícia; Amaral, Margarida; Pepperkok, Rainer; Matos, Paulo. "Plasma membrane-specific interactome analysis reveals calpain 1 as a druggable modulator of rescued Phe508del-CFTR cell surface stability". Paper presented in SINAL 2019 ¿ 10th Meeting on Signal Transduction, 2019.
    10.1109/elektro.2016.7512136
  5. Camelo, Carolina; Peneda, Catarina; Coyaud, Étienne; Raught, Brian; Câmara, Ana I.; Carmona, Bruno; Pinto, Francisco; Narinho, H. Susana; Soares, Helena. "Unraveling the role of TBCCD1 protein on cell size control: the regulation of cytoskeleton dynamics and cell junctions". 2016.
  6. Friães, Ana; Silva-Costa, C.; Pinto, Francisco; Ramirez, Mário; Melo-Cristino, Jose. "Identification of clones with enhanced invasive capacity among Group A Streptococci isolated in Portugal". Paper presented in XVIII Lancefield International Symposium, 2011.
  7. Silva-Costa, C.; Friães, Ana; Pinto, Francisco; Vaz Filipa; Fernandes Paulo; Carriço, Joao A.; Melo-Cristino, José; Ramirez, Mário. "Re-evaluating the appropriateness of using emm typing to define group A streptococci clones". Paper presented in 8th International Meeting on Microbial Epidemiological Markers (IMMEM 8), 2008.
  8. Silva-Costa, C.; Pinto, Francisco; Ramirez, Mário; Melo-Cristino, José. "Decrease in macrolide resistance and clonal instability among Streptococcus pyogenes in spite of increased macrolide consumption". Paper presented in 18th European Congress of Clinical Microbiology and Infectious Diseases (ECCMID), 2008.
Journal article
  1. Sena, Filipa V.; Sousa, Filipe M.; Pereira, Ana R.; Catarino, Teresa; Cabrita, Eurico J.; Pinho, Mariana G.; Pinto, Francisco R.; Pereira, Manuela M.. "The two alternative NADH:quinone oxidoreductases from Staphylococcus aureus: two players with different molecular and cellular roles". Microbiology Spectrum 12 8 (2024): http://dx.doi.org/10.1128/spectrum.04152-23.
    Published • 10.1128/spectrum.04152-23
  2. McGuire, Daniel; Pinto, Francisco; Costa, Telma; Cruz, Joana; Sousa, Rui; de Sousa, Miguel Leão; Martins, Carmo; et al. "Fire4CAST – a new integrative epidemiological forecasting model for the accurate prediction of infection risk and effective control of fire blight in Pyrus orchards". Journal of Plant Pathology (2024): http://dx.doi.org/10.1007/s42161-024-01622-2.
    10.1007/s42161-024-01622-2
  3. K.R. Saranya; E.R. Vimina; F.R. Pinto. "TransNeT-CGP: A cluster-based comorbid gene prioritization by integrating transcriptomics and network-topological features". Computational Biology and Chemistry (2024): https://doi.org/10.1016/j.compbiolchem.2024.108038.
    10.1016/j.compbiolchem.2024.108038
  4. Carrolo, Margarida; Miranda, João A. I.; Vilhais, Guilherme; Quintela, António; Sousa, Mário Fontes e; Costa, Diogo Alpuim; Pinto, Francisco R.. "Metastatic organotropism: a brief overview". Frontiers in Oncology 14 (2024): http://dx.doi.org/10.3389/fonc.2024.1358786.
    10.3389/fonc.2024.1358786
  5. Guillem Santamaria; Francisco R. Pinto. "Bioinformatic Analysis of Metabolomic Data: From Raw Spectra to Biological Insight". BioChem (2024): https://doi.org/10.3390/biochem4020005.
    10.3390/biochem4020005
  6. McGuire, Daniel; Costa, Telma; Tenreiro, Ana; Cruz, Joana; Sousa, Rui; de Sousa, Miguel Leão; Martins, Carmo; et al. "Use of immuno-flow cytometry and real-time PCR disclose the epidemiological behaviour of Erwinia amylovora populations during the winter in Portuguese pear orchards". Journal of Plant Pathology (2024): http://dx.doi.org/10.1007/s42161-023-01561-4.
    Published • 10.1007/s42161-023-01561-4
  7. Diallo, Mickael; Pimenta, Constança; Murtinheira, Fernanda; Martins-Alves, Daniela; Pinto, Francisco R.; da Costa, André Abrantes; Letra-Vilela, Ricardo; et al. "Asymmetric post-translational modifications regulate the nuclear translocation of STAT3 homodimers in response to leukemia inhibitory factor". Cellular Oncology 47 3 (2023): 1065-1070. http://dx.doi.org/10.1007/s13402-023-00911-9.
    10.1007/s13402-023-00911-9
  8. Marina L. Garcia-Vaquero; Marjorie Heim; Barbara Flix; Marcelo Pereira; Lucile Palin; Tânia M. Marques; Francisco R. Pinto; et al. "Analysis of asymptomatic Drosophila models for ALS and SMA reveals convergent impact on functional protein complexes linked to neuro-muscular degeneration". BMC Genomics 24 1 (2023): http://dx.doi.org/10.1186/s12864-023-09562-4.
    10.1186/s12864-023-09562-4
  9. Guillem Santamaria; Chen Liao; Chloe Lindberg; Yanyan Chen; Zhe Wang; Kyu Rhee; Francisco Rodrigues Pinto; Jinyuan Yan; Joao B Xavier. "Evolution and regulation of microbial secondary metabolism". eLife (2022): https://doi.org/10.7554/eLife.76119.
    10.7554/eLife.76119
  10. Guillem Santamaria; Paula Ruiz-Rodriguez; Chantal Renau-Mínguez; Francisco R. Pinto; Mireia Coscollá. "In Silico Exploration of Mycobacterium tuberculosis Metabolic Networks Shows Host-Associated Convergent Fluxomic Phenotypes". Biomolecules 12 3 (2022): 376-376. https://doi.org/10.3390/biom12030376.
    10.3390/biom12030376
  11. Marina L. García-Vaquero; Margarida Gama-Carvalho; Francisco R. Pinto; Javier De Las Rivas. "Biological interacting units identified in human protein networks reveal tissue-functional diversification and its impact on disease". Computational and Structural Biotechnology Journal 20 (2022): 3764-3778. http://dx.doi.org/10.1016/j.csbj.2022.07.006.
    10.1016/j.csbj.2022.07.006
  12. Daniel V. Olivença; Eberhard O. Voit; Francisco R. Pinto. "ENaC regulation by phospholipids and DGK explained through mathematical modeling". Scientific Reports (2020): https://doi.org/10.1038/s41598-020-70630-w.
    10.1038/s41598-020-70630-w
  13. Santos, João D.; Pinto, Francisco R.; Ferreira, João F.; Amaral, Margarida D.; Zaccolo, Manuela; Farinha, Carlos M.. "Cytoskeleton regulators CAPZA2 and INF2 associate with CFTR to control its plasma membrane levels under EPAC1 activation". Biochemical Journal 477 13 (2020): 2561-2580. http://dx.doi.org/10.1042/bcj20200287.
    Published • 10.1042/bcj20200287
  14. Cláudia Almeida Loureiro; Francisco R. Pinto; Patrícia Barros; Paulo Matos; Peter Jordan. "A SYK/SHC1 pathway regulates the amount of CFTR in the plasma membrane". Cellular and Molecular Life Sciences (2020): https://doi.org/10.1007/s00018-020-03448-4.
    10.1007/s00018-020-03448-4
  15. Ana M. Matos; Francisco R. Pinto; Patrícia Barros; Margarida D. Amaral; Rainer Pepperkok; Paulo Matos; Matos, Ana M.; et al. "Inhibition of calpain 1 restores plasma membrane stability to pharmacologically rescued Phe508del-CFTR variant". Journal of Biological Chemistry (2019): jbc.RA119.008738-jbc.RA119.008738. https://doi.org/10.1074/jbc.RA119.008738.
    10.1074/jbc.RA119.008738
  16. Daniel V. Olivença; Luis L. Fonseca; Eberhard O. Voit; Francisco R. Pinto. "Thickness of the airway surface liquid layer in the lung is affected in cystic fibrosis by compromised synergistic regulation of the ENaC ion channel". Journal of The Royal Society Interface (2019): https://doi.org/10.1098/rsif.2019.0187.
    10.1098/rsif.2019.0187
  17. Dias, Oscar; Saraiva, João; Faria, Cristiana; Ramirez, Mario; Pinto, Francisco; Rocha, Isabel. "iDS372, a Phenotypically Reconciled Model for the Metabolism of Streptococcus pneumoniae Strain R6". Frontiers in Microbiology 10 (2019): http://dx.doi.org/10.3389/fmicb.2019.01283.
    10.3389/fmicb.2019.01283
  18. Loureiro, Cláudia Almeida; Santos, João D.; Matos, Ana Margarida; Jordan, Peter; Matos, Paulo; Farinha, Carlos M.; Pinto, Francisco R.. "Network Biology Identifies Novel Regulators of CFTR Trafficking and Membrane Stability". Frontiers in Pharmacology 10 (2019): http://dx.doi.org/10.3389/fphar.2019.00619.
    10.3389/fphar.2019.00619
  19. Marina L. Garcia-Vaquero; Margarida Gama-Carvalho; Javier De Las Rivas; Francisco R. Pinto. "Searching the overlap between network modules with specific betweeness (S2B) and its application to cross-disease analysis". Scientific Reports (2018): https://doi.org/10.1038/s41598-018-29990-7.
    10.1038/s41598-018-29990-7
  20. Daniel V. Olivença; Inna Uliyakina; Luis L. Fonseca; Margarida D. Amaral; Eberhard O. Voit; Francisco R. Pinto. "A Mathematical Model of the Phosphoinositide Pathway". Scientific Reports (2018): https://doi.org/10.1038/s41598-018-22226-8.
    10.1038/s41598-018-22226-8
  21. Sara F. Fernandes; Rita Fior; Francisco Pinto; Margarida Gama-Carvalho; Leonor Saúde. "Fine-tuning of fgf8a expression through alternative polyadenylation has a selective impact on Fgf-associated developmental processes". Biochimica et Biophysica Acta (BBA) - Gene Regulatory Mechanisms 1861 9 (2018): 783-793. https://doi.org/10.1016/j.bbagrm.2018.07.012.
    10.1016/j.bbagrm.2018.07.012
  22. Carolina Camelo; Filipe Vilas-Boas; Andreia Pereira Cepeda; Carla Real; Joana Barros-Martins; Francisco Pinto; Helena Soares; H. Susana Marinho; Luisa Cyrne. "Opi1p translocation to the nucleus is regulated by hydrogen peroxide in Saccharomyces cerevisiae". Yeast (2017): https://doi.org/10.1002%2Fyea.3240.
    10.1002/yea.3240
  23. Gama-Carvalho, M.; Garcia-Vaquero, M. L.; Pinto, F. R.; Besse, F.; Weis, J.; Voigt, A.; Schulz, J. B.; De Las Rivas, J.. "Linking Amyotrophic Lateral Sclerosis and Spinal Muscular Atrophy through RNA-transcriptome homeostasis: a genomics perspective". J Neurochem (2017): https://www.ncbi.nlm.nih.gov/pubmed/28054357.
    10.1111/jnc.13945
  24. Valente, C.; Dawid, S.; Pinto, F. R.; Hinds, J.; Simões, A. S.; Gould, K. A.; Mendes, L. A.; de Lencastre, H.; Sá-Leão, R.. "The blp Locus of Streptococcus pneumoniae Plays a Limited Role in the Selection of Strains That Can Cocolonize the Human Nasopharynx". Appl Environ Microbiol 82 17 (2016): 5206-15.
    10.1128/AEM.01048-16
  25. Valente, C.; Hinds, J.; Gould, K. A.; Pinto, F. R.; de Lencastre, H.; Sa-Leao, R.. "Impact of the 13-valent pneumococcal conjugate vaccine on Streptococcus pneumoniae multiple serotype carriage". Vaccine 34 34 (2016): 4072-4078. http://gateway.webofknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcAuth=ORCID&SrcApp=OrcidOrg&DestLinkType=FullRecord&DestApp=WOS_CPL&KeyUT=WOS:000380604000025&KeyUID=WOS:000380604000025.
    10.1016/j.vaccine.2016.06.017
  26. Carrolo, Margarida; Pinto, Francisco Rodrigues; Melo-Cristino, Jose; Ramirez, Mario. "Pherotype Influences Biofilm Growth and Recombination in Streptococcus pneumoniae". Plos One 9 3 (2014): http://gateway.webofknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcAuth=ORCID&SrcApp=OrcidOrg&DestLinkType=FullRecord&DestApp=WOS_CPL&KeyUT=WOS:000333348500089&KeyUID=WOS:000333348500089.
    10.1371/journal.pone.0092138
  27. Cardoso, Liliana Sofia; Suissas, Claudia Elvas; Ramirez, Mario; Antunes, Marilia; Pinto, Francisco Rodrigues. "Comparison of alternative mixture model methods to analyze bacterial CGH experiments with multi-genome arrays". BMC research notes 7 (2014): 148-148. http://gateway.webofknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcAuth=ORCID&SrcApp=OrcidOrg&DestLinkType=FullRecord&DestApp=MEDLINE&KeyUT=MEDLINE:24629208&KeyUID=MEDLINE:24629208.
    10.1186/1756-0500-7-148
  28. Costa, A.; Afonso, J.; Osório, C.; Gomes, A.L.; Caiado, F.; Valente, J.; Aguiar, S.I.; et al. "MiR-363-5p regulates endothelial cell properties and their communication with hematopoietic precursor cells". Journal of Hematology and Oncology 6 1 (2013): http://www.scopus.com/inward/record.url?eid=2-s2.0-84887928259&partnerID=MN8TOARS.
    10.1186/1756-8722-6-87
  29. Friães, A.; Pinto, F.R.; Silva-Costa, C.; Ramirez, M.; Melo-Cristino, J.. "Superantigen gene complement of Streptococcus pyogenes - Relationship with other typing methods and short-term stability". European Journal of Clinical Microbiology and Infectious Diseases 32 1 (2013): 115-125. http://www.scopus.com/inward/record.url?eid=2-s2.0-84872539465&partnerID=MN8TOARS.
    10.1007/s10096-012-1726-3
  30. Friães, A.; Pinto, F.R.; Silva-Costa, C.; Ramirez, M.; Melo-Cristino, J.. "Group A streptococci clones associated with invasive infections and pharyngitis in Portugal present differences in emm types, superantigen gene content and antimicrobial resistance". BMC Microbiology 12 (2012): http://www.scopus.com/inward/record.url?eid=2-s2.0-84872274958&partnerID=MN8TOARS.
    10.1186/1471-2180-12-280
  31. Gomes, Ricardo A.; Franco, Catarina; Da Costa, Goncalo; Planchon, Sebastien; Renaut, Jenny; Ribeiro, Raquel M.; Pinto, Francisco; et al. "The Proteome Response to Amyloid Protein Expression In Vivo". Plos One 7 11 (2012): http://gateway.webofknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcAuth=ORCID&SrcApp=OrcidOrg&DestLinkType=FullRecord&DestApp=WOS_CPL&KeyUT=WOS:000311821000186&KeyUID=WOS:000311821000186.
    10.1371/journal.pone.0050123
  32. Tendeiro, R.; Foxall, R.B.; Baptista, A.P.; Pinto, F.; Soares, R.S.; Cavaleiro, R.; Valadas, E.; et al. "PD-1 and its ligand PD-L1 are progressively up-regulated on CD4 and CD8 T-cells in HIV-2 infection irrespective of the presence of viremia". AIDS 26 9 (2012): 1065-1071. http://www.scopus.com/inward/record.url?eid=2-s2.0-84861528314&partnerID=MN8TOARS.
    10.1097/QAD.0b013e32835374db
  33. Valente, C.; Hinds, J.; Pinto, F.; Brugger, S.D.; Gould, K.; Mühlemann, K.; de Lencastre, H.; Sá-Leão, R.. "Decrease in pneumococcal co-colonization following vaccination with the seven-valent pneumococcal conjugate vaccine". PLoS ONE 7 1 (2012): http://www.scopus.com/inward/record.url?eid=2-s2.0-84855809538&partnerID=MN8TOARS.
    10.1371/journal.pone.0030235
  34. Severiano, A.; Pinto, F.R.; Ramirez, M.; Carriço, J.A.. "Adjusted Wallace coefficient as a measure of congruence between typing methods". Journal of Clinical Microbiology 49 11 (2011): 3997-4000. http://www.scopus.com/inward/record.url?eid=2-s2.0-80355145041&partnerID=MN8TOARS.
    10.1128/JCM.00624-11
  35. Severiano, A.; Carriço, J.A.; Robinson, D.A.; Ramirez, M.; Pinto, F.R.. "Evaluation of Jackknife and Bootstrap for defining confidence intervals for pairwise agreement measures". PLoS ONE 6 5 (2011): http://www.scopus.com/inward/record.url?eid=2-s2.0-79956190902&partnerID=MN8TOARS.
    10.1371/journal.pone.0019539
  36. Sá-Leao, R.; Pinto, F.; Aguiar, S.; Nunes, S.; Carriço, J.A.; Frazao, N.; Gonçalves-Sousa, N.; et al. "Analysis of invasiveness of pneumococcal serotypes and clones circulating in portugal before widespread use of conjugate vaccines reveals heterogeneous behavior of clones expressing the same serotype". Journal of Clinical Microbiology 49 4 (2011): 1369-1375. http://www.scopus.com/inward/record.url?eid=2-s2.0-79953881891&partnerID=MN8TOARS.
    10.1128/JCM.01763-10
  37. Carrolo, M.; Frias, M.J.; Pinto, F.R.; Melo-Cristino, J.; Ramirez, M.; Carrolo, Margarida; Frias, Maria João; et al. "Prophage spontaneous activation promotes DNA release enhancing biofilm formation in Streptococcus pneumoniae". PLoS ONE 5 12 (2010): http://www.scopus.com/inward/record.url?eid=2-s2.0-78650883397&partnerID=MN8TOARS.
    10.1371/journal.pone.0015678
  38. Aguiar, S.I.; Pinto, F.R.; Nunes, S.; Serrano, I.; Melo-Cristino, J.; Sá-Leão, R.; Ramirez, M.; De Lencastre, H.. "Denmark14-230 clone as an increasing cause of pneumococcal infection in Portugal within a background of diverse serotype 19A lineages". Journal of Clinical Microbiology 48 1 (2010): 101-108. http://www.scopus.com/inward/record.url?eid=2-s2.0-73949151881&partnerID=MN8TOARS.
    10.1128/JCM.00665-09
  39. Carrolo, M.; Pinto, F.R.; Melo-Cristino, J.; Ramirez, M.. "Pherotypes are driving genetic differentiation within Streptococcus pneumoniae". BMC Microbiology 9 (2009): http://www.scopus.com/inward/record.url?eid=2-s2.0-70349656631&partnerID=MN8TOARS.
    10.1186/1471-2180-9-191
  40. Aguiar, S.I.; Serrano, I.; Pinto, F.R.; Melo-Cristino, J.; Ramirez, M.. "Changes in Streptococcus pneumoniae serotypes causing invasive disease with non-universal vaccination coverage of the seven-valent conjugate vaccine". Clinical Microbiology and Infection 14 9 (2008): 835-843. http://www.scopus.com/inward/record.url?eid=2-s2.0-50149095416&partnerID=MN8TOARS.
    10.1111/j.1469-0691.2008.02031.x
  41. Pinto, F.R.; Aguiar, S.I.; Melo-Cristino, J.; Ramirez, M.. "Optimal control and analysis of two-color genomotyping experiments using bacterial multistrain arrays". BMC Genomics 9 (2008): http://www.scopus.com/inward/record.url?eid=2-s2.0-44649164484&partnerID=MN8TOARS.
    10.1186/1471-2164-9-230
  42. Aguiar, S.I.; Serrano, I.; Pinto, F.R.; Melo-Cristino, J.; Ramirez, M.. "The presence of the pilus locus is a clonal property among pneumococcal invasive isolates". BMC Microbiology 8 (2008): http://www.scopus.com/inward/record.url?eid=2-s2.0-41149167131&partnerID=MN8TOARS.
    10.1186/1471-2180-8-41
  43. Silva-Costa, C.; Pinto, F.R.; Ramirez, M.; Melo-Cristino, J.. "Decrease in macrolide resistance and clonal instability among Streptococcus pyogenes in Portugal". Clinical Microbiology and Infection 14 12 (2008): 1152-1159. http://www.scopus.com/inward/record.url?eid=2-s2.0-57749088762&partnerID=MN8TOARS.
    10.1111/j.1469-0691.2008.02104.x
  44. Pinto, F.R.; Melo-Cristino, J.; Ramirez, M.. "A confidence interval for the wallace coefficient of concordance and its application to microbial typing methods". PLoS ONE 3 11 (2008): http://www.scopus.com/inward/record.url?eid=2-s2.0-58149200162&partnerID=MN8TOARS.
    10.1371/journal.pone.0003696
  45. Pinto, F.R.; Carriço, J.A.; Ramirez, M.; Almeida, J.S.. "Ranked adjusted rand: Integrating distance and partition information in a measure of clustering agreement". BMC Bioinformatics 8 (2007): http://www.scopus.com/inward/record.url?eid=2-s2.0-33847331585&partnerID=MN8TOARS.
    10.1186/1471-2105-8-44
  46. Carriço, J.A.; Silva-Costa, C.; Melo-Cristino, J.; Pinto, F.R.; De Lencastre, H.; Almeida, J.S.; Ramirez, M.. "Illustration of a common framework for relating multiple typing methods by application to macrolide-resistant Streptococcus pyogenes". Journal of Clinical Microbiology 44 7 (2006): 2524-2532. http://www.scopus.com/inward/record.url?eid=2-s2.0-33746255226&partnerID=MN8TOARS.
    10.1128/JCM.02536-05
  47. Pina, C.; Pinto, F.; Feijó, J.A.; Becker, J.D.. "Gene family analysis of the Arabidopsis pollen transcriptome reveals biological implications for cell growth, division control, and gene expression regulation". Plant Physiology 138 2 (2005): 744-756. http://www.scopus.com/inward/record.url?eid=2-s2.0-26944493068&partnerID=MN8TOARS.
    10.1104/pp.104.057935
  48. Carriço, J.A.; Pinto, F.R.; Simas, C.; Nunes, S.; Sousa, N.G.; Frazão, N.; De Lencastre, H.; Almeida, J.S.. "Assessment of band-based similarity coefficients for automatic type and subtype classification of microbial isolates analyzed by pulsed-field gel electrophoresis". Journal of Clinical Microbiology 43 11 (2005): 5483-5490. http://www.scopus.com/inward/record.url?eid=2-s2.0-27744601905&partnerID=MN8TOARS.
    10.1128/JCM.43.11.5483-5490.2005
  49. Pinto, F.R.; Cowart, L.A.; Hannun, Y.A.; Rohrer, B.; Almeida, J.S.. "Local correlation of expression profiles with gene annotations - Proof of concept for a general conciliatory method". Bioinformatics 21 7 (2005): 1037-1045. http://www.scopus.com/inward/record.url?eid=2-s2.0-16344377693&partnerID=MN8TOARS.
    10.1093/bioinformatics/bti074
  50. Rohrer, B.; Pinto, F.R.; Hulse, K.E.; Lohr, H.R.; Zhang, L.; Almeida, J.S.. "Multidestructive Pathways triggered in photoreceptor cell death of the RD mouse as determined through gene expression profiling". Journal of Biological Chemistry 279 40 (2004): 41903-41910. http://www.scopus.com/inward/record.url?eid=2-s2.0-4744338189&partnerID=MN8TOARS.
    10.1074/jbc.M405085200
  51. Cowart, L.A.; Okamoto, Y.; Pinto, F.R.; Gandy, J.L.; Almeida, J.S.; Hannun, Y.A.. "Roles for sphingolipid biosynthesis in mediation of specific programs of the heat stress response determined through gene expression profiling". Journal of Biological Chemistry 278 32 (2003): 30328-30338. http://www.scopus.com/inward/record.url?eid=2-s2.0-0043031395&partnerID=MN8TOARS.
    10.1074/jbc.M300656200
Preprint
  1. Guillem Santamaria; Francisco R Pinto. "A Guide for the Bioinformatic Analysis of Metabolomics Data". 2024. https://doi.org/10.20944/preprints202402.0461.v1.
    10.20944/preprints202402.0461.v1
  2. Fernanda Murtinheira; Ana Sofia Boasinha; Joao Belo; Luana Macedo; Elisa Farsetti; Tiago T. Robalo; Vukosava M. Torres; et al. "Subcellular, biochemical and biophysical alterations in two glial cell models of ARSACS". 2024. https://doi.org/10.1101/2024.04.15.589510.
    10.1101/2024.04.15.589510
  3. Carmona, Bruno; Camelo, Carolina; Mehraz, Manon; Lemullois, Michel; Faria, Mariana Lince; Coyaud, Étienne; Marinho, H. Susana; et al. "The maintenance of centriole appendages and motile cilia basal body anchoring relies on TBCCD1". 2023. http://dx.doi.org/10.1101/2023.07.26.549647.
    10.1101/2023.07.26.549647
  4. Marina Garcia-Vaquero; Marjorie Heim; Barbara Flix; Marcelo Pereira; Lucile Palin; Tânia M. Marques; Francisco R. Pinto; et al. "Analysis of pre-symptomatic Drosophila models for ALS and SMA reveals convergent impact on functional protein complexes linked to neuro-muscular degeneration". 2022. https://doi.org/10.1101/2022.06.20.496821.
    10.1101/2022.06.20.496821
Activities

Oral presentation

Presentation title Event name
Host (Event location)
2022 Exploring cancer tissue specificities through protein physical interaction networks 8th International Iberian Biophysics Congress
(Bilbao, Spain)
2019 Network biology approaches in the identification of novel pharmacological targets – the case of cystic fibrosis Encontro Ciência ’19
(Lisboa, Portugal)
2019 Predicting protein annotations using the expected network interaction between related diseases or cellular processes MABioS Seminar, Institut de Mathématiques de Marseille, Université d'Aix-Marseille
(Marseille, France)
2019 Cross Disease Network Analysis 6th Portuguese Meeting on Bioengineering (ENBENG), IEEE, February 22-23, Lisboa, Portugal
(Lisboa, Portugal)
2018 S2B (Double Specific Betweenness): a novel cross-disease network analysis method applied to motor neuron degeneration EMBO Workshop: Integrating Systems Biology: From Networks to Mechanisms to Models, April 15-17, EMBL, Heidelberg, Germany
(Heidelberg, Germany)
2017 Specific Betweeness: finding molecular bridges between diseases III Semana da Bioengenharia, Intituto Superior Técnico, Lisboa, Portugal
(Lisboa, Portugal)
2016 Specific (x2) Betweeness: finding molecular bridges between diseases Oeiras Advanced Studies Seminar, Instituto Gulbenkian de Ciência, Oeiras, Portugal
(Oeiras, Portugal)
2013 Search for coherent gene modules that predict Streptococcus pneumoniae strain invasiveness Frontiers in Systems and Synthetic Biology ’13 (FSSB’13), March 20-24, Atlanta, Georgia, USA
(Atlanta, United States)
2012 Search for cellular network components that predict invasiveness of Streptococcus pneumoniae strains III Jornadas de Bioquímica da Universidade do Minho, 26 e 27 de Março, Braga, Portugal
(Braga, Portugal)
2011 Asymmetry of age group sizes contributes to high child carriage and leads to the underestimation of pneumococcal transmission dynamics in adults 10th European Meeting on the Molecular Biology of the Pneumococcus, June 23-26, Amsterdão, Holanda.
(Amsterdam, Netherlands)
2009 Estimating Simultaneous and Differential Responses to Random Perturbations in Gene Regulatory Networks JB2009 - Jornadas de Bioinformatica 2009, Novembro 3-6, Lisboa, Portugal
(Lisboa, Portugal)
2008 Bacterial multistrain genomotyping arrays: optimal choice of control in two-color experiments. 18th European Congress of Clinical Microbiology and Infectious Diseases, April 18-22, Barcelona, Spain.
(Barcelona, Spain)
2006 A probabilistic approach to study yeast’s gene regulatory network Advanced Workshop on Regulatory Networks 2006 AWRN06, Instituto Gulbenkian de Ciência, Oeiras, Portugal
(Oeiras, Portugal)
2005 How to weight multiple transcription factors of the same gene BKDB2005 - Bioinformatics: Knowledge Discovery in Biology, June 17, Lisboa, Portugal
(Lisboa, Portugal)
2004 Microarray data analysis: what can we do with all these numbers? International Postgraduate Programme in Life and Health Sciences 2004, Universidade do Minho, Escola de Ciências da Saúde, May 24th-27th, Braga, Portugal
(Braga, Portugal)
2003 A correlação entre o transcriptoma e os circuitos regulatórios de S. cereviseae Workshop de Bioinformática, V Jornadas de Biologia Aplicada, Universidade do Minho, Campus de Gualtar, 10-12 de Novembro, Braga, Portugal.
(Braga, Portugal)

Supervision

Thesis Title
Role 		Degree Subject (Type)
Institution / Organization
2023 - Current Identification of tissue specific dependencies between cancer driver gene mutations and their interactors abundances
Supervisor
 Bioinformática e Biologia Computacional (Master)
Universidade de Lisboa Faculdade de Ciências, Portugal
2022 - Current Knowledge-infusion adapters and multi-layer networks to predict cancer driver genes
Co-supervisor
 Ciências da Computação (PhD)
Universidade de Lisboa Faculdade de Ciências, Portugal
2022 - Current Towards understanding and restoring the function of the NKX6-2 transcriptional regulator in normal and pathological conditions
Co-supervisor
 Bioquímica (PhD)
Universidade de Lisboa Faculdade de Ciências, Portugal
2022 - Current E(xtraterrestris). Coli: Adapting genome-scale metabolic models to non-standard thermodynamical constraints
Co-supervisor
 Bioinformática e Biologia Computacional (Master)
Universidade de Lisboa Faculdade de Ciências, Portugal
2017 - Current Integrative network approach for identification of new proteins involved in NMD
Supervisor
 Biologia (PhD)
Universidade de Lisboa Faculdade de Ciências, Portugal
2021 - 2023 Understanding Metastasis Organotropism Patterns Through Within-cell and Between-cells Molecular Interaction Networks
Supervisor
 Bioquimica e Biomedicina (Master)
Universidade de Lisboa Faculdade de Ciências, Portugal
2018 - 2023 Metabolomics and genomics of microbial infections and gut microbiome dynamics in patients undergoing allogeneic hematopoietic stem cell transplantation
Supervisor
 Biologia (PhD)
Universidade de Lisboa Faculdade de Ciências, Portugal
2021 - 2022 Development of a machine learning-based pipeline able to predict genes associated with diseases and cell processes using interpretable network embeddings
Supervisor
 Bioinformática e Biologia Computacional (Master)
Universidade de Lisboa Faculdade de Ciências, Portugal
2020 - 2021 Discovery of tissue specific network properties associated with cancer driver genes
Supervisor
 Bioquímica (Master)
Universidade de Lisboa Faculdade de Ciências, Portugal
2019 - 2020 Extensive validation of network methods to predict the overlap between disease modules
Supervisor
 Bioinformática e Biologia Computacional (Master)
Universidade de Lisboa Faculdade de Ciências, Portugal
2018 - 2019 Combination of Topological Indices in Network Analysis: a Computational Approach
Co-supervisor
 Bioinformática e Biologia Computacional (Master)
Universidade de Lisboa Faculdade de Ciências, Portugal
2017 - 2019 Epidemiologia da insuficiência renal crónica e anemia associada em adultos
Co-supervisor of Sandrine Marques Gordino
 Bioquímica (Master)
Universidade de Lisboa Faculdade de Ciências, Portugal
2017 - 2018 Development of a computacional approach to predict the activity of new, lead-like, Kv modulators for chronic pain therapy
Co-supervisor
 Bioquímica (Master)
Universidade de Lisboa Faculdade de Ciências, Portugal
2017 - 2018 Cross disease network analysis
Supervisor
 Engenharia Biomédica e Biofísica (Master)
Universidade de Lisboa Faculdade de Ciências, Portugal
2015 - 2018 A mathematical model of the phosphoinositide pathway in human pulmonary epithelial cells
Supervisor
 Biologia (PhD)
Universidade de Lisboa Faculdade de Ciências, Portugal
2015 - 2016 Exploring the interactions between neuron degeneration and RNA homeostasis through biological network analysis
Supervisor
 Bioquímica (Master)
Universidade de Lisboa Faculdade de Ciências, Portugal
2014 - 2015 Evolution of modularity in biological signalling networks
Supervisor
 Bioquímica (Master)
Universidade de Lisboa Faculdade de Ciências, Portugal
2013 - 2014 A stochastic model of gene expression including splicing events
Supervisor
 Bioinformática e Biologia Computacional (Master)
Universidade de Lisboa Faculdade de Ciências, Portugal
2012 - 2014 Pesquisa de módulos de genes associados à invasividade de Streptococcus pneumoniae usando semelhanças semânticas
Supervisor
 Bioquímica (Master)
Universidade de Lisboa Faculdade de Ciências, Portugal
2011 - 2012 Identificação de genes associados com o potencial invasivo de Streptococcus pneumoniae
Co-supervisor of Luisa Moreira Seco
 Bioestatística (Master)
Universidade de Lisboa Faculdade de Ciências, Portugal
2011 - 2012 Search for coherent gene modules that predict Streptococcus pneumoniae strain invasiveness
Supervisor of Rui Ribeiro Catarino
 Bioquímica (Master)
Universidade de Lisboa Faculdade de Ciências, Portugal
2008 - 2009 Classificação de genes em hibridação genómica comparativa de estirpes de Streptococcus pneumoniae
Supervisor of Liliana Cardoso
 Bioestatística (Master)
Universidade de Lisboa Faculdade de Ciências, Portugal
2008 - 2009 Computational Tools for the Metabolic Reconstruction of Streptococcus pneumoniae
Co-supervisor of Daniel Oliveira Santos Conceição
 Bioinformática (Master)
Universidade do Minho, Portugal

Event organisation

Event name
Type of event (Role) 		Institution / Organization
2018 - Current Member of the organising committee of the Workshop in Integrative Approaches in Neurodegeneration, Faculdade de Ciências da Universidade de Lisboa, June 21-23, 2018 (2018)
Workshop (Member of the Organising Committee)
 Universidade de Lisboa Faculdade de Ciências, Portugal
2009 - Current Member of the organizing committee of JB2009 - Jornadas de Bioinformatica 2009, Lisboa, Portugal (2009)
Conference (Member of the Organising Committee)
 Instituto Gulbenkian de Ciência, Portugal

Jury of academic degree

Topic
Role 		Candidate name (Type of degree)
Institution / Organization
2023 Computational Methodologies for Exploring the Role of MicroRNAs in Complex Disorders and MicroRNA Mediated Disease Association Prediction
(Thesis) Main arguer
 Sujamol S (PhD)
Amrita School of Arts & Sciences - Kochi Campus, India
2023 Development of a recommender system based on life and health sciences literature
(Thesis) Main arguer
 Maria Teresa Hipólito da Cunha (Master)
Universidade de Lisboa Faculdade de Ciências, Portugal
2023 Unraveling compound taxonomies in untargeted metabolomics through artificial intelligence
(Thesis) Main arguer
 Henrique dos Santos Silva (Master)
Universidade de Lisboa Faculdade de Ciências, Portugal
2022 The impact of the Human papilloma virus type 16 on non-coding RNAs in Head and neck cancers
(Thesis) Main arguer
 Dayna Mason (PhD)
University of Technology Sydney, Australia
2022 COMPUTATIONAL METHODOLOGIES FOR IDENTIFYING KEY GENES IN COMORBIDITY THROUGH PROTEIN – PROTEIN INTERACTION NETWORK ANALYSIS
(Thesis) Main arguer
 NIKHILA T. SURESH (PhD)
Amrita School of Arts & Sciences - Kochi Campus, India
2022 Genomic Characterisation of Streptococcus dysgalactiae subsp. equisimilis Associated with Respiratory Tract Infections
(Thesis) Main arguer
 Filipe Barbosa Valcovo (Master)
Universidade de Lisboa Instituto Superior Técnico, Portugal
2022 Novel cell models to study Cystic Fibrosis – from disease mechanisms to new therapeutic approaches
(Thesis) Arguer
 Lúcia Alexandra Rosa dos Santos (PhD)
2021/05/19 Bioinformatic analysis and deep learning on large-scale human transcriptomic data: studies on aging, Alzheimers neurodegeneration and cancer
(Thesis) Main arguer
 Óscar Gonzalez Velazco (PhD)
2021 Development of a Corpus for User-based Scientific Question Answering
(Thesis) Main arguer
 Miguel Ângelo Conde Vieira (Master)
Universidade de Lisboa Faculdade de Ciências, Portugal
2021 Extracting Negative Biomedical Relations from Literature
(Thesis) Main arguer
 Leonor Horta Torcato (Master)
Universidade de Lisboa Faculdade de Ciências, Portugal
2021 Binary Similarity Measures and Mass-Difference Network Analysis as Effective Tools in Metabolomics Data Analysis
(Thesis) Main arguer
 Francisco Maria Reis Ventura Rosado Traquete (Master)
Universidade de Lisboa Faculdade de Ciências, Portugal
2021 A Benchmark for Biomedical Knowledge Graph based Similarity
(Thesis) Main arguer
 Carlota Maria Alegre Branco Ferreira Cardoso (Master)
Universidade de Lisboa Faculdade de Ciências, Portugal
2020 Computational modeling of TGF-¿ signaling
(Thesis) Main arguer
 Márcia Raquel Gomes Carvalho de Abreu (Master)
Universidade de Lisboa Faculdade de Ciências, Portugal
2019 A Machine Learning Based Drug Discovery Pipeline: Finding New Therapies for Cystic Fibrosis
(Thesis) Main arguer
 Paulo Nuno Hilário Teixeira de Sousa (Master)
Universidade de Lisboa Faculdade de Ciências, Portugal
2019 Exploring biomedical ontologies, personalized pagerank and semantic similarity in the entity linking task
(Thesis) Main arguer
 Pedro Simões Ruas (Master)
Universidade de Lisboa Faculdade de Ciências, Portugal
2019 Extracting Phenotype-Gene Relations from Biomedical Literature Using Distant Supervision and Deep Learning
(Thesis) Main arguer
 Diana Francisco de Sousa (Master)
Universidade de Lisboa Faculdade de Ciências, Portugal
2019 How to make a single structure per cell? Lessons from X chromosome inactivation and antigen receptor gene recombination
(Thesis) Arguer
 Delphine Pessoa (PhD)
Universidade Nova de Lisboa Instituto de Tecnologia Química e Biológica, Portugal
2019 Tackling the molecular basis of lipid metabolism: from candidate genes testing in a disease cohort to multi-omics approaches in unselected populations
(Thesis) Arguer
 Niccolò Rossi (PhD)
Universidade de Lisboa Faculdade de Ciências, Portugal
2018/09/14 Bioinformatics applied to human genomics and proteomics: development of algorithms and methods for discovery of molecular signatures derived from omic data and for the construction of coexpression and interaction networks.
(Thesis) Main arguer
 Francisco José Campos-Laborie (PhD)
Universidad de Salamanca, Spain
2018 How cells initiate Epithelial-to-Mesenchymal Transition. A computational modelling of celular and supra-cellular networks to unravel the control of EMT
(Thesis) Arguer
 Ricardo Jorge Fonseca Tavares Godinho Pais (PhD)
Universidade Nova de Lisboa Instituto de Tecnologia Química e Biológica, Portugal
2018 The endoplasmic reticulum quality control : dissecting protein networks in cystic fibrosis
(Thesis) Arguer
 Sara Inês de Ascensão Tavares Canato (PhD)
2015/08/28 Integrated analysis of transcriptional regulation of human adipogenesis and cell-type selective disease association of high regulatory load genes.
(Thesis) Main arguer
 Mafalda Galhardo (PhD)
Université du Luxembourg, Luxembourg
2014 Characterization of Streptococcus pyogenes associated with tonsillo-pharyngitis in Portugal with particular emphasis on macrolide resistance
(Thesis) Arguer
 Ana Catarina Costa (PhD)
Universidade de Lisboa Faculdade de Medicina, Portugal
2013 In vivo metabolic pathway analysis of Enterococcus faecalis for uncovering key pathogenicity factors
(Thesis) Main arguer
 Carla Andreia Freixo Portela (PhD)
Universidade do Minho, Portugal
2012 EXPERIMENTAL VALIDATION OF NEW DRUGS FOR CALORIE RESTRICTION FROM COMPUTATIONAL MODELS
(Thesis) Main arguer
 Rute Monteiro Teixeira (Master)
Universidade de Lisboa Faculdade de Ciências, Portugal
2012 Coupling metabolic footprinting and flux balance analysis to predict how single gene knockouts perturb microbial metabolism
(Thesis) Main arguer
 Gonçalo dos Santos Correia (Master)
Universidade de Lisboa Faculdade de Ciências, Portugal
2010 Classification of clinical expression time series: A case study in patients with Multiple Sclerosis
(Thesis) Main arguer
 André Valerio Raposo Carreiro (Master)
Universidade de Lisboa Instituto Superior Técnico, Portugal
2010 Estudo computacional das interacções proteína-proteína
(Thesis) Main arguer
 Sérgio Miguel Cardoso Marcelino Dos Santos (Master)
Universidade de Lisboa Faculdade de Ciências, Portugal
2010 Structural and semantic similarity metrics for chemical compound classification
(Thesis) Main arguer
 João Diogo Silva Ferreira (Master)
Universidade de Lisboa Faculdade de Ciências, Portugal
2010 Model discrimination in time-course kinetics : the glyoxalase pathway in S. cerevisiae
(Thesis) Arguer
 Nuno Filipe Gonçalves das Lages (PhD)
Universidade de Lisboa Faculdade de Ciências, Portugal
2009 Cell biology informatics: two informatic tools for the study of evolutionary cell biology
(Thesis) Main arguer
 Filipe Bernardes da Silva Tavares Cadete (Master)
Universidade de Lisboa Faculdade de Ciências, Portugal
2008 Aplicação de espectroscopia de FT-IR para a serotipagem e avaliação da susceptibilidade à penicilina em Streptococcus pneumoniae
(Thesis) Main arguer
 Mónica Cancela de Abreu Miranda (Master)
Universidade de Lisboa Faculdade de Medicina, Portugal

Ad Hoc journal article review

Journal title (ISSN) Publisher
2023 - Current Electronics
2023 - Current Entropy
2022 - Current Journal of Personalized Medicine
2022 - Current Frontiers in Genetics
2022 - Current Metabolites
2022 - Current Pharmaceutics
2022 - Current International Journal of Molecular Sciences
2021 - Current Cancers
2021 - Current Biomedicines
2021 - Current Genes
2021 - Current IEEE/ACM Transactions on Computational Biology and Bioinformatics
2021 - Current Heliyon
2021 - Current Molecular Omics
2020 - Current Scientific Reports
2020 - Current Briefings in Bioinformatics
2019 - Current PLOS Computational Biology
2018 - Current Database
2018 - Current FEMS Yeast Research
2015 - Current BioMed Research International
2015 - Current Computer Methods and Programs in Biomedicine
2012 - Current PLoS One
2010 - Current BMC Medical Genomics

Association member

Society Organization name Role
2018/12/17 - Current Sociedade Portuguesa de Bioquímica Membro do Conselho Directivo

Committee member

Activity description
Role 		Institution / Organization
2024/09/09 - Current Facilitator of the Systems Biology and Microbial Biotechnology Community
Coordinator
 BioData.pt, Portugal

Conference scientific committee

Conference name Conference host
2013 - Current 4th international conference on bioinformatics models, methods and algoritms, 2013 Barcelona, Espanha
2010 - Current JB2010 -Jornadas de Bioinformática 2010 Málaga, Espanha
2010 - Current International Conference on Information Technology in Bio and Medical Informatics 2010 Bilbau, Espanha
2024 - 2024 XXII National Congress of Biochemistry University of Aveiro
2007 - 2008 BIRD - Bioinformatics Research and Development

Consulting

Activity description Institution / Organization
2022 - Current Statistical review of studies submitted for publication on the Society's Journal. Sociedade Portuguesa de Pediatria, Portugal

Evaluation committee

Activity description
Role 		Institution / Organization Funding entity
2016 - Current Scientific project evaluator for the Romanian Science funding agency UEFISCDI
Evaluator
 Unitatea Executiva pentru Finantarea Invatamantului Superior a Cercetarii Dezvoltarii si Inovarii, Romania Unitatea Executiva pentru Finantarea Invatamantului Superior a Cercetarii Dezvoltarii si Inovarii
2022 - 2023 Part of jury for the evaluation and selection of applications for postdoctoral research contracts at the University of Salamanca, within the program USAL4Excellence
Evaluator
 Universidad de Salamanca, Spain

Journal scientific committee

Journal title (ISSN) Publisher
2019/06/01 - Current Scientific Reports (2045-2322) Springer Science and Business Media LLC
Distinctions

Award

2001 Best final degree grades in Faculty of Sciences, University of Lisbon
Banco Espírito Santo e Comercial de Lisboa, Portugal
2000 Merit Scholarship
Universidade de Lisboa Faculdade de Ciências, Portugal
1999 Merit Scholarship
Universidade de Lisboa Faculdade de Ciências, Portugal
1997 Merit Scholarship
Universidade de Lisboa Faculdade de Ciências, Portugal
1996 3rd prize for freshmen's academic performance
Fundação da Faculdade de Ciências da Universidade de Lisboa, Portugal

Other distinction

2020 Honorable mention (Menção Honrosa) for Excellence in Teaching
Universidade de Lisboa Faculdade de Ciências, Portugal