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I graduated in Bioinformatics, in 2005, from University of Lisbon, with a specialization in software development and in using deterministic mathematical models for data analysis. I developed my PhD also in Bioinformatics, in 2010, from University of Reading. During this time I applied Bayesian inference using genetic data. Afterwards, I have done a 1-year post-doc where I analysed a large database with whole-genome data using Bayesian methods. Later, I did a 2-years post-doc in Infectious Diseases using mathematical manipulation and computation-intensive statistical tools to capture dynamics in transmission models. Finally, I have done another 2-years post-doc analysing small and large datasets using statistical based programming tools, while continuing to apply statistical tools to analyse genetic data. At the moment, I am working in the Portuguese NSI in Survey Methodology and in the application of Data Science tools to combined micro- and macro-data from questionnaires and to administrative data. Due to my background, my interests are focused mainly on the development and use of software for mathematical and statistical analysis, as well as, on the creation and upkeep of databases. Meanwhile, I have been shifting my main interest to Social Science, particularly, to the fields of Population and Social Conditions. I consider that these fields can make important contributions to a sustainable development of the society. As such, I become attracted to the use of computer-based statistical and mathematical analysis to extract potentially important relations between demographic and socio-economic factors.
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Identification

Personal identification

Full name
Joao Sollari Allegro Machado Lopes

Citation names

  • Lopes, Joao Sollari

Author identifiers

Ciência ID
591B-6DEB-ECF9
ORCID iD
0000-0001-5670-2069
Google Scholar ID
https://scholar.google.pt/citations?user=uYeCHmkAAAAJ=en&authuser=1
Researcher Id
A-1493-2013
Scopus Author Id
35094054800

Telephones

Telephone
  • 218426100 (Professional)

Addresses

  • Instituto Nacional de Estatística. Av. António José de Almeida, 1000-043, Lisboa, Lisboa, Portugal (Professional)

Websites

Knowledge fields

  • Exact Sciences - Computer and Information Sciences - Bioinformatics
  • Exact Sciences - Mathematics - Statistics and Probability
  • Exact Sciences - Mathematics - Applied Mathematics
  • Medical and Health Sciences - Health Sciences - Infectious Diseases
  • Medical and Health Sciences - Health Sciences - Epidemiology
  • Natural sciences - Biological Sciences - Evolutionary Biology
  • Natural sciences - Biological Sciences - Genetics and Heredity
  • Social Sciences - Economics and Business - Econometrics
  • Social Sciences - Sociology - Social Topics
  • Social Sciences - Sociology - Demography

Languages

Language Speaking Reading Writing Listening Peer-review
English Advanced (C1) Advanced (C1) Advanced (C1) Advanced (C1)
Spanish; Castilian Intermediate (B1) Intermediate (B1) Beginner (A1) Intermediate (B1)
French Beginner (A1) Intermediate (B1) Beginner (A1) Beginner (A1)
Italian Beginner (A1) Intermediate (B1) Beginner (A1) Beginner (A1)
Education
Degree Classification
2010/05/05
Concluded
 PhD in Life Sciences (Doctor of Philosophy)
University of Reading School of Biological Sciences, United Kingdom
"Software development in population genetics" (THESIS/DISSERTATION)
 n/a
2005/10/14
Concluded
 Estágio do final de curso de Biologia ramo Científico (Outros)
Universidade de Lisboa Faculdade de Ciências, Portugal
"Desenvolvimento de software para modelacao do crescimento de Sparus aurata em aquacultura" (THESIS/DISSERTATION)
 18 (0 a 20)
2005/10/14
Concluded
 Biologia ramo Científico (Licenciatura)
Universidade de Lisboa Faculdade de Ciências, Portugal
"n/a" (THESIS/DISSERTATION)
 15 (0 a 20)
1999/08/12
Concluded
 n/a (Ensino secundário)
Escola Secundária de Odivelas, Portugal
"n/a" (THESIS/DISSERTATION)
 18 (0 a 20)
Affiliation

Science

Category
Host institution 		Employer
2013/08/01 - 2015/11/30 Postdoc (Research) Instituto Superior de Psicologia Aplicada Centro de Investigacao, Portugal
Instituto Gulbenkian de Ciência, Portugal
2011/04/01 - 2015/11/30 Postdoc (Research) Instituto Gulbenkian de Ciência, Portugal
2010/04/01 - 2011/03/31 Postdoc (Research) Centro de Ciências do Mar, Portugal
2005/08/01 - 2005/09/30 Research Trainee (Research) Swansea University Department of Biosciences, United Kingdom
2004/09/06 - 2005/09/30 Research Trainee (Research) Universidade de Lisboa Faculdade de Ciências, Portugal

Teaching in Higher Education

Category
Host institution 		Employer
2007/09/03 - 2008/06/27 Tutor (University Teacher) University of Reading School of Biological Sciences, United Kingdom

Other Careers

Category
Host institution 		Employer
2015/12/01 - Current Técnico Superior (Técnico Superior) Instituto Nacional de Estatistica, Portugal
2002/10/01 - 2004/08/31 Técnico de Informática Estagiário (Técnico de informática) Universidade de Lisboa Instituto Superior de Economia e Gestão, Portugal
Projects

Grant

Designation Funders
2013/08/01 - 2015/11/30 Molecular mechanisms and evolutionary implications of social plasticity
info:eu-repo/grantAgreement/FCT/3599-PPCDT/129982/PT
Post-doc Fellow
Instituto Gulbenkian de Ciência, Portugal

Instituto Superior de Psicologia Aplicada Centro de Investigacao, Portugal
UK Research and Innovation
Concluded
2013/07 - 2013/08 Developing the Framework for an Epidemic Forecast Infrastructure
info:eu-repo/grantAgreement/EC/SEVENTH FRAMEWORK PROGRAMME/231807/EU
Post-doc Fellow
Instituto Gulbenkian de Ciência, Portugal
 Fundação para a Ciência e a Tecnologia
Concluded
2013/02 - 2013/06 Unravelling pneumococcal interactions in the nasopharyngeal niche
info:eu-repo/grantAgreement/FCT/3599-PPCDT/98289/PT
Post-doc Fellow
Instituto Gulbenkian de Ciência, Portugal
 UK Research and Innovation
Concluded
2011/04 - 2013/01 Exploring pathogen diversity in disease epidemiology and vaccine research
info:eu-repo/grantAgreement/FCT/3599-PPCDT/103484/PT
Post-doc Fellow
Instituto Gulbenkian de Ciência, Portugal
 UK Research and Innovation
Concluded
2010/04 - 2011/03 The origin and early diversification of plants: a phylogenomic approach employing novel composition-heterogeneous methods
info:eu-repo/grantAgreement/FCT/3599-PPCDT/99565/PT
Post-doc Fellow
Centro de Ciências do Mar, Portugal
 Fundação para a Ciência e a Tecnologia
Concluded
2009/01/01 - 2010/03 EXPLORE THE USE OF BAYESIAN STATISTIC METHODS FOR APPLIED POPULATION GENETICS AND PHYLOGENETIC PROBLEMS
info:eu-repo/grantAgreement/FCT/SFRH/SFRH2%FBD2%F435882%F2008/PT
PhD Student Fellow
University of Reading School of Biological Sciences, United Kingdom
 UK Research and Innovation
Concluded
2006/03/01 - 2008/12 Computational Statistical Methods for Population Genomics
EP/C533550/1
PhD Student Fellow
Engineering and Physical Sciences Research Council, United Kingdom
 UK Research and Innovation
Concluded
Outputs

Publications

Book chapter
  1. Lopes, Joao; Moura, Marco; Quaresma, Sonia. "Labour Market Attractiveness in the EU at country-level". In Classificacao e analise de dados: Metodos e Aplicacoes, edited by Bacelar-Nicolau, H.; Sousa, F.; Marcelo, C.; Ferreira, A.S.; Infante, P.; Figueiredo, A., 191-200. lisbon, Portugal: Instituto Nacional de Estatistica, 2019.
    Published
  2. Lopes, Joao. "10 Years of Software Development for Approximate Bayesian Computation". In Horizons in Computer Science Research, edited by Clary, T. S., 35-53. New York, United States: Nova Science Publishers Inc., 2011.
    Published
Journal article
  1. Roleira, António; Oliveira, Gonçalo A.; Lopes, João S.; Oliveira, Rui F.. "Audience Effects in Territorial Defense of Male Cichlid Fish Are Associated with Differential Patterns of Activation of the Brain Social Decision-Making Network". Frontiers in Behavioral Neuroscience 11 (2017): http://dx.doi.org/10.3389/fnbeh.2017.00105.
    Published • 10.3389/fnbeh.2017.00105
  2. Gomes, M. Gabriela M.; Gjini, Erida; Lopes, Joao S.; Souto-Maior, Caetano; Rebelo, Carlota. "A theoretical framework to identify invariant thresholds in infectious disease epidemiology". Journal of Theoretical Biology 395 (2016): 97-102. http://dx.doi.org/10.1016/j.jtbi.2016.01.029.
    Published • 10.1016/j.jtbi.2016.01.029
  3. Oliveira, Rui F.; Simões, José M.; Teles, Magda C.; Oliveira, Catarina R.; Becker, Jorg D.; Lopes, João S.. "Assessment of fight outcome is needed to activate socially driven transcriptional changes in the zebrafish brain". Proceedings of the National Academy of Sciences 113 5 (2016): E654-E661. http://dx.doi.org/10.1073/pnas.1514292113.
    Published • 10.1073/pnas.1514292113
  4. Lopes, João Sollari; Abril-de-Abreu, Rodrigo; Oliveira, Rui F.. "Brain Transcriptomic Response to Social Eavesdropping in Zebrafish (Danio rerio)". PLOS ONE 10 12 (2015): e0145801. http://dx.doi.org/10.1371/journal.pone.0145801.
    Published • 10.1371/journal.pone.0145801
  5. Teles MC; Almeida O; Lopes JS; Oliveira RF. "Social interactions elicit rapid shifts in functional connectivity in the social decision-making network of zebrafish.". (2015): http://europepmc.org/abstract/med/26423839.
    10.1098/rspb.2015.1099
  6. Pinho ST; Rodrigues P; Andrade RF; Serra H; Lopes JS; Gomes MG. "Impact of tuberculosis treatment length and adherence under different transmission intensities.". (2015): http://europepmc.org/abstract/med/26163050.
    10.1016/j.tpb.2015.06.004
  7. Arenas M; Lopes JS; Beaumont MA; Posada D. "CodABC: a computational framework to coestimate recombination, substitution, and molecular adaptation rates by approximate Bayesian computation.". (2015): http://europepmc.org/abstract/med/25577191.
    10.1093/molbev/msu411
  8. Delphine Pessoa; Caetano Souto-Maior; Erida Gjini; Joao S. Lopes; Bruno Ceña; Cláudia T. Codeço; M. Gabriela M. Gomes; Roland R. Regoes. "Unveiling Time in Dose-Response Models to Infer Host Susceptibility to Pathogens". PLoS Comput Biol 10 8 (2014): e1003773-e1003773. http://dx.doi.org/10.1371/journal.pcbi.1003773.
    10.1371/journal.pcbi.1003773
  9. Caetano Souto-Maior; Joao S. Lopes; Erida Gjini; Claudio J. Struchiner; Luis Teixeira; M. Gabriela M. Gomes. "Heterogeneity in symbiotic effects facilitates Wolbachia establishment in insect populations". Theor Ecol 8 1 (2014): 53-65. http://dx.doi.org/10.1007/s12080-014-0235-7.
    10.1007/s12080-014-0235-7
  10. Almeida O; Gonçalves-de-Freitas E; Lopes JS; Oliveira RF. "Social instability promotes hormone-behavior associated patterns in a cichlid fish.". (2014): http://europepmc.org/abstract/med/24973663.
    10.1016/j.yhbeh.2014.05.007
  11. B. Li; J. S. Lopes; P. G. Foster; T. M. Embley; C. J. Cox. "Compositional Biases among Synonymous Substitutions Cause Conflict between Gene and Protein Trees for Plastid Origins". Molecular Biology and Evolution 31 7 (2014): 1697-1709. http://dx.doi.org/10.1093/molbev/msu105.
    10.1093/molbev/msu105
  12. Lopes JS; Rodrigues P; Pinho ST; Andrade RF; Duarte R; Gomes MG. "Interpreting measures of tuberculosis transmission: a case study on the Portuguese population.". (2014): http://europepmc.org/abstract/med/24941996.
    10.1186/1471-2334-14-340
  13. Parisi, A.; Lopes, J.S.; Nunes, A.; Gomes, M.G.M.. "Heterogeneity in antibody range and the antigenic drift of influenza A viruses". Ecological Complexity 14 (2013): 157-165. http://www.scopus.com/inward/record.url?eid=2-s2.0-84877153145&partnerID=MN8TOARS.
    10.1016/j.ecocom.2012.12.001
  14. Lopes, J.S.; Arenas, M.; Posada, D.; Beaumont, M.A.. "Coestimation of recombination, substitution and molecular adaptation rates by approximate Bayesian computation". Heredity (2013): http://www.scopus.com/inward/record.url?eid=2-s2.0-84886939439&partnerID=MN8TOARS.
    10.1038/hdy.2013.101
  15. Lopes, J.S.; Marques, I.; Soares, P.; Nebenzahl-Guimaraes, H.; Costa, J.; Miranda, A.; Duarte, R.; et al. "SNP typing reveals similarity in Mycobacterium tuberculosis genetic diversity between Portugal and Northeast Brazil". Infection, Genetics and Evolution 18 (2013): 238-246. http://www.scopus.com/inward/record.url?eid=2-s2.0-84879517694&partnerID=MN8TOARS.
    10.1016/j.meegid.2013.04.028
  16. Gomes, M.G.; Aguas, R.; Lopes, J.S.; Nunes, M.C.; Rebelo, C.; Rodrigues, P.; Struchiner, C.J.. "How host heterogeneity governs tuberculosis reinfection?". Proceedings. Biological sciences / The Royal Society 279 1737 (2012): 2473-2478. http://www.scopus.com/inward/record.url?eid=2-s2.0-84865612754&partnerID=MN8TOARS.
    10.1098/rspb.2011.2712
  17. Batini, C.; Lopes, J.; Behar, D.M.; Calafell, F.; Jorde, L.B.; Van Der Veen, L.; Quintana-Murci, L.; et al. "Insights into the demographic history of African pygmies from complete mitochondrial genomes". Molecular Biology and Evolution 28 2 (2011): 1099-1110. http://www.scopus.com/inward/record.url?eid=2-s2.0-78751503886&partnerID=MN8TOARS.
    10.1093/molbev/msq294
  18. Lopes, J.S.; Boessenkool, S.. "The use of approximate Bayesian computation in conservation genetics and its application in a case study on yellow-eyed penguins". Conservation Genetics 11 2 (2010): 421-433. http://www.scopus.com/inward/record.url?eid=2-s2.0-77952098598&partnerID=MN8TOARS.
    10.1007/s10592-009-0032-9
  19. Lopes, J.S.; Beaumont, M.A.. "ABC: A useful Bayesian tool for the analysis of population data". Infection, Genetics and Evolution 10 6 (2010): 825-832. http://www.scopus.com/inward/record.url?eid=2-s2.0-77954035029&partnerID=MN8TOARS.
    10.1016/j.meegid.2009.10.010
  20. Lopes, J.S.; Balding, D.; Beaumont, M.A.. "PopABC: A program to infer historical demographic parameters". Bioinformatics 25 20 (2009): 2747-2749. http://www.scopus.com/inward/record.url?eid=2-s2.0-70349978987&partnerID=MN8TOARS.
    10.1093/bioinformatics/btp487
  21. Palero, F.; Lopes, J.; Abellaó, P.; MacPherson, E.; Pascual, M.; Beaumont, M.A.. "Rapid radiation in spiny lobsters (Palinurus spp) as revealed by classic and ABC methods using mtDNA and microsatellite data". BMC Evolutionary Biology 9 1 (2009): http://www.scopus.com/inward/record.url?eid=2-s2.0-72449123214&partnerID=MN8TOARS.
    10.1186/1471-2148-9-263
Thesis / Dissertation
  1. Lopes, Joao. "Software development in population genetics". PhD, University of Reading School of Biological Sciences, 2009. https://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.529977.
  2. Lopes, Joao. "Criação de uma aplicação para modelar o crescimento da dourada (Sparus aurata) em aquacultura". Degree, Universidade de Lisboa Faculdade de Ciências, 2005. http://hdl.handle.net/10451/7590.
Working paper
  1. Lopes, Joao; Moura, Marco; Quaresma, Sonia. 2018. "Labour market attractiveness in the EU". https://ec.europa.eu/eurostat/web/products-statistical-working-papers/-/KS-TC-18-002.
    10.2785/252238
Activities

Oral presentation

Presentation title Event name
Host (Event location)
2017/11/03 Mismatch between jobs and skills in the EU Big Data in Finance, Retail and Commerce
Centro de Estatistica e Aplicacoes (Lisboa, Portugal)
2017/10/18 Discrepância entre postos de trabalho e competências na UE SPE 2017
Sociedade Portuguesa de Estatistica (Lisboa, Portugal)
2017/09/11 Labour Market Attractiveness in the EU From Prototype to Production
Eurostat (Thessaloniki, Greece)
2017/04/26 Mismatch between jobs and skills in the EU Jornadas de Classificacao e Analise de Dados 2017
Classificacao e Analise de Dados (Porto, Portugal)
2015/05/07 TB transmission model: Portugal as a case study O significado dos dados: a biologia quantitativa, a biominformática e a compreensão da vida
Instituto Superior de Psicologia Aplicada (Lisboa, Portugal)
2014/06/30 Coestimation of Recombination, Molecular Adaptation and substitution rates by approximate Baysian computation Postdoc seminars
Instituto Gulbenkian de Ciência (Oeiras, Portugal)
2014/02/04 Retreat IBBG 2014 IBBG 2004
Integrative Behavioural Biology Group (Milfontes, Portugal)
2013/04/04 Protection vs Fecundity: modeling a trade-off Heterogeneity in Host-Pathogen Systems 2
Instituto Gulbenkian de Ciência (Oeiras, Portugal)
2013/02/11 TB transmission model: Portugal as a case-study Seminar EAO
Instituto Gulbenkian de Ciência (Oeiras, Portugal)
2012/10/15 MTBC gentic diversity in Portugal and Northeast Brazil 2º Encontro de Bolseiros da Fundacao Calouste Gulbenkian nas areas das Doencas Tropicais Negligenciadas e das Ciencias da Saude
Fundação Calouste Gulbenkian (Lisboa, Portugal)
2012/09/27 ABC Basics Workshop at Fiocruz September 2012
Fiocruz (Rio de Janeiro, Brazil)
2012/05/30 Tuberculosis reinfection patterns reveal host heterogeneity Postdoc seminars
Instituto Gulbenkian de Ciência (Oeiras, Portugal)
2012/03/05 MTBC strains identification Tuberculosis Meeting
Instituto Gulbenkian de Ciência (Oeiras, Portugal)
2011/10/26 Infectious diseases dynamics Post-doc Retreat 2011
Instituto Gulbenkian de Ciência (Cascais, Portugal)
2011/10/24 Hidden heterogeneity in interventions Seminar EAO
Instituto Gulbenkian de Ciência (Oeiras, Portugal)
2011/07/20 Multi-strain SIR models with cross-immunity Expand meeting
Instituto Gulbenkian de Ciência (Oeiras, Portugal)
2011/01/21 Coestimation of Recombination and Molecular Adaptation by approximate Bayesian computation Seminar
Instituto Gulbenkian de Ciência (Oeiras, Portugal)
2009/09/23 ABC: learning populations history 11th ICZEGAR
Hellenic Zoological Society (Heraklion, Greece)
2009/09/11 ABC: learning populations history MMEE 2009
University of Bristol (Bristol, United Kingdom)
2009/09/06 ABC: studying historical demographic parameters ConGen: Evolutionary and physiological adaptation to climate induced environmental changes
European Science Foundation (Bialowieza, Poland)
2009/05/25 ABC: studying historical demographic parameters ConGen: Integrating Population Genetics and Conservation Biology meeting
European Science Foundation (Trondheim, Norway)
2009/02/09 ABC: estimating historic demographic parameters Evolution: The experience
The University of Melbourne (Melbourne, Australia)
2009/01/12 ABC: estimating historic demographic parameters Environmental forum
University of Reading School of Biological Sciences (Reading, United Kingdom)
2009/01/08 Introduction to Bayesian methods in population genetics Seminar
University of Oxford (Oxford, United Kingdom)
2008/12/16 ABC: estimating historic demographic parameters PopGroup 2008
Genetics Society (Cardiff, United Kingdom)
2008/11/30 ABC: general applications MEEGID IX
Infection, Genetics and Evolution (Irvine, United States)
2008/06/17 ABC: studying demogarphic historic parameters Biological School EB 2008
University of Reading School of Biological Sciences (Reading, United Kingdom)
2008/06/11 ABC: studying demographic historic parameters MIEP 2008
Centre National de la Recherche Scientifique (Montpellier, France)
2008/06/08 ABC: studying demographic historic parameters SMBE 2008
Society for Molecular Biology and Evolution (Barcelona, Spain)
2008/04/02 ABC: simple short somewhat happy ending research story Environmental forum
University of Reading School of Biological Sciences (Reading, United Kingdom)
2007/09/21 ABC: adding summary statistics ConGen: Population genetics modelling and habitat fragmentation
Instituto Gulbenkian de Ciência (Oeiras, Portugal)
2007/06/26 ABC: method details & space for improvements Biological School EB 2007
University of Reading School of Biological Sciences (Reading, United Kingdom)
2007/06/19 ABC: acet MCM2007
University of Reading Advanced Computing and Emerging Technologies (Reading, United Kingdom)
2007/06/08 ABC: uncertainties Estimating demographic parameters from genetic data
Congress Universitaire de Suisse Occidentale (La Fouly, Switzerland)
2007/01/10 ABC: simplified overview PopGroup 2006
Genetics Society (Manchester, United Kingdom)
2006/12/21 ABC: simplified overview II ENBE 2006
Centro de Investigação em Biodiversidade e Recursos Geneticos (Porto, Portugal)
2006/12/15 ABC: Practical overview Recent Advances in Statistical Genetics and Bioinformatics
Newton Institute (Cambridge, United Kingdom)
2006/07/03 ABC presentation Biological School EB 2006
University of Reading School of Biological Sciences (Reading, United Kingdom)

Supervision

Thesis Title
Role 		Degree Subject (Type)
Institution / Organization
2013/02/04 - 2014/09/11 Insights into tuberculosis: a survival analysis of time to reccurence
Co-supervisor
 Biostatistics (Master)
Universidade de Lisboa Faculdade de Ciências, Portugal

Course / Discipline taught

Academic session Degree Subject (Type) Institution / Organization
2019/02 - 2019/02 Introduction to Data Science (Outros) Instituto Nacional de Estatistica, Portugal
2017/07 - 2017/07 Introduction to Data Mining Data Mining (Outros) Instituto Nacional de Estatistica, Portugal
2010/03 - 2010/03 Approximate Bayesian Computation: Introductory course Bayesian Statistics (Outros) Centro de Ciências do Mar, Portugal
2008/01 - 2008/03 Microevolution Biological Sciences (Bachelor) University of Reading School of Biological Sciences, United Kingdom
2008/01 - 2008/03 Genes and Chromosomes (Bachelor) University of Reading School of Biological Sciences, United Kingdom
2008/01 - 2008/03 Animal Behaviour Biological Sciences (Bachelor) University of Reading School of Biological Sciences, United Kingdom
2007/09 - 2007/12 Macroevolution Biological Sciences (Bachelor) University of Reading School of Biological Sciences, United Kingdom
Distinctions

Award

2009 Arthur Hosier/Meyer Sassoon Travel Award
University of Reading, United Kingdom

Other distinction

2017 5th place (in 22) European Big Data Hackathon 2017
Eurostat, Luxembourg
2008 winner of the "Biotechnology Young Entrepreneurs Scientists" competition
Biotechnology and Biological Sciences Research Council, United Kingdom