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Pedro G. Ferreira graduated in Systems and Informatics Engineering from the University of Minho in 2002 and completed his PhD in Artificial Intelligence from the same University in 2007. From 2008 to 2012, he was a Postdoctoral Fellow at the Bioinformatics and Genomics Laboratory, Center for Genomic Regulation, Barcelona. From 2012 to 2014, he joined as a Postdoctoral Fellow the Functional Population Genomics and Genetics of Complex Traits group, School of Medicine, University of Geneva. During his two postdocs, he was involved in five major international consortia: ICGC-CLL, ENCODE, GEUVADIS, SYSCOL and GTEx. He published several papers in high-profile journals, including multidisciplinary journals: Nature, Science, Nature Communications, Scientific Reports, PNAS and eLife. Other papers were published in top ranking specialized journals including Genome Biology, Genome Research, American Journal of Human Genetics, Nature Cell Biology, RNA or Leukemia. He is an author of 3 book chapters and 2 books. He has an h-index of 28, summing > 26 000 citations. In 2015, he was awarded an FCT Investigator Starting grant and he joined Ipatimup/i3s. He received the Research Award 2015 and 2019 from Portuguese Society of Human Genetics - SPGH and the Microsoft Azure Research Award for Data Science 2017. He was an Invited Assistant Professor at Department of Informatics at University of Minho from 2015 to 2018, teaching Bioinformatics and Data Analysis at Masters degree level. In the last years, he supervised 1 Post-doc, 2 PhD students, 8 Master students, 2 Research assistants and 12 undergraduate students. Currently supervises 5 PhD students and 5 Master students. He has experience in genomics start-up environment where he developed information systems for personal genomics data interpretation. Since early 2019 he is an Assistant Professor at the Department of Computer Science, Faculty of Sciences of University of Porto. He is the director of the specialisation course and the Master in Bioinformatics and Computational Biology from the University of Porto. He is leading the installation committee for a bachelor degree in Bioinformatics.  He is a partner of a bioinformatics data analysis company with national and international clients, including hospitals, diagnostics clinics and research centers. His main research focus in the development of methods for a diverse set of problems in genomic data science. In particular, he is interested in unraveling the role of genomics on the human health and disease. In order to achieve this goal he applies and develops data-analytical models using machine learning and probabilistic methods to analyze and interpret diverse, complex and large-scale genomic datasets.
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Identification

Personal identification

Full name
Pedro Gabriel Dias Ferreira
Date of birth
1978/05/10
Gender
Male

Citation names

  • Ferreira, Pedro G.

Author identifiers

Ciência ID
6E1E-0D58-A2D6
ORCID iD
0000-0003-3838-8664
Google Scholar ID
https://scholar.google.com/citations?user=X097-20AAAAJ
Researcher Id
J-6379-2013
Scopus Author Id
13405242500

Email addresses

  • pgferreira@fc.up.pt (Professional)

Addresses

  • Rua Campo Alegre 1021/1055, FC6, 4169-007, Porto, Porto, 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 Proficiency (C2) Proficiency (C2) Proficiency (C2) Proficiency (C2) Proficiency (C2)
Spanish; Castilian Advanced (C1) Advanced (C1) Advanced (C1) Advanced (C1) Advanced (C1)
English Proficiency (C2) Proficiency (C2) Proficiency (C2) Proficiency (C2) Proficiency (C2)
Education
Degree Classification
2022/10/14
Concluded
 Ciência de Computadores (Título de Agregado)
Universidade do Porto Faculdade de Ciências, Portugal
"Agregado no ramo de conhecimento de Ciência de Computadores. / Habilitation in Computer Science." (THESIS/DISSERTATION)
2007
Concluded
 Doutoramento em Informática (Doutoramento)
Universidade do Minho Escola de Engenharia, Portugal
"Sequence Pattern Mining in Biochemical Data" (THESIS/DISSERTATION)
 Unanimidade
2002
Concluded
 Licenciatura em Engenharia de Sistemas e Informática (Licenciatura)
Universidade do Minho Escola de Engenharia, Portugal
"Engenharia de Sistemas e Informática" (THESIS/DISSERTATION)
 16
Affiliation

Science

Category
Host institution 		Employer
2019/03/01 - Current Researcher (Research) Instituto de Engenharia de Sistemas e Computadores Tecnologia e Ciência, Portugal
Instituto de Engenharia de Sistemas e Computadores, Portugal
2015/05/01 - Current Researcher (Research) Universidade do Porto Instituto de Investigação e Inovação em Saúde, Portugal
2015/05/01 - 2019/01/31 Auxiliary Researcher (Research) Universidade do Porto Instituto de Patologia e Imunologia Molecular, Portugal
2012/11/01 - 2014/06/01 Postdoc (Research) Universite de Geneve Faculte de Medecine, Switzerland
2008/01/01 - 2012/11/01 Postdoc (Research) Centre de Regulació Genòmica, Spain
2003/10/01 - 2007/09/01 Researcher (Research) Universidade do Minho Escola de Engenharia, Portugal
2002/04/01 - 2002/10/01 Visiting Researcher (Research) Philips Research, Natuurkunde Laboratorium, IST, Netherlands

Teaching in Higher Education

Category
Host institution 		Employer
2019/02/01 - Current Assistant Professor (University Teacher) Universidade do Porto Faculdade de Ciências, Portugal
Universidade do Porto Faculdade de Ciências, Portugal

Others

Category
Host institution 		Employer
2014/08/01 - 2015/04/01 Senior Bioinformatics Specialist Coimbra Genomics SA, Portugal
2003/01/01 - 2003/09/01 Software Engineer Escripóvoa Software House Lda, Portugal
2001/06/01 - 2001/08/01 Software Programmer Avel Electrónica Lda, Portugal
Projects

Grant

Designation Funders
2008/01 - 2010/12 Searching for high level rules in protein folding and unfolding: from amyloid diseases to protein structure prediction
Provided by PTCRIS: 72838
 Universidade de Coimbra

Contract

Designation Funders
2018/06/01 - Current Solving the 3D chromatin structure of CDH1 locus to identify disease-associated mechanisms
POCI-01-0145-FEDER-030164
Researcher
Universidade do Porto Instituto de Investigação e Inovação em Saúde, Portugal
 Fundação para a Ciência e a Tecnologia
Ongoing
2018/06/01 - Current AVC em translação: Biomarcadores para diagnóstico e decisão terapêutica no AVC isquémico
POCI-01-0145-FEDER-031674
Researcher
Universidade do Porto Instituto de Investigação e Inovação em Saúde, Portugal
 Fundação para a Ciência e a Tecnologia
Ongoing
2018/06/01 - Current NaSA - Neoantigen signature algorithm to predict immunotherapy response
POCI-01-0145-FEDER-032018
Researcher
Universidade do Porto Instituto de Investigação e Inovação em Saúde, Portugal
 Fundação para a Ciência e a Tecnologia
Ongoing
2018/06/01 - Current Tregs in cancer immune response
POCI-01-0145-FEDER-032462
Researcher
Universidade do Porto Instituto de Investigação e Inovação em Saúde, Portugal
Ongoing
2018/06 - Current Tregs in cancer immune response
POCI-01-0145-FEDER-032462
 N/A
2020/01 - 2020/07 Transcriptomics-based prediction of human phenotypes using scalable and secure machine learning approaches
CPCA/A2/2640/2020
 CPCA/A2/2640/2020
2017/06/01 - 2020/05/30 GenomePT – National Laboratory for Genome Sequencing and Analysis
POCI-01-0145-FEDER-022184
Researcher
Universidade do Porto Instituto de Investigação e Inovação em Saúde, Portugal
Ongoing
2017/01/01 - 2020/01/01 Training in Extracellular vesicles: for benefit in Health & Disease
H2020-MSCA-ITN-2016/H2020-MSCA-ITN-2016, Grant nº 722148
Researcher
Universidade do Porto Instituto de Investigação e Inovação em Saúde, Portugal
Ongoing
2016/02/01 - 2019/07/31 The yin and yang of somatic mutations in cancer immunosurveillance
PTDC/BIM-MEC/2834/2014
Researcher
Universidade do Porto Instituto de Investigação e Inovação em Saúde, Portugal
Ongoing
2015/05/01 - 2019/01/31 Understanding the impact of acquired and germline genetic variants in the complexity of gastric cancer
IF/01127/2014
Principal investigator
Universidade do Porto Instituto de Patologia e Imunologia Molecular, Portugal
 Fundação para a Ciência e a Tecnologia
Concluded

Other

Designation Funders
2016/01/01 - Current Advancing cancer research: from basic knowledgment to application II
ORTE-01-0145-FEDER-000029
Researcher
Universidade do Porto Instituto de Investigação e Inovação em Saúde, Portugal
2017/05/01 - 2018/04/30 Understanding gender differential susceptibility to cancer through large-scale data analysis with correlation networks and deep neural networks.
.
Principal investigator
Universidade do Porto Instituto de Investigação e Inovação em Saúde, Portugal
 Microsoft Azure
Concluded
Outputs

Publications

Book
  1. Ferreira, Pedro G.. Bioinformatics Algorithms Design and Implementation in Python. Elsevier. 2018.
    Published
  2. Ferreira, Pedro G.. Análise e exploração de dados com o R. FCA Editora. 2017.
    Published
  3. Alves, R.; Ferreira, P.; Ribeiro, J.; Belo, O.. Detecting abnormal patterns in call graphs based on the aggregation of relevant vertex measures. 2012.
    10.1007/978-3-642-31488-9_8
  4. Silva, C.G.; Ferreira, P.G.; Azevedo, P.J.; Brito, R.M.M.. Using data mining techniques to probe the role of hydrophobic residues in protein folding and unfolding simulations. 2009.
    10.4018/978-1-60566-816-1.ch012
  5. Ferreira, P.G.; Azevedo, P.J.. Deterministic pattern mining on genetic sequences. 2009.
    10.4018/978-1-60566-766-9.ch013
  6. Ferreira, P.G.; Silva, C.G.; Azevedo, P.J.; Brito, R.M.M.. Spatial clustering of molecular dynamics trajectories in protein unfolding simulations. 2009.
    10.1007/978-3-642-02504-4_14
  7. Ferreira, P.G.; Azevedo, P.J.. Deterministic motif mining in protein databases. 2007.
    10.4018/978-1-59904-645-7.ch006
  8. Ferreira, P.G.; Azevedo, P.J.; Silva, C.G.; Brito, R.M.M.. Mining approximate motifs in time series. 2006.
  9. Ferreira, P.; Alves, R.; Belo, O.; Cortesão, L.. Establishing fraud detection patterns based on signatures. 2006.
    10.1007/11790853_41
  10. Ferreira, P.G.; Azevedo, P.J.. Protein sequence pattern mining with constraints. 2005.
    10.1007/11564126_14
  11. Ferreira, P.G.; Azevedo, P.J.. Protein sequence classification through relevant sequence mining and bayes classifiers. 2005.
    10.1007/11595014_24
  12. Alves, R.; Belo, O.; Cavalcanti, F.; Ferreira, P.. Clickstreams, the basis to establish user navigation patterns on web sites. 2004.
Conference paper
  1. Ferreira, P.G.; Azevedo, P.J.. "Evaluating protein motif significance measures: A case study on prosite patterns". 2007.
    10.1109/CIDM.2007.368869
  2. Librelotto, G.R.; Machado, H.T.; Martins, M.; Ferreira, P.G.D.; Ramalho, J.C.; Henriques, P.R.. "Topic maps applied to PubMed". 2007.
  3. Ferreira, P.G.; Silva, C.G.; Brito, R.M.M.; Azevedo, P.J.. "A closer look on protein unfolding simulations through hierarchical clustering". 2007.
Journal article
  1. Moreno, Marta; Vilaça, Ricardo; Ferreira, Pedro G.. "Scalable transcriptomics analysis with Dask: applications in data science and machine learning". BMC Bioinformatics 23 1 (2022): http://dx.doi.org/10.1186/s12859-022-05065-3.
    10.1186/s12859-022-05065-3
  2. "Predicting Gastric Cancer Molecular Subtypes from Gene Expression Data". Proceedings 54 1 (2020): 59-59. http://dx.doi.org/10.3390/proceedings2020054059.
    10.3390/proceedings2020054059
  3. Ferreira, Pedro G.. "The GTEx Consortium atlas of genetic regulatory effects across human tissues.". Science (New York, N.Y.) (2020): https://europepmc.org/articles/PMC7737656.
    10.1126/science.aaz1776
  4. Ferreira, Pedro G.. "Gender Differential Transcriptome in Gastric and Thyroid Cancers.". Frontiers in genetics (2020): https://europepmc.org/articles/PMC7406663.
    10.3389/fgene.2020.00808
  5. 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
  6. Ferreira, Pedro G.. "Integrated Analysis of Structural Variation and RNA Expression of FGFR2 and Its Splicing Modulator ESRP1 Highlight the ESRP1amp-FGFR2norm-FGFR2-IIIchigh Axis in Diffuse Gastric Cancer.". Cancers (2019): https://europepmc.org/articles/PMC7017189.
    10.3390/cancers12010070
  7. Pedro G. Ferreira; Manuel Muñoz-Aguirre; Ferran Reverter; Caio P. Sá Godinho; Abel Sousa; Alicia Amadoz; Reza Sodaei; et al. "The effects of death and post-mortem cold ischemia on human tissue transcriptomes". Nature Communications 9 1 (2018): https://doi.org/10.1038/s41467-017-02772-x.
    10.1038/s41467-017-02772-x
  8. Aguet, F.; Brown, A.A.; Castel, S.E.; Davis, J.R.; He, Y.; Jo, B.; Mohammadi, P.; et al. "Genetic effects on gene expression across human tissues". Nature 550 7675 (2017): 204-213. http://www.scopus.com/inward/record.url?eid=2-s2.0-85031313737&partnerID=MN8TOARS.
    10.1038/nature24277
  9. Tukiainen, T.; Villani, A.-C.; Yen, A.; Rivas, M.A.; Marshall, J.L.; Satija, R.; Aguirre, M.; et al. "Landscape of X chromosome inactivation across human tissues". Nature 550 7675 (2017): 244-248. http://www.scopus.com/inward/record.url?eid=2-s2.0-85031299871&partnerID=MN8TOARS.
    10.1038/nature24265
  10. Tan, M.H.; Li, Q.; Shanmugam, R.; Piskol, R.; Kohler, J.; Young, A.N.; Liu, K.I.; et al. "Dynamic landscape and regulation of RNA editing in mammals". Nature 550 7675 (2017): 249-254. http://www.scopus.com/inward/record.url?eid=2-s2.0-85031298074&partnerID=MN8TOARS.
    10.1038/nature24041
  11. Bryois, J.; Buil, A.; Ferreira, P.G.; Panousis, N.I.; Brown, A.A.; Viñuela, A.; Planchon, A.; et al. "Time-dependent genetic effects on gene expression implicate aging processes". Genome Research 27 4 (2017): 545-552. http://www.scopus.com/inward/record.url?eid=2-s2.0-85017531409&partnerID=MN8TOARS.
    10.1101/gr.207688.116
  12. Li, X.; Kim, Y.; Tsang, E.K.; Davis, J.R.; Damani, F.N.; Chiang, C.; Hess, G.T.; et al. "The impact of rare variation on gene expression across tissues". Nature 550 7675 (2017): 239-243. http://www.scopus.com/inward/record.url?eid=2-s2.0-85031302505&partnerID=MN8TOARS.
    10.1038/nature24267
  13. Cummings, B.B.; Marshall, J.L.; Tukiainen, T.; Lek, M.; Donkervoort, S.; Foley, A.R.; Bolduc, V.; et al. "Improving genetic diagnosis in Mendelian disease with transcriptome sequencing". Science Translational Medicine 9 386 (2017): http://www.scopus.com/inward/record.url?eid=2-s2.0-85018570855&partnerID=MN8TOARS.
    10.1126/scitranslmed.aal5209
  14. Alves-Rodrigues, I.; Ferreira, P.G.; Moldón, A.; Vivancos, A.P.; Hidalgo, E.; Guigó, R.; Ayté, J.. "Spatiotemporal Control of Forkhead Binding to DNA Regulates the Meiotic Gene Expression Program". Cell Reports 14 4 (2016): 885-895. http://www.scopus.com/inward/record.url?eid=2-s2.0-84958123507&partnerID=MN8TOARS.
    10.1016/j.celrep.2015.12.074
  15. Ferreira, P.G.; Oti, M.; Barann, M.; Wieland, T.; Ezquina, S.; Friedländer, M.R.; Rivas, M.A.; et al. "Sequence variation between 462 human individuals fine-tunes functional sites of RNA processing". Scientific Reports 6 (2016): http://www.scopus.com/inward/record.url?eid=2-s2.0-84987596952&partnerID=MN8TOARS.
    10.1038/srep32406
  16. Arous, C.; Ferreira, P.G.; Dermitzakis, E.T.; Halban, P.A.. "Short term exposure of beta cells to low concentrations of interleukin-1ß improves insulin secretion through focal adhesion and actin remodeling and regulation of gene expression". Journal of Biological Chemistry 290 10 (2015): 6653-6669. http://www.scopus.com/inward/record.url?eid=2-s2.0-84925004057&partnerID=MN8TOARS.
    10.1074/jbc.M114.611111
  17. Arous, C.; Ferreira, P.G.; Dermitzakis, E.T.; Halban, P.A.. "Erratum: Short term exposure of beta cells to low concentrations of interleukin-1ß improves insulin secretion through focal adhesion and actin remodeling and regulation of gene expression (Journal of Biological Chemistr (2015) 290 (6653-6669))". Journal of Biological Chemistry 290 23 (2015): http://www.scopus.com/inward/record.url?eid=2-s2.0-84930660827&partnerID=MN8TOARS.
    10.1074/jbc.A114.611111
  18. Bassaganyas, L.; Beà, S.; Escaramís, G.; Tornador, C.; Salaverria, I.; Zapata, L.; Drechsel, O.; et al. "Corrigendum: Sporadic and reversible chromothripsis in chronic lymphocytic leukemia revealed by longitudinal genomic analysis". Leukemia 29 3 (2015): http://www.scopus.com/inward/record.url?eid=2-s2.0-84924408200&partnerID=MN8TOARS.
    10.1038/leu.2014.309
  19. Melé, M.; Ferreira, P.G.; Reverter, F.; DeLuca, D.S.; Monlong, J.; Sammeth, M.; Young, T.R.; et al. "The human transcriptome across tissues and individuals". Science 348 6235 (2015): 660-665. http://www.scopus.com/inward/record.url?eid=2-s2.0-84929015296&partnerID=MN8TOARS.
    10.1126/science.aaa0355
  20. Patalano, S.; Vlasova, A.; Wyatt, C.; Ewels, P.; Camara, F.; Ferreira, P.G.; Asher, C.L.; et al. "Molecular signatures of plastic phenotypes in two eusocial insect species with simple societies". Proceedings of the National Academy of Sciences of the United States of America 112 45 (2015): 13970-13975. http://www.scopus.com/inward/record.url?eid=2-s2.0-84946763289&partnerID=MN8TOARS.
    10.1073/pnas.1515937112
  21. Rivas, M.A.; Pirinen, M.; Conrad, D.F.; Lek, M.; Tsang, E.K.; Karczewski, K.J.; Maller, J.B.; et al. "Effect of predicted protein-truncating genetic variants on the human transcriptome". Science 348 6235 (2015): 666-669. http://www.scopus.com/inward/record.url?eid=2-s2.0-84929015299&partnerID=MN8TOARS.
    10.1126/science.1261877
  22. Ardlie, K.G.; DeLuca, D.S.; Segrè, A.V.; Sullivan, T.J.; Young, T.R.; Gelfand, E.T.; Trowbridge, C.A.; et al. "The Genotype-Tissue Expression (GTEx) pilot analysis: Multitissue gene regulation in humans". Science 348 6235 (2015): 648-660. http://www.scopus.com/inward/record.url?eid=2-s2.0-84929001104&partnerID=MN8TOARS.
    10.1126/science.1262110
  23. Borel, C.; Ferreira, P.G.; Santoni, F.; Delaneau, O.; Fort, A.; Popadin, K.Y.; Garieri, M.; et al. "Biased allelic expression in human primary fibroblast single cells". American Journal of Human Genetics 96 1 (2015): 70-80. http://www.scopus.com/inward/record.url?eid=2-s2.0-84920733410&partnerID=MN8TOARS.
    10.1016/j.ajhg.2014.12.001
  24. Greger, L.; Su, J.; Rung, J.; Ferreira, P.G.; Lappalainen, T.; Dermitzakis, E.T.; Brazma, A.. "Tandem RNA chimeras contribute to transcriptome diversity in human population and are associated with intronic genetic variants". PLoS ONE 9 8 (2014): http://www.scopus.com/inward/record.url?eid=2-s2.0-84940247886&partnerID=MN8TOARS.
    10.1371/journal.pone.0104567
  25. Ferreira, P.G.; Jares, P.; Rico, D.; Gómez-López, G.; Martínez-Trillos, A.; Villamor, N.; Ecker, S.; et al. "Transcriptome characterization by RNA sequencing identifies a major molecular and clinical subdivision in chronic lymphocytic leukemia". Genome Research 24 2 (2014): 212-226. http://www.scopus.com/inward/record.url?eid=2-s2.0-84893699492&partnerID=MN8TOARS.
    10.1101/gr.152132.112
  26. Ongen, H.; Andersen, C.L.; Bramsen, J.B.; Oster, B.; Rasmussen, M.H.; Ferreira, P.G.; Sandoval, J.; et al. "Putative cis-regulatory drivers in colorectal cancer". Nature 512 1 (2014): 87-90. http://www.scopus.com/inward/record.url?eid=2-s2.0-84905581513&partnerID=MN8TOARS.
    10.1038/nature13602
  27. Monlong, J.; Calvo, M.; Ferreira, P.G.; Guigó, R.. "Identification of genetic variants associated with alternative splicing using sQTLseekeR". Nature Communications 5 (2014): http://www.scopus.com/inward/record.url?eid=2-s2.0-84907346176&partnerID=MN8TOARS.
    10.1038/ncomms5698
  28. Ferreira, P.G.; Dermitzakis, E.T.. "Immune response is a personal matter". eLife 2013 2 (2013): http://www.scopus.com/inward/record.url?eid=2-s2.0-84880642705&partnerID=MN8TOARS.
    10.7554/eLife.00899
  29. Ferreira, P.G.; Patalano, S.; Chauhan, R.; Ffrench-Constant, R.; Gabaldón, T.; Guigó, R.; Sumner, S.. "Transcriptome analyses of primitively eusocial wasps reveal novel insights into the evolution of sociality and the origin of alternative phenotypes". Genome Biology 14 2 (2013): http://www.scopus.com/inward/record.url?eid=2-s2.0-84874214846&partnerID=MN8TOARS.
    10.1186/gb-2013-14-2-r20
  30. Lappalainen, T.; Sammeth, M.; Friedländer, M.R.; 'T Hoen, P.A.C.; Monlong, J.; Rivas, M.A.; Gonzàlez-Porta, M.; et al. "Transcriptome and genome sequencing uncovers functional variation in humans". Nature 501 7468 (2013): 506-511. http://www.scopus.com/inward/record.url?eid=2-s2.0-84885645853&partnerID=MN8TOARS.
    10.1038/nature12531
  31. Bava, F.-A.; Eliscovich, C.; Ferreira, P.G.; Miñana, B.; Ben-Dov, C.; Guigó, R.; Valcácel, J.; Méndez, R.. "CPEB1 coordinates alternative 3'-UTR formation with translational regulation". Nature 495 7439 (2013): 121-125. http://www.scopus.com/inward/record.url?eid=2-s2.0-84874732911&partnerID=MN8TOARS.
    10.1038/nature11901
  32. Bassaganyas, L.; Beà, S.; Escaramís, G.; Tornador, C.; Salaverria, I.; Zapata, L.; Drechsel, O.; et al. "Sporadic and reversible chromothripsis in chronic lymphocytic leukemia revealed by longitudinal genomic analysis". Leukemia 27 12 (2013): 2376-2379. http://www.scopus.com/inward/record.url?eid=2-s2.0-84890437212&partnerID=MN8TOARS.
    10.1038/leu.2013.127
  33. Plass, M.; Codony-Servat, C.; Ferreira, P.G.; Vilardell, J.; Eyras, E.. "RNA secondary structure mediates alternative 3'ss selection in Saccharomyces cerevisiae". RNA 18 6 (2012): 1103-1115. http://www.scopus.com/inward/record.url?eid=2-s2.0-84861390545&partnerID=MN8TOARS.
    10.1261/rna.030767.111
  34. Dunham, I.; Kundaje, A.; Aldred, S.F.; Collins, P.J.; Davis, C.A.; Doyle, F.; Epstein, C.B.; et al. "An integrated encyclopedia of DNA elements in the human genome". Nature 489 7414 (2012): 57-74. http://www.scopus.com/inward/record.url?eid=2-s2.0-84865790047&partnerID=MN8TOARS.
    10.1038/nature11247
  35. Djebali, S.; Davis, C.A.; Merkel, A.; Dobin, A.; Lassmann, T.; Mortazavi, A.; Tanzer, A.; et al. "Landscape of transcription in human cells". Nature 489 7414 (2012): 101-108. http://www.scopus.com/inward/record.url?eid=2-s2.0-84865757142&partnerID=MN8TOARS.
    10.1038/nature11233
  36. Vieira, J.; Ferreira, P.G.; Aguiar, B.; Fonseca, N.A.; Vieira, C.P.. "Evolutionary patterns at the RNase based gametophytic self - Incompatibility system in two divergent Rosaceae groups (Maloideae and Prunus)". BMC Evolutionary Biology 10 1 (2010): http://www.scopus.com/inward/record.url?eid=2-s2.0-77953954949&partnerID=MN8TOARS.
    10.1186/1471-2148-10-200
  37. Novoa, I.; Gallego, J.; Ferreira, P.G.; Mendez, R.. "Mitotic cell-cycle progression is regulated by CPEB1 and CPEB4-dependent translational control". Nature Cell Biology 12 5 (2010): 447-456. http://www.scopus.com/inward/record.url?eid=2-s2.0-77951978351&partnerID=MN8TOARS.
    10.1038/ncb2046
  38. Ferreira, P.G.; Azevedo, P.J.. "Evaluating deterministic motif significance measures in protein databases". Algorithms for Molecular Biology 2 1 (2007): http://www.scopus.com/inward/record.url?eid=2-s2.0-44449158817&partnerID=MN8TOARS.
    10.1186/1748-7188-2-16
Preprint
  1. Delora Baptista; Pedro G. Ferreira; Miguel Rocha. "A systematic evaluation of deep learning methods for the prediction of drug synergy in cancer". Preprint. 2022. https://doi.org/10.1101/2022.05.16.492054.
    10.1101/2022.05.16.492054
Activities

Oral presentation

Presentation title Event name
Host (Event location)
2018/05 Data Science na era da revolução dos dados / Data Science in the era of data revolution Invited talk at Supercomputing and Data Science Workshop.
(Braga)
2018/05 Large-scale data analysis for the characterization of human gene expression patterns across hundreds of individuals and dozens of tissues Invited Open Class at Universidade Nova de Lisboa
Universidade Nova de Lisboa (Lisboa, Portugal)
2018/03 Characterization of human gene expression patterns across hundreds of individuals and dozens of tissues Invited talk at Barcelona Supercomputing Center
Alfonso Valencia (Barcelona, Spain)
2017/09/15 Bioinformatics and Computational Biology: a personal perspective. Invited talk at University of Minho at 10th anniversary of the masters in Bioinformatics.
Miguel Rocha
2017/06 The human postmortem transcriptome across 36 tissues Invited talk at ICVS - Life and Health Sciences Research Institute
Rui Reis (Braga, Portugal)
2017/05 The life of genes after death: The human postmortem transcriptome across 36 tissues. Seminar Series at i3s.
(porto, Portugal)
2017/03 Large-scale data analysis for the characterization of human gene expression patterns across hundreds of individuals and dozens of tissues Invited talk at Department of Informatics at Instituto Superior Técnico
Ana Teresa Freitas (Lisboa, Portugal)
2016/07 Patterns of gene expression variation in human populations across tissues and individuals Invited talk at The Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute (EMBL-EBI)
Richard Durbin (Cambridge, United Kingdom)
2016/06 Patterns of gene expression variation in human populations across tissues and individuals: methods behind the scenes Invited talk at the 2nd Porto Meeting in Mathematics and Biology
Paulo Aguiar (Porto, Portugal)
2016/05 Poster presentation at the 29th Annual Meeting on The Biology of Genomes. Poster presentation at the 29th Annual Meeting on The Biology of Genomes.
(Cold Spring Harbor, United States)
2016/04 Patterns of gene expression variation in human populations across tissues and individuals Invited talk at 7th Symposium on Bioengineering organized by NEB-FEUP/ICBAS, FEUP
Students of Bioengineering Association (porto, Portugal)
2016/03 Patterns of gene expression variation in human populations across tissues and individuals Invited talk at 17th Meeting Portugaliae Genetica.
(porto, Portugal)

Supervision

Thesis Title
Role 		Degree Subject (Type)
Institution / Organization
2022 - 2026 Deepening the understanding of Alzheimer's disease risk and progression: a multimodal approach.
Co-supervisor
 Bioinformatics (PhD)
Universidade do Porto Faculdade de Ciências, Portugal
2021 - 2025 Integration of multi-modal genomics datasets with expert data: a patient centered approach to improve diagnosis and prognosis (2021.07092.BD).
Supervisor
 Bioinformatics (PhD)
Universidade do Porto Faculdade de Ciências, Portugal
2021 - 2025 BioPredictor: a tool to predict the outcome of molecular alterations (SFRH/BD/05763/2020).
Co-supervisor
 Bioinformatics (PhD)
Universidade do Porto Faculdade de Ciências, Portugal
2022 - 2023 Exploring the Human Phenotype-Gene Network
Supervisor
 Bioinformática e Biologia Computacional (Master)
Universidade do Porto Faculdade de Ciências, Portugal
2022 - 2023 A multi-caller pipeline to maximize the output of somatic exome sequencing analysis
Co-supervisor
 Bioinformática e Biologia Computacional (Master)
Universidade do Porto Faculdade de Ciências, Portugal
2022 - 2023 Novos Antídotos para o Veneno da Víbora Terciopelo
Co-supervisor
 Bioinformática e Biologia Computacional (Master)
Universidade do Porto Faculdade de Ciências, Portugal
2019 - 2023 Transcriptomics-based prediction of human phenotypes using scalable and secure machine learning approaches (SFRH/BD/145707/2019).
Supervisor
 Bioinformatics (PhD)
Universidade do Porto Faculdade de Ciências, Portugal
2019 - 2023 Towards a Modular and Scalable Privacy-preserving Machine Learning Framework (SFRH/BD/146528/2019).
Co-supervisor
 Informatics (PhD)
Universidade do Minho, Portugal
2021 - 2022 Understanding the impact of Mycobacterium tuberculosis complex diversity in tuberculosis
Co-supervisor
 Bioinformática e Biologia Computacional (Master)
Universidade do Porto Faculdade de Ciências, Portugal
2021 - 2022 Modelling and Predicting Acute Ischaemic Stroke Outcomes
Co-supervisor
 Bioinformática e Biologia Computacional (Master)
Universidade do Porto Faculdade de Ciências, Portugal
2021 - 2022 RISK - New RNA signatures of therapy evasion in Cancer
Co-supervisor
 Bioinformática e Biologia Computacional (Master)
Universidade do Porto Faculdade de Ciências, Portugal
2017 - 2022 A framework for predicting drug sensitivity and synergy in cancer cells using deep learning
Co-supervisor
 Informatics (PhD)
2020 - 2021 Analysis and comparison tool for multiple variant calling results from germline NGS data with clinical applications
Co-supervisor
 Bioinformática e Biologia Computacional (Master)
Universidade do Porto Faculdade de Ciências, Portugal
2020 - 2021 NRfinder: A pipeline for the characterization of the number and type of nuclear receptors in a genomic sequence
Co-supervisor
 Bioinformática e Biologia Computacional (Master)
Universidade do Porto Faculdade de Ciências, Portugal
2020 - 2021 A model validation pipeline for healthy tissue genome-scale metabolic models.
Co-supervisor
 Bioinformática (Master)
Universidade do Minho, Portugal
2020 - 2021 Developing deep learning methods to predict phenotypes and clinical outcomes from transcriptomics data
Co-supervisor
 Bioinformática (Master)
Universidade do Minho, Portugal
2017 - 2021 Study of control of protein abundance using multi-omics data from cancer samples
Supervisor
 Biomedical / Bioinformatics (PhD)
Universidade do Porto Instituto de Ciências Biomédicas Abel Salazar, Portugal
2019 - 2020 Evaluating clustering and high- dimensionality reduction techniques for genomics data.
Supervisor
 Bioinformática e Biologia Computacional (Master)
Universidade do Porto Faculdade de Ciências, Portugal
2019 - 2020 Data analysis of clinical datasets to support laboratory diagnostics using machine learning.
Supervisor
 Ciência de Dados (Data Science) (Master)
Universidade do Porto Faculdade de Ciências, Portugal
2019 - 2020 HSA/CD42: a cardiomyocyte precursor biomarker and/or a gateway to cardiomyogenesis.
Co-supervisor
 Bioinformática e Biologia Computacional (Master)
Universidade do Porto Faculdade de Ciências, Portugal
2019 - 2020 Neoantigen Signature Automatized Pipeline to predict Immunotherapy response
Supervisor
 Bioinformática e Biologia Computacional (Master)
Universidade do Porto Faculdade de Ciências, Portugal
2017 - 2018 Implementation and comparison of computational pipelines for variant calling in sequencing data
Supervisor
 Bioinformática (Master)
Universidade do Minho, Portugal
2017 - 2018 Mining cancer genomic data with Probabilistic Logic Programming
Supervisor
 Bioinformática (PhD)
Universidade do Minho, Portugal
2017 - 2018 Pathogen identification in human cancer cells
Co-supervisor
 Engenharia Informática e Computação (Master)
Universidade do Porto Faculdade de Engenharia, Portugal
2017 - 2018 Sentiment analysis from medical records
Co-supervisor
 Engenharia Informática (Master)
Universidade do Minho, Portugal
2016 - 2017 Developing Deep Learning tools for cancer using omics data
Co-supervisor
 Bioinformática (Master)
Universidade do Minho, Portugal
2016 - 2017 Deep Learning for genomic data analysis
Co-supervisor
 Engenharia Informática e Computação (Master)
Universidade do Porto Faculdade de Engenharia, Portugal
2016 - 2016 Post-doc fellowship from the José Castillejo program for Spanish young doctors
Supervisor
 Bioinformatics (Other)
Universidade do Porto Instituto de Patologia e Imunologia Molecular, Portugal
2015 - 2016 Análise de padrões em dados genómicos multi- plataforma disponíveis pelo TCGA.
Supervisor
 Bioinformática (Master)
Universidade do Minho, Portugal
2015 - 2016 Identification of pathogens in human cell cancers
Co-supervisor
 Engenharia Informática e Computação (Master)
Universidade do Porto Faculdade de Engenharia, Portugal
2015 - 2016 Assessing the impact of alternative splicing in thyroid cancer
Co-supervisor
 Engenharia Informática e Computação (Master)
Universidade do Porto Faculdade de Engenharia, Portugal
2014 - 2015 A Computational platform for assessing the impact of alternative splicing in cancer
Co-supervisor
 Engenharia Informática e Computação
Universidade do Porto Faculdade de Engenharia, Portugal

Conference scientific committee

Conference name Conference host
2021/04 - Current 10th International Conference on Data Science, Technology and Applications (DATA 2021)
2021/03 - Current 30th International Joint Conference on Artificial Intelligence
2021/03 - Current 7th-8th International Conference on Algorithms for Computational Biology (AlCoB 2020 & 2021)
2021 - Current 13th International Conference on Knowledge Discovery and Information Retrieval (KDIR 2021)
2021 - Current European Society of Human Genetics (Bioinformatics and Computational methods section; 2016 & 2017 & 2021)
2018 - Current Technical Committee (Data Science) and Reviewer for Inforum (2018)
2017 - Current IEEE International Conference on Data Science and Advanced Analytics (2017)
2017 - Current Technical Committee and Reviewer for International Conference on Computational Chemistry and Biology (2017)
2009 - Current 6th International Meeting Computational Intelligence Methods for Bioinformatics and Biostatistics
2017 - 2021 International Conference on Practical Applications of Computational Biology & Bioinformatics

Evaluation committee

Activity description
Role 		Institution / Organization Funding entity
2022 - 2022 Reviewer for FCT and Google Initiative for AI in Portugal (CPCA-IAC)
Evaluator
 Rede Nacional de Computação Avançada, Portugal
2021 - 2021 Call on Advanced Computing Projects (2nd edition)
Evaluator
 Rede Nacional de Computação Avançada, Portugal
2020/05 - 2020/06 Reviewer for the Portuguese Agency for Evaluation and Accreditation of Higher Education of three proposals on Master Courses submitted by Portuguese Universities (2020).
Evaluator
2013 - 2013 Post-Doctoral Return programme, for young post-doc researchers returning to France, from the Agence Nationale de Recherche, France, 2013
Evaluator
 Agence nationale de la recherche, France

Journal scientific committee

Journal title (ISSN) Publisher
2021/01/04 - Current Knowledge and Information Systems Springer
2021 - Current ACM Transactions on Intelligent Systems and Technology
2020 - Current Cancers MDPI
2017/01/01 - Current PeerJ PerrJ Publishing
Distinctions

Award

2019 Best Paper Award
2016 Best work (on other tumors category) on the Symposium of the Portuguese Society of Oncology
2015 Basic Research Award 2015
2015 2nd place on EU SME eHealth Competition (Part of the team at Coimbra Genomics that developed award-winning system ELSIE©)
2002 Prémio de Mérito Escolar
Universidade do Minho, Portugal
2002 Bolsa de estudo por Mérito Escolar
2001 Prémio de Mérito Escolar
Universidade do Minho, Portugal
2000 Prémio de Mérito Escolar
Universidade do Minho, Portugal
2000 2º lugar ”O Comércio Tradicional no trilho do Comércio Electrónico”
1999 Prémio de Mérito Escolar
Universidade do Minho, Portugal

Other distinction

2020 5 Highly cited papers according to Web of Science
2020 1 Paper in Hot papers in field according to Web of Science
2020 3 Recommended papers for special significance in the field
2019 Paper among top-50 most accessed papers in Nature Comminations
2017 Azure for Research Award: Data Science
Microsoft Research, United States
2015 FCT Investigator Starting Grant 2014 [IF/01127/2014]
Fundação para a Ciência e a Tecnologia, Portugal
2014 F1000Prime (recommended by the F1000Prime Faculty as being of special significance)
2007 Bolsa de apresentação em conferência
IEEE Computational Intelligence Society, United States