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Engineering and biotechnology background. Over the years, I have moved between ’wet-’ and ’dry-lab’ environments, and prioritized efforts in acquiring a unique expertise in the broad fields of genomics and genome dynamics. My current interests are on identifying emerging challenges in the relatively young research field of epigenomics, and on developing novel methods that can fundamentally address these challenges. My long term goal is to obtain biological insights that can be translated into more accurate disease diagnosis and more effective treatment for certain bacterial pathogens.
Identification

Personal identification

Full name
Pedro Henrique Couto Oliveira

Citation names

  • Oliveira, PH

Author identifiers

Ciência ID
EE15-8FA6-CD75
ORCID iD
0000-0003-3161-8367

Websites

Knowledge fields

  • Engineering and Technology - Industrial Biotechnology
  • Natural sciences - Biological Sciences
  • Exact Sciences - Computer and Information Sciences

Languages

Language Speaking Reading Writing Listening Peer-review
Portuguese Advanced (C1) Advanced (C1) Advanced (C1) Advanced (C1)
English Advanced (C1) Advanced (C1) Advanced (C1) Advanced (C1)
French Intermediate (B1) Intermediate (B1) Intermediate (B1) Intermediate (B1)
Spanish; Castilian Beginner (A1) Intermediate (B1) Beginner (A1) Beginner (A1)
Chinese Beginner (A1) Intermediate (B1) Beginner (A1) Beginner (A1)
Education
Degree Classification
2006 - 2010
Concluded
 Biotecnologia (Doutoramento)
Universidade de Lisboa, Portugal
"Structural Instability in Plasmid Biopharmaceuticals" (THESIS/DISSERTATION)
 Aprovado
2008 - 2009
Concluded
 Bioengineering (Outros)
Massachusetts Institute of Technology, United States
2005 - 2005
Concluded
 Bioengineering (Outros)
University of London, United Kingdom
1999 - 2005
Concluded
 Engenharia Biológica (Licenciatura)
Universidade de Lisboa, Portugal
 16
Affiliation

Science

Category
Host institution 		Employer
2016/10/01 - Current Principal Investigator (Research) Icahn School of Medicine at Mount Sinai, United States
2013/01 - 2016 Postdoc (Research) Institut Pasteur, France
2010 - 2012/12/31 Postdoc (Research) Universidade de Lisboa Instituto Superior Técnico Campus Taguspark, Portugal
Outputs

Publications

Book chapter
  1. Oliveira, PH. "DNA instability in bacterial genomes: causes and consequences". In Genome Analysis: Current Procedures and Applications, 261-284. UK, United Kingdom: Horizon Press, 2014.
    Published
  2. Oliveira, PH; Prazeres, Duarte M. F.; Monteiro, Gabriel A.. "Structural and segregational instability in plasmid biology". In Plasmids: Genetics, Applications and Health, 79-100. NY, United States: Nova Publishers, 2012.
    Published
  3. João Carlos Marcos; Oliveira, PH. "Biofármacos: Desafios e Limitações". In Conversas com Ciência, 63-65. Braga, Portugal, Portugal: Escola de Ciências da Universidade do Minho, 2012.
    Published
Conference paper
  1. Oliveira, Pedro H.; Boura, Joana S.; Abecasis, Manuel M.; da Silva, Claudia Lobato; Cabral, Joaquim M. S.. "An appraisal of genetic stability in human mesenchymal stem cells". Paper presented in 2011 1st Portuguese Meeting in Bioengineering ¿ The Challenge of the XXI Century (ENBENG), Lisbon, Portugal, 2011.
    Published • 10.1109/ENBENG.2011.6026040
Conference poster
  1. Oliveira, PH; Touchon, M.; Rocha, E. P. C.. "Genetic mobility and the distribution of restriction modification systems in prokaryotes". Paper presented in EMBO Conference on Microbiology after the Genomics Revolution: Genomes 2014, 2014.
  2. Oliveira, PH; Touchon, M.; Rocha, E. P. C.. "Genetic mobility and the distribution of restriction modification systems in prokaryotes". Paper presented in 13th European Conference on Computational Biology (ECCB 2014) (Selected for F1000 Posters), 2014.
  3. Oliveira, PH; Boura, Joana S.; Abecasis, Manuel M.; Gimble, Jeffrey M.; da Silva, Cláudia Lobato; Cabral, Joaquim M.S.. "Effect of hypoxia and long-term culture on the genomic stability and mitochondrial performance of human mesenchymal stem cells expanded in vitro for clinical applications". Paper presented in 15th European Congress on Biotechnology-Biocrossroads, 2012.
  4. Gomes, A.G.; Oliveira, PH. "Comparative genomic analysis indicates strand compositional asymmetries as regional landmarks in plasmid evolution". Paper presented in 15th European Congress on Biotechnology-Biocrossroads, 2012.
  5. Oliveira, PH; Gonçalves, G.A.L.; Lewis, Leslie A; Prazeres, Duarte M. F.; Monteiro, Gabriel A. "Preferential transposition of the mobile element IS2 into AT- and GC-skew polarity switches". Paper presented in 15th European Congress on Biotechnology-Biocrossroads, 2012.
  6. Gonçalves, G.A.L.; Oliveira, PH; Lewis, Leslie A; Prazeres, Duarte M. F.; Monteiro, Gabriel A.. "Identification of IS2 transposition in pVAX1-based plasmid, a common vector for DNA vaccine development". Paper presented in 15th European Congress on Biotechnology-Biocrossroads, 2012.
  7. Oliveira, PH; Boura, Joana S.; Abecasis, Manuel M.; Gimble, J.; da Silva, Claudia Lobato; Cabral, Joaquim M. S.. "An appraisal of genetic stability during the ex-vivo expansion of human mesenchymal stem cells". Paper presented in 11th International Symposium on Mutations in the Genome, 2011.
  8. Oliveira, PH; da Silva, Claudia Lobato; Cabral, Joaquim M. S.. "Unusual DNA structures and instability motifs correlate with human mitochondrial deletion breakpoints involved in genetic disorders and cancer". Paper presented in 11th International Symposium on Mutations in the Genome, 2011.
  9. Lopes, G.; Oliveira, Pedro H.; Prather, Kristala L. J.; Prazeres, Duarte M. F.; Monteiro, Gabriel A.. "Rational engineering of E. coli strains and vectors for improved manufacturing of plasmid biopharmaceuticals". Paper presented in 2nd MIT-Portugal Annual Conference: Creating Value through Systems Thinking, 2010.
  10. Monteiro, Gabriel A.; Prazeres, Duarte M. F.; Fonseca, L.P.; Martins, S.; Oliveira, Pedro H.; Azzoni, A.; Lima, J.. "Quality control and monitoring of plasmid biopharmaceuticals". Paper presented in Ist Scientific Meeting of the Institute for Biotechnology and Bioengineering (IBB), 2009.
  11. Monteiro, Gabriel A.; Prazeres, Duarte M. F.; Azzoni, A.; Ribeiro, Sofia C.; Carvalho, J.; Oliveira, Pedro H.; Freitas, S.; et al. "Design and stability of plasmid vectors". Paper presented in Ist Scientific Meeting of the Institute for Biotechnology and Bioengineering (IBB), 2009.
  12. Oliveira, PH; Prather, Kristala L. J.; Prazeres, Duarte M.F.; Monteiro, Gabriel A.. "Rational engineering of E. coli strains and vectors for improved manufacturing of plasmid biopharmaceuticals". Paper presented in 1st MIT-Portugal Annual Conference: Engineering for Better Jobs, 2009.
  13. Oliveira, PH; Prazeres, Duarte M. F.; Monteiro, Gabriel A.. "Hotspots for recombination are widespread among plasmid vectors". Paper presented in 3rd FEMS congress, 2009.
  14. Oliveira, PH; Prather, Kristala Jones; Prazeres, Duarte M. F.; Monteiro, Gabriel A.. "Genome-wide analysis of DNA repeats in bacterial plasmids identifies genetically unstable hotspots and candidate regions for minimization". Paper presented in 8th European Symposium on Biochemical Engineering Science (ESBES), 2009.
  15. Oliveira, PH; Prazeres, Duarte M.F.; Monteiro, Gabriel A.. "Plasmid DNA instability mediated by direct repeats and type-2 insertion sequences". Paper presented in EMBO conference Recombination Mechanisms, 2008.
  16. Oliveira, PH; Prazeres, Duarte M. F.; Monteiro, Gabriel A.. "Plasmid recombination by direct repeats and type 2 insertion sequences". Paper presented in XIIIrd MicroBiotec, 2007.
  17. Oliveira, PH; Marques, Marco P.C.; Santos, Ricardo; Claudino, M.; Monteiro, Gabriel A.; Cabral, J.M.S.. "Searching for a multipurpose Mycobacterium". Paper presented in XIIIrd MicroBiotec, 2007.
  18. Oliveira, PH; Nunes, S.C.; Ribeiro, Sofia C.; Prazeres, Duarte M. F.; Monteiro, Gabriel A.. "Kanamycin-induced recombination in E. coli cells harbouring plasmids with direct repeats". Paper presented in 32nd FEBS Congress – Molecular Machines, 2007.
  19. Oliveira, PH; Ribeiro, Sofia C.; Prazeres, Duarte M. F.; Monteiro, Gabriel A.. "Deletions in Escherichia coli plasmids harbouring direct repeats – Environmental factors and the adaptive response". Paper presented in XVth National Congress of Biochemistry, 2006.
  20. Oliveira, PH; Linde, E.; Baganz, F.; Ward, J.; Krabben, P.. "From genome to improved antibiotic production by Saccharopolyspora erythraea". Paper presented in ExGen - Exploiting Genomics Grant Holders, 2006.
  21. Aleixo, Ana I.; Oliveira, Pedro H.; Diogo, Hermínio P.; Minas da Piedade, Manuel E.. "Enthalpies of formation of alkaline metal acetates". Paper presented in 6th Mediterranean Conference on Calorimetry and Thermal Analysis, 2003.
Journal article
  1. Pedro H. Oliveira; Marie Touchon; Jean Cury; Eduardo P. C. Rocha. "Author Correction: The chromosomal organization of horizontal gene transfer in bacteria". Nature Communications (2020): https://doi.org/10.1038/s41467-020-15091-5.
    10.1038/s41467-020-15091-5
  2. Pedro H. Oliveira; Gang Fang. "Conserved DNA Methyltransferases: A Window into Fundamental Mechanisms of Epigenetic Regulation in Bacteria". Trends in Microbiology (2020): https://doi.org/10.1016/j.tim.2020.04.007.
    10.1016/j.tim.2020.04.007
  3. Pedro H. Oliveira; John W. Ribis; Elizabeth M. Garrett; Dominika Trzilova; Alex Kim; Ognjen Sekulovic; Edward A. Mead; et al. "Epigenomic characterization of Clostridioides difficile finds a conserved DNA methyltransferase that mediates sporulation and pathogenesis". Nature Microbiology (2020): https://doi.org/10.1038/s41564-019-0613-4.
    10.1038/s41564-019-0613-4
  4. Cury J; Oliveira PH; de la Cruz F; Rocha EPC. "Host range and genetic plasticity explain the co-existence of integrative and extrachromosomal mobile genetic elements.". Molecular biology and evolution (2018): http://europepmc.org/abstract/med/29905872.
    10.1093/molbev/msy123
  5. Oliveira, Pedro H; Touchon, Marie; Cury, Jean; Rocha, Eduardo P. C.. "The chromosomal organization of horizontal gene transfer in bacteria". Nature Communications 8 1 (2017): 1-11. https://www.nature.com/articles/s41467-017-00808-w.
    Published • 10.1038/s41467-017-00808-w
  6. Oliveira, Pedro H; Touchon, Marie; Rocha, Eduardo P. C.. "Regulation of genetic flux between bacteria by restriction–modification systems". Proceedings of the National Academy of Sciences XX (2016): 201603257-201603257. www.pnas.org/cgi/doi/10.1073/pnas.1603257113.
    Published • 10.1073/pnas.1603257113
  7. Oliveira, Pedro H; Silva, Cláudia Lobatoda; Cabral, Joaquim M. S.. "Genomic instability in human stem cells: Current status and future challenges". STEM CELLS 32 11 (2014): 2824-2832. http://onlinelibrary.wiley.com/doi/10.1002/stem.1796/abstract.
    Published • 10.1002/stem.1796
  8. Gonçalves, Geisa A. L.; Oliveira, Pedro H; Gomes, Ana G.; Prather, Kristala L. J.; Lewis, Leslie A; Prazeres, Duarte M. F.; Monteiro, Gabriel A. "Evidence that the insertion events of IS2 transposition are biased towards abrupt compositional shifts in target DNA and modulated by a diverse set of culture parameters". Applied Microbiology and Biotechnology 98 15 (2014): 6609-6619. http://link.springer.com/article/10.1007%2Fs00253-014-5695-6.
    Published • 10.1007/s00253-014-5695-6
  9. Oliveira, P. H.; Touchon, M.; Rocha, E. P. C.. "The interplay of restriction-modification systems with mobile genetic elements and their prokaryotic hosts". Nucleic Acids Research 42 16 (2014): 10618-10631. http://www.ncbi.nlm.nih.gov/pubmed/25120263.
    Published • 10.1093/nar/gku734
  10. Oliveira, Pedro H.; Lobato da Silva, Cláudia; Cabral, Joaquim M. S.. "An Appraisal of Human Mitochondrial DNA Instability: New Insights into the Role of Non-Canonical DNA Structures and Sequence Motifs". PLoS ONE 8 3 (2013): e59907-e59907. http://dx.plos.org/10.1371/journal.pone.0059907.
    Published • 10.1371/journal.pone.0059907
  11. Oliveira, Pedro H; Mairhofer, Juergen. "Marker-free plasmids for biotechnological applications – implications and perspectives". Trends in Biotechnology 31 9 (2013): 539-547. http://www.ncbi.nlm.nih.gov/pubmed/23830144.
    Published • 10.1016/j.tibtech.2013.06.001
  12. Lewis, Leslie A; Astatke, Mekbib; Umekubo, Peter T; Alvi, Shaheen; Saby, Robert; Afrose, Jehan; Oliveira, Pedro H; Monteiro, Gabriel A; Prazeres, Duarte M. F.. "Protein-DNA Interactions Define the Mechanistic Aspects of Circle formation and Insertion Reactions in IS2 Transposition". Mobile DNA 3 1 (2012): 1-1. http://www.mobilednajournal.com/content/3/1/1.
    Published • 10.1186/1759-8753-3-1
  13. Oliveira, Pedro H.; Boura, Joana S.; Abecasis, Manuel M.; Gimble, Jeffrey M.; da Silva, Cláudia Lobato; Cabral, Joaquim M.S.. "Impact of hypoxia and long-term cultivation on the genomic stability and mitochondrial performance of ex vivo expanded human stem/stromal cells". Stem Cell Research 9 3 (2012): 225-236. http://www.sciencedirect.com/science/article/pii/S1873506112000694.
    Published • 10.1016/j.scr.2012.07.001
  14. Borlido, L.; Azevedo, A.M.; Sousa, A.G.; Oliveira, P.H.; Roque, A.C.A.; Aires-Barros, M.R.. "Fishing human monoclonal antibodies from a CHO cell supernatant with boronic acid magnetic particles". Journal of Chromatography B 903 1 (2012): 163-170. http://www.sciencedirect.com/science/article/pii/S1570023212004151.
    Published • 10.1016/j.jchromb.2012.07.014
  15. Oliveira, Pedro H.; Prather, Kristala L. J.; Prazeres, Duarte M. F.; Monteiro, Gabriel A.. "Mutation detection in plasmid-based biopharmaceuticals". Biotechnology Journal 6 4 (2011): 378-391. http://onlinelibrary.wiley.com/doi/10.1002/biot.201000372/abstract.
    Published • 10.1002/biot.201000372
  16. Oliveira, Pedro H.; Prather, Kristala Jones; Prazeres, Duarte M. F.; Monteiro, Gabriel A.. "Analysis of DNA repeats in bacterial plasmids reveals the potential for recurrent instability events". Applied Microbiology and Biotechnology 87 6 (2010): 2157-2167. http://rd.springer.com/article/10.1007/s00253-010-2671-7.
    Published • 10.1007/s00253-010-2671-7
  17. Oliveira, Pedro H.; Prather, Kristala Jones; Prazeres, Duarte M.F.; Monteiro, Gabriel A.. "Structural instability of plasmid biopharmaceuticals: challenges and implications". Trends in Biotechnology 27 9 (2009): 503-511. http://www.sciencedirect.com/science/article/pii/S0167779909001164.
    Published • 10.1016/j.tibtech.2009.06.004
  18. Oliveira, Pedro H.; Prazeres, Duarte M.F.; Monteiro, Gabriel A.. "Deletion formation mutations in plasmid expression vectors are unfavored by runaway amplification conditions and differentially selected under kanamycin stress". Journal of Biotechnology 143 4 (2009): 231-238. http://www.ncbi.nlm.nih.gov/pubmed/19665504.
    Published • 10.1016/j.jbiotec.2009.08.002
  19. Ribeiro, Sofia C.; Oliveira, Pedro H.; Prazeres, Duarte M. F.; Monteiro, Gabriel A.. "High Frequency Plasmid Recombination Mediated by 28 bp Direct Repeats". Molecular Biotechnology 40 3 (2008): 252-260. http://link.springer.com/article/10.1007%2Fs12033-008-9082-3?LI=true.
    Published • 10.1007/s12033-008-9082-3
  20. Oliveira, Pedro H.; Lemos, Francisco; Monteiro, Gabriel A.; Prazeres, Duarte M.F.. "Recombination frequency in plasmid DNA containing direct repeats—predictive correlation with repeat and intervening sequence length". Plasmid 60 2 (2008): 159-165. http://www.sciencedirect.com/science/article/pii/S0147619X08000590.
    Published • 10.1016/j.plasmid.2008.06.004
  21. Oliveira, P.H.; Batagov, A.; Ward, J.; Baganz, F.; Krabben, P.. "Identification of erythrobactin, a hydroxamate-type siderophore produced by Saccharopolyspora erythraea". Letters in Applied Microbiology 42 4 (2006): 375-380. http://onlinelibrary.wiley.com/doi/10.1111/j.1472-765X.2006.01849.x/full.
    Published • 10.1111/j.1472-765X.2006.01849.x
  22. Aleixo, Ana I.; Oliveira, Pedro H.; Diogo, Hermínio P.; Minas da Piedade, Manuel E.. "Enthalpies of formation and lattice enthalpies of alkaline metal acetates". Thermochimica Acta 428 1-2 (2005): 131-136. http://www.sciencedirect.com/science/article/pii/S0040603104004988.
    Published • 10.1016/j.tca.2004.11.004
Activities

Oral presentation

Presentation title Event name
Host (Event location)
2015 Restriction-modification systems as key players in horizontal gene transfer and genome diversification 7th New England Biolabs (NEB) Meeting
New England Biolabs (NEB) (Poland, Poland)
2013 A comparative genomics approach provides new insights into the distribution and evolutionary history of restriction modification systems in bacteria Annual Meeting of the Society for Molecular Biology and Evolution
(Chicago, United States)
2013 Mechanistic definition of IS2 transposition and the basis for its non-random insertional specificity in relevant DNA-based biopharmaceuticals.
(China)
2012 Biological Reactors in Health and Biotechnology
(Portugal)
2012 An appraisal of human mtDNA instability: role of DNA topology and composition 3rd Scientific Meeting of the Institute for Biotechnology and Bioengineering
(Lisbon, Portugal)
2012 An appraisal of human mtDNA instability: role of DNA topology and sequence motifs 15th European Congress on Biotechnology-Biocrossroads
(Istanbul, Turkey)
2011 An appraisal of genetic stability in human mesenchymal stem cells 1st Portuguese Meeting in Bioengineering
(Lisbon, Portugal)
2011 Genetic stability during the ex-vivo expansion of human mesenchymal stem cells for clinical applications 6th International Meeting of the Portuguese Society for Stem Cells and Cellular Therapy (SPCE-TC)
(Cantanhede, Portugal)
2010 Structural instability in plasmid biopharmaceuticals for DNA vaccination 2nd Scientific Meeting of the Institute for Biotechnology and Bioengineering
(Braga, Portugal)
2010 Bias in human mitochondrial DNA repeat distribution correlates with common deletion/amplification breakpoints involved in genetic disorders and cancer 5th International Meeting of the Portuguese Society for Stem Cells and Cellular Therapy (SPCE-TC)
(Guimarães, Portugal)
2009 Structural instability in plasmid vectors for DNA vaccination MicroBiotec 2009
(Vilamoura, Portugal)
2009 The sunny side of mycobacteria 30th Annual Congress of the European Society of Mycobacteriology
(Porto, Portugal)
2009 III International Conference on Environmental, Industrial and Microbial Biotechnology (BioMicroWorld) III International Conference on Environmental, Industrial and Microbial Biotechnology (BioMicroWorld)
(Lisbon, Portugal)
2006 Stress-induced mutation in E. coli cells harbouring plasmids with direct repeats – The adaptive response 31st FEBS Congress – Molecules in health and disease
(Istanbul, Turkey)
2005 Exploring the substrate spectrum of the antibiotic producing bacteria Saccharopolyspora erythraea 12th European Congress on Biotechnology
(Copenhagen, Denmark)

Event participation

Activity description
Type of event 		Event name
Institution / Organization
2014 - 2014 Genetic mobility and the distribution of restriction modification systems in prokaryotes
Meeting
 Department Days of Institut Pasteur
Institut Pasteur, France
2013 - 2013 Mechanistic definition of IS2 transposition and the basis for its non-random insertional specificity in relevant DNA-based biopharmaceuticals
Congress
 3rd Annual World Congress of Molecular and Cell Biology
2011 - 2011 Biofármacos: Desafios e Limitações
Round table
 Tertúlias FNACiência
2011 - 2011 Da sala de aula ao laboratório – Uma experiência na primeira pessoa
Conference
 Jornadas de Engenharia Química e Biológica (JEQB)
Instituto Superior Técnico, Portugal

Journal scientific committee

Journal title (ISSN) Publisher
2012/02/01 - Current Biotechnology Research International
Current Pharmaceutica Analytica Acta
Current Acta Biomaterialia
Current Food Technology and Biotechnology
Current PLoS ONE
Current Cell Death and Differentiation
Current BMC Genomics
Current Cell and Tissue Research
Current FEMS Microbiology Letters
Current Nucleic Acids Research
Current Bioinformatics
Current Scientific Reports
Current Biomed Research International
Distinctions

Other distinction

2010 Top-Cited Article
Elsevier, Portugal