Jorge dos Santos Oliveira (B815-6E71-E324)

Curriculum Vitae

Jorge dos Santos Oliveira

JORGE DOS SANTOS OLIVEIRA. Completed the Mestrado integrado in Engenharia Biológica in 2013 by Universidade de Lisboa Instituto Superior Técnico and Doutoramento in PhD in Biotechnology from Northeast Biotechnology Network Program (RENORBIO) in 2018/05/31 by Universidade Federal do Rio Grande do Norte. Is Chief Technical Officer - Technical Coordinator in BioData.pt, Invited Assistant Professor in Universidade de Lisboa Instituto Superior Técnico and Researcher in Instituto de Engenharia de Sistemas e Computadores Investigação e Desenvolvimento em Lisboa. Currently is focused on several health data related projects, namely the EU Digital Europe Funded Genomic Data Infrastructure where he is responsible for the technical implementation of the infrastructure in Portugal.

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Identification

Personal identification

Full name: Jorge dos Santos Oliveira
Gender: Male

Citation names

OLIVEIRA, JORGE

Author identifiers

Ciência ID: B815-6E71-E324
ORCID iD: 0000-0001-6425-2176

Email addresses

jorge.oliveira@tecnico.ulisboa.pt (Professional)

Websites

biodata.pt (Professional)
https://web.tecnico.ulisboa.pt/jorge.oliveira/ (Personal)

Knowledge fields

Exact Sciences - Computer and Information Sciences - Bioinformatics
Engineering and Technology

Languages

Language	Speaking	Reading	Writing	Listening	Peer-review
Portuguese (Mother tongue)
English	Proficiency (C2)	Proficiency (C2)	Proficiency (C2)	Proficiency (C2)	Proficiency (C2)
Spanish; Castilian	Upper intermediate (B2)	Advanced (C1)	Advanced (C1)	Advanced (C1)	Beginner (A1)

Education

	Degree	Classification
2022/01 - 2022/10 Concluded	Executive Masters in Management of Research Infrastructures (Pós-Graduação) Università degli Studi di Milano-Bicocca, Italy
2015/05/01 - 2018/05/31 Concluded	PhD in Biotechnology from Northeast Biotechnology Network Program (RENORBIO) (Doutoramento) Major in Biotechnology in Natural Resources Universidade Federal do Rio Grande do Norte, Brazil "Prospection of genes related to hydrocarbon biodegradation and surfactant production using computational approaches" (THESIS/DISSERTATION)
2013 Concluded	Engenharia Biológica (Mestrado integrado) Major in Bioinformática Universidade de Lisboa Instituto Superior Técnico, Portugal "Identification of microRNAs and analysis of their expression in Eucalyptus globulus" (THESIS/DISSERTATION)

Affiliation

Science

	Category Host institution	Employer
2023/01/01 - Current	Researcher (Research)	Instituto de Engenharia de Sistemas e Computadores Investigação e Desenvolvimento em Lisboa, Portugal

2018/06/01 - 2021/06/30	Postdoc (Research)	Instituto de Engenharia de Sistemas e Computadores Investigação e Desenvolvimento em Lisboa, Portugal
	Instituto de Engenharia de Sistemas e Computadores Investigação e Desenvolvimento em Lisboa, Portugal
2015 - 2018	Researcher (Research)	Universidade Federal do Rio Grande do Norte, Brazil
	Universidade Federal do Rio Grande do Norte Centro de Biociências, Brazil
2014/05 - 2015	Visiting Researcher (Research)	Laboratório Nacional de Computação Científica, Brazil
	Laboratório Nacional de Computação Científica, Brazil
2011/06/01 - 2014	Researcher (Research)	Instituto de Engenharia de Sistemas e Computadores Investigação e Desenvolvimento em Lisboa, Portugal
	Instituto de Engenharia de Sistemas e Computadores Investigação e Desenvolvimento em Lisboa, Portugal

Teaching in Higher Education

	Category Host institution	Employer
2023/01/01 - Current	Invited Assistant Professor (University Teacher)	Universidade de Lisboa Instituto Superior Técnico, Portugal

Others

	Category Host institution	Employer
2021/09/13 - Current	Chief Technical Officer - Technical Coordinator	BioData.pt, Portugal
	Instituto Gulbenkian de Ciência, Portugal

Projects

Grant

	Designation	Funders
2023/11 - Current	Genomic Data Infrastructure - Providing access to genomic data to improve research, policy making and healthcare across Europe 101081813 Researcher	European Union
2018/08/01 - 2021/08/31	Biodata.pt - Portuguese Infrastructure of Biological Data 022231 Research Fellow Instituto de Engenharia de Sistemas e Computadores Investigação e Desenvolvimento em Lisboa, Portugal	Fundação para a Ciência e a Tecnologia, I.P.
2015/06/01 - 2018/05/31	Prospection of genes related to hydrocarbon biodegradation and surfactant production using computational approaches PPG-RENORBIO Universidade Federal do Rio Grande do Norte Centro de Biociências, Brazil	Coordenação de Aperfeiçoamento de Pessoal de Nível Superior Concluded
2015/07/01 - 2015/10/31	Large-Scale Data Management in Cloud Environments (DataStorm) EXCL/EEI-ESS/0257/2012 Research Fellow Instituto de Engenharia de Sistemas e Computadores Investigação e Desenvolvimento em Lisboa, Portugal	Fundação para a Ciência e a Tecnologia Concluded
2014/06 - 2015/05	Prospection of genes related to hydrocarbon biodegradation and surfactant production using computational approaches E-26/101.230/2014 Laboratório Nacional de Computação Científica, Brazil	Fundação Carlos Chagas Filho de Amparo à Pesquisa do Estado do Rio de Janeiro
2012/03 - 2015/02	CAMP - Computational Analysis of MicroRNAs in Plants 122534 Provided by PTCRIS: 122534	Fundação para a Ciência e a Tecnologia, I.P.
2010/03 - 2013/08	Did you ask for something small? The microRNAs power in a Eucalyptus tension world! (the microEGo project) 98179 Provided by PTCRIS: 98179	Fundação para a Ciência e a Tecnologia, I.P.

Contract

	Designation	Funders
2019/01/01 - 2019/12/31	Instituto de Engenharia de Sistemas e Computadores, Investigação e Desenvolvimento em Lisboa UID/CEC/50021/2019 Instituto de Engenharia de Sistemas e Computadores Investigação e Desenvolvimento em Lisboa, Portugal	Fundação para a Ciência e a Tecnologia Concluded

Other

	Designation	Funders
2021/09 - 2023/07	ELIXIR-CONVERGE - Connect and align ELIXIR Nodes to deliver sustainable FAIR life-science data management services 871075 Researcher	European Commission Concluded

Outputs

Publications

Journal article

Flora D'Anna; Niclas Jareborg; Mijke Jetten; Minna Ahokas; Pinar Alper; Robert Andrews; Korbinian Bösl; et al. "A research data management (RDM) community for ELIXIR [version 1; peer review: 2 approved with reservations]". (2024): https://f1000research.com/articles/13-230/v1.
10.12688/f1000research.146301.1
Cláudia P Godinho; Margarida Palma; Jorge Oliveira; Marta N Mota; Miguel Antunes; Miguel C Teixeira; Pedro T Monteiro; Isabel Sá-Correia. "The N.C.Yeastract and CommunityYeastract databases to study gene and genomic transcription regulation in non-conventional yeasts". FEMS Yeast Research 21 6 (2021): https://doi.org/10.1093/femsyr/foab045.
10.1093/femsyr/foab045
Pais, Pedro; Oliveira, Jorge; Almeida, Vanda; Yilmaz, Melike; Monteiro, Pedro T.; Teixeira, Miguel C.. "Transcriptome-wide differences between Saccharomyces cerevisiae and Saccharomyces cerevisiae var. boulardii: Clues on host survival and probiotic activity based on promoter sequence variability". Genomics 113 2 (2021): 530-539. http://dx.doi.org/10.1016/j.ygeno.2020.11.034.
Published • 10.1016/j.ygeno.2020.11.034
Araújo, W. J.; Oliveira, J. S.; Araújo, S. C. S.; Minnicelli, C. F.; Silva-Portela, R. C. B.; da Fonseca, M. M. B.; Freitas, J. F.; et al. "Microbial Culture in Minimal Medium With Oil Favors Enrichment of Biosurfactant Producing Genes". Frontiers in Bioengineering and Biotechnology 8 (2020): http://dx.doi.org/10.3389/fbioe.2020.00962.
10.3389/fbioe.2020.00962
Monteiro, Pedro T; Oliveira, Jorge; Pais, Pedro; Antunes, Miguel; Palma, Margarida; Cavalheiro, Mafalda; Galocha, Mónica; et al. "YEASTRACT+: a portal for cross-species comparative genomics of transcription regulation in yeasts". Nucleic Acids Research 48 D1 (2019): D642-D649. http://dx.doi.org/10.1093/nar/gkz859.
Open access • Published • 10.1093/nar/gkz859
Amanda P. Napp; José Evandro S. Pereira; Jorge S. Oliveira; Rita C.B. Silva-Portela; Lucymara F. Agnez-Lima; Maria C.R. Peralba; Fátima M. Bento; et al. "Comparative metagenomics reveals different hydrocarbon degradative abilities from enriched oil-drilling waste". Chemosphere 209 (2018): 7-16. https://doi.org/10.1016/j.chemosphere.2018.06.068.
10.1016/j.chemosphere.2018.06.068
Guerra AB; Oliveira JS; Silva-Portela RCB; Araújo W; Carlos AC; Vasconcelos ATR; Freitas AT; et al. "Metagenome enrichment approach used for selection of oil-degrading bacteria consortia for drill cutting residue bioremediation.". Environmental pollution (Barking, Essex : 1987) (2018): http://europepmc.org/abstract/med/29353803.
10.1016/j.envpol.2018.01.014
Jorge S. Oliveira; Wydemberg J. Araújo; Ricardo M. Figueiredo; Rita C. B. Silva-Portela; Alaine de Brito Guerra; Sinara Carla da Silva Araújo; Carolina Minnicelli; et al. "Biogeographical distribution analysis of hydrocarbon degrading and biosurfactant producing genes suggests that near-equatorial biomes have higher abundance of genes with potential for bioremediation". BMC Microbiology 17 1 (2017): https://doi.org/10.1186%2Fs12866-017-1077-4.
10.1186/s12866-017-1077-4
Oliveira JS; Araújo W; Lopes Sales AI; Brito Guerra Ad; Silva Araújo SC; de Vasconcelos AT; Agnez-Lima LF; Freitas AT. "BioSurfDB: knowledge and algorithms to support biosurfactants and biodegradation studies.". (2015): http://europepmc.org/abstract/med/25833955.
10.1093/database/bav033
OLIVEIRA, JORGE. "A Computational Approach for MicroRNA Identification in Plants". J Data Mining Genomics Proteomics (2013): http://omicsonline.org/a-computational-approach-for-microrna-identification-in-plants-combining-genome-based-predictions-with-rna-seq-data-2153-0602.1000130.php?aid=14889.
10.4172/2153-0602.1000130

Activities

Oral presentation

	Presentation title	Event name Host (Event location)
2016/12/01	A study on eco-geographical influence on hydrocarbon-degrading and surfactant producing gene diversity using public-data	XXI Encontro de Genética do Nordeste (Recife, Brazil)
2014/12/01	Biosurfactants and Biodegradation Database	5th International Symposium in Biochemistry of Macromolecules and Biotechnology Sociedade Brasileira de Bioquímica e Biologia Molecular (Natal, Brazil)

Event participation

	Activity description Type of event	Event name Institution / Organization
2021/02/04 - 2021/02/04	First National Summit to raise awareness and gather scientists addressing microbiome research in Portugal, organized by The Portuguese Microbiome Community Conference	First Microbiome PT Summit BioData.pt, Portugal Instituto Gulbenkian de Ciência, Portugal
2020/01/14 - 2020/01/14	Value Creation For Heathcare System's Genomics Data Meeting	Team Meeting BioData.pt Instituto de Biologia Molecular e Celular, Portugal
2019/05/29 - 2019/05/29	Community Yeastract: a comparative genomics cool platform for the analysis of transcriptional regulatory networks in yeast species Meeting	Cools Tools Meeting BioData.pt, Portugal
2019/02/21 - 2019/02/22	YEASTRACT+: a comparative genomics platform for the analysis of transcriptional regulatory networks in yeast species Conference	Bioinformatics Open Days Universidade do Minho, Portugal

Jury of academic degree

	Topic Role	Candidate name (Type of degree) Institution / Organization
2019/10	Unveiling the molecular basis of S. boulardii probiotic activity: through the construction of a global promoter survey computational tool and transcriptomics analyses (Thesis) Main arguer	Maria Vanda Pinto de Almeida Sá Dias (Master) Universidade de Lisboa Instituto Superior Técnico, Portugal