I obtained a MSc in Biological Engineering from Instituto Superior Técnico in 2013 (evaluated in 16/20) with a dissertation on Identification of microRNAs and analysis of their expression in Eucalyptus globulus (evaluated 20/20), with Professor Ana Teresa Freitas and Dr. Jorge Paiva, in collaboration between Knowledge Discovery and Bioinformatics Group of INESC-ID and the Institute of Scientific and Tropical Research, both located in Lisbon.
I obtained my PhD in Biotechnology from the Federal University of Rio Grande do Norte, Brazil (2018), in a collaboration with INESC-ID in Lisbon and the National Laboratory of Scientific Computation in Rio de Janeiro. This work, in the field of Metagenomics applied to oil exploration, was supervised by Professors Lucymara Lima, Ana Teresa Freitas and Ana Tereza Vasconcelos, yielding several tools, still in use today, in this specific domain of metagenomics.
Additionally, during my PhD I completed two semesters of teaching experience, teaching the subjects of Evolutionary Genetics and Introduction to Bioinformatics.
During all my academic life, I gave great importance to extracurricular skills, having participated in various student groups such as the Board of European Students of Technology (BEST), the Students Association, where I was administrator and treasurer, and the School's Pedagogical Council, in which I belonged to the executive committee.
This academic path, based on biological engineering and a specialization in bioinformatics is unusual, and has given me the opportunity to be invited to several projects were I was able to close the gap between biologists and computer scientists, allowing me to use and develop tools with real knowledge of its application.
Currently my main interests are in the development of user-friendly tools and pipelines for analysis and interpretation of genomic or metagenomic sequencing data.
Participation in Projects
Jun 2018 - Present Research grant from the project Biodata.pt - Infraestrutura Portuguesa de Dados Biológicos (candidatura 02223 - Portugal 2020) funded by FCT/MCTES.
Jan 2016 - Apr 2018: Research Grant from the project Prospeção de genes aplicados a biodegradação de hidrocarbonetos e produção de surfactantes utilizando abordagens computacionais, a collaboration project betweeen INESC-ID and Universidade Federal do Rio Grande do Norte, Natal, Brazil, supported by GALP-energia Brazil.
Aug 2015 - Oct 2015: Research Grant from the FCT funded project DATASTORM: LARGE-SCALE DATA MANAGEMENT IN CLOUD ENVIRONMENTS (EXCL/EEI-ESS/0257/2012).
Jun 2014 - Jun 2015: Reverse-Sandwich PhD Grant from FAPERJ, Brazil: Search for genes applied to the biodegradation of hydrocarbons and surfactant production using computational approaches (E-26/101.230/2014).
Aug 2013 - Jun 2014: Research Grant in the FCT funded project CAMP: Computational Analysis of MicroRNAs in Plants (PTDC/EIA-EIA/122534/2010).
Apr 2012 - Jan 2013: Research Grant in the FCT funded project microEgo: Did you ask for something small? The microRNAs power in a Eucalyptus tension world! (PTDC/AGR-GPL/098179/2008).
Monteiro PT, Oliveira JS, Pais P, et al. YEASTRACT+: a portal for cross-species comparative genomics of transcription regulation in yeasts. Nucleic Acids Research. doi:10.1093/nar/gkz859. (2019).
Napp AP, Pereira JES, Oliveira JS, Silva-Portela RCB, Agnez-Silva LF, Peralba MCR, Bento FM, Passaglia LMP, Thompson CE, Vainstein MH, Comparative metagenomics reveals different hydrocarbon degradative abilities from enriched oil-drilling waste, Chemosphere, Available online 11 June 2018, ISSN 0045-6535, https://doi.org/10.1016/j.chemosphere.2018.06.068.
Guerra AB, Oliveira JS, Silva-Portela RCB, et al. Metagenome Enrichment Approach Used For Selection Of Oil-Degrading
Bacteria Consortia For Drill Cutting Residue Bioremediation. Environmental Pollution (Barking, Essex: 1987), V. 235, P.
869-880, Jan. (2018).
Oliveira JS, Araújo W, Figueiredo RM, 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 Microbiol (2017).
Oliveira JS, Araúo W, Lopes Sales AI., et al. BioSurfDB: knowledge and algorithms to support biosurfactants and biodegradation studies. Database (Oxford) Vol. 2015: article ID bav033; doi:10.1093/database/bav033. (2015).
Oliveira JS, Mendes ND, Carocha V, Graça C, Paiva JA, et al. A Computational Approach for MicroRNA Identification in Plants: Combining Genome-Based Predictions with RNA-Seq Data. J Data Mining Genomics Proteomics 4:130. doi: 10.4172/2153-0602.1000130. (2013).
International Conferences (Proceedings)
Miguel E. Coimbra, Jorge S. Oliveira, Luís Russo, Ana Tereza Vasconcelos, Lucymara F. A. Lima, Ana Teresa Freitas. Técnicas computacionais para metagenómica adaptadas à prospecção de genes envolvidos na biodegradação de hidrocarbonetos e produção de surfactantes. Congresso Luso-Moçambicano de Engenharia. April 2014.
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, Aline Cardoso Carlos, Ana Tereza Ribeiro de Vasconcelos, Ana Teresa Freitas and Lucymara F. Agnez-Lima, A study on eco-geographical influence on hydrocarbon-degrading and surfactant producing gene diversity using public-data. XXI Encontro de Genética do Nordeste,
Recife, PE, Brazil. Dec. 2016. Oral Presentation.
Oliveira JS, Freitas AT, Araújo SCS, Sales AIL, Guerra AB, Araújo WJ, Lima LFA, Vasconcelos, ATR. Biosurfactants and Biodegradation Database. XII Reunião Regional da SBB and 5th International Symposium in Biochemistry of Macromolecules and Biotechnolog / Dec. 2014. - Natal, RN Brazil. Poster awarded with merit prize.
Jorge dos Santos Oliveira, Identification of microRNAs and analysis of their expression in Eucalyptus globulus, Bioinformatics Open Day, Apr. 2013. Oral presentation.
Paiva JAP, Carocha VJ, Graça CS, Mendes ND, Oliveira JS, Pera S, Amaral AJ, Quilhó T, Rodrigues JC, Leal L, Fevereiro P, Grima-Pettenati J and Freitas AT. 2014. Unraveling miRNA Post-Transcriptional Regulation Mechanisms behind Eucalyptus globulus Wood Formation. International Plant & Animal Genome XXIII / January 11-15, 2014 - San Diego, CA, USA.
Carocha VJ, Graça CS, Mendes ND, Oliveira JS, Amaral AJ, Neves L, Araújo C, Pera S, Fevereiro P, Grima-Pettenati J, Freitas AT, and Paiva JAP. 2013. The microEGo project: unraveling post-transcriptional regulation mechanisms on Eucalyptus wood formation. International Plant & Animal Genome XXII / January 11-15, 2013 - San Diego, CA, USA.
Carocha VJ, Graça CS, Mendes ND, Oliveira JS, Pera SI, Amaral AJ, Neves L, Araújo C, Fevereiro P, Grima-Pettenati J, Freitas AT and Paiva JAP. 2013. The microEGo PROJECT: unraveling post-transcriptional regulation mechanisms on Eucalyptus wood formation. XIII Congresso Luso-Espanhol de Fisiologia Vegetal. Faculdade de Ciências da Universidade de Lisboa. Campo Grande, 24-28 Julho 2013.
Ricardo Figueiredo and Jorge dos Santos Oliveira and Nuno D. Mendes and Ana T. Freitas, Identification of regulatory networks from the prediction of miRNAs and their targets, INESC-ID Tec. Rep. 4/2015, Jan 2015.
Gulbenkian Training Programme in Bioinformatics courses, IGC, Oeiras (Portugal):
2013 - Analysing Whole-Genome Shotgun Metagenomic Data
2012 - Automated and Reproducible Analysis of NGS Data
2012 - Biostatistical Foundations in Bioinformatics
2013 - Analysing Whole-Genome Shotgun Metagenomic Data
My main interrest outside research is MUSIC. I like to play guitar, mainly Blues and Swing Jazz; I also love woodwork and electronics, related to guitars mostly; general bricolage and sports.
You can follow my humble contribution to music in my Youtube Channel HERE: