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João Carlos Sequeira da Costa has a college degree in Biochemistry (2015) and a master's degree in Bioinformatics with specialization in Information Technologies (2017) in University of Minho. He is a PhD student in Chemical and Biological Engineering in University of Minho. He participated in three research projects as research fellow. He has published two papers in conference proceedings, four papers in international peer reviewed journals (2 Q1, 1 Q2 and 1 Q3, according to Scimago in 2022) and one abstract in Bioinformatics Open Days 2018. He has one oral presentation at an international congress, two at national congresses, and three posters in Bioinformatics Open Days conferences. He has assisted in the supervision of four master thesis in Bioinformatics. He has developed a bioinformatics pipeline for integrated analysis of omics data, two tools for functional annotation of proteins and one tool for representation of genomic potential and gene differential expression in metabolic maps. He has participated in two proteomics courses, one in 2018 (36 hours) and one in 2019 (28 hours). He has helped organize several bioinformatics events: a MATLAB workshop (2016), Bioinformatics Open Days (2017) and a proteomics workshop (2019). Most frequent terms to contextualize his scientific activity are: metagenomics; metatranscriptomics; metaproteomics; next-generation sequencing; mass spectrometry. He is currently working in Engineering and Technology Sciences and Bioinformatics applied to Environmental Biotechnology. His scientific interests are the study of complex microbial communities and interactions between microorganisms and materials by using bioinformatics tools.
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Identification

Personal identification

Full name
João Carlos Sequeira da Costa

Citation names

  • Sequeira, João C.

Author identifiers

Ciência ID
E910-B758-A0E2
ORCID iD
0000-0002-2691-9950

Email addresses

  • jsequeira@ceb.uminho.pt (Professional)

Knowledge fields

  • Engineering and Technology - Environmental Biotechnology

Languages

Language Speaking Reading Writing Listening Peer-review
Portuguese (Mother tongue)
English Advanced (C1) Proficiency (C2) Advanced (C1) Proficiency (C2) Advanced (C1)
Education
Degree Classification
2015/09/01 - 2017/12/15
Concluded
 Bioinformática (Mestrado)
Universidade do Minho Escola de Engenharia, Portugal
"Development of an automated pipeline for meta-omics data analysis" (THESIS/DISSERTATION)
 17
2012/09/01 - 2015/07/31
Concluded
 Bioquímica (Licenciatura)
Universidade do Minho Escola de Ciências, Portugal
"Genetic Scale Metabolic Model of a CD4+ T lymphocyte infected with HIV-1" (THESIS/DISSERTATION)
 16
Affiliation

Science

Category
Host institution 		Employer
2017/09/10 - 2019/05/31 Researcher (Research) Universidade do Minho Centro de Engenharia Biológica, Portugal
Projects

Grant

Designation Funders
2017/09/10 - 2018/03/31 Novel anaerobes for a biobased economy
info:eu-repo/grantAgreement/EC/SEVENTH FRAMEWORK PROGRAMME/323009/EU
Research Fellow
European Commission
Concluded

Contract

Designation Funders
2022/01 - Current GLOMICAVE
952908
Researcher
Technology Centre of Catalonia Eurecat, Spain
 European Union's Research and Innovation
Ongoing
2022/01/01 - 2024/12/31 O papel dos materiais condutores na aceleração da produção de metano a partir de resíduos em processos de digestão anaeróbia
PTDC/BTA-BTA/2249/2021
Universidade do Minho, Portugal

Universidade do Porto Faculdade de Engenharia, Portugal

Universidade do Minho Centro de Engenharia Biológica, Portugal
Fundação para a Ciência e a Tecnologia
Ongoing
2018/06/01 - 2019/05/31 MORE - Enhanced microbial oil bioremediation by ferric minerals
PTDC/AAG-TEC/3500/2014
Research Fellow
Universidade do Minho Centro de Engenharia Biológica, Portugal
Ongoing
Outputs

Publications

Conference abstract
  1. Sequeira, João C.; Pereira, Vítor; Alves, Maria Madalena; Rocha, Miguel; Salvador, Andreia F.. Corresponding author: Salvador, Andreia F.. "Individual-Based Modeling elucidates about the role of nanomaterials on methane production". Paper presented in BOD 2024 - XIII Bioinformatics Open Days, Braga, 2024.
  2. Freitas, P José; Sequeira, João C.; Diogo Cachetas; Rocha, Miguel; Salvador, Andreia F.. "Prediction of plastic-degrading enzymes in omics data from marine environments". Paper presented in Bioinformatics Open Days 2023, Braga, 2023.
  3. Sequeira, João C.; Pereira, Vítor; Alves, Maria Madalena; Rocha, Miguel; Salvador, Andreia F.. "A user-friendly bioinformatics pipeline for metaproteogenomics data analysis". Paper presented in Bioinformatics Open Days, Braga, 2023.
Conference paper
  1. OLIVEIRA, ALEXANDRE; Cunha, Emanuel; Cruz, Fernando; Capela, João; Sequeira, João C.; Sampaio, Marta; Óscar Dias. Corresponding author: Óscar Dias. "Towards a multivariate analysis of genome-scale metabolic models derived from the BiGG models database". Paper presented in PACBB 2021, Salamanca, 2021.
    Published
  2. Sequeira, J.C.; Rocha, M.; Madalena Alves, M.; Salvador, A.F.. "MOSCA: An automated pipeline for integrated metagenomics and metatranscriptomics data analysis". Paper presented in Practical Applications of Computational Biology and Bioinformatics, 12th International Conference, Toledo, 2018.
    Published • 10.1007/978-3-319-98702-6_22
Conference poster
  1. Sequeira, João C.; Pereira, Vítor; Alves, Maria Madalena; Rocha, Miguel; Salvador, Andreia F.. Corresponding author: Salvador, Andreia F.. "User-friendly and reproducible Metaproteogenomics: studying communities on all levels of life". Paper presented in BOD 2023 - XII Bioinformatics Open Days, 2023.
  2. Sequeira, João C.; Pereira, Vítor; Alves, Maria Madalena; Rocha, Miguel; Salvador, Andreia F.. Corresponding author: Salvador, Andreia F.. "Uncovering the role of conductive nanomaterials on anaerobic digestion". Paper presented in Ciência 2023, 2023.
  3. Sequeira, João C.; Pereira, Vítor; Alves, Maria Madalena; Rocha, Miguel; Salvador, Andreia F.. Corresponding author: Salvador, Andreia F.. "Metaproteogenomics analysis of an anaerobic bioreactor with the MOSCA pipeline". Paper presented in 2nd Microbiome PT Summit, 2023.
  4. Sequeira, João C.; Rocha, Miguel; Alves, M. Madalena; Salvador, Andreia F.. "Improving analysis of meta-omics data with the MOSCA framework". Paper presented in 4th International Conference on Biogas Microbiology, 2022.
  5. Sequeira, João C.; Miguel Rocha; Alves, M. Madalena; Salvador, Andreia F.. Corresponding author: Salvador, Andreia F.. "UPIMAPI, reCOGnizer and KEGGCharter: three tools for functional annotation". Paper presented in Bioinformatic Open Days 2021, 2021.
  6. Sequeira, João C.; M. Rocha; M. Madalena Alves; Andreia F. Salvador. "Development of an automated pipeline for metagenomics and metatranscriptomics data analyses". Paper presented in Bioinformatics Open Days 2018, 2018.
Journal article
  1. Sequeira, João C.; Rocha, Miguel; Alves, M. Madalena; Salvador, Andreia F.. Corresponding author: Salvador, Andreia F.. "UPIMAPI, reCOGnizer and KEGGCharter: Bioinformatics tools for functional annotation and visualization of (meta)-omics datasets". Computational and Structural Biotechnology Journal 20 (2022): 1798-1810. http://dx.doi.org/10.1016/j.csbj.2022.03.042.
    Published • 10.1016/j.csbj.2022.03.042
  2. Martins, Valdo R.; Freitas, Carlos J. B.; Castro, A. Rita; Silva, Rita M.; Gudiña, Eduardo J.; Sequeira, João C.; Salvador, Andreia F.; Pereira, M. Alcina; Cavaleiro, Ana J.. "Corksorb Enhances Alkane Degradation by Hydrocarbonoclastic Bacteria". Frontiers in Microbiology 12 (2021): http://dx.doi.org/10.3389/fmicb.2021.618270.
    Published • 10.3389/fmicb.2021.618270
  3. Cavaleiro, Ana J.; Guedes, Ana P.; Silva, Sérgio A.; Arantes, Ana L.; Sequeira, João C.; Salvador, Andreia F.; Sousa, Diana Z.; Stams, Alfons J. M.; Alves, M. Madalena. "Effect of Sub-Stoichiometric Fe(III) Amounts on LCFA Degradation by Methanogenic Communities". Microorganisms 8 9 (2020): 1375. http://dx.doi.org/10.3390/microorganisms8091375.
    Published • 10.3390/microorganisms8091375
  4. Sequeira, João C.; Miguel Rocha; M. Madalena Alves; Andreia F. Salvador. "A rapid bioinformatics workflow for functional annotation of omics and meta-omics datasets". in preparation, to be submitted to Microbial Ecology (2020):
  5. Sequeira, João C.. "Modelling Interactions between Microorganisms and Nanomaterials: A Review of Mathematical and Multi-dimensional Methods". In preparation, to be submitted to Biotechnology Advances (2020):
  6. Sequeira, João C.. "MOSCA 2.0: a bioinformatics framework for metagenomics, metatranscriptomics and metaproteomics data analysis". In preparation, to be submitted to Frontiers in Microbiology (2020):
Online resource
  1. Sequeira, João C.; Miguel Rocha; M. Madalena Alves; Andreia F. Salvador. UPIMAPI - UniProt Id Mapping through API. 2020. https://github.com/iquasere/UPIMAPI.
  2. Sequeira, João C.; Miguel Rocha; M. Madalena Alves; Andreia F. Salvador. reCOGnizer - a tool for domain based annotation with the COG database. 2020. https://github.com/iquasere/reCOGnizer.
  3. Sequeira, João C.. KEGGCharter - A tool for representing genomic potential and transcriptomic expression into KEGG pathways. 2020.
Thesis / Dissertation
  1. Sequeira, João C.. "Development of an automated pipeline for meta-omics data analysis". Master, Universidade do Minho Escola de Engenharia, 2017. http://hdl.handle.net/1822/56113.
Activities

Oral presentation

Presentation title Event name
Host (Event location)
2022/05/11 Improving analysis of meta-omics data with the MOSCA framework International Conference on Biogas Microbiology
(Braga, Portugal)
2018/06/21 MOSCA: an automated pipeline for integrated metagenomics and metatranscriptomics data analysis (presenting author) 12th International Conference on Practical Applications of Computational Biology & Bioinformatics
Universidad de Castilla-La Mancha (Toledo, Spain)
2018/03/16 Development of an automated pipeline for metagenomics and metatranscriptomics data analyses Bioinformatics Open Days 2018
(Braga, Portugal)

Event organisation

Event name
Type of event (Role) 		Institution / Organization
2017/02/22 - 2017/02/24 Bioinformatics Open Days 2017 (2017/02/22 - 2017/02/24)
Conference (Member of the Organising Committee)
 Núcleo de Estudos de Bioinformática da Universidade do Minho, Portugal
2016/10/01 - 2016/10/10 Introduction to matrices; introduction to MATLAB (2016/10/10 - 2016/10/10)
Workshop (Co-organisor)
 Núcleo de Estudos de Bioinformática da Universidade do Minho, Portugal

Event participation

Activity description
Type of event 		Event name
Institution / Organization
2018/05/28 - 2018/06/01 Proteomics Data Analysis 2018 (36 hours of intensive hands-on training)
Workshop
 Proteomics Data Analysis 2018
The Gulbenkian Training Programme in Bioinformatics, Portugal
2014/07/11 - 2015/02/01 Foldit, a game about de novo protein design
Call
 De novo protein design by citizen scientists
The Foldit Team, United States

Association member

Society Organization name Role
2013/09/10 - Current Associação Recreativa e Cultura Universitária do Minho Música, organização de eventos

Mentoring / Tutoring

Topic Student name
2021/10/27 - 2022/10/31 Development of a knowledgebase for plastics' biodegradation Joana Marques Gabriel
2021/10/27 - 2022/10/31 Development of Genome-Scale Metabolic Models for methanogens and syntrophic co-cultures Mariana Sofia Gomes Coelho
2021/10/19 - 2022/10/31 Mining metagenomics datasets for novel plastic-degrading enzymes José Pedro Silva Freitas
2021/10/19 - 2022/10/31 Development of MOSGUITO: a user-friendly graphical interface for meta-omics data analyses José Henrique Lopes Pereira
2021/03/16 - 2021/06/30 Methanobacterium formicicum Metabolic Model Diogo Macedo Cachetas
2021/03/08 - 2021/06/30 Development of MOSGUITO for the interactive visualization of results from MOSCA José Henrique Lopes Pereira