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Rui Sotero Rodrigues Machado is currently a Post-Doctoral Fellow at ICArEHB working on the theme "DOPE - Domestication of Oppium Poppy in Europe". He concluded a Biology degree in 2010 - Universidade do Algarve and a Masters degree in Biomedical Sciences on 2014 at Universidade do Algarve with an evaluation of 17. Completed the PhD in Mechanisms of Disease and Regenerative Medicine on 2021 at Universidade of Algarve with an evaluation of Very Good. He published 10 articles in international journals and participated in the development of 6 webtools in the areas of stem cells, protein interaction and cardiac development. Additionally, he co-supervised 3 monographies for the completion of biomedical sciences degree. Works in the area(s) related to Bioinformatics, Molecular Biology and recently in the study of the evolution of agricultural societies and domestication. He uses Computational Biology and Bioinformatics as a way of answering biologically relevant questions. He is keen on Open Science and the 3R's in science (Repeatability, Reproducibility, and Replicability) and is always open to establish new collaborations.
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Identification

Personal identification

Full name
Rui Sotero Rodrigues Machado

Citation names

  • Machado, Rui SR
  • Machado, Rui
  • RSR Machado
  • Machado, RSR

Author identifiers

Ciência ID
5D19-8F5F-3CE1
ORCID iD
0000-0002-4080-2353
Google Scholar ID
dxieA2oAAAAJ
Scopus Author Id
55991033900

Email addresses

  • rsmachado@ualg.pt (Professional)

Websites

Knowledge fields

  • Exact Sciences - Computer and Information Sciences - Bioinformatics
  • Natural sciences - Biological Sciences - Molecular Biology
  • Humanities - History and Archaeology - Archaeology

Languages

Language Speaking Reading Writing Listening Peer-review
Portuguese (Mother tongue)
English Advanced (C1) Advanced (C1) Advanced (C1) Proficiency (C2)
Spanish; Castilian Upper intermediate (B2) Upper intermediate (B2) Intermediate (B1) Upper intermediate (B2)
French Beginner (A1) Elementary (A2) Beginner (A1) Elementary (A2)
Education
Degree Classification
2015/01/01 - 2021/12/03
Concluded
 Mecanismos de Doença e Medicina Regenerativa (associação) (Doutoramento)
Major in Sem especialidade
Universidade do Algarve, Portugal
"Identification of novel key factors of heart development using a systems biology approach" (THESIS/DISSERTATION)
2011/09/12 - 2014/02/14
Concluded
 Ciências Biomédicas (Mestrado)
Universidade do Algarve, Portugal
"Analysis of the transcriptional regulatory network: underlying heart development" (THESIS/DISSERTATION)
 17
2006/09/21 - 2010/09/05
Concluded
 Biologia (Licenciatura)
Major in Ciências Biomédicas
Universidade do Algarve, Portugal
"Analysis the innate defence genes in clams (Ruditapes decussatus) and how the infection parasites affecting those genes" (THESIS/DISSERTATION)
 14
Affiliation

Science

Category
Host institution 		Employer
2022/07/08 - Current Postdoc (Research) Universidade do Algarve - Campus de Gambelas, Portugal
Universidade do Algarve Centro Interdisciplinar de Arqueologia e Evolução do Comportamento Humano, Portugal
2020/06/01 - 2021/12/31 Researcher (Research) Universidade do Algarve, Portugal
Universidade do Algarve Faculdade de Ciências e Tecnologia, Portugal
2014/05/01 - 2014/12/31 Researcher (Research) Centro de Ciências do Mar, Portugal
Universidade do Algarve Faculdade de Ciências e Tecnologia, Portugal
2012/10/01 - 2012/12/31 Researcher (Research) Universidade do Algarve Faculdade de Ciências e Tecnologia, Portugal
Universidade do Algarve Faculdade de Ciências e Tecnologia, Portugal

Positions / Appointments

Category
Host institution 		Employer
2007/01/01 - 2009/12/31 Member of the Pedagogical Council of the Faculdade do Mar e do Ambiente Universidade do Algarve, Portugal
Universidade do Algarve - Campus de Gambelas, Portugal

Others

Category
Host institution 		Employer
2015 - 2021 PhD Student Fundação para a Ciência e a Tecnologia, Portugal
Universidade Nova de Lisboa Faculdade de Ciências Médicas, Portugal
(...)
2011/03/21 - 2011/05/21 Laboratory technician assistant St Cecilia's College, Ireland
St Cecilia's College, Ireland
Projects

Grant

Designation Funders
2015/01/01 - 2019/03/15 Identification of novel key factors of heart development using a systems biology approach
PD/BD/105894/2014 Ref.ª CRM:0010478
PhD Student Fellow

Contract

Designation Funders
2022/07/08 - Current DOPE - Domestication of the Opium poppy in Prehistoric Europe
PTDC/HAR-ARQ/1709/2021
Post-doc Fellow
2020/06/01 - 2021/12/31 GenomePT
POCI-01-0145-FEDER-022184
Master Student Fellow
2014/05/01 - 2014/12/31 Proteína relacionada com hormona paratiróide e Stanniocalcina: novas hormonas metabólicas?
PTDC /MAR/121279/2010
Master Student Fellow
2012/10/01 - 2012/12/31 Alternative splicing and its impact on molecular interaction networks during stem cell differentiation.
PTDC/BIA-GEN/116519/2010
Research Fellow
Outputs

Publications

Conference abstract
  1. Aurélie, Salavert; Machado, RSR; Antolín, Ferran; Oliveira, Hugo Rafael. "Outcomes of interdisciplinary projects on the domestication of opium poppy". Paper presented in International Workgroup of Palaeoethnobotany, Groningen, 2025.
    Submitted
  2. Utge, José; Machado, Rui SR; Oliveira, Hugo Rafael; Aurélie, Salavert. Corresponding author: Utge, José. "ADN ancien, muséomique, problématique des vieux spécimens et de leur intégrité physique". Paper presented in DNA-ID, Paris, 2024.
    Accepted
  3. Oliveira, Hugo Rafael; Machado, Rui SR; López, Bernardo. Corresponding author: Oliveira, Hugo Rafael. "West side story? The possibility of independent prehistoric crop domestication in the western Europe". Paper presented in International Work Group for Paleoethnobotany Research Group, Basque country (San Sebastian), 2024.
    Submitted
  4. Oliveira, Hugo Rafael; Machado, Rui SR; Antolín, Ferran; Aurélie, Salavert. "The origins and spread of opium poppy (Papaver somniferum L.)". Paper presented in 30th European Association of Archaeologists Annual Meeting, Rome, 2024.
    Accepted
Conference poster
  1. Machado, Rui; Pinto, JP; Sachinidis, A; Futschik, M. "HeartmiR: An Open Access Database of miR-mRNA Interactions in the Context of Late Heart Development". Paper presented in 2º meeting Heart without Boarders International Conference, 2017.
  2. Machado, Rui; Sabour, D; Pinto, JP; Rohani, S; Hescheler, J; Futschik, M; Sachinidis, A. "Parallel genome-wide profiling of RNA and miRNA indicates extensive regulation of embryonic heart development by non-coding RNAs". Paper presented in 2º meeting Heart without Boarders International Conference, 2017.
  3. Machado, Rui; Sabour, D; Pinto, JP; Braganca, J; Sachinidis, Agapios; Futschik, Matthias. ""HEARTI ToolBox: An online platform for the analysis in silico of cardiogenesis".". Paper presented in 9th International Meeting of the Stem Cell Network NRW, 2017.
  4. Pinto, José Pedro; Kalathur, Ravi; Oliveira, DA; Barata, Tania; Machado, Rui; Machado, Susana; Pacheco-Leyva, Ivette; Futschik, Matthias. "SCIS Toolbox: Design and implementation of online tools for in silico stem cell biology". Paper presented in 9th International Meeting of the Stem Cell Network NRW, 2017.
  5. Oliveira, Daniel; Machado, Rui SR; Duarte, Isabel; Pacheco-Leyva, Ivette; Justo, T; Pinto, JP; Braganca, Jose; Futschik, Matthias. "From Stem Cells 2 Heart: Finding novel candidate isoforms and genes for cardiomyogenesis". Paper presented in 9th International Meeting of the Portuguese society for Stem cells and Cell therapies, 2015.
  6. Machado, Rui; Pinto, JP; Oliveira, DV; Duarte, I; Machado, S; Bragança, J; Futschik, M. "A meta-analysis study of stem cell differentiation in the context of cardiogenesis". Paper presented in 9th International Meeting of the Portuguese society for Stem cells and Cell therapies, 2015.
  7. Machado, S; Kalathur, R.K.; Oliveira, D; Barata, T; Machado, Rui; Pacheco-Leyva, I; Duarte, I; Futschik, M. "StemCellNet: an interactive platform for network-oriented investigations in stem cell biology". Paper presented in 9th International Meeting of the Portuguese society for Stem cells and Cell therapies, 2015.
  8. Oliveira, D; Machado, Rui; Pacheco-Leyva, I; Duarte, I; Justo, T; Pinto, J; Belo, J; Futschik, M. "From Stem Cells 2 heart: Finding novel candidate genes for cardiomyogenesis". Paper presented in 1º meeting 1º meeting Heart without Boarders International Conference, 2014.
  9. Pinto, J; Kalathur, R; Machado, Rui; Xavier, J; Braganca, J; Futschik, M. "StemCellNet: an interactive platform for network-oriented investigations in stem cell biology". Paper presented in 1º meeting Heart without Boarders International Conference, 2014.
  10. Machado, Rui; Pinto, J; Braganca, J; Futschik, M. "What a heart makes or breaks: A meta-analysis of gene expression profiles". Paper presented in 8th International Meeting of the Portuguese Society for Stem Cells and Cell Therapies, 2013.
  11. Pinto, J; Machado, Rui; Kalathur, R; Futschik, M. "StemCellNet: A web-based Platform for Assembly and Analysis of Molecular Interaction Networks in Stem Cells". Paper presented in 8th International Meeting of the Portuguese Society for Stem Cells and Cell Therapies, 2013.
Journal article
  1. Mekonnen, Degsew; Gomes, Ana; Machado, Rui SR; Oliveira, Hugo Rafael. Corresponding author: Mekonnen, Degsew. "The Genomics of T'ef and Finger Millet Domestication and Spread". Philosophical Transactions B (2025):
    Under revision
  2. Wallach, Thomas; Mossmann, Zoé J.; Szczepek, Michal; Wetzel, Max; Machado, Rui; Raden, Martin; Miladi, Milad; et al. "MicroRNA-100-5p and microRNA-298-5p released from apoptotic cortical neurons are endogenous Toll-like receptor 7/8 ligands that contribute to neurodegeneration". Molecular Neurodegeneration 16 1 (2021): http://dx.doi.org/10.1186/s13024-021-00498-5.
    10.1186/s13024-021-00498-5
  3. Machado, Rui; Sachinidis, Agapios; Futschik, Matthias E.. Corresponding author: Machado, Rui. "Detection of Novel Potential Regulators of Stem Cell Differentiation and Cardiogenesis through Combined Genome-Wide Profiling of Protein-Coding Transcripts and microRNAs". Cells 10 9 (2021): 2477. http://dx.doi.org/10.3390/cells10092477.
    10.3390/cells10092477
  4. João M. A. Santos; Leonardo Mendes-Silva; Vanessa Afonso; Gil Martins; Machado, Rui; João A. Lopes; Leonor Cancela; et al. "Exogenous WNT5A and WNT11 proteins rescue CITED2 dysfunction in mouse embryonic stem cells and zebrafish morphants". Cell Death & Disease 10 8 (2019): https://doi.org/10.1038%2Fs41419-019-1816-6.
    10.1038/s41419-019-1816-6
  5. Ghezzo, M; Fernandes, M; Pacheco-Leyva, I; Rodrigues, P; Machado, Rui; Araújo, M; Kalathur, R; et al. "FoxN1-dependent thymic epithelial cells promote T-cell leukemia development.". Carcinogenesis (2018): https://doi.org/10.1093/carcin/bgy127.
    10.1093/carcin/bgy127
  6. Machado, Rui; Sabour, D; Pinto, J; Rohani, S; Sahito, R; Hescheler, J; Futschik, M; Sachinidis, A. "Parallel Genome-wide Profiling of Coding and Non-coding RNAs to Identify Novel Regulatory Elements in Embryonic and Maturated Heart.". Molecular therapy. Nucleic acids (2018): https://europepmc.org/articles/PMC6023836.
    10.1016/j.omtn.2018.04.018
  7. Pinto, J.P.; Machado, Rui; Magno, R.; Oliveira, D.V.; MacHado, S.; Andrade, R.P.; Braganca, J.; Duarte, I.; Futschik, M.E.. "StemMapper: A curated gene expression database for stem cell lineage analysis". Nucleic Acids Research 46 D1 (2018): D788-D793. http://www.scopus.com/inward/record.url?eid=2-s2.0-85040935381&partnerID=MN8TOARS.
    10.1093/nar/gkx921
  8. Pinto, J.P.; Kalathur, R.K.; Oliveira, D.V.; Barata, T.; Machado, Rui; Machado, S.; Pacheco-Leyva, I.; Duarte, I.; Futschik, M.E.. "StemChecker: A web-based tool to discover and explore stemness signatures in gene sets". Nucleic Acids Research 43 W1 (2015): W72-W77. http://www.scopus.com/inward/record.url?eid=2-s2.0-84979856605&partnerID=MN8TOARS.
    10.1093/nar/gkv529
  9. Pinto, J.P.; Machado, R.S.R.; Xavier, J.M.; Futschik, M.E.. "Targeting molecular networks for drug research". Frontiers in Genetics 5 JUN (2014): http://www.scopus.com/inward/record.url?eid=2-s2.0-84906249332&partnerID=MN8TOARS.
    10.3389/fgene.2014.00160
  10. Pinto, J.P.; Reddy Kalathur, R.K.; Machado, Rui; Xavier, J.M.; Bragança, J.; Futschik, M.E.. "StemCellNet: An interactive platform for network-oriented investigations in stem cell biology". Nucleic Acids Research 42 W1 (2014): http://www.scopus.com/inward/record.url?eid=2-s2.0-84904816435&partnerID=MN8TOARS.
    10.1093/nar/gku455
  11. Kalathur, R.K.R.; Pinto, J.P.; Hernández-Prieto, M.A.; Machado, Rui; Almeida, D.; Chaurasia, G.; Futschik, M.E.. "UniHI 7: An enhanced database for retrieval and interactive analysis of human molecular interaction networks". Nucleic Acids Research 42 D1 (2014): http://www.scopus.com/inward/record.url?eid=2-s2.0-84891763323&partnerID=MN8TOARS.
    10.1093/nar/gkt1100
Thesis / Dissertation
  1. "Identification of novel key factors of heart development using a systems biology approach". PhD, Universidade Nova de Lisboa Faculdade de Ciências Médicas, 2021.
  2. "Analysis of the transcriptional regulatory network: underlying heart development". Master, Universidade do Algarve Faculdade de Ciências e Tecnologia, 2014.

Other

Dataset
  1. Machado, Rui. UniHI: comprehensive database of human molecular interactions, functional annotation, disease assocation and drug target information. http://www.unihi.org/.
  2. Machado, Rui. StemMapper: manually curated database containing gene expression data for different lineages of Stem Cells (SCs) from human and mouse.. http://stemmapper.sysbiolab.eu/.
  3. Machado, Rui. StemCellNet: interactive web server & database for network analysis and visualization in stem cell biology. http://stemcellnet.sysbiolab.eu/.
  4. Machado, Rui. temCellNet: interactive web server & database for network analysis and visualization in stem cell biology. http://stemcellnet.sysbiolab.eu/.
  5. Machado, Rui. HeartmiR: database and webserver for querying of relevant miRNA-mRNA interactions for late heart development in mouse. http://heartmir.sysbiolab.eu/.
  6. Machado, Rui. HeartEXpress: database for query and visualisation of integrated expression datasets associated with cardiomyogenesis. http://heartexpress.sysbiolab.eu/.
Activities

Oral presentation

Presentation title Event name
Host (Event location)
2024/03/15 Lecture to Msc Students: "DOPE: Domestication of the opium poppy in Prehistoric Europe"
Universidade do Algarve
2023/10/10 Lecture to PhD students: "DOPE: Domestication of the opium poppy in Prehistoric Europe"
Universidade do Algarve
2023 DOPE: Domestication of the opium poppy in Prehistoric Europe ICArEHB Internal Seminars
ICarEHB
2018/09/11 Parallel Genome-wide Profiling of Coding and Non-coding RNAs to Identify Novel Regulatory Elements in Embryonic and Maturated Heart 3rd CBMR/ProRegeM Meeting
CBMR/ProRegeM (Faro, Portugal)
2017/10/13 The HEARTI and SCIS toolboxes: A Swiss Army Knife for Stem Cell Biology in silico. 10th Sociedade Portuguesa de Células Estaminais e Terapia Celular (SPCETC)
Sociedade Portuguesa de Células Estaminais e Terapia Celular (Covilhã, Portugal)
2017/09/08 The HEARTI and SCIS toolboxes: A Swiss Army Knife for Stem Cell Biology in silico 2nd CBMR/ProRegeM Annual Meeting
CBMR/ProRegeM (Faro, Portugal)

Supervision

Thesis Title
Role 		Degree Subject (Type)
Institution / Organization
2015/11/01 - 2016/07/31 From mouse to man: A cardiogenesis transcriptomics analysis in R
Co-supervisor
 Ciências Biomédicas (Degree)
Universidade do Algarve Faculdade de Ciências e Tecnologia, Portugal
2015/11/01 - 2016/07/31 Identification of human bone disease associated SNPs within CNE common to Bony Vertebrates across Phyla
Co-supervisor
 Ciências Biomédicas (Degree)
Universidade do Algarve Faculdade de Ciências e Tecnologia, Portugal
2013/05/01 - 2013/06/30 Functional characterization and comparison of genes associated with an identity of stem cells and oncogenesis
Co-supervisor
 Ciências Biomédicas (Degree)
Universidade do Algarve Faculdade de Ciências e Tecnologia, Portugal

Event organisation

Event name
Type of event (Role) 		Institution / Organization
2016/05/30 - 2019/05/31 Workshops in R programming language - Advanced Training - ATT: R for absolute beginners May 30th and 31st, 2016 (2016/05/30 - 2016/05/31)
Workshop (Co-organisor)
 Universidade do Algarve Faculdade de Ciências e Tecnologia, Portugal

Centro de Ciências do Mar, Portugal
2019 - 2019 Workshops in R programming language - Advanced Training - ATT: R for absolute beginners May 27th and 28th, 2019 (2019 - 2019)
Workshop (Co-organisor)
2018/09/11 - 2018/09/11 3rd CBMR/ProRegeM Annual Meeting (2018 - 2018)
Meeting (Member of the Organising Committee)
 Universidade do Algarve, Portugal
2018/09/08 - 2018/09/08 2nd CBMR/ProRegeM Annual Meeting (2018 - 2018)
Meeting (Member of the Organising Committee)
 Universidade do Algarve, Portugal
2018 - 2018 Workshops in R programming language- Advanced Training - ATT: R for absolute beginners June 4th and 5th, 2018 (2018 - 2018)
Workshop (Co-organisor)
 Universidade do Algarve Faculdade de Ciências e Tecnologia, Portugal

Centro de Ciências do Mar, Portugal
2017/09/08 - 2017/09/08 1st CBMR/ProRegeM Annual Meeting (2017/09/08 - 2017/09/08)
Meeting (Member of the Organising Committee)
 Universidade do Algarve, Portugal
2017 - 2017 Workshops in R programming language- Advanced Training - ATT: R for absolute beginners May 29th and 30th and June 5th and 6th, 2017 (2017 - 2017)
Workshop (Co-organisor)
 Universidade do Algarve Faculdade de Ciências e Tecnologia, Portugal

Centro de Ciências do Mar, Portugal
2016/09/14 - 2016/09/16 Workshop in Marine Genomics (2016 - 2016)
Workshop (Member of the Organising Committee)
 Centro de Ciências do Mar, Portugal
2015 - 2015 Workshops in R programming language - Advanced Training - ATT: R for absolute beginners September 23rd and 24th, 2015 (2015 - 2015)
Workshop (Co-organisor)
 Universidade do Algarve Faculdade de Ciências e Tecnologia, Portugal

Event participation

Activity description
Type of event 		Event name
Institution / Organization
2017/05/17 - 2017/05/18 Presentation of the poster "HEARTI ToolBox: An online platform for the analysis in silico of cardiomyogenesis" at the 7th Bioinformatics and Stem Cells Satellite Meeting
Meeting
 7th Bioinformatics and Stem Cells Satellite Meeting
Universitätsmedizin Rostock, Germany
2017/05/16 - 2017/05/17 Presentation of the poster "HEARTI ToolBox: An online platform for the analysis in silico of cardiomyogenesis" at the international congress promoted by the Stem Cell Network NRW - Germany, Munster
Congress
 9th International Meeting of the Stem Cell Network
2016/06/19 - 2016/06/23 Course in comparative genomics, covering genome analysis and exploration, pair-wise comparisons of genomes, comparisons of multiple genomes, evolutionary inference using a computational biology approach.
Workshop
 EMBO practical course - Computational Biology: Genomes to Systems
European Molecular Biology Laboratory, Germany
2016/04/04 - 2016/04/15 Revolution VI: descriptive statistics, hypothesis testing, modeling and spatial analysis of societies diversity
Workshop
Centro de Ciências do Mar, Portugal
Distinctions

Other distinction

2016 FCT/DAAD Transnational cooperation
Fundação para a Ciência e a Tecnologia, Portugal

Deutscher Akademischer Austauschdienst, Germany
2016 Student travel grant
European Molecular Biology Laboratory, Germany
2015 PhD grant
Fundação para a Ciência e a Tecnologia, Portugal