Rui S. R. Machado - PhD Student

ProRegeM - PhD Programme on Regenerative Medicine

Centre for Molecular and Structural Biomedicine

Faculty of Sciences and Technology (Building 8)

University of Algarve

Phone: + 351 289 800 100 (ext. 7177, Gab. 3.14)

Scientific Interests

* System Biology

* Interaction Networks

* Stem Cells

* Next Generation Sequencing

* Microarray

Academic Degrees

* 2010: Licenciate Degree in Biology, University of Algarve, Portugal

* 2014: Master´s Degree in Biomedical Sciences, University of Algarve, Portugal

Academic and Professional Experience

* 2014: Master Research Grant for bioinformatics analysis under the theme "Parathyroid hormone-related protein and Stanniocalcin: new metabolic hormones?" at Centro Ciencias do Mar (CCMAR), University of Algarve.

* 2014: Master Degree thesis: "Analysis of the transcriptional regulatory network underlying heart development"

* 2011: EU Leonardo Da Vinci grant for work in Science/Education. St. Cecilia's College, Londonderry, Northern Ireland, United Kingdom

* 2010: Biology Degree Project: Analysis of inate defensive genes in clams (Ruditapes decussatus) and how parasitic infection affects those genes

Current Research

* Analysis of the transcriptional regulatory network underlying heart development

Publications

* Rui Machado, Agapios Sachinidis and Matthias E. Futschik (2021) 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), 2477 (pdf+html)

* João Santos, Leonardo Mendes-Silva, Vanessa Afonso, Gil Martins, Rui Machado, João Lopes, Leonor Cancela, Matthias Futschik, Agapios Sachinidis, Paulo Gavaia, and José Bragança (2019) Exogenous Wnt5a and Wnt11 proteins rescue Cited2 dysfunction in mouse embryonic stem cells and zebrafish morphants, Cell Death & Disease volume 10, Article number: 582 (pdf + html )

* Marinella N Ghezzo, Mónica T Fernandes, Ivette Pacheco-Leyva, Pedro M Rodrigues, Rui S Machado, Marta A S Araújo, Ravi K Kalathur, Matthias E Futschik, Nuno L Alves and Nuno R dos Santos; FoxN1-dependent thymic epithelial cells promote T-cell leukemia development, Carcinogenesis 39, 12, 1463 - 1476 (pdf+html)

* Davood Sabour, Rui S.R. Machado, José P. Pinto, Susan Rohani, Raja G.A. Sahito, Jürgen Hescheler, Matthias E. Futschik and Agapios Sachinidis (2018) Parallel Genome-wide Profiling of Coding and Non-coding RNAs to Identify Novel Regulatory Elements in Embryonic and Maturated Heart, Molecular Therapy - Nucleic Acids, 12, 158-173 (pdf+html)

*José Pinto, Rui Machado, Ramiro Magno, Daniel Oliveira, Susana Machado, Raquel Andrade, José Bragança, Isabel Duarte & Matthias Futschik (2018) StemMapper: A Curated Gene Expression Database for Stem Cell Lineage Analysis, Nucleic Acids Research D1: D788 - D793 (pdf+html)

*José P. Pinto, Ravi K. Kalathur, Daniel V. Oliveira, Tânia Barata, Rui S. R. Machado, Susana Machado, Ivette Pacheco-Leyva, Isabel Duarte and Matthias E. Futschik. StemChecker: a web-based tool to discover and explore stemness signatures in gene sets, Nucleic Acids Research 43 (W1): W72-W77 (pdf + html)

* Ravi K. Kalathur, José P. Pinto,Miguel A. Hernández-Prieto, Rui S.R. Machado, Dulce Almeida, Gautam Chaurasia and Matthias Futschik (2014) UniHI 7: an enhanced database for retrieval and interactive analysis of human molecular interaction networks, Nucleic Acids Research, Database issue, 42 (D1): D408-D414 (html, pdf)

*José P. Pinto, Ravi K.R. Kalathur, Rui S. R. Machado , Joana M. Xavier, José Bragança, and Matthias E. Futschik(2014) StemCellNet: an interactive platform for network-oriented investigations in stem cell biology. Nucleic Acids Research 42:W154-W160. (pdf+html)

*José P. Pinto, Rui Machado, Joana G. Xavier and Matthias E. Futschik(2014) Targeting molecular networks for drug research. Frontiers in Genetics 5: 160 (pdf + html )

Presentations

*Rui S. R. Machado, José P. Pinto, Davood Sabour, José Bragança, A. Sachinidis and Matthias E. Futschik (2017) HEARTI ToolBox: An online platform for the analysis in silico of cardiomyogenesis, Poster presentation, 10th International Meeting of the Stem Cell Network NRW, Münster, Germany

*José Pedro Pinto, Ravi Kalathur, Daniel V. Oliveira, Tânia Barata, Rui Machado, Susana Machado, Ivette Pacheco-Leyva, Joana M. Xavier, José Bragança, Isabel Duarte and Matthias Futschik (2016) SCIS Toolbox: Design and implementation of online tools for in silico stem cell biology, INFORUM 2016, Lisbon, Portugal

*Rui Machado (2016) Identification of key factors of heart regeneration using a systems biology approach, ProRegeM, Annual Meeting 2016, Lisbon, Portugal

*RS Machado, JP Pinto, DV Oliveira, I. Duarte, S Machado, J Bragança & M Futschik (2015) A meta-analysis study of stem cell differentiation in the context of cardiogenesis.9th International Meeting of the Portuguese society for Stem cells and Cell therapies. Oeiras. Portugal.

*DV Oliveira, I Duarte, RS Machado, I Pacheco-Leyva, T Justo, JP Pinto, S Machado, JA Belo, J Bragança & ME Futschik(2015) From Stem Cells 2 Heart: Finding novel candidate isoforms and genes for cardiomyogenesis. 9th International Meeting of the Portuguese society for Stem cells and Cell therapies. Oeiras. Portugal.

*S Machado, R Kalathur, DV Oliveira, T Barata, R Machado, I Pacheco-Leyva, I Duarte, M Futschik, J Pinto (2015) StemChecker: a web-based tool to discover and explore stemness signatures in gene sets.9th International Meeting of the Portuguese society for Stem cells and Cell therapies. Oeiras. Portugal.

*JP Pinto, R Kalathur, RS Machado, J Xavier, J Bragança & ME Futschik (2015) StemCellNet: an interactive platform for network -oriented investigations in stem cell biology. 9th International Meeting of the Portuguese society for Stem cells and Cell therapies. Oeiras. Portugal.

* J. Pinto, R. Kalathur,R. Machado , J. Xavier, J. Bragança, and M.E Futschik (2014) StemCellNet: an interactive platform for network-oriented investigations in stem cell biology, Heart without Boarders, International Conference, Porto, Portugal (abstract)

*D Oliveira,R. Machado, I. Pacheco-Leyva, I. Duarte, T. Justo , J. Pinto, J. Belo, J. Bragança and M. Futschik (2014) From Stem Cells 2 heart: Finding novel candidate genes for cardiomyogenesis, Heart without Boarders, International Conference, Porto, Portugal (abstract)

* Rui S.R. Machado, José Pedro B. G. P. Pinto, José Bragança and Matthias E. Futschik (2013) What a heart makes or breaks: A meta-analysis of gene expression profiles , 8th International Meeting of the Portuguese Society for Stem Cells and Cell Therapies, Faro, Portugal

* José Pedro B. G. P. Pinto, Rui S.R. Machado, Ravi K.R. Kalathur, and Matthias E. Futschik (2013) StemCellNet: A web-based Platform for Assembly and Analysis of Molecular Interaction Networks in Stem Cells, 8th International Meeting of the Portuguese Society for Stem Cells and Cell Therapies, Faro, Portugal