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José Pedro B. G. P. Pinto - Postdoctoral Fellow

Centre for Molecular and Structural Biomedicine

Faculty of Sciences and Technology (Building 8,Lab 1.5)

University of Algarve

Phone: + 351 289 800 100 (extn. 7292 )


Journals

[8] Ravi Kiran Reddy Kalathur, José Pedro Pinto, Biswanath Sahoo, Gautam Chaurasia & Matthias E. Futschik (2017) HDNetDB: A Molecular Interaction Database for Network-Oriented Investigations into Huntington's Disease, Scientific Reports 7: 5216 (pdf+html)

[7] 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 (2015). StemChecker: a web-based tool to discover and explore stemness signatures in gene sets, Nucleic Acids Research 43 (W1): W72-W77 (pdf + html)

[6] 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)

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

[4] Ravi K. Kalathur, José P. Pinto, Miguel A. Hernández-Prieto, Rui S.R. Machado, Dulce Almeida, Gautam Chaurasia and Matthias Futschik 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)

[3] A. Lourenço, S. Carneiro, J.P. Pinto, M. Rocha, E.C. Ferreira, I. Rocha. A Study on the Short and Long-Term Regulation of E. coli Metabolic Pathways. Journal of Integrative Bioinformatics. 8(3), 1-15, 2011. Indexed by Scimago (Q1) and DBLP;

[ Repository]

[2] I. Rocha, P. Maia, P. Evangelista, P. Vilaça, S. Soares, J.P. Pinto, J. Nielsen, K.R. Patil, E.C. Ferreira, M. Rocha. OptFlux: an open-source software platform for in silico metabolic engineering. BMC Systems Biology, 4(45), 2010 (IF 3.71) Highly accessed paper: http://www.biomedcentral.com/1752-0509/4/45 Indexed by ISI JCR 2010 FI 3.565 (Q1), Scimago (Q1) e Scopus;

[ Repository]

[1] M. Rocha, P. Maia, R. Mendes, J.P. Pinto, E.C. Ferreira, J. Nielsen, K.R. Patil, I. Rocha. Natural computation meta-heuristics for the in silico optimization of microbial strains. BMC Bioinformatics, 9(499), BioMed Central, November 2008. Indexed by ISI JCR 2010 FI 3.029 (Q1), Scimago (Q1), Scopus e DBLP

[ Repository]

Conference Proceeding

[4] J.P. Pinto, I. Rocha, M. Rocha. Highlighting Metabolic Strategies Using Network Analysis over Strain Optimization Results. Proc. Pattern Recognition in Bioinformatics (PRIB 2011), Lecture Notes in Computer Science, vol. 7036, pp. 109-120, Springer, Delft, Nov. 2011. Indexed by Scopus, DBLP and Scimago (Q2);

[ Repository]

[5] A. Lourenço, S. Carneiro, J.P. Pinto, M. Rocha, E.C. Ferreira, I. Rocha. Interpreting the Regulatory Interplay in E. coli Metabolic Pathways. Proceedings of Conference on Practical Applications of Bioinformatics and Computational Biology (PACBB 2011), Advances on Intelligent and Soft Computing, vol. 93, pp. 303-312, Springer, April 2011. Indexed by ISI WoS; Scopus; DBLP; Scimago (Q4)

[ Repository]

[6] J.P. Pinto, I. Rocha, M. Rocha. A software tool for network topology analysis under a metabolic engineering perspective. Proceedings of the ACM Conference on Bioinformatics and Computational Biology (ACM BCB 2010), pp. 569- 578, ACM Press, August 2010. Indexed by Scopus; DBLP

[7] J.P. Pinto, O. Dias, A. Lourenço, S. Carneiro, E.C. Ferreira, I. Rocha, M. Rocha. Data Integration Issues in the Reconstruction of the Genome-scale Metabolic Model of Zymomonas mobillis. Proceedings IWPACBB'08, pp. 92-101, Series: Advances on Soft Computing, Springer Verlag, Salamanca, October 2008. Indexed by ISI WoS; Scopus; DBLP; Scimago (Q4);

[ Repository]

[8] M. Rocha, R. Mendes, P. Maia, J.P. Pinto, I. Rocha, E.C. Ferreira. Evaluating Simulated Annealing Algorithms in the Optimization of Bacterial Strains. Proceedings EPIA 2007, Lecture Notes in Artificial Intelligence, pp. 473-484, vol. 4874, Springer, Guimarães, December 2007. Indexed by ISI WoS; Scopus, DBLP and Scimago (Q2);

[ Repository]

[9] M. Rocha, J.P. Pinto, I. Rocha, E.C. Ferreira. Evaluating Evolutionary Algorithms and Differential Evolution for the Online Optimization of Fermentation Processes. Proceedings EvoBio’2007, Lecture Notes on Computer Science, vol. 4447, pp. 236-246, Springer, Valencia, April 2007. Indexed by ISI WoS, Scopus, DBLP and Scimago (Q2)

[ Repository]

[10] M. Rocha, J.P. Pinto, I. Rocha, E.C. Ferreira. Optimization of Bacterial Strains with Variable-Sized Evolutionary Algorithms. Proceedings IEEE Symposium on Computational Intelligence in Bioinformatics and Computational Biology, pp. 331-337, IEEE Press, Honolulu, USA, April 2007. Indexed by ISI WoS; DBLP;

[ Repository]

Book Chapters

[11] R. Mendes, I. Rocha, J.P. Pinto, E.C. Ferreira, M. Rocha. Differential Evolution for the Offline and Online Optimization of Fed-Batch Fermentation Processes. In U.K. Chakraborty (ed.), Advances on Differential Evolution. Series: Studies in Computational Intelligence, vol. 143. chap. 13, pp. 299-318, Springer, 2008. Indexed: Scopus; Scimago (Q4)

[ Repository]

Posters and presentations

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

J Pinto, Machado, R Kalathur, DV Oliveira, T Barata, R Machado, S Machado, I Pacheco-Leyva, I Duarte, M Futschik (2016) StemChecker: a web-based tool to discover and explore stemness signatures in gene sets. Bioinformatics Open Days, Braga, 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.

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.

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.

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.

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)

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

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

PRIB 2011, The Netherlands, Delft: Highlighting Metabolic Strategies using Network Analysis over Strain Optimization Results.

RECOMB 2010, Portugal, Lisbon: A software tool for network topology analysis under a Metabolic Engineering perspective.

Software Developed

StemChecker Web server for detection of stemness signatures in gene lists provided by the user.

StemCellNet Web server for network-oriented investigations in stem cell biology

InBiNA Tool for analysing biological networks; roll: main programmer.

OptFlux Platform for Metabolic Engineering; roll: programmer.

TNA4OptFlux Plug-in for OptFlux which adds metabolic network creation and analysis functionalities.