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Jose A. Arjona-Medinaphone: +43-732-2468-4480 e-mail: arjona@bioinf.jku.at Room: S3 327 (Computer Science Building, Science Park 3) |
CV
Education
- Currently Phd. Student at Johannes Kepler University (JKU), Linz, Austria. Under supervision of Prof. Sepp Hochreiter
- Doctor by University of Malaga (UMA), Spain. 2017. (Supervisor Prof. Oswaldo Trelles). Doctoral thesis Presentation Slides
- Master degree on Software Engineering and Artificial Intelligence, UMA, Malaga, Spain. 2013
- Master degree on Electronics Systems for Intelligent Environments, UMA, Malaga, Spain. 2011
- Pedagogical Certificate Aptitude, UMA, Malaga, Spain. 2008
- Technical Telecommunication Engineering, UMA, Malaga, Spain. 2007
- Professional Intermediate-level Music, Manuel Carra, Malaga, Spain, Esp. Piano. 2007
Honors, Awards and Fellowships
- Doctoral thesis grade: "Sobresaliente Cum laude" and "Mención Europea" honors. Title: "Algorithms and methods for large-scale genome rearrangements identification". 2017
- Marie Curie Actions fellowship, Industry Academia Partnerships and Pathways (IAPP), MrSymbiomath project. 2014
- Final Degree Project grade: "Matricula de honor". Title: "Segmentation and 3D reconstruction of bone tissue in medical imaging from computerized axial tomography”. 2007
Employment record
- 2016- : present: Research Assistant, Institute of Bioinformatics, Johannes Kepler University, Linz, Austria
- 2016-2016: Researcher, Computer Architecture department. University of Malaga. Bit-Lab Group, Proj: Plataforma tecnógica de Recursos Biomoleculares y Bioinformáticos Málaga, Spain
- 2014-2016: Software Development, RISC Software GmbH, High Performance, Cloud and Symbolic Computing in Big-Data problems applied to mathematical modeling of Comparative genomics (mrSymBioMath), Industry-Academia Partnership and Pathways (IAPP) - Marie Curie Programme-EU. Hagenberg (Linz), Austria
- 2013-2014: Researcher, University of Malaga. Computer Architecture department. Bit- Lab Group, Proj. Red de Investigación de Reacciones Adversas a Alergenos y fármacos (RIRAAF) RD12/0013., Instituto de Salud Carlos III - Programa Redes RETICS. Málaga, Spain
- 2009-2012: High School Teacher, JUNTA DE ANDALUCIA. Andalucía, Spain
Research topics
- Reinforcement Learning
- Actor-critic models
- Deep Learning and Neural Networks
- Comparative Genomics
- Bioinformatics algorithms
Selected publications
- (2016) Refining borders of genome-rearrangements including repetitions, J. A. Arjona-Medina and O. Trelles, BMC Genomics, 2016, 17(Suppl 8):804. DOI:10.1186/s12864-016-3069-4
- (2016) Computational workflow for the fine-grained analysis of metagenomic samples, Esteban Pérez-Wohlfeil, José Arjona-Medina, Óscar Torreño-Tirado, Eugenia Ulzurrun, Oswaldo Trelles, BMC Genomics,2016, 17(Suppl 8):802. DOI:10.1186/s12864-016-3063-x
- (2016) Computational Synteny Block: A framework to identify Evolutionary Events, Jose A. Arjona-Medina and Oswaldo Trelles, IEEE Transactions on NanoBioscience, 2016, 15 (4)pp. 1-11.
Conferences and poster
- Speeding up Semantic Segmentation for Autonomous Driving, Michael Treml*, José Arjona-Medina*, Thomas Unterthiner*, Rupesh Durg esh, Felix Friedmann, Peter Schuberth, Andreas Mayr, Martin Heusel, Markus Hofmarche r, Michael Widrich, Bernhard Nessler, Sepp Hochreiter Machine Learning for Intelligent Transportation Systems, in conjunction with Neural Information Processing Systems (NIPS), 2016, link
- Refining borders of genome-rearrangements using repetitions, J. A. Arjona-Medina and O. Trelles, SolBio International Conference 2016 on "Bioinformatics & Computational Biology for Innovative Genomics”ť April, 2016. Riviera Maya, MÉXICO.
- Computational workflow for the fine-grained analysis of metagenomic samples, Esteban Pérez-Wohlfeil, José Arjona-Medina, Óscar Torreño-Tirado, Eugenia Ulzurrun, Oswaldo Trelles, SolBio International Conference 2016 on "Bioinformatics & Computational Biology for Innovative Genomics”ť April, 2016. Riviera Maya, MÉXICO.
- GECKO-MGV: Evolution Events driven tool for enhanced visual analysis of multi-genome comparisons, S. Díaz Del Pino, J. A. Arjona-Medina, O. Torreño, S. Benavides and O. Trelles, International Work-Conference on Bioinformatics and Biomedical Engineering IWBBIO 2016. April, 2016. Granada (SPAIN).
- Computational Synteny Block: A framework to identify Evolutionary Events, Jose A. Arjona-Medina and Oswaldo Trelles, IEEE International Conference on Bioinformatics and Biomedicine (BIBM), 2015, pp. 5-12.
- Experimental Study of Local Alignment Distributions in the Comparison of Large Genomic Sequences, Jose A. Arjona-Medina, Oscar Torreño Tirado, Noura Chelbat and Oswaldo Trelles, ISCB-Latin America x-Meeting on Bioinformatics with BSB & SoiBio. Belo Horizonte, Brazil October 28 - 30, 2014.
- Software for featuring genome evolution, Jose A. Arjona-Medina, Oscar Torreño Tirado and Oswaldo Trelles, European Conference on Computational Biology, Strasbourgh, France, 7th - 10th of September 2014.
- Digital Signal Processing applied to the identification of Evolutionary Events, Jose A. Arjona-Medina, Oscar Torreño Tirado and Oswaldo Trelles, 4to Congreso Argentino de Bioinformática y Biología Computacional y 4ta Conferencia Internacional de la Sociedad Iberoamericana de Bioinformática (SoIBio).
Teaching
- Practical course on Galaxy, SolBio International Conference 2016 on "Bioinformatics & Computational Biology for Innovative Genomics”ť April, 2016. Riviera Maya, MÉXICO.
- Special Topics in Bioinformatics: Breaking the computational barriers in pairwise genome comparison, Johannes Kepler University. Linz, Austria
- High School Teacher (2009-2012)