Publications

Journal Papers

2014

Analyzing Phylogenetic Trees with Timed and Probabilistic Model Checking: The Lactose Persistance Case Study. J.I. Requeno and J.M. Colom. Journal of Integrative Bioinformatics, 11(3). 2014


2013

Model checking software for phylogenetic trees using distribution and database methods. J.I. Requeno and J.M. Colom. Journal of Integrative Bioinformatics, 10(3). 2013.

Temporal Logics for Phylogenetic Analysis via Model Checking. J.I. Requeno, G. de Miguel Casado, R. Blanco and J.M. Colom. IEEE/ACM Transactions on Computational Biology and Bioinformatics, 10(4): 1058-1070. 2013.


2011

Rebooting the human mitochondrial phylogeny: an automated and scalable methodology with expert knowledge. R. Blanco, E. Mayordomo, J. Montoya and E. Ruiz-Pesini. BMC Bioinformatics, 12(174): 29 pp. 2011.

 

Conference Papers

2015

Conservation in Mitochondrial DNA: Parallelized Estimation and Alignment Influence. F.Merino-Casallo, J. Álvarez-Jarreta and E. Mayordomo. Proceedings of the IEEE International Conference on Bioinformatics and Biomedicine (BIBM 2015), 1434-1440. 2015.


2014

PhyloFlow: A fully customizable and automatic workflow for phylogenetic reconstruction. J. Álvarez-Jarreta, G. de Miguel Casado and E. Mayordomo. Proceedings of the IEEE International Conference on Bioinformatics and Biomedicine (BIBM 2014), 1-7. 2014.

Timed and Probabilistic Model Checking over Phylogenetic Trees. J.I. Requeno and J.M. Colom. 8th International Conference on Practical Applications of Computational Biology & Bioinformatics (PACBB 2014). 2014.

PhyloFlow: A Fully Customizable and Automatic Workflow for Phylogeny Estimation. J. Álvarez-Jarreta, G. de Miguel Casado and E. Mayordomo. 13th European Conference on Computational Biology (ECCB 2014). 2014.

PhyloViewer: A Viewer for Large Phylogenies. J. Álvarez-Jarreta, G. de Miguel Casado and E. Mayordomo. 13th European Conference on Computational Biology (ECCB 2014). 2014.


2013

Speeding Up Phylogenetic Model Checking. J.I. Requeno and J.M. Colom. 7th International Conference on Practical Applications of Computational Biology and Bioinformatics (PACBB 2013), 222: 119-126. 2013.


2012

PHYSER: An Algorithm to Detect Sequencing Errors from Phylogenetic Information. J. Álvarez-Jarreta, E. Mayordomo, and E. Ruiz-Pesini. Proceedings of the 6th International Conference on Practical Applications of Computational Biology & Bioinformatics (PACBB 2012). Springer-Verlag Advances in Soft Computing, 154: 105-112. 2012.

Sliced Model Checking for Phylogenetic Analysis. J.I. Requeno, R. Blanco, G. de Miguel Casado and J.M. Colom. Proceedings of the 6th International Conference on Practical Applications of Computational Biology & Bioinformatics (PACBB 2012). Springer-Verlag Advances in Soft Computing, 154. 2012.

Compact representation of biological sequences using set decision diagrams. J.I. Requeno and J.M. Colom. Proceedings of the 6th International Conference on Practical Applications of Computational Biology & Bioinformatics (PACBB 2012). Springer-Verlag Advances in Soft Computing, 154. 2012.


2011

Workflows with model selection: a multilocus approach to phylogenetic analysis. J. Álvarez, R. Blanco and E. Mayordomo. Proceedings of the 5th International Conference on Practical Applications of Computational Biology & Bioinformatics (PACBB 2011). Springer-Verlag Advances in Soft Computing, 93/2011: 39-47. 2011.

Phylogenetic Analysis Using an SMV Tool. J.I. Requeno, R. Blanco, G. de Miguel Casado and J.M. Colom. Proceedings of the 5th International Conference on Practical Applications of Computational Biology & Bioinformatics (PACBB 2011). Springer-Verlag Advances in Soft Computing, 93/2011: 167-174. 2011.

Simplification Methods for Maximum Parsimony: A Relational View. R. Blanco. Proceedings of the IEEE International Conference on Bioinformatics and Biomedicine (BIBM 2011): 49-56. 2011.


2010

Scalable Phylogenetics through Input Preprocessing. R. Blanco, E. Mayordomo, E. Montes, R. Mayo and A. Alberto. Advances in Bioinformatics: Proceedings of the 4th International Workshop on Practical Applications of Computational Biology & Bioinformatics (IWPACBB 2010). Springer-Verlag Advances in Soft Computing, 74/2010: 123-130. 2010.

Temporal Logics for Phylogenetic Analysis via Model Checking. R. Blanco, G. de Miguel, J.I. Requeno and J.M. Colom. Proceedings of the IEEE International Conference on Bioinformatics and Biomedicine (BIBM 2010): 152-157. 2010.

Structural parsimony: Reductions in sequence space. R. Blanco. Proceedings of the IEEE International Conference on Bioinformatics and Biomedicine (BIBM 2010): 47-61. 2010.


2009

Building maintainable, exhaustive human mitochondrial phylogenies. R. Blanco and E. Mayordomo. 17th Annual International Conference on Intelligent Systems for Molecular Biology/8th European Conference. 2009.

ZARAMIT: a system for the evolutionary study of human mitochondrial DNA. R. Blanco and E. Mayordomo. Proceedings of the 3rd International Workshop on Practical Applications of Computational Biology & Bioinformatics (IWPACBB 2009, within IWANN 2009). Springer-Verlag Lecture Notes in Computer Science, 5518: 1139-1142. 2009.

Exhaustive mitochondrial phylogenetics: challenges and solutions. R. Blanco and E. Mayordomo. 9th Workshop on Algorithms in Bioinformatics (WABI 2009). 2009.