Publications

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58 entries « 1 of 2 »

2020

L. Melgar-García and D. Gutiérrez-Avilés and C. Rubio-Escudero and A. Troncoso

High-content screening images streaming analysis using the STriGen methodology (Conference)

SAC 35th Annual ACM Symposium on Applied Computing, 2020.

(Links | BibTeX | Tags: bioinformatics)

F. M. Delgado-Chaves and F. Gómez-Vela and F. Divina and M. García-Torres and D. S. Rodríguez-Baena

Computational Analysis of the Global Effects of Ly6E in the Immune Response to Coronavirus Infection Using Gene Networks (Journal Article)

Genes, 11 (7), pp. 831-864, 2020.

(Abstract | BibTeX | Tags: bioinformatics)

T. Vanhaeren and F. Divina and M. García-Torres and F. Gómez-Vela and W. Vanhoof and P. M. Martínez-García

A Comparative Study of Supervised Machine Learning Algorithms for the Prediction of Long-Range Chromatin Interactions (Journal Article)

Genes, 11 (9), pp. 985, 2020.

(Abstract | BibTeX | Tags: bioinformatics)

2019

F. M Delgado-Chaves and F. Gómez-Vela and M. García-Torres and F. Divina and J. Luis Vázquez Noguera

Computational Inference of Gene Co-Expression Networks for the identification of Lung Carcinoma Biomarkers: An Ensemble Approach (Journal Article)

Genes, 10 (12), pp. 962, 2019.

(Abstract | Links | BibTeX | Tags: bioinformatics)

F. Gómez-Vela and F. M Delgado-Chaves and D.S. Rodríguez-Baena and M. García-Torres and F. Divina

Ensemble and Greedy Approach for the Reconstruction of Large Gene Co-Expression Networks (Journal Article)

Entropy, 21 (12), pp. 1139, 2019.

(Abstract | Links | BibTeX | Tags: bioinformatics)

E.L. Mangas and A. Rubio and R. Álvarez-Marín and G. Labrador-Herrera and J. Pachón and M. Eugenia Pachón-Ibáñez and F. Divina and A.J. Pérez-Pulido

Pangenome of Acinetobacter baumannii uncovers two groups of genomes, one of them with genes involved in CRISPR/Cas defence systems associated with the absence of plasmids and exclusive genes for biofilm formation (Journal Article)

Microbial Genomics, pp. mgen000309, 2019.

(Abstract | Links | BibTeX | Tags: bioinformatics)

2018

D. Gutiérrez-Avilés and R. Giráldez and F. J. Gil-Cumbreras and C. Rubio-Escudero

TRIQ: a new method to evaluate triclusters (Journal Article)

BioData Mining, 11 (1), pp. 15, 2018.

(Abstract | Links | BibTeX | Tags: bioinformatics, time series)

J. A. Nepomuceno and A. Troncoso and J. S. Aguilar-Ruiz

Pairwise gene GO-based measures for biclustering of high-dimensional expression data (Journal Article)

BioData Mining, 11 (4), 2018.

(Abstract | Links | BibTeX | Tags: bioinformatics)

P. Manuel Martínez-García and M. García-Torres and F. Divina and F. Gómez-Vela and F. Cortés-Ledesma

Analysis of Relevance and Redundance on Topoisomerase 2b (TOP2B) Binding Sites: A Feature Selection Approach (Conference)

International Conference on the Applications of Evolutionary Computation, 2018.

(Links | BibTeX | Tags: bioinformatics)

E. Pereda and M. García-Torres and B. Melián and S. Ma~nas and L. Méndez and J. González

The Blessing of Dimensionality: Feature Selection Outperforms Functional Connectivity-based Feature Transformation to Classify ADHD Subjects from EEG Patterns of Phase Synchronisation (Journal Article)

PLoS ONE, 13 (8), 2018.

(Links | BibTeX | Tags: bioinformatics)

2016

D. Gutiérrez-Avilés and C. Rubio-Escudero

TRIQ: A Comprehensive Evaluation Measure for Triclustering Algorithms (Conference)

Hybrid Artificial Intelligent Systems: 11th International Conference, HAIS 2016, Seville, Spain, April 18-20, 2016, Proceedings, Lecture Notes in Computer Science 2016.

(Links | BibTeX | Tags: bioinformatics, time series)

J. A. Nepomuceno and A. Troncoso and I. Nepomuceno and J. S. Aguilar-Ruiz

Biclustering of gene expression data based on SimUI semantic similarity measure (Conference)

HAIS 11th International Conference on Hybrid Artificial Intelligence Systems, Lecture Notes in Computer Science 2016.

(Links | BibTeX | Tags: bioinformatics)

2015

D. Gutiérrez-Avilés and C. Rubio-Escudero

MSL: A Measure to Evaluate Three-dimensional Patterns in Gene Expression Data (Journal Article)

Evolutionary Bioinformatics, 11 , pp. 121—135, 2015.

(Abstract | Links | BibTeX | Tags: bioinformatics, time series)

J. A. Nepomuceno and A. Troncoso and J. S. Aguilar-Ruiz

Scatter Search-based identification of local patterns with positive and negative correlations in gene expression data (Journal Article)

Applied Soft Computing, 35 , pp. 637-651, 2015.

(Abstract | Links | BibTeX | Tags: bioinformatics)

A. E. Marquez-Chamorro and G. Asencio-Cortes and C. E. Santiesteban-Toca and J. S. Aguilar-Ruiz

Soft computing methods for the prediction of protein tertiary structures: A survey (Journal Article)

Applied Soft Computing, (35), pp. 398-410, 2015, ISSN: 1568-4946.

(Abstract | Links | BibTeX | Tags: bioinformatics)

G. Asencio-Cortes and J. S. Aguilar-Ruiz and A. E. Marquez-Chamorro

An Efficient Nearest Neighbor Method for Protein Contact Prediction (Conference)

Hybrid Artificial Intelligent Systems, 2015, ISBN: 978-3-319-19644-2.

(Abstract | BibTeX | Tags: bioinformatics)

J. A. Nepomuceno and A. Troncoso and J. S. Aguilar-Ruiz

Integrating biological knowledge based on functional annotations for biclustering of gene expression data (Journal Article)

Computers Methods and Programs in Biomedicine, 119 (3), pp. 163-180, 2015.

(Abstract | Links | BibTeX | Tags: bioinformatics)

2014

D. Gutiérrez-Avilés and C. Rubio-Escudero

Mining 3D Patterns from Gene Expression Temporal Data: A New Tricluster Evaluation Measure (Journal Article)

The Scientific World Journal, 2014 , pp. 1-16, 2014.

(Abstract | Links | BibTeX | Tags: bioinformatics, time series)

D. Gutiérrez-Avilés and C. Rubio-Escudero

LSL: A new measure to evaluate triclusters (Conference)

2014 IEEE International Conference on Bioinformatics and Biomedicine (BIBM), 2014.

(Links | BibTeX | Tags: bioinformatics, time series)

A. E. Marquez-Chamorro and G. Asencio-Cortes and F. Divina and J. S. Aguilar-Ruiz

Evolutionary decision rules for predicting protein contact maps (Journal Article)

Pattern Analysis and Applications, 4 (17), pp. 725-737, 2014, ISSN: 1433-7541.

(Abstract | Links | BibTeX | Tags: bioinformatics)

D. Gutiérrez-Avilés and C. Rubio-Escudero and F. Martínez-Álvarez and J.C. Riquelme

TriGen: A genetic algorithm to mine triclusters in temporal gene expression data (Journal Article)

Neurocomputing, 132 , pp. 42-53, 2014.

(Abstract | Links | BibTeX | Tags: bioinformatics)

2013

M. García-Torres and R. Arma~nanzas and C. Bielza and P. Larra~naga

Comparison of metaheuristic strategies for peakbin selection in proteomic mass spectrometry data (Journal Article)

Information Sciences, 222 , pp. 229-246, 2013.

(Links | BibTeX | Tags: bioinformatics, feature selection)

2012

G. Asencio-Cortes and J. S. Aguilar-Ruiz and A. E. Marquez-Chamorro and R. Ruiz and C. E. Santiesteban-Toca

Prediction of Mitochondrial Matrix Protein Structures Based on Feature Selection and Fragment Assembly (Conference)

Evolutionary Computation, Machine Learning and Data Mining in Bioinformatics, Springer Berlin Heidelberg, Berlin, Heidelberg, 2012, ISBN: 978-3-642-29066-4.

(Abstract | BibTeX | Tags: bioinformatics)

A. E. Marquez-Chamorro and F. Divina and J. S. Aguilar-Ruiz and J. Bacardit and G. Asencio-Cortes and C. E. Santiesteban-Toca

A NSGA-II Algorithm for the Residue-Residue Contact Prediction (Conference)

Evolutionary Computation, Machine Learning and Data Mining in Bioinformatics, Springer Berlin Heidelberg, Berlin, Heidelberg, 2012, ISBN: 978-3-642-29066-4.

(Abstract | BibTeX | Tags: bioinformatics)

C. E. Santiesteban-Toca and G. Asencio-Cortes and A. E. Marquez-Chamorro and J. S. Aguilar-Ruiz

Short-Range Interactions and Decision Tree-Based Protein Contact Map Predictor (Conference)

Evolutionary Computation, Machine Learning and Data Mining in Bioinformatics, Springer Berlin Heidelberg, Berlin, Heidelberg, 2012, ISBN: 978-3-642-29066-4.

(Abstract | BibTeX | Tags: bioinformatics)

D. Gutiérrez-Avilés and F. Martínez-Álvarez and C. Rubio-Escudero and J. C. Riquelme

Finding motifs in DNA sequences (Workshop)

Spanish Conference on Technologies and Fuzzy Logic (ESTYLF'12), 2012.

(BibTeX | Tags: bioinformatics)

2011

A. E. Marquez-Chamorro and F. Divina and J. S. Aguilar-Ruiz and G. Asencio-Cortes

A multi-objective genetic algorithm for the Protein Structure Prediction (Conference)

2011 11th International Conference on Intelligent Systems Design and Applications, 2011, ISSN: 2164-7151.

(Links | BibTeX | Tags: bioinformatics)

D. Gutiérrez-Avilés and C. Rubio-Escudero and J. C. Riquelme

Revisiting the yeast cell cycle problem with the improved TriGen algorithm (Conference)

2011 Third World Congress on Nature and Biologically Inspired Computing, 2011.

(Links | BibTeX | Tags: bioinformatics, time series)

D. Gutiérrez-Avilés and C. Rubio-Escudero and J. C. Riquelme

Unravelling the Yeast Cell Cycle Using the TriGen Algorithm (Conference)

Advances in Artificial Intelligence, 2011.

(Links | BibTeX | Tags: bioinformatics, time series)

J. A. Nepomuceno and A. Troncoso and J. S. Aguilar-Ruiz

Biclustering of Gene Expression Data by Correlation-Based Scatter Search (Journal Article)

BioData Mining, 4 (3), 2011.

(Abstract | Links | BibTeX | Tags: bioinformatics)

J. A. Nepomuceno and A. Troncoso and J. S. Aguilar-Ruiz

Inferring Genes Coexpression Networks with Biclustering Based on Scatter Search (Conference)

ISDA 11th International Conference on Intelligent Systems Design and Applications, 2011.

(Links | BibTeX | Tags: bioinformatics)

J. A. Nepomuceno and A. Troncoso and J. S. Aguilar-Ruiz

A Local Search in Scatter Search for Improving Biclusters (Conference)

NABIC 3th Congress on Natural and Biologically Inspired Computing, 2011.

(Links | BibTeX | Tags: bioinformatics)

G. Asencio-Cortes and J. S. Aguilar-Ruiz

Predicting protein distance maps according to physicochemical properties (Conference)

8 , 2011, ISSN: 1613-4516.

(Links | BibTeX | Tags: bioinformatics)

A. E. Marquez-Chamorro and F. Divina and J. S. Aguilar-Ruiz and G. Asencio-Cortes

Residue-Residue Contact Prediction Based on Evolutionary Computation (Conference)

5th International Conference on Practical Applications of Computational Biology & Bioinformatics (PACBB 2011), Springer Berlin Heidelberg, 2011, ISBN: 978-3-642-19914-1.

(Abstract | BibTeX | Tags: bioinformatics)

G. Asencio-Cortes and J. S. Aguilar-Ruiz and A. E. Marquez-Chamorro

Prediction of Protein Distance Maps by Assembling Fragments According to Physicochemical Similarities (Conference)

5th International Conference on Practical Applications of Computational Biology & Bioinformatics (PACBB 2011), 2011, ISBN: 978-3-642-19914-1.

(Abstract | BibTeX | Tags: bioinformatics)

A. E. Marquez-Chamorro and F. Divina and J. S. Aguilar-Ruiz and G. Asencio-Cortes

An Evolutionary Approach for Protein Contact Map Prediction (Conference)

Evolutionary Computation, Machine Learning and Data Mining in Bioinformatics, 2011, ISBN: 978-3-642-20389-3.

(Abstract | BibTeX | Tags: bioinformatics)

G. Asencio-Cortes and J. S. Aguilar-Ruiz and A. E. Marquez-Chamorro

A Nearest Neighbour-Based Approach for Viral Protein Structure Prediction (Conference)

Evolutionary Computation, Machine Learning and Data Mining in Bioinformatics, 2011, ISBN: 978-3-642-20389-3.

(Abstract | BibTeX | Tags: bioinformatics)

C. E. Santiesteban-Toca and A. E. Marquez-Chamorro and G. Asencio-Cortes and J. S. Aguilar-Ruiz

A Decision Tree-Based Method for Protein Contact Map Prediction (Conference)

Evolutionary Computation, Machine Learning and Data Mining in Bioinformatics, 2011, ISBN: 978-3-642-20389-3.

(Abstract | BibTeX | Tags: bioinformatics)

C. Rubio-Escudero and F. Martínez-Álvarez and M. Martínez-Ballesteros and J. C. Riquelme

On the use of algorithms to discover motifs in DNA sequences (Conference)

IEEE International Conference on Intelligent Systems Design and Applications (ISDA'11), 2011.

(Links | BibTeX | Tags: bioinformatics)

F. Gómez-Vela and F. Martínez-Álvarez and C. D. Barranco and N. Díaz-Díaz and D. S. Rodríguez-Baena and J. S. Aguilar-Ruiz

Pattern recognition in biological time series (Conference)

Conference of the Spanish Association for Artificial Intelligence (CAEPIA'11), Lecture Notes in Artificial Intelligence 2011.

(Links | BibTeX | Tags: bioinformatics, time series)

R. Arma~nanzas and Y. Saeys and I. Inza and M. García-Torres and C. Bielza and Y. van~de~Peer and P. Larra~naga

Peakbin selection in mass spectrometry data using a consensus approach with estimation of distribution algorithms (Journal Article)

IEEE/ACM Transactions on Computational Biology and Bioinformatics, 8 (3), pp. 760-774, 2011.

(Links | BibTeX | Tags: bioinformatics)

2010

J. A. Nepomuceno and A. Troncoso and J. S. Aguilar-Ruiz

Correlation-Based Scatter Search for Discovering Biclusters from Gene Expression Data (Conference)

EvoBio 8th European Conference on Evolutionary Computation Machine Learning an Data Mining in Bioinformatics, Lecture Notes in Computer Science 2010.

(Links | BibTeX | Tags: bioinformatics)

J. A. Nepomuceno and A. Troncoso and J. S. Aguilar-Ruiz

Evolutionary Metaheuristic for Biclustering Based on Linear Correlations Among Genes (Conference)

SAC 25th Symposium on Applied Computing, 2010.

(Links | BibTeX | Tags: bioinformatics)

A. E. Marquez-Chamorro and F. Divina and J. S. Aguilar-Ruiz and G. Asencio-Cortes

Alpha Helix Prediction Based on Evolutionary Computation (Conference)

Pattern Recognition in Bioinformatics, 2010, ISBN: 978-3-642-16001-1.

(Abstract | BibTeX | Tags: bioinformatics)

G. Asencio-Cortes and J. S. Aguilar-Ruiz

Importancia de las Propiedades Fisico-Quimicas de los Aminoacidos en la Prediccion de Estructuras de Proteinas usando Vecinos mas Cercanos (Conference)

XV Congreso Español sobre Tecnologias y Logica Fuzzy, ISBN: 978-84-92944-02-6., 2010.

(Abstract | BibTeX | Tags: bioinformatics)

2009

J. A. Nepomuceno and A. Troncoso and J. S. Aguilar-Ruiz

An Overlapping Control-Biclustering Algorithm from Gene Expression Data (Conference)

ISDA 9th International Conference on Intelligent Systems Design and Applications, 2009.

(Links | BibTeX | Tags: bioinformatics)

J. A. Nepomuceno and A. Troncoso and J. S. Aguilar-Ruiz

Un Algoritmo de Biclustering Basado en Búsqueda Dispersa y Algoritmos Genéticos (Workshop)

CAEPIA XIII Conferencia de la Asociación Española para la Inteligencia Artificial. EvaBio II Workshop Español sobre Extracción y Validación de Conocimiento en Bases de Datos Biomédicas, 2009.

(BibTeX | Tags: bioinformatics)

J. A. Nepomuceno and A. Troncoso and J. S. Aguilar-Ruiz

A Hybrid Metaheuristic for Biclustering Based on Sccater Search and Genetic Algorithms (Conference)

PRIB 4th International Conference on Pattern Recognition in Bioinformatics, Lecture Notes in Bioinformatics 2009.

(Links | BibTeX | Tags: bioinformatics)

G. Asencio-Cortes and J. S. Aguilar-Ruiz

Prediccion de Estructuras de Proteinas mediante Vecinos mas Cercanos usando Caracteristicas Inherentes a los Aminoacidos (Conference)

II Workshop Español sobre Extraccion y Validacion de Conocimientos en Base de Datos Biomedicas, 2009.

(Abstract | BibTeX | Tags: bioinformatics)

2008

C. Rubio-Escudero and F. Martínez-Álvarez and R. Romero-Záliz and I. Zwir

Classification of gene expression using Expectation Maximization (Conference)

IEEE International Conference on Hybrid Intelligent Systems (HIS'08), 2008.

(Links | BibTeX | Tags: bioinformatics)

58 entries « 1 of 2 »