Personal information

bioinformatics, mathematical optimization, metaheuristics, high performance computing
Spain

Biography

My name is David Rodríguez Penas (Santiago de Compostela, 1987), and I am a researcher in computer science, bioinformatics and optimization. Currently, I am a postdoctoral research associate at IIM-CSIC (Marine Research Institute, Spanish National Research Council).
I received my BASc in Computer Engineering from the University of Santiago de Compostela (USC) in 2011 and my MSc in High-Performance Scientific Computing from USC in 2012, achieving USC Best Master's thesis Award.
In June 2017, I obtained my European PhD at the University of A Coruña (UDC), developed under the supervision of Professor Julio R Banga (IIM-CSIC), in collaboration with Professors Patricia González and Ramón Doallo, from Computer Architecture Group (GAC-UDC). I obtained the top qualification of "Sobresaliente Cum Laude" and the UDC Best PhD Thesis Award 2016-2017.
During 2017-2019, I was a postdoc researcher from the Institute of Mathematics (IMAT-USC), from the University of Santiago de Compostela, working on a set of projects related to High-Performance Computing (HPC) and Operations Research (OR) fields. In that period, I collaborated with Professors Balbina Casas Méndez and Julio González Díaz, members of MODESTyA research group, led by Professor Wenceslao González Manteiga.
Later, I obtained the Xunta postdoctoral grant 2019 to develop a research project related to logistic optimization using HPC techniques and heuristic methods. Thus, I was a visiting researcher in the Edinburgh Research Group in Optimization (ERGO) at the University of Edinburgh, collaborating with Professor Sergio Garcia Quiles in facility location optimization problems. Besides, this project also allowed me to collaborate with Professors José F Oliveira and M Antónia Carravilla at the University of Oporto.
Finally, I returned to IIM-CSIC in April 2021. This time, I am collaborating with Julio R Banga under CanPathPro, EU project, developing research tasks related to optimization and computer science in the context of bioinformatics.

Activities

Employment (7)

Misión Biológica de Galicia: Pontevedra, Galicia, ES

2022-12-29 to present | Postdoctoral Researcher (Computational Biology Lab)
Employment
Source: Self-asserted source
David R Penas

Spanish National Research Council (funded by EU H2020 project CanPathPro): Vigo, Galicia, ES

2021-04-01 to 2021-11-01 | Post-doctoral Researcher (Marine Research Institute)
Employment
Source: Self-asserted source
David R Penas

University of Edinburgh (funded by Xunta de Galicia via University of Santiago de Compostela): Edinburgh, Scotland, GB

2019-10 to 2021-04 | Visiting researcher (ERGO group, School of Mathematics)
Employment
Source: Self-asserted source
David R Penas

Technological Institute for Industrial Mathematics (ITMATI) : Santiago de Compostela, Galicia, ES

2019-06 to 2019-10 | Post-doctoral Researcher
Employment
Source: Self-asserted source
David R Penas

University of Santiago de Compostela: Santiago de Compostela, Galicia, ES

2017-09 to 2019-06 | Post-doc (Institute of Mathematics (IMAT))
Employment
Source: Self-asserted source
David R Penas

University of A Coruña: A Coruña, Galicia, ES

2016-12 to 2017-09 | Research assistant (Department of Computer Engineering)
Employment
Source: Self-asserted source
David R Penas

Spanish National Research Council: Vigo, Galicia, ES

2012-12 to 2016-12 | PhD Student (Marine Research Institute)
Employment
Source: Self-asserted source
David R Penas

Education and qualifications (3)

University of A Coruña: A Coruña, Galicia, ES

2017 | PhD Computer Science (Computer Architecture Group)
Education
Source: Self-asserted source
David R Penas

University of Santiago de Compostela: Santiago de Compostela, Galicia, ES

2012 | MSc in high performance computing
Education
Source: Self-asserted source
David R Penas

University of Santiago de Compostela: Santiago de Compostela, Galicia, ES

2011 | BSc in computer engineering
Education
Source: Self-asserted source
David R Penas

Professional activities (5)

Asociación Española de Inteligencia Artificial: A Coruna, Galicia, ES

2018 to present
Membership
Source: Self-asserted source
David R Penas

Sociedade Galego para a Promoción da Estatística e da Investigación de Operacións (SGAPEIO): Galicia, ES

2017 to present
Membership
Source: Self-asserted source
David R Penas

Institute of Mathematics : Santiago de Compostela, Galicia, ES

2018 to 2019 | Non-permanent researcher (University of Santiago de Compostela)
Membership
Source: Self-asserted source
David R Penas

University of A Coruña: A Coruña, Galicia, ES

2017 | Outstanding PhD Student Award
Distinction
Source: Self-asserted source
David R Penas

University of Santiago de Compostela: Santiago de Compostela, Galicia, ES

2012 | Best Master's Thesis of the Year Award (Escola Técnica Superior de Enxeñería (ETSE), University of Santiago de Compostela)
Distinction
Source: Self-asserted source
David R Penas

Funding (3)

Postdoctoral researcher funded by Xunta de Galicia Grant program 2019

2019-10 to 2021-10 | Grant
Xunta de Galicia (Santiago de Compostela, ES)
GRANT_NUMBER:

ED481B-2019-010

Source: Self-asserted source
David R Penas

Post-doctoral Investigation contracts in mathematics

2017-09 to 2019-06 | Salary award
Institute of Mathematics, University of Santiago de Compostela (Santiago de Compostela, ES)
GRANT_NUMBER:

2017-AD005

Source: Self-asserted source
David R Penas

Research Staff Training (FPI) grant

2012-12 to 2016-12 | Grant
Ministerio de Economía, Fomento y Turismo (Madrid, ES)
GRANT_NUMBER:

BES-2012-054889

Source: Self-asserted source
David R Penas

Works (19)

Optimal evaluation of energy yield and driving force in microbial metabolic pathway variants

PLOS Computational Biology
2023-05 | Journal article
Contributors: Ahmed Taha; Mauricio Patón; David R Penas; Julio R Banga; Jorge Rodríguez
Source: Self-asserted source
David R Penas

A new two‐phase heuristic for a problem of food distribution with compartmentalized trucks and trailers

International Transactions in Operational Research
2023-03 | Journal article | Author
Part of ISSN: 0969-6016
Part of ISSN: 1475-3995
Contributors: Laura Davila-Pena; David R Penas; Balbina Virginia Casas Méndez
Source: Self-asserted source
David R Penas

Computational advances in polynomial optimization: RAPOSa, a freely available global solver

Journal of Global Optimization
2023-03 | Journal article
Part of ISSN: 0925-5001
Part of ISSN: 1573-2916
Contributors: Brais González Rodríguez; Joaquín Ossorio-Castillo; Julio González-Díaz; Ángel M. González-Rueda; David R. Penas; Diego Rodríguez-Martínez
Source: Self-asserted source
David R Penas

Application of decomposition techniques in a wildfire suppression optimization model

Optimization and Engineering
2023-03-09 | Journal article
Part of ISSN: 1389-4420
Part of ISSN: 1573-2924
Contributors: Jorge Rodríguez-Veiga; David R. Penas; Ángel M. González-Rueda; María José Ginzo-Villamayor
Source: Self-asserted source
David R Penas

Searching for genetic interactions in complex disease by using distance correlation

2020-12-09 | Preprint
Source: Self-asserted source
David R Penas

A metaheuristic penalty approach for the starting point in nonlinear programming

RAIRO - Operations Research
2020-03 | Journal article
Part of ISSN: 0399-0559
Part of ISSN: 1290-3868
Source: Self-asserted source
David R Penas

Enhanced global optimization methods applied to complex fisheries stock assessment models

Applied Soft Computing
2019 | Journal article
Source: Self-asserted source
David R Penas

Hybrid parallel multimethod hyperheuristic for mixed-integer dynamic optimization problems in computational systems biology

2019-05-08 | Journal article
Part of ISSN: 0920-8542
Part of ISSN: 1573-0484
Source: Self-asserted source
David R Penas

Multimethod Optimization for Reverse Engineering of Complex Biological Networks

Proceedings of the 6th International Workshop on Parallelism in Bioinformatics
2018 | Conference paper
Part of ISBN: 978-1-4503-6531-4
Source: Self-asserted source
David R Penas

Multimethod optimization in the cloud: A case-study in systems biology modelling

Concurrency Computation
2018 | Journal article
EID:

2-s2.0-85044570366

Contributors: González, P.; Penas, D.R.; Pardo, X.C.; Banga, J.R.; Doallo, R.
Source: Self-asserted source
David R Penas via Scopus - Elsevier

A cloud-based enhanced differential evolution algorithm for parameter estimation problems in computational systems biology

Cluster Computing
2017 | Journal article
EID:

2-s2.0-85017518623

Contributors: Teijeiro, D.; Pardo, X.C.; Penas, D.R.; González, P.; Banga, J.R.; Doallo, R.
Source: Self-asserted source
David R Penas via Scopus - Elsevier

Evaluation of parallel differential evolution implementations on MapReduce and spark

Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)
2017 | Book
EID:

2-s2.0-85020410999

Contributors: Teijeiro, D.; Pardo, X.C.; Penas, D.R.; González, P.; Banga, J.R.; Doallo, R.
Source: Self-asserted source
David R Penas via Scopus - Elsevier

Parameter estimation in large-scale systems biology models: A parallel and self-adaptive cooperative strategy

BMC Bioinformatics
2017 | Journal article
EID:

2-s2.0-85009961427

Contributors: Penas, D.R.; González, P.; Egea, J.A.; Doallo, R.; Banga, J.R.
Source: Self-asserted source
David R Penas via Scopus - Elsevier

Using the Cloud for Parameter Estimation Problems: Comparing Spark vs MPI with a Case-Study

2017 17th IEEE/ACM International Symposium on Cluster, Cloud and Grid Computing (CCGRID)
2017 | Conference paper
Source: Self-asserted source
David R Penas
grade
Preferred source (of 2)‎

A parallel metaheuristic for large mixed-integer dynamic optimization problems, with applications in computational biology

PLOS ONE
2017-08 | Journal article
Source: Self-asserted source
David R Penas
grade
Preferred source (of 2)‎

Enhanced parallel differential evolution algorithm for problems in computational systems biology

Applied Soft Computing Journal
2015 | Journal article
EID:

2-s2.0-84928812317

Contributors: Penas, D.R.; Banga, J.R.; González, P.; Doallo, R.
Source: Self-asserted source
David R Penas via Scopus - Elsevier

Parallel metaheuristics in computational biology: An asynchronous Cooperative enhanced Scatter Search method

Procedia Computer Science
2015 | Conference paper
EID:

2-s2.0-84939209790

Contributors: Penas, D.R.; González, P.; Egea, J.A.; Banga, J.R.; Doallo, R.
Source: Self-asserted source
David R Penas via Scopus - Elsevier

A parallel differential evolution algorithm for parameter estimation in dynamic models of biological systems

Advances in Intelligent Systems and Computing
2014 | Book
EID:

2-s2.0-84921772409

Contributors: Penas, D.R.; Banga, J.R.; González, P.; Doallo, R.
Source: Self-asserted source
David R Penas via Scopus - Elsevier

A study of semantic proximity between archetype terms based on SNOMED CT relationships

Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)
2013 | Book
EID:

2-s2.0-84879812545

Contributors: Allones, J.L.; Penas, D.; Taboada, M.; Martinez, D.; Tellado, S.
Source: Self-asserted source
David R Penas via Scopus - Elsevier