Dr. MIGUEL ARENAS - web page

 

PhD in Bioinformatics
Phone: +34 686364287

I am interested in Bioinformatics applied in the area of evolutionary analysis at the Molecular Level. 
My areas of research include molecular evolution, mutation, recombination, molecular adaptation and phylogenetics. Indeed, I am also interested in the study of the evolution effects on the structure and function of biological macromolecules.

 PUBLICATIONS - CV
    SOFTWARE    PHOTOS


PUBLICATIONS

 1. Arenas, M. and Posada, D. 2007. Recodon: Coalescent simulation of coding DNA sequences with recombination, migration and demography. BMC Bioinformatics, 8:458. Highly accessed. pdf

2. Arenas, M.; Valiente, G.; Posada, D. 2008. Characterization of Reticulate Networks based on the Coalescent with Recombination. Molecular Biology and Evolution, 25(12):2517-2520. pdf 

3. Arenas, M.; Villaverde, M. C.; Sussman, F. 2009. Prediction and Analysis of Binding Affinities for Chemically Diverse HIV-1 PR Inhibitors by the Modified SAFE_p Approach. Journal of Computational Chemistry, 30(8):1229-1240. pdf

4. Perez-Losada, M.; Posada, D.; Arenas, M.; Jobes, D.V.; Sinangil, F.; Berman, P.W. and Crandall, K.A. 2009. Ethnic differences in the adaptation rate of HIV gp120 from a vaccine trial. Retrovirology, 6:67. pdf

5. Arenas, M. and Posada, D. 2010. Coalescent simulation of intracodon recombination. Genetics, 184(2):429-437. pdf

6. Arenas, M. and Posada, D. 2010. The effect of recombination on the reconstruction of ancestral sequences. Genetics, 184(4):1133-1139. Issue highlights. pdf

7. Arenas, M.; Patricio M.; Posada D.; Valiente G. 2010. Characterization of Phylogenetic Networks with NetTest. BMC Bioinformatics, 11:268. pdf

8. Arenas, M. and Posada D. 2010. Computational design of centralized HIV-1 genes. Current HIV Research, 8(8):613-621. pdf

9. Perez-Losada, M.; Jobes, D.V.; Sinangil, F.; Crandall, K.A.; Arenas, M.; Posada, D. and Berman, P.W. 2011. Phylodynamics of HIV-1 from a Phase III AIDS Vaccine Trial in Bangkok, Thailand. PLoS ONE, 6(3): e16902. pdf

10. Arenas, M. and Posada D. 2012. Simulation of Coding Sequence Evolution. In "Codon Evolution: Mechanisms and Models". Eds., Cannarozzi G.M. and Schneider A. Oxford University Press. Pp. 126-132. pdf

11. Arenas, M.; Ray, N.; Currat, M. and Excoffier, L. 2012. Consequences of Range Contractions and Range Shifts on Molecular Diversity. Molecular Biology and Evolution, 29(1):207-218. pdf


ACADEMIC ACTIVITY - RESEARCH HISTORY

 2012 (May) - Currently
- Postdoctoral position with Prof. Ugo Bastolla. Protein evolution.
Centre for Molecular Biology "Severo Ochoa". CSIC - Autonomous University of Madrid (Spain).
2010 (August) - 2012 (April)
 - Postdoctoral position with Prof. Laurent Excoffier. Effects of heterogeneity dynamics on molecular diversity.
Department of Ecology and Evolution. University of Bern (Switzerland).
2010 (April-July)
- Postdoctoral position with Prof. David Posada. Molecular evolution of HIV-1.
Department of Biochemistry, Genetics and Immunology. University of Vigo (Spain).
2005 - 2010
- Ph.D. Thesis: Applications of the Coalescent with Recombination in Molecular Evolution. pdf
    Cum Laude with highest honors. Supervised by David Posada. 26/02/2010.
    Special Prize of Best Thesis of the University of Vigo.
2003 - 2005
- M.Sc. in Organic Chemistry and Certificate of Advanced Studies (DEA).
Department of Organic Chemistry, University of Santiago de Compostela (Spain).
2003 - 2004
- Graduate in Chemistry. Majors in Organic Chemistry.
Department of Organic Chemistry and unit associated to the CSIC, University of Santiago de Compostela.
1997 - 2003
- BSc. in Chemistry. Majors in Chemistry of Materials (Inorganic Chemistry) and Chemistry of Bioactive Compounds (Organic Chemistry).
University of Santiago de Compostela.

PLACES

2012 - Currently. Postdoctoral position. Centre for Molecular Biology "Severo Ochoa" - Autonomous University of Madrid, Madrid (Spain), with Professor Ugo Bastolla. From 16-05-2012 to currently.
2010 - 2012. Postdoctoral position. University of Bern, Bern (Switzerland), with Professor Laurent Excoffier. From 16-08-2010 to 30-04-2012.
Effects of heterogeneity dynamics on molecular diversity.
2009. Visiting Scientist. School of Biological Sciences - University of Reading, Reading (UK), with Dr. Mark Beaumont. From 26-02-2009 to 30-04-2009 and from 24-08-2009 to 24-09-2009.
Approximate Bayesian Computation (ABC).
2008. Visiting Scientist. Department of Biology - Brigham Young University, Utah (USA), with Professor Keith A. Crandall. From 08-08-2008 to 10-11-2008.
Bioinformatic analysis DNA sequences. Development of genetic algorithms.
2007. Visiting Scientist. Institute of Health Carlos III - ISCIII, Madrid (Spain), with Dr. Cecilio Lopez Galindez. From 21-09-2007 to 21-12-2007.
Analysis of HIV-1 DNA sequences.

RESEARCH PROJECTS

2010-2012. SCALES - Securing the conservation of biodiversity across administrative levels and spatial, temporal, and ecological scales. European Project. sWP 2.2: Genetic Diversity Scaling. 7th Framework Programme (FP7), Theme 6, Grant #226852.
Main researcher: Prof. L. Excoffier. Institute of Ecology and Evolution. University of Bern (Switzerland).
2007-2009. Computational design of centralized genes with recombination: implications for the AIDS vaccine.
Main researcher: Prof. D. Posada. Department of Biochemistry, Genetics and Immunology. University of Vigo (Spain).
2005-2007. Incorporation of sugars in polipeptide chains. Design, synthesis and structural study of poly substituted carboxylic 2-aminecycloalcane acid peptide.
Main researcher: Prof. R.J. Estevez. Department of Organic Chemistry, University of Santiago de Compostela.

CONGRESS/SYMPOSIUM COMMUNICATIONS

2012. SCALES Meeting- Securing the conservation of biodiversity across administrative levels and spatial, temporal, and ecological scales (SCALES2012). Nicosia (Cyprus). March, 19-23.
- sWP 2.2: Genetic Diversity Scaling. (oral)
2012. Swiss Institute of Bioinformatics Meeting (SIB2012). Biel/Bienne (Switzerland). January, 30-31.
- Principal component analysis of European human range expansion and contraction.
2011. Evolution 2011. Norman, Oklahoma (USA). June, 17-21.
- Evolutionary Patterns in Population History of Marine Bacteria.
2011. SCALES Meeting- Securing the conservation of biodiversity across administrative levels and spatial, temporal, and ecological scales (SCALES2011). Sofia (Bulgaria). April, 12-15.
- sWP 2.2: Genetic Diversity Scaling. (oral)
2011. Swiss Institute of Bioinformatics Meeting (SIB2011). Biel/Bienne (Switzerland). January, 31 - February, 1.
- Implications of Range Contractions and Range Shifts on Molecular Diversity.
2010. Evolutionary and ecological genomics of adaptation. Fribourg (Switzerland). September, 2-3.
2010. Annual Meeting of the Society of Molecular Biology and Evolution (SMBE). Lyon (France). July, 4-8.
- Coestimation of recombination, adaptation and substitution rates using approximate Bayesian computation.
2010. XVIII Seminario de Genética de Poblaciones y evolución. (XVIII Meeting of Population Genetics and Evolution). Guitiriz (Spain). May, 5-7.
- Inference of ancestral sequences, recombination and adaptation from recombining sequences.
2009. II Xornada Galega de Bioinformatica. (Second Galician Meeting on Bioinformatics). Santiago de Compostela (Spain). December, 4.
- Coalescent simulation of coding sequences with recombination and other evolutionary processes.
- The Impact of Recombination on the Reconstruction of Ancestral Sequences.
2009. Jornadas de Bioinformática "JB2009", Lisbon, (Portugal). November, 3-6.
- Coalescent simulation of coding sequences with recombination, migration, selection, demographics and longitudinal sampling. (oral)
- Recombination biases the reconstruction of ancestral DNA and protein sequences.
2009. Understanding emergence of infectious diseases: focus on new experimental and theoretical approaches to virus evolution. Jacques Monod Conferences. Roscoff (France). September, 26-30.
- Ancestral sequence reconstruction in the presence of recombination: Implications for HIV-1.
2009. 16th International HIV Dynamics and Evolution. University of Oxford, Oxford (UK). April, 4-7.
- Accuracy of ancestral sequence reconstruction in the presence of recombination: Implications for HIV-1.
2009. International Workshop in Memoriam of Angel Ramirez Ortiz. Structural Bioinformatics and Beyond. Madrid (Spain). January, 26-28.
- Simulation of coding sequences in the ancestral recombination graph.
2008. Cesga-Finis Terrae Computational Science Conference. Santiago de Compostela (Spain). June, 12.
2008. Annual Meeting of the Society of Molecular Biology and Evolution (SMBE). Barcelona (Spain). June, 5-8.
- A new coalescence algorithm to simulate DNA sequences with intra-codon recombination.
2008. I Xornada Galega de Bioinformatica. (First Galician Meeting on Bioinformatics). University of A Coruña. A Coruña (Spain). April, 4.
2008. VIII Jornadas de Bioinformatica. (VIII Meeting on Bioinformatics). Centro de Investigacion Principe Felipe. Valencia (Spain). February, 13-15.
2008. 52nd Biophysical Society Annual Meeting 2008. Long Beach, CA (USA). February, 2-6.
- Predicting inhibitor binding affinities: the SAFE_p approach.
2007. XXXVI Congreso de la Real Sociedad Española de Genetica. (XXXVI Symposium of the Spanish Real Society of Genetics). Leon (Spain). September, 18-21.
- Nuevo software para la simulacion de secuencias de ADN mediante coalescencia con recombinacion, migracion, demografia y modelos de codones
(A new software for simulate DNA sequences by coalescence with recombination, migration, demographics and codon models).
2007. Current Challenges and Problems in Phylogenetics. Isaac Newton Institute for Mathematical Sciences, Cambrige (UK). September, 3-7.
- Coalescent simulations with complex models.
2005. XXX Reunion Bienal de la Real Sociedad Española de Quimica (RSEQ). (XXX Symposium of the Spanish Real Society of Chemistry). Lugo (Spain). September, 19-23.
- Desarrollo de un nuevo metodo de prediccion de afinidad de inhibidores de la proteasa del VIH-1. (Development of a new method for affinity prediction of HIV-1 protease inhibitors).
2004. 5th Spanish-Italian Symposium on Organic Chemistry (SISOC-5). Santiago de Compostela (Spain). September, 10-13.
- Intramolecular Metal Catalyzed Cyclization of Cyclopropenes and Alkenes.
- Synthesis of Triphenylene Derivatives by Palladium-Catalyzed Cyclotrimerization of Arynes.


TEACHING IN COURSES AND INVITED SEMINARS

2012. Seminar. Simulation of molecular data by the coalescent with recombination, migration and demographics. February, 22. Invited by Maria Anisimova. Swiss Federal Institute of Technology (ETH), Zurich (Switzerland). 
2011. Course. Introduction to Coalescent Theory. Section: Coalescent Simulation of Coding Data. September, 5-8. University of Bern (Switzerland).
2011. Seminar. Consequences of Range Contractions and Range Shifts on Molecular Diversity. February, 10. Invited by Olivier François. University of Grenoble (France). 
2010. Seminar. Applications of the coalescent with recombination in molecular evolution. October, 4. Invited by Laurent Excoffier. University of Bern (Switzerland). 
2006-09. Teacher of General Genetics for Biology degree. Department of Biochemistry, Genetics and Immunology, University of Vigo.
2004-05. Teacher of Practical Lessons for Chemistry degree. Laboratory of Organic Chemistry Department, University of Santiago de Compostela.
2004-05. Personal Assistant of Computational Service at University of Santiago de Compostela. Computational Net Rooms (RAI) in the Faculty of Chemistry.
2004. Teacher for primary and high school level at the Private School Ana Maria Parada in Villagarcia de Arosa (Spain).


OTHER SCIENTIFIC INFORMATION

- Membership of the Official College of Chemistry of Galicia, 2009.
- Membership of SMBE Society for Molecular Biology and Evolution, 2008.
- Young membership of Real Spanish Society of Chemistry, from 2005.
- Reviewer of the Journals: Bioinformatics; Journal of Infection, Genetics and Evolution; Molecular Ecology; Molecular Phylogenetics and Evolution; PLoS Computational Biology; PLoS ONE.


PRIZES AND FELLOWSHIPS

- Fellowship from The Ministry of Science of Spain for PostDoc (Juan de la Cierva, 2012-2015), at The Bioinformatics Unit, Centre for Molecular Biology "Severo Ochoa". CSIC - University Autonoma of Madrid.
- Special Prize of Best Thesis in the University of Vigo in 2010.
- Fellowship from The Ministry of Science of Spain for PhD student (FPI, 2005-2009), at The Department of Biochemistry, Genetics and Immunology. University of Vigo.
- Several Fellowships from The Ministry of Education and Science of Spain for visiting labs in USA, UK and Spain. Also Felloships from The University of Vigo for travelling to diverse Meetings.

COURSES AND WORKSHOPS

2009. Bioinformática estructural: Modelización y Simulación de Moléculas Biológicas. (Structural Bioinformatics: Modellization and Simulation of Biological Molecules). University of Santiago de Compostela. November, 30 - December, 3. Santiago de Compostela (Spain).
2009. Optimizacion del uso de la jerarquia de memoria. (Optimization of the use of memory hierarchy). GHPC (Galician network of high-performance computing) and University of La Coruña. October, 13-15. Santiago de Compostela (Spain).
2008. Workshop on Molecular Evolution. MBL - Marine Biological Laboratory. July, 27 - August, 8. Woods Hole, Boston (MA), (USA).
2008. Matematica computacional. (Computational mathematics). i-MATH (Ingenio Mathematica) and CESGA (Superior center of supercomputation of Galicia). June, 30 - July, 4. Santiago de Compostela (Spain).
2008. Molecular Markers and Population Genetics. Gulbenkian Institute of Science. June, 23-27. Oeiras, Lisbon (Portugal).
2008. Seminario de Tecnologias del Instituto Nacional de Bioinformatica. (Seminar on Technologies of the Bioinformatics National Institute). May, 29. Santiago de Compostela, (Spain).
2007. Chrom Forum VWR. Institute of Health Carlos III - ISCIII. October, 2. Majadahonda, Madrid, (Spain).
2007. Elementary Bioinformatic Skills. Gulbenkian Institute of Science. May, 20-25. Oeiras, Lisbon (Portugal).
2006. Workshop on Coalescent Theory. Gulbenkian Institute of Science. June, 21-24. Oeiras, Lisbon (Portugal).
2006. Phylogenetics and Genealogies of DNA: Reconstruction and Applications. Certfem, University of Barcelona. July, 4-14. Barcelona (Spain).
2005. The challenge of energy sources in the XXI century. Department of Physical Chemistry, University of Santiago de Compostela and Xunta de Galicia.
2005. The radioactive isotopes. Department of Physical Chemistry, University of Santiago de Compostela and Xunta de Galicia.
2005. Sustainable development and clean production. University of Santiago de Compostela, Consello Social and Xunta de Galicia.
2004. Pc: Operating and Components. University of Santiago de Compostela.
2003-04. Pedagogic Aptitude Certificate (CAP). ICE, Institute of education science. University of Santiago de Compostela.
2003. Bioactive compounds obtained from residues of food and agriculture industry and forest industry. Chemistry Faculty, University of Santiago de Compostela.
2003. Initiation to the operation in chemical plants. Santiago de Compostela (Spain). Participation of Repsol YPF, ISE and University of Santiago de Compostela.
2003. Microsoft Access. University of Santiago de Compostela.
2003. DreamWeaver. University of Santiago de Compostela.
2003. First aids. Red Cross, Villagarica de Arosa, Pontevedra (Spain).
2002. Visual Programming: Visual Basic. University of Santiago de Compostela.
2002. Making a web site with FrontPage. University of Santiago de Compostela.

COMPUTING SKILLS

  • Software Systems & Programs
    • Windows and Macintosh, Basic, MS-DOS, UNIX and Linux.
    • Science programs. Bioinformatic software: Chemical software (ChemOffice, Mestre C, InsightII, Charmm, SAFE_p, etc.) and Genetic software (MrBayes, OmegaMap, Beast, PAML, Hyphy, phyml, PAUP, SplitsTree, TCS, BLAST, ClustalX/W, MacClade, BioEdit, OmegaMap, TreeView, FigTree, etc.). Other: Scifinder, Xcode, Codewarrior, etc.
    • Other basic programs. Office: Word, Excel, Access, Power Point, FrontPage.. Antivirus, AntiSpyware, Photo Express, Corel Draw, Adobe Ilustrator, WinZip, Acrobat.. and much more.
    • Supercomputers, Clusters.
  • Internet
    • Explorer, Netscape, Safari and Firefox. Email.
    • Design and making of web sites. DreamWeaver and Front Page. HTML.
    • File Transfer Programs, FTP.
  • Programming Languages


INDUSTRY JOBS

 2005. Professional training for chemistry at Ence S.A. Company. Industry of the wood. Laboratory Sections.
2003. Professional training for chemistry at Brenntag Quimica S.A. Company. Industry of chemical compounds (bleaches, organic solvents, soaps, etc) - Laboratory Section.
2002. Professional training for chemistry at Metalgrafica Gallega S.A. Company. Industry of metallic containers. Department of Quality Control.



More photos of Miguel Arenas
- UP -

Miguel Arenas Busto, 1983 (4 years old)

Old Miguel Arenas web page


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Created: October 28, 2008
Last updated: May 17, 2012