Research Assistant Professor
  Biology Department, Boston College

Welcome!

Ivan Dotu

Who I am:

I am a Research Assistant Professor at the Biology Department at Boston College.

I was born in Madrid, Spain, although I lived in Barcelona for 9 years. I moved back to Madrid to start high school there and I later studied Computer Science at the Universidad Europea de Madrid. I did my phD in Universidad Autonoma de Madrid where I defended my thesis in September 2006.

After defending my thesis I worked as a professor at Universidad Europea de Madrid, teaching Algorithms and Operations Research. I was also a researcher at Universidad Carlos III at the same time.

In 2007 I was awarded a Fundacion Caja Madrid Grant to do a postdoc at Brown University under the supervision of Professor Pascal Van Hentenryck. The theme of this postdoc was combinatorial optimization for computational biology problems. During this time I also collaborated with Professor Peter Clote, director of the lab of Computational Biology at Boston College.

At the beginning of October 2009 I received an O-1 visa and I started working at Dynadec, an optimization software company based in Rhode Island where I was a Senior Software Engineer.

In October 2010 I started my current appointment as Research Assistant Professor at the Biology Department of Boston College, where I am part of Professor Clote's lab.

My research interest are broad. In a technical level I am interested in Constraint Programming and Local Search methods. In a problem level I am interested in Computational Biology, where I have worked in problems as diverse as Protein Tertiary Structure, RNA segmentation or riboswitch energy barrier.

I was Program Committee of AAAI-08 and I am (or have been) reviewer for conferences such as CP, SAT or AAAI, and journals such as Constraints, Journal of Mathematical Biology, Transactions on Computational Biology and Bioinformatics and Nucleic Acids Research.

Publications:                                                                                                                                Top

Here you have a list of my publications:
- - Published papers
  1. Ivan Dotu, Manuel Cebrian, Pascal Van Hentenryck and Peter Clote, "On Lattice Protein Structure Prediction Revisited". To appear in Transactions on Computational Biology and Bioinformatics.
  2. Ivan Dotu, Miguel A. Patricio, A. Berlanga,  J. Garcia, Jose M. Molina, "Improving video tracking performance by means of Tabu Search in Intelligent Visual Surveillance Systems".  To appear in Journal of Heuristics.
  3. Ivan Dotu, William A. Lorenz, Pascal Van Hentenryck and Peter Clote, " RNA structural segmentation". In PSB'10 Proceedings, 2010.
  4. Ivan Dotu, William A. Lorenz, Pascal Van Hentenryck and Peter Clote, "Computing folding pathways between RNA secondary structures". In Nucleic Acids Research Journal.
  5. Miguel A. Patricio, Ivan Dotu, A. Berlanga,  J. Garcia, Jose M. Molina, "Discrete Optimization Algorithms in Real-Time Visual Tracking". In Applied Artificial Intelligence journal, 2009.
  6. Ivan Dotu, Pascal Van Hentenryck, Miguel A. Patricio, A. Berlanga,  J. Garcia, Jose M. Molina, "Real-Time Tabu Search for Video Tracking Association". In CP'09 Proceedings, 2009.
  7. Ivan Dotu, J. Garcia, A. Berlanga, Jose M. Molina, "A Meta-level Evolutionary Strategy for  Many-criteria Design. Application to Improving Tracking Filters". In Advanced Engineering Informatics, 2008.
  8. Ivan Dotu, Manuel Cebrian, Pascal Van Hentenryck and Peter Clote, "Protein Structure Prediciton with Large Neighborhood Constraint Programming Search". In CP'08 Proceedings, 2008.
  9. Manuel Cebrian, Ivan Dotu, Pascal Van Hentenryck and Peter Clote, "Protein Structure Prediciton on the Face Centered Cubic Lattice by Local Search". In AAAI'08 Proceedings, 2008.
  10. Carlos Cotta, Ivan Dotu, Antonio J. Fernandez and Pascal Van Hentenryck, "Local Search-Based Hybrid Algorithms for Finding Golomb Rulers", In Constraints Journal 12(3): 263-291, 2007.
  11. Ivan Dotu and Pascal Van Hentenryck, "Scheduling Social Tournaments Locally", In AI Communications Journal, Special Issue on Constraint Programming for Planning and Scheduling, 20(3): 151-162, 2007.
  12. Carlos Cotta, Ivan Dotu, Antonio J. Fernandez and Pascal Van Hentenryck, "Scheduling Social Golfers with Memetic Evolutionary Programming", In Proceedings of HM'06, October 2006.
  13. Ivan Dotu and Pascal Van Hentenryck, "A Note on Low Autocorrelation Binary Sequences", In Proceedings of CP'06, September 2006.
  14. Carlos Cotta, Ivan Dotu, Antonio J. Fernandez and Pascal Van Hentenryck, "A Memetic Approach for Golomb Rulers", In Proceedings of PPSN'06, Reykjavik, Iceland, September 2006.
  15. Manuel Cebrián and Ivan Dotu, "GRASP-Evolution for Constraint Satisfaction Problems", In Proceedings of  GECCO-06, Seattle, USA, July 2006.
  16. Ivan Dotu, Alvaro del Val and Pascal van Hentenryck, "Scheduling Social Tournaments", In Proceedings of CP-05, Sitges, Spain.
  17. Ivan Dotu and Pascal Van Hentenryck, “A Simple Hybrid Evolutionary Algortihm for Finding Golomb Rulers” In Proceedings of IEEE CEC'05 Proceedings, Edimburgh, September 2005.
  18. Ivan Dotu and Pascal Van Hentenryck, “Scheduling Social Golfers Locally”,In CPAIOR'05 Proceedings, Prague, May 2005.
  19. Carlos Ansótegui, Alvaro del Val, Iván Dotú, Cèsar Fernández y Felip Manyà, “Modeling Choices in Quasigroup Completion: SAT vs. CSP”. In AAAI'04 Proceedings, San José,California, USA, July 2004.
  20. Iván Dotú, Álvaro del Val and Manuel Cebrián, “Channeling Constraints and Value Ordering in the QuasiGroup Completion Problem”. In IJCAI'03 Proceedings, pages 1372-1373, Acapulco, México, August 2003.
  21. Iván Dotú, Álvaro del Val and Manuel Cebrián, “Redundant Modeling for the QuasiGroup Completion Problem”. In CP'03 Proceedings, Kinsale, Ireland, September 2003.
  22. Iván Dotú, Juan de Lara, “Rapid Prototyping by Means of Meta-Modelling and Graph Grammars. An Example with Constraint Satisfaction”. In Jornadas de Ingeniería del Software y Bases de Datos, JISBD’03.
- Thesis
"Towards Hybrid Methods for Solving Hard Combiantorial Optimization Problems", Universidad Autonoma de Madrid, September 2006.

Conferences:                                                                                                                                 Top


Organizer and Chairman of the "Problem Solving and Applications Seminar" in Colmenarejo, Madrid, June of 2007.

Presenter at the following conferences:

  1. CAEPIA'09 - Tutorial in Comet. Seville, Spain, November 2009.
  2. INFORMS'09, San Diego, USA, October 2009.
  3. CP'09, Lisbon, Portugal, September 2009.
  4. MIT Bioinformatics Seminar, Cambridge, USA, May 2009.
  5. Telefonica Research Seminars, Madrid, Spain, September 2008.
  6. CP'05, Sitges, Spain, October 2005.
  7. CPAIOR'05, Prague, Czech Republic, May 2005.
  8. CP'03, Kinsale, Ireland, October 2003.
  9. Problem Solving Seminar, Barcelona, Spain, May 2003.

Teaching:                                                                                                                                      Top


  1. UNIVERSIDAD EUROPEA DE MADRID, 2006/2007.
    Algorithms and Operations Research. Undergraduate.
  2. UNIVERSIDAD AUTONOMA DE MADRID, 2002-2004.
    Labs of Methodology of Programming and Data Structures. Undergraduate.

Links:                                                                                                                                             Top


Contact:                                                                                                                                         Top


Postdocs and/or research stays with own funding are welcome, please contact me at:

Biology Department,
Boston College
Chesnut Hill, MA 02467
contact@
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