Christine Gaspin, permanent researcher INRA Toulouse, Dept. de Biométrie et Intelligence Artificielle Chemin de Borde Rouge, BP 27 Castanet-Tolosan 31326 Cedex, France Christine.Gaspin@toulouse.inra.fr Phone: (+33).5.61.28.52.82 Fax: (+33).5.61.28.53.35

• Research
• Scientific collaborations
• Tools and software
• Publications

Research themes

• Computer science : constraint satisfaction and optimization techniques originating from artificial intelligence and operations research to constrained
• Computational biology : RNA structure determination ; structured pattern searching ; genetic markers ordering...

Collaborations

• CNRS/IBMC of Strasbourg (FRANCE)
  Collaboration with E. Westhof on the development of tools dedicated to RNA structure analysis.
• IBCG/CNRS of Toulouse (FRANCE)
  Collaboration with B. Michot and J.-P. Bachellerie on the development of tools dedicated to RNA structure analysis.
• INRA laboratory associated to the university of Gand (BELGIUM)
  Collaboration with P. Rouze on gene prediction

Tools & Softwares

• Con'FLEX: a C++ library dedicated to the expression and the resolution of (fuzzy) CSP.
• Drawna : available on request to E. Westhof (westhof@ibmc.u-strasbg.fr)
• RNAsearch : computes RNA secondary structures display without overlapping. Actually works in ESSA.
• SAPSSARN: computes RNA secondary structures within the CSP framework.
• ESSA: edition and analysis of RNA secondary structures.
• CARThAGÈNE: solves marker ordering problems and can also join genetic maps on simple pedigrees: backcross and RI (ri self, ri sib) up to now. This is still a prototype, but you may ask T. Schiex the binaries if you are interested.

Publications

Journals

• Mission scheduling
  C. Gaspin
  Journal of Telematics and Informatics, Vol. 6, pp. 159-169, 1989.

• Automatic Display of RNA Secondary Structures
  G. Muller, C. Gaspin, A. Etienne & E. Westhof
  CABIOS, Vol. 9, Num. 5, pp. 551-561, 1993.

• DRAWNA : a program for drawing schematic views of nucleic acids
  Ch. Massire, Ch. Gaspin & E. Westhof
  J. Mol. Graphics, Vol. 12, pp. 201-207, September, 1994.

• Determination assistee par ordinateur de structures secondaires d'ARN (in french)
  C. Gaspin, P. Bourret & E. Westhof
  Technique et science informatiques (TSI), Vol. 14, Num. 2, pp. 141-160, 1995.

• An interactive framework for RNA secondary structure prediction with a dynamical treatment of constraints
  C. Gaspin & E. Westhof
  Journal of Molecular Biology, Vol. 254, pp. 163-174, 1995.

• Satisfaction de contraintes et biologie moléculaire (in french)
  C. Gaspin, C. Bessière, A. Moisan & T. Schiex
  Revue d'Intelligence Artificielle, Vol. 9, Num. 3, pp. 355-381, 1995.

• An interactive computer tool for the analysis of RNA molecules on the basis of their secondary structure
  F. Chetouani, P. Monestie, P. Thebault, C. Gaspin & B. Michot
  Nucleic Acids Research, Vol. 25, 1997.

Conferences

• Reseaux neuromimetiques, Machines de Boltzmann avec accoutumance et sensibilisation (in french)
  P. Bourret & C. Gaspin
  IVemes journees neurosciences et sciences de l'ingenieur,Marseilles,mai 1988.

• Neural networks for optimal planning of a camera on board a satellite
  P. Bourret, C. Gaspin & M. Samuelides
  Neuro-Nimes,November, 1988.

• Scheduling space operations by a Boltzmann machine
  C. Gaspin & P. Bourret
  n'Euro88, Paris, June 6-9, 1988.

• Annealing used with Boltzmann machines
  P. Bourret, A. Bouju & C. Gaspin
  Proc. INNC90, Vol. 2, Paris, 1990.

• Programmation lineaire en variables bivalentes sur modeles discrets: traduction de contraintes (in french)
  C. Gaspin
  Proc. of Neuro-Nimes 1990, Nimes, Novembre, 1990.

• Computation of RNAs secondary structures by a boltzmann machine
  P. Bourret & C. Gaspin
  Proc. of the international AMSE conference, Neural networks methodologies and applications in system, control vsion and genetics, San Diego, California, May 29-31,1991.

• A neural based approach of constraints satisfaction problems
  P. Bourret & C. Gaspin
  Proc. of IJCNN92, Baltimore, 1992.

• Prediction de structures d'acides ribonucleiques (in french)
  C. Gaspin & E. Westhof
  Proc. of the XXIVemes journees de Statistiques de Bruxelles, Bruxelles, 22 mai, 1992.

• Determination de structures secondaires et tertiaires d'acides ribonucleiques(in french)
  C. Gaspin & E. Westhof
  Colloques annuel de la societe francaise de biophysique, Figeac, 1993.

• Modelisation d'ARN catalytiques : du 2D au 3D (in french)
  E. Westhof & C. Gaspin
  Septiemes Entretiens du Centre Jacques Cartier, Computer Science and molecular biology, Lyon (France), November 30th, December 2nd, 1994.

• The determination of the secondary structure of ribonucleic acids as a constraint satisfaction problem
  C. Gaspin & E. Westhof
  Colloquium Molecular Bioinformatics IEE94, London, England, 1994.

• Lazy Arc Consistency
  T. Schiex, J-C. Régin, C. Gaspin & G. Verfaillie
  Proc. of AAAI'96. Portland(OR), 1996.

• Constructing and Joining Maximum Likelihood Genetic Maps
  T. Schiex, C. Gaspin, V. Laurent & B. Mangin
  To appear in the proc. of EUCARPIA'97, Poznan, Poland, May 1997.

• CARThAGENE: Constructing and Joining Maximum Likelihood Genetic Maps
  T. Schiex & C. Gaspin
  Proc. of ISMB'97. Halkidiki, Greece, June 1997.

• Genetic Algorithms for Genetic Mapping
  C. Gaspin & T. Schiex
  In Proc. of EA-97, Nimes, France, 1997.

Contribution to edited books

• The determination of secondary structures of RNA as a constraint satisfaction problem
  C. Gaspin & E. Westhof
  Advances in molecular bioinformatics, IOS Press, Ed. S. Schulze-Kremer, Frontiers in Artificial Intelligence and Applications, 1994.

• DNA and RNA structure prediction
  E. Westhof, P. Auffinger & C. Gaspin
  In M. Bishop & C. Rawlings (Ed.), DNA and Protein Sequence Analysis, A practical Approach, Chapter 14, IRL Press, 1996.

• RNA structure prediction
  E. Westhof & C. Gaspin
  Encyclopedia of Molecular Biology. To appear.

Posters

• Automatic translation of constraints for solving optimization problems by neural networks
  C. Gaspin
  Proc. of IJCNN90, Vol. III, San Diego, California, June 17-21, 1990.

Workshop papers

• Maximal constraint satisfaction problems
  C. Gaspin & J.-C. Regin
  CP97 workshop on the applications of constraints to bioinformatics and biocomputing, Austria, october 27th - november 1st, 1997.

Seminars

• Autour des molécules d'arn : Introduction aux problèmes et aux solutions algorithmiques.
  C. Gaspin
  Seminaire bio-informatique sur l'ARN à l'institut Pasteur, organisé par Marie-France Sagot, Dec. 1997, Material available at the team level.