Overall Objectives
Scientific Foundations
New Results
Contracts and Grants with Industry
Other Grants and Activities


Publications of the year

Doctoral Dissertations and Habilitation Theses

T. Bourquard.
Exploitation des algorithmes génétiques pour la prédiction de structures de complexes protéine-protéine, Laboratoire de Recherche en Informatique (LRI) – Université Paris-XI/Paris Sud, December 2009, Ph. D. Thesis.
M. Djelloul.
Algorithmes de graphes pour la recherche de motifs récurrents dans les structures tertiaires d'ARN, Laboratoire de Recherche en Informatique (LRI) – Université Paris-XI/Paris Sud, December 2009, Ph. D. Thesis.
B. Rance.
Fouille et intégration de données biologiques hétérogènes, Laboratoire de Recherche en Informatique (LRI) – Université Paris-XI/Paris Sud, September 2009, Ph. D. Thesis.

Articles in International Peer-Reviewed Journal

Z. Bao, S. Cohen-Boulakia, S. Davidson, P. Girard.
PDiffView: Viewing the Difference in Provenance of Workflow Results, in: PVLDB, Proc. of the 35th Int. Conf. on Very Large Data Bases, 2009, vol. 2, no 2, p. 1638-1641.
K. Darty, A. Denise, Y. Ponty.
VARNA: Interactive drawing and editing of the RNA secondary structure, in: Bioinformatics, Apr 2009, vol. 25, no 15, p. 1974–1975
A. Ivashchenko, G. Boldina, A. Turmagambetova, M. Régnier.
Using profiles based on hydropathy properties to define essential regions for splicing, in: International Journal of Biological Sciences, 2009, vol. 5, 10 p. p
A. Lopes, M. Schmidt am Busch, T. Simonson.
Computational design of protein:ligand binding: modifying the specificity of asparaginyl-tRNA synthetase, in: J. Comp. Chem., 2009, vol. in press, 0000 p.
G. Park, H.-K. Hwang, P. Nicodème, W. Szpankowski.
Profile of Tries, in: SIAM journal on Computing, 2009, vol. 38, no 5, p. 1821-1880.
M. Schmidt am Busch, D. Mignon, T. Simonson.
Computational protein design as a tool for fold recognition, in: Proteins, 2009, vol. 77, p. 139–158.

Invited Conferences

S. Davidson, Y. Chen, P. Sun, S. Cohen-Boulakia.
On User Views in Scientific Workflow Systems (Invited Paper), in: Proc. of the the First Int. Workshop on the role of Semantic Web in Provenance Management (ISWC 2009 Workshop), 2009.

International Peer-Reviewed Conference/Proceedings

Z. Bao, S. Cohen-Boulakia, S. Davidson, A. Eyal, S. Khanna.
Differencing Provenance in Scientific Workflows, in: Proc. of the 25th Int. Conf. on Data Engineering (ICDE), IEEE, 2009, p. 808-819.
T. Bourquard, J. Bernauer, J. Azé, A. Poupon.
Comparing Voronoi and Laguerre tessellations in the protein-protein docking context, in: Sixth annual International Symposium on Voronoi Diagrams, Danemark Copenhagen, F. Anton and J. Andreas Bærentzen - Technical University of Denmark, 2009
S. Cohen-Boulakia, K. Masini.
BioBrowsing: Making the Most of the Data Available in Entrez, in: 21st Int. Conf. in Scientific and Statistical Database Management (SSDBM), LNCS 5566, Springer, 2009, p. 283-291.
B. Rance, J.-F. Gibrat, C. Froidevaux.
An adaptive combination of matchers: application to the mapping of biological ontologies for genome annotation, in: Data Integration in the Life Sciences, DILS 2009, N. W. Paton, P. Missier, C. Hedeler (editors), Lecture Notes in Computer Science, Springer, 2009, vol. 5647, p. 113-126.
C. Saule, A. Denise.
Counting RNA pseudoknotted structures, in: Proceedings of ISMB/ECCB, Stockholm, June 2009.
V. D. Tran, P. Chassignet, J.-M. Steyaert.
Prediction of super-secondary structure in alpha-helical and beta-barrel transmembrane proteins, in: Highlights from the Fifth International Society for Computational Biology (ISCB) Student Council Symposium, 2009, vol. 10, no Suppl 13, O3 p

Scientific Books (or Scientific Book chapters)

P. Amar, F. Képes, V. Norris, G. Bernot.
Proceedings of the Nice 2009 spring school on Modelling Complex Biological Systems in the context of genomics, EDP Sciences, 2009.
S. Cohen-Boulakia, W. C. Tan.
Provenance in Scientific Databases, in: Encyclopedia of Database Systems, Springer US, 2009, p. 2202-2207.
Z. Lacroix, C. R. Kothari, P. Mork, R. Rifaieh, M. Wilkinson, J. Freire, S. Cohen-Boulakia.
Biological Resource Discovery, in: Encyclopedia of Database Systems, Springer US, 2009, p. 220-223.
Z. Lacroix, C. R. Kothari, P. Mork, M. Wilkinson, S. Cohen-Boulakia.
Biological Metadata Management, in: Encyclopedia of Database Systems, Springer US, 2009, p. 215-219.
V. Norris, P. Amar, M. Aimar, P. Ballet, A.-F. Batto, G. Barlovatz, G. Bernot, G. Beslon, A. Cabin, S. Chevalier, A. Delaune, J.-M. Delosme, E. Fanchon, H. Gao, N. Glade, Y. Grondin, D. Hernandez-Verdun, L. Janniere, F. Képes, C. Lange, G. Legent, C. Loutelier-Bourhis, F. Molina, N. Orange, D. Raine, C. Ripoll, M. Thellier, A. Thierry, P. Tracqui, A. Zemirline.
Hyperstructures 2008-2009, in: Modelling Complex Biological Systems in the Context of Genomics, EDP Sciences, 2009, p. 71–84.
M. Régnier, Z. Kirakossian, E. Furletova, M. Roytberg.
A Word Counting Graph, in: London Algorithmics 2008: Theory and Practice (Texts in Algorithmics), J. Chan, J. W. Daykin, M. Sohel Rahman (editors), London College Publications, 06 2009, p. 10–43

Other Publications

A. Denise, Y. Ponty, M. Termier.
Controlled non-uniform random generation of decomposable structures, 2009, Submitted to Theoretical Computer Science.
C. Herrbach, A. Denise, S. Dulucq.
Average complexity of the Jiang-Wang-Zhang pairwise tree alignment algorithm and of a RNA secondary structure alignment algorithm, 2009, Submitted to Theoretical Computer Science.
C. Saule, M. Régnier, J.-M. Steyaert, A. Denise.
Counting RNA pseudoknots, 2009, submitted to SFCA/FPSAC'10 : San Francisco, USA, 2010 and to workshop "Algorithmique, combinatoire du texte et applications en bio-informatique", Montpellier, janvier 2010.