Bibliography

Publications of the year

Doctoral Dissertations and Habilitation Theses

[1]

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.

[2]

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.

[3]

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

[4]

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, n^o 2, p. 1638-1641.

[5]

K. Darty, A. Denise, Y. Ponty.
VARNA: Interactive drawing and editing of the RNA secondary structure, in: Bioinformatics, Apr 2009, vol. 25, n^o 15, p. 1974–1975
http://bioinformatics.oxfordjournals.org/cgi/content/abstract/btp250.

[6]

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
http://hal.inria.fr/inria-00429780/en/.

[7]

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.

[8]

G. Park, H.-K. Hwang, P. Nicodème, W. Szpankowski.
Profile of Tries, in: SIAM journal on Computing, 2009, vol. 38, n^o 5, p. 1821-1880.

[9]

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

[10]

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

[11]

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.

[12]

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
http://hal.inria.fr/inria-00429618/en/.

[13]

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.

[14]

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.

[15]

C. Saule, A. Denise.
Counting RNA pseudoknotted structures, in: Proceedings of ISMB/ECCB, Stockholm, June 2009.

[16]

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, n^o Suppl 13, O3 p
http://www.biomedcentral.com/1471-2105/10/S13/O3.

Scientific Books (or Scientific Book chapters)

[17]

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.

[18]

S. Cohen-Boulakia, W. C. Tan.
Provenance in Scientific Databases, in: Encyclopedia of Database Systems, Springer US, 2009, p. 2202-2207.

[19]

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.

[20]

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.

[21]

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.

[22]

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
http://hal.archives-ouvertes.fr/inria-00437147/en/.

Other Publications

[23]

A. Denise, Y. Ponty, M. Termier.
Controlled non-uniform random generation of decomposable structures, 2009, Submitted to Theoretical Computer Science.

[24]

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.

[25]

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.