Bibliography

Major publications by the team in recent years

• 1B. Bouvier, R. Grunberg, M. Nilges, F. Cazals.
  
  Shelling the Voronoi interface of protein-protein complexes reveals patterns of residue conservation, dynamics and composition, in: Proteins: structure, function, and bioinformatics, 2009, vol. 76, n^o 3, pp. 677–692.
• 2F. Cazals.
  
  Effective nearest neighbors searching on the hyper-cube, with applications to molecular clustering, in: Proc. 14th Annu. ACM Sympos. Comput. Geom., 1998, pp. 222–230.
• 3F. Cazals, F. Chazal, T. Lewiner.
  
  Molecular shape analysis based upon the Morse-Smale complex and the Connolly function, in: ACM SoCG, San Diego, USA, 2003.
• 4F. Cazals, T. Dreyfus.
  
  Multi-scale Geometric Modeling of Ambiguous Shapes with Toleranced Balls and Compoundly Weighted $\alpha$-shapes, in: Symposium on Geometry Processing, Lyon, B. Levy, O. Sorkine (editors), 2010, Also as Inria Tech report 7306.
• 5F. Cazals, J. Giesen.
  
  Delaunay Triangulation Based Surface Reconstruction, in: Effective Computational Geometry for curves and surfaces, J.-D. Boissonnat, M. Teillaud (editors), Springer-Verlag, Mathematics and Visualization, 2006.
• 6F. Cazals, C. Karande.
  
  An algorithm for reporting maximal $c$-cliques, in: Theoretical Computer Science, 2005, vol. 349, n^o 3, pp. 484–490.
• 7F. Cazals, S. Loriot.
  
  Computing the exact arrangement of circles on a sphere, with applications in structural biology, in: Computational Geometry: Theory and Applications, 2009, vol. 42, n^o 6-7, pp. 551–565, Preliminary version as Inria Tech report 6049.
• 8F. Cazals, F. Proust, R. Bahadur, J. Janin.
  
  Revisiting the Voronoi description of Protein-Protein interfaces, in: Protein Science, 2006, vol. 15, n^o 9, pp. 2082–2092.
• 9T. Dreyfus, V. Doye, F. Cazals.
  
  Assessing the Reconstruction of Macro-molecular Assemblies with Toleranced Models, in: Proteins: structure, function, and bioinformatics, 2012, vol. 80, n^o 9, pp. 2125–2136.
• 10S. Loriot, S. Sachdeva, K. Bastard, C. Prevost, F. Cazals.
  
  On the Characterization and Selection of Diverse Conformational Ensembles, in: IEEE/ACM Transactions on Computational Biology and Bioinformatics, 2011, vol. 8, n^o 2, pp. 487–498.
• 11N. Malod-Dognin, A. Bansal, F. Cazals.
  
  Characterizing the Morphology of Protein Binding Patches, in: Proteins: structure, function, and bioinformatics, 2012, vol. 80, n^o 12, pp. 2652–2665.

Publications of the year

Articles in International Peer-Reviewed Journals

• 12R. Castro, L. Jouneau, H. Pham, O. Bouchez, V. Giudicelli, M. Lefranc, E. Quillet, A. Benmansour, F. Cazals, A. Six, S. Fillatreau, O. Sunyer, P. Boudinot.
  
  Teleost Fish Mount Complex Clonal IgM and IgT Responses in Spleen upon Systemic Viral Infection, in: PLoS Pathog, 2013, vol. 9, n^o 1.
  
  http://hal.inria.fr/hal-00779835
• 13T. Dreyfus, V. Doye, F. Cazals.
  
  Probing a Continuum of Macro-molecular Assembly Models with Graph Templates of Sub-complexes, in: Proteins: Structure, Function, and Bioinformatics, 2013, In press. [ DOI : 10.1002/prot.24313 ]
  
  http://hal.inria.fr/hal-00849795

International Conferences with Proceedings

• 14D. Agarwal, J. Araujo, C. Caillouet, F. Cazals, D. Coudert, S. Perennes.
  
  Connectivity Inference in Mass Spectrometry based Structure Determination, in: European Symposium on Algorithms, Sophia-Antipolis, France, France, H. Bodlaender, G. Italiano (editors), Lecture Notes in Computer Science - LNCS, Springer, 2013, vol. 8125, pp. 289-300. [ DOI : 10.1007/978-3-642-40450-4_25 ]
  
  http://hal.inria.fr/hal-00849873

Books or Proceedings Editing

• 15F. Cazals, P. Kornprobst (editors)
  
  Modeling in Computational Biology and Medicine: A Multidisciplinary Endeavor, Springer, 2013, 315 p. [ DOI : 10.1007/978-3-642-31208-3 ]
  
  http://hal.inria.fr/hal-00845616

Internal Reports

• 16D. Agarwal, J. Araujo, C. Caillouet, F. Cazals, D. Coudert, S. Pérennes.
  
  Connectivity Inference in Mass Spectrometry based Structure Determination, Inria, June 2013, n^o RR-8320, 23 p.
  
  http://hal.inria.fr/hal-00837496
• 17D. Agarwal, F. Cazals, N. Malod-Dognin.
  
  Stoichiometry Determination for Mass-spectrometry Data: the Interval Case, Inria, February 2013, n^o RR-8101, 52 p.
  
  http://hal.inria.fr/hal-00741491
• 18F. Cazals, T. Dreyfus, S. Sachdeva, S. Nisarg.
  
  Greedy Geometric Optimization Algorithms for Collection of Balls, Inria, January 2013, n^o RR-8205, 26 p.
  
  http://hal.inria.fr/hal-00777892
• 19F. Cazals, A. Roth, C. Robert, M. Christian.
  
  Towards Morse Theory for Point Cloud Data, Inria, July 2013, n^o RR-8331, 37 p.
  
  http://hal.inria.fr/hal-00848753

Other Publications

• 20C. Garate, S. Zaidenberg, J. Badie, F. Bremond.
  
  Group Tracking and Behavior Recognition in Long Video Surveillance Sequences, January 2014, VISAPP - 9th International Joint Conference on Computer Vision, Imaging and Computer Graphics Theory and Applications.
  
  http://hal.inria.fr/hal-00879734

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• 22F. Alber, S. Dokudovskaya, L. Veenhoff, W. Zhang, J. Kipper, D. Devos, A. Suprapto, O. Karni-Schmidt, R. Williams, B. Chait, A. Sali, M. Rout.
  
  The molecular architecture of the nuclear pore complex, in: Nature, 2007, vol. 450, n^o 7170, pp. 695–701.
• 23F. Alber, F. Förster, D. Korkin, M. Topf, A. Sali.
  
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  On Itinerant Water Molecules and Detectability of Protein-Protein Interfaces through Comparative Analysis of Homologues, in: JMB, 2007, vol. 369, n^o 2, pp. 584–595.
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  Integrating statistical pair potentials into protein complex prediction, in: Proteins, 2007, vol. 69, pp. 511–520.
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  Geometry and Topology in Hamiltonian Dynamics and Statistical Mechanics, Springer, 2007.
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  Fast and Reliable Analysis of Molecular Motion Using Proximity Relations and Dimensionality Reduction, in: Proteins: Structure, Function, and Bioinformatics, 2007, vol. 67, n^o 4, pp. 897–907.
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