Bibliography

Major publications by the team in recent years

• 1F. Cazals, P. Kornprobst (editors)
  
  Modeling in Computational Biology and Medicine: A Multidisciplinary Endeavor, Springer, 2013. [ DOI : 10.1007/978-3-642-31208-3 ]
  
  http://hal.inria.fr/hal-00845616
• 2D. Agarwal, J. Araujo, C. Caillouet, F. Cazals, D. Coudert, S. Pérennes.
  
  Connectivity Inference in Mass Spectrometry based Structure Determination, in: European Symposium on Algorithms (Springer LNCS 8125), Sophia Antipolis, France, H. Bodlaender, G. Italiano (editors), Springer, 2013, pp. 289–300.
  
  http://hal.inria.fr/hal-00849873
• 3B. 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.
• 4F. 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, pp. 351-360.
• 5F. 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, pp. 1713-1722, Also as Inria Tech report 7306.
• 6F. 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.
• 7F. Cazals, C. Karande.
  
  An algorithm for reporting maximal $c$-cliques, in: Theoretical Computer Science, 2005, vol. 349, n^o 3, pp. 484–490.
• 8F. 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.
• 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

Doctoral Dissertations and Habilitation Theses

• 12D. Agarwal.
  
  Topics in mass spectrometry based structure determination, Université Nice Sophia Antipolis, May 2015.
  
  https://tel.archives-ouvertes.fr/tel-01176554
• 13A. Lhéritier.
  
  Nonparametric Methods for Learning and Detecting Multivariate Statistical Dissimilarity, Université Nice Sophia Antipolis, November 2015.
  
  https://hal.inria.fr/tel-01245946

Articles in International Peer-Reviewed Journals

• 14D. Agarwal, C. Caillouet, D. Coudert, F. Cazals.
  
  Unveiling Contacts within Macro-molecular assemblies by solving Minimum Weight Connectivity Inference Problems, in: Molecular and Cellular Proteomics, April 2015, 27 p. [ DOI : 10.1074/mcp.M114.047779 ]
  
  https://hal.inria.fr/hal-01245401
• 15J.-D. Boissonnat, D. Mazauric.
  
  On the complexity of the representation of simplicial complexes by trees, in: Theoretical Computer Science, February 2016, vol. 617, 17 p. [ DOI : 10.1016/j.tcs.2015.12.034 ]
  
  https://hal.inria.fr/hal-01259806
• 16F. Cazals, T. Dreyfus, D. Mazauric, A. Roth, C. Robert.
  
  Conformational Ensembles and Sampled Energy Landscapes: Analysis and Comparison, in: Journal of Computational Chemistry, May 2015, vol. 36, n^o 6, 18 p.
  
  https://hal.archives-ouvertes.fr/hal-01245395

International Conferences with Proceedings

• 17F. Cazals, A. Lhéritier.
  
  Beyond Two-sample-tests: Localizing Data Discrepancies in High-dimensional Spaces, in: IEEE/ACM International Conference on Data Science and Advanced Analytics, Paris, France, P. Gallinari, J. Kwok, G. Pasi, O. Zaiane (editors), October 2015, 29 p.
  
  https://hal.inria.fr/hal-01245408

Internal Reports

• 18F. Cazals, A. Lhéritier.
  
  Beyond Two-sample-tests: Localizing Data Discrepancies in High-dimensional Spaces, Inria, March 2015, n^o RR-8734, 29 p.
  
  https://hal.inria.fr/hal-01159235
• 19A. Lhéritier, F. Cazals.
  
  A Sequential Nonparametric Two-Sample Test, Inria, March 2015, n^o RR-8704, 18 p.
  
  https://hal.inria.fr/hal-01135608
• 20S. Marillet, P. Boudinot, F. Cazals.
  
  High Resolution Crystal Structures Leverage Protein Binding Affinity Predictions, Inria, March 2015, n^o RR-8733.
  
  https://hal.inria.fr/hal-01159641
• 21S. Marillet, M.-P. Lefranc, P. Boudinot, F. Cazals.
  
  Dissecting Interfaces of Antibody -Antigen Complexes: from Ligand Specific Features to Binding Affinity Predictions, Inria Sophia Antipolis, September 2015, n^o RR-8770, 61 p.
  
  https://hal.inria.fr/hal-01191462
• 22A. Roth, T. Dreyfus, C. H. Robert, F. Cazals.
  
  Hybridizing rapidly growing random trees and basin hopping yields an improved exploration of energy landscapes, Inria, September 2015, n^o RR-8768, 29 p.
  
  https://hal.inria.fr/hal-01191028

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• 24F. Alber, S. Dokudovskaya, L. Veenhoff, W. Zhang, J. Kipper, D. Devos, A. Suprapto, O. Karni-Schmidt, R. Williams, B. Chait, A. Sali, M. Rout.
  
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• 25F. Alber, F. Förster, D. Korkin, M. Topf, A. Sali.
  
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• 26O. Becker, A. D. Mackerell, B. Roux, M. Watanabe.
  
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