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  • The Inria's Research Teams produce an annual Activity Report presenting their activities and their results of the year. These reports include the team members, the scientific program, the software developed by the team and the new results of the year. The report also describes the grants, contracts and the activities of dissemination and teaching. Finally, the report gives the list of publications of the year.

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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
  • 3D. 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, 2015, vol. 14, pp. 2274–2282. [ DOI : 10.1074/mcp.M114.047779 ]

    https://hal.archives-ouvertes.fr/hal-01078378
  • 4J. Carr, D. Mazauric, F. Cazals, D. J. Wales.

    Energy landscapes and persistent minima, in: The Journal of Chemical Physics, 2016, vol. 144, no 5, 4 p. [ DOI : 10.1063/1.4941052 ]

    https://www.repository.cam.ac.uk/handle/1810/253412
  • 5F. 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.
  • 6F. Cazals, T. Dreyfus.

    The Structural Bioinformatics Library: modeling in biomolecular science and beyond, in: Bioinformatics, 2017, vol. 7, no 33, pp. 1–8. [ DOI : 10.1093/bioinformatics/btw752 ]

    http://sbl.inria.fr
  • 7F. Cazals, T. Dreyfus, D. Mazauric, A. Roth, C. Robert.

    Conformational Ensembles and Sampled Energy Landscapes: Analysis and Comparison, in: J. of Computational Chemistry, 2015, vol. 36, no 16, pp. 1213–1231. [ DOI : 10.1002/jcc.23913 ]

    https://hal.archives-ouvertes.fr/hal-01076317
  • 8F. Cazals, T. Dreyfus, S. Sachdeva, N. Shah.

    Greedy Geometric Algorithms for Collections of Balls, with Applications to Geometric Approximation and Molecular Coarse-Graining, in: Computer Graphics Forum, 2014, vol. 33, no 6, pp. 1–17. [ DOI : 10.1111/cgf.12270 ]

    http://hal.inria.fr/hal-00777892
  • 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, no 9, pp. 2125–2136.
  • 10T. 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, vol. 81, no 11, pp. 2034–2044. [ DOI : 10.1002/prot.24313 ]

    http://hal.inria.fr/hal-00849795
  • 11N. Malod-Dognin, A. Bansal, F. Cazals.

    Characterizing the Morphology of Protein Binding Patches, in: Proteins: structure, function, and bioinformatics, 2012, vol. 80, no 12, pp. 2652–2665.
  • 12S. Marillet, P. Boudinot, F. Cazals.

    High Resolution Crystal Structures Leverage Protein Binding Affinity Predictions, in: Proteins: structure, function, and bioinformatics, 2015, vol. 1, no 84, pp. 9–20. [ DOI : 10.1002/prot.24946 ]

    https://hal.inria.fr/hal-01159641
  • 13A. Roth, T. Dreyfus, C. Robert, F. Cazals.

    Hybridizing rapidly growing random trees and basin hopping yields an improved exploration of energy landscapes, in: J. Comp. Chem., 2016, vol. 37, no 8, pp. 739–752. [ DOI : 10.1002/jcc.24256 ]

    https://hal.inria.fr/hal-01191028
Publications of the year

Articles in International Peer-Reviewed Journals

  • 14N. Cohen, F. Havet, D. Mazauric, I. Sau, R. Watrigant.

    Complexity dichotomies for the Minimum F -Overlay problem, in: Journal of Discrete Algorithms, September 2018, vol. 52-53, pp. 133-142. [ DOI : 10.1016/j.jda.2018.11.010 ]

    https://hal.inria.fr/hal-01947563
  • 15A. Lhéritier, F. Cazals.

    A Sequential Non-Parametric Multivariate Two-Sample Test, in: IEEE Transactions on Information Theory, May 2018, vol. 64, no 5, pp. 3361-3370.

    https://hal.inria.fr/hal-01968190
  • 16S. Magadan, L. Jouneau, M. Puelma Touzel, S. Marillet, W. Chara, A. Six, E. Quillet, T. Mora, A. Walczak, F. Cazals, O. Sunyer, S. Fillatreau, P. Boudinot.

    Origin of Public Memory B Cell Clones in Fish After Antiviral Vaccination, in: Frontiers in Immunology, September 2018, vol. 9.

    https://hal.inria.fr/hal-01968155

International Conferences with Proceedings

  • 17J. Bensmail, D. Mazauric, F. Mc Inerney, N. Nisse, S. Pérennes.

    Localiser une cible dans un graphe, in: ALGOTEL 2018 - 20èmes Rencontres Francophones sur les Aspects Algorithmiques des Télécommunications, Roscoff, France, May 2018.

    https://hal.inria.fr/hal-01774827
  • 18J. Bensmail, D. Mazauric, F. Mc Inerney, N. Nisse, S. Pérennes.

    Sequential Metric Dimension, in: 16th Workshop on Approximation and Online Algorithms (WAOA 2018), Helsinki, Finland, August 2018.

    https://hal.inria.fr/hal-01883712
  • 19J.-C. Bermond, A. Chaintreau, G. Ducoffe, D. Mazauric.

    How long does it take for all users in a social network to choose their communities?, in: 9th International Conference on Fun with Algorithms (FUN 2018), La Maddalena, Italy, 2018.

    https://hal.inria.fr/hal-01780627
  • 20F. Cazals, D. Mazauric, R. Tetley, R. Watrigant.

    Comparaison de deux clusterings par couplage entre clusters de clusters, in: ALGOTEL 2018 - 20èmes Rencontres Francophones sur les Aspects Algorithmiques des Télécommunications, Roscoff, France, May 2018.

    https://hal.inria.fr/hal-01774440

Internal Reports

Other Publications

  • 24J.-C. Bermond, D. Mazauric, V. Misra, P. Nain.

    Distributed Link Scheduling in Wireless Networks, January 2019, working paper or preprint.

    https://hal.inria.fr/hal-01977266
  • 25F. Cazals, R. Tetley.

    Multiscale analysis of structurally conserved motifs, July 2018, working paper or preprint.

    https://hal.inria.fr/hal-01968176
  • 26R. Tetley, F. Cazals.

    Characterizing molecular flexibility by combining lRMSD measures, July 2018, working paper or preprint.

    https://hal.inria.fr/hal-01968175
  • 27R. Tetley, F. Cazals.

    Hybrid sequence-structure based HMM models leverage the identification of homologous proteins: the example of class II fusion proteins, July 2018, working paper or preprint.

    https://hal.inria.fr/hal-01968177
References in notes
  • 28F. Alber, S. Dokudovskaya, L. Veenhoff, W. Zhang, J. Kipper, D. Devos, A. Suprapto, O. Karni-Schmidt, R. Williams, B. Chait, M. Rout, A. Sali.

    Determining the architectures of macromolecular assemblies, in: Nature, Nov 2007, vol. 450, pp. 683-694.
  • 29F. 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, no 7170, pp. 695–701.
  • 30F. Alber, F. Förster, D. Korkin, M. Topf, A. Sali.

    Integrating Diverse Data for Structure Determination of Macromolecular Assemblies, in: Ann. Rev. Biochem., 2008, vol. 77, pp. 11.1–11.35.
  • 31O. Becker, A. D. Mackerell, B. Roux, M. Watanabe.

    Computational Biochemistry and Biophysics, M. Dekker, 2001.
  • 32A.-C. Camproux, R. Gautier, P. Tuffery.

    A Hidden Markov Model derived structural alphabet for proteins, in: J. Mol. Biol., 2004, pp. 591-605.
  • 33M. L. Connolly.

    Analytical molecular surface calculation, in: J. Appl. Crystallogr., 1983, vol. 16, no 5, pp. 548–558.
  • 34R. Dunbrack.

    Rotamer libraries in the 21st century, in: Curr Opin Struct Biol, 2002, vol. 12, no 4, pp. 431-440.
  • 35B. Escoffier, L. Gourvès, J. Monnot.

    Strategic coloring of a graph, in: Internet Mathematics, 2012, vol. 8, no 4, pp. 424–455.
  • 36A. Fernandez, R. Berry.

    Extent of Hydrogen-Bond Protection in Folded Proteins: A Constraint on Packing Architectures, in: Biophysical Journal, 2002, vol. 83, pp. 2475-2481.
  • 37A. Fersht.

    Structure and Mechanism in Protein Science: A Guide to Enzyme Catalysis and Protein Folding, Freeman, 1999.
  • 38M. Gerstein, F. Richards.

    Protein geometry: volumes, areas, and distances, in: The international tables for crystallography (Vol F, Chap. 22), M. G. Rossmann, E. Arnold (editors), Springer, 2001, pp. 531–539.
  • 39H. Gohlke, G. Klebe.

    Statistical potentials and scoring functions applied to protein-ligand binding, in: Curr. Op. Struct. Biol., 2001, vol. 11, pp. 231-235.
  • 40J. Janin, S. Wodak, M. Levitt, B. Maigret.

    Conformations of amino acid side chains in proteins, in: J. Mol. Biol., 1978, vol. 125, pp. 357–386.
  • 41J. Kleinberg, K. Ligett.

    Information-sharing in social networks, in: Games and Economic Behavior, 2013, vol. 82, pp. 702–716.
  • 42V. K. Krivov, M. Karplus.

    Hidden complexity of free energy surfaces for peptide (protein) folding, in: PNAS, 2004, vol. 101, no 41, pp. 14766-14770.
  • 43E. Meerbach, C. Schutte, I. Horenko, B. Schmidt.

    Metastable Conformational Structure and Dynamics: Peptides between Gas Phase and Aqueous Solution, in: Analysis and Control of Ultrafast Photoinduced Reactions. Series in Chemical Physics 87, O. Kuhn, L. Wudste (editors), Springer, 2007.
  • 44I. Mihalek, O. Lichtarge.

    On Itinerant Water Molecules and Detectability of Protein-Protein Interfaces through Comparative Analysis of Homologues, in: JMB, 2007, vol. 369, no 2, pp. 584–595.
  • 45J. Mintseris, B. Pierce, K. Wiehe, R. Anderson, R. Chen, Z. Weng.

    Integrating statistical pair potentials into protein complex prediction, in: Proteins, 2007, vol. 69, pp. 511–520.
  • 46M. Pettini.

    Geometry and Topology in Hamiltonian Dynamics and Statistical Mechanics, Springer, 2007.
  • 47E. Plaku, H. Stamati, C. Clementi, L. Kavraki.

    Fast and Reliable Analysis of Molecular Motion Using Proximity Relations and Dimensionality Reduction, in: Proteins: Structure, Function, and Bioinformatics, 2007, vol. 67, no 4, pp. 897–907.
  • 48D. Rajamani, S. Thiel, S. Vajda, C. Camacho.

    Anchor residues in protein-protein interactions, in: PNAS, 2004, vol. 101, no 31, pp. 11287-11292.
  • 49D. Reichmann, O. Rahat, S. Albeck, R. Meged, O. Dym, G. Schreiber.

    From The Cover: The modular architecture of protein-protein binding interfaces, in: PNAS, 2005, vol. 102, no 1, pp. 57-62.
  • 50F. Richards.

    Areas, volumes, packing and protein structure, in: Ann. Rev. Biophys. Bioeng., 1977, vol. 6, pp. 151-176.
  • 51G. Rylance, R. Johnston, Y. Matsunaga, C.-B. Li, A. Baba, T. Komatsuzaki.

    Topographical complexity of multidimensional energy landscapes, in: PNAS, 2006, vol. 103, no 49, pp. 18551-18555.
  • 52G. Schreiber, L. Serrano.

    Folding and binding: an extended family business, in: Current Opinion in Structural Biology, 2005, vol. 15, no 1, pp. 1–3.
  • 53M. Sippl.

    Calculation of Conformational Ensembles from Potential of Mean Force: An Approach to the Knowledge-based prediction of Local Structures in Globular Proteins, in: J. Mol. Biol., 1990, vol. 213, pp. 859-883.
  • 54C. Summa, M. Levitt, W. DeGrado.

    An atomic environment potential for use in protein structure prediction, in: JMB, 2005, vol. 352, no 4, pp. 986–1001.
  • 55S. Wodak, J. Janin.

    Structural basis of macromolecular recognition, in: Adv. in protein chemistry, 2002, vol. 61, pp. 9–73.