Modeling in Computational Biology and Medicine: A Multidisciplinary Endeavor
F. Cazals, and P. Kornprobst (Editors)
Springer, 2013
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Simpler protein domain identification using spectral clustering
F. Cazals, and J. Herrmann, and E. Sarti
Submitted
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Modeling the dynamics of proteins: techniques from geometry, kinematics, and statistics
T. O'Donnell, and F. Cazals
Submitted
Subspace-Embedded Spherical Clusters: a novel cluster model for compact clusters of arbitrary dimension
F. Cazals, and L. Goldenberg, and S. Suren
Submitted
Conflict coloring problems: (theory, complexity, algorithm), and application to multi-resolution modeling in structural bioinformatics
F. Cazals, and F. Havet, and D. Mazauric, and V.H. Nguyen
Submitted
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Geometric constraints within tripeptides and the existence of tripeptide reconstructions
T. O'Donnell, and V. Agashe, and F. Cazals
J. Comp. Chem., 44 (13), 2023
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Overlaying a hypergraph with a graph with bounded maximum degree
Fr{\'e}d{\'e}ric Havet, and Dorian Mazauric, and Viet-Ha Nguyen, and R{\'e}mi Watrigant
Discrete Applied Mathematics, , 2022
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Non-existence of stable social groups in information-driven networks
Augustin Chaintreau, and Guillaume Ducoffe, and Dorian Mazauric
Theory of Computing Systems, , 2022
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Efficient computation of the the volume of a polytope in high-dimensions using Piecewise Deterministic Markov Processes
A. Chevallier, and F. Cazals, and P. Fearnhead
AISTATS, 2022
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Improved polytope volume calculations based on Hamiltonian Monte Carlo with boundary reflections and sweet arithmetics
A. Chevallier, and S. Pion, and F. Cazals
J. of Computational Geometry, 13 (1), 2022
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Fr\'echet mean and $p$-mean on the unit circle: decidability, algorithm, and applications to clustering on the flat torus
F. Cazals, and B. Delmas, and T. O'Donnell
Symposium on Experimental Algorithms, 2021
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Overlaying a Hypergraph with a Graph with Bounded Maximum Degree
Fr{\'{e}}d{\'{e}}ric Havet, and Dorian Mazauric, and Viet{-}Ha Nguyen, and R{\'{e}}mi Watrigant
Algorithms and Discrete Applied Mathematics - 6th International Conference, CALDAM 2020, Hyderabad, India, February 13-15, 2020, Proceedings, 2020
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Distributed Link Scheduling in Wireless Networks
Jean-Claude Bermond, and Dorian Mazauric, and Vishal Misra, and Philippe Nain
Discrete Mathematics, Algorithms and Applications, NA (NA), 2020
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Sequential Metric Dimension
Julien Bensmail, and Dorian Mazauric, and Fionn Mc Inerney, and Nicolas Nisse, and St{\'e}phane P{\'e}rennes
Algorithmica, NA (NA), 2020
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Wang-Landau algorithm: an adapted random walk to boost convergence
A. Chevallier, and F. Cazals
J. of Computational Physics, 410 (1), 2020
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Low-Complexity Nonparametric Bayesian Online Prediction with Universal Guarantees
A. Lh\'eritier, and F. Cazals
NeurIPS, 2019
Comparing two clusterings using matchings between clusters of clusters
F. Cazals, and D. Mazauric, and R. Tetley, and R. Watrigant
ACM J. of Experimental Algorithms, 24 (1), 2019
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Complexity dichotomies for the Minimum F-Overlay problem
N. Cohen, and F. Havet, and D. Mazauric, and I. Sau, and R. Watrigant
Journal of Discrete Algorithms, 52-53, 2018
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How long does it take for all users in a social network to choose their communities?
J.-C. Bermond, and A. Chaintreau, and G. Ducoffe, and D. Mazauric
9th International Conference on Fun with Algorithms, 2018
A Sequential Non-Parametric Multivariate Two-Sample Test
A. Lh\'eritier, and F. Cazals
IEEE Transactions on Information Theory, 64 (5), 2018
Maximum flow under proportional delay constraint
Pierre Bonami, and Dorian Mazauric, and Yann Vax{\`e}s
Theoretical Computer Science, NA, 2017
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Complexity Dichotomies for the Minimum F-Overlay Problem
N. Cohen, and F. Havet, and D. Mazauric, and I. Sau, and R. Watrigant
IWOCA 2017, 2017
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On the complexity of the representation of simplicial complexes by trees
J-D. Boissonnat, and D. Mazauric
Theoretical Computer Science, 617, 2016
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Experimental Evaluation of a Branch and Bound Algorithm for Computing Pathwidth and Directed Pathwidth
David Coudert, and Dorian Mazauric, and Nicolas Nisse
ACM Journal of Experimental Algorithmics, 21 (1), 2016
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Well Balanced Designs for Data Placement
Jean-Claude Bermond, and Alain Jean-Marie, and Dorian Mazauric, and Joseph Yu
Journal of Combinatorial Designs, 24 (2), 2016
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Beyond Two-sample-tests: Localizing Data Discrepancies in High-dimensional Spaces
F. Cazals, and A. Lh\'eritier
IEEE/ACM International Conference on Data Science and Advanced Analytics, 2015
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Greedy Geometric Algorithms for Collections of Balls, with Applications to Geometric Approximation and Molecular Coarse-Graining
F. Cazals, and T. Dreyfus, and S. Sachdeva, and N. Shah
Computer Graphics Forum, 33 (6), 2014
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Connectivity Inference in Mass Spectrometry based Structure Determination
D. Agarwal, and J. Araujo, and C. Caillouet, and F. Cazals, and D. Coudert, and S. P{\'e}rennes
European Symposium on Algorithms (Springer LNCS 8125), 2013
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Reconstructing 3D compact sets
F. Cazals, and D. Cohen-Steiner
Computational Geometry Theory and Applications, 45 (1-2), 2011
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Computing the Volume of Union of Balls: a Certified Algorithm
F. Cazals, and H. Kanhere, and S. Loriot
ACM Transactions on Mathematical Software, 38 (1), 2011
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Shape Matching by Localized Calculations of Quasi-isometric Subsets,with Applications to the Comparison of Protein Binding Patches
F. Cazals, and N. Malod-Dognin
International Conference on Pattern Recognition in Bioinformatics, 2011
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Multi-scale Geometric Modeling of Ambiguous Shapes with Toleranced Balls and Compoundly Weighted $\alpha$-shapes
F. Cazals, and T. Dreyfus
Symposium on Geometry Processing, 2010
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Design of the CGAL Spherical Kernel and application to arrangements of circles on a sphere
P. Castro, and F. Cazals, and S. Loriot, and M. Teillaud
Computational Geometry: Theory and Applications, 42 (6-7), 2009
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Computing the exact arrangement of circles on a sphere, with applications in structural biology
F. Cazals, and S. Loriot
Computational Geometry: Theory and Applications, 42 (6-7), 2009
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A note on the problem of reporting maximal cliques
F. Cazals, and C. Karande
Theoretical Computer Science, 407 (1--3), 2008
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Robust construction of the three-dimensional flow complex
F. Cazals, and A. Parameswaran, and S. Pion
ACM Symposium on Computational Geometry, 2008
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Algorithm 889: Jet fitting 3---A Generic C++ Package for Estimating the Differential Properties on Sampled Surfaces via Polynomial Fitting
F. Cazals, and M. Pouget
ACM Transactions on Mathematical Software, 35 (3), 2008
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Computing the exact arrangement of circles on a sphere, with applications in structural biology
F. Cazals, and S. Loriot
ACM Symposium on Computational Geometry, Video/Multimedia track, 2007
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A mini-review of clustering algorithms and their theoretical properties, with applications to molecular science
F. Cazals
Journal of Innovative Materials in Extreme Conditions, 5 (1), 2024. In honor of the 66th birthday of Christian Schoen.
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Discriminating physiological from non-physiological interfaces in structures of protein complexes: a community-wide study
H. Schweke, and Q. Xu, and G. Tauriello, and L. Pantolini, and T. Schwede, and F. Cazals, and A. Lhéritier, and J. Fernandez-Recio, and L. Rodríguez-Lumbreras, and O. Schueler-Furman, and J.K. Varga, and B. Jim\'enez-Garc\'ia, and M.F. R\'eau, and A. Bonvin, and C. Savojardo, and P-L. Martelli, and R. Casadio, and J. Tubiana, and H. Wolfson, and R. Oliva, and D. Barradas-Bautista, and T. Ricciardelli, and L. Cavallo, and C. Venclovas, and K. Olechnovic, and R. Guerois, and J. Andreani, and J. Martin, and X. Wang, and D. Kihara, and A. Marchand, and B. Correia, and X. Zou, and S. Dey, and R. Dunbrack, and E. Levy, and S. Wodak
Proteomics, 23 (17), 2023
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Enhanced conformational exploration of protein loops using a global parameterization of the backbone geometry
T. O'Donnell, and F. Cazals
J. Comp. Chem., 44 (11), 2023
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AlignMe: an update of the web server for alignment of membrane protein sequences
Ren\'e Staritzbichler, and Emily Yaklich, and Edoardo Sarti, and Nikola Ristic, and Peter Hildebrand, and Lucy Forrest
Nucleic Acids Research, (), 2022
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iBIS2Analyzer: a web server for a phylogeny-driven coevolution analysis of protein families
Francesco Oteri, and Edoardo Sarti, and Francesca Nadalin, and Alessandra Carbone
Nucleic Acids Research, (), 2022
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Crystal structure of chloroplast fructose-1,6-bisphosphate aldolase from the green alga Chlamydomonas reinhardtii
Th\'eo {Le Moigne}, and Edoardo Sarti, and Antonin Nourisson, and Mirko Zaffagnini, and Alessandra Carbone, and St\'ephane Lemaire, and Julien Henri
Journal of Structural Biology, 214 (3), 2022
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Gene prioritization based on random walks with restarts and absorbing states, to define gene sets regulating drug pharmacodynamics from single-cell analyses
A. Sales-de-Queiroz, and G. Cruz, and A. Jean-Marie, and D. Mazauric, and J. Roux, and F. Cazals
PLOS One, 17 (11), 2022
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Tripeptide loop closure: a detailed study of reconstructions based on Ramachandran distributions
T. O'Donnell, and C.H. Robert, and F. Cazals
Proteins: structure, function, and bioinformatics, 90 (3), 2022
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Boosting the analysis of protein interfaces with Multiple Interface String Alignment: illustration on the spikes of coronaviruses
S. Bereux, and B. Delmas, and F. Cazals
Proteins: structure, function, and bioinformatics, 90 (3), 2022
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SARS-CoV-2 Through the Lens of Computational Biology:How bioinformatics is playing a key role in the study of the virus and its origins
Samuel Alizon, and Fr{\'e}d{\'e}ric Cazals, and St{\'e}phane Guindon, and Claire Lemaitre, and Tristan Mary-Huard, and Anna Niarakis, and Mika{\"e}l Salson, and Celine Scornavacca, and H{\'e}l{\`e}ne Touzet
Report 2021
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Studying dynamics without explicit dynamics: a structure-based study of the export mechanism by AcrB
M. Simsir, and I. Broutin, and I. Mus-Veteau, and F. Cazals
Proteins: structure, function, and bioinformatics, 89, 2021
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Characterizing molecular flexibility by combining lRMSD measures
F. Cazals, and R. Tetley
Proteins: structure, function, and bioinformatics, 87 (5), 2019
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Survey of the analysis of continuous conformational variability of biological macromolecules by electron microscopy
C. Sorzano, and A. Jim{\'e}nez, and J. Mota, and J. Vilas, and D. Maluenda, and M. Mart{\'i}nez, and E. Ram{\'i}rez-Aportela, and T. Majtner, and J. Segura, and R. S{\'a}nchez-Garc{\'i}a, and Y. Rancel, and L. Ca{\~n}o, and P. Conesa, and R. Melero, and S. Jonic, and J. Vargas, and F. Cazals, and Z. Freyberg, and J. Krieger, and I. Bahar, and R. Marabini, and J. Carazo
Acta Crystallographica Section F, 75 (1), 2019
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Origin of public memory B cell clones in fish after antiviral vaccination
S. Magadan, and L. Jouneau, and M. Touzel, and S. Marillet, and W. Chaara, and A. Six, and E. Quillet, and T. Mora, and A. Walczak, and F. Cazals, and O. Sunyer, and S. Fillatreau, and P. Boudinot
Frontiers in immunology, 9 (NA), 2018
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Anti-interleukin-6 signalling therapy rebalances the disturbed cytokine production of B cells from patients with active rheumatoid arthritis
S. Fleischer, and S. Ries, and P. Shen, and A. Lh\'eritier, and F. Cazals, and G. Burmester, and T. D\"orner, and S. Fillatreau
European Journal of Immunology, 48 (1), 2017 -- DOI
Novel Structural Parameters of Ig--Ag Complexes Yield a Quantitative Description of Interaction Specificity and Binding Affinity
S. Marillet, and M-P. Lefranc, and P. Boudinot, and F. Cazals
Frontiers in immunology, 34 (8), 2017
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The Structural Bioinformatics Library: modeling in biomolecular science and beyond
F. Cazals, and T. Dreyfus
Bioinformatics, 7 (33), 2017
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Predicting binding poses and affinities for protein - ligand complexes in the 2015 D3R Grand Challenge using a physical model with a statistical parameter estimation
S. Grudinin, and M. Kadukova, and A. Eisenbarth, and S. Marillet, and F. Cazals
J. of Computer-Aided Molecular Design, 9 (30), 2016
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Energy landscapes and persistent minima
J. Carr, and D. Mazauric, and F. Cazals, and D. Wales
The Journal of Chemical Physics, 144 (5), 2016
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Hybridizing rapidly growing random trees and basin hopping yields an improved exploration of energy landscapes
A. Roth, and T. Dreyfus, and C.H. Robert, and F. Cazals
J. Comp. Chem., 37 (8), 2016
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High Resolution Crystal Structures Leverage Protein Binding Affinity Predictions
S. Marillet, and P. Boudinot, and F. Cazals
Proteins: structure, function, and bioinformatics, 1 (84), 2015
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Unveiling Contacts within Macro-molecular assemblies by solving Minimum Weight Connectivity Inference Problems
D. Agarwal, and C. Caillouet, and D. Coudert, and F. Cazals
Molecular and Cellular Proteomics, 14, 2015
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Conformational Ensembles and Sampled Energy Landscapes: Analysis and Comparison
F. Cazals, and T. Dreyfus, and D. Mazauric, and A. Roth, and C.H. Robert
J. Comp. Chem., 36 (16), 2015
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Ciruvis: a web-based tool for rule networks and interaction detection using rule-based classifiers
Susanne Bornel{\"o}v, and Simon Marillet, and Jan Komorowski
BMC bioinformatics, 15 (1), 2014
Teleost fish mount complex clonal IgM and IgT responses in spleen upon systemic viral infection
R. Castro, and L. Journeau, and H.P. Pham, and O. Bouchez, and V. Giudicelli, and M-P. Lefranc, and E. Quillet, and A. Benmansour, and F. Cazals, and A. Six, and S. Fillatreau, and O. Sunyer, and P. Boudinot
PLOS Pathogens, 9 (1), 2013
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Modeling Macro-molecular Complexes : a Journey Across Scales
F. Cazals, and T. Dreyfus, and C.H. Robert
in Modeling in Computational Biology and Medicine: : A Multidisciplinary Endeavor (Editors: F. Cazals, and P. Kornprobst), Springer, 2013
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Probing a Continuum of Macro-molecular Assembly Models with Graph Templates of Sub-complexes
T. Dreyfus, and V. Doye, and F. Cazals
Proteins: structure, function, and bioinformatics, 81 (11), 2013
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Assessing the Reconstruction of Macro-molecular Assemblies with Toleranced Models
T. Dreyfus, and V. Doye, and F. Cazals
Proteins: structure, function, and bioinformatics, 80 (9), 2012
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Characterizing the Morphology of Protein Binding Patches
N. Malod-Dognin, and A. Bansal, and F. Cazals
Proteins: structure, function, and bioinformatics, 80 (12), 2012
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On the Characterization and Selection of Diverse Conformational Ensembles
S. Loriot, and S. Sachdeva, and K. Bastard, and C. Prevost, and F. Cazals
IEEE/ACM Transactions on Computational Biology and Bioinformatics, 8 (2), 2011
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Revisiting the Voronoi description of Protein-Protein interfaces: Algorithms
F. Cazals
International Conference on Pattern Recognition in Bioinformatics, 2010
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Spectral Techniques to Explore Point Clouds in Euclidean Space, with Applications to Collective Coordinates in Structural Biology
F. Cazals, and F. Chazal, and J. Giesen
in Nonlinear Computational Geometry (Editors: Ioannis Emiris, and Frank Sottile, and Thorsten Theobald), Springer, 2010
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Modeling Macro-Molecular Interfaces with Intervor
S. Loriot, and F. Cazals
Bioinformatics, 26 (7), 2010
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ESBTL: efficient PDB parser and data structure for the structural and geometric analysis of biological macromolecules
S. Loriot, and F. Cazals, and J. Bernauer
Bioinformatics, 26 (8), 2010
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Shelling the Voronoi interface of protein-protein complexes reveals patterns of residue conservation, dynamics and composition
B. Bouvier, and R. Grunberg, and M. Nilg{\`e}s, and F. Cazals
Proteins: structure, function, and bioinformatics, 76 (3), 2009
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A geometric knowledge-based biogeom-grained scoring potential for structure prediction evaluation
S. Loriot, and F. Cazals, and M. Levitt, and J. Bernauer
JOBIM, 2009
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Algorithmique des graphes pour les r\'eseaux et la biologie structurale computationnelle
D. Mazauric
Habilitation thesis from Universit\'e C\^ote d'Azur, 2021
Problèmes de graphes motivés par des modèles basse et haute résolution de grands assemblages de protéines
Thi Nguyen
PhD thesis from Universit\'e C\^ote d'Azur, 2021
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Modélisation structurale des pompes à efflux de la famille des RND: de la résistance aux antibiotiques à la résistance à la chimiothérapie
M. Simsir
PhD thesis from Universit\'e C\^ote d'Azur, 2020
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Marches al\'eatoires pour l’estimation de densit\'es d'\'etats et de volume de convexes en grande dimension
A. Chevallier
PhD thesis from Universit\'e C\^ote d'Azur, 2019
Analyse mixte de prot\'eines bas\'ee sur la s\'equence et la structure -- applications \`a l'annotation fonctionnelle
R. Tetley
PhD thesis from Universit\'e C\^ote d'Azur, 2018
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Modeling the antibody response: from the structure of immunoglobulin - antigen complexes to the clonal complexity of heavy chain repertoires
S. Marillet
PhD thesis from Univ. of Nice Sophia Antipolis, 2016
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Topics in mass spectrometry based structure determination
D. Agarwal
PhD thesis from Univ. of Nice Sophia Antipolis, 2015
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Nonparametric methods for learning and detecting multivariate statistical dissimilarity
A. Lh{\'e}ritier
PhD thesis from Univ. of Nice Sophia Antipolis, 2015
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Multi-scale modeling and analysis of ambiguous macro-molecular assemblies, with applications to the nuclear pore complex
T. Dreyfus
PhD thesis from Univ. of Nice Sophia Antipolis, 2011
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Arrangements de Cercles sur une Sph\`ere: Algorithmes et Applications aux Mod\`eles Mol\'eculaires Represent\'es par une Union de Boules
S. Loriot
PhD thesis from Univ. de Bourgogne, 2008
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L'intelligence artificielle au défi du design de protéines : des prouesses et limites d’AlphaFold
F. Cazals
TheConversation, (), 2022
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Graphes et Algorithmes -- Jeux grandeur nature
D. Mazauric
Inria, 2016
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Graphes et Algorithmes -- Jeux grandeur nature
D. Mazauric
Inria, 2016
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Multiscale analysis of structurally conserved motifs
F. Cazals, and R. Tetley
Preprint, NA (NA), 2020
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A generic framework for Wang-Landau type algorithms
A. Chevallier, and F. Cazals
Preprint, NA (NA), 2020
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Hybrid sequence-structure based HMM models leverage the identification of homologous proteins: the example of class II fusion proteins
R. Tetley, and J. Fedry, and P. Guardado-Calvo, and F. Rey, and F. Cazals
Preprint, NA (NA), 2019
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Extracting the Core Structural Connectivity Network: Guaranteeing Network Connectedness Through a Graph-Theoretical Approach
Demian Wassermann, and Dorian Mazauric, and Guillermo Gallardo-Diez, and Rachid Deriche
MICCAI 2016, 2016
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Optimal transportation problems with connectivity constraints
F. Cazals, and D. Mazauric
Inria Tech report 8991, 2016
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Stoichiometry Determination for Mass-spectrometry Data: the Interval Case
D. Agarwal, and F. Cazals, and N. Malod-Dognin
Inria Tech report 8101, 2014
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Towards Morse theory for point cloud data
F. Cazals, and C. Mueller, and C. Robert, and C.A. Roth
Inria Tech report 8331, 2013
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