**Modeling in Computational Biology and Medicine: A Multidisciplinary Endeavor**

F. Cazals, and P. Kornprobst (Editors)

Springer, 2013

pdf -- DOI

**Characterizing molecular flexibility by combining lRMSD measures**

F. Cazals, and R. Tetley

Submitted

pdf -- DOI

**Multiscale analysis of structurally conserved motifs**

F. Cazals, and R. Tetley

Submitted

pdf -- DOI

**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

Submitted

pdf -- DOI

**Wang-Landau Algorithm: an adapted random walk to boost convergence**

A. Chevallier, and F. Cazals

Submitted

pdf

**Hamiltonian Monte Carlo with boundary reflections, and application to polytope volume calculations**

A. Chevallier, and S. Pion, and F. Cazals

Submitted

pdf

**Comparing two clusterings using matchings between clusters of clusters**

F. Cazals, and D. Mazauric, and R. Tetley, and R. Watrigant

Submitted. Available as Inria tech report:

pdf

**Optimal transportation problems with connectivity constraints**

F. Cazals, and D. Mazauric

Submitted. Available as Inria tech report:

pdf

**A Sequential Non-Parametric Multivariate Two-Sample Test**

A. Lh\'eritier, and F. Cazals

IEEE Transactions on Information Theory, 64 (5), 2018

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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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**Ridges and umbilics of polynomial parametric surfaces**

F. Cazals, and J.-C. Faug{\`e}re, and M. Pouget, and F. Rouillier* in *Computational Methods for Algebraic Spline Surfaces II (Editors: B. Juettler, and R. Piene), Springer, 2006

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**The implicit structure of ridges of a smooth parametric surface**

F. Cazals, and J.-C. Faug{\`e}re, and M. Pouget, and F. Rouillier

Computer Aided Geometric Design, 23 (7), 2006

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**Delaunay Triangulation Based Surface Reconstruction**

F. Cazals, and J. Giesen* in *Effective Computational Geometry for curves and surfaces (Editors: J.-D. Boissonnat, and M. Teillaud), Springer-Verlag, Mathematics and Visualization, 2006

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**The conformal alpha shapes filtration**

F. Cazals, and J. Giesen, and M. Pauly, and A. Zomorodian

The Visual Computer, 22 (8), 2006

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**Conformal Alpha Shapes**

F. Cazals, and J. Giesen, and M. Pauly, and A. Zomorodian

Symposium on Point Based Graphics, 2005

**An algorithm for reporting maximal $c$-cliques**

F. Cazals, and C. Karande

Theoretical Computer Science, 349 (3), 2005

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**Differential topology and geometry of smooth embedded surfaces: selected topics**

F. Cazals, and M. Pouget

Int. J. of Computational Geometry and Applications, 15 (5), 2005

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**Estimating Differential Quantities using Polynomial fitting of Osculating Jets**

F. Cazals, and M. Pouget

Computer Aided Geometric Design, 22 (2), 2005

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**Accurate Interactive Specular Reflections on Curved Objects**

P. Estalella, and I. Martin, and G. Drettakis, and D. Tost, and O. Devillers, and F. Cazals

Vision, Modeling, and Visualization, 2005

**On the angular defect of triangulations and the pointwise approximation of curvatures**

V. Borrelli, and F. Cazals, and J-M. Morvan

Computer Aided Geometric Design, 20 (6), 2003

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**Randomized Jumplists: A Jump-and-Walk Dictionary Data Structure**

H. Bronnimann, and F. Cazals, and M. Durand

STACS, 2003

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**Molecular shape analysis based upon the Morse-Smale complex and the Connolly function**

F. Cazals, and F. Chazal, and T. Lewiner

ACM Symposium on Computational Geometry, 2003

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**Estimating Differential Quantities using Polynomial fitting of Osculating Jets**

F. Cazals, and M. Pouget

Symp. on Geometry Processing, 2003

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**Smooth Surface Reconstruction via Natural Neighbour Interpolation of Distance Functions**

J.-D. Boissonnat, and F. Cazals

Computational Geometry Theory and Applications, 22 (1), 2002

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**Non-intrusive Debugging and Incremental Visualization with the Geometric Stethoscope**

F. Cazals

J. of Graphics Tools, 7 (2), 2002

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**Coarse-to-fine surface simplification with geometric guarantees**

J.-D. Boissonnat, and F. Cazals

Euromcs, 2001

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**Natural Coordinates of Points on a Surface**

J.-D. Boissonnat, and F. Cazals

Computational Geometry Theory and Applications, 19 (2), 2001

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**Smooth surface reconstruction via natural neighbour interpolation of distance functions**

J.-D. Boissonnat, and F. Cazals

ACM Symposium on Computational Geometry, 2000

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**Data structures and basic algorithms**

F. Cazals* in *Mesh Generation. Application to finite elements (Editors: P. Frey, and P.-L. George), Oxford, 2000

**Programming with CGAL: The Example of Triangulations**

J.-D. Boissonnat, and F. Cazals, and F. Da, and O. Devillers, and S. Pion, and F. Rebufat, and M. Teillaud, and M. Yvinec

ACM Symposium on Computational Geometry, 1999

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**Effective nearest neighbors searching on the hyper-cube, with applications to molecular clustering**

F. Cazals

ACM Symposium on Computational Geometry, 1998

pdf

**Combinatorial properties of one-dimensional arrangements**

F. Cazals

Experimental Mathematics, 6 (1), 1997

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**Effect of tolerancing on the relative position of parts in an assembly**

F. Cazals, and J-C. Latombe

IEEE International Conference on Robotics and Automation, 1997

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**Bucket-like space partitioning data structures with applications to ray tracing**

F. Cazals, and C. Puech

ACM Symposium on Computational Geometry, 1997

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**Algorithms for computing the union and the intersection of toleranced polygons**

F. Cazals, and G.D. Ramkumar

Artificial Intelligence for Engineering Design, Analysis and Manufacturing, 11 (4), 1997

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**Assembly sequencing with toleranced parts**

J-C. Latombe, and R. Wilson, and F. Cazals

Computer Aided Design, 29 (2), 1997

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**Filtering, clustering and hierarchy construction: a new solution for ray-tracing complex scenes**

F. Cazals, and G. Drettakis, and C. Puech

Euromcs, 1995

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**Survey of the analysis of continuous conformational variability of biological macromolecules by electron microscopy**

C.O.S. Sorzano, and A. Jim\'enez, and J. Mota, and J.L. Vilas, and D. Maluenda, and M. Mart\'inez, and E. Ram\'irez-Aportela, and T. Majtner, and J. Segura, and R. S\'anchez-Garc\'ia, and Y. Rancel, and L. no, and P. Conesa, and S. Jonic, and J. Vargas, and F. Cazals, and Z. Freyberg, and J. Krieger, and I. Bahar, and R. Marabini, and J.M. Carazo

Acta Crystalographica Section F, NA (), 2018

**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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**Dissecting Interfaces of Antibody - Antigen Complexes: from Ligand Specific Features to Binding Affinity Predictions**

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 -- DOI

**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

pdf -- DOI

**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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**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

pdf -- DOI

**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

pdf -- DOI

**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

pdf -- DOI

**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

pdf

**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

pdf -- DOI

**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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**Revisiting the Voronoi description of Protein-Protein interfaces**

F. Cazals, and F. Proust, and R. Bahadur, and J. Janin

Protein Science, 15 (9), 2006

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**$2D$-Structure Drawings of Similar Molecules**

J.-D. Boissonnat, and F. Cazals, and J. Fl{\"o}totto

Graph Drawing: 8th international symposium, 2000

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**Computational Geometry and Topology: Concepts, Algorithms, Applications**

F. Cazals

Habilitation from Univ. Nice Sophia Antipolis, 2006

**Structures de donn\'ees hi\'erarchiques non recursives et probl\`emes de proximit\'e**

F. Cazals

PhD thesis (Th\`ese de doctorat) from Univ. Paris VII, 1997

**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), 2018 -- DOI

**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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**La morphologie des contacts entre bio-mol\'ecules**

F. Cazals

Pour la Science, Juillet - Ao\^ut (), 2006

**Topology driven algorithms for ridge extraction on meshes**

F. Cazals, and M. Pouget

Inria Tech report 5526, 2005

pdf

**Combinatorics of Non-Crossing Configurations**

F. Cazals

Studies in Automatic Combinatorics, Vol. 2, 1997

pdf

**Monomer-Dimer Tilings**

F. Cazals

Studies in Automatic Combinatorics, Vol. 2, 1997

pdf

**Some integral geometry tools to estimate the complexity of 3d scenes**

F. Cazals, and M. Sbert

Inria Tech report 3204, 1997

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