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Centric selection: a way to tune the exploration/exploitation trade-off

 David Simoncini , Sébastien Verel , Philippe Collard , Manuel Clergue
GECCO'09, Jul 2009, Montreal, Canada. pp.891--898, ⟨10.1145/1569901.1570023⟩
Communication dans un congrès hal-00410191v1
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Anisotropic selection in cellular genetic algorithms

 David Simoncini , Sébastien Verel , Philippe Collard , Manuel Clergue
Genetic And Evolutionary Computation Conference, Jul 2006, Seatle, United States. pp.559 - 566, ⟨10.1145/1143997.1144098⟩
Communication dans un congrès hal-00164697v1
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From Cells to Islands: An unified Model of Cellular Parallel Genetic Algorithms

 David Simoncini , Philippe Collard , Sébastien Verel , Manuel Clergue
7th International Conference on Cellular Automata For Research and Industry - ACRI 2006, Sep 2006, Perpignan, France. pp.248-257
Communication dans un congrès hal-00164669v1
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A preliminary investigation of anisotropic selection in celullar genetic algorithms

 David Simoncini , Sébastien Verel , Manuel Clergue , Philippe Collard
Poster at Evolution Artificielle, 7th International Conference, Oct 2005, Lillle, France
Communication dans un congrès hal-00164913v1

Population-Based Sampling and Fragment-Based De Novo Protein Structure Prediction

 David Simoncini , Kam Y.J. Zhang
Encyclopedia of Bioinformatics and Computational Biology - Reference Work 2019, 1, Elsevier, pp.774-784, 2019, 978-0-12-811432-2. ⟨10.1016/B978-0-12-809633-8.20507-4⟩
Chapitre d'ouvrage hal-02945383v1

Guaranteed Discrete Energy Optimization on Large Protein Design Problems

 David Simoncini , David Allouche , Simon de Givry , Céline Delmas , Sophie Barbe , et al.
Journal of Chemical Theory and Computation, 2015, 11 (12), pp.5980 - 5989. ⟨10.1021/acs.jctc.5b00594⟩
Article dans une revue hal-02637306v1
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Approximate counting with deterministic guarantees for affinity computation

 Clément Viricel , David Simoncini , David Allouche , Simon de Givry , Sophie Barbe , et al.
3. International Conference on Modelling, Computation and Optimization in Information Systems and Management Sciences - MCO 2015, Université de Lorraine (UL). FRA., May 2015, Metz, France. 500 p., ⟨10.1007/978-3-319-18167-7_15⟩
Communication dans un congrès hal-01269259v1
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On the Influence of Selection Operators on Performances in Cellular Genetic Algorithms

 David Simoncini , Philippe Collard , Sébastien Verel , Manuel Clergue
IEEE Congress on Evolutionary Computation CEC2007, Sep 2007, singapore, Singapore. pp.4706-4713
Communication dans un congrès hal-00164789v1
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Seven Amino Acid Types Suffice to Create the Core Fold of RNA Polymerase

 Sota Yagi , Aditya K Padhi , Jelena Vucinic , Sophie Barbe , Thomas Schiex , et al.
Journal of the American Chemical Society, In press, 143 (39), pp.15998-16006. ⟨10.1021/jacs.1c05367⟩
Article dans une revue hal-03360584v1

Evolution-Inspired Computational Design of Symmetric Proteins

 Arnout R. D. Voet , David Simoncini , Jeremy R. H. Tame , Kam Y. J. Zhang
Computational Protein Design, 1529, SPRINGER, pp.14, 2017, Methods in Molecular Biology, 978-1-4939-6635-6. ⟨10.1007/978-1-4939-6637-0_16⟩
Chapitre d'ouvrage hal-02789574v1

Computational Enzyme Design through deterministic optimization and counting

 Thomas Schiex , Seydou Traoré , David Simoncini , Sophie Barbe , Simon de Givry , et al.
3DSig Structural Bioinformatics and Computational Biophysics 2015, Jul 2015, Dublin, Ireland
Communication dans un congrès hal-01605405v1
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Computational design of symmetrical eight-bladed β-propeller proteins

 Hiroki Noguchi , Christine Addy , David Simoncini , Staf Wouters , Bram Mylemans , et al.
International Union of Crystallography journal, 2019, 6 (1), pp.46-55. ⟨10.1107/S205225251801480X⟩
Article dans une revue hal-02154353v1

Balancing exploration and exploitation in population-based sampling improves fragment-based de novo protein structure prediction

 David Simoncini , Thomas Schiex , Kam Y.J. Zhang
Proteins, 2017, 85 (5), pp.852-858. ⟨10.1002/prot.25244⟩
Article dans une revue hal-01607119v1
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Fitness Landscape Analysis around the Optimum in Computational Protein Design

 David Simoncini , Sophie Barbe , Thomas Schiex , Sébastien Verel
Genetic and Evolutionary Computation Conference (GECCO) 2018, Jul 2018, Kyoto, Japan. pp.355-362
Communication dans un congrès hal-01823638v1
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Constraint Programming and Graphical models - Pushing data into your models, The protein design case.

 Thomas Schiex , Sophie Barbe , David Simoncini , Jelena Vucinic , Manon Ruffini , et al.
23rd International Symposium on Mathematical Programming (ISMP-18), Jul 2018, Bordeaux, France
Communication dans un congrès hal-02154354v1

Quality assessment of predicted protein models using energies calculated by the fragment molecular orbital method

 David Simoncini , Hiroya Nakata , Koji Ogata , Shinichiro Nakamura , Kam Zhang
Molecular Informatics, 2015, 34 (2-3), pp.97--104. ⟨10.1002/minf.201400108⟩
Article dans une revue istex hal-03213976v1
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Iterated local search with partition crossover for computational protein design

 François Beuvin , Simon De Givry , Thomas Schiex , Sébastien Verel , David Simoncini
Proteins - Structure, Function and Bioinformatics, 2021, 89 (11), pp.1522-1529. ⟨10.1002/prot.26174⟩
Article dans une revue hal-03298736v1
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Positive multistate protein design

 Jelena Vucinic , David Simoncini , Manon Ruffini , Sophie Barbe , Thomas Schiex
Bioinformatics, 2020, ⟨10.1093/bioinformatics/btz497⟩
Article dans une revue hal-02625007v1

Computational design of a self-assembling symmetrical β-propeller protein

 Arnout Voet , Hiroki Noguchi , Christine Addy , David Simoncini , Daiki Terada , et al.
Proceedings of the National Academy of Sciences of the United States of America, 2014, 111 (42), pp.15102--15107. ⟨10.1073/pnas.1412768111⟩
Article dans une revue hal-03266953v1
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Complete Combinatorial Mutational Enumeration of a protein functional site enables sequence-landscape mapping and identifies highly-mutated variants that retain activity

 Mireia Solà Colom , Jelena Vucinic , Jared Adolf-Bryfogle , James W Bowman , Sébastien Verel , et al.
2024
Pré-publication, Document de travail hal-04432033v1
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Guaranteed Weighted Counting for Affinity Computation: Beyond Determinism and Structure

 Clement Viricel , David Simoncini , Sophie Barbe , Thomas Schiex
CP16 - 22nd International Conference on the Principles and Practice of Constraint Programming, Sep 2016, Toulouse, France. pp.18, ⟨10.1007/978-3-319-44953-1_46⟩
Communication dans un congrès hal-01828389v1

PB1764: Segmentation and classification of Bone Marrow Cells from multi-precision numerization of Bone Marrow Smears (BMS) from patients with Acute Myeloid Leukemia (AML) using AI techniques

 Achraf Bennis , Philippe Leleux , Alban Canali , Caroline De Pourtales , Sandrine Mouysset , et al.
HemaSphere, 2023, 7 (S3), pp.e5127496. ⟨10.1097/01.HS9.0000973912.51274.96⟩
Article dans une revue hal-04298189v1
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A structural homology approach for computational protein design with flexible backbone

 David Simoncini , Kam y J Zhang , Thomas Schiex , Sophie Barbe
Bioinformatics, 2019, 35 (14), ⟨10.1093/bioinformatics/bty975⟩
Article dans une revue hal-02114756v1
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Cost Function Networks to Solve Large Computational Protein Design Problems

 David Allouche , Sophie Barbe , Simon de Givry , George Katsirelos , Yahia Lebbah , et al.
Malek Masmoudi, Bassem Jarboui, Patrick Siarry. Operations Research and Simulation in healthcare, Springer, pp.81-102, 2021, 978-3-030-45223-0. ⟨10.1007/978-3-030-45223-0_4⟩
Chapitre d'ouvrage hal-02177634v1
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