D
David Allouche
Researcher at Institut national de la recherche agronomique
Publications - 28
Citations - 752
David Allouche is an academic researcher from Institut national de la recherche agronomique. The author has contributed to research in topics: Graphical model & Solver. The author has an hindex of 14, co-authored 26 publications receiving 680 citations. Previous affiliations of David Allouche include Paul Sabatier University & Saab Automobile AB.
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Journal ArticleDOI
Gene Regulatory Network Reconstruction Using Bayesian Networks, the Dantzig Selector, the Lasso and Their Meta-Analysis
Matthieu Vignes,Jimmy Vandel,David Allouche,Nidal Ramadan-Alban,Christine Cierco-Ayrolles,Thomas Schiex,Brigitte Mangin,Simon de Givry +7 more
TL;DR: A simple yet very powerful meta-analysis is proposed, which combines a wide panel of methods ranging from Bayesian networks to penalised linear regressions to analyse gene regulatory networks from different genetical genomics data sets and was ranked first among the teams participating in Challenge 3A.
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A new framework for computational protein design through cost function network optimization
Seydou Traoré,Seydou Traoré,David Allouche,Isabelle André,Isabelle André,Simon de Givry,George Katsirelos,Thomas Schiex,Sophie Barbe,Sophie Barbe +9 more
TL;DR: It is shown that the CFN-based approach is able to solve optimality a variety of complex designs that could often not be solved using a usual CPD-dedicated tool or state-of-the-art exact operations research tools.
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Computational protein design as an optimization problem
David Allouche,Isabelle André,Sophie Barbe,Jessica Davies,Simon de Givry,George Katsirelos,Barry O'Sullivan,Steve Prestwich,Thomas Schiex,Seydou Traoré +9 more
TL;DR: The CPD problem is introduced and some of the main approaches that have been used by structural biologists to solve it, with an emphasis on the exact method embodied in the dead-end elimination/A? algorithm (DEE/A?).
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Guaranteed Discrete Energy Optimization on Large Protein Design Problems.
David Simoncini,David Allouche,Simon de Givry,Céline Delmas,Sophie Barbe,Sophie Barbe,Sophie Barbe,Thomas Schiex +7 more
TL;DR: An exact deterministic method combining branch and bound, arc consistency, and tree-decomposition is used to provenly identify the global minimum energy sequence-conformation on full-redesign problems, defining search spaces of size up to 10(234).
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Simple Two-Body Cation−Water Interaction Potentials Derived from ab Initio Calculations. Comparison to Results Obtained with an Empirical Approach
TL;DR: In this article, the effective Lennard-Jone (LJ) parameters for the most hydrated H2On systems were calculated on M(H2O)n systems with n = 1, 2, 4, or 6.