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Exhaustively characterizing feasible logic models of a signaling network using Answer Set Programming

 Carito Guziolowski , Santiago Videla , Federica Eduati , Sven Thiele , Thomas Cokelaer , et al.
Bioinformatics, 2013, 29 (18), pp.2320-2326. ⟨10.1093/bioinformatics/btt393⟩
Article dans une revue hal-00853704v1

Properties of seismic noise at the Virgo site

 F. Acernese , P. Amico , N. Arnaud , D. Babusci , R. Barill , et al.
Edoardo Amaldi International Conference on Gravitational Waves 5, Jul 2003, Tirrenia, Pise, Italy. pp.S433-S440
Communication dans un congrès in2p3-00021604v1

First locking of the VIRGO central area interferometer with suspension hierarchical control

 F. Acernese , P. Amico , N. Arnaud , D. Babusci , R. Barill , et al.
Astroparticle Physics, 2004, 20, pp.629-640
Article dans une revue in2p3-00021612v1
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Mtfp1 ablation enhances mitochondrial respiration and protects against hepatic steatosis

 Cecilia Patitucci , Juan Diego Hernández-Camacho , Elodie Vimont , Thomas Cokelaer , Thibault Chaze , et al.
2023
Pré-publication, Document de travail pasteur-04093359v1
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Spectrum': Spectral Analysis in Python

 Thomas Cokelaer , Juergen Hasch
Journal of Open Source Software, 2017, 2 (18), pp.348. ⟨10.21105/joss.00348⟩
Article dans une revue pasteur-03111917v1
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Telomere-to-telomere assemblies of 142 strains characterize the genome structural landscape in Saccharomyces cerevisiae

 Samuel O’donnell , Jia-Xing Yue , Omar Abou Saada , Nicolas Agier , Claudia Caradec , et al.
Nature Genetics, 2023, 55 (8), pp.1390 - 1399. ⟨10.1038/s41588-023-01459-y⟩
Article dans une revue hal-04305689v1
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Sequana': a Set of Snakemake NGS pipelines

 Thomas Cokelaer , Dimitri Desvillechabrol , Rachel Legendre , Mélissa Cardon
Journal of Open Source Software, 2017, 2 (16), pp.352. ⟨10.21105/joss.00352⟩
Article dans une revue pasteur-03111935v1
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Autotransporters drive biofilm formation and auto-aggregation in the diderm Firmicute Veillonella parvula

 Nathalie Bechon , Alicia Jiménez-Fernández , Jerzy Witwinowski , Emilie Bierque , Najwa Taïb , et al.
Journal of Bacteriology, 2020, ⟨10.1128/JB.00461-20⟩
Article dans une revue pasteur-02924221v1

Sensitivity Analysis of Light Interception to Geometrical Traits of Apple Trees: an in silico Study based on MAppleT model

 Ligi Han , Jean-Christophe Soulié , Frédéric Boudon , David da Silva , Thomas Cokelaer , et al.
9th International Symposium on Modelling in Fruit Research and Orchard Management, 2011, Saint-Jean-sur-Richelieu, Canada
Communication dans un congrès hal-00828858v1
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Dynamics of extended-spectrum beta-lactamase-producing Enterobacterales colonization in long-term carriers following travel abroad

 Laurence Armand-Lefèvre , Emilie Rondinaud , Dimitri Desvillechabrol , Jimmy Mullaert , Olivier Clermont , et al.
Microbial Genomics, 2021, 7 (7), pp.000576. ⟨10.1099/mgen.0.000576⟩
Article dans une revue pasteur-03509051v1

Astrophysically Triggered Searches for Gravitational Waves: Status and Prospects

 B. Abbott , R. Abbott , R. Adhikari , P. Ajith , B. Allen , et al.
Classical and Quantum Gravity, 2008, 25, pp.114051. ⟨10.1088/0264-9381/25/11/114051⟩
Article dans une revue in2p3-00260101v1

Sensitivity analysis of light interception to geometrical traits of Apple trees: an in silico study based on MAppleT Model

 Liqi Han , Jean-Christophe Soulie , Frédéric Boudon , David da Silva , Thomas Cokelaer , et al.
9. International Symposium on modelling in Fruit Research and Orchard management, International Society for Horticultural Science (ISHS). Louvain, INT., Jun 2011, Saint-Jean-Sur-Richelieu, Canada
Communication dans un congrès hal-01269213v1
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Reprohackathons: promoting reproducibility in bioinformatics through training

 Thomas Cokelaer , Sarah Cohen-Boulakia , Frédéric Lemoine
Bioinformatics, 2023, 39 (Sup 1), pp.i11 - i20. ⟨10.1093/bioinformatics/btad227⟩
Article dans une revue hal-04402365v1
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Search for non-Gaussian events in the data of the VIRGO E4 engineering run

 F. Acernese , P. Amico , N. Arnaud , D. Babusci , G. Ballardin , et al.
Gravitational Wave Data Analysis Workshop 7, 2003, Kyoto, Japan. pp.623-632
Communication dans un congrès in2p3-00014167v1
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Scientific workflow for reusing plant/FSPM models

 Jérôme Chopard , Christophe Pradal , Daniel Barbeau , Thomas Cokelaer , Christophe Godin
MODSIM2011. 19th International Congress on Modelling and Simulation, Modelling and Simulation Society of Australia and New Zealand, Dec 2011, Perth, Australia. pp.968-974
Communication dans un congrès hal-00790635v1

First LIGO search for gravitational wave bursts from cosmic (super)strings

 F. Robinet , B. P. Abbott , R. Abbott , R. Adhikari , P. Ajith , et al.
Physical Review D, 2009, 80, pp.062002. ⟨10.1103/PhysRevD.80.062002⟩
Article dans une revue in2p3-00428981v1

Last stage control and mechanical transfer function measurement of the Virgo suspensions

 A. Bozzi , C. Bourgoin , S. Cortese , A. Errico , D. Enard , et al.
Review of Scientific Instruments, 2002, 73, pp.2143-2149
Article dans une revue in2p3-00011764v1

Network topology and parameter estimation: from experimental design methods to gene regulatory network kinetics using a community based approach

 Pablo Meyer , Thomas Cokelaer , Deepak Chandran , Kyung Kim , Po-Ru Loh , et al.
BMC Systems Biology, 2014, 8 (1), ⟨10.1186/1752-0509-8-13⟩
Article dans une revue hal-01823890v1
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Complete Genome Sequences of Bioluminescent Staphylococcus aureus Strains Xen31 and Xen36, Derived from Two Clinical Isolates

 Océane Blaise , Clarisse Leseigneur , Thomas Cokelaer , Elena Capuzzo , Nadira Frescaline , et al.
Microbiology Resource Announcements, 2023, 12 (3), pp.e0002423. ⟨10.1128/mra.00024-23⟩
Article dans une revue pasteur-04120590v1
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L-Py: an L-system simulation framework for modeling plant architecture development based on a dynamic language

 Frédéric Boudon , Christophe Pradal , Thomas Cokelaer , Przemyslaw Prusinkiewicz , Christophe Godin
Frontiers in Plant Science, 2012, 3 (76), doi: 10.3389/fpls.2012.00076. ⟨10.3389/fpls.2012.00076⟩
Article dans une revue cirad-00703085v1
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Efficient randomization of biological networks while preserving functional characterization of individual nodes

 Francesco Iorio , Marti Bernardo-Faura , Andrea Gobbi , Thomas Cokelaer , Giuseppe Jurman , et al.
BMC Bioinformatics, 2016, 17 (1), pp.542. ⟨10.1186/s12859-016-1402-1⟩
Article dans une revue pasteur-03112917v1
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Sequanix: a dynamic graphical interface for Snakemake workflows

 Dimitri Desvillechabrol , Rachel Legendre , Claire Rioualen , Christiane Bouchier , Jacques van Helden , et al.
Bioinformatics, 2018, 34 (11), pp.1934 - 1936. ⟨10.1093/bioinformatics/bty034⟩
Article dans une revue hal-01874933v1

Status of VIRGO

 F. Acernese , P. Amico , N. Arnaud , C. Arnault , D. Babusci , et al.
Gravitational Wave Data Analysis Workshop 7, Dec 2003, Kyoto, Japan. pp.S609-S616
Communication dans un congrès in2p3-00021574v1

A local control system for the test masses of the Virgo gravitational wave detector

 F. Acernese , P. Amico , N. Arnaud , D. Babusci , R. Barill , et al.
Astroparticle Physics, 2004, 20, pp.617-628
Article dans une revue in2p3-00021613v1

Search for gravitational-wave bursts associated with gamma-ray bursts using data from LIGO Science Run 5 and Virgo Science Run 1

 B.P. Abbott , R. Abbott , F. Acernese , R. Adhikari , P. Ajith , et al.
The Astrophysical Journal, 2010, 715, pp.1438-1452. ⟨10.1088/0004-637X/715/2/1438⟩
Article dans une revue in2p3-00421376v1
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Low CCR5 expression protects HIV-specific CD4+ T cells of elite controllers from viral entry

 Mathieu Claireaux , Rémy Robinot , Jérôme Kervevan , Mandar Patgaonkar , Isabelle Staropoli , et al.
Nature Communications, 2022, 13 (1), pp.521. ⟨10.1038/s41467-022-28130-0⟩
Article dans une revue pasteur-03654265v1
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A Landscape of Pharmacogenomic Interactions in Cancer

 Francesco Iorio , Theo Knijnenburg , Daniel Vis , Graham Bignell , Michael Menden , et al.
Cell, 2016, 166 (3), pp.740-754. ⟨10.1016/j.cell.2016.06.017⟩
Article dans une revue pasteur-03112918v1
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SARS‐CoV‐2‐related bat virus behavior in human‐relevant models sheds light on the origin of COVID‐19

 Sarah Temmam , Xavier Montagutelli , Cécile Herate , Flora Donati , Béatrice Regnault , et al.
EMBO Reports, 2023, 24 (4), pp.e56055. ⟨10.15252/embr.202256055⟩
Article dans une revue pasteur-04072738v1
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Competition-based Model of Pruning: Applications to Apple Trees

 Thomas Cokelaer , Damien Fumey , Yann Guédon , Evelyne Costes , Christophe Godin
6th International Workshop on Functional-Structural Plant Models, 2010, Davis, CA, United States. pp.87-89
Communication dans un congrès hal-00831776v1
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Sequana Coverage: Detection and Characterization of Genomic Variations using Running Median and Mixture Models

 Dimitri Desvillechabrol , Christiane Bouchier , Sean Kennedy , Thomas Cokelaer
GigaScience, 2018, 7 (12), pp.giy110. ⟨10.1093/gigascience/giy110⟩
Article dans une revue pasteur-02552049v1
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