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authIdHal_s : sophie-abby
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Phylogenetic modeling of lateral gene transfer reconstructs the pattern and relative timing of speciations.

Gergely J Szöllosi , Bastien Boussau , Sophie S Abby , Eric Tannier , Vincent Daubin
Proceedings of the National Academy of Sciences of the United States of America, 2012, 109 (43), pp.17513-17518. ⟨10.1073/pnas.1202997109⟩
Journal articles hal-00740292v1
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Ubiquinone Biosynthesis over the Entire O2 Range: Characterization of a Conserved O2-Independent Pathway

Ludovic Pelosi , Chau-Duy-Tam Vo , Sophie Saphia Abby , Laurent Loiseau , Bérengère Rascalou , et al.
mBio, 2019, 10 (4), ⟨10.1128/mBio.01319-19⟩
Journal articles hal-02183791v1
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Lateral gene transfer as a support for the tree of life.

Sophie S Abby , Eric Tannier , Manolo Gouy , Vincent Daubin
Proceedings of the National Academy of Sciences of the United States of America, 2012, 109 (13), pp.4962-4967. ⟨10.1073/pnas.1116871109⟩
Journal articles hal-00752055v1
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Investment in rapid growth shapes the evolutionary rates of essential proteins.

Sara Vieira-Silva , Marie Touchon , Sophie S Abby , Eduardo P C Rocha
Proceedings of the National Academy of Sciences of the United States of America, 2011, 108 (50), pp.20030-5. ⟨10.1073/pnas.1110972108⟩
Journal articles pasteur-00655553v1
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Diversification of the type IV filament superfamily into machines for adhesion, protein secretion, DNA uptake, and motility

Rémi Denise , Sophie S. Abby , Eduardo P. C. Rocha
PLoS Biology, 2019, 17 (7), pp.e3000390. ⟨10.1371/journal.pbio.3000390⟩
Journal articles pasteur-02263349v1
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Bacteria in Ostreococcus tauri cultures – friends, foes or hitchhikers?

Sophie S Abby , Marie Touchon , Aurelien de Jode , Nigel Grimsley , Gwenael Piganeau
Frontiers in Microbiology, 2014, 5, pp.505. ⟨10.3389/fmicb.2014.00505⟩
Journal articles hal-01321228v1
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MacSyFinder: a program to mine genomes for molecular systems with an application to CRISPR-Cas systems.

Sophie S Abby , Bertrand Néron , Hervé Ménager , Marie Touchon , Eduardo P C Rocha
PLoS ONE, 2013, 9 (10), pp.e110726. ⟨10.1371/journal.pone.0110726⟩
Journal articles pasteur-01080418v1
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Identification of protein secretion systems in bacterial genomes

Sophie S. Abby , Jean Cury , Julien Guglielmini , Bertrand Néron , Marie Touchon , et al.
Scientific Reports, 2016, 6, ⟨10.1038/srep23080⟩
Journal articles pasteur-01374967v1
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Identifying Conjugative Plasmids and Integrative Conjugative Elements with CONJscan

Jean Cury , Sophie S. Abby , Olivia Doppelt-Azeroual , Bertrand Néron , Eduardo P C Rocha
Fernando de la Cruz. Horizontal Gene Transfer : Methods and Protocols, Springer Science; Business Media, pp.265-283, 2019, 978-1-4939-9876-0. ⟨10.1007/978-1-4939-9877-7_19⟩
Book sections pasteur-02867882v1
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The evolution of protein secretion systems by co-option and tinkering of cellular machineries

Rémi Denise , Sophie S. Abby , Eduardo Rocha
Trends in Microbiology, 2020, 28 (5), pp.372-386. ⟨10.1016/j.tim.2020.01.005⟩
Journal articles pasteur-02626815v1
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The Non-Flagellar Type III Secretion System Evolved from the Bacterial Flagellum and Diversified into Host-Cell Adapted Systems

Sophie S. Abby , Eduardo P. C. Rocha
PLoS Genetics, 2012, 8 (9), pp.e1002983. ⟨10.1371/journal.pgen.1002983.s017⟩
Journal articles pasteur-01374947v1

Testing for independence between evolutionary processes

Abdelkader Behdenna , Joël Pothier , Sophie S. Abby , Guillaume Achaz , Amaury Lambert
Systematic Biology, 2016, 65 (5), pp.812-823. ⟨10.1093/sysbio/syw004⟩
Journal articles hal-01490961v1
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Candidatus Nitrosocaldus cavascurensis, an Ammonia Oxidizing, Extremely Thermophilic Archaeon with a Highly Mobile Genome

Sophie S. Abby , Michael Melcher , Melina Kerou , Mart Krupovic , Michaela Stieglmeier , et al.
Frontiers in Microbiology, 2018, 9, pp.28. ⟨10.3389/fmicb.2018.00028⟩
Journal articles hal-01702026v1
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MacSyFinder v2: Improved modelling and search engine to identify molecular systems in genomes

Bertrand Néron , Rémi Denise , Charles Coluzzi , Marie Touchon , Eduardo P.C. Rocha , et al.
Peer Community Journal, 2023, 3, pp.e28. ⟨10.24072/pcjournal.250⟩
Journal articles pasteur-04060331v2

Identification of Protein Secretion Systems in Bacterial Genomes Using MacSyFinder.

Sophie S. Abby , Eduardo P C Rocha
Methods in Molecular Biology, 2018, Bacterial protein secretion systems, 1615, pp.1-21. ⟨10.1007/978-1-4939-7033-9_1⟩
Journal articles hal-01677379v1