Recherche - Archive ouverte HAL Accéder directement au contenu

Filtrer vos résultats

30 résultats
Page :
triés par
Image document

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⟩
Article dans une revue hal-01702026v1
Image document

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⟩
Article dans une revue pasteur-04060331v2
Image document

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⟩
Article dans une revue pasteur-01374967v1
Image document

Advances in bacterial pathways for the biosynthesis of ubiquinone

 Sophie S. Abby , Katayoun Kazemzadeh , Charles Vragniau , Ludovic Pelosi , Fabien Pierrel
Biochimica biophysica acta (BBA) - Bioenergetics, 2020, 1861 (11), pp.148259. ⟨10.1016/j.bbabio.2020.148259⟩
Article dans une revue hal-02944115v1
Image document

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⟩
Chapitre d'ouvrage pasteur-02867882v1
Image document

Genome wide transcriptomic analysis of the soil ammonia oxidizing archaeon Nitrososphaera viennensis upon exposure to copper limitation

 Carolina Reyes , Logan Hodgskiss , Melina Kerou , Thomas Pribasnig , Sophie S. Abby , et al.
The International Society of Microbiologial Ecology Journal, 2020, 14 (11), pp.2659-2674. ⟨10.1038/s41396-020-0715-2⟩
Article dans une revue hal-02992775v1
Image document

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⟩
Article dans une revue hal-00752055v1

Comparative genomics and the evolution of prokaryotes

 Sophie S. Abby , Vincent Daubin
Trends in Microbiology, 2007, 15, pp.135-141
Article dans une revue hal-00434649v1
Image document

Geochemical transition zone powering microbial growth in subsurface sediments

 Rui Zhao , José Mogollón , Sophie S. Abby , Christa Schleper , Jennifer Biddle , et al.
Proceedings of the National Academy of Sciences of the United States of America, 2020, pp.202005917. ⟨10.1073/pnas.2005917117⟩
Article dans une revue hal-03079193v1
Image document

Ancestral Reconstructions Decipher Major Adaptations of Ammonia-Oxidizing Archaea upon Radiation into Moderate Terrestrial and Marine Environments

 Sophie S. Abby , Melina Kerou , Christa Schleper
mBio, 2020, 11 (5), ⟨10.1128/mBio.02371-20⟩
Article dans une revue hal-02992748v1

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⟩
Article dans une revue hal-01677379v1

Diversification of ubiquinone biosynthesis via gene duplications, transfers, losses, and parallel evolution

 Katayoun Kazemzadeh , Ludovic Pelosi , Clothilde Chenal , Sophie-Carole Chobert , Mahmoud Hajj Chehade , et al.
Molecular Biology and Evolution, 2023, 40 (10), pp.msad219. ⟨10.1093/molbev/msad219⟩
Article dans une revue hal-04256893v1
Image document

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⟩
Article dans une revue hal-00740292v1
Image document

Les transferts horizontaux de gènes et l’arbre de la vie

 Vincent Daubin , Sophie S. Abby
Médecine/Sciences, 2012, 28 (8-9), pp.695 - 698. ⟨10.1051/medsci/2012288007⟩
Article dans une revue hal-01913973v1
Image document

Towards Molecular Understanding of the Functional Role of UbiJ-UbiK2 Complex in Ubiquinone Biosynthesis by Multiscale Molecular Modelling Studies

 Romain Launay , Elin Teppa , Carla Martins , Sophie S Abby , Fabien Pierrel , et al.
International Journal of Molecular Sciences, 2022, 23 (18), ⟨10.3390/ijms231810323⟩
Article dans une revue hal-03800688v1

MacSyFinder

 Bertrand Néron , Sophie Abby , Eduardo Rocha
2023, ⟨swh:1:dir:b7595ff8d8bfbb327f63ae0dc8f33314f46c0996;origin=https://github.com/gem-pasteur/macsyfinder;visit=swh:1:snp:d01ecf21ed904146f244bad043bf052f2d2f8d0d;anchor=swh:1:rev:1821de180b026abe24043305cbfbdcf5e63d2881⟩
Logiciel hal-04372564v1
Image document

Detecting lateral gene transfers by statistical reconciliation of phylogenetic forests

 Sophie S. Abby , Eric Tannier , Manolo Gouy , Vincent Daubin
BMC Bioinformatics, 2010, 11 (324), pp.13. ⟨10.1186/1471-2105-11-324⟩
Article dans une revue inria-00527151v1
Image document

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⟩
Article dans une revue pasteur-01374947v1

Robust Frankia phylogeny, species delineation and intraspecies diversity based on Multi-Locus Sequence Analysis (MLSA) and Single-Locus Strain Typing (SLST) adapted to a large sample size

 Adrien C Pozzi , Hector Bautista-Guerrero , Sophie S. Abby , Aude P Herrera-Belaroussi , Danis Abrouk , et al.
Systematic and Applied Microbiology, 2018, 41 (4), pp.311-323. ⟨10.1016/j.syapm.2018.03.002⟩
Article dans une revue hal-02313880v1
Image document

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⟩
Article dans une revue pasteur-02626815v1

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⟩
Article dans une revue hal-01490961v1

Proteomics and comparative genomics of Nitrososphaera viennensis reveal the core genome and adaptations of archaeal ammonia oxidizers

 Melina Kerou , Pierre Offre , Luis Valledor , Sophie S. Abby , Michael Melcher , et al.
Proceedings of the National Academy of Sciences of the United States of America, 2016, 113 (49), pp.E7937-E7946. ⟨10.1073/pnas.1601212113⟩
Article dans une revue hal-03412776v1
Image document

Identification of protein secretion systems in bacterial genomes using MacSyFinder version 2

 Sophie S. Abby , Rémi Denise , Eduardo Pc Rocha
2023
Pré-publication, Document de travail hal-04257010v1
Image document

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⟩
Article dans une revue hal-02183791v1
Image document

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⟩
Article dans une revue hal-01321228v1

Ammonia Oxidation by the Arctic Terrestrial Thaumarchaeote Candidatus Nitrosocosmicus arcticus Is Stimulated by Increasing Temperatures

 Ricardo Alves , Melina Kerou , Anna Zappe , Romana Bittner , Sophie S. Abby , et al.
Frontiers in Microbiology, 2019, 10, ⟨10.3389/fmicb.2019.01571⟩
Article dans une revue hal-02313925v1
Image document

Genomes of Thaumarchaeota from deep sea sediments reveal specific adaptations of three independently evolved lineages

 Melina Kerou , Rafael Ponce-Toledo , Rui Zhao , Sophie S. Abby , Miho Hirai , et al.
The International Society of Microbiologial Ecology Journal, 2021, 15 (9), pp.2792-2808. ⟨10.1038/s41396-021-00962-6⟩
Article dans une revue hal-03365290v1
Image document

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⟩
Article dans une revue pasteur-01080418v1
Image document

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⟩
Article dans une revue pasteur-00655553v1
Image document

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⟩
Article dans une revue pasteur-02263349v1
Page :