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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⟩
Journal articles hal-02313925v1
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Fishing for barcodes in the Torrent: from COI to complete mitogenomes on NGS platforms

Damien Hinsinger , Régis Debruyne , Maeva Thomas , Gaël Denys , Marion I. Mennesson , et al.
DNA Barcodes, 2015, 3 (1), pp.170-186. ⟨10.1515/dna-2015-0019⟩
Journal articles mnhn-02309917v1
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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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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.
ISME Journal, 2021, 15 (9), pp.2792-2808. ⟨10.1038/s41396-021-00962-6⟩
Journal articles hal-03365290v1

Universal and idiosyncratic characteristic lengths in bacterial genomes

Ivan Junier , Paul Frémont , Olivier Rivoire
Physical Biology, 2018, 15 (3), pp.035001. ⟨10.1088/1478-3975/aab4ac⟩
Journal articles hal-01972786v1

Mutator genomes decay, despite sustained fitness gains, in a long-term experiment with bacteria

Alejandro Couce , Larissa Viraphong Caudwell , Christoph Feinauer , Thomas Hindré , Jean-Paul Feugeas , et al.
Proceedings of the National Academy of Sciences of the United States of America, 2017, 114 (43), pp.E9026 - E9035. ⟨10.1073/pnas.1705887114⟩
Journal articles hal-01653591v1

The goat domestication process inferred from large-scale mitochondrial DNA analysis of wild and domestic individuals

S. Naderi , H. R. Rezaei , F. Pompanon , Michaël G. B. Blum , R. Negrini , et al.
Proceedings of the National Academy of Sciences of the United States of America, 2008, 105 (46), pp.17659-17664. ⟨10.1073/pnas.0804782105⟩
Journal articles halsde-00377989v1

Ocular manifestations of syphilis: recent cases over a 2.5-year period.

Cindy Puech , Stéphane Gennai , Patricia Pavese , Isabelle Pelloux , Max Maurin , et al.
Graefe's Archive for Clinical and Experimental Ophthalmology, 2010, 248 (11), pp.1623-9. ⟨10.1007/s00417-010-1481-z⟩
Journal articles istex hal-00993906v1

Guns, germs and dogs: On the origin of Leishmania chagasi

Raphaël Leblois , Katrin Kuhls , Olivier François , Gabriele Schönian , Thierry Wirth
Infection, Genetics and Evolution, 2011, 11 (5), pp.1091-1095. ⟨10.1016/j.meegid.2011.04.004⟩
Journal articles istex hal-02931001v1

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⟩
Journal articles hal-03412776v1
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Reducing the ionizing radiation background does not significantly affect the evolution of Escherichia coli populations over 500 generations

Nathanael Lampe , Pierre Marin , Marianne Coulon , Pierre Micheau , Lydia Maigne , et al.
Scientific Reports, 2019, 9 (1), pp.14891. ⟨10.1038/s41598-019-51519-9⟩
Journal articles hal-02337251v1
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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.
ISME Journal, 2020, 14 (11), pp.2659-2674. ⟨10.1038/s41396-020-0715-2⟩
Journal articles hal-02992775v1

Contrasting effects of historical contingency on phenotypic and genomic trajectories during a two-step evolution experiment with bacteria

Jessica Plucain , Antonia Suau , Stéphane Cruveiller , Claudine Médigue , Dominique Schneider , et al.
BMC Evolutionary Biology, 2016, 16 (1), ⟨10.1186/s12862-016-0662-8⟩
Journal articles hal-01653387v1
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Machine learning methods are useful for Approximate Bayesian Computation in evolution and ecology

Michael Blum
Peer Community in Evolutionary Biology, 2017, ⟨10.24072/pci.evolbiol.100036⟩
Journal articles hal-01637362v1
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Diversity and survival of artificial lifeforms under sedimentation and random motion

Nicolas Glade , Olivier Bastien , Pascal Ballet
Theorie in den Biowissenschaften / Theory in Biosciences, 2017, 136 (364), pp.153. ⟨10.1007/s12064-017-0254-1⟩
Journal articles hal-01582506v1

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⟩
Journal articles hal-02313880v1
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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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A western Sahara centre of domestication inferred from pearl millet genomes

Concetta Burgarella , Philippe Cubry , Ndjido A Kane , Rajeev K Varshney , Cedric Mariac , et al.
Nature Ecology & Evolution, 2018, 2 (9), pp.1377-1380. ⟨10.1038/s41559-018-0643-y⟩
Journal articles halshs-03958403v1

Fibrillin influence on plastid ultrastructure and pigment content in tomato fruit.

Andrew J Simkin , Joël Gaffé , Jean-Pierre Alcaraz , Jean-Pierre Carde , Peter M Bramley , et al.
Phytochemistry, 2007, 68 (11), pp.1545-56. ⟨10.1016/j.phytochem.2007.03.014⟩
Journal articles istex hal-00801236v1

The Genetical Bandwidth Mapping: A spatial and graphical representation of population genetic structure based on the Wombling method

Alain Cercueil , Olivier Francois , S. Manel
Theoretical Population Biology, 2007, 71 (3), pp.332-341. ⟨10.1016/j.tpb.2007.01.007⟩
Journal articles istex halsde-00283758v1

Tempo and mode of genome evolution in a 50,000-generation experiment

Olivier Tenaillon , Jeffrey E. Barrick , Noah Ribeck , Daniel E. Deatherage , Jeffrey L. Blanchard , et al.
Nature, 2016, 536 (7615), pp.165 - 170. ⟨10.1038/nature18959⟩
Journal articles hal-01653393v1

Oral administration of viable Bifidobacterium pseudolongum strain Patronus modified colonic microbiota and increased mucus layer thickness in rat

Irène Mangin , Flore Marques Dossou-Yovo , Christophe Lévêque , Marie-Vincent Dessoy , Olivier Sawoo , et al.
FEMS Microbiology Ecology, 2018, 94 (11), ⟨10.1093/femsec/fiy177⟩
Journal articles hal-01980169v1

The amino-terminal region of dense granule protein 6 of Toxoplasma gondii stimulates IFN-γ production by microglia

Qila Sa , Corinne Mercier , Marie-France Cesbron-Delauw , Yasuhiro Suzuki
Microbes and Infection, 2020, ⟨10.1016/j.micinf.2019.12.003⟩
Journal articles hal-02470435v1
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LFMM 2: Fast and Accurate Inference of Gene-Environment Associations in Genome-Wide Studies

Kevin Caye , Basile Jumentier , Johanna Lepeule , Olivier François
Molecular Biology and Evolution, 2019, 36 (4), pp.852-860. ⟨10.1093/molbev/msz008⟩
Journal articles inserm-03179375v1
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Non-linear frequency-dependent selection promotes long-term coexistence between bacteria species

Noémie Harmand , Valentine Federico , Thomas Hindre , Thomas Lenormand
Ecology Letters, 2019, 22, pp.1192-1202. ⟨10.1111/ele.13276⟩
Journal articles hal-02099952v1

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
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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⟩
Journal articles hal-02992748v1

Genetic Basis of Exploiting Ecological Opportunity During the Long-Term Diversification of a Bacterial Population

Jessika Consuegra , Jessica Plucain , Joël Gaffé , Thomas Hindré , Dominique Schneider
Journal of Molecular Evolution, 2017, 85 (1-2), pp.26 - 36. ⟨10.1007/s00239-017-9802-z⟩
Journal articles hal-01653588v1
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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⟩
Journal articles hal-03079193v1