Portfolio item number 1
Short description of portfolio item number 1
Posts by Collection
portfolio
Portfolio item number 2
Short description of portfolio item number 2
projects
Genome Annotation
We develop software and methods to improve genome annotations.
Bacterial Secretion Systems
We study the evolution and diversity of bacterial secretion systems.
Bioenergetics and Quinones
We study the evolution of metabolic pathways involved in bioenergetics.
Origin of Life consortium
We are involved in the Astrobiology consortium in Grenoble.
publications
Comparative genomics and the evolution of prokaryotes
Published in , 1969
Recommended citation: S. Abby, V. Daubin. Comparative genomics and the evolution of prokaryotes, Trends in Microbiology, March 2007 https://linkinghub.elsevier.com/retrieve/pii/S0966842X07000224
Detecting lateral gene transfers by statistical reconciliation of phylogenetic forests
Published in , 1969
Recommended citation: S. S. Abby, E. Tannier, M. Gouy, V. Daubin. Detecting lateral gene transfers by statistical reconciliation of phylogenetic forests, BMC Bioinformatics, December 2010 https://bmcbioinformatics.biomedcentral.com/articles/10.1186/1471-2105-11-324
Investment in rapid growth shapes the evolutionary rates of essential proteins
Published in , 1969
Recommended citation: S. Vieira-Silva, M. Touchon, S. S. Abby, E. P. C. Rocha. Investment in rapid growth shapes the evolutionary rates of essential proteins, Proceedings of the National Academy of Sciences, December 2011 http://www.pnas.org/cgi/doi/10.1073/pnas.1110972108
Immune Subversion and Quorum-Sensing Shape the Variation in Infectious Dose among Bacterial Pathogens
Published in , 1969
Recommended citation: J. A. Gama, S. S. Abby, S. Vieira-Silva, F. Dionisio et al.. Immune Subversion and Quorum-Sensing Shape the Variation in Infectious Dose among Bacterial Pathogens, PLoS Pathogens, February 2012 https://dx.plos.org/10.1371/journal.ppat.1002503
Lateral gene transfer as a support for the tree of life
Published in , 1969
Recommended citation: S. S. Abby, E. Tannier, M. Gouy, V. Daubin. Lateral gene transfer as a support for the tree of life, Proceedings of the National Academy of Sciences, March 2012 http://www.pnas.org/cgi/doi/10.1073/pnas.1116871109
Les transferts horizontaux de gènes et l’arbre de la vie
Published in , 1969
Recommended citation: V. Daubin, S. Abby. Les transferts horizontaux de gènes et l’arbre de la vie, médecine/sciences, August 2012 http://www.medecinesciences.org/10.1051/medsci/2012288007
The Non-Flagellar Type III Secretion System Evolved from the Bacterial Flagellum and Diversified into Host-Cell Adapted Systems
Published in , 1969
Recommended citation: S. S. Abby, E. P. C. Rocha. The Non-Flagellar Type III Secretion System Evolved from the Bacterial Flagellum and Diversified into Host-Cell Adapted Systems, PLoS Genetics, September 2012 https://dx.plos.org/10.1371/journal.pgen.1002983
A Single Amino Acid Substitution Changes the Self-Assembly Status of a Type IV Piliation Secretin
Published in , 1969
Recommended citation: N. N. Nickerson, S. S. Abby, E. P. C. Rocha, M. Chami et al.. A Single Amino Acid Substitution Changes the Self-Assembly Status of a Type IV Piliation Secretin, Journal of Bacteriology, September 2012 http://jb.asm.org/content/194/18/4951
Phylogenetic modeling of lateral gene transfer reconstructs the pattern and relative timing of speciations
Published in , 1969
Recommended citation: G. J. Szollosi, B. Boussau, S. S. Abby, E. Tannier et al.. Phylogenetic modeling of lateral gene transfer reconstructs the pattern and relative timing of speciations, Proceedings of the National Academy of Sciences, October 2012 http://www.pnas.org/cgi/doi/10.1073/pnas.1202997109
Key components of the eight classes of type IV secretion systems involved in bacterial conjugation or protein secretion
Published in , 1969
Recommended citation: J. Guglielmini, B. Néron, S. S. Abby, M. P. Garcillán-Barcia et al.. Key components of the eight classes of type IV secretion systems involved in bacterial conjugation or protein secretion, Nucleic Acids Research, May 2014 http://academic.oup.com/nar/article/42/9/5715/1253976/Key-components-of-the-eight-classes-of-type-IV
MacSyFinder: A Program to Mine Genomes for Molecular Systems with an Application to CRISPR-Cas Systems
Published in , 1969
Recommended citation: S. S. Abby, B. Néron, H. Ménager, M. Touchon et al.. MacSyFinder: A Program to Mine Genomes for Molecular Systems with an Application to CRISPR-Cas Systems, PLoS ONE, October 2014 https://dx.plos.org/10.1371/journal.pone.0110726
Bacteria in Ostreococcus tauri cultures – friends, foes or hitchhikers?
Published in , 1969
Recommended citation: S. S. Abby, M. Touchon, A. De Jode, N. Grimsley et al.. Bacteria in Ostreococcus tauri cultures – friends, foes or hitchhikers?, Frontiers in Microbiology, November 2014 http://journal.frontiersin.org/article/10.3389/fmicb.2014.00505/abstract
Identification of protein secretion systems in bacterial genomes
Published in , 1969
Recommended citation: S. S. Abby, J. Cury, J. Guglielmini, B. Néron et al.. Identification of protein secretion systems in bacterial genomes, Scientific Reports, March 2016 http://www.nature.com/articles/srep23080
Testing for Independence between Evolutionary Processes
Published in , 1969
Recommended citation: A. Behdenna, J. Pothier, S. S. Abby, A. Lambert et al.. Testing for Independence between Evolutionary Processes, Systematic Biology, September 2016 https://academic.oup.com/sysbio/article-lookup/doi/10.1093/sysbio/syw004
Proteomics and comparative genomics of extitNitrososphaera viennensis reveal the core genome and adaptations of archaeal ammonia oxidizers
Published in , 1969
Recommended citation: M. Kerou, P. Offre, L. Valledor, S. S. Abby et al.. Proteomics and comparative genomics of \textitNitrososphaera viennensis reveal the core genome and adaptations of archaeal ammonia oxidizers, Proceedings of the National Academy of Sciences, December 2016 http://www.pnas.org/lookup/doi/10.1073/pnas.1601212113
Identification of Protein Secretion Systems in Bacterial Genomes Using MacSyFinder
Published in , 1969
Recommended citation: S. S. Abby, E. P. C. Rocha. Identification of Protein Secretion Systems in Bacterial Genomes Using MacSyFinder, 2017 http://link.springer.com/10.1007/978-1-4939-7033-9_1
Asynchronous division by non-ring FtsZ in the gammaproteobacterial symbiont of Robbea hypermnestra
Published in , 1969
Recommended citation: N. Leisch, N. Pende, P. M. Weber, H. R. Gruber-Vodicka et al.. Asynchronous division by non-ring FtsZ in the gammaproteobacterial symbiont of Robbea hypermnestra, Nature Microbiology, January 2017 http://www.nature.com/articles/nmicrobiol2016182
Candidatus Nitrosocaldus cavascurensis, an Ammonia Oxidizing, Extremely Thermophilic Archaeon with a Highly Mobile Genome
Published in , 1969
Recommended citation: S. S. Abby, M. Melcher, M. Kerou, M. Krupovic et al.. Candidatus Nitrosocaldus cavascurensis, an Ammonia Oxidizing, Extremely Thermophilic Archaeon with a Highly Mobile Genome, Frontiers in Microbiology, January 2018 http://journal.frontiersin.org/article/10.3389/fmicb.2018.00028/full
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
Published in , 1969
Recommended citation: A. C. Pozzi, H. H. Bautista-Guerrero, S. S. Abby, A. Herrera-Belaroussi et al.. 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, Systematic and Applied Microbiology, July 2018 https://linkinghub.elsevier.com/retrieve/pii/S0723202018301139
Ammonia Oxidation by the Arctic Terrestrial Thaumarchaeote Candidatus Nitrosocosmicus arcticus Is Stimulated by Increasing Temperatures
Published in , 1969
Recommended citation: R. J. E. Alves, M. Kerou, A. Zappe, R. Bittner et al.. Ammonia Oxidation by the Arctic Terrestrial Thaumarchaeote Candidatus Nitrosocosmicus arcticus Is Stimulated by Increasing Temperatures, Frontiers in Microbiology, July 2019 https://www.frontiersin.org/article/10.3389/fmicb.2019.01571/full
Diversification of the type IV filament superfamily into machines for adhesion, protein secretion, DNA uptake, and motility
Published in , 1969
Recommended citation: R. Denise, S. S. Abby, E. P. C. Rocha. Diversification of the type IV filament superfamily into machines for adhesion, protein secretion, DNA uptake, and motility, PLOS Biology, July 2019 https://journals.plos.org/plosbiology/article?id=10.1371/journal.pbio.3000390
Ubiquinone Biosynthesis over the Entire O $_ extrm2$ Range: Characterization of a Conserved O $_ extrm2$ -Independent Pathway
Published in , 1969
Recommended citation: L. Pelosi, C.-D.-T. Vo, S. S. Abby, L. Loiseau et al.. Ubiquinone Biosynthesis over the Entire O $_\textrm2$ Range: Characterization of a Conserved O $_\textrm2$ -Independent Pathway, mBio, August 2019 https://journals.asm.org/doi/10.1128/mBio.01319-19
Identifying Conjugative Plasmids and Integrative Conjugative Elements with CONJscan
Published in , 1969
Recommended citation: J. Cury, S. S. Abby, O. Doppelt-Azeroual, B. Néron et al.. Identifying Conjugative Plasmids and Integrative Conjugative Elements with CONJscan, 2020 http://link.springer.com/10.1007/978-1-4939-9877-7_19
The Evolution of Protein Secretion Systems by Co-option and Tinkering of Cellular Machineries
Published in , 1969
Recommended citation: R. Denise, S. S. Abby, E. P. Rocha. The Evolution of Protein Secretion Systems by Co-option and Tinkering of Cellular Machineries, Trends in Microbiology, May 2020 https://linkinghub.elsevier.com/retrieve/pii/S0966842X2030007X
Ancestral Reconstructions Decipher Major Adaptations of Ammonia-Oxidizing Archaea upon Radiation into Moderate Terrestrial and Marine Environments
Published in , 1969
Recommended citation: S. S. Abby, M. Kerou, C. Schleper. Ancestral Reconstructions Decipher Major Adaptations of Ammonia-Oxidizing Archaea upon Radiation into Moderate Terrestrial and Marine Environments, mBio, October 2020 https://journals.asm.org/doi/10.1128/mBio.02371-20
Advances in bacterial pathways for the biosynthesis of ubiquinone
Published in , 1969
Recommended citation: S. S. Abby, K. Kazemzadeh, C. Vragniau, L. Pelosi et al.. Advances in bacterial pathways for the biosynthesis of ubiquinone, Biochimica et Biophysica Acta (BBA) - Bioenergetics, November 2020 https://linkinghub.elsevier.com/retrieve/pii/S0005272820301092
Genome wide transcriptomic analysis of the soil ammonia oxidizing archaeon Nitrososphaera viennensis upon exposure to copper limitation
Published in , 1969
Recommended citation: C. Reyes, L. H. Hodgskiss, M. Kerou, T. Pribasnig et al.. Genome wide transcriptomic analysis of the soil ammonia oxidizing archaeon Nitrososphaera viennensis upon exposure to copper limitation, The ISME Journal, November 2020 http://www.nature.com/articles/s41396-020-0715-2
Geochemical transition zone powering microbial growth in subsurface sediments
Published in , 1969
Recommended citation: R. Zhao, J. M. Mogollón, S. S. Abby, C. Schleper et al.. Geochemical transition zone powering microbial growth in subsurface sediments, Proceedings of the National Academy of Sciences, December 2020 http://www.pnas.org/lookup/doi/10.1073/pnas.2005917117
Genomes of Thaumarchaeota from deep sea sediments reveal specific adaptations of three independently evolved lineages
Published in , 1969
Recommended citation: M. Kerou, R. I. Ponce-Toledo, R. Zhao, S. S. Abby et al.. Genomes of Thaumarchaeota from deep sea sediments reveal specific adaptations of three independently evolved lineages, The ISME Journal, September 2021 https://www.nature.com/articles/s41396-021-00962-6
Towards Molecular Understanding of the Functional Role of UbiJ-UbiK2 Complex in Ubiquinone Biosynthesis by Multiscale Molecular Modelling Studies
Published in , 1969
Recommended citation: R. Launay, E. Teppa, C. Martins, S. S. Abby et al.. Towards Molecular Understanding of the Functional Role of UbiJ-UbiK2 Complex in Ubiquinone Biosynthesis by Multiscale Molecular Modelling Studies, International Journal of Molecular Sciences, September 2022 https://www.mdpi.com/1422-0067/23/18/10323
MacSyFinder v2: Improved modelling and search engine to identify molecular systems in genomes
Published in , 1969
Recommended citation: B. Néron, R. Denise, C. Coluzzi, M. Touchon et al.. MacSyFinder v2: Improved modelling and search engine to identify molecular systems in genomes, Peer Community Journal, March 2023 https://peercommunityjournal.org/articles/10.24072/pcjournal.250/
Structural Space of the Duffy Antigen/Receptor for Chemokines’ Intrinsically Disordered Ectodomain 1 Explored by Temperature Replica-Exchange Molecular Dynamics Simulations
Published in , 1969
Recommended citation: A. Kranjc, T. J. Narwani, S. S. Abby, A. G. De Brevern. Structural Space of the Duffy Antigen/Receptor for Chemokines’ Intrinsically Disordered Ectodomain 1 Explored by Temperature Replica-Exchange Molecular Dynamics Simulations, International Journal of Molecular Sciences, August 2023 https://www.mdpi.com/1422-0067/24/17/13280
Diversification of ubiquinone biosynthesis extitvia gene duplications, transfers, losses, and parallel evolution
Published in , 1969
Recommended citation: K. Kazemzadeh, L. Pelosi, C. Chenal, S.-C. Chobert et al.. Diversification of ubiquinone biosynthesis \textitvia gene duplications, transfers, losses, and parallel evolution, Molecular Biology and Evolution, October 2023 https://academic.oup.com/mbe/advance-article/doi/10.1093/molbev/msad219/7288468
Identification of Protein Secretion Systems in Bacterial Genomes Using MacSyFinder Version 2
Published in , 1969
Recommended citation: S. S. Abby, R. Denise, E. P. C. Rocha. Identification of Protein Secretion Systems in Bacterial Genomes Using MacSyFinder Version 2, 2024 https://link.springer.com/10.1007/978-1-0716-3445-5_1
talks
Talk 1 on Relevant Topic in Your Field
Published:
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Conference Proceeding talk 3 on Relevant Topic in Your Field
Published:
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teaching
Teaching experience 1
Undergraduate course, University 1, Department, 2014
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Teaching experience 2
Workshop, University 1, Department, 2015
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