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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

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

Paper Title Number 1

Published in Journal 1, 1900

This paper is about the number 1. The number 2 is left for future work.

Recommended citation: Your Name, You. (2009). "Paper Title Number 1." Journal 1. 1(1). http://academicpages.github.io/files/paper1.pdf

Paper Title Number 2

Published in Journal 1, 1900

This paper is about the number 2. The number 3 is left for future work.

Recommended citation: Your Name, You. (2010). "Paper Title Number 2." Journal 1. 1(2). http://academicpages.github.io/files/paper2.pdf

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

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

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

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

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

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

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

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

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

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

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

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

Paper Title Number 3

Published in Journal 1, 1900

This paper is about the number 3. The number 4 is left for future work.

Recommended citation: Your Name, You. (2015). "Paper Title Number 3." Journal 1. 1(3). http://academicpages.github.io/files/paper3.pdf

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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, September 2022 http://biorxiv.org/lookup/doi/10.1101/2022.09.02.506364

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

Published in , 1969

Recommended citation: S. S. Abby, R. Denise, E. P. Rocha. Identification of protein secretion systems in bacterial genomes using MacSyFinder version 2, January 2023 http://biorxiv.org/lookup/doi/10.1101/2023.01.06.522999

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

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Future Blog Post

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Published: January 01, 2199

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Blog Post number 4

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Published: August 14, 2015

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Blog Post number 3

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Published: August 14, 2014

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Blog Post number 2

less than 1 minute read

Published: August 14, 2013

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Blog Post number 1

less than 1 minute read

Published: August 14, 2012

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Portfolio item number 1

Short description of portfolio item number 1

Portfolio item number 2

Short description of portfolio item number 2

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.

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

Talk 1 on Relevant Topic in Your Field

Published: March 01, 2012

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Tutorial 1 on Relevant Topic in Your Field

Published: March 01, 2013

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Talk 2 on Relevant Topic in Your Field

Published: February 01, 2014

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Conference Proceeding talk 3 on Relevant Topic in Your Field

Published: March 01, 2014

This is a description of your conference proceedings talk, note the different field in type. You can put anything in this field.

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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