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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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/
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
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
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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