CV

Current Position

• Since 2017: CNRS researcher
  • Université Grenoble Alpes
  • TIMC lab
  • TrEE team
  • CompBio@TrEE group

Education

• B.S. in Biology and Computer Sciences, Paris 7 University, 2004
• M.S. in Biology and Computer Sciences, Paris 7 University, 2006
• Ph.D in Bioinformatics, Lyon 1 University, 2010
• Habilitation, “Chemistry and Life Sciences” Doctoral School, U. Grenoble Alpes, 2024

Academic experience

• 2015-2016: Postdoctoral Researcher & Marie Curie Fellow
  • University of Vienna
  • Topic: Evolution and adaptation of Thaumarchaeota to moderate environments
  • Supervision: Christa Schleper
• 2010-2014: Postdoctoral Researcher
  • Pasteur Institute, Paris
  • Topic: Molecular evolution of bacterial secretion systems
  • Supervision: Eduardo Rocha
• 2006-2010: PhD Student
  • Laboratoire de Biométrie et Biologie Evolutive, Lyon 1 University
  • Topic: Phylogenetics and evolutionary genomics of prokaryotes
  • Supervision: Vincent Daubin & Manolo Gouy

PhD thesis supervisions

• PhD thesis of Dr. Rémi Denise (2017-2019).
  • Co-supervision with Dr. Eduardo Rocha.
  • Topic: “Co-option de systèmes moléculaires complexes de la membrane bactérienne et archéenne”
  • Insitut Pasteur, Paris.
• PhD thesis of Sophie-Carole Chobert (2021-).
  • Co-supervision with Dr. Fabien Pierrel.
  • Topic: “Etude de l’origine et de la diversification des voies de biosynthèse des quinones respiratoires”
  • TIMC lab, Grenoble.
• PhD thesis of Morgane Roger-Margueritat (2022-).
  • Co-supervision with Dr. Fabien Pierrel.
  • Topic: “Mécanismes d’échanges de quinones et impact sur le microbiote intestinal”
  • TIMC lab, Grenoble.
• PhD thesis of Sandy Frank Ngaha (2023-).
  • Co-supervision with Dr. Nelle Varoquaux.
  • TIMC lab, Grenoble.

Editorial and scientific outreach activities

• PCI Microbiology
  • Managing board member
  • https://microbiol.peercommunityin.org/
• PCI Genomics, PCI Evolutionary Biology
  • Recommender
  • Check out: https://peercommunityin.org/current-pcis/
• French Microbiology Society
  • Board member of the “Biodiversité & Evolution” section.
• Organization of conferences:
  • 2023 French Alphy/AIEM meeting, Grenoble (Joint meeting for “Alignment and Phylogeny”, and “Interdisciplinary Approaches for Molecular Evolution” CNRS work groups)
  • 2021 Alphy meeting, virtual edition.

Publications

See: https://scholar.google.fr/citations?hl=en&user=pJ3h0iMAAAAJ&view_op=list_works

Comparative genomics and the evolution of prokaryotes

S. Abby, V. Daubin. Comparative genomics and the evolution of prokaryotes, Trends in Microbiology, March 2007

Detecting lateral gene transfers by statistical reconciliation of phylogenetic forests

S. S. Abby, E. Tannier, M. Gouy, V. Daubin. Detecting lateral gene transfers by statistical reconciliation of phylogenetic forests, BMC Bioinformatics, December 2010

Investment in rapid growth shapes the evolutionary rates of essential proteins

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

Immune Subversion and Quorum-Sensing Shape the Variation in Infectious Dose among Bacterial Pathogens

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

Lateral gene transfer as a support for the tree of life

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

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

V. Daubin, S. Abby. Les transferts horizontaux de gènes et l’arbre de la vie, médecine/sciences, August 2012

The Non-Flagellar Type III Secretion System Evolved from the Bacterial Flagellum and Diversified into Host-Cell Adapted Systems

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

A Single Amino Acid Substitution Changes the Self-Assembly Status of a Type IV Piliation Secretin

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

Phylogenetic modeling of lateral gene transfer reconstructs the pattern and relative timing of speciations

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

Key components of the eight classes of type IV secretion systems involved in bacterial conjugation or protein secretion

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

MacSyFinder: A Program to Mine Genomes for Molecular Systems with an Application to CRISPR-Cas Systems

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

Bacteria in Ostreococcus tauri cultures – friends, foes or hitchhikers?

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

Identification of protein secretion systems in bacterial genomes

S. S. Abby, J. Cury, J. Guglielmini, B. Néron et al.. Identification of protein secretion systems in bacterial genomes, Scientific Reports, March 2016

Testing for Independence between Evolutionary Processes

A. Behdenna, J. Pothier, S. S. Abby, A. Lambert et al.. Testing for Independence between Evolutionary Processes, Systematic Biology, September 2016

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

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

Identification of Protein Secretion Systems in Bacterial Genomes Using MacSyFinder

S. S. Abby, E. P. C. Rocha. Identification of Protein Secretion Systems in Bacterial Genomes Using MacSyFinder, 2017

Asynchronous division by non-ring FtsZ in the gammaproteobacterial symbiont of Robbea hypermnestra

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

Candidatus Nitrosocaldus cavascurensis, an Ammonia Oxidizing, Extremely Thermophilic Archaeon with a Highly Mobile Genome

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

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

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

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

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

Diversification of the type IV filament superfamily into machines for adhesion, protein secretion, DNA uptake, and motility

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

Ubiquinone Biosynthesis over the Entire O $_ extrm2$ Range: Characterization of a Conserved O $_ extrm2$ -Independent Pathway

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

Identifying Conjugative Plasmids and Integrative Conjugative Elements with CONJscan

J. Cury, S. S. Abby, O. Doppelt-Azeroual, B. Néron et al.. Identifying Conjugative Plasmids and Integrative Conjugative Elements with CONJscan, 2020

The Evolution of Protein Secretion Systems by Co-option and Tinkering of Cellular Machineries

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

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

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

Advances in bacterial pathways for the biosynthesis of ubiquinone

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

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

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

Geochemical transition zone powering microbial growth in subsurface sediments

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

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

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

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

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

MacSyFinder v2: Improved modelling and search engine to identify molecular systems in genomes

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

Structural Space of the Duffy Antigen/Receptor for Chemokines’ Intrinsically Disordered Ectodomain 1 Explored by Temperature Replica-Exchange Molecular Dynamics Simulations

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

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

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

Identification of Protein Secretion Systems in Bacterial Genomes Using MacSyFinder Version 2

S. S. Abby, R. Denise, E. P. C. Rocha. Identification of Protein Secretion Systems in Bacterial Genomes Using MacSyFinder Version 2, 2024