Curriculum Vitae

Current Position

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

Education

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

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

Ongoing

PhD thesis of Timothée Salzat-Hervouette (2024-)
- Co-supervision with Dr. Fabien Pierrel
- Topic: Evolution of phototrophic bacteria
PhD thesis of Emma Bouvet (2024-)
- Co-supervision with Dr. Ludovic Pelosi
- Topic: Evolution of quinone biosynthetic pathways
PhD thesis of Sandy Frank Ngaha (2023-)
- Co-supervision with Dr. Nelle Varoquaux
- Topic: machine learning and genome annotation
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”

Past

PhD thesis of Sophie-Carole Chobert (2021-2024)
- Co-supervision with Dr. Fabien Pierrel
- Topic: “Etude de l’origine et de la diversification des voies de biosynthèse des quinones respiratoires”
- Location: TIMC lab, Grenoble
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”
- Location: Insitut Pasteur, Paris

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
- 2022-2025 – Board member of the “Biodiversité & Evolution” section.
Since 2021 – Member of the editorial board of Environmental Microbiology
Organization of conferences:
- 2025 BactoGre - annual meeting of microbiologists in Grenoble
- 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
- Since 2022 – Member of the Program Committee for the French national bioinformatics meeting (JOBIM “Journées Ouvertes En Biologie, Informatique Et Mathématiques”)

Expert activities

2024 – HCERES expert
Since 2024 – Member of hiring panels for two tenured positions
2023-2024 – Nominated member of the national committee of the CNRS “coNRS” (section 21 « Organisation, expression, évolution des génomes »), in charge of the evaluation and recruitment of CNRS researchers (since 2023)
2019-2024 – Expert reviewer for the European Commission (Marie Skłodowska-Curie Individual Fellowship)
Since 2017 – Part of fifteen PhD committees
Two software and several genome annotation tools developed

Fundings & awards

2023 – CNRS Bronze medal
2023-2028 – co-PI (partner) of two collaborative ANR projects (340k€ for the team), ADAPT2Q and AbiSYM.
2022-2025 – co-PI of the renewed Université Grenoble Alpes consortium/project “Cross Disciplinary Project - Origin of Life” (PI: Xavier Delfosse, astronomer at IPAG, 600k€, ~60k€ for the team)
2021-2025 – PI of a 42 months ANR project (AAPG 2021 call) (232k€), QUINEVOL
2020-2021 – PI of a 18 months project (IDEX Grenoble Alpes Université “Initiatives de Recherche Stratégiques”) (19k€)
2017-2019 – PI of a 2y Grenoble Alpes data Institute workpackage (Grenoble Alpes Data Institute, ANR-15-IDEX-02) (6k€)
2016-2017 – 2y Marie Skłodowska-Curie Individual Fellowship (IF-EF), European Commission, H2020 framework (192k€), THAUMECOPHYL

Publications

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

A novel quinone biosynthetic pathway illuminates the evolution of aerobic metabolism

F. J. Elling, F. Pierrel, S.-C. Chobert, S. S. Abby et al.. A novel quinone biosynthetic pathway illuminates the evolution of aerobic metabolism, Proc. Natl. Acad. Sci. U.S.A., February 2025

Dynamic quinone repertoire accompanied the diversification of energy metabolism in extitPseudomonadota

S.-C. Chobert, M. Roger-Margueritat, L. Flandrin, S. Berraies et al.. Dynamic quinone repertoire accompanied the diversification of energy metabolism in \textitPseudomonadota, The ISME Journal, January 2025

Structural Reconstruction of extitE. coli Ubi Metabolon Using an AlphaFold2-Based Computational Framework

R. Launay, S.-C. Chobert, S. S. Abby, F. Pierrel et al.. Structural Reconstruction of \textitE. coli Ubi Metabolon Using an AlphaFold2-Based Computational Framework, J. Chem. Inf. Model., July 2024

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

Bacteria in Ostreococcus tauri cultures â€“ friends, foes or hitchhikers?

S. S. Abby, M. Touchon, A. De Jode, N. Grimsley et al.. Bacteria in Ostreococcus tauri cultures â€“ friends, foes or hitchhikers?, Frontiers in Microbiology, November 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

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

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

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

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

Sophie Abby