Team TrEE
Phone: 04 57 42 18 98
Address: Bâtiment Jean Roget, Place du Commandant Nal, Domaine de la Merci
Office: 512-B

I received a bi-disciplinary education in biology and computational sciences. I'm an evolutionary biologist, particularly interested in the mechanisms of diversification of prokaryotes (archaea and bacteria). I study these at different scales: from enzymes, to macromolecular complexes, and genome dynamics with respect to environmental adaptations. When needed, I design new computational methods in the field of comparative genomics and phylogenomics. 

  • 2017 - now: CNRS researcher
  • 2015 - 2017: Post-doc at the University of Vienna (Christa Schleper's lab) ; Marie-Curie fellow (2016-2017)
  • 2010 - 2014: Post-doc at the Pasteur Institute (Eduardo Rocha's lab)
  • 2010: phD at the University of Lyon (LBBE lab, superv. by Vincent Daubin and Manolo Gouy)

Here the link to my personal, up-to-date website.


Designed software and tools

- Prunier: software for phylogenetic identification of lateral gene transfers.

- MacSyFinder: software for the modeling and detection of macromolecular systems in genomes.

- TXSScan: a MacSyFinder-based tool for the detection of bacterial secretion systems and appendages in genomes.

- Cas-Finder: a MacSyFinder-based tool for the detection and classification of CRISPR-associated (Cas) systems in genomes.

- TXSSdb, a queryable database of bacterial protein secretion systems in genomes (data from Abby et al., Scientific Reports, 2016).

- Secreton: an online queryable database of bacterial Type III secretion systems (T3SS) and flagella in genomes (data from Abby and Rocha, Plos Genetics, 2012).

Research themes

Microbial evolution ; Molecular evolution ; Phylogenetics ; Comparative genomics ; Metagenomics ; Bioinformatics

Supervised thesis
Sophie-Carole CHOBERT : "Etude de l'origine et de la diversification des voies de biosynthèse des quinones respiratoires"
Flora GAUDILLIERE : "Rôle des séquences d'insertion dans l'évolution des génomes bactériens"

See my Google scholar profile or Pubmed that should list all my publications. 


Selected publications


2020 – Denise R, Abby SS*, Rocha EPC*.

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

Trends Microbiol. 2020 May;28(5):372-386. doi: 10.1016/j.tim.2020.01.005. Epub 2020 Feb 13.


2020 – Abby SS, Kazemzadeh K, Vragniau C, Pelosi L, Pierrel F.

Advances in bacterial pathways for the biosynthesis of ubiquinone.

Biochim Biophys Acta Bioenerg. 2020 Jul 12;1861(11):148259. doi: 10.1016/j.bbabio.2020.148259.


2019 – Denise R, Abby SS*, Rocha EPC*.

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

PLoS Biology, Public Library of Science, 2019, 17 (7), pp.e3000390. ;10.1371/journal.pbio.3000390

* co-senior authors


2019 – Pelosi L*, Vo C*, Abby SS, Loiseau L, Rascalou B, Hajj Chehade M, Faivre B, Goussé M, Chenal C, Touati N, Binet L, Cornu D, Fyfe CD, Fontecave M, Barras F, Lombard M, Pierrel F.

Ubiquinone Biosynthesis over the Entire O2 Range: Characterization of a Conserved O2−Independent Pathway.

mBio, 2019, 10 (4);10.1128/mBio.01319−19

* these authors contributed equally


2018 Abby SS*, Melcher M*, Kerou M, Krupovic M, Stieglmeier M, Rossel C, Pfeifer K, Schleper C.

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

Frontiers in Microbiology. 2018 Jan 26;9:28. doi: 10.3389/fmicb.2018.00028. * Authors contributed equally.



2016Abby SS, Cury J, Guglielmini J, Néron B, Touchon M, Rocha EP.

Identification of protein secretion systems in bacterial genomes.

Scientific Reports. 2016 Mar 16;6:23080. doi: 10.1038/srep23080.


2014Abby SS, Néron B, Ménager H, Touchon M, Rocha EP.

MacSyFinder: a program to mine genomes for molecular systems with an application to CRISPR-Cas systems.

PLoS One. 2014 Oct 17;9(10):e110726. doi: 10.1371/journal.pone.0110726.


2012  Abby SS, Rocha EPC. 

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

PLoS Genetics 8 (9), e1002983


2012  Abby SS, Tannier E, Gouy M, Daubin V.

Lateral gene transfer as a support for the tree of life*

Proceedings of the National Academy of Sciences 109 (13), 4962-4967 *Featured in "This Week in PNAS".


Invited communications

Scientific events

  • 2021: Organization of the French Alphy (comparative genomics work group) meeting




One post-doc position is currently available: we are looking for a postdoc to use phylogenomics and co-evolution approaches to study the emergence and evolution of enzymes' functions. 

We are looking for a highly motivated young scientist with a strong background in computational biology, evolutionary genomics or mathematical methods, with a strong interest to investigate evolution of biological functions.
Please send your CV, a motivation letter, and the names and contact information of two references to "sophie.abby" and "ivan.junier" (both For more details, informal enquiries are also welcome!

We regularly offer training positions, feel free to contact us spontaneously! 


Ongoing projects

  • Design of "system-level" annotation tools using comparative genomics. See: 
  • Study of the evolution of cellular machineries evolution, in particular protein secretion systems and related appendages
  • Investigation of the evolution of biosynthetic pathways, and in particular, of that of the quinones involved in bioenergetics


Ongoing fundings

  • 3.5y "JCJC" funding by the ANR (232k€, ANR-21-CE02-0018, 2021)
  • 2y funding by the IDEX Grenoble Alpes Université “Initiatives de Recherche Stratégiques” (19k€, 2020)


Past fundings

  • 2y Grenoble Alpes data Institute workpackage (6k€, Grenoble Alpes Data Institute supported by the ANR-15-IDEX-02 project, 2017)
  • 2y Marie Skłodowska-Curie Individual Fellowship (192k€, IF-EF), European Commission, H2020 framework