Team GEM
Phone: 04 76 63 75 36
Address: Bâtiment Jean Roget, Domaine de la Merci
Office: 513

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 this aspect 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)

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).


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




Selected publications



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.


2017 Abby SS, Rocha EPC.

Identification of Protein Secretion Systems in Bacterial Genomes Using MacSyFinder.

Methods in Molecular Biology. 2017;1615:1-21. doi:10.1007/978-1-4939-7033-9_1.


2016 – Kerou M, Offre P, Valledor L, Abby SS, Melcher M, Nagler M, Weckwerth W, Schleper C.

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

Proceedings of the National Academy of Sciences USA. 2016 Dec 6;113(49):E7937-E7946.


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".


2010  Abby SS, Tannier E, Gouy M, Daubin V.

Detecting lateral gene transfers by statistical reconciliation of phylogenetic forests

BMC bioinformatics 11 (1), 324

Invited communications