Department of Ecogenetics and Systems Biology - Division of Archaea Biology and Ecogenomics

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Dr. Sophie Abby

Room: 1.092
1090 Wien, Althanstraße 14 (UZA I)
T: +43-1-4277-76515
F: +43-1-4277-876515

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I'm a biologist, I own a bi-disciplinary Master degree in Biology and Computer Sciences and a PhD in bioinformatics. When necessary, I develop bioinformatics methods to tackle biological questions of interest for me (Prunier, MacSyFinder, TXSScan) or I use methods developed by others (phylogeny, comparative genomics...).

'm deeply interested in evolutionary biology, and more particularly in molecular evolution. I have a strong interest in the formidable capacity of bacteria and archaea to adapt to different conditions (milieu, lifestyle...). I've studied lateral gene transfers in bacteria and archaea, a way to acquire new genetic material, and potentially, new functions. I've reconstructed the different steps of the evolution of the bacterial type III secretion system (a virulence factor found in various pathogens) from the bacterial flagellum, dedicated in a very different function: motility.

I've joined Christa Schleper's group, I'm focusing on the evolution of genomic features of ammonia-oxidising archaea (AOA), the Thaumarchaeota. In order to obtain a detailed picture of their diversification in different environments, I'm attempting to obtain complete genomes for organisms representative of AOA's diversity, either from environmental metagenomes, or from cultures grown in the lab. This will enable me to conduct a broad comparative genomics analysis. Ultimately, I hope to get insights into the acquisition of the ammonia-oxidising metabolism, and into Thaumarchaeota's conquest of many various environments, from hot springs, to deep-sea sediments and garden soils.


  • 2010 PhD in bioinformatics and evolutionary genomics. Thesis: "The Relevance of Lateral Gene Transfers to Understand the Evolutionary History of Prokaryotes" [french]Supervisors: Dr V. Daubin and Dr M. Gouy (Bioinformatics and Evolutionary Genomics group, Laboratory of Biometry and Evolutionary Biology, UMR CNRS 5558, University Lyon 1, France).
  • 2004-2006 Bi-disciplinary Master degree (MCs and BCs), Biology and Computer sciences, Paris 7 University. Thesis: "Wide-scale analysis of gene trees congruence: development of an automatic method", June 2006 [french]Thesis: "Development of a scoring function to assess pairwise structural alignments based on hydrophobic clusters information", May 2005 [french]

2006-2010 - Teaching assistant at University Lyon 1, school of Biological Sciences:

  • Applied mathematics for natural sciences (University Lyon 1)
  • Biostatistics and Bioinformatics (University Lyon 1)
  • Molecular phylogeny (INSA engineering school of Lyon)


  • Since 2015 Postdoctoral position at the University of Vienna (Austria), Department of Ecogenomics and Systems Biology, in Prof. C. Schleper's "Archaea Biology and Ecogenomics" group. I'm currently focusing on the reconstruction of Thaumarchaeota genomes that are cultivated in the lab.
  • 2010-2014 Postdoctoral position at the CNRS/Pasteur Institute (Paris, France) in Dr. E. Rocha's "Microbial evolutionary genomics" group. I was mostly interested in the evolution and diversification of bacterial protein secretion systems. To do that, I developed new methods to detect them in genomes, and used phylogenomic approaches to reconstruct their evolutionary history
  • 2006-2010 PhD student at CNRS/University Lyon 1 (Lyon, France), "Laboratoire de Biométrie et de Biologie Evolutive", under the supervision of Dr. V. Daubin and Dr. M. Gouy. I focused on prokaryotic phylogeny and lateral gene transfers (LGT). I developed a new method to detect LGT, and could show LGT are powerful phylogenetic markers, and thus are useful to evaluate phylogenies
  • 2006 6 months internship at CNRS/University Lyon 1 (Lyon, France), "Laboratoire de Biométrie et de Biologie Evolutive", under the supervision of Dr. V. Daubin and Dr. M. Gouy. I demonstrated the ability to use more phylogenetic markers than usually to reconstruct phylogenetic trees with phylogenomic approaches
  • 2005 3 months internship at "Equipe Génomique Analytique" of the lab INSERM-U511 (Paris, France), under the supervision of Dr. A. Carbone. I developed an index to assess the quality of protein structures alignments
  • 2002 2 months internship as a computer scientist in Apic S.A. (now “1-Spatial”, Paris area, France), editor of Geographic Information Systemsin collaboration with the "Centre Scientifique des Îles du Lérins" (Cannes, France). I created queries of spatial marine ecological data to trace the progression of algae on the Mediterranean sea floor.

2016-2018 Marie Skłodowska-Curie Individual Fellowship (IF-EF), European Commission
2006-2010 Fellowship of the French Department of Research and Higher Education
2007 Travel award of the Society for General Microbiology, England


  • Co-supervision of a Master student, Tobias Reinelt with Dr. Melina Kerou (post-doc in the team) and Prof. Christa Schleper
  • Co-supervision of a Master student, Rémi Denise with Dr. Eduardo Rocha (Institut Pasteur, Paris)


Research articles

  • Abby SS, Cury J, Guglielmini J, Néron B, Touchon M, Rocha EPC (2016) Identification of protein secretion systems in bacterial genomes. Scientific Reports 6, Article number: 23080. doi:10.1038/srep23080.
  • Behdenna A, Pothier J, Abby SS, Lambert A, Achaz A (2016) Testing dependencies between evolutionary processes. Systematic Biology (in press).
  • Abby SS, Néron B, Ménager H, Touchon M, Rocha EPC (2014) MacSyFinder: a program to mine genomes for molecular systems with an application to CRISPR-cas systems. PLoS ONE 9(10): e110726. doi: 10.1371/journal.pone.0110726.
  • Abby SS, Touchon M, De Jode A, Grimsley N, Piganeau G (2014) Bacteria in tauricultures - friends, foes or hitchhikers? Frontiers in Microbiology 5:505. doi: 10.3389/fmicb.2014.00505.
  • Guglielmini J, Néron B, Abby SS, Garcillán-Barcia MP, de la Cruz F, Rocha EPC (2014) Key components of the eight classes of type IV secretion systems involved in bacterial conjugation or protein secretion. Nucleic Acids Research 42 (9): 5715-27. doi: 10.1093/nar/gku194.
  • Abby SS, Rocha EPC (2012) The Non-Flagellar Type III Secretion System Evolved from the Bacterial Flagellum and Diversified into Host-Cell Adapted Systems. PLoS Genetics 8 (9): e1002983. doi: 10.1371/journal.pgen.1002983.
  • Abby SS, Tannier E, Gouy M, Daubin V (2012) Lateral gene transfer as a support for the tree of life. Proceedings of the National Academy of Sciences USA 109 (13): 4962-4967. doi: 10.1073/pnas.1116871109.
  • Nickerson NN, Abby SS, Rocha EPC, Chami M, Pugsley AP (2012) A Single Amino Acid Substitution Changes the Self-Assembly Status of a Type IV Piliation Secretin. Journal of Bacteriology 194(18): 4951-4958. doi: 10.1128/JB.00798-12.
  • Gama JA, Abby SS, Vieira-Silva S, Dionisio F, Rocha EPC (2012) Immune Subversion and Quorum-Sensing Shape the Variation in Infectious Dose among Bacterial Pathogens. PLoS Pathogens 8(2): e1002503. doi: 10.1371/journal.ppat.1002503.
  • Szöllősi GJ, Boussau B, Abby SS, Tannier E, Daubin V (2012) Phylogenetic modeling of lateral gene transfer reconstructs the pattern and relative timing of speciations. Proceedings of the National Academy of Sciences USA 109(43): 17513-17518. doi: 10.1073/pnas.1202997109.
  • Vieira-Silva S, Touchon M, Abby SS, Rocha EPC (2011) Investment in rapid growth shapes the evolutionary rates of essential proteins. Proceedings of the National Academy of Sciences USA 108(50): 20030-20035. doi: 10.1073/pnas.1110972108.
  • Abby S, Tannier E, Gouy M, Daubin V (2010) Detecting lateral gene transfers by statistical reconciliation of phylogenetic forests. BMC bioinformatics 11(1): 324. doi: 10.1186/1471-2105-11-324.

Reviews and Briefs

  • Daubin V, Abby S (2012) Healing the tree of life with lateral gene transfers [french] Médecine sciences: M/S 28(8-9): 695.
  • Abby S, Daubin V (2007) Comparative genomics and the evolution of prokaryotes. Trends in microbiology 15(3): 135-141.

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