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Testing for Independence between Evolutionary Processes.

Behdenna A, Pothier J, Abby SS, Lambert A, Achaz G.

Syst Biol. 2016 May 21. pii: syw004. [Epub ahead of print]


Identification of protein secretion systems in bacterial genomes.

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

Sci Rep. 2016 Mar 16;6:23080. doi: 10.1038/srep23080.


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

Abby SS, Touchon M, De Jode A, Grimsley N, Piganeau G.

Front Microbiol. 2014 Nov 7;5:505. doi: 10.3389/fmicb.2014.00505. eCollection 2014.


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

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

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


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

Guglielmini J, Néron B, Abby SS, Garcillán-Barcia MP, de la Cruz F, Rocha EP.

Nucleic Acids Res. 2014 May;42(9):5715-27. doi: 10.1093/nar/gku194. Epub 2014 Mar 12.


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

Szöllosi GJ, Boussau B, Abby SS, Tannier E, Daubin V.

Proc Natl Acad Sci U S A. 2012 Oct 23;109(43):17513-8. doi: 10.1073/pnas.1202997109. Epub 2012 Oct 4.


The non-flagellar type III secretion system evolved from the bacterial flagellum and diversified into host-cell adapted systems.

Abby SS, Rocha EP.

PLoS Genet. 2012 Sep;8(9):e1002983. doi: 10.1371/journal.pgen.1002983. Epub 2012 Sep 27.


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

Nickerson NN, Abby SS, Rocha EP, Chami M, Pugsley AP.

J Bacteriol. 2012 Sep;194(18):4951-8. doi: 10.1128/JB.00798-12. Epub 2012 Jul 6.


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

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

Proc Natl Acad Sci U S A. 2012 Mar 27;109(13):4962-7. doi: 10.1073/pnas.1116871109. Epub 2012 Mar 13.


Immune subversion and quorum-sensing shape the variation in infectious dose among bacterial pathogens.

Gama JA, Abby SS, Vieira-Silva S, Dionisio F, Rocha EP.

PLoS Pathog. 2012 Feb;8(2):e1002503. doi: 10.1371/journal.ppat.1002503. Epub 2012 Feb 2.


Investment in rapid growth shapes the evolutionary rates of essential proteins.

Vieira-Silva S, Touchon M, Abby SS, Rocha EP.

Proc Natl Acad Sci U S A. 2011 Dec 13;108(50):20030-5. doi: 10.1073/pnas.1110972108. Epub 2011 Nov 30.


Detecting lateral gene transfers by statistical reconciliation of phylogenetic forests.

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

BMC Bioinformatics. 2010 Jun 15;11:324. doi: 10.1186/1471-2105-11-324.

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