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Martinez-Hernandez F, Diop A, Garcia-Heredia I, Bobay LM, Martinez-Garcia M. Unexpected myriad of co-occurring strains in one of the most abundant and microdiverse viral populations on Earth. ISME J (in press).

Stott CM, Bobay LM. Impact of homologous recombination on core genome phylogenies. BMC Genomics. 2020; 21:1-10.


Buton A, Bobay LM. Evolution of Chi motifs in Proteobacteria. G3 (bethesda). 2021; 11:jkaa054.

Harris CD, Torrance EL, Raymann K, Bobay LM. CoreCruncher: fast and robust construction of core genomes in large prokaryotic datasets. Molecular Biology and Evolution. Mol Biol Evol. 2020; 38:727-734.


Bobay LM, Wissel EF, Raymann K. Strain Structure and Dynamics Revealed by Targeted Deep Sequencing of the Honey Bee Gut Microbiome. mSphere. 2020; 5 (4).

Bobay LM. CoreSimul: a forward-in-time simulator of genome evolution for prokaryotes modeling homologous recombination. BMC Bioinformatics. 2020; 21:1-7.

Bobay LM. The prokaryotic species concept and challenges. The Pangenome. 2020. 21-49

Bobay LM, Raymann K. Population genetics of host-associated microbiomes. Curr Mol Biol Rep. 2019; 5:128-139. doi: 10.1007/s40610-019-00122-y.

Bobay LM, Ochman H. Factors driving effective population size and pan-genome evolution in bacteria. BMC Evol Biol. 2018; 18:153.

Bobay LM, Ochman H. Biological species in the viral world. Proc Natl Acad Sci U S A. 2018; 115:6040-6045.

Bobay LM, Ellis BS, Ochman H. ConSpeciFix: Classifying prokaryotic species based on gene flow. Bioinformatics. 2018. doi: 10.1093/bioinformatics/bty400.


Raymann K*, Bobay LM*, Moran NA. Antibiotics reduce genetic diversity of core species in the honeybee gut microbiome. Molecular ecology. 2017; 27:2057-2066.


Bobay LM, Ochman H. Impact of recombination on the base composition of Bacteria and Archaea. Molecular biology and evolution. 2017; 34:2627-2636.


Bobay LM, Ochman H. Biological species are universal across Life’s domains. Genome biology and evolution. 2017; 9:491-501.


Bobay LM, Ochman H. The Evolution of Bacterial Genome Architecture. Frontiers in genetics. 2017; 8:72.


Wexler AG, Bao Y, Whitney JC, Bobay LM, Xavier JB, Schofield WB, Barry NA, Russell AB, Tran BQ, Goo YA, Goodlett DR, Ochman H, Mougous JD, Goodman AL. Human symbionts inject and neutralize antibacterial toxins to persist in the gut. Proceedings of the National Academy of Sciences USA. 2016; 13:3639-44.


Douam F*, Bobay LM*, Maurin G, Fresquet J, Calland N, Maisse C, Durand T, Cosset FL, Féray C, Lavillette D. Specialization of hepatitis C virus envelope glycoproteins for B-lymphocytes in chronically infected patients. Journal of Virology. 2015; 90:992-1008.


Bobay LM, Traverse CC, Ochman H. Impermance of bacterial clones. Proceedings of the National Academy of Sciences USA 2015; 112:8893-900.


Henry M, Bobay LM, Chevallereau A, Saussereau E, Ceyssens PJ, Debarbieux L. The search for therapeutic bacteriophages uncovers one new subfamily and two new genera of Pseudomonas-infecting Myoviridae. PLoS One. 2015; 10:e0117163.


Touchon M, Bobay LM, Rocha EP. The chromosomal accomodation and domestication of mobile genetic elements. Current Opinion in Microbiology. 2014; 22:22-29.


Bobay LM, Touchon M, Rocha EP. Pervasive domestication of defective prophages by bacteria. Proceedings of the National Academy of Sciences USA 2014; 111:12127-12132.


Bobay LM, Touchon M, Rocha EP. Manipulating or superseding host recombination functions: a dilemma that shapes phage evolvability. PLoS Genetics. 2013; 9: e1003825.


Raymann K, Bobay LM, Doak TG, Lynch M, Gribaldo S. A genomic survey of reb homologs suggests widespread occurrence of R-bodies in proteobacteria. G3 (Bethesda). 2013; 3:505-16.


Bobay LM, Rocha EP, Touchon M. The adaptation of temperate bacteriophages to their host genomes. Molecular Biology and Evolution. 2013; 30:737-751.


Deghorain M, Bobay LM, Smeesters PR, Bousbata S, Vermeersch M, Perez-Morga D, Drèze PA,

Rocha EP, Touchon M, Van Melderen L. Characterization of novel phages isolated in coagulase-negative staphylococci reveals evolutionary relationships with Staphylococcus aureus phages. Journal of Bacteriology. 2012; 194:5829-39.


Lynch M, Bobay LM, Catania F, Gout JF, Rho M. The repatterning of eukaryotic genomes by random genetic drift. Annual Reviews of Genomics and Human Genetics. 2011; 12:347-66.


* These authors contributed equally to this work

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