Louis-Marie Jean Fabrice Bobay

MetaStrainer: Accurate reconstruction of bacterial strain genotypes from short-read metagenomic samples.

Sharaf, H., & Bobay, L.-M. (2026, March 3).

Prevalence and Evolutionary Implications of Genome Rearrangements in Bacteria

Martinez-Gutierrez, C. A., Huang, Y., & Bobay, L.-M. (2026, January 14). (R. Hershberg, Ed.). Genome Biology and Evolution.

Co-occurrence is associated with horizontal gene transfer across marine bacteria independent of phylogeny

Douglas, G. M., Tromas, N., Gaudin, M., Lypaczewski, P., Bobay, L.-M., Shapiro, B. J., & Chaffron, S. (2025, March 28).

Co-occurrence is associated with horizontal gene transfer across marine bacteria independent of phylogeny

Douglas, G. M., Tromas, N., Gaudin, M., Lypaczewski, P., Bobay, L.-M., Shapiro, B. J., & Chaffron, S. (2025, December 10). The ISME Journal.

Introgression impacts the evolution of bacteria, but species borders are rarely fuzzy

Diop, A., Douglas, G. M., & Bobay, L.-M. (2025, November 13). Nature Communications.

MetaStrainer: Accurate reconstruction of bacterial strain genotypes from short-read metagenomic samples.

Sharaf, H., & Bobay, L.-M. (2025, December 9). Zenodo (CERN European Organization for Nuclear Research).

MetaStrainer: Accurate reconstruction of bacterial strain genotypes from short-read metagenomic samples.

Sharaf, H., & Bobay, L.-M. (2025, December 9). Zenodo (CERN European Organization for Nuclear Research).

Co-evolution and Gene Transfers Drive Speciation Patterns in Host-Associated Bacteria

Stott, C., Diop, A., Raymann, K., & Bobay, L.-M. (2024, December 1). (H. Hendrickson, Ed.). Molecular Biology and Evolution, Vol. 41.

Evolution of homologous recombination rates across bacteria

Torrance, E. L., Burton, C., Diop, A., & Bobay, L.-M. (2024, April 24). Proceedings of the National Academy of Sciences, Vol. 121.

Evolution of homologous recombination rates across bacteria

Proceedings of the National Academy of Sciences, 121(18), e2316302121.

Homologous Recombination Shapes the Architecture and Evolution of Bacterial Genomes

Torrance, E. L., Diop, A., & Bobay, L.-M. (2024, June 3).

Homologous recombination shapes the architecture and evolution of bacterial genomes

Torrance, E. L., Diop, A., & Bobay, L.-M. (2024, December 11). Nucleic Acids Research.

Introgression impacts the evolution of bacteria, but species borders are rarely fuzzy

Diop, A., & Bobay, L.-M. (2024, May 9).

Prevalence and Dynamics of Genome Rearrangements in Bacteria and Archaea

Martinez-Gutierrez, C. A., & Bobay, L.-M. (2024, October 5).

Tractidigestivibacter montrealensis sp. nov., a new member of human gut microbiota isolated from a healthy volunteer

FEMS Microbiology Letters, 370.

Gene flow and introgression are pervasive forces shaping the evolution of bacterial species

Genome Biology, 23(1).

Genome-wide transcriptome analysis of the orphan crop tef (Eragrostis tef (Zucc.) Trotter) under long-term low calcium stress

Scientific Reports, 12(1).

Correction to: Unexpected myriad of co-occurring viral strains and species in one of the most abundant and microdiverse viruses on Earth

Martinez-Hernandez, F., Diop, A., Garcia-Heredia, I., Bobay, L.-M., & Martinez-Garcia, M. (2021, December 24). The ISME Journal, Vol. 16, pp. 1199–1199.

Evolution of Chi motifs in Proteobacteria

Buton, A., & Bobay, L.-M. (2021, January 1). (M. Zetka, Ed.). G3 Genes Genomes Genetics, Vol. 11, pp. 1–7.

Unexpected myriad of co-occurring viral strains and species in one of the most abundant and microdiverse viruses on Earth

The ISME Journal, 16(4), 1025–1035.

CoreCruncher: Fast and Robust Construction of Core Genomes in Large Prokaryotic Data Sets

Molecular Biology and Evolution, 38(2), 727–734.

CoreSimul: a forward-in-time simulator of genome evolution for prokaryotes modeling homologous recombination

Bobay, L.-M. (2020, June 24). BMC Bioinformatics, Vol. 21.

Evolution of Chi motifs in Proteobacteria

Buton, A., & Bobay, L.-M. (2020, August 14). BioRxiv (Cold Spring Harbor Laboratory).

Impact of homologous recombination on core genome phylogenies

Stott, C. M., & Bobay, L.-M. (2020, December 2). Research Square (Research Square).

Impact of homologous recombination on core genome phylogenies

Stott, C. M., & Bobay, L.-M. (2020, June 8).

Impact of homologous recombination on core genome phylogenies

BMC Genomics, 21(1).

Recombination events are concentrated in the spike protein region of Betacoronaviruses

Bobay, L.-M., O’Donnell, A. C., & Ochman, H. (2020, December 17). (H. Tang, Ed.). PLoS Genetics, Vol. 16, p. e1009272.

Strain Structure and Dynamics Revealed by Targeted Deep Sequencing of the Honey Bee Gut Microbiome

MSphere, 5(4).

The Prokaryotic Species Concept and Challenges

Population Genetics of Host-Associated Microbiomes

Current Molecular Biology Reports, 5(3), 128–139.

Biological species in the viral world

Bobay, L.-M., & Ochman, H. (2018, May 21). Proceedings of the National Academy of Sciences, Vol. 115, pp. 6040–6045.

ConSpeciFix: classifying prokaryotic species based on gene flow

Bioinformatics, 34(21), 3738–3740.

Factors driving effective population size and pan-genome evolution in bacteria

Bobay, L.-M., & Ochman, H. (2018, October 12). BMC Evolutionary Biology, Vol. 18.

Heredity: A Very Short Introduction

Bobay, L.-M. (2018, August 17). Journal of Mammalogy, Vol. 9.

Antibiotics reduce genetic diversity of core species in the honeybee gut microbiome

Molecular Ecology, 27(8), 2057–2066.

Biological Species Are Universal across Life’s Domains

Genome Biology and Evolution, 9(3), 491–501.

Impact of Recombination on the Base Composition of Bacteria and Archaea

Molecular Biology and Evolution, 34(10), 2627–2636.

The Evolution of Bacterial Genome Architecture

Frontiers in Genetics, 8.

Human symbionts inject and neutralize antibacterial toxins to persist in the gut

Proceedings of the National Academy of Sciences, 113(13), 3639–3644.

Impermanence of bacterial clones

Proceedings of the National Academy of Sciences, 112(29), 8893–8900.

Specialization of Hepatitis C Virus Envelope Glycoproteins for B Lymphocytes in Chronically Infected Patients

Journal of Virology, 90(2), 992–1008.

The Search for Therapeutic Bacteriophages Uncovers One New Subfamily and Two New Genera of Pseudomonas-Infecting Myoviridae

PLOS ONE, 10(1), e0117163.

Pervasive domestication of defective prophages by bacteria

Proceedings of the National Academy of Sciences, 111(33), 12127–12132.

The chromosomal accommodation and domestication of mobile genetic elements

Current Opinion in Microbiology, 22, 22–29.

A Genomic Survey of Reb Homologs Suggests Widespread Occurrence of R-Bodies in Proteobacteria

G3 Genes|Genomes|Genetics, 3(3), 505–516.

Manipulating or Superseding Host Recombination Functions: A Dilemma That Shapes Phage Evolvability

PLoS Genetics, 9(9), e1003825.

Characterization of Novel Phages Isolated in Coagulase-Negative Staphylococci Reveals Evolutionary Relationships with Staphylococcus aureus Phages

Journal of Bacteriology, 194(21), 5829–5839.

The Adaptation of Temperate Bacteriophages to Their Host Genomes

Molecular Biology and Evolution, 30(4), 737–751.

The Repatterning of Eukaryotic Genomes by Random Genetic Drift

Annual Review of Genomics and Human Genetics, 12(1), 347–366.

L'évolution c'est tout simple!

Paris: Vuibert.