Author
Listed by name: these papers carry no ORCID for this author, so different people with the same name may be mixed together.
12 papers
Recent·Most cited
M. Escalera-Zamudio, C. Tan, L. van Dorp, F. Balloux
The paper investigates the evolutionary origins of the BA.2.86 SARS-CoV-2 variant, finding it evolved through multiple transmission chains and recombination, not a single chronic infection.
bioRxiv · Jul 18, 2024 · PreprintEvolutionary Biology
M. N. Osnes, O. B. Brynildsrud, K. Alfsnes, L. van Dorp, S. A. McKeand, J. Ross, K. Town, J. De Korne-Elenbaas, A. van Dam, S. Bruisten, B. F. de Blasio, D. A. Caugant, Y. H. Grad, D. A. Williamson, F. Balloux, , V. Eldholm
This study reconstructs the global population dynamics of Neisseria gonorrhoeae using phylogenomic analysis, revealing expanding effective population size and distinct transmission patterns between Norway and Victoria, Australia.
bioRxiv · Aug 2, 2023 · PreprintMicrobiology
M. Milighetti, Y. Peng, C. C. S. Tan, M. Mark, G. Nageswaran, S. Byrne, T. Ronel, T. Peacock, A. Mayer, A. Chandran, J. Rosenheim, M. Wheelan, X. Yao, G. Liu, S. L. Felce, , B. Chain
The paper identifies high frequency naive T cell precursors that drive rapid T cell responses during early SARS-COV-2 and LCMV infections.
bioRxiv · Nov 8, 2022Immunology
S. Holtsmark Nielsen, L. van Dorp, C. J. Houldcroft, A. G. Pedersen, M. E. Allentoft, L. Vinner, A. Margaryan, E. Pavlova, V. Chasnyk, P. Nikolskiy, V. Pitulko, V. N. Pimenoff, F. Balloux, M. Sikora
The paper analyzes ancient virus genomes from 31,600-year-old human remains, showing that common childhood infections originated in the Pleistocene.
bioRxiv · Jun 28, 2021 · PreprintEvolutionary Biology
M. Acman, R. Wang, L. van Dorp, L. P. Shaw, Q. Wang, N. Luhmann, Y. Yuyao, S. Sun, H. Chen, H. Wang, F. Balloux
This study tracks the global spread of the carbapenem resistance gene blaNDM by analyzing genomic contexts and mobile genetic elements across 6000 bacterial genomes.
bioRxiv · Jan 14, 2021 · PreprintMicrobiology
F. Lassalle, S. M. M. Dastgheib, F.-J. Zhao, J. Zhang, S. Verbarg, A. Fruhling, H. Brinkmann, T. H. Osborne, J. Sikorski, F. Balloux, X. Didelot, J. M. Santini, J. Petersen
This paper reclassifies Pseudorhizobium species based on genomic analysis and identifies key functions for adaptation to extreme environments.
bioRxiv · Jul 3, 2020Microbiology
L. P. Shaw, A. D. Wang, D. Dylus, M. Meier, G. Pogacnik, C. Dessimoz, F. Balloux
The paper compiles a large host-pathogen association database and analyzes factors influencing host range and zoonotic potential across bacteria and viruses.
bioRxiv · Mar 21, 2020Ecology
L. P. Shaw, H. Bassam, C. P. Barnes, A. S. Walker, N. Klein, F. Balloux
The paper develops a quantitative stability landscape model to analyze microbiome recovery after antibiotics and finds support for long-term state transitions in gut and salivary microbiomes after ciprofloxacin and clindamycin.
bioRxiv · Mar 4, 2019Microbiology
L. P. Shaw, R. M. Doyle, E. Kavaliunaite, H. Spencer, F. Balloux, G. Dixon, K. A. Harris
This study finds that children with cystic fibrosis have multiple subpopulations of Mycobacterium abscessus with different antimicrobial resistance profiles, not all captured by sputum isolates.
bioRxiv · Oct 5, 2018Microbiology
R. Wang, L. van Dorp, L. Shaw, P. Bradley, Q. Wang, X. Wang, L. Jin, Q. Zhang, Y. Liu, A. Rieux, T. Dorai-Schneiders, L. A. Weinert, Z. Iqbal, X. Didelot, H. Wang, F. Balloux
The paper analyzes the global spread of the mcr-1 gene by sequencing isolates and phylogenetic analysis, finding all mcr-1 elements originated from a single mobilization event in the mid-2000s.
bioRxiv · Nov 17, 2017Microbiology
L. Shaw, A. L. R. Ribeiro, A. P. Levine, N. Pontikos, F. Balloux, A. W. Segal, A. P. Roberts, A. Smith
This study shows that shared environment, not genetics, shapes the oral microbiome in a large family, with household effects persisting even after individuals move out.
bioRxiv · Apr 26, 2017Microbiology