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Listed by name: these papers carry no ORCID for this author, so different people with the same name may be mixed together.
10 papers
Recent·Most cited
C. Yang, H. Qiu, S. L. Svensson, C. Ni, S. Gao, Z. Jia, H. Wen, L. Xie, W. Xu, Y. Qin, S. Lin, J. Wang, Y. Zhang, Y. Li, M. Jiang, , D. Falush
The paper investigates gene loss in Vibrio parahaemolyticus pandemic clones, showing it drives wave succession through environmental and transmission advantages.
Nature Ecology & Evolution · Aug 27, 2025Peer-reviewedMicrobiology
E. Tourrette, R. C. Torres, S. L. Svensson, T. Matsumoto, K. A. Fauzia, R. I. Alfaray, R.-K. Vilaichone, V. P. Tuan, HelicobacterGenomicsConsortium, D. Wang, L. Olsson, A. Yadegar, Z. Zhou, Y. Yamaoka, K. Thorell, D. Falush
The paper identifies a new ecospecies of Helicobacter pylori, 'Hardy', found in Indigenous populations and animal-adapted lineages, with distinct genetic features and evolutionary history.
bioRxiv · Apr 28, 2023 · PreprintMicrobiology
H. A. Thorpe, E. Tourrette, K. Yahara, F. F. Vale, S. Liu, M. Oleastro, T. Alarcon, T. Perets, S. Latifi-Navid, Y. Yamaoka, B. Martinez-Gonzalez, I. Karayiannis, T. Karamitros, D. Sgouras, W. Elamin, , D. Falush
This study shows H. pylori has spread repeatedly from Africa by replacing strains with deleterious mutations through migration and selection.
bioRxiv · Jun 5, 2021Evolutionary Biology
Y. You, K. Thorell, L. He, K. Yahara, Y. Yamaoka, J.-H. Cha, K. Murakami, Y. Katsura, TEAMHp, I. Kobayashi, D. Falush, J. Zhang
This study identifies genomic differentiation in Helicobacter pylori across East Asia, linking specific SNPs to cancer risk and geographic adaptation.
bioRxiv · Jun 5, 2021Microbiology
A. J. Taylor, K. Yahara, B. Pascoe, L. Mageiros, E. Mourkas, J. K. Calland, S. Puranen, M. D. Hitchings, K. A. Jolley, C. M. Kobras, S. C. Bayliss, N. J. Williams, A. H. van Vliet, J. Parkhill, M. C. Maiden, , S. K. Sheppard
The paper shows that recombination in bacteria can overcome genomic disharmony through a two-hit epistasis model, allowing beneficial gene combinations to be reinstated in new genetic backgrounds.
bioRxiv · Mar 15, 2021 · PreprintMicrobiology
Y. Cui, C. Yang, H. Qiu, H. Wang, R. Yang, D. Falush
The paper identifies coadapted genetic elements in Vibrio parahaemolyticus through genome-wide screening, revealing complex interactions and ecological strategies.
bioRxiv · Dec 3, 2019Microbiology
A. Criscuolo, S. Issenhuth-Jeanjean, X. Didelot, K. Thorell, J. Hale, J. Parkhill, N. Thomson, F.-X. Weill, D. Falush, S. Brisse
This study investigates the speciation and hybridization history of Salmonella, identifying eleven phylogroups and revealing complex hybridization events that challenge traditional speciation models.
bioRxiv · Apr 5, 2019Microbiology
C. Yang, Y. Cui, X. Didelot, R. Yang, D. Falush
The paper estimates recombination scaled effective population size in 21 bacterial species and finds only two show signs of panmixia, suggesting panmixia is unstable in bacteria.
bioRxiv · Jan 19, 2019 · PreprintMicrobiology
C. Yang, X. Pei, Y. Wu, L. Yan, Y. Yan, Y. Song, N. Coyle, J. Martinez-Urtaza, C. Quince, Q. Hu, M. Jiang, E. Feil, D. Yang, Y. Song, D. Zhou, , Y. Cui
The paper analyzes genomic data from 1,103 Vibrio parahaemolyticus isolates to show recent genetic mixing among four populations due to increased human-mediated dispersal.
bioRxiv · Jan 19, 2019Microbiology
M. Malinsky, E. Trucchi, D. Lawson, D. Falush
The paper introduces RADpainter and fineRADstructure to infer population structure from RADseq data, demonstrating their effectiveness with example datasets.
bioRxiv · Jun 16, 2016Evolutionary Biology