Shanghai Institute of Material Medical Chinese Academy of Sciences

Biography

Daniel Falush was graduated with his B.A. degree in statistical genetics from the University of Cambridge and received his Ph.D. degree in the University College London. He is an internationally recognized researcher in population genomics and computational biology, best known as a co-developer of the widely used STRUCTURE algorithm. His work combines theory and large-scale genomic data to uncover patterns of human evolution and microbial adaptation, with high-impact publications in Nature and Science.

Education

1991.06 B.A. Hons Mathematical Tripos, University of Cambridge

1998.06 Ph.D. Department of Biology, University College London

Work Experience：

2019.09 – Present Professor, Shanghai Institute of Materia Medica (Shanghai Institute of Immunity and Infection /Institut Pasteur of Shanghai), Chinese Academy of Sciences

2014.09 – 2019.08 MRC Senior Research Fellow, University of Swansea and University of Bath

2014.05 – 2014.07 Project Professor, University of Tokyo

2010.09 – 2014.08 Senior Scientist, Max Planck Institute for Evolutionary Anthropology, Leipzig

2008.01 – 2010.08 Senior Research Fellow, Department of Microbiology, University College Cork

2003.10 – 2007.09 Wellcome Trust Career Development Fellow, Department of Statistics, University of Oxford

2000.09 – 2003.09 Postdoctoral Researcher, Max Planck Institute for Infection Biology, Berlin

1998.10 – 2000.08 Japan Society for the Promotion of Science Fellow, Department of Mathematical Biology, Kyushu University

Research Directions

1. Coadaptive variation in recombinogenic bacteria

2. Study organisms: Helicobacter pylori and Vibrio parahaemolyticus

3. Statistical genetic analysis of coadaptation

4. Expanding genomic resources

5. Biomedical and ecological relevance

Grants & Research Projects

2024-2026 NSFC PGP RFIS-III RMB 3.92 Million

2022-2023 National Foreign Expert RMB 0.48 Million

2023 Shanghai Foreign Expert RMB 0.15Million

2022-2025 MOST RMB 3.25 Million

2022-2024 NSFC Japan RMB 0.2 Million

2022-2025 NSFC General RMB 0.58 Million

2014-2019 Named fellow, MRC CLIMB Consortium (to S Sheppard and M Pallen).

2008-2010 Named fellow, Science Foundation of Ireland (to M Achtman) €3m

2008-2012 Wellcome Trust Project Grant £287,000 (host P Green).

2003-2007 Wellcome Trust Research Career Development Fellowship £340,000

2004-2006 EPA Cephalosporin Junior Research Fellowship, Linacre College

1993-1997 Wellcome Trust Prize Studentship in Mathematical Biology £70,000

Achievements

1. Published more than 90 papers in leading journals including Nature and Science, with over 51,000 citations and an h-index of 60 (Google Scholar).

2. Developed several influential software tools in population genetics and statistical genomics including Chromopainter, fineSTRUCTURE, GLOBETROTTER, fineRADstructure, OrderedPaintin, badMIXTURE ClonalFrame, ClonalOrigin, SimMLST, Genoplast, STRUCTURE V2.0, METAPALETTE, LINEAGE.

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Social Titles

1. Associate editor of Molecular Biology and Evolution (2011 to present).

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Awards & Honors

1. Shanghai Magnolia Sliver Award

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Pubilcations

Selected Publications

1. Froschauer K, Svensson SL., Gelhausen R, Fiore E, Kible P, Klaude A, Kucklick M, Fuchs S, Eggenhofer F, Yang C, Falush D, Engelmann S, Backofen R & Sharma CM., Complementary Ribo-seq approaches map the translatome and provide a small protein census in the foodborne pathogen Campylobacter jejuni. Nat Commun 16, 3078 (2025).doi: https://doi.org/10.1038/s41467-025-58329-w. (SCI-E/PubMed)

2. Thorell K, Muñoz-Ramírez ZY, Wang D, Sandoval-Motta S, Boscolo Agostini R, Ghirotto S, Torres RC; HpGP Research Network; Falush D*, Camargo MC, Rabkin CS. The Helicobacter pylori Genome Project: insights into H. pylori population structure from analysis of a worldwide collection of complete genomes. Nature Communications, 14, 8184 (2023).doi: https://doi.org/10.1038/s41467-023-43562-y. (SCI-E/PubMed)

3.Thorpe HA, Tourrette E, Yahara K, Vale FF, Liu S, Oleastro M, Alarcon T, Perets TT, Latifi-Navid S, Yamaoka Y, Martinez-Gonzalez B, Karayiannis I, Karamitros T, Sgouras DN, Elamin W, Pascoe B, Sheppard SK, Ronkainen J, Aro P, Engstrand L, Agreus L, Suerbaum S, Thorell K, Falush D*. Repeated out-of-Africa expansions of Helicobacter pylori driven by replacement of deleterious mutations. Nature Communications, 6484(2022).doi: https://doi.org/10.1038/s41467-022-34475-3. (SCI-E/PubMed)

4.You Y, Thorell K, He L, Yahara K, Yamaoka Y, Cha J, Murakami K, Katsura Y, Kobayashi I, Falush D*, Zhang J. Genomic differentiation within East Asian Helicobacter pylori. Microbial genomics,8(2). (2022). doi:https://doi.org/10.1099/mgen.0.000676. (SCI-E/PubMed)

4. Calland, JK, Pascoe B, Bayliss SC, Mourkas E, Berthenet E, Thorpe HA, Hitchings MD, Feil EJ, Corander J, Blaser MJ, Falush D*, Sheppard SK. Quantifying bacterial evolution in the wild: a birthday problem for Campylobacter lineages. PLoS genetics, 17(9), e1009829. (2021). doi: https://doi.org/10.1371/journal.pgen.1009829. (SCI-E/PubMed)

5. Cui YJ, Yang, C, Qiu H, Wang H, Yang R, Falush D*. The landscape of coadaptation in Vibrio parahaemolyticus. Elife, 9, e54136. (2020).doi: https://doi.org/10.7554/eLife.54136. (SCI-E/PubMed)

6. Yang C, Pei X, Wu Y, Yan L, Yan Y, Song Y, Coyle NM, Martinez-Urtaza J, Quince C, Hu Q, Jiang M, Feil E, Yang D, Song Y, Zhou D, Yang R, Falush D*, Cui Y. Recent mixing of Vibrio parahaemolyticus populations. The ISME journal, 13(10), 2578-2588. (2019).doi: https://doi.org/10.1038/s41396-019-0461-5. (SCI-E/PubMed)

7.Criscuolo A, Issenhuth-Jeanjean S, Didelot X, Thorell K, Hale J, Parkhill J, Thomson NR, Weill FX, Falush D*, Brisse S. The speciation and hybridization history of the genus Salmonella. Microbial genomics, 5(8). (2019).doi: https://doi.org/10.1099/mgen.0.000284. (SCI-E/PubMed)

8.Yang C, Pei X, Wu Y, Yan L, Yan Y, Song Y, Coyle NM, Martinez-Urtaza J, Quince C, Hu Q, Jiang M, Feil E, Yang D, Song Y, Zhou D, Yang R, Falush D*, Cui Y. Recent mixing of Vibrio parahaemolyticus populations. The ISME journal, 13(10), 2578-2588. (2019).doi: https://doi.org/10.1038/s41396-019-0461-5. (SCI-E/PubMed)

9. Lawson D, van Dorp L, Falush D*. A tutorial on how not to overinterpret STRUCTURE or ADMIXTURE bareplots. Nature Communications 2018 9: 3258.doi: https://doi.org/10.1038/s41467-018-05257-7. (SCI-E/PubMed)

10. Berthenet E, Yahara K, Thorell K, Pascoe B, Meric G, Mikhail JM, Engstrand L, Enroth H, Burette A, Megraud F, Varon C, Atherton JC, Smith S, Wilkinson TS, Hitchings MD, Falush D*, Sheppard SK. A GWAS on Helicobacter pylori strains points to genetic variants associated with gastric cancer risk. BMC Biology 2018, 16:84.doi: https://doi.org/10.1186/s12915-018-0550-3.(SCI-E/PubMed)

11. Thorell K, Yahara K, Berthenet E, Lawson DJ, Mikhail J, Kato I, Mendez A, Rizzato C, Bravo MM, Suzuki R, Yamaoka Y, Torres J, Sheppard SK, Falush D*. Rapid evolution of distinct Helicobacter pylori subpopulations in the Americas. Plos Genetics. 2017;13(2).doi:https://doi.org/10.1371/journal.pgen.100654.6

(SCI-E/PubMed)

12. Yahara K, Didelot X, Jolley KA, Kobayashi I, Maiden MCJ, Sheppard SK, Falush D*. The Landscape of Realized Homologous Recombination in Pathogenic Bacteria. Molecular Biology and Evolution. 2016;33(2):456-71.doi: https://doi.org/10.1093/molbev/msv237. (SCI-E/PubMed)

13.Page AJ, Cummins CA, Hunt M, Wong VK, Reuter S, Holden MTG, Fookes M, Falush D, Keane JA, Parkhill J. Roary: rapid large-scale prokaryote pan genome analysis. Bioinformatics. 2015;31(22):3691-3.

Doi: https://doi.org/10.1093/bioinformatics/btv421. (SCI-E/PubMed)

13. Nell S, Eibach D, Montano V, Maady A, Nkwescheu A, Siri J, Elamin WF, Falush D, Linz B, Achtman M, Moodley Y, Suerbaum S. Recent Acquisition of Helicobacter pylori by Baka Pygmies. Plos Genetics. 2013;9(9).doi:https://doi.org/10.1371/journal.pgen.1003775. (SCI-E/PubMed)

13.Sheppard SK, Didelot X, Meric G, Torralbo A, Jolley KA, Kelly DJ, Bentley SD, Maiden MCJ, Parkhill J, Falush D*. Genome-wide association study identifies vitamin B-5 biosynthesis as a host specificity factor in Campylobacter. Proceedings of the National Academy of Sciences of the United States of America. 2013;110(29):11923-7.doi: https://doi.org/10.1073/pnas.1305559110. (SCI-E/PubMed)

14. Lawson DJ, Hellenthal G, Myers S, Falush D*. Inference of Population Structure using Dense Haplotype Data. Plos Genetics. 2012;8(1).doi: https://doi.org/10.1371/journal.pgen.1002453. (SCI-E/PubMed)

15.Didelot X, Bowden R, Street T, Golubchik T, Spencer C, McVean G, Sangal V, Anjum MF, Achtman M, Falush D, Donnelly P. Recombination and Population Structure in Salmonella enterica. Plos Genetics. 2011;7(7).doi: https://doi.org/10.1371/journal.pgen.1002191. (SCI-E/PubMed)

16.Didelot X, Lawson D, Darling A, Falush D. Inference of Homologous Recombination in Bacteria Using Whole-Genome Sequences. Genetics. 2010;186(4):1435-U567.doi: https://doi.org/10.1534/genetics.110.120121. (SCI-E/PubMed)

17.Didelot X, Achtman M, Parkhill J, Thomson NR, Falush D*. A bimodal pattern of relatedness between the Salmonella Paratyphi A and Typhi genomes: Convergence or divergence by homologous recombination? Genome Research. 2007;17(1):61-8.doi: http://www.genome.org/cgi/doi/10.1101/gr.5512906. (SCI-E/PubMed)

18.Harter AV, Gardner KA, Falush D, Lentz DL, Bye RA, Rieseberg LH. Origin of extant domesticated sunflowers in eastern North America. Nature. 2004;430(6996):201-5.doi:https://doi.org/10.1038/nature02

710. (SCI-E/PubMed)

19.Falush D, Stephens M, Pritchard JK. Inference of population structure using multilocus genotype data: Linked loci and correlated allele frequencies. Genetics. 2003;164(4):1567-87.doi: https://doi.org/10.1

093/genetics/164.4.1567. (SCI-E/PubMed)

20.Falush D, Kraft C, Taylor NS, Correa P, Fox JG, Achtman M, Suerbaum S. Recombination and mutation during long-term gastric colonization by Helicobacter pylori: Estimates of clock rates, recombination size, and minimal age. Proceedings of the National Academy of Sciences of the United States of America. 2001;98(26):15056-doi:https://doi.org/10.1073/pnas.251396098. (SCI-E/PubMed)

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