Browse by UCL people
Group by: Type | Date
Number of items: 76.
2025
Marshall, AF;
Balloux, F;
Brown, L;
Flach, E;
Richardson, A;
Steeves, TE;
Spiro, S;
... Brekke, P; + view all
(2025)
True fertilisation failure in captivity is rare.
Global Ecology and Conservation
, 61
, Article e03687. 10.1016/j.gecco.2025.e03687.
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2024
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Kepp, Kasper P;
Aavitsland, Preben;
Ballin, Marcel;
Balloux, Francois;
Baral, Stefan;
Bardosh, Kevin;
Bauchner, Howard;
... Ioannidis, John PA; + view all
(2024)
Panel stacking is a threat to consensus statement validity.
Journal of Clinical Epidemiology
, 173
, Article 111428. 10.1016/j.jclinepi.2024.111428.
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Nimmo, Camus;
Ortiz, Arturo Torres;
Tan, Cedric CS;
Pang, Juanita;
Acman, Mislav;
Millard, James;
Padayatchi, Nesri;
... van Dorp, Lucy; + view all
(2024)
Detection of a historic reservoir of bedaquiline/clofazimine resistance-associated variants in Mycobacterium tuberculosis.
Genome Medicine
, 16
(1)
, Article 34. 10.1186/s13073-024-01289-5.
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Tan, Cedric CS;
van Dorp, Lucy;
Balloux, Francois;
(2024)
The evolutionary drivers and correlates of viral host jumps.
Nature Ecology & Evolution
10.1038/s41559-024-02353-4.
(In press).
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Wang, Ruobing;
Zhang, Anru;
Sun, Shijun;
Yin, Guankun;
Wu, Xingyu;
Ding, Qi;
Wang, Qi;
... Wang, Hui; + view all
(2024)
Increase in antioxidant capacity associated with the successful subclone of hypervirulent carbapenem-resistant Klebsiella pneumoniae ST11-KL64.
Nature Communications
, 15
, Article 67. 10.1038/s41467-023-44351-3.
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2023
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Kuchipudi, Suresh V;
Tan, Cedric;
van Dorp, Lucy;
Lichtveld, Maureen;
Pickering, Bradley;
Bowman, Jeff;
Mubareka, Samira;
(2023)
Coordinated surveillance is essential to monitor and mitigate the evolutionary impacts of SARS-CoV-2 spillover and circulation in animal hosts.
Nature Ecology and Evolution
, 7
pp. 956-959.
10.1038/s41559-023-02082-0.
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Marshall, Ashleigh F;
Balloux, François;
Hemmings, Nicola;
Brekke, Patricia;
(2023)
Systematic review of avian hatching failure and implications for conservation.
Biological Reviews
10.1111/brv.12931.
(In press).
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Tan, Cedric CS;
Trew, Jahcub;
Peacock, Thomas P;
Mok, Kai Yi;
Hart, Charlie;
Lau, Kelvin;
Ni, Dongchun;
... Savolainen, Vincent; + view all
(2023)
Genomic screening of 16 UK native bat species through conservationist networks uncovers coronaviruses with zoonotic potential.
Nature Communications
, 14
(1)
, Article 3322. 10.1038/s41467-023-38717-w.
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Van Dorp, Lucy;
Nimmo, Camus;
Ortiz, Arturo Torres;
Pang, Juanita;
Acman, Mislav;
Tan, Cedric CS;
Millard, James;
... Balloux, François; + view all
(2023)
Detection of a reservoir of bedaquiline / clofazimine resistance associated variants in Mycobacterium tuberculosis predating the antibiotic era.
BioRxiv: Cold Spring Harbor, NY, USA.
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2022
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Acman, Mislav;
Wang, Ruobing;
van Dorp, Lucy;
Shaw, Liam P;
Wang, Qi;
Luhmann, Nina;
Yin, Yuyao;
... Balloux, Francois; + view all
(2022)
Role of mobile genetic elements in the global dissemination of the carbapenem resistance gene blaNDM.
Nature Communications
, 13
(1)
, Article 1131. 10.1038/s41467-022-28819-2.
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Balloux, François;
Tan, Cedric;
Swadling, Leo;
Richard, Damien;
Jenner, Charlotte;
Maini, Mala;
van Dorp, Lucy;
(2022)
The past, current and future epidemiological dynamic of SARS-CoV-2.
Oxford Open Immunology
, 3
(1)
, Article iqac003. 10.1093/oxfimm/iqac003.
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Ford, CE;
Brookes, LM;
Skelly, E;
Sergeant, C;
Jordine, T;
Balloux, F;
Nichols, RA;
(2022)
Non-Lethal Detection of Frog Virus 3-Like (RUK13) and Common Midwife Toad Virus-Like (PDE18) Ranaviruses in Two UK-Native Amphibian Species.
Viruses
, 14
(12)
, Article 2635. 10.3390/v14122635.
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Gopalakrishnan, Shyam;
Ebenesersdóttir, S Sunna;
Lundstrøm, Inge KC;
Turner-Walker, Gordon;
Moore, Kristjan HS;
Luisi, Pierre;
Margaryan, Ashot;
... Gilbert, M Thomas P; + view all
(2022)
The population genomic legacy of the second plague pandemic.
Current Biology
10.1016/j.cub.2022.09.023.
(In press).
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Swadling, L;
Diniz, MO;
Schmidt, NM;
Amin, OE;
Chandran, A;
Shaw, E;
Pade, C;
... Maini, MK; + view all
(2022)
Pre-existing polymerase-specific T cells expand in abortive seronegative SARS-CoV-2.
Nature
, 601
pp. 110-117.
10.1038/s41586-021-04186-8.
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Tan, Cedric CS;
Lam, Su Datt;
Richard, Damien;
Owen, Christopher J;
Berchtold, Dorothea;
Orengo, Christine;
Nair, Meera Surendran;
... Balloux, François; + view all
(2022)
Transmission of SARS-CoV-2 from humans to animals and potential host adaptation.
Nature Communications
, 13
(1)
, Article 2988. 10.1038/s41467-022-30698-6.
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2021
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Chen, H;
Yin, Y;
van Dorp, L;
Shaw, LP;
Gao, H;
Acman, M;
Yuan, J;
... Balloux, F; + view all
(2021)
Drivers of methicillin-resistant Staphylococcus aureus (MRSA) lineage replacement in China.
Genome Medicine
, 13
, Article 171. 10.1186/s13073-021-00992-x.
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de-Dios, T;
Carrión, P;
Olalde, I;
Llovera Nadal, L;
Lizano, E;
Pàmies, D;
Marques-Bonet, T;
... Lalueza-Fox, C; + view all
(2021)
Salmonella enterica from a soldier from the 1652 siege of Barcelona (Spain) supports historical transatlantic epidemic contacts.
iScience
, 24
(9)
, Article 103021. 10.1016/j.isci.2021.103021.
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Lassalle, F;
Dastgheib, SMM;
Zhao, F-J;
Zhang, J;
Verbarg, S;
Frühling, A;
Brinkmann, H;
... Petersen, J; + view all
(2021)
Phylogenomics reveals the basis of adaptation of Pseudorhizobium species to extreme environments and supports a taxonomic revision of the genus.
Systematic and Applied Microbiology
, 44
(1)
, Article 126165. 10.1016/j.syapm.2020.126165.
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Qutob, N;
Salah, Z;
Richard, D;
Darwish, H;
Sallam, H;
Shtayeh, I;
Najjar, O;
... van Dorp, L; + view all
(2021)
Genomic epidemiology of the first epidemic wave of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) in Palestine.
Microbial Genomics
, 7
(6)
, Article 000584. 10.1099/mgen.0.000584.
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Richard, D;
Pruvost, O;
Balloux, F;
Boyer, C;
Rieux, A;
Lefeuvre, P;
(2021)
Time-calibrated genomic evolution of a monomorphic bacterium during its establishment as an endemic crop pathogen.
Molecular Ecology
, 30
(8)
pp. 1823-1835.
10.1111/mec.15770.
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Tan, CCS;
Acman, M;
van Dorp, L;
Balloux, F;
(2021)
Metagenomic evidence for a polymicrobial signature of sepsis.
Microbial Genomics
, 7
(9)
10.1099/mgen.0.000642.
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Tan, CCS;
Owen, CJ;
Tham, CYL;
Bertoletti, A;
van Dorp, L;
Balloux, F;
(2021)
Pre-existing T cell-mediated cross-reactivity to SARS-CoV-2 cannot solely be explained by prior exposure to endemic human coronaviruses.
Infection, Genetics and Evolution
, 95
, Article 105075. 10.1016/j.meegid.2021.105075.
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Torres Ortiz, A;
Coronel, J;
Vidal, JR;
Bonilla, C;
Moore, DAJ;
Gilman, RH;
Balloux, F;
... Grandjean, L; + view all
(2021)
Genomic signatures of pre-resistance in Mycobacterium tuberculosis.
Nature Communications
, 12
, Article 7312. 10.1038/s41467-021-27616-7.
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van Dorp, L;
Houldcroft, CJ;
Richard, D;
Balloux, F;
(2021)
COVID-19, the first pandemic in the post-genomic era.
Current Opinion in Virology
10.1016/j.coviro.2021.07.002.
(In press).
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White, AE;
De-Dios, T;
Carrión, P;
Bonora, GL;
Llovera, L;
Cilli, E;
Lizano, E;
... Lalueza-Fox, C; + view all
(2021)
Genomic Analysis of 18th-Century Kazakh Individuals and Their Oral Microbiome.
Biology
, 10
(12)
, Article 1324. 10.3390/biology10121324.
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2020
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Acman, M;
Van Dorp, L;
Santini, JM;
Balloux, F;
(2020)
Large-scale network analysis captures biological features of bacterial plasmids.
Nature Communications
, 11
, Article 2452. 10.1038/s41467-020-16282-w.
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Bharucha, T;
Oeser, C;
Balloux, F;
Brown, JR;
Carbo, EC;
Charlett, A;
Chiu, CY;
... Field, N; + view all
(2020)
STROBE-metagenomics: a STROBE extension statement to guide the reporting of metagenomics studies.
Lancet Infectious Diseases
, 20
(10)
E251-E260.
10.1016/S1473-3099(20)30199-7.
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Curtis, D;
Balloux, F;
(2020)
Editorial: Topical ethical issues in the publication of human genetics research.
Annals of Human Genetics
, 84
(4)
pp. 313-314.
10.1111/ahg.12382.
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De-Dios, T;
Van Dorp, L;
Charlier, P;
Morfopoulou, S;
Lizano, E;
Bon, C;
Le Bitouzé, C;
... Lalueza-Fox, C; + view all
(2020)
Metagenomic analysis of a blood stain from the French revolutionary Jean-Paul Marat (1743–1793).
Infection, Genetics and Evolution
, 80
, Article 104209. 10.1016/j.meegid.2020.104209.
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Grandjean, L;
Johana, M;
Robert, G;
gilman, R;
paudshcart, J;
rokadiya, S;
bonilla, C;
... Balloux, F; + view all
(2020)
Association Between Bacterial Homoplastic Variants and Radiological Pathology in Tuberculosis.
Thorax
, 75
(7)
pp. 584-591.
10.1136/thoraxjnl-2019-213281.
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Nimmo, C;
Brien, K;
Millard, J;
Grant, AD;
Padayatchi, N;
Pym, AS;
O'Donnell, M;
... Balloux, F; + view all
(2020)
Dynamics of within-host Mycobacterium tuberculosis diversity and heteroresistance during treatment.
EBioMedicine
, 55
, Article 102747. 10.1016/j.ebiom.2020.102747.
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Nimmo, C;
Millard, J;
Brien, K;
Moodley, S;
van Dorp, L;
Lutchminarain, K;
Wolf, A;
... O'Donnell, M; + view all
(2020)
Bedaquiline resistance in drug-resistant tuberculosis HIV co-infected patients.
[Letter].
European Respiratory Journal
, 55
(6)
, Article 1902383. 10.1183/13993003.02383-2019.
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Nimmo, C;
Millard, J;
van Dorp, L;
Brien, K;
Moodley, S;
Wolf, A;
Grant, AD;
... O'Donnell, M; + view all
(2020)
Population-level emergence of bedaquiline and clofazimine resistance-associated variants among patients with drug-resistant tuberculosis in southern Africa: a phenotypic and phylogenetic analysis.
The Lancet Microbe
, 1
(4)
e165-e174.
10.1016/S2666-5247(20)30031-8.
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Osnes, MN;
Van Dorp, L;
Brynildsrud, OB;
Alfsnes, K;
Schneiders, T;
Templeton, KE;
Yahara, K;
... Eldholm, V; + view all
(2020)
Antibiotic Treatment Regimes as a Driver of the Global Population Dynamics of a Major Gonorrhea Lineage.
Molecular Biology and Evolution
, Article msaa282. 10.1093/molbev/msaa282.
(In press).
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Shaw, LP;
Wang, AD;
Dylus, D;
Meier, M;
Pogacnik, G;
Dessimoz, C;
Balloux, F;
(2020)
The phylogenetic range of bacterial and viral pathogens of vertebrates.
Molecular Ecology
, 29
(17)
pp. 3361-3379.
10.1111/mec.15463.
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van Dorp, L;
Acman, M;
Richard, D;
Shaw, LP;
Ford, CE;
Ormond, L;
Owen, CJ;
... Balloux, F; + view all
(2020)
Emergence of genomic diversity and recurrent mutations in SARS-CoV-2.
Infection, Genetics and Evolution
, 83
, Article 104351. 10.1016/j.meegid.2020.104351.
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Van Dorp, L;
Richard, D;
Tan, CCS;
Shaw, LP;
Acman, M;
Balloux, F;
(2020)
No evidence for increased transmissibility from recurrent mutations in SARS-CoV-2.
Nature Communications
, 11
, Article 5986. 10.1038/s41467-020-19818-2.
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2019
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de-Dios, T;
van Dorp, L;
Gelabert, P;
Carøe, C;
Sandoval-Velasco, M;
Fregel, R;
Escosa, R;
... Lalueza-Fox, C; + view all
(2019)
Genetic affinities of an eradicated European Plasmodium falciparum strain.
Microbial Genomics
10.1099/mgen.0.000289.
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Farrer, RA;
Chang, M;
Davis, MJ;
van Dorp, L;
Yang, D-H;
Shea, T;
Sewell, TR;
... Kwon-Chung, KJ; + view all
(2019)
A New Lineage of Cryptococcus gattii (VGV) Discovered in the Central Zambezian Miombo Woodlands.
MBio
, 10
(6)
, Article e02306-19. 10.1128/mBio.02306-19.
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Nimmo, C;
Shaw, LP;
Doyle, R;
Williams, R;
Brien, K;
Burgess, C;
Breuer, J;
... Pym, AS; + view all
(2019)
Whole genome sequencing Mycobacterium tuberculosis directly from sputum identifies more genetic diversity than sequencing from culture.
BMC Genomics
, 20
(1)
, Article 389. 10.1186/s12864-019-5782-2.
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Price, S;
Leung, W;
Owen, C;
Puschendorf, R;
Sergeant, C;
Cunningham, A;
Balloux, F;
... Nichols, R; + view all
(2019)
Effects of historic and projected climate change on the range and impacts of an emerging wildlife disease.
Global Change Biology
, 25
(8)
pp. 2648-2660.
10.1111/gcb.14651.
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Shaw, LP;
Doyle, RM;
Kavaliunaite, E;
Spencer, H;
Balloux, F;
Dixon, G;
Harris, KA;
(2019)
Children With Cystic Fibrosis Are Infected With Multiple Subpopulations of Mycobacterium abscessus With Different Antimicrobial Resistance Profiles.
Clinical Infectious Diseases
, 69
(10)
pp. 1678-1686.
10.1093/cid/ciz069.
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Shaw, LP;
Bassam, H;
Barnes, CP;
Walker, AS;
Klein, N;
Balloux, F;
(2019)
Modelling microbiome recovery after antibiotics using a stability landscape framework.
The ISME Journal
, 13
(7)
pp. 1845-1856.
10.1038/s41396-019-0392-1.
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van Dorp, L;
Gelabert, P;
Rieux, A;
de Manuel, M;
de-Dios, T;
Gopalakrishnan, S;
Carøe, C;
... Lalueza-Fox, C; + view all
(2019)
Plasmodium vivax Malaria viewed through the lens of an eradicated European strain.
Molecular Biology and Evolution
10.1093/molbev/msz264.
(In press).
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van Dorp, L;
Wang, Q;
Shaw, LP;
Acman, M;
Brynildsrud, OB;
Eldholm, V;
Wang, R;
... Wang, H; + view all
(2019)
Rapid phenotypic evolution in multidrug-resistant Klebsiella pneumoniae hospital outbreak strains.
Microbial Genomics
10.1099/mgen.0.000263.
(In press).
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Wegner, F;
Lassalle, F;
Depledge, DP;
Balloux, F;
Breuer, J;
(2019)
Co-evolution of sites under immune selection shapes Epstein-Barr Virus population structure.
Molecular Biology and Evolution
10.1093/molbev/msz152.
(In press).
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2018
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Balloux, F;
Brønstad Brynildsrud, O;
van Dorp, L;
Shaw, LP;
Chen, H;
Harris, KA;
Wang, H;
(2018)
From Theory to Practice: Translating Whole-Genome Sequencing (WGS) into the Clinic.
Trends in Microbiology
, 26
(12)
pp. 1035-1048.
10.1016/j.tim.2018.08.004.
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Brynildsrud, OB;
Pepperell, CS;
Suffys, P;
Grandjean, L;
Monteserin, J;
Debech, N;
Bohlin, J;
... Eldholm, V; + view all
(2018)
Global Expansion of Mycobacterium Tuberculosis Lineage 4 Shaped by Colonial Migration and Local Adaptation.
Science Advances
, 4
(10)
, Article eaat5869. 10.1126/sciadv.aat5869.
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Farrer, RA;
Ford, CB;
Rhodes, J;
Delorey, T;
May, RC;
Fisher, MC;
Cloutman-Green, E;
... Cuomo, CA; + view all
(2018)
Transcriptional Heterogeneity of Cryptococcus gattii VGII Compared with Non-VGII Lineages Underpins Key Pathogenicity Pathways.
mSphere
, 3
(5)
, Article e00445-18. 10.1128/mSphere.00445-18.
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Lassalle, F;
Spagnoletti, M;
Fumagalli, M;
Shaw, L;
Dyble, M;
Walker, C;
Thomas, MG;
... Balloux, F; + view all
(2018)
Oral microbiomes from hunter-gatherers and traditional farmers reveal shifts in commensal balance and pathogen load linked to diet.
Molecular Ecology
, 27
(1)
pp. 182-195.
10.1111/mec.14435.
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O'Hanlon, SJ;
Rieux, A;
Farrer, RA;
Rosa, GM;
Waldman, B;
Bataille, A;
Kosch, TA;
... Fisher, MC; + view all
(2018)
Recent Asian origin of chytrid fungi causing global amphibian declines.
Science
, 360
(6389)
pp. 621-627.
10.1126/science.aar1965.
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Wang, R;
van Dorp, L;
Shaw, LP;
Bradley, P;
Wang, Q;
Wang, X;
Jin, L;
... Balloux, F; + view all
(2018)
The global distribution and spread of the mobilized colistin resistance gene mcr-1.
Nat Commun
, 9
, Article 1179. 10.1038/s41467-018-03205-z.
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2017
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Balloux, F;
van Dorp, L;
(2017)
Q&A: What are pathogens, and what have they done to and for us?
BMC Biology
, 15
, Article 91. 10.1186/s12915-017-0433-z.
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Jeffares, DC;
Jolly, C;
Hoti, M;
Speed, D;
Shaw, L;
Rallis, C;
Balloux, F;
... Sedlazeck, FJ; + view all
(2017)
Transient structural variations have strong effects on quantitative traits and reproductive isolation in fission yeast.
Nature Communications
, 8
, Article 14061. 10.1038/ncomms14061.
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Leung, WTM;
Thomas-Walters, L;
Garner, TWJ;
Balloux, F;
Durrant, C;
Price, SJ;
(2017)
A quantitative-PCR based method to estimate ranavirus viral load following normalisation by reference to an ultraconserved vertebrate target.
Journal of Virological Methods
, 249
pp. 147-155.
10.1016/j.jviromet.2017.08.016.
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Shaw, L;
Ribeiro, ALR;
Levine, AP;
Pontikos, N;
Balloux, F;
Segal, AW;
Roberts, AP;
(2017)
The Human Salivary Microbiome Is Shaped by Shared Environment Rather than Genetics: Evidence from a Large Family of Closely Related Individuals.
MBio
, 8
(5)
, Article e01237-17. 10.1128/mBio.01237-17.
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2016
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Eldholm, V;
Balloux, F;
(2016)
Antimicrobial Resistance in Mycobacterium tuberculosis: The Odd One Out.
Tends in Microbiology
, 24
(8)
pp. 637-648.
10.1016/j.tim.2016.03.007.
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Eldholm, V;
Pettersson, JH-O;
Brynildsrud, OB;
Kitchen, A;
Rasmussen, EM;
Lillebaek, T;
Ronning, JO;
... Balloux, F; + view all
(2016)
Armed conflict and population displacement as drivers of the evolution and dispersal of Mycobacterium tuberculosis.
Proceedings of the National Academy of Sciences of the United States of America
, 113
(48)
pp. 13881-13886.
10.1073/pnas.1611283113.
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Eldholm, V;
Rieux, A;
Monteserin, J;
Lopez, JM;
Palmero, D;
Lopez, B;
Ritacco, V;
... Balloux, F; + view all
(2016)
Impact of HIV co-infection on the evolution and transmission of multidrug-resistant tuberculosis.
eLife
, 5
, Article e16644. 10.7554/eLife.16644.
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Lassalle, F;
Depledge, DP;
Reeves, MB;
Brown, AC;
Christiansen, MT;
Tutill, HJ;
Williams, RJ;
... Breuer, J; + view all
(2016)
Islands of linkage in an ocean of pervasive recombination reveals two-speed evolution of human cytomegalovirus genomes.
Virus Evolution
, 2
(1)
, Article vew017. 10.1093/ve/vew017.
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Mallick, S;
Li, H;
Lipson, M;
Mathieson, I;
Gymrek, M;
Racimo, F;
Zhao, M;
... Reich, D; + view all
(2016)
The Simons Genome Diversity Project: 300 genomes from 142 diverse populations.
Nature
, 538
(7624)
pp. 201-206.
10.1038/nature18964.
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Rieux, A;
Balloux, F;
(2016)
Inferences from tip-calibrated phylogenies: a review and a practical guide.
Molecular Ecology
, 25
(9)
pp. 1911-1924.
10.1111/mec.13586.
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Shaw, L;
Harjunmaa, U;
Doyle, R;
Mulewa, S;
Charlie, D;
Maleta, K;
Callard, R;
... Klein, N; + view all
(2016)
Distinguishing the Signals of Gingivitis and Periodontitis in Supragingival Plaque: A Cross-Sectional Cohort Study in Malawi.
Applied and Enviromental Microbiology
, 82
(19)
pp. 6057-6067.
10.1128/AEM.01756-16.
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2015
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Eldholm, V;
Monteserin, J;
Rieux, A;
Lopez, B;
Sobkowiak, B;
Ritacco, V;
Balloux, F;
(2015)
Four decades of transmission of a multidrug-resistant Mycobacterium tuberculosis outbreak strain.
Nature Communications
, 6
, Article 7119. 10.1038/ncomms8119.
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Jeffares, DC;
Rallis, C;
Rieux, A;
Speed, D;
Převorovský, M;
Mourier, T;
Marsellach, FX;
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