Publications
Genomic screening of 16 UK native bat species through conservationist networks uncovers coronaviruses with zoonotic potential
Nature Communications 2023 14:1
Cedric C S Tan, Jahcub Trew, Thomas P Peacock, Kai Yi Mok, Charlie Hart, Kelvin Lau, Dongchun Ni, C David, L Orme, Emma Ransome, William D Pearse, Christopher M Coleman, Dalan Bailey, Nazia Thakur, Jessica L Quantrill, Ksenia Sukhova, Damien Richard, Laura Kahane, Guy Woodward, Thomas Bell, Lisa Worledge, Joe Nunez-Mino, Wendy Barclay, Lucy Van Dorp, Francois Balloux, Vincent Savolainen
Identification of Evolutionary Trajectories Shared across Human Betacoronaviruses
Genome Biology and Evolution
Marina Escalera-Zamudio, Sergei L Kosakovsky Pond, Natalia Viña, Bernardo Gutiérrez, Rhys P D Inward, Julien Thézé, Lucy van Dorp, Hugo G Castelán-Sánchez, Thomas A Bowden, Oliver G Pybus, Ruben J G Hulswit
Coordinated surveillance is essential to monitor and mitigate the evolutionary impacts of SARS-CoV-2 spillover and circulation in animal hosts
Nature Ecology & Evolution 2023 7:7
Suresh V. Kuchipudi, Cedric Tan, Lucy van Dorp, Maureen Lichtveld, Bradley Pickering, Jeff Bowman, Samira Mubareka, Francois Balloux
Population structure and hybridisation in a population of Hawaiian feral chickens
Heredity
Maria Luisa Martin Cerezo, Saioa Lopez, Lucy van Dorp, Garrett Hellenthal, Martin Johnsson, Eben Gering, Rie Henriksen, Dominic Wright
The population genomic legacy of the second plague pandemic
Current Biology
Shyam Gopalakrishnan, S. Sunna Ebenesersdóttir, Inge K.C. Lundstrøm, Gordon Turner-Walker, Kristjan H.S. Moore, Pierre Luisi, Ashot Margaryan, Michael D. Martin, Martin Rene Ellegaard, Ólafur Magnússon, Ásgeir Sigurðsson, Steinunn Snorradóttir, Droplaug N. Magnúsdóttir, Jason E. Laffoon, Lucy van Dorp, Xiaodong Liu, Ida Moltke, María C. Ávila-Arcos, Joshua G. Schraiber, Simon Rasmussen, David Juan, Pere Gelabert, Toni de-Dios, Anna K. Fotakis, Miren Iraeta-Orbegozo, Åshild J. Vågene, Sean Dexter Denham, Axel Christophersen, Hans K. Stenøien, Filipe G. Vieira, Shanlin Liu, Torsten Günther, Toomas Kivisild, Ole Georg Moseng, Birgitte Skar, Christina Cheung, Marcela Sandoval-Velasco, Nathan Wales, Hannes Schroeder, Paula F. Campos, Valdís B. Guðmundsdóttir, Thomas Sicheritz-Ponten, Bent Petersen, Jostein Halgunset, Edmund Gilbert, Gianpiero L. Cavalleri, Eivind Hovig, Ingrid Kockum, Tomas Olsson, Lars Alfredsson, Thomas F. Hansen, Thomas Werge, Eske Willerslev, Francois Balloux, Tomas Marques-Bonet, Carles Lalueza-Fox, Rasmus Nielsen, Kári Stefánsson, Agnar Helgason, M. Thomas P. Gilbert
Ancient herpes simplex 1 genomes reveal recent viral structure in Eurasia
Science Advances
Meriam Guellil, Lucy van Dorp, Sarah A. Inskip, Jenna M. Dittmar, Lehti Saag, Kristiina Tambets, Ruoyun Hui, Alice Rose, Eugenia D’Atanasio, Aivar Kriiska, Liivi Varul, A. M. H. C. Koekkelkoren, Rimma D. Goldina, Craig Cessford, Anu Solnik, Mait Metspalu, Johannes Krause, Alexander Herbig, John E. Robb, Charlotte J. Houldcroft, Christiana L. Scheib
The past, current and future epidemiological dynamic of SARS-CoV-2
Oxford Open Immunology
François Balloux, Cedric Tan, Leo Swadling, Damien Richard, Charlotte Jenner, Mala Maini, Lucy van Dorp
Transmission of SARS-CoV-2 from humans to animals and potential host adaptation
Nature Communications
Cedric C S Tan, Su Datt Lam, Damien Richard, Christopher J Owen, Dorothea Berchtold, Christine Orengo, Meera Surendran Nair, Suresh V Kuchipudi, Vivek Kapur, Lucy van Dorp, Francois Balloux
Role of mobile genetic elements in the global dissemination of the carbapenem resistance gene blaNDM
Nature Communications
Mislav Acman, Ruobing Wang, Lucy van Dorp, Liam P Shaw, Qi Wang, Nina Luhmann, Yuyao Yin, Shijun Sun, Hongbin Chen, Hui Wang, Francois Balloux
Genomic Analysis of 18th-Century Kazakh Individuals and Their Oral Microbiome
Biology
Anna E. White, Toni de-Dios, Pablo Carrión, Gian Luca Bonora, Laia Llovera, Elisabetta Cilli, Esther Lizano, Maral K. Khabdulina, Daniyar T. Tleugabulov, Iñigo Olalde, Tomàs Marquès-Bonet, François Balloux, Davide Pettener, Lucy van Dorp, Donata Luiselli, Carles Lalueza-Fox
Drivers of methicillin-resistant Staphylococcus aureus (MRSA) lineage replacement in China
Genome Medicine
Hongbin Chen, Yuyao Yin, Lucy van Dorp, Liam P. Shaw, Hua Gao, Mislav Acman, Jizhen Yuan, Fengning Chen, Shijun Sun, Xiaojuan Wang, Shuguang Li, Yawei Zhang, Rhys A. Farrer, Hui Wang, Francois Balloux
Pre-existing polymerase-specific T cells expand in abortive seronegative SARS-CoV-2
Nature
Leo Swadling, Mariana O. Diniz, Nathalie M. Schmidt, Oliver E. Amin, Aneesh Chandran, Emily Shaw, Corinna Pade, Joseph M. Gibbons, Nina Le Bert, Anthony T. Tan, Anna Jeffery-Smith, Cedric C. S. Tan, Christine Y. L. Tham, Stephanie Kucykowicz, Gloryanne Aidoo-Micah, Joshua Rosenheim, Jessica Davies, Marina Johnson, Melanie P. Jensen, George Joy, Laura E. McCoy, Ana M. Valdes, Benjamin M. Chain, David Goldblatt, Daniel M. Altmann, Rosemary J. Boyton, Charlotte Manisty, Thomas A. Treibel, James C. Moon, Hakam Abbass, Aderonke Abiodun, Mashael Alfarih, Zoe Alldis, Mervyn Andiapen, Jessica Artico, João B. Augusto, Georgina L. Baca, Sasha N. L. Bailey, Anish N. Bhuva, Alex Boulter, Ruth Bowles, Rosemary J. Boyton, Olivia V. Bracken, Ben O'Brien, Tim Brooks, Natalie Bullock, David K. Butler, Gabriella Captur, Nicola Champion, Carmen Chan, David Collier, Jorge Couto Sousa, Xose Couto-Parada, Teresa Cutino-Moguel, Rhodri H. Davies, Brooke Douglas, Cecilia Di Genova, Keenan Dieobi-Anene, Anaya Ellis, Karen Feehan, Malcolm Finlay, Marianna Fontana, Nasim Forooghi, Celia Gaier, Derek Gilroy, Matt Hamblin, Gabrielle Harker, Jacqueline Hewson, Lauren M. Hickling, Aroon D. Hingorani, Lee Howes, Alun Hughes, Gemma Hughes, Rebecca Hughes, Ivie Itua, Victor Jardim, Wing-Yiu Jason Lee, Melanie Jensen, Jessica Jones, Meleri Jones, George Joy, Vikas Kapil, Hibba Kurdi, Jonathan Lambourne, Kai-Min Lin, Sarah Louth, Vineela Mandadapu, Áine McKnight, Katia Menacho, Celina Mfuko, Oliver Mitchelmore, Christopher Moon, Sam M. Murray, Mahdad Noursadeghi, Ashley Otter, Susana Palma, Ruth Parker, Kush Patel, Babita Pawarova, Steffen E. Petersen, Brian Piniera, Franziska P. Pieper, Daniel Pope, Mary Prossora, Lisa Rannigan, Alicja Rapala, Catherine J. Reynolds, Amy Richards, Matthew Robathan, Genine Sambile, Amanda Semper, Andreas Seraphim, Mihaela Simion, Angelique Smit, Michelle Sugimoto, Stephen Taylor, Nigel Temperton, Stephen Thomas, George D. Thornton, Art Tucker, Jessry Veerapen, Mohit Vijayakumar, Sophie Welch, Theresa Wodehouse, Lucinda Wynne, Dan Zahedi, Lucy van Dorp, Francois Balloux, Aine McKnight, Mahdad Noursadeghi, Antonio Bertoletti, Mala K. Maini
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
Cedric C.S. Tan, Christopher J. Owen, Christine Y.L. Tham, Antonio Bertoletti, Lucy van Dorp, Francois Balloux
Salmonella enterica from a soldier from the 1652-siege of Barcelona (Spain) supports historical transatlantic epidemic contacts
iScience
Toni De-Dios, Pablo Carrion, Inigo Olalde, Laia Llovera Nadal, Esther Lizano, Didac Pamies, Tomas Marques-Bonet, Francois Balloux, Lucy van Dorp, Carles Lalueza-Fox
Metagenomic evidence for a polymicrobial signature of sepsis
Microbial Genomics
Cedric Chih Shen Tan, Mislav Acman, Lucy van Dorp, Francois Balloux
COVID-19, the first pandemic in the post-genomic era
Current Opinion in Virology
Lucy van Dorp, Charlotte J Houldcroft, Damien Richard, François Balloux
The epidemiology of Plasmodium vivax among adults in the Democratic Republic of the Congo
Nature Communications
Nicholas F. Brazeau, Cedar L. Mitchell, Andrew P. Morgan, Molly Deutsch-Feldman, Oliver John Watson, Kyaw L. Thwai, Pere Gelabert, Lucy van Dorp, Corinna Y. Keeler, Andreea Waltmann, Michael Emch, Valerie Gartner, Ben Redelings, Gregory A. Wray, Melchior K. Mwandagalirwa, Antoinette K. Tshefu, Joris L. Likwela, Jessie K. Edwards, Robert Verity, Jonathan B. Parr, Steven R. Meshnick, Jonathan J. Juliano
Genomic epidemiology of the first epidemic wave of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) in Palestine
Microbial Genomics
Nouar Qutob, Zaidoun Salah, Damien Richard, Hisham Darwish, Husam Sallam, Issa Shtayeh, Osama Najjar, Mahmoud Ruzayqat, Dana Najjar, Francois Balloux, Lucy van Dorp
Evidence of the interplay of genetics and culture in Ethiopia
Nature Communications
Saioa Lopez, Ayele Tarekegn, Gavin Band, Lucy van Dorp, Nancy Bird, Sam Morris, Tamiru Oljira, Ephrem Mekonnen, Endashaw Bekele, Roger Blench, Mark G. Thomas, Neil Bradman, Garrett Hellenthal
How Does Large-Scale Genomic Analysis Shape Our Understanding of COVID Variants in Real Time?
Cell Systems
Lucy van Dorp, MukiS Shey, Elodie Ghedin, Franziska Michor, Eugene V. Koonin, Katie Hampson
No evidence for increased transmissibility from recurrent mutations in SARS-CoV-2
Nature Communications
Lucy van Dorp, Damien Richard, Cedric C. S. Tan, Liam P. Shaw, Mislav Acman, Francois Balloux
Antibiotic treatment regimes as a driver of the global population dynamics of a major gonorrhea lineage
Molecular Biology and Evolution
Magnus N Osnes, Lucy van Dorp, Ola B Brynildsrud, Kristian Alfsnes, Thamarai Schneiders, Kate E Templeton, Koji Yahara, Francois Balloux, Dominique A Caugant, Vegard Eldholm
SARS-CoV-2 spike protein predicted to form complexes with host receptor protein orthologues from a broad range of mammals
Scientific Reports
Su. D. Lam, Nicola. Bordin, Vaishali. P. Waman, Harry. M. Scholes, Paul. Ashford, Neeladri. Sen, Lucy. van Dorp, Clemens. Rauer, Natalie. L. Dawson, Camilla S. M. Pang, Mahnaz. Abbasian, Ian. Sillitoe, Sarah. J. L. Edwards, Franca. Fraternali, Jonathan. G. Lees, Jo. M. Santini, Christine. A. Orengo
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
Camus Nimmo, James Millard, Lucy van Dorp, Kayleen Brien, Sashen Moodley, Allison Wolf, Alison D Grant, Nesri Padayatchi, Alexander S Pym, Francois Balloux, Max O'Donnell
STROBE-metagenomics: a STROBE extension statement to guide the reporting of metagenomics studies.
The Lancet. Infectious diseases
Tehmina Bharucha, Clarissa Oeser, Francois Balloux, Julianne R Brown, Ellen C Carbo, Andre Charlett, Charles Y Chiu, Eric C J Claas, Marcus C Goffau, Jutte J C Vries, Marc Eloit, Susan Hopkins, Jim F Huggett, Duncan MacCannell, Sofia Morfopoulou, Avindra Nath, Denise M O'Sullivan, Lauren B Reoma, Liam P Shaw, Igor Sidorov, Patricia J Simner, Le Van Tan, Emma C Thomson, Lucy van Dorp, Michael R Wilson, Judith Breuer, Nigel Field
Emergence of genomic diversity and recurrent mutations in SARS-CoV-2
Infection, Genetics and Evolution
Lucy van Dorp, Mislav Acman, Damien Richard, Liam P. Shaw, Charlotte E. Ford, Louise Ormond, Christopher J. Owen, Juanita Pang, Cedric C.S. Tan, Florencia A.T. Boshier, Arturo Torres Ortiz, Francois Balloux
Large-scale network analysis captures biological features of bacterial plasmids
Nature Communications
Mislav Acman, Lucy van Dorp, Joanne M. Santini, Francois Balloux
Bedaquiline resistance in drug-resistant tuberculosis HIV co-infected patients.
The European respiratory journal
Camus Nimmo, James Millard, Kayleen Brien, Sashen Moodley, Lucy van Dorp, Keeren Lutchminarain, Allison Wolf, Alison D Grant, Francois Balloux, Alexander S Pym, Nesri Padayatchi, Max O'Donnell
Eugenics history: university geneticists respond
Nature
Andrew Pomiankowski, Mark G. Thomas, Steve Jones, Rosemary Ekong, Lucy van Dorp, Nikolas Maniatis, Nick Lane, Adam Rutherford, Catherine Walker, Dallas Swallow
Metagenomic analysis of a blood stain from the French revolutionary Jean-Paul Marat (1743–1793)
Infection, Genetics and Evolution
Antonio De-Dios, Lucy van Dorp, Philippe Charlier, Sofia Morfopoulou, Esther Lizano, Celine Bon, Corinne Le Bitouzé, Marina Alvarez-Estape, Tomas Marques-Bonet, Francois Balloux, Carles Lalueza-Fox
Discordant bioinformatic predictions of antimicrobial resistance from whole-genome sequencing data of bacterial isolates: an inter-laboratory study
Microbial Genomics
Ronan M. Doyle, Denise M. O'Sullivan, Sean D. Aller, Sebastian Bruchmann, Taane Clark, Andreu Coello Pelegrin, Martin Cormican, Ernest Diez Benavente, Matthew J. Ellington, Elaine McGrath, Yair Motro, Thi Phuong Thuy Nguyen, Jody Phelan, Liam P. Shaw, Richard A. Stabler, Alex Belkum, Lucy van Dorp, Neil Woodford, Jacob Moran-Gilad, Jim F. Huggett, Kathryn A. Harris
Plasmodium vivax Malaria viewed through the lens of an eradicated European strain
Molecular Biology and Evolution
Lucy van Dorp, Pere Gelabert, Adrien Rieux, Marc Manuel, Toni De-Dios, Shyam Gopalakrishnan, Christian Caroe, Marcela Sandoval-Velasco, Rosa Fregel, Inigo Olalde, Raul Escosa, Carles Aranda, Silvie Huijben, Ivo Mueller, Tomas Marques-Bonet, Francois Balloux, M Thomas P Gilbert, Carles Lalueza-Fox
A New Lineage of Cryptococcus gattii (VGV) Discovered in the Central Zambezian Miombo Woodlands.
mBio
Rhys A Farrer, Miwha Chang, Michael J Davis, Lucy van Dorp, Dong-Hoon Yang, Terrance Shea, Thomas R Sewell, Wieland Meyer, Francois Balloux, Hannah M Edwards, Duncan Chanda, Geoffrey Kwenda, Mathieu Vanhove, Yun C Chang, Christina A Cuomo, Matthew C Fisher, Kyung J Kwon-Chung
Genetic affinities of an eradicated European Plasmodium falciparum strain
Microbial Genomics
Antonio De-Dios, Lucy van Dorp, Pere Gelabert, Christian Caroe, Marcela Sandoval-Velasco, Rosa Fregel, Raul Escosa, Carles Aranda, Silvie Huijben, Francois Balloux, M. Thomas P. Gilbert, Carles Lalueza-Fox
Ancient genomes indicate population replacement in Early Neolithic Britain
Nature Ecology and Evolution
Selina Brace, Yoan Diekmann, Tom J. Booth, Lucy van Dorp, Zuzana Faltyskova, Nadin Rohland, Swapan Mallick, Inigo Olalde, Matthew Ferry, Megan Michel, Jonas Oppenheimer, Nasreen Broomandkhoshbacht, Kristin Stewardson, Rui Martiniano, Susan Walsh, Manfred Kayser, Sophy Charlton, Garrett Hellenthal, Ian Armit, Rick Schulting, Oliver E. Craig, Alison Sheridan, Mike Parker Pearson, Chris Stringer, David Reich, Mark G. Thomas, Ian Barnes
Rapid phenotypic evolution in multidrug-resistant Klebsiella pneumoniae hospital outbreak strains
Microbial Genomics
Lucy van Dorp, Qi Wang, Liam P. Shaw, Mislav Acman, Ola B. Brynildsrud, Vegard Eldholm, Ruobing Wang, Hua Gao, Yuyao Yin, Hongbin Chen, Chuling Ding, Rhys A. Farrer, Xavier Didelot, Francois Balloux, Hui Wang
Genetic legacy of state centralization in the Kuba Kingdom of the Democratic Republic of the Congo.
Proceedings of the National Academy of Sciences of the United States of America
Lucy van Dorp, Sara Lowes, Jonathan L Weigel, Naser Ansari-Pour, Saioa Lopez, Javier Mendoza-Revilla, James A Robinson, Joseph Henrich, Mark G Thomas, Nathan Nunn, Garrett Hellenthal
From Theory to Practice: Translating Whole-Genome Sequencing (WGS) into the Clinic.
Trends in Microbiology
Francois Balloux, Ola Bronstad Brynildsrud, Lucy van Dorp, Liam P Shaw, Hongbin Chen, Kathryn A Harris, Hui Wang, Vegard Eldholm
A tutorial on how (not) to over-interpret STRUCTURE/ADMIXTURE bar plots
Nature Communications
Daniel Falush, Lucy van Dorp, Daniel Lawson
The global distribution and spread of the mobilized colistin resistance gene mcr-1
Nature Communications
Ruobing Wang, Lucy van Dorp, Liam P. Shaw, Phelim Bradley, Qi Wang, Xiaojuan Wang, Longyang Jin, Qing Zhang, Yuqing Liu, Adrien Rieux, Thamarai Dorai-Schneiders, Lucy Anne Weinert, Zamin Iqbal, Xavier Didelot, Hui Wang, Francois Balloux
Population genomic analysis of elongated skulls reveals extensive female-biased immigration in Early Medieval Bavaria.
Proceedings of the National Academy of Sciences of the United States of America
Krishna R Veeramah, Andreas Rott, Melanie Gross, Lucy van Dorp, Saioa Lopez, Karola Kirsanow, Christian Sell, Jens Blocher, Daniel Wegmann, Vivian Link, Zuzana Hofmanova, Joris Peters, Bernd Trautmann, Anja Gairhos, Jochen Haberstroh, Bernd Paffgen, Garrett Hellenthal, Brigitte Haas-Gebhard, Michaela Harbeck, Joachim Burger
Destructive sampling natural science collections: an overview for museum professionals and researchers
Journal of Natural Science Collections
Jan Freedman, Lucy van Dorp, Selina Brace
Q&A: What are pathogens, and what have they done to and for us?
BMC Biology
Francois Balloux, Lucy van Dorp
The Genetic Legacy of Zoroastrianism in Iran and India: Insights into Population Structure, Gene Flow, and Selection
American Journal of Human Genetics
Saioa. Lopez, Mark G. Thomas, Lucy van Dorp, Naser Ansari-Pour, Sarah Stewart, Abigail L. Jones, Erik Jelinek, Lounes Chikhi, Tudor Parfitt, Neil Bradman, Michael E. Weale, Garrett Hellenthal
Feralisation targets different genomic loci to domestication in the chicken
Nature Communications
Martin Johnsson, Eben Gering, Pamela Willis, Saioa Lopez, Lucy van Dorp, Garrett Hellenthal, Rie Henriksen, Urban Friberg, Dominic Wright
Early Neolithic genomes from the eastern Fertile Crescent.
Science
Farnaz Broushaki, Mark G Thomas, Vivian Link, Saioa Lopez, Lucy van Dorp, Karola Kirsanow, Zuzana Hofmanova, Yoan Diekmann, Lara M Cassidy, David Diez-Del-Molino, Athanasios Kousathanas, Christian Sell, Harry K Robson, Rui Martiniano, Jens Blocher, Amelie Scheu, Susanne Kreutzer, Ruth Bollongino, Dean Bobo, Hossein Davudi, Olivia Munoz, Mathias Currat, Kamyar Abdi, Fereidoun Biglari, Oliver E Craig, Daniel G Bradley, Stephen Shennan, Krishna Veeramah, Marjan Mashkour, Daniel Wegmann, Garrett Hellenthal, Joachim Burger
Early farmers from across Europe directly descended from Neolithic Aegeans.
Proceedings of the National Academy of Sciences of the United States of America
Zuzana Hofmanova, Susanne Kreutzer, Garrett Hellenthal, Christian Sell, Yoan Diekmann, David Diez-Del-Molino, Lucy van Dorp, Saioa Lopez, Athanasios Kousathanas, Vivian Link, Karola Kirsanow, Lara M Cassidy, Rui Martiniano, Melanie Strobel, Amelie Scheu, Kostas Kotsakis, Paul Halstead, Sevi Triantaphyllou, Nina Kyparissi-Apostolika, Dushka Urem-Kotsou, Christina Ziota, Fotini Adaktylou, Shyamalika Gopalan, Dean M Bobo, Laura Winkelbach, Jens Blocher, Martina Unterlander, Christoph Leuenberger, Ciler Cilingiroğlu, Barbara Horejs, Fokke Gerritsen, Stephen J Shennan, Daniel G Bradley, Mathias Currat, Krishna R Veeramah, Daniel Wegmann, Mark G Thomas, Christina Papageorgopoulou, Joachim Burger
Human Dispersal Out of Africa: A Lasting Debate
Evolutionary Bioinformatics Online
Saioa Lopez, Lucy van Dorp, Garrett Hellenthal
Evidence for a common origin of blacksmiths and cultivators in the Ethiopian Ari within the last 4500 Years: Lessons for clustering-based inference
PLoS Genetics
Lucy van Dorp, David Balding, Simon Myers, Luca Pagani, Chris Tyler-Smith, Endashaw Bekele, Ayele Tarekegn, Mark G. Thomas, Neil Bradman, Garrett Hellenthal