Dynamic co-evolution of transposable elements and the piRNA pathway in African cichlid fishes.

Autor: Almeida MV; Department of Biochemistry, University of Cambridge, Tennis Court Road, Cambridge, CB2 1GA, UK.; Wellcome/CRUK Gurdon Institute, University of Cambridge, Tennis Court Road, Cambridge, CB2 1QN, UK., Blumer M; Department of Genetics, University of Cambridge, Downing Street, Cambridge, CB2 3EH, UK.; These authors contributed equally., Yuan CU; Department of Biochemistry, University of Cambridge, Tennis Court Road, Cambridge, CB2 1GA, UK.; Wellcome/CRUK Gurdon Institute, University of Cambridge, Tennis Court Road, Cambridge, CB2 1QN, UK.; Department of Genetics, University of Cambridge, Downing Street, Cambridge, CB2 3EH, UK.; These authors contributed equally., Sierra P; Department of Genetics, University of Cambridge, Downing Street, Cambridge, CB2 3EH, UK., Price JL; Department of Biochemistry, University of Cambridge, Tennis Court Road, Cambridge, CB2 1GA, UK.; Wellcome/CRUK Gurdon Institute, University of Cambridge, Tennis Court Road, Cambridge, CB2 1QN, UK., Quah FX; Department of Biochemistry, University of Cambridge, Tennis Court Road, Cambridge, CB2 1GA, UK.; Department of Genetics, University of Cambridge, Downing Street, Cambridge, CB2 3EH, UK., Friman A; National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892, USA.; Biophysics Graduate Program, Institute for Physical Science and Technology, University of Maryland, College Park, Maryland 20742, USA., Dallaire A; Department of Biochemistry, University of Cambridge, Tennis Court Road, Cambridge, CB2 1GA, UK.; Wellcome/CRUK Gurdon Institute, University of Cambridge, Tennis Court Road, Cambridge, CB2 1QN, UK.; Comparative Fungal Biology, Royal Botanic Gardens Kew, Jodrell Laboratory, Richmond TW9 3DS, UK., Vernaz G; Wellcome/CRUK Gurdon Institute, University of Cambridge, Tennis Court Road, Cambridge, CB2 1QN, UK.; Department of Genetics, University of Cambridge, Downing Street, Cambridge, CB2 3EH, UK.; Present address: Zoological Institute, Department of Environmental Sciences, University of Basel, Vesalgasse 1, Basel, 4051, Switzerland., Putman ALK; Department of Biochemistry, University of Cambridge, Tennis Court Road, Cambridge, CB2 1GA, UK.; Wellcome/CRUK Gurdon Institute, University of Cambridge, Tennis Court Road, Cambridge, CB2 1QN, UK.; Department of Genetics, University of Cambridge, Downing Street, Cambridge, CB2 3EH, UK., Smith AM; School of Natural Sciences, University of Hull, Hull, HU6 7RX, UK., Joyce DA; School of Natural Sciences, University of Hull, Hull, HU6 7RX, UK., Butter F; Institute of Molecular Biology (IMB), Quantitative Proteomics, Ackermannweg 4, Mainz, 55128, Germany.; Institute of Molecular Virology and Cell Biology, Friedrich-Loeffler-Institute, Südufer, Greifswald, 17493, Germany., Haase AD; National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892, USA., Durbin R; Department of Genetics, University of Cambridge, Downing Street, Cambridge, CB2 3EH, UK.; Wellcome Sanger Institute, Tree of Life, Wellcome Genome Campus, Hinxton, CB10 1SA, UK., Santos ME; Department of Zoology, University of Cambridge, Downing Street, Cambridge, CB2 3EJ, UK., Miska EA; Department of Biochemistry, University of Cambridge, Tennis Court Road, Cambridge, CB2 1GA, UK.; Wellcome/CRUK Gurdon Institute, University of Cambridge, Tennis Court Road, Cambridge, CB2 1QN, UK.; Wellcome Sanger Institute, Tree of Life, Wellcome Genome Campus, Hinxton, CB10 1SA, UK.

Publikováno v: BioRxiv : the preprint server for biology [bioRxiv] 2024 Apr 01. Date of Electronic Publication: 2024 Apr 01.

SC3s: efficient scaling of single cell consensus clustering to millions of cells.

Autor: Quah FX; Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, CB10 1SA, UK.; The Gurdon Institute, University of Cambridge, Tennis Court Road, Cambridge, CB2 1QN, UK., Hemberg M; Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, CB10 1SA, UK. mhemberg@bwh.harvard.edu.; Evergrande Center for Immunologic Diseases, Harvard Medical School and Brigham and Women's Hospital, 75 Francis Street, Boston, MA, 02115, USA. mhemberg@bwh.harvard.edu.

Publikováno v: BMC bioinformatics [BMC Bioinformatics] 2022 Dec 12; Vol. 23 (1), pp. 536. Date of Electronic Publication: 2022 Dec 12.

Visualizing variation within Global Pneumococcal Sequence Clusters (GPSCs) and country population snapshots to contextualize pneumococcal isolates.

Autor: Gladstone RA; Parasites and microbes, Wellcome Sanger InstituteHinxton, UK., Lo SW; Parasites and microbes, Wellcome Sanger InstituteHinxton, UK., Goater R; Centre for Genomic Pathogen Surveillance, Wellcome Genome CampusHinxton, UK.; Big Data Institute, Li Ka Shing Centre for Health Information and Discovery, University of Oxford, Oxford, UK., Yeats C; Centre for Genomic Pathogen Surveillance, Wellcome Genome CampusHinxton, UK.; Big Data Institute, Li Ka Shing Centre for Health Information and Discovery, University of Oxford, Oxford, UK., Taylor B; Centre for Genomic Pathogen Surveillance, Wellcome Genome CampusHinxton, UK.; Big Data Institute, Li Ka Shing Centre for Health Information and Discovery, University of Oxford, Oxford, UK., Hadfield J; Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA., Lees JA; Faculty of Medicine, School of Public Health, Imperial College London, UK., Croucher NJ; Faculty of Medicine, School of Public Health, Imperial College London, UK., van Tonder AJ; Parasites and microbes, Wellcome Sanger InstituteHinxton, UK.; Department of Veterinary Medicine, University of Cambridge, Cambridge, UK., Bentley LJ; Parasites and microbes, Wellcome Sanger InstituteHinxton, UK., Quah FX; Parasites and microbes, Wellcome Sanger InstituteHinxton, UK., Blaschke AJ; Division of Pediatric Infectious Diseases, Department of Pediatrics, School of Medicine, University of Utah, 295 Chipeta Way, Salt Lake City, UT, 84108, USA., Pershing NL; Division of Pediatric Infectious Diseases, Department of Pediatrics, School of Medicine, University of Utah, 295 Chipeta Way, Salt Lake City, UT, 84108, USA., Byington CL; University of California Health, Oakland, CA, USA., Balaji V; Christian Medical College, Vellore, India., Hryniewicz W; National Medicines Institute, Division of Clinical Microbiology and Infection Prevention, Warsaw, Poland., Sigauque B; Fundação Manhiça / Centro de Investigação em Saúde da Manhiça (CISM), Maputo Mozambique, Instituto Nacional de Saúde, inistério de Saúde, Maputo, Mozambique., Ravikumar KL; Central Research Laboratory, Department of Microbiology, Kempegowda Institute of Medical Sciences Hospital & Research Center, Bangalore, India., Almeida SCG; Center of Bacteriology, Adolfo Lutz Institute, São Paulo, Brazil., Ochoa TJ; Instituto de Medicina Tropical, Universidad Peruana Cayetano Heredia, Lima, Peru., Ho PL; Department of Microbiology and Carol Yu Centre for Infection, The University of Hong Kong, Queen Mary Hospital, Hong Kong, PR China., du Plessis M; Centre for Respiratory Diseases and Meningitis, National Institute for Communicable Diseases, Johannesburg, South Africa., Ndlangisa KM; Centre for Respiratory Diseases and Meningitis, National Institute for Communicable Diseases, Johannesburg, South Africa., Cornick JE; Malawi-Liverpool-Wellcome-Trust, Malawi., Kwambana-Adams B; NIHR Global Health Research Unit on Mucosal Pathogens, Division of Infection and Immunity, University College London, London, UK.; WHO Collaborating Centre for New Vaccines Surveillance, Medical Research Council Unit The Gambia at The London School of Hygiene & Tropical Medicine, Fajara, The Gambia., Benisty R; The Faculty of Health Sciences, Ben-Gurion University of the NegevBeer-Sheva, Israel., Nzenze SA; Medical Research Council: Respiratory and Meningeal Pathogens Research Unit, University of the Witwatersrand, Johannesburg, South Africa.; Department of Science and Technology/National Research Foundation: Vaccine Preventable Diseases, University of the Witwatersrand, Johannesburg, South Africa., Madhi SA; Medical Research Council: Respiratory and Meningeal Pathogens Research Unit, University of the Witwatersrand, Johannesburg, South Africa.; Department of Science and Technology/National Research Foundation: Vaccine Preventable Diseases, University of the Witwatersrand, Johannesburg, South Africa., Hawkins PA; Rollins School Public Health, Emory University, GA, USA., Pollard AJ; Oxford Vaccine Group, Department of Paediatrics, University of Oxford, and the NIHR Oxford Biomedical Research Centre, Oxford, UK., Everett DB; Queens Research Institute, University of Edinburgh, UK., Antonio M; WHO Collaborating Centre for New Vaccines Surveillance, Medical Research Council Unit The Gambia at The London School of Hygiene & Tropical Medicine, Fajara, The Gambia., Dagan R; The Faculty of Health Sciences, Ben-Gurion University of the NegevBeer-Sheva, Israel., Klugman KP; Rollins School Public Health, Emory University, GA, USA., von Gottberg A; Department of Microbiology and Carol Yu Centre for Infection, The University of Hong Kong, Queen Mary Hospital, Hong Kong, PR China., Metcalf BJ; Centers for Disease Control and Prevention, Atlanta, GA, USA., Li Y; Centers for Disease Control and Prevention, Atlanta, GA, USA., Beall BW; Centers for Disease Control and Prevention, Atlanta, GA, USA., McGee L; Centers for Disease Control and Prevention, Atlanta, GA, USA., Breiman RF; Rollins School Public Health, Emory University, GA, USA.; Emory Global Health Institute, Atlanta, GA, USA., Aanensen DM; Centre for Genomic Pathogen Surveillance, Wellcome Genome CampusHinxton, UK.; Big Data Institute, Li Ka Shing Centre for Health Information and Discovery, University of Oxford, Oxford, UK., Bentley SD; Parasites and microbes, Wellcome Sanger InstituteHinxton, UK., The Global Pneumococcal Sequencing Consortium; See the full list of the The Global Pneumococcal Sequencing Consortium members, in acknowledgements.

Publikováno v: Microbial genomics [Microb Genom] 2020 May; Vol. 6 (5). Date of Electronic Publication: 2020 Apr 29.