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In vitro susceptibilities of Stenotrophomonas maltophilia isolates to antimicrobial agents commonly used for related infections: Results from the Antimicrobial Testing Leadership and Surveillance (ATLAS) program, 2004-2020

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International journal of antimicrobial agents 2023年第2期62卷 106878页

作者： Yu-Lin Lee Chun-Eng Liu Wen-Chien Ko Po-Ren Hsueh Department of Internal Medicine Chung Shan Medical University Hospital Taichung Taiwan School of Medicine Chung Shan Medical University Taichung Taiwan Institute of Genomics and Bioinformatics National Chung Hsing University Taichung Taiwan. Department of Internal Medicine Changhua Christian Hospital Changhua Taiwan. Department of Medicine College of Medicine National Cheng Kung University Tainan Taiwan. Departments of Laboratory Medicine and Internal Medicine China Medical University Hospital Taichung Taiwan School of Medicine China Medical University Taichung Taiwan Ph.D Program for Aging School of Medicine China Medical University Taichung Taiwan Departments of Laboratory Medicine and Internal Medicine National Taiwan University Hospital National Taiwan University College of Medicine Taipei Taiwan. Electronic address: hsporen@***.

Stenotrophomonas maltophilia is an emerging opportunistic pathogen for which there are limited therapeutic options because of intrinsic multidrug resistance. S. maltophilia isolates were collected as part of the Antimicrobial Testing Leadership and Surveillance (ATLAS) program and minimum inhibitory concentrations (MICs) were determined using broth microdilution methods. Susceptibility was interpreted according to Clinical and Laboratory Standards Institute (CLSI) breakpoints. Isolates with tigecycline MIC ≤2 mg/L were defined as susceptible, using the United States Food and Drug Administration criteria of Enterobacterales. A total of 2330 S. maltophilia isolates were collected from 47 countries worldwide in the ATLAS program from 2004 to 2020. Most patients were hospitalized (92.3%, 2151/2330) and respiratory tract infections (47.8%, 1114/2330) were the most common source of isolates. Minocycline had the highest susceptibility rate (98.8%), followed by levofloxacin (85.0%), trimethoprim-sulfamethoxazole (TMP-SMX) (84.4%), and ceftazidime (53.7%). A total of 98.3% (2290/2330) of S. maltophilia isolates had tigecycline MIC ≤2 mg/L. Among the S. maltophilia isolates exhibiting resistance to levofloxacin and ceftazidime, 89.3% (150/168) and 97.3% (692/711), respectively, were susceptible to tigecycline. Eight countries provided more than 30 isolates and were selected for comparison. Geographical difference in antimicrobial resistance was significant for levofloxacin, minocycline, and tigecycline (all P<0.05) but not for ceftazidime (P=0.467). These in vitro data demonstrated that minocycline had a higher susceptibility rate than levofloxacin and ceftazidime, and that tigecycline could be an alternative or salvage option for the treatment of S. maltophilia infections.

关键词： Levofloxacin Minocycline Multidrug resistance Stenotrophomonas maltophilia Tigecycline

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Author Correction: Genomic footprints of activated telomere maintenance mechanisms in cancer (Dec, 10.1038/s41467-019-13824-9, 2022)

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NATURE COMMUNICATIONS 2022年第1期13卷 1-1页

作者： Sieverling, Lina Hong, Chen Koser, Sandra D. Ginsbach, Philip Kleinheinz, Kortine Hutter, Barbara Braun, Delia M. Cortes-Ciriano, Isidro Xi, Ruibin Kabbe, Rolf Park, Peter J. Eils, Roland Schlesner, Matthias Brors, Benedikt Rippe, Karsten Jones, David T. W. Feuerbach, Lars Division of Applied Bioinformatics German Cancer Research Center (DKFZ) 69120 Heidelberg Germany Faculty of Biosciences Heidelberg University 69120 Heidelberg Germany Division of Applied Bioinformatics German Cancer Research Center (DKFZ) Heidelberg Germany Faculty of Biosciences Heidelberg University Heidelberg Germany Division of Theoretical Bioinformatics German Cancer Research Center (DKFZ) 69120 Heidelberg Germany Department for Bioinformatics and Functional Genomics Institute for Pharmacy and Molecular Biotechnology (IPMB) and BioQuant 69120 Heidelberg Germany Division of Theoretical Bioinformatics German Cancer Research Center (DKFZ) Heidelberg Germany Institute of Pharmacy and Molecular Biotechnology and BioQuant Heidelberg University Heidelberg Germany German Cancer Consortium (DKTK) Heidelberg Germany National Center for Tumor Diseases (NCT) Heidelberg Heidelberg Germany Heidelberg Center for Personalized Oncology (DKFZ-HIPO) German Cancer Research Center (DKFZ) Heidelberg Germany German Cancer Consortium (DKTK) German Cancer Research Center (DKFZ) Heidelberg Germany Division of Chromatin Networks German Cancer Research Center (DKFZ) and BioQuant 69120 Heidelberg Germany Department of Biomedical Informatics Harvard Medical School Boston Massachusetts 02115 USA Department of Chemistry Centre for Molecular Science Informatics University of Cambridge Cambridge CB2 1EW UK Ludwig Center at Harvard Medical School Boston Massachusetts 02115 USA Department of Biomedical Informatics Harvard Medical School Boston MA USA Department of Chemistry Centre for Molecular Science Informatics University of Cambridge Cambridge UK Ludwig Center at Harvard Medical School Boston MA USA School of Mathematical Sciences and Center for Statistical Science Peking University Beijing 100871 China Heidelberg University Heidelberg Germany New BIH Digital Health Center Berlin Institute of Health (BIH) and Charité - Universitätsmedizin Berlin Berlin Germany Bioi

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High-depth African genomes inform human migration and health (vol 586, pg 741, 2020)

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NATURE 2021年第7856期592卷 E26-E26页

作者： Choudhury, Ananyo Aron, Shaun Botigue, Laura R. Sengupta, Dhriti Botha, Gerrit Bensellak, Taoufik Wells, Gordon Kumuthini, Judit Shriner, Daniel Fakim, Yasmina J. Ghoorah, Anisah W. Dareng, Eileen Odia, Trust Falola, Oluwadamilare Adebiyi, Ezekiel Hazelhurst, Scott Mazandu, Gaston Nyangiri, Oscar A. Mbiyavanga, Mamana Benkahla, Alia Kassim, Samar K. Mulder, Nicola Adebamowo, Sally N. Chimusa, Emile R. Muzny, Donna Metcalf, Ginger Gibbs, Richard A. Matovu, Enock Bucheton, Bruno Hertz-Fowler, Christiane Koffi, Mathurin Macleod, Annette Mumba-Ngoyi, Dieudonne Noyes, Harry Nyangiri, Oscar A. Simo, Gustave Simuunza, Martin Rotimi, Charles Ramsay, Michele Choudhury, Ananyo Choudhury, Ananyo Aron, Shaun Botigue, Laura Sengupta, Dhriti Botha, Gerrit Bensellak, Taoufik Wells, Gordon Kumuthini, Judit Shriner, Daniel Fakim, Yasmina J. Ghoorah, Anisah W. Dareng, Eileen Odia, Trust Falola, Oluwadamilare Adebiyi, Ezekiel Hazelhurst, Scott Mazandu, Gaston Nyangiri, Oscar A. Mbiyavanga, Mamana Benkahla, Alia Kassim, Samar K. Mulder, Nicola Adebamowo, Sally N. Chimusa, Emile R. Rotimi, Charles Ramsay, Michele Adeyemo, Adebowale A. Lombard, Zane Hanchard, Neil A. Adebamowo, Clement Agongo, Godfred Boua, Romuald P. Oduro, Abraham Sorgho, Hermann Landoure, Guida Cisse, Lassana Diarra, Salimata Samassekou, Oumar Anabwani, Gabriel Matshaba, Mogomotsi Joloba, Moses Kekitiinwa, Adeodata Mardon, Graeme Mpoloka, Sununguko W. Kyobe, Samuel Mlotshwa, Busisiwe Mwesigwa, Savannah Retshabile, Gaone Williams, Lesedi Wonkam, Ambroise Moussa, Ahmed Adu, Dwomoa Ojo, Akinlolu Burke, David Salako, Babatunde O. Matovu, Enock Bucheton, Bruno Hertz-Fowler, Christiane Koffi, Mathurin Macleod, Annette Mumba-Ngoyi, Dieudonne Noyes, Harry Nyangiri, Oscar A. Simo, Gustave Simuunza, Martin Awadalla, Philip Bruat, Vanessa Gbeha, Elias Adeyemo, Adebowale A. Lombard, Zane Hanchard, Neil A. Sydney Brenner Institute for Molecular Bioscience Faculty of Health Sciences University of the Witwatersrand Johannesburg South Africa School of Electrical and Information Engineering University of the Witwatersrand Johannesburg South Africa Division of Human Genetics National Health Laboratory Service and School of Pathology Faculty of Health Sciences University of the Witwatersrand Johannesburg South Africa Navrongo Health Research Centre Navrongo Ghana Clinical Research Unit of Nanoro Institut de Recherche en Sciences de la Sante Bobo-Dioulasso Burkina Faso Center for Research in Agricultural Genomics (CRAG) Plant and Animal Genomics Program CSIC-IRTA-UAB-UB Barcelona Spain Computational Biology Division and H3ABioNet Department of Integrative Biomedical Sciences IDM University of Cape Town Cape Town South Africa System and Data Engineering Team Abdelmalek Essaadi University ENSA Tangier Morocco Centre for Proteomic and Genomic Research (CPGR) Cape Town South Africa South African National Bioinformatics Institute University of the Western Cape Bellville South Africa Africa Health Research Institute Durban South Africa Center for Research on Genomics and Global Health National Human Genome Research Institute National Institutes of Health Bethesda MD USA Department of Agriculture and Food Science Faculty of Agriculture University of Mauritius Reduit Mauritius Department of Digital Technologies Faculty of Information Communication & Digital Technologies University of Mauritius Reduit Mauritius Department of Public Health and Primary Care University of Cambridge Cambridge UK Institute of Human Virology Nigeria Abuja Nigeria Department of Epidemiology and Public Health University of Maryland School of Medicine University of Maryland Baltimore Baltimore MD USA University of Maryland Greenebaum Comprehensive Cancer Center University of Maryland School of Medicine University of Maryland Baltimore Baltimore MD USA Institute of Human Virology and Greeneba

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An Open-Source Knowledge Graph Ecosystem for the Life Sciences

arXiv

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arXiv 2023年

作者： Callahan, Tiffany J. Tripodi, Ignacio J. Stefanski, Adrianne L. Cappelletti, Luca Taneja, Sanya B. Wyrwa, Jordan M. Casiraghi, Elena Matentzoglu, Nicolas A. Reese, Justin Silverstein, Jonathan C. Hoyt, Charles Tapley Boyce, Richard D. Malec, Scott A. Unni, Deepak R. Joachimiak, Marcin P. Robinson, Peter N. Mungall, Christopher J. Cavalleri, Emanuele Fontana, Tommaso Valentini, Giorgio Mesiti, Marco Gillenwater, Lucas A. Santangelo, Brook Vasilevsky, Nicole A. Hoehndorf, Robert Bennett, Tellen D. Ryan, Patrick B. Hripcsak, George Kahn, Michael G. Bada, Michael Baumgartner, William A. Hunter, Lawrence E. Computational Bioscience Program University of Colorado Anschutz Medical Campus AuroraCO80045 United States Department of Biomedical Informatics Columbia University Irving Medical Center New YorkNY10032 United States Computer Science Department Interdisciplinary Quantitative Biology University of Colorado Boulder BoulderCO80301 United States AnacletoLab Computer Science Department University of Milan 20122 Italy Intelligent Systems Program University of Pittsburgh PittsburghPA15260 United States Department of Physical Medicine and Rehabilitation School of Medicine University of Colorado Anschutz Medical Campus AuroraCO80045 United States Division of Environmental Genomics and Systems Biology Lawrence Berkeley National Laboratory BerkeleyCA94720 United States Semanticly Ltd Athens Greece Department of Biomedical Informatics University of Pittsburgh School of Medicine PittsburghPA15206 United States Laboratory of Systems Pharmacology Harvard Medical School BostonMA02115 United States Division of Translational Informatics University of New Mexico School of Medicine AlbuquerqueNM87131 United States SIB Swiss Institute of Bioinformatics Basel Switzerland Berlin Institute of Health at Charité-Universitatsmedizin Berlin10117 Germany ELLIS European Laboratory for Learning and Intelligent Systems Germany Department of Biomedical Informatics University of Colorado School of Medicine AuroraCO80045 United States Data Collaboration Center Critical Path Institute 1840 E River Rd. Suite 100 TucsonAZ85718 United States Computer Electrical and Mathematical Sciences & Engineering Division Computational Bioscience Research Center King Abdullah University of Science and Technology Thuwal23955-6900 Saudi Arabia Department of Pediatrics University of Colorado School of Medicine AuroraCO80045 United States Janssen Research and Development RaritanNJ08869 United States Division of General Internal Medicine University of Colorado School of Medicine A

Translational research requires data at multiple scales of biological organization. Advancements in sequencing and multi-omics technologies have increased the availability of these data, but researchers face significant integration challenges. Knowledge graphs (KGs) are used to model complex phenomena, and methods exist to construct them automatically. However, tackling complex biomedical integration problems requires flexibility in the way knowledge is modeled. Moreover, existing KG construction methods provide robust tooling at the cost of fixed or limited choices among knowledge representation models. PheKnowLator (Phenotype Knowledge Translator) is a semantic ecosystem for automating the FAIR (Findable, Accessible, Interoperable, and Reusable) construction of ontologically grounded KGs with fully customizable knowledge representation. The ecosystem includes KG construction resources (e.g., data preparation APIs), analysis tools (e.g., SPARQL endpoints and abstraction algorithms), and benchmarks (e.g., prebuilt KGs and embeddings). We evaluated the ecosystem by systematically comparing it to existing open-source KG construction methods and by analyzing its computational performance when used to construct 12 large-scale KGs. With flexible knowledge representation, PheKnowLator enables fully customizable KGs without compromising performance or usability. © 2023, CC BY.

关键词： Ecosystems

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Natural variation in the parameters of innate immune cells is preferentially driven by genetic factors (vol 19, pg 302, 2018)

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NATURE IMMUNOLOGY 2018年第6期19卷 645-645页

作者： Patin, Etienne Hasan, Milena Bergstedt, Jacob Rouilly, Vincent Libri, Valentina Urrutia, Alejandra Alanio, Cecile Scepanovic, Petar Hammer, Christian Joensson, Friederike Beitz, Benoit Quach, Helene Lim, Yoong Wearn Hunkapiller, Julie Zepeda, Magge Green, Cherie Piasecka, Barbara Leloup, Claire Rogge, Lars Huetz, Francois Peguillet, Isabelle Lantz, Olivier Fontes, Magnus Di Santo, James P. Thomas, Stephanie Fellay, Jacques Duffy, Darragh Quintana-Murci, Lluis Albert, Matthew L. Unit of Human Evolutionary Genetics Department of Genomes & Genetics Institut Pasteur Paris France CNRS UMR 2000 Paris France Center of Bioinformatics Biostatistics and Integrative Biology Institut Pasteur Paris France Center for Translation Research Institut Pasteur Paris France Department of Automatic Control Lund University Lund Sweden International Group for Data Analysis Institut Pasteur Paris France Laboratory of Dendritic Cell Immunobiology Department of Immunology Institut Pasteur Paris France INSERM U1223 Paris France Department of Cancer Immunology Genentech South San Francisco CA USA School of Life Sciences École Polytechnique Fédérale de Lausanne Lausanne Switzerland Swiss Institute of Bioinformatics Lausanne Switzerland Antibodies in Therapy and Pathology Department of Immunology Institut Pasteur Paris France INSERM U760 Paris France Department of Human Genetics Genentech South San Francisco CA USA Employee Donation Program Genentech South San Francisco CA USA Department of Development Sciences Genentech South San Francisco CA USA Immunoregulation Unit Department of Immunology Institut Pasteur Paris France INSERM U783 Faculté de Médecine Site Necker-Enfants Malades Université Paris Descartes Paris France Lymphocyte Population Biology CNRS URA 1961 Institut Pasteur Paris France Center of Clinical Investigations CIC-BT1428 IGR/Curie Paris France Department of Biopathology Institut Curie Paris France Equipe Labellisée de la Ligue de Lutte Contre le Cancer Institut Curie Paris France INSERM/Institut Curie U932 Paris France Centre for Mathematical Sciences Lund University Lund Sweden Innate Immunity Unit Institut Pasteur Paris France St. Giles Laboratory of Human Genetics of Infectious Diseases Rockefeller Branch Rockefeller University New York NY USA Laboratory of Human Genetics of Infectious Diseases Necker Branch INSERM U1163 Necker Hospital for Sick Children Paris France Paris Descartes University Imagine Insti

The quantification and characterization of circulating immune cells provide key indicators of human health and disease. To identify the relative effects of environmental and genetic factors on variation in the parameters of innate and adaptive immune cells in homeostatic conditions, we combined standardized flow cytometry of blood leukocytes and genome-wide DNA genotyping of 1,000 healthy, unrelated people of Western European ancestry. We found that smoking, together with age, sex and latent infection with cytomegalovirus, were the main non-genetic factors that affected variation in parameters of human immune cells. Genome-wide association studies of 166 immunophenotypes identified 15 loci that showed enrichment for disease-associated variants. Finally, we demonstrated that the parameters of innate cells were more strongly controlled by genetic variation than were those of adaptive cells, which were driven by mainly environmental exposure. Our data establish a resource that will generate new hypotheses in immunology and highlight the role of innate immunity in susceptibility to common autoimmune diseases.

关键词： Activated Lymphocyte Genetic factors Immunity Nonspecific Immune Cell Variation

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γ-Linolenic acid in maternal milk drives cardiac metabolic maturation (vol 618, pg 365, 2023)

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NATURE 2023年第7968期619卷 E24-E24页

作者： Paredes, Ana Justo-Mendez, Raquel Jimenez-Blasco, Daniel Nunez, Vanessa Calero, Irene Villalba-Orero, Maria Alegre-Marti, Andrea Fischer, Thierry Gradillas, Ana Sant'Anna, Viviane Aparecida Rodrigues Were, Felipe Huang, Zhiqiang Hernansanz-Agustin, Pablo Contreras, Carmen Martinez, Fernando Camafeita, Emilio Vazquez, Jesus Ruiz-Cabello, Jesus Area-Gomez, Estela Sanchez-Cabo, Fatima Treuter, Eckardt Bolanos, Juan Pedro Estebanez-Perpina, Eva Ruperez, Francisco Javier Barbas, Coral Enriquez, Jose Antonio Ricote, Mercedes Cardiovascular Regeneration Program Centro Nacional de Investigaciones Cardiovasculares (CNIC) Madrid Spain Departamento de Medicina y Cirugía Animal Universidad Complutense de Madrid (UCM) Madrid Spain CIBER de Fragilidad y Envejecimiento Saludable (CIBERFES) Madrid Spain Institute of Functional Biology and Genomics (IBFG) University of Salamanca CSIC Salamanca Spain Institute for Biomedical Research of Salamanca (IBSAL) Salamanca Spain Department of Biochemistry and Molecular Biomedicine Institute of Biomedicine (IBUB) of the University of Barcelona (UB) Barcelona Spain Department of Immunology and Oncology Centro Nacional de Biotecnología-Consejo Superior de Investigaciones Científicas (CNB/CSIC) Campus Universidad Autónoma de Madrid (UAM) Madrid Spain Centro de Metabolómica y Bioanálisis (CEMBIO) Facultad de Farmacia Universidad San Pablo-CEU CEU Universities Madrid Spain Bioinformatics Unit Centro Nacional de Investigaciones Cardiovasculares (CNIC) Madrid Spain CIBER de Enfermedades Cardiovasculares (CIBERCV) Madrid Spain Department of Biosciences and Nutrition Karolinska Institutet Huddinge Sweden Proteomics Unit Centro Nacional de Investigaciones Cardiovasculares (CNIC) Madrid Spain CIC biomaGUNE Basque Research and Technology Alliance (BRTA) San Sebastian Spain Ikerbasque Basque Foundation for Science Bilbao Spain CIBER de Enfermedades Respiratorias (CIBERES) Madrid Spain Departamento de Ciencias Farmacéuticas Facultad de Farmacia Universidad Complutense Madrid (UCM) Madrid Spain Departament of Cellular and Molecular Biology Centro de Investigaciones Biológicas Margarita Salas-CSIC Madrid Spain Department of Neurology Columbia University Medical Campus New York NY USA

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A clonal expression biomarker associates with lung cancer mortality (vol 25, pg 1540, 2019)

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NATURE MEDICINE 2020年第7期26卷 1148-1148页

作者： Biswas, Dhruva Birkbak, Nicolai J. Rosenthal, Rachel Hiley, Crispin T. Lim, Emilia L. Papp, Krisztian Boeing, Stefan Krzystanek, Marcin Djureinovic, Dijana La Fleur, Linnea Greco, Maria Doeme, Balazs Fillinger, Janos Brunnstrom, Hans Wu, Yin Moore, David A. Skrzypski, Marcin Abbosh, Christopher Litchfield, Kevin Al Bakir, Maise Watkins, Thomas B. K. Veeriah, Selvaraju Wilson, Gareth A. Jamal-Hanjani, Mariam Moldvay, Judit Botling, Johan Chinnaiyan, Arul M. Micke, Patrick Hackshaw, Allan Bartek, Jiri Csabai, Istvan Szallasi, Zoltan Herrero, Javier McGranahan, Nicholas Swanton, Charles Cancer Research UK Lung Cancer Centre of Excellence University College London Cancer Institute Paul O’Gorman Building London UK Bill Lyons Informatics Centre University College London Cancer Institute Paul O’Gorman Building London UK Cancer Evolution and Genome Instability Laboratory The Francis Crick Institute London UK Department of Molecular Medicine Aarhus University Aarhus Denmark Bioinformatics Research Centre Aarhus University Aarhus Denmark Department of Physics of Complex Systems ELTE Eötvös Loránd University Budapest Hungary Bioinformatics and Biostatistics The Francis Crick Institute London UK Danish Cancer Society Research Center Copenhagen Denmark Department of Immunology Genetics and Pathology Uppsala University Uppsala Sweden Genomics Equipment Park The Francis Crick Institute London UK Department of Tumor Biology National Korányi Institute of Pulmonology Semmelweis University Budapest Hungary Division of Thoracic Surgery Comprehensive Cancer Center Medical University of Vienna Vienna Austria Department of Thoracic Surgery National Institute of Oncology Semmelweis University Budapest Hungary Department of Pathology National Korányi Institute of Pulmonology Semmelweis University Budapest Hungary Department of Pathology National Institute of Oncology Budapest Hungary Lund University Laboratory Medicine Region Skåne Department of Clinical Sciences Lund Pathology Lund Sweden Department of Pathology UCL Cancer Institute London UK Department of Oncology and Radiotherapy Medical University of Gdansk Gdansk Poland SE-NAP Brain Metastasis Research Group 2nd Department of Pathology Semmelweis University Budapest Hungary Michigan Center for Translational Pathology University of Michigan Ann Arbor USA Department of Pathology University of Michigan Ann Arbor USA Rogel Cancer Center University of Michigan Ann Arbor USA Department of Urology University of Michigan Ann Arbor USA Howard Hughes Medical Institute University of Michigan An

An amendment to this paper has been published and can be accessed via a link at the top of the paper.

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The European Reference Genome Atlas: piloting a decentralised approach to equitable biodiversity genomics

NPJ Biodiversity

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NPJ Biodiversity 2024年第1期3卷 28页

作者： Mc Cartney, Ann M. Formenti, Giulio Mouton, Alice De Panis, Diego Marins, Luísa S. Leitão, Henrique G. Diedericks, Genevieve Kirangwa, Joseph Morselli, Marco Salces-Ortiz, Judit Escudero, Nuria Iannucci, Alessio Natali, Chiara Svardal, Hannes Fernández, Rosa De Pooter, Tim Joris, Geert Strazisar, Mojca Wood, Jonathan M. D. Herron, Katie E. Seehausen, Ole Watts, Phillip C. Shaw, Felix Davey, Robert P. Minotto, Alice Fernández, José M. Böhne, Astrid Alegria, Carla Alioto, Tyler Alves, Paulo C. Amorim, Isabel R. Aury, Jean-Marc Backstrom, Niclas Baldrian, Petr Baltrunaite, Laima Barta, Endre Bedhom, Bertrand Belser, Caroline Bergsten, Johannes Bertrand, Laurie Bilandija, Helena Binzer-Panchal, Mahesh Bista, Iliana Blaxter, Mark Borges, Paulo A. V. Dias, Guilherme Borges Bosse, Mirte Brown, Tom Bruggmann, Rémy Buena-Atienza, Elena Burgin, Josephine Buzan, Elena Cariani, Alessia Casadei, Nicolas Chiara, Matteo Chozas, Sergio Jr, Fedor Čiampor Crottini, Angelica Cruaud, Corinne Cruz, Fernando Dalen, Love Biase, Alessiode Delcampo, Javier Delic, Teo Dennis, Aliceb. Derks, Martijn F. L. Diroma, Maria Angela Djan, Mihajla Duprat, Simone Eleftheriadi, Klara Feulner, Philine G. D. Flot, Jean-François Forni, Giobbe Fosso, Bruno Fournier, Pascal Fournier-Chambrillon, Christine Gabaldon, Toni Garg, Shilpa Gissi, Carmela Giupponi, Luca Gomez-Garrido, Jessica González, Josefa Grilo, Miguel L. Grüning, Björn Guerin, Thomas Guiglielmoni, Nadege Gut, Marta Haesler, Marcel P. Hahn, Christoph Halpern, Balint Harrison, Peter W. Heintz, Julia Hindrikson, Maris Höglund, Jacob Howe, Kerstin Hughes, Graham M. Istace, Benjamin Cock, Mark J. Janžekovič, Franc Jonsson, Zophonias O. Joye-Dind, Sagane Koskimäki, Janne J. Krystufek, Boris Kubacka, Justyna Kuhl, Heiner Kusza, Szilvia Labadie, Karine Lähteenaro, Meri Lantz, Henrik Lavrinienko, Anton Leclère, Lucas Lopes, Ricardo Jorge Madsen, Ole Magdelenat, Ghislaine Magoga, Giulia Manousaki, Tereza Mappes, Tapio Marques, Joao Pedro Redondo, Gemma I. Martinez Maumus, Florian McCarthy, Shane A. M Genomics Institute University of California SantaCruz CA United States TheVertebrate Genome Laboratory The Rockefeller University NewYork NY United States Department of Biology University of Florence Sesto Fiorentino Italy InBios-Conservation Genetics Laboratory University of Liege Liege Belgium Leibniz Institut für Zoo und Wildtierforschung Berlin Germany Berlin Center for Genomics in Biodiversity Research Berlin Germany Department of Biology University of Antwerp Antwerp Belgium Institute of Zoology University of Cologne Cologne Germany Department of Chemistry Life Sciences and Environmental Sustainability University of Parma Parma Italy Institute of Evolutionary Biology (CSIC-Universitat Pompeu Fabra Barcelona Spain Naturalis Biodiversity Center Leiden Netherlands Neuromics Support Facility VIB Center for Molecular Neurology VIB Antwerp Belgium Neuromics Support Facility Department of Biomedical SciencesUniversity ofAntwerp Antwerp Belgium Tree of Life WellcomeSanger Institute Cambridge Hinxton United Kingdom School of Biology and Environmental Science University College Dublin Belfield Ireland Aquatic Ecology & Evolution Institute of Ecology & Evolution University of Bern Bern Switzerland Department of Fish Ecology & Evolution Eawag Kastanienbaum Switzerland Department of Biological and Environmental Science University of Jyvaskyla Jyvaskyla Finland The EarlhamInstitute NorwichResearchPark Norwich United Kingdom Digital Science London United Kingdom Barcelona Supercomputing Center Spanish National Bioinformatics Institute ELIXIR Spain Getafe Spain Leibniz Institute for the Analysis of Biodiversity Change Museum Koenig Bonn Bonn Germany CE3C—Centre for Ecology Evolution and Environmental Changes & CHANGE—Global Change and Sustainability Institute Faculdade de Ciências Universidade de Lisboa Campo Grande Lisboa Portugal Centro Nacional de Análisis Genómico (CNAG) Barcelona Spain Universitat de Barcelona (UB) Barcelona Spain CIBIO Cen

A genomic database of all Earth’s eukaryotic species could contribute to many scientific discoveries;however, only a tiny fraction of species have genomic information available. In 2018, scientists across the world united under the Earth BioGenome Project (EBP), aiming to produce a database of highquality reference genomes containing all ~1.5 million recognized eukaryotic species. As the European node of the EBP, the European Reference Genome Atlas (ERGA) sought to implement a new decentralised, equitable and inclusive model for producing reference genomes. For this, ERGA launched a Pilot Project establishing the first distributed reference genome production infrastructure and testing it on 98 eukaryotic species from 33 European countries. Here we outline the infrastructure and explore its effectiveness for scaling high-quality reference genome production, whilst considering equity and inclusion. The outcomes and lessons learned provide a solid foundation for ERGA while offering key learnings to other transnational, national genomic resource projects and the EBP. © The Author(s) 2024, corrected publication 2024.

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Author Correction: Antibodies from dengue patients with prior exposure to Japanese encephalitis virus are broadly neutralizing against Zika virus

Communications biology

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Communications biology 2024年第1期7卷 252页

作者： Gielenny M Salem Jedhan Ucat Galula Shang-Rung Wu Jyung-Hurng Liu Yen-Hsu Chen Wen-Hung Wang Sheng-Fan Wang Cheng-Sheng Song Fan-Chi Chen Adrian B Abarientos Guan-Wen Chen Cheng-I Wang Day-Yu Chao Graduate Institute of Microbiology and Public Health College of Veterinary Medicine National Chung Hsing University Taichung City 402 Taiwan. Institute of Oral Medicine School of Dentistry College of Medicine National Cheng Kung University Tainan City 701 Taiwan. Institute of Basic Medical Sciences College of Medicine National Cheng Kung University Tainan City 701 Taiwan. Graduate Institute of Genomics and Bioinformatics College of Life Sciences National Chung Hsing University Taichung City 40227 Taiwan. School of Medicine College of Medicine National Sun Yat-Sen University Kaohsiung City 80424 Taiwan. Center for Tropical Medicine and Infectious Disease Research Kaohsiung Medical University Kaohsiung City 80708 Taiwan. Division of Infectious Diseases Department of Internal Medicine Kaohsiung Medical University Hospital Kaohsiung Medical University Kaohsiung City 80708 Taiwan. Department of Medical Laboratory Science and Biotechnology Kaohsiung Medical University Kaohsiung City 80708 Taiwan. Doctoral Program in Microbial Genomics National Chung Hsing University and Academia Sinica Taichung City 402 Taiwan. Singapore Immunology Network Agency for Science Technology and Research (A*STAR) 8A Biomedical Grove Immunos Singapore 138648 Singapore. Graduate Institute of Microbiology and Public Health College of Veterinary Medicine National Chung Hsing University Taichung City 402 Taiwan. dychao@nchu.edu.tw. Doctoral Program in Microbial Genomics National Chung Hsing University and Academia Sinica Taichung City 402 Taiwan. dychao@nchu.edu.tw. Department of Post-Baccalaureate Medicine College of Medicine National Chung Hsing University Taichung City 402 Taiwan. dychao@nchu.edu.tw.

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Patterns of somatic structural variation in human cancer genomes (vol 578, pg 112, 2020)

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NATURE 2023年第7948期614卷 E38-E38页

作者： Li, Yilong Roberts, Nicola D. Wala, Jeremiah A. Shapira, Ofer Schumacher, Steven E. Kumar, Kiran Khurana, Ekta Waszak, Sebastian Korbel, Jan O. Haber, James E. Imielinski, Marcin Weischenfeldt, Joachim Beroukhim, Rameen Campbell, Peter J. Cancer Genome Project Wellcome Trust Sanger Institute Hinxton UK Totient Inc Cambridge MA USA Wellcome Sanger Institute Wellcome Genome Campus Hinxton UK Department of Haematology University of Cambridge Cambridge UK Cambridge University Hospitals NHS Foundation Trust Cambridge UK Korea Advanced Institute of Science and Technology Daejeon South Korea Department of Zoology Genetics and Physical Anthropology University of Santiago de Compostela Santiago de Compostela Spain Centre for Research in Molecular Medicine and Chronic Diseases (CIMUS) University of Santiago de Compostela Santiago de Compostela Spain The Biomedical Research Centre (CINBIO) University of Vigo Vigo Spain Centre for Research in Molecular Medicine and Chronic Diseases (CiMUS) Universidade de Santiago de Compostela Santiago de Compostela Spain Department of Zoology Genetics and Physical Anthropology (CiMUS) Universidade de Santiago de Compostela Santiago de Compostela Spain The Biomedical Research Centre (CINBIO) Universidade de Vigo Vigo Spain The Broad Institute of Harvard and MIT Cambridge MA USA Bioinformatics and Integrative Genomics Harvard University Cambridge MA USA Department of Cancer Biology Dana-Farber Cancer Institute Boston MA USA Broad Institute of MIT and Harvard Cambridge MA USA Department of Medical Oncology Dana-Farber Cancer Institute Boston MA USA Harvard Medical School Boston MA USA Massachusetts General Hospital Center for Cancer Research Charlestown MA USA Dana-Farber Cancer Institute Boston MA USA Department of Biostatistics and Computational Biology Dana-Farber Cancer Institute and Harvard Medical School Boston MA USA Weill Cornell Medical College New York NY USA Department of Physiology and Biophysics Weill Cornell Medicine New York NY USA Institute for Computational Biomedicine Weill Cornell Medicine New York NY USA Controlled Department and Institution New York NY USA Englander Institute for Precision Medicine Weill Cornell Medicine Ne

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