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Correction: ColistinDose, a Mobile App for Determining Intravenous Dosage Regimens of Colistimethate in Critically Ill Adult Patients: Clinician-Centered Design and Development Study

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JMIR mHealth and uHealth 2020年第12期8卷 e26593页

作者： Xueliang Hua Chen Li Jason M Pogue Varun S Sharma Ilias Karaiskos Keith S Kaye Brian T Tsuji Phillip J Bergen Yan Zhu Jiangning Song Jian Li Independent Researcher Santa Clara CA United States. Department of Biochemistry and Molecular Biology Monash University Melbourne Australia. Infection and Immunity Program Biomedicine Discovery Institute Monash University Melbourne Australia. Institute of Molecular Systems Biology Department of Biology ETH Zurich Zurich Switzerland. Department of Clinical Pharmacy University of Michigan College of Pharmacy Ann Arbor MI United States. 1st Internal Medicine and Infectious Diseases Department Hygeia Hospital Marousi Greece. Department of Internal Medicine University of Michigan Medical School Ann Arbor MI United States. Laboratory for Antimicrobial Dynamics NYS Center of Excellence in Bioinformatics & Life Sciences Buffalo NY United States. School of Pharmacy and Pharmaceutical Sciences University at Buffalo Buffalo NY United States. Department of Microbiology Monash University Melbourne Australia. Monash Centre for Data Science Faculty of Information Technology Monash University Melbourne Australia.

[This corrects the article DOI: 10.2196/20525.].

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Correction to: Specific Susceptibility to COVID-19 in Adults with Down Syndrome

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Neuromolecular medicine 2021年第4期23卷 572-573页

作者： Tomer Illouz Arya Biragyn Milana Frenkel-Morgenstern Orly Weissberg Alessandro Gorohovski Eugene Merzon Ilan Green Florencia Iulita Lisi Flores-Aguilar Mara Dierssen Ilario De Toma Hefziba Lifshitz Stylianos E Antonarakis Eugene Yu Yann Herault Marie-Claude Potier Alexandra Botté Randall Roper Benjamin Sredni Ronit Sarid Jacqueline London William Mobley Andre Strydom Eitan Okun The Leslie and Susan Gonda Multidisciplinary Brain Research Center Bar-Ilan University 5290002 Ramat-Gan Israel. The Paul Feder Laboratory On Alzheimer's Disease Research Bar-Ilan University 5290002 Ramat-Gan Israel. Laboratory of Molecular Biology and Immunology NIA Baltimore MD 21224 USA. Cancer Genomics and BioComputing of Complex Diseases Lab Azrieli Faculty of Medicine Bar-Ilan University Safed Israel. Leumit Health Services Department of Family Medicine Sackler School of Medicine Tel Aviv University Tel Aviv-Yafo Israel. Sant Pau Memory Unit Department of Neurology Hospital de La Santa Creu I Sant Pau Barcelona Spain. Biomedical Research Institute Sant Pau Universitat Autònoma de Barcelona Barcelona Spain. Center of Biomedical Investigation Network for Neurodegenerative Diseases (CIBERNED) Madrid Spain. Alzheimer-Down Unit Fundación Catalana Síndrome de Down Barcelona Spain. Department of Anatomy and Cell Biology McGill University Montreal Canada. Center for Genomic Regulation The Barcelona Institute for Science and Technology Barcelona Spain. University Pompeu Fabra Barcelona Spain. Biomedical Research Networking Center for Rare Diseases (CIBERER) Barcelona Spain. Cellular & Systems Neurobiology Systems Biology Program The Barcelona Institute of Science and Technology Centre for Genomic Regulation (CRG) Dr. Aiguader 88 08003 Barcelona Spain. Universitat Pompeu Fabra (UPF) Barcelona Spain. Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER) Madrid Spain. School of Education Bar-Ilan University 5290002 Ramat-Gan Israel. Department of Genetic Medicine and Development University of Geneva 1211 Geneva Switzerland. Medigenome Swiss Institute of Genomic Medicine 1207 Geneva Switzerland. iGE3 Institute of Genetics and Genomics of Geneva 1211 Geneva Switzerland. The Children's Guild Foundation Down Syndrome Research Program Genetics and Genomics Program and Department of Cancer Genetics and Genomics Roswell Park Comprehensi

A correction to this paper has been published: https://***/10.1007/s12017-021-08657-z

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Proceedings of the 16th Annual UT-KBRIN bioinformatics Summit 2016: bioinformatics

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BMC bioinformatics 2017年第9期18卷 1-9页

作者： Eric C. Rouchka Juw Won Park Julia H. Chariker David A. Tieri Shreedharkumar Rajurkar Vikas Singh Nishchal K. Verma Yan Cui Mark Farman Bradford Condon Jolanta Jaromczyk Neil Moore Jerzy Jaromczyk Daniel Harris Patrick Calie Eun Kyong Shin Robert L. Davis Arash Shaban-Nejad Joshua M. Mitchell Hunter N. B. Moseley Robert M. Flight Qing Jun Wang Richard M. Higashi Teresa W-M Fan Andrew N. Lane Liangqun Lu Bernie J Daigle Jr. Xi Chen Andrey Smelter Jerzy W. Jaromczyk Bailey K. Phan Nathaniel J. Serpico Ethan G. Toney Li Chen Caroline E. Melton Jennifer R. Mandel Bernie J. Daigle Jr. Hao Chen Kazi I. Zaman Ramin Homayouni Patrick J. Trainor Andrew P. DeFilippis Samantha M. Carlisle Shesh N. Rai Department of Computer Engineering and Computer Science University of Louisville Duthie Center for Engineering Louisville KY 40292 USA Kentucky Biomedical Research Infrastructure (KBRIN) Bioinformatics Core 522 East Gray Street Louisville KY 40292 USA Department of Psychological and Brain Sciences University of Louisville Louisville KY 40292 USA Department of Anatomical Sciences and Neurobiology University of Louisville Louisville KY 40292 USA Department of Electrical Engineering IIT Kanpur India Department of Microbiology Immunology and Biochemistry University of Tennessee Health Science Center Memphis TN 38103 USA Center for Integrative and Translational Genomics University of Tennessee Health Science Center Memphis TN 38103 USA Department of Plant Pathology University of Kentucky Lexington KY 40546 USA UK Healthcare Genomics University of Kentucky Lexington KY 40536 USA Department of Entomology & Plant Pathology University of Tennessee Knoxville TN 37996 USA Department of Forestry University of Kentucky Lexington KY 40506 USA Department of Computer Science University of Kentucky Lexington KY 40506 USA Department of Computer Science University of Kentucky Lexington KY 40508 USA Department of Biological Sciences Eastern Kentucky University Richmond KY 40475 USA University of Tennessee Health Science Center – Oak-Ridge National Lab (UTHSC-ORNL) Center for Biomedical Informatics Department of Pediatrics Memphis TN 38103 USA Department of Molecular & Cellular Biochemistry University of Kentucky Lexington KY 40536 USA Markey Cancer Center University of Kentucky Lexington KY 40536 USA Center for Environmental and Systems Biochemistry University of Kentucky Lexington KY 40536 USA Institute for Biomedical Informatics University of Kentucky Lexington KY 40536 USA Department of Molecular and Cellular Biochemistry University of Kentucky Lexington KY 40536 USA Department of Statistics University of Kentucky Louisville KY

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The IBEX Imaging Knowledge-Base: A Community Resource Enabling Adoption and Development of Immunofluoresence Imaging Methods

arXiv

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arXiv 2024年

作者： Yaniv, Ziv Anidi, Ifeanyichukwu U. Arakkal, Leanne Arroyo-Mejías, Armando J. Beuschel, Rebecca T. Börner, Katy Chu, Colin J. Clark, Beatrice Clatworthy, Menna R. Colautti, Jake Coscia, Fabian Croteau, Joshua Denha, Saven Dever, Rose Dutra, Walderez O. Fritzsche, Sonja Fullam, Spencer Gerner, Michael Y. Gola, Anita Gollob, Kenneth J. Hernandez, Jonathan M. Hor, Jyh Liang Ichise, Hiroshi Jing, Zhixin Jonigk, Danny Kandov, Evelyn Kastenmüller, Wolfgang Koenig, Joshua F.E. Kothurkar, Aanandita Kortekaas, Rosa K. Kreins, Alexandra Y. Lamborn, Ian T. Lin, Yuri Morais, Katia Luciano Pereira Lunich, Aleksandra Luz, Jean C.S. MacDonald, Ryan B. Makranz, Chen Maltez, Vivien I. McDonough, John E. Moriarty, Ryan V. Ocampo-Godinez, Juan M. Olyntho, Vitoria M. Oxenius, Annette Padhan, Kartika Remmert, Kirsten Richoz, Nathan Schrom, Edward C. Shang, Wanjing Shi, Lihong Shih, Rochelle M. Speranza, Emily Stierli, Salome Teichmann, Sarah A. Veres, Tibor Z. Vierhout, Megan Wachter, Brianna T. Williams, Margaret Zangger, Nathan Germain, Ronald N. Radtke, Andrea J. Bioinformatics and Computational Bioscience Branch National Institute of Allergy and Infectious Diseases National Institutes of Health BethesdaMD United States Critical Care Medicine and Pulmonary Branch National Heart Lung and Blood Institute National Institutes of Health BethesdaMD United States Lymphocyte Biology Section Laboratory of Immune System Biology NIAID NIH BethesdaMD United States Department of Intelligent Systems Engineering Indiana University BloomingtonIN United States UCL Institute of Ophthalmology NIHR Moorfields Biomedical Research Centre London United Kingdom Cambridge Institute for Therapeutic Immunology and Infectious Diseases University of Cambridge Department of Medicine Molecular Immunity Unit Laboratory of Molecular Biology Cambridge United Kingdom McMaster Immunology Research Centre Schroeder Allergy and Immunology Research Institute Department of Medicine Faculty of Health Sciences McMaster University HamiltonON Canada Spatial Proteomics Group Berlin Germany Department of Business Development BioLegend Inc. San DiegoCA United States Functional Immunogenomics Unit National Institute of Arthritis and Musculoskeletal and Skin Diseases National Institutes of Health BethesdaMD United States Laboratory of Cell-Cell Interactions Department of Morphology Institute of Biological Sciences Universidade Federal de Minas Gerais MG Belo Horizonte Brazil Division of Rheumatology Rush University Medical Center ChicagoIL United States Department of Immunology University of Washington School of Medicine SeattleWA United States Robin Chemers Neustein Laboratory of Mammalian Cell Biology and Development The Rockefeller University New YorkNY United States Hospital Israelita Albert Einstein SP Sao Paulo Brazil Surgical Oncology Program National Cancer Institute National Institutes of Health BethesdaMD United States Institute of Pathology Aachen Medical University RWTH Aachen Aachen Germany Hannover Germany Würzburg Institute

The iterative bleaching extends multiplexity (IBEX) Knowledge-Base is a central portal for researchers adopting IBEX and related 2D and 3D immunofluorescence imaging methods. The design of the Knowledge-Base is modeled after efforts in the open-source software community and includes three facets: a development platform (GitHub), static website, and service for data archiving. The Knowledge-Base facilitates the practice of open science throughout the research life cycle by providing validation data for recommended and non-recommended reagents, e.g., primary and secondary antibodies. In addition to reporting negative data, the Knowledge-Base empowers method adoption and evolution by providing a venue for sharing protocols, videos, datasets, software, and publications. A dedicated discussion forum fosters a sense of community among researchers while addressing questions not covered in published manuscripts. Together, scientists from around the world are advancing scientific discovery at a faster pace, reducing wasted time and effort, and instilling greater confidence in the resulting data. © 2024, CC BY.

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Meeting Report from the Second "Minimum Information for Biological and Biomedical Investigations" (MIBBI) workshop

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Standards in genomic sciences 2010年第3期3卷 259-66页

作者： Carsten Kettner Dawn Field Susanna-Assunta Sansone Chris Taylor Jan Aerts Nigel Binns Andrew Blake Cedrik M Britten Ario de Marco Jennifer Fostel Pascale Gaudet Alejandra González-Beltrán Nigel Hardy Jan Hellemans Henning Hermjakob Nick Juty Jim Leebens-Mack Eamonn Maguire Steffen Neumann Sandra Orchard Helen Parkinson William Piel Shoba Ranganathan Philippe Rocca-Serra Annapaola Santarsiero David Shotton Peter Sterk Andreas Untergasser Patricia L Whetzel Beilstein-Institut Frankfurt am Main Germany Centre for Ecology & Hydrology UK Oxford e-Research Centre University of Oxford UK The European Bioinformatics Institute (EBI) UK Faculty of Engineering - ESAT/SCD Leuven University Leuven-Heverlee Belgium Division of Pathway Medicine University of Edinburgh Medical School Edinburgh UK MRC Harwell UK Medical Department University Medical Center Johannes Gutenberg University-Mainz Mainz Germany Consortium for Genomic Technology Milano Italy University of Nova Gorica Nova Gorica Slovenia NIEHS NIH US National Toxicology Program USA Swiss Institute of Bioinformatics Geneva Switzerland Computational and Systems Medicine and Department of Computer Science University College London London UK Department of Computer Science Aberystwyth University Aberystwyth UK Center for Medical Genetics Ghent University Ghent Belgium Department of Plant Biology University of Georgia Athens USA Department of Stress- and Developmental Biology Institute for Plant Biochemistry Halle Germany Peabody Museum of Natural History Yale University New Haven USA Macquarie University Sydney Australia National University of Singapore Singapore Cancer Pharmacology The Mario Negri Institute for Pharmacological Research Milan Italy Image Bioinformatics Research Group Department of Zoology University of Oxford Oxford UK Wellcome Trust Sanger Institute UK Zentrum für Molekulare Biologie der Universität Heidelberg Heidelberg Germany The National Center for Biomedical Ontology / Stanford Center for Biomedical Informatics Research Stanford University Stanford USA

This report summarizes the proceedings of the second workshop of the 'Minimum Information for Biological and Biomedical Investigations' (MIBBI) consortium held on Dec 1-2, 2010 in Rüdesheim, Germany through the sponsorship of the Beilstein-Institute. MIBBI is an umbrella organization uniting communities developing Minimum Information (MI) checklists to standardize the description of data sets, the workflows by which they were generated and the scientific context for the work. This workshop brought together representatives of more than twenty communities to present the status of their MI checklists and plans for future development. Shared challenges and solutions were identified and the role of MIBBI in MI checklist development was discussed. The meeting featured some thirty presentations, wide-ranging discussions and breakout groups. The top outcomes of the two-day workshop as defined by the participants were: 1) the chance to share best practices and to identify areas of synergy; 2) defining a series of tasks for updating the MIBBI Portal; 3) reemphasizing the need to maintain independent MI checklists for various communities while leveraging common terms and workflow elements contained in multiple checklists; and 4) revision of the concept of the MIBBI Foundry to focus on the creation of a core set of MIBBI modules intended for reuse by individual MI checklist projects while maintaining the integrity of each MI project. Further information about MIBBI and its range of activities can be found at http://***/.

关键词： Minimum Information European bioinformatics Institute Biomedical Ontology Stable Link Breakout Group

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The importance of transparency and reproducibility in artificial intelligence research

arXiv

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arXiv 2020年

作者： Haibe-Kains, Benjamin Adam, George Alexandru Hosny, Ahmed Khodakarami, Farnoosh Waldron, Levi Wang, Bo McIntosh, Chris Kundaje, Anshul Greene, Casey S. Hoffman, Michael M. Leek, Jeffrey T. Huber, Wolfgang Brazma, Alvis Pineau, Joelle Tibshirani, Robert Hastie, Trevor Ioannidis, John P.A. Quackenbush, John Aerts, Hugo J.W.L. Princess Margaret Cancer Centre University Health Network TorontoON Canada Department of Medical Biophysics University of Toronto TorontoON Canada Department of Computer Science University of Toronto TorontoON Canada Ontario Institute for Cancer Research TorontoON Canada Vector Institute for Artificial Intelligence TorontoON Canada Program Brigham and Women's Hospital Harvard Medical School BostonMA United States Radiation Oncology and Radiology Dana-Farber Cancer Institute Brigham and Women's Department of Epidemiology and Biostatistics Institute for Implementation Science in Population Health CUNY Graduate School of Public Health and Health Policy New YorkNY United States Peter Munk Cardiac Centre University Health Network TorontoON Canada Hospital Harvard Medical School BostonMA United States Department of Genetics Stanford University School of Medicine StanfordCA United States Dept. of Systems Pharmacology and Translational Therapeutics Perelman School of Medicine University of Pennsylvania PhiladelphiaPA United States Childhood Cancer Data Lab Alex's Lemonade Stand Foundation PhiladelphiaPA United States Department of Biostatistics Johns Hopkins Bloomberg School of Public Health BaltimoreMD United States European Molecular Biology Laboratory Genome Biology Unit Heidelberg Germany European Molecular Biology Laboratory European Bioinformatics Institute EMBL-EBI Hinxton United Kingdom McGill University MontrealQC Canada Montreal Institute for Learning Algorithms QC Canada StanfordCA United States Department of Biomedical Data Science Stanford University School of Medicine StanfordCA United States Departments of Medicine of Health Research and Policy and of Biomedical Data Science Stanford University School of Medicine StanfordCA United States Department of Statistics Stanford University School of Humanities and Sciences StanfordCA United States Department of Biostatistics Harvard T.H Chan School of Public Health BostonMA Un

In their study, McKinney et al. showed the high potential of artificial intelligence for breast cancer screening. However, the lack of detailed methods and computer code undermines its scientific value. We identify obstacles hindering transparent and reproducible AI research as faced by McKinney et al and provide solutions with implications for the broader field. Copyright © 2020, The Authors. All rights reserved.

关键词： Artificial intelligence

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Author Correction: Perspectives on ENCODE

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Nature 2022年第7909期605卷 E4页

作者： Michael P Snyder Thomas R Gingeras Jill E Moore Zhiping Weng Mark B Gerstein Bing Ren Ross C Hardison John A Stamatoyannopoulos Brenton R Graveley Elise A Feingold Michael J Pazin Michael Pagan Daniel A Gilchrist Benjamin C Hitz J Michael Cherry Bradley E Bernstein Eric M Mendenhall Daniel R Zerbino Adam Frankish Paul Flicek Richard M Myers Department of Genetics School of Medicine Stanford University Palo Alto CA USA. mpsnyder@stanford.edu. Cardiovascular Institute Stanford School of Medicine Stanford CA USA. mpsnyder@stanford.edu. Functional Genomics Cold Spring Harbor Laboratory Cold Spring Harbor NY USA. University of Massachusetts Medical School Program in Bioinformatics and Integrative Biology Worcester MA USA. Department of Thoracic Surgery Clinical Translational Research Center Shanghai Pulmonary Hospital The School of Life Sciences and Technology Tongji University Shanghai China. Bioinformatics Program Boston University Boston MA USA. Yale University New Haven CT USA. Ludwig Institute for Cancer Research University of California San Diego La Jolla CA USA. Center for Epigenomics University of California San Diego La Jolla CA USA. Department of Biochemistry and Molecular Biology The Pennsylvania State University University Park PA USA. Altius Institute for Biomedical Sciences Seattle WA USA. Department of Genome Sciences University of Washington Seattle WA USA. Department of Medicine University of Washington Seattle WA USA. Department of Genetics and Genome Sciences Institute for Systems Genomics UConn Health Farmington CT USA. National Human Genome Research Institute National Institutes of Health Bethesda MD USA. Department of Genetics School of Medicine Stanford University Palo Alto CA USA. Broad Institute and Department of Pathology Massachusetts General Hospital and Harvard Medical School Boston MA USA. Biological Sciences University of Alabama in Huntsville Huntsville AL USA. HudsonAlpha Institute for Biotechnology Huntsville AL USA. European Molecular Biology Laboratory European Bioinformatics Institute Wellcome Genome Campus Cambridge UK.

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Publisher Correction: Comprehensive molecular characterization of mitochondrial genomes in human cancers

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Nature genetics 2023年第5期55卷 893页

作者： Yuan Yuan Young Seok Ju Youngwook Kim Jun Li Yumeng Wang Christopher J Yoon Yang Yang Inigo Martincorena Chad J Creighton John N Weinstein Yanxun Xu Leng Han Hyung-Lae Kim Hidewaki Nakagawa Keunchil Park Peter J Campbell Han Liang Department of Bioinformatics and Computational Biology The University of Texas MD Anderson Cancer Center Houston TX USA. Cancer Genome Project Wellcome Trust Sanger Institute Hinxton UK. Graduate School of Medical Science and Engineering Korea Advanced Institute of Science and Technology Daejeon Korea. Department of Health Science and Technology Samsung Advanced Institute for Health Science and Technology Sungkyunkwan University School of Medicine Seoul Korea. Quantitative and Computational Biosciences Graduate Program Baylor College of Medicine Houston TX USA. Division of Biostatistics The University of Texas Health Science Center at Houston School of Public Health Houston TX USA. Department of Medicine and Dan L. Duncan Cancer Center Division of Biostatistics Baylor College of Medicine Houston TX USA. Department of Systems Biology The University of Texas MD Anderson Cancer Center Houston TX USA. Department of Applied Mathematics and Statistics Johns Hopkins University Baltimore MD USA. Department of Biochemistry and Molecular Biology The University of Texas Health Science Center at Houston McGovern Medical School Houston TX USA. Department of Biochemistry Ewha Womans University School of Medicine Seoul Korea. Laboratory for Cancer Genomics RIKEN Center for Integrative Medical Sciences Yokohama Japan. Division of Hematology/Oncology Samsung Medical Center Sungkyunkwan University School of Medicine Seoul Korea. kpark@skku.edu. Cancer Genome Project Wellcome Trust Sanger Institute Hinxton UK. pc8@sanger.ac.uk. Cambridge University Hospitals NHS Foundation Trust Cambridge UK. pc8@sanger.ac.uk. Department of Bioinformatics and Computational Biology The University of Texas MD Anderson Cancer Center Houston TX USA. hliang1@***. Quantitative and Computational Biosciences Graduate Program Baylor College of Medicine Houston TX USA. hliang1@***. Department of Systems Biology The University of Texas MD Anderson Cancer Center Houston TX USA. hliang1@mdanderson

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The IBEX Knowledge-Base: Achieving more together with open science

arXiv

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arXiv 2024年

作者： Radtke, Andrea J. Anidi, Ifeanyichukwu Arakkal, Leanne Arroyo-Mejias, Armando Beuschel, Rebecca T. Börner, Katy Chu, Colin J. Clark, Beatrice Clatworthy, Menna R. Colautti, Jake Croteau, Joshua Denha, Saven Dever, Rose Dutra, Walderez O. Fritzsche, Sonja Fullam, Spencer Gerner, Michael Y. Gola, Anita Gollob, Kenneth J. Hernandez, Jonathan M. Hor, Jyh Liang Ichise, Hiroshi Jing, Zhixin Jonigk, Danny Kandov, Evelyn Kastenmüller, Wolfgang Koenig, Joshua F.E. Kothurkar, Aanandita Kreins, Alexandra Y. Lamborn, Ian Lin, Yuri Morais, Katia Luciano Pereira Lunich, Aleksandra Luz, Jean C.S. MacDonald, Ryan B. Makranz, Chen Maltez, Vivien I. Moriaty, Ryan V. Ocampo-Godinez, Juan M. Olyntho, Vitoria M. Padhan, Kartika Remmert, Kirsten Richoz, Nathan Schrom, Edward C. Shang, Wanjing Shi, Lihong Shih, Rochelle M. Speranza, Emily Stierli, Salome Teichmann, Sarah A. Veres, Tibor Z. Vierhout, Megan Wachter, Brianna T. Wade-Vallance, Adam K. Williams, Margaret Zangger, Nathan Germain, Ronald N. Yaniv, Ziv Lymphocyte Biology Section Center for Advanced Tissue Imaging Laboratory of Immune System Biology National Institute of Allergy and Infectious Diseases National Institutes of Health BethesdaMD United States Critical Care Medicine and Pulmonary Branch National Heart Lung and Blood Institute National Institutes of Health BethesdaMD United States Lymphocyte Biology Section Laboratory of Immune System Biology National Institute of Allergy and Infectious Diseases National Institutes of Health BethesdaMD United States Department of Intelligent Systems Engineering Indiana University BloomingtonIN United States UCL Institute of Ophthalmology NIHR Moorfields Biomedical Research Centre London United Kingdom Cambridge Institute for Therapeutic Immunology and Infectious Diseases University of Cambridge Department of Medicine Molecular Immunity Unit Laboratory of Molecular Biology Cambridge United Kingdom McMaster Immunology Research Centre Schroeder Allergy and Immunology Research Institute Department of Medicine Faculty of Health Sciences McMaster University HamiltonON Canada Department of Business Development BioLegend Inc. San DiegoCA United States Functional Immunogenomics Unit National Institute of Arthritis and Musculoskeletal and Skin Diseases National Institutes of Health BethesdaMD United States Laboratory of Cell-Cell Interactions Department of Morphology Institute of Biological Sciences Universidade Federal de Minas Gerais MG Belo Horizonte Brazil Spatial Proteomics Group Berlin Germany Division of Rheumatology Rush University Medical Center ChicagoIL United States Department of Immunology University of Washington School of Medicine SeattleWA United States Robin Chemers Neustein Laboratory of Mammalian Cell Biology and Development The Rockefeller University New YorkNY United States Hospital Israelita Albert Einstein SP Sao Paulo Brazil Surgical Oncology Program National Cancer Institute National Institutes of Health BethesdaMD United St

Iterative Bleaching Extends multipleXity (IBEX) is a versatile method for highly multiplexed imaging of diverse tissues. Based on open science principles, we created the IBEX Knowledge-Base, a resource for reagents, p... 详细信息

关键词： Cleaning

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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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