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Author Correction: Profiling immunoglobulin repertoires across multiple human tissues using RNA sequencing

Nature communications 2020年第1期11卷 4499页

作者： Igor Mandric Jeremy Rotman Harry Taegyun Yang Nicolas Strauli Dennis J Montoya William Van Der Wey Jiem R Ronas Benjamin Statz Douglas Yao Velislava Petrova Alex Zelikovsky Roberto Spreafico Sagiv Shifman Noah Zaitlen Maura Rossetti K Mark Ansel Eleazar Eskin Serghei Mangul Department of Computer Science University of California Los Angeles 404 Westwood Plaza Los Angeles CA 90095 USA. Department of Clinical Pharmacy School of Pharmacy University of Southern California 1540 Alcazar Street Los Angeles CA 90033 USA. Bioinformatics Interdepartmental Ph.D. Program University of California Los Angeles 611 Charles E. Young Drive East Los Angeles CA 90095-1570 USA. Biomedical Sciences Graduate Program University of California San Francisco 1675 Owens Street Suite 310 San Francisco CA 94143-0523 USA. Department of Molecular Cell and Developmental Biology University of California Los Angeles 610 Charles E. Young Drive South Los Angeles CA 90095 USA. Department of Microbiology Immunology and Molecular Genetics University of California Los Angeles 609 Charles E. Young Drive East Los Angeles CA 90095 USA. Program in Bioinformatics and Integrative Genomics Harvard Medical School 10 Shattuck Street Suite 514 Boston MA 02115 USA. Wellcome Trust Sanger Institute Wellcome Genome Campus Hinxton Cambridge CB10 1SA UK. Department of Computer Science Georgia State University 33 Gilmer Street SE Atlanta GA 30303 USA. The Laboratory of Bioinformatics I.M. Sechenov First Moscow State Medical University Moscow 119991 Russia. Institute for Quantitative and Computational Biosciences University of California Los Angeles 611 Charles E. Young Drive East Los Angeles CA 90095 USA. Department of Genetics The Institute of Life Sciences The Hebrew University of Jerusalem Jerusalem 9190401 Israel. Department of Medicine University of California San Francisco 533 Parnassus Avenue San Francisco CA 94143 USA. Immunogenetics Center Department of Pathology and Laboratory Medicine David Geffen School of Medicine University of California Los Angeles 1000 Veteran Avenue Los Angeles CA 90095-1652 USA. Sandler Asthma Basic Research Center Department of Microbiology and Immunology University of California San Francisco 513 Parnass

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

关键词： computational biology and bioinformatics Adaptive immunity Immunogenetics B cells

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GWAS meta-analysis of over 29,000 people with epilepsy identifies 26 risk loci and subtype-specific genetic architecture

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Nature genetics 2023年第9期55卷 1471-1482页

作者： Remi Stevelink Dorothee Kasteleijn-Nolst Trenite Bobby P. C. Koeleman Dick Lindhout Anja C. M. Sonsma Ciarán Campbell Gianpiero L. Cavalleri Norman Delanty Hany El-Naggar Austin Lacey Peter Widdess-Walsh Colin P. Doherty Siwei Chen Claire Churchhouse Mark J. Daly Yen-Chen A. Feng Daniel P. Howrigan Mitja I. Kurki Benjamin M. Neale Aarno Palotie Wei Zhou Namrata Gupta Henrike O. Heyne Bassel Abou-Khalil Kevin F. Haas R. S. Taneja Oluyomi M. Adesoji Michael Nothnagel Peter Nürnberg Thomas Sander Zaid Afawi Ilan Blatt Amos D. Korczyn Elisabetta Amadori Ganna Balagura Antonella Riva Marcello Scala Paolo Scudieri Pasquale Striano Federico Zara Michele Iacomino Francesca Madia Alison Anderson Patrick Kwan Terence J. O’Brien Slavé Petrovski K. Meng Tan Marian Todaro Joseph Anderson Danielle M. Andrade Quratulain Zulfiqar Ali Grazia Annesi Pauls Auce Andreja Avbersek Simona Balestrini Vera Braatz Claudia B. Catarino Krishna Chinthapalli Jennifer Jamnadas-Khoda Dalia Kasperavičiūte Costin Leu Josemir W. Sander Sanjay M. Sisodiya Sara Zagaglia Melanie Bahlo Karen L. Oliver Mark D. Baker Beata Fonferko-Shadrach William O. Pickrell Carmen Barba Claudia Bianchini Viola Doccini Renzo Guerrini Davide Mei Martino Montomoli Elena Parrini Annalisa Vetro Karen Barboza Fabrice Bartolomei Thomas Bast Bernhard J. Steinhoff Larry Baum Stacey S. Cherny Pak Sham Tobias Baumgartner Christian E. Elger Kerstin Hallmann Wolfram S. Kunz Rainer Surges Randi von Wrede Gábor Zsurka Betül Baykan Nerses Bebek Yeşim Kesim Albert J. Becker Susanne Schoch Felicitas Becker Caitlin A. Bennett Samuel F. Berkovic Stephanie L. Leech Brigid M. Regan Ingrid E. Scheffer Bianca Berghuis Ahmad Beydoun Wassim Nasreddine Francesca Bisulli Lidia Di Vito Lorenzo Ferri Tania Giangregorio Laura Licchetta Raffaella Minardi Barbara Mostacci Carlotta Stipa Paolo Tinuper Lorenzo Muccioli Federica Pondrelli Dheeraj R. Bobbili Emadeldin Hassanin Roland Krause Zied Landoulsi Patrick May Ingo Borggraefe Christian Bosselmann Christian Hengsbach Josua Kegele Stephen Lauxmann Department of Genetics University Medical Center Utrecht Utrecht The Netherlands Stichting Epilepsie Instellingen Nederland (SEIN) Heemstede The Netherlands School of Pharmacy and Biomolecular Sciences The Royal College of Surgeons in Ireland Dublin Ireland The FutureNeuro Research Centre Dublin Ireland Department of Neurology Beaumont Hospital Dublin Ireland Department of Neurology St. James’s Hospital Dublin Ireland Analytic and Translational Genetics Unit Department of Medicine Massachusetts General Hospital and Harvard Medical School Boston MA USA Program in Medical and Population Genetics Broad Institute of MIT and Harvard Cambridge MA USA Stanley Center for Psychiatric Research Broad Institute of Harvard and M.I.T Cambridge MA USA Institute for Molecular Medicine Finland (FIMM) University of Helsinki Helsinki Finland Psychiatric & Neurodevelopmental Genetics Unit Department of Psychiatry Massachusetts General Hospital and Harvard Medical School Boston MA USA Division of Biostatistics Institute of Epidemiology and Preventive Medicine College of Public Health National Taiwan University Taipei Taiwan Hasso Plattner Institute Digital Health Center University of Potsdam Potsdam Germany Hasso Plattner Institute Mount Sinai School of Medicine New York City NY USA Department of Neurology Vanderbilt University Medical Center Nashville TN USA Cologne Center for Genomics (CCG) University of Cologne Faculty of Medicine and University Hospital Cologne Cologne Germany University Hospital Cologne Cologne Germany Department of Neurology Charité Universitaetsmedizin Berlin Campus Virchow-Clinic Berlin Germany Tel-Aviv University Sackler Faculty of Medicine Ramat Aviv Israel Department of Neurology Sheba Medical Center Ramat Gan Israel Department of Neurosciences Rehabilitation Ophthalmology Genetics Maternal and Child Health University of Genova Genova Italy IRCCS Istituto Giannina Gaslini Genova Italy Department of Medicine University of Melbour

Epilepsy is a highly heritable disorder affecting over 50 million people worldwide, of which about one-third are resistant to current treatments. Here we report a multi-ancestry genome-wide association study including 29,944 cases, stratified into three broad categories and seven subtypes of epilepsy, and 52,538 controls. We identify 26 genome-wide significant loci, 19 of which are specific to genetic generalized epilepsy (GGE). We implicate 29 likely causal genes underlying these 26 loci. SNP-based heritability analyses show that common variants explain between 39.6% and 90% of genetic risk for GGE and its subtypes. Subtype analysis revealed markedly different genetic architectures between focal and generalized epilepsies. Gene-set analyses of GGE signals implicate synaptic processes in both excitatory and inhibitory neurons in the brain. Prioritized candidate genes overlap with monogenic epilepsy genes and with targets of current antiseizure medications. Finally, we leverage our results to identify alternate drugs with predicted efficacy if repurposed for epilepsy treatment.

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Author Correction: Pan-cancer analysis of whole genomes identifies driver rearrangements promoted by LINE-1 retrotransposition

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Nature genetics 2023年第6期55卷 1080页

作者： Bernardo Rodriguez-Martin Eva G Alvarez Adrian Baez-Ortega Jorge Zamora Fran Supek Jonas Demeulemeester Martin Santamarina Young Seok Ju Javier Temes Daniel Garcia-Souto Harald Detering Yilong Li Jorge Rodriguez-Castro Ana Dueso-Barroso Alicia L Bruzos Stefan C Dentro Miguel G Blanco Gianmarco Contino Daniel Ardeljan Marta Tojo Nicola D Roberts Sonia Zumalave Paul A Edwards Joachim Weischenfeldt Montserrat Puiggròs Zechen Chong Ken Chen Eunjung Alice Lee Jeremiah A Wala Keiran M Raine Adam Butler Sebastian M Waszak Fabio C P Navarro Steven E Schumacher Jean Monlong Francesco Maura Niccolo Bolli Guillaume Bourque Mark Gerstein Peter J Park David C Wedge Rameen Beroukhim David Torrents Jan O Korbel Iñigo Martincorena Rebecca C Fitzgerald Peter Van Loo Haig H Kazazian Kathleen H Burns Peter J Campbell Jose M C Tubio Department of Zoology Genetics and Physical Anthropology Universidade de Santiago de Compostela Santiago de Compostela Spain. 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. Transmissible Cancer Group Department of Veterinary Medicine University of Cambridge Cambridge UK. The Biomedical Research Centre (CINBIO) Universidade de Vigo Vigo Spain. Wellcome Sanger Institute Wellcome Genome Campus Cambridge UK. Genome Data Science Institute for Research in Biomedicine (IRB Barcelona) The Barcelona Institute of Science and Technology (BIST) Barcelona Spain. Institucio Catalana de Recerca i Estudis Avançats (ICREA) Barcelona Spain. The Francis Crick Institute London UK. Department of Human Genetics University of Leuven Leuven Belgium. Genomes and Disease Centre for Research in Molecular Medicine and Chronic Diseases (CIMUS) Universidade de Santiago de Compostela Santiago de Compostela Spain. Graduate School of Medical Science and Engineering Korea Advanced Institute of Science and Technology Daejeon South Korea. Cancer Ageing and Somatic Mutation Programme Wellcome Sanger Institute Cambridge UK. Department of Biochemistry Genetics and Immunology University of Vigo Vigo Spain. Galicia Sur Health Research Institute Vigo Spain. Faculty of Science and Technology University of Vic-Central University of Catalonia (UVic-UCC) Vic Spain. Barcelona Supercomputing Center (BSC) Barcelona Spain. Experimental Cancer Genetics Wellcome Sanger Institute Cambridge UK. Oxford Big Data Institute University of Oxford Oxford UK. DNA Repair and Genome Integrity Centre for Research in Molecular Medicine and Chronic Diseases (CIMUS) Universidade de Santiago de Compostela Santiago de Compostela Spain. Department of Biochemistry and Molecular Biology Universidade de Santiago de Compostela Santiago de Compostela Spain. Medical R

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The Network Zoo: a multilingual package for the inference and analysis of gene regulatory networks

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Genome biology 2023年第1期24卷 45页

作者： Marouen Ben Guebila Tian Wang Camila M Lopes-Ramos Viola Fanfani Des Weighill Rebekka Burkholz Daniel Schlauch Joseph N Paulson Michael Altenbuchinger Katherine H Shutta Abhijeet R Sonawane James Lim Genis Calderer David G P van IJzendoorn Daniel Morgan Alessandro Marin Cho-Yi Chen Qi Song Enakshi Saha Dawn L DeMeo Megha Padi John Platig Marieke L Kuijjer Kimberly Glass John Quackenbush Department of Biostatistics Harvard T.H. Chan School of Public Health Boston MA USA. Present Address: Biology Department Boston College Chestnut Hill MA USA. Channing Division of Network Medicine Brigham and Women's Hospital and Harvard Medical School Boston MA USA. Present Address: Lineberger Comprehensive Cancer Center University of North Carolina at Chapel Hill Chapel Hill NC USA. Present Address: CISPA Helmholtz Center for Information Security Saarbrücken Germany. Present Address: Genospace LLC Boston MA USA. Department of Biochemistry and Molecular Biology Pennsylvania State University College of Medicine Hershey PA USA. Present Address: Department of Medical Bioinformatics University Medical Center Göttingen Göttingen Germany. Present Address: Center for Interdisciplinary Cardiovascular Sciences Division of Cardiovascular Medicine Department of Medicine Brigham and Women's Hospital Boston MA USA. Department of Molecular and Cellular Biology University of Arizona Tucson AZ USA. Present Address: Monoceros Biosystems LLC San Diego CA USA. Center for Molecular Medicine Norway Nordic EMBL Partnership University of Oslo Oslo Norway. Department of Pathology Leiden University Medical Center Leiden The Netherlands. Present Address: Department of Pathology Stanford University School of Medicine Palo Alto CA USA. Present Address: School of Biomedical Sciences Hong Kong University Pokfulam Hong Kong. Expert Analytics AS Oslo Norway. Dana-Farber Cancer Institute Boston MA USA. Present Address: Institute of Biomedical Informatics National Yang Ming Chiao Tung University Taipei 112 Taiwan. Present Address: Computational Biology Department Carnegie Mellon University Pittsburgh PA USA. Leiden Center for Computational Oncology Leiden University Leiden The Netherlands. Department of Biostatistics Harvard T.H. Chan School of Public Health Boston MA USA. johnq@hsph.harvard.edu. Channing Division of Network Medicine Brigham and Women's Hospital and Har

Inference and analysis of gene regulatory networks (GRNs) require software that integrates multi-omic data from various sources. The Network Zoo (netZoo; ***) is a collection of open-source methods to infer GRNs, conduct differential network analyses, estimate community structure, and explore the transitions between biological states. The netZoo builds on our ongoing development of network methods, harmonizing the implementations in various computing languages and between methods to allow better integration of these tools into analytical pipelines. We demonstrate the utility using multi-omic data from the Cancer Cell Line Encyclopedia. We will continue to expand the netZoo to incorporate additional methods.

关键词： Gene regulation Multi-omic analysis Network biology Open-source software

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Author Correction: An atlas of dynamic chromatin landscapes in mouse fetal development

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Nature 2020年第7831期586卷 E31页

作者： David U Gorkin Iros Barozzi Yuan Zhao Yanxiao Zhang Hui Huang Ah Young Lee Bin Li Joshua Chiou Andre Wildberg Bo Ding Bo Zhang Mengchi Wang J Seth Strattan Jean M Davidson Yunjiang Qiu Veena Afzal Jennifer A Akiyama Ingrid Plajzer-Frick Catherine S Novak Momoe Kato Tyler H Garvin Quan T Pham Anne N Harrington Brandon J Mannion Elizabeth A Lee Yoko Fukuda-Yuzawa Yupeng He Sebastian Preissl Sora Chee Jee Yun Han Brian A Williams Diane Trout Henry Amrhein Hongbo Yang J Michael Cherry Wei Wang Kyle Gaulton Joseph R Ecker Yin Shen Diane E Dickel Axel Visel Len A Pennacchio Bing Ren Ludwig Institute for Cancer Research La Jolla CA USA. Center for Epigenomics University of California San Diego School of Medicine La Jolla CA USA. Environmental Genomics and Systems Biology Division Lawrence Berkeley National Laboratory Berkeley CA USA. Department of Surgery and Cancer Imperial College London London UK. Bioinformatics and Systems Biology Graduate Program University of California San Diego La Jolla CA USA. Biomedical Sciences Graduate Program University of California San Diego School of Medicine La Jolla CA USA. Department of Pediatrics University of California San Diego School of Medicine La Jolla CA USA. Department of Cellular and Molecular Medicine University of California San Diego School of Medicine La Jolla CA USA. Department of Biochemistry and Molecular Biology Penn State School of Medicine Hershey PA USA. Stanford University School of Medicine Department of Genetics Stanford CA USA. Genomic Analysis Laboratory Salk Institute for Biological Studies La Jolla CA USA. Division of Biology and Biological Engineering California Institute of Technology Pasadena CA USA. Howard Hughes Medical Institute Salk Institute for Biological Studies La Jolla CA USA. Institute for Human Genetics and University of California San Francisco San Francisco CA USA. Department of Neurology University of California San Francisco San Francisco CA USA. Environmental Genomics and Systems Biology Division Lawrence Berkeley National Laboratory Berkeley CA USA. avisel@lbl.gov. US Department of Energy Joint Genome Institute Berkeley CA USA. avisel@lbl.gov. School of Natural Sciences University of California Merced Merced CA USA. avisel@lbl.gov. Environmental Genomics and Systems Biology Division Lawrence Berkeley National Laboratory Berkeley CA USA. lapennacchio@lbl.gov. US Department of Energy Joint Genome Institute Berkeley CA USA. lapennacchio@lbl.gov. Comparative Biochemistry Program University of California Berkeley Berkeley CA USA

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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Causes of blindness and vision impairment in 2020 and trends over 30 years, and prevalence of avoidable blindness in relation to VISION 2020: the Right to Sight: an analysis for the Global Burden of Disease Study (vol 2, pg 144, 2021)

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LANCET GLOBAL HEALTH 2021年第4期9卷 E408-E408页

作者： Steinmetz, Jaimie D. Vision and Eye Research Institute Anglia Ruskin University Cambridge United Kingdom Biomedical Informatics Seoul National University Hospital Seoul South Korea Institute for Health Metrics and Evaluation University of Washington Seattle WA United States Department of Health Metrics Sciences School of Medicine University of Washington Seattle WA United States Institute of Health Services Research Yonsei University Seoul South Korea Department of Ophthalmology University of Washington Seattle WA United States Department of Mathematics Imperial College London London United Kingdom WHO Collaborating Centre for Public Health Education and Training Imperial College London London United Kingdom Department of Primary Care and Public Health Imperial College London London United Kingdom School of Population and Global Health University of Melbourne Carlton VIC Australia School of Optometry and Vision Science UNSW Sydney NSW Australia Brien Holden Vision Institute Sydney Australia Department of Ophthalmology University of Adelaide Adelaide SA Australia Department of Parasitology and Mycology Jahrom University of Medical Sciences Jahrom Iran Department of Clinical Sciences University of Sharjah Sharjah United Arab Emirates Ophthalmic Research Center Shahid Beheshti University of Medical Sciences Tehran Iran Department of Ophthalmology Shahid Beheshti University of Medical Sciences Tehran Iran Research Institute for Endocrine Sciences Shahid Beheshti University of Medical Sciences Tehran Iran Ophthalmic Epidemiology Research Center Shahid Beheshti University of Medical Sciences Tehran Iran Health Services Management Department Qazvin University of Medical Sciences Qazvin Iran Department of Systems Populations and Leadership University of Michigan Ann Arbor MI United States Department of Medicine Sofia Ismail Memorial Medical Centre Bogura Bangladesh The Fred Hollows Foundation Sydney NSW Australia Berhan Public Health & Eye Care Consultancy Addis A

Hospital El Salvador: a novel paradigm of intensive care in response to COVID-19 in central America. Lancet Glob Health 2021;9: e241?42?In this Comment, the conflict of interest statement should have included the following: ?By virtue of their roles within a public hospital or the Ministry of Health, MB, LC, WH, and XS are government employees. The findings and conclusions in the Comment are only those of the authors.? This correction has been made as of Feb 26, 2021.

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Author Correction: Cell segmentation-free inference of cell types from in situ transcriptomics data

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Nature communications 2021年第1期12卷 4103页

作者： Jeongbin Park Wonyl Choi Sebastian Tiesmeyer Brian Long Lars E Borm Emma Garren Thuc Nghi Nguyen Bosiljka Tasic Simone Codeluppi Tobias Graf Matthias Schlesner Oliver Stegle Roland Eils Naveed Ishaque Berlin Institute of Health at Charité-Universitätsmedizin Berlin Digital Health Center Kapelle-Ufer 2 10117 Berlin Germany. Faculty of Biosciences Heidelberg University Heidelberg Germany. Division of Computational Genomics and System Genetics German Cancer Research Center (DKFZ) Heidelberg Germany. Department of Computer Science Boston University Boston MA USA. Allen Institute for Brain Science Seattle WA USA. Division of molecular neurobiology Department of medical biochemistry and biophysics Karolinska Institutet Stockholm Sweden. Bioinformatics and Omics Data Analytics German Cancer Research Center (DKFZ) Heidelberg Germany. Genome Biology Unit European Molecular Biology Laboratory (EMBL) Heidelberg Germany. Berlin Institute of Health at Charité-Universitätsmedizin Berlin Digital Health Center Kapelle-Ufer 2 10117 Berlin Germany. roland.eils@bih-charite.de. Health Data Science Unit Heidelberg University Hospital Heidelberg Germany. roland.eils@bih-charite.de. Berlin Institute of Health at Charité-Universitätsmedizin Berlin Digital Health Center Kapelle-Ufer 2 10117 Berlin Germany. naveed.ishaque@bih-charite.de.

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Author Correction: Guidelines for public database submission of uncultivated virus genome sequences for taxonomic classification

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Nature biotechnology 2023年第9期41卷 1346页

作者： Evelien M Adriaenssens Simon Roux J Rodney Brister Ilene Karsch-Mizrachi Jens H Kuhn Arvind Varsani Tong Yigang Alejandro Reyes Cédric Lood Elliot J Lefkowitz Matthew B Sullivan Robert A Edwards Peter Simmonds Luisa Rubino Sead Sabanadzovic Mart Krupovic Bas E Dutilh Quadram Institute Bioscience Norwich Research Park Rosalind Franklin Road Norwich UK. evelien.adriaenssens@quadram.ac.uk. United States Department of Energy Joint Genome Institute Lawrence Berkeley National Laboratory Berkeley CA USA. National Center for Biotechnology Information National Library of Medicine National Institutes of Health Bethesda MD USA. Integrated Research Facility at Fort Detrick National Institute of Allergy and Infectious Diseases National Institutes of Health Fort Detrick Frederick MD USA. The Biodesign Center for Fundamental and Applied Microbiomics Arizona State University Tempe AZ USA. Structural Biology Research Unit Department of Clinical Laboratory Sciences University of Cape Town Cape Town South Africa. Beijing Advanced Innovation Center for Soft Matter Science and Engineering College of Life Science and Technology Beijing University of Chemical Technology Beijing China. Max Planck Tandem Group in Computational Biology Department of Biological Sciences Universidad de los Andes Bogotá Colombia. Centre of Microbial and Plant Genetics Department of Microbial and Molecular Systems KU Leuven Leuven Belgium. Laboratory of Gene Technology Department of Biosystems KU Leuven Leuven Belgium. Institute of Biodiversity Faculty of Biological Sciences Cluster of Excellence Balance of the Microverse Friedrich Schiller University Jena Jena Germany. Department of Microbiology University of Alabama at Birmingham Birmingham AL USA. Department of Microbiology The Ohio State University Columbus OH USA. Department of Civil Environmental and Geodetic Engineering The Ohio State University Columbus OH USA. Center of Microbiome Science The Ohio State University Columbus OH USA. College of Science and Engineering Flinders University Bedford Park South Australia Australia. Nuffield Department of Medicine University of Oxford South Parks Road Oxford UK. Consiglio Nazionale delle Ricerche Istituto per la Protezione Sostenibile delle Piante

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Erratum to: A survey of best practices for RNA-seq data analysis

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Genome biology 2016年第1期17卷 181页

作者： Ana Conesa Pedro Madrigal Sonia Tarazona David Gomez-Cabrero Alejandra Cervera Andrew McPherson Michal Wojciech Szcześniak Daniel J Gaffney Laura L Elo Xuegong Zhang Ali Mortazavi Institute for Food and Agricultural Sciences Department of Microbiology and Cell Science University of Florida Gainesville FL 32603 USA. aconesa@ufl.edu. Centro de Investigación Príncipe Felipe Genomics of Gene Expression Laboratory 46012 Valencia Spain. aconesa@ufl.edu. Wellcome Trust Sanger Institute Wellcome Trust Genome Campus Hinxton Cambridge CB10 1SA UK. pm12@sanger.ac.uk. Wellcome Trust-Medical Research Council Cambridge Stem Cell Institute Anne McLaren Laboratory for Regenerative Medicine Department of Surgery University of Cambridge Cambridge CB2 0SZ UK. pm12@sanger.ac.uk. Centro de Investigación Príncipe Felipe Genomics of Gene Expression Laboratory 46012 Valencia Spain. Department of Applied Statistics Operations Research and Quality Universidad Politécnica de Valencia 46020 Valencia Spain. Unit of Computational Medicine Department of Medicine Karolinska Institutet Karolinska University Hospital 171 77 Stockholm Sweden. Center for Molecular Medicine Karolinska Institutet 17177 Stockholm Sweden. Unit of Clinical Epidemiology Department of Medicine Karolinska University Hospital L8 17176 Stockholm Sweden. Science for Life Laboratory 17121 Solna Sweden. Systems Biology Laboratory Institute of Biomedicine and Genome-Scale Biology Research Program University of Helsinki 00014 Helsinki Finland. School of Computing Science Simon Fraser University Burnaby V5A 1S6BC Canada. Department of Bioinformatics Institute of Molecular Biology and Biotechnology Adam Mickiewicz University in Poznań 61-614 Poznań Poland. Wellcome Trust Sanger Institute Wellcome Trust Genome Campus Hinxton Cambridge CB10 1SA UK. Turku Centre for Biotechnology University of Turku and Åbo Akademi University FI-20520 Turku Finland. Key Lab of Bioinformatics/Bioinformatics Division TNLIST and Department of Automation Tsinghua University Beijing 100084 China. School of Life Sciences Tsinghua University Beijing 100084 China. Department of Developmental and Cell Biolo

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Automatic Extraction of Medication Mentions from Tweets-Overview of the BioCreative VII Shared Task 3 Competition

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Database : the journal of biological databases and curation 2023年第2023期2023卷 baac108页

作者： Davy Weissenbacher Karen O'Connor Siddharth Rawal Yu Zhang Richard Tzong-Han Tsai Timothy Miller Dongfang Xu Carol Anderson Bo Liu Qing Han Jinfeng Zhang Igor Kulev Berkay Köprü Raul Rodriguez-Esteban Elif Ozkirimli Ammer Ayach Roland Roller Stephen Piccolo Peijin Han V G Vinod Vydiswaran Ramya Tekumalla Juan M Banda Parsa Bagherzadeh Sabine Bergler João F Silva Tiago Almeida Paloma Martinez Renzo Rivera-Zavala Chen-Kai Wang Hong-Jie Dai Luis Alberto Robles Hernandez Graciela Gonzalez-Hernandez Department of Computational Biomedicine Cedars-Sinai Medical Center Los Angeles CA USA. DBEI The Perelman School of Medicine University of Pennsylvania Philadelphia PA USA. Department of Computer Science and Information Engineering National Central University No. 300 Zhongda Rd Zhongli District Taoyuan 320 Taiwan. IoX Center National Taiwan University Da'an District Section 4 Roosevelt Rd No. 1 Barry Lam Hall Taipei 106 Taiwan. Research Center for Humanities and Social Sciences Academia Sinica No. 128 Section 2 Academia Rd Nangang District Taipei 115 Taiwan. Computational Health Informatics Program Boston Children's Hospital Boston MA USA. Department of Pediatrics Harvard Medical School Boston MA USA. NVIDIA Santa Clara CA USA. Department of Statistics Florida State University Tallahassee FL USA. Data and Analytics Chapter F. Hoffmann-La Roche Ltd Switzerland. Pharmaceutical Research and Early Development Roche Innovation Center Basel Switzerland. Speech and Language Technology Lab DFKI Berlin Germany. Department of Biology Brigham Young University Provo UT USA. Department of Computational Medicine and Bioinformatics Medical School University of Michigan Ann Arbor MI USA. Department of Learning Health Sciences Medical School University of Michigan Ann Arbor MI USA. School of Information University of Michigan Ann Arbor MI USA. Department of Computer Science Georgia State University Atlanta GA USA. CLaC Labs Concordia University Montreal Canada. DETI Institute of Electronics and Informatics Engineering of Aveiro University of Aveiro Portugal. Department of Computation University of A Coruña Spain. Computer Science and Engineering Department Universidad Carlos III de Madrid Madrid Spain. Big Data Laboratory Chunghwa Telecom Laboratories Taoyuan Taiwan. Department of Computer Science National Yang Ming Chiao Tung University Hsinchu Taiwan. Department of Electrical Engineering College of Electrical Engineering and Computer Sci

This study presents the outcomes of the shared task competition BioCreative VII (Task 3) focusing on the extraction of medication names from a Twitter user's publicly available tweets (the user's 'timeline'). In general, detecting health-related tweets is notoriously challenging for natural language processing tools. The main challenge, aside from the informality of the language used, is that people tweet about any and all topics, and most of their tweets are not related to health. Thus, finding those tweets in a user's timeline that mention specific health-related concepts such as medications requires addressing extreme imbalance. Task 3 called for detecting tweets in a user's timeline that mentions a medication name and, for each detected mention, extracting its span. The organizers made available a corpus consisting of 182 049 tweets publicly posted by 212 Twitter users with all medication mentions manually annotated. The corpus exhibits the natural distribution of positive tweets, with only 442 tweets (0.2%) mentioning a medication. This task was an opportunity for participants to evaluate methods that are robust to class imbalance beyond the simple lexical match. A total of 65 teams registered, and 16 teams submitted a system run. This study summarizes the corpus created by the organizers and the approaches taken by the participating teams for this challenge. The corpus is freely available at https://***/tasks/biocreative-vii/track-3/. The methods and the results of the competing systems are analyzed with a focus on the approaches taken for learning from class-imbalanced data.

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