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Erratum for Wang et al., "Clinically Applicable System for Rapidly Predicting Enterococcus faecium Susceptibility to Vancomycin"

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Microbiology spectrum 2022年第1期10卷 e0261021页

作者： Hsin-Yao Wang Chia-Ru Chung Chao-Jung Chen Ko-Pei Lu Yi-Ju Tseng Tzu-Hao Chang Min-Hsien Wu Wan-Ting Huang Ting-Wei Lin Tsui-Ping Liu Tzong-Yi Lee Jorng-Tzong Horng Jang-Jih Lu Department of Laboratory Medicine Chang Gung Memorial Hospitalgrid.413801.f at Linkou Taoyuan City Taiwan. Ph.D. Program in Biomedical Engineering Chang Gung Universitygrid.145695.a Taoyuan City Taiwan. Department of Computer Science and Information Engineering National Central Universitygrid.37589.30 Taoyuan City Taiwan. Graduate Institute of Integrated Medicine China Medical Universitygrid.254145.3 Taichung Taiwan. Proteomics Core Laboratory China Medical Universitygrid.254145.3 Hospital Taichung Taiwan. Graduate Program in Biomedical Information Yuan-Ze University Taoyuan City Taiwan. Department of Information Management Chang Gung Universitygrid.145695.a Taoyuan City Taiwan. Graduate Institute of Biomedical Informatics Taipei Medical University Taipei City Taiwan. Clinical Big Data Research Center Taipei Medical University Hospital Taipei City Taiwan. Graduate Institute of Biomedical Engineering Chang Gung Universitygrid.145695.a Taoyuan City Taiwan. Division of Haematology/Oncology Department of Internal Medicine Chang Gung Memorial Hospitalgrid.413801.f at Linkou Taoyuan City Taiwan. Biosensor Group Biomedical Engineering Research Center Chang Gung Universitygrid.145695.a Taoyuan City Taiwan. Department of Pathology Kaohsiung Chang Gung Memorial Hospitalgrid.413801.f and Chang Gung University College of Medicine Kaohsiung Taiwan. School of Life and Health Sciences The Chinese University of Hong Kong Shenzhen China. Warshel Institute for Computational Biology The Chinese University of Hong Kong Shenzhen China. Department of Bioinformatics and Medical Engineering Asia University Taichung City Taiwan. School of Medicine Chang Gung Universitygrid.145695.a Taoyuan City Taiwan. Department of Medical Biotechnology and Laboratory Science Chang Gung Universitygrid.145695.a Taoyuan City Taiwan.

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46. PAN-CANCER ANALYSIS OF ORTHOTOPIC PATIENT DERIVED XENOGRAFTS FROM BRAIN METASTASES

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Neuro-Oncology Advances 2020年第SUPPLEMENT_2期2卷 ii9-ii9页

作者： Zeng, Yu Pelton, Kristine Yerrum, Smitha Kao, Pei-Lun Sinai, Claire Tran, Tony Sinha, Rileen Shetty, Aniket Tolstorukov, Michael Y Jaber, Aliya Freitas, Dylan E Pisano, William Verselis, Sigitas J Herbert, Zach T Lin, Nancy U Zhao, Jean J Weinstock, David M Chukwueke, Ugonma N Aizer, Ayal A Chiocca, E Antonio Bi, Wenya Linda Wen, Patrick Y Lee, Eudocia Q Nayak, Lakshmi Meredith, David M Santagata, Sandro Chow, Kin-Hoe Ligon, Keith L Department of Oncologic Pathology Dana-Farber Cancer Institute Boston MA USA Department of Neurosurgery Xiangya Hospital Central South University Changsha China Center for Patient Derived Models Dana-Farber Cancer Institute Boston MA USA Bioinformatics and Data Science Group Informatics and Analytics Department Dana-Farber Cancer Institute Boston MA USA Molecular Diagnostics Laboratory Dana-Farber Cancer Institute Boston MA USA The Molecular Biology Core Facilities Dana-Farber Cancer Institute Boston MA USA Department of Medical Oncology Dana-Farber Cancer Institute Boston Boston MA USA Department of Cancer Biology Dana-Farber Cancer Institute Boston MA USA Department of Radiation Oncology Dana-Farber/Brigham and Women’s Cancer Center Harvard Medical School Boston MA USA Department of Neurosurgery Brigham and Women’s Hospital Boston MA USA Department of Pathology Brigham and Women’s Hospital Boston MA USA

Brain metastases (BM) are a leading cause of cancer death and prognosis remains poor despite treatment advances at other sites. Models are central to therapeutic development, but few orthotopic patient-derived xenograft (PDX) models of BM exist. To represent diversity across BM types, we established a program to create orthotopic PDX at scale from all BM patients. To date BM were received from 100 patients and PDX attempted by direct brain injection (PDX, n=89) or injection of low passage patient-derived cell lines (PDCLX, n=11). We created 65 successful BM PDX from 13 cancers: 17 lung (55% take), 15 breast (68%), 6 melanoma (75%), 5 CNS lymphoma (83%), 3 gastrointestinal (75%), 2 esophageal (40%), 2 ovarian (67%), 1 sarcoma (100%), 1 laryngeal (100%), 1 prostate (100%), 1 pancreatic (100%), 1 uterine adenosarcoma (100%), and 1 yolk sac tumor (100%). Take rate was similar for models derived from patients with prior chemotherapy-only versus immune/targeted therapy-only (63 vs 58%). Fifteen patients had live tumor and matching PBMCs archived for modeling in vitro immunotherapy responses. Mean time to moribund among different cancer types ranged from 27 days (yolk sac tumor) to 177.5 days (ovarian). BM PDX had a favorable timeline for preclinical study (90% moribund at 180 days). All PDX matched the patient driver SNVs and copy aberrations, even at >P4. No significant differences noted by immunodeficient strain (SCID versus NSG) or injection site (orthotopic versus heterotopic). Explants from BM PDX were able to generate long-term cell lines (60%) or short-term cultures with qualitative concordance of model-to-patient responses to targeted therapy (Osimertinib, EGFRi) and immunotherapy (Pembrolizumab, PD1i). Genomic and clinical data were used to create the DFCI BM PDX cBioPortal for public release and models distribution will be available through the DFCI center for Patient Derived Models.

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TMOD-03. PAN-CANCER ANALYSIS OF ORTHOTOPIC PATIENT DERIVED XENOGRAFTS FROM BRAIN METASTASES

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Neuro-Oncology 2020年第SUPPLEMENT_2期22卷 ii228–ii228页

作者： Yu Zeng Kristine Pelton Smitha Yerrum Pei-Lun Kao Claire Sinai Tony Tran Rileen Sinha Aniket Shetty Michael Tolstorukov Aliya Jaber Dylan Freitas William Pisano Sigitas J Verselis Zach T Herbert Nancy Lin Jean J Zhao David M Weinstock Ugonma Chukwueke Ayal A Aizer E Antonio Chiocca Wenya Linda Bi Patrick Wen Eudocia Lee Lakshmi Nayak David Meredith Sandro Santagata Kin Hoe Chow Keith Ligon Department of Oncologic Pathology Dana-Farber Cancer Institute Boston MA USA Center for Patient Derived Models Dana-Farber Cancer Institute Boston MA USA Data Science and Bioinformatics Group Dana-Farber Cancer Institute Boston MA USA Molecular Diagnostics Laboratory Dana-Farber Cancer Institute Boston MA USA The Molecular Biology Core Facilities Dana-Farber Cancer Institute Boston MA USA Dana Farber Cancer Institute Boston MA USA Department of Cancer Biology Dana-Farber Cancer Institute Boston MA USA Department of Medical Oncology Dana-Farber Cancer Institute Boston MA USA Department of Radiation Oncology Dana-Farber/Brigham and Women’s Cancer Center Harvard Medical School Boston MA USA Brigham and Women’s Hospital and Harvard Medical School Boston MA USA Department of Neurosurgery Brigham and Women’s Hospital Boston MA USA Department of Pathology Brigham and Women’s Hospital Boston MA USA

Brain metastases (BM) are a leading cause of cancer death and prognosis remains poor despite treatment advances at other sites. Models are central to therapeutic development, but few orthotopic patient-derived xenograft (PDX) models of BM exist. To represent diversity across BM types, we established a program to create orthotopic PDX at scale from all BM patients. To date BM were received from 100 patients and PDX attempted by direct brain injection (PDX, n=89) or injection of low passage patient-derived cell lines (PDCLX, n=11). We created 65 successful BM PDX from 13 cancers: 17 lung (55% take), 15 breast (68%), 6 melanoma (75%), 5 CNS lymphoma (83%), 3 gastrointestinal (75%), 2 esophageal (40%), 2 ovarian (67%), 1 sarcoma (100%), 1 laryngeal (100%), 1 prostate (100%), 1 pancreatic (100%), 1 uterine adenosarcoma (100%), and 1 yolk sac tumor (100%). Take rate was similar for models derived from patients with prior chemotherapy-only versus immune/targeted therapy-only (63 vs 58%). Fifteen patients had live tumor and matching PBMCs archived for modeling in vitro immunotherapy responses. Mean time to moribund among different cancer types ranged from 27 days (yolk sac tumor) to 177.5 days (ovarian). BM PDX had a favorable timeline for preclinical study (90% moribund at 180 days). All PDX retained high fidelity to the patient driver SNVs and copy aberrations, even at >P4. No significant differences noted by immunodeficient strain (SCID versus NSG) or injection site (orthotopic versus heterotopic). Explants from BM PDX were able to generate long-term cell lines (60%) or short-term cultures with qualitative concordance of model-to-patient responses to targeted therapy (Osimertinib, EGFRi) and immunotherapy (Pembrolizumab, PD1i). Genomic and clinical data were used to create the DFCI BM PDX cBioPortal for public release and models distribution will be available through the DFCI center for Patient Derived Models.

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Publisher Correction: A meta-analysis of genome-wide association studies identifies multiple longevity genes

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Nature communications 2021年第1期12卷 2463页

作者： Joris Deelen Daniel S Evans Dan E Arking Niccolò Tesi Marianne Nygaard Xiaomin Liu Mary K Wojczynski Mary L Biggs Ashley van der Spek Gil Atzmon Erin B Ware Chloé Sarnowski Albert V Smith Ilkka Seppälä Heather J Cordell Janina Dose Najaf Amin Alice M Arnold Kristin L Ayers Nir Barzilai Elizabeth J Becker Marian Beekman Hélène Blanché Kaare Christensen Lene Christiansen Joanna C Collerton Sarah Cubaynes Steven R Cummings Karen Davies Birgit Debrabant Jean-François Deleuze Rachel Duncan Jessica D Faul Claudio Franceschi Pilar Galan Vilmundur Gudnason Tamara B Harris Martijn Huisman Mikko A Hurme Carol Jagger Iris Jansen Marja Jylhä Mika Kähönen David Karasik Sharon L R Kardia Andrew Kingston Thomas B L Kirkwood Lenore J Launer Terho Lehtimäki Wolfgang Lieb Leo-Pekka Lyytikäinen Carmen Martin-Ruiz Junxia Min Almut Nebel Anne B Newman Chao Nie Ellen A Nohr Eric S Orwoll Thomas T Perls Michael A Province Bruce M Psaty Olli T Raitakari Marcel J T Reinders Jean-Marie Robine Jerome I Rotter Paola Sebastiani Jennifer Smith Thorkild I A Sørensen Kent D Taylor André G Uitterlinden Wiesje van der Flier Sven J van der Lee Cornelia M van Duijn Diana van Heemst James W Vaupel David Weir Kenny Ye Yi Zeng Wanlin Zheng Henne Holstege Douglas P Kiel Kathryn L Lunetta P Eline Slagboom Joanne M Murabito Max Planck Institute for Biology of Ageing Cologne Germany. Joris.Deelen@age.mpg.de. Molecular Epidemiology Department of Biomedical Data Sciences Leiden University Medical Center Leiden The Netherlands. Joris.Deelen@age.mpg.de. California Pacific Medical Center Research Institute San Francisco CA USA. DEvans@***. McKusick-Nathans Institute of Genetic Medicine Department of Genetic Medicine Johns Hopkins University School of Medicine Baltimore MD USA. Alzheimer Center Amsterdam Department of Neurology Amsterdam Neuroscience Vrije Universiteit Amsterdam Amsterdam UMC Amsterdam The Netherlands. Department of Clinical Genetics Amsterdam UMC Amsterdam The Netherlands. Delft Bioinformatics Lab Delft University of Technology Delft The Netherlands. The Danish Aging Research Center Department of Public Health University of Southern Denmark Odense C Denmark. BGI-Shenzhen Shenzhen China. China National Genebank BGI-Shenzhen Shenzhen China. Division of Statistical Genomics Department of Genetics Washington University School of Medicine Saint Louis MO USA. Department of Biostatistics University of Washington Seattle WA USA. Cardiovascular Health Research Unit Department of Medicine University of Washington Seattle WA USA. Department of Epidemiology Erasmus MC Rotterdam The Netherlands. Department of Biology Faculty of Natural Science University of Haifa Haifa Israel. Departments of Medicine and Genetics Albert Einstein College of Medicine Bronx NY USA. Institute for Social Research Survey Research Center University of Michigan Ann Arbor MI USA. Department of Biostatistics Boston University School of Public Health Boston MA USA. School of Public Health Department of Biostatistics University of Michigan Ann Arbor MI USA. Icelandic Heart Association Kópavogur Iceland. Department of Clinical Chemistry Fimlab Laboratories and Finnish Cardiovascular Research Center-Tampere Faculty of Medicine and Health Technology Tampere University Tampere Finland. I

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Author Correction: Federated learning enables big data for rare cancer boundary detection

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Nature communications 2023年第1期14卷 436页

作者： Sarthak Pati Ujjwal Baid Brandon Edwards Micah Sheller Shih-Han Wang G Anthony Reina Patrick Foley Alexey Gruzdev Deepthi Karkada Christos Davatzikos Chiharu Sako Satyam Ghodasara Michel Bilello Suyash Mohan Philipp Vollmuth Gianluca Brugnara Chandrakanth J Preetha Felix Sahm Klaus Maier-Hein Maximilian Zenk Martin Bendszus Wolfgang Wick Evan Calabrese Jeffrey Rudie Javier Villanueva-Meyer Soonmee Cha Madhura Ingalhalikar Manali Jadhav Umang Pandey Jitender Saini John Garrett Matthew Larson Robert Jeraj Stuart Currie Russell Frood Kavi Fatania Raymond Y Huang Ken Chang Carmen Balaña Jaume Capellades Josep Puig Johannes Trenkler Josef Pichler Georg Necker Andreas Haunschmidt Stephan Meckel Gaurav Shukla Spencer Liem Gregory S Alexander Joseph Lombardo Joshua D Palmer Adam E Flanders Adam P Dicker Haris I Sair Craig K Jones Archana Venkataraman Meirui Jiang Tiffany Y So Cheng Chen Pheng Ann Heng Qi Dou Michal Kozubek Filip Lux Jan Michálek Petr Matula Miloš Keřkovský Tereza Kopřivová Marek Dostál Václav Vybíhal Michael A Vogelbaum J Ross Mitchell Joaquim Farinhas Joseph A Maldjian Chandan Ganesh Bangalore Yogananda Marco C Pinho Divya Reddy James Holcomb Benjamin C Wagner Benjamin M Ellingson Timothy F Cloughesy Catalina Raymond Talia Oughourlian Akifumi Hagiwara Chencai Wang Minh-Son To Sargam Bhardwaj Chee Chong Marc Agzarian Alexandre Xavier Falcão Samuel B Martins Bernardo C A Teixeira Flávia Sprenger David Menotti Diego R Lucio Pamela LaMontagne Daniel Marcus Benedikt Wiestler Florian Kofler Ivan Ezhov Marie Metz Rajan Jain Matthew Lee Yvonne W Lui Richard McKinley Johannes Slotboom Piotr Radojewski Raphael Meier Roland Wiest Derrick Murcia Eric Fu Rourke Haas John Thompson David Ryan Ormond Chaitra Badve Andrew E Sloan Vachan Vadmal Kristin Waite Rivka R Colen Linmin Pei Murat Ak Ashok Srinivasan J Rajiv Bapuraj Arvind Rao Nicholas Wang Ota Yoshiaki Toshio Moritani Sevcan Turk Joonsang Lee Snehal Prabhudesai Fanny Morón Jacob Mandel Konstantinos Kamnitsas Ben Glocker Luke V M Dixon Matthew Williams Peter Zamp Center for Biomedical Image Computing and Analytics (CBICA) University of Pennsylvania Philadelphia PA USA. Department of Radiology Perelman School of Medicine University of Pennsylvania Philadelphia PA USA. Department of Pathology and Laboratory Medicine Perelman School of Medicine University of Pennsylvania Philadelphia PA USA. Department of Informatics Technical University of Munich Munich Bavaria Germany. Intel Corporation Santa Clara CA USA. Department of Neuroradiology Heidelberg University Hospital Heidelberg Germany. Clinical Cooperation Unit Neuropathology German Cancer Consortium (DKTK) within the German Cancer Research Center (DKFZ) Heidelberg Germany. Department of Neuropathology Heidelberg University Hospital Heidelberg Germany. Division of Medical Image Computing German Cancer Research Center Heidelberg Germany. Pattern Analysis and Learning Group Department of Radiation Oncology Heidelberg University Hospital Heidelberg Germany. Neurology Clinic Heidelberg University Hospital Heidelberg Germany. Department of Radiology & Biomedical Imaging University of California San Francisco San Francisco CA USA. Symbiosis Center for Medical Image Analysis Symbiosis International University Pune Maharashtra India. Department of Neuroimaging and Interventional Radiology National Institute of Mental Health and Neurosciences Bangalore Karnataka India. Department of Radiology School of Medicine and Public Health University of Wisconsin Madison WI USA. Department of Medical Physics School of Medicine and Public Health University of Wisconsin Madison WI USA. Leeds Teaching Hospitals Trust Department of Radiology Leeds UK. Department of Radiology Brigham and Women's Hospital Harvard Medical School Boston MA USA. Athinoula A. Martinos Center for Biomedical Imaging Massachusetts General Hospital Charlestown MA USA. Catalan Institute of Oncology Badalona Spain. Consorci MAR Parc de Salut de Barcelona Catalonia Spain. Department of Radiology (IDI

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Author Correction: Genetic effects on the timing of parturition and links to fetal birth weight

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Nature genetics 2023年第7期55卷 1250页

作者： Pol Solé-Navais Christopher Flatley Valgerdur Steinthorsdottir Marc Vaudel Julius Juodakis Jing Chen Triin Laisk Abigail L LaBella David Westergaard Jonas Bacelis Ben Brumpton Line Skotte Maria C Borges Øyvind Helgeland Anubha Mahajan Matthias Wielscher Frederick Lin Catherine Briggs Carol A Wang Gunn-Helen Moen Robin N Beaumont Jonathan P Bradfield Abin Abraham Gudmar Thorleifsson Maiken E Gabrielsen Sisse R Ostrowski Dominika Modzelewska Ellen A Nohr Elina Hypponen Amit Srivastava Octavious Talbot Catherine Allard Scott M Williams Ramkumar Menon Beverley M Shields Gardar Sveinbjornsson Huan Xu Mads Melbye William Lowe Luigi Bouchard Emily Oken Ole B Pedersen Daniel F Gudbjartsson Christian Erikstrup Erik Sørensen Rolv T Lie Kari Teramo Mikko Hallman Thorhildur Juliusdottir Hakon Hakonarson Henrik Ullum Andrew T Hattersley Line Sletner Mario Merialdi Sheryl L Rifas-Shiman Thora Steingrimsdottir Denise Scholtens Christine Power Jane West Mette Nyegaard John A Capra Anne H Skogholt Per Magnus Ole A Andreassen Unnur Thorsteinsdottir Struan F A Grant Elisabeth Qvigstad Craig E Pennell Marie-France Hivert Geoffrey M Hayes Marjo-Riitta Jarvelin Mark I McCarthy Deborah A Lawlor Henriette S Nielsen Reedik Mägi Antonis Rokas Kristian Hveem Kari Stefansson Bjarke Feenstra Pål Njolstad Louis J Muglia Rachel M Freathy Stefan Johansson Ge Zhang Bo Jacobsson Department of Obstetrics and Gynaecology Sahlgrenska Academy Institute of Clinical Science University of Gothenburg Gothenburg Sweden. pol.sole.navais@gu.se. Department of Obstetrics and Gynaecology Sahlgrenska Academy Institute of Clinical Science University of Gothenburg Gothenburg Sweden. deCODE genetics/Amgen Reykjavik Iceland. Center for Diabetes Research Department of Clinical Science University of Bergen Bergen Norway. Division of Biomedical Informatics Cincinnati Children's Hospital Medical Center Cincinnati OH USA. Department of Pediatrics University of Cincinnati College of Medicine Cincinnati OH USA. Estonian Genome Centre Institute of Genomics University of Tartu Tartu Estonia. Department of Biological Sciences Vanderbilt University Nashville TN USA. Novo Nordisk Foundation Center for Protein Research University of Copenhagen Copenhagen Denmark. Department of Obstetrics and Gynaecology Copenhagen University Hospital Hvidovre Hvidovre Denmark. Methods and Analysis Statistics Denmark Copenhagen Denmark. K.G. Jebsen Center for Genetic Epidemiology Department of Public Health and Nursing Norwegian University of Science and Technology Trondheim Norway. Department of Epidemiology Research Statens Serum Institut Copenhagen Denmark. MRC Integrative Epidemiology Unit University of Bristol Bristol UK. Population Health Sciences Bristol Medical School University of Bristol Bristol UK. Department of Genetics and Bioinformatics Health Data and Digitalization Norwegian Institute of Public Health Oslo Norway. Wellcome Trust Centre for Human Genetics University of Oxford Oxford UK. Genentech South San Francisco CA USA. Department of Epidemiology and Biostatistics MRC-PHE Centre for Environment and Health School of Public Health Imperial College London London UK. Department of Dermatology Medical University of Vienna Vienna Austria. Northwestern University Feinberg School of Medicine Chicago IL USA. Department of Population Medicine Harvard M

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Introducing evolutionary biologists to the analysis of big data: Guidelines to organize extended bioinformatics training courses

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Evolution: Education and Outreach 2018年第1期11卷 1-10页

作者： Faria, Rui Triant, Deborah Perdomo-Sabogal, Alvaro Overduin, Bert Bleidorn, Christoph Santana, Clara Isabel Bermudez Langenberger, David Indrischek, Henrike Aerts, Jan Engelhardt, Jan Engelken, Johannes Liebal, Katja Fasold, Mario Robb, Sofia Grath, Sonja Kolora, Sree Rohit Raj Carvalho, Tiago Salzburger, Walter Jovanovic, Vladimir Nowick, Katja CIBIO Centro de Investigação em Biodiversidade e Recursos Genéticos InBIO Laboratório Associado Universidade Do Porto Campus Agrário de Vairão Vairão 4485-661 Portugal IBE Institute of Evolutionary Biology (CSIC-UPF) Department of Experimental and Health Sciences Pompeu Fabra University Doctor Aiguader 88 Barcelona 08003 Spain Department of Animal and Plant Sciences University of Sheffield Sheffield United Kingdom Department of Biochemistry and Molecular Genetics University of Virginia Charlottesville 22908 VA United States TFome Research Group Bioinformatics Group Interdisciplinary Center of Bioinformatics Department of Computer Science University of Leipzig Härtelstrasse 16-18 Leipzig 04107 Germany Paul-Flechsig-Institute for Brain Research University of Leipzig Jahnallee 59 Leipzig 04109 Germany Faculty for Biology Chemistry and Pharmacy Freie Universität Berlin Königin-Luise-Straße 1-3 Berlin 14195 Germany Edinburgh Genomics University of Edinburgh Ashworth Laboratories King's Buildings Charlotte Auerbach Road Edinburgh EH9 3FL United Kingdom Museo Nacional de Ciencias Naturales Spanish Research Council (CSIC) José Gutiérrez Abascal 2 Madrid 28006 Spain German Centre for Integrative Biodiversity Research (IDiv) Halle-Jena-Leipzig Deutscher Platz 5e Leipzig 04103 Germany Grupo Rnomica Teórica y Computacional Departamento de Biologia Universidad Nacional de Colombia Bogota Colombia EcSeq Bioinformatics GmbH Sternwartenstraße 29 Leipzig 04103 Germany Computational Biology Department of Target Sciences GlaxoSmithKline Gunnels Wood Road Stevenage SG1 2NY United Kingdom Computational EvoDevo Group Department of Computer Science University of Leipzig Härtelstrasse 16-18 Leipzig 04107 Germany Bioinformatics Group Department of Computer Science University of Leipzig Härtelstrasse 16-18 Leipzig 04107 Germany Visual Data Analysis Lab ESAT/STADIUS KU Leuven Kasteelpark Arenberg 10 Leuven 3001 Belgium Imec KU Leuven Leuven Belgiu

Research in evolutionary biology has been progressively influenced by big data such as massive genome and transcriptome sequencing data, scalar measurements of several phenotypes on tens to thousands of individuals, as well as from collecting worldwide environmental data at an increasingly detailed scale. The handling and analysis of such data require computational skills that usually exceed the abilities of most traditionally trained evolutionary biologists. Here we discuss the advantages, challenges and considerations for organizing and running bioinformatics training courses of 2-3 weeks in length to introduce evolutionary biologists to the computational analysis of big data. Extended courses have the advantage of offering trainees the opportunity to learn a more comprehensive set of complementary topics and skills and allowing for more time to practice newly acquired competences. Many organizational aspects are common to any course, as the need to define precise learning objectives and the selection of appropriate and highly motivated instructors and trainees, among others. However, other features assume particular importance in extended bioinformatics training courses. To successfully implement a learning-by-doing philosophy, sufficient and enthusiastic teaching assistants (TAs) are necessary to offer prompt help to trainees. Further, a good balance between theoretical background and practice time needs to be provided and assured that the schedule includes enough flexibility for extra review sessions or further discussions if desired. A final project enables trainees to apply their newly learned skills to real data or case studies of their interest. To promote a friendly atmosphere throughout the course and to build a close-knit community after the course, allow time for some scientific discussions and social activities. In addition, to not exhaust trainees and TAs, some leisure time needs to be organized. Finally, all organization should be done while keeping

关键词： Active learning bioinformatics Evolutionary biology Extended course Genomics High-throughput-sequencing Programming Sustainable course

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Correction to: Recommendations for the nomenclature of enteroviruses and rhinoviruses

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Archives of virology 2020年第6期165卷 1515页

作者： P Simmonds A E Gorbalenya H Harvala T Hovi N J Knowles A M Lindberg M S Oberste A C Palmenberg G Reuter T Skern C Tapparel K C Wolthers P C Y Woo R Zell Nuffield Department of Experimental Medicine University of Oxford Oxford UK. Peter.Simmonds@ndm.ox.ac.uk. Department of Medical Microbiology Leiden University Medical Center Leiden The Netherlands. Faculty of Bioengineering and Bioinformatics Lomonosov Moscow State University Moscow Russia. Department of Biomedical Data Sciences Leiden University Medical Center Leiden The Netherlands. National Microbiology Service NHS Blood and Transplant London UK. Finnish Institute for Health and Welfare Helsinki Finland. The Pirbright Institute Pirbright Woking UK. Department of Chemistry and Biomedical Sciences Linnaeus University Kalmar Sweden. Division of Viral Diseases Centers for Disease Control and Prevention Atlanta GA USA. Department of Biochemistry Institute for Molecular Virology Madison WI USA. Department of Medical Microbiology and Immunology Medical School University of Pécs Pecs Hungary. Max Perutz Labs Medical University of Vienna Vienna Austria. Department of Microbiology and Molecular Medicine Faculty of Medicine University of Geneva Geneva Switzerland. Department of Medical Microbiology Academic Medical Center University of Amsterdam Amsterdam The Netherlands. Department of Microbiology The University of Hong Kong Hong Kong SAR China. Division of Experimental Virology Institute of Medical Microbiology Jena University Hospital Jena Germany.

Unfortunately, one of the affiliations of author "A. E. Gorbalenya" was missed in original version. The affiliation is updated here.

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Corrigendum to: Recommendations to enhance rigor and reproducibility in biomedical research

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GigaScience 2020年第9期9卷 giaa103页

作者： Jaqueline J Brito Jun Li Jason H Moore Casey S Greene Nicole A Nogoy Lana X Garmire Serghei Mangul Department of Clinical Pharmacy School of Pharmacy University of Southern California 1985 Zonal Avenue Los Angeles CA 90089 USA. Department of Computational Medicine & Bioinformatics Medical School University of Michigan 1301 Catherine Street Ann Arbor MI 48109 USA. Department of Biostatistics Epidemiology and Informatics Institute for Biomedical Informatics University of Pennsylvania 3700 Hamilton Walk Philadelphia PA 19104 USA. Department of Systems Pharmacology and Translational Therapeutics Perelman School of Medicine University of Pennsylvania 3400 Civic Center Boulevard Philadelphia PA 19104 USA. Childhood Cancer Data Lab Alex's Lemonade Stand 1429 Walnut St Floor 10 Philadelphia PA 19102 USA. GigaScience 26/F Kings Wing Plaza 2 1 On Kwan Street Shek Mun N.T. Hong Kong. Quantitative and Computational Biology University of Southern California Los Angeles CA 90089 USA.

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IG- MYC + neoplasms with precursor B-cell phenotype are molecularly distinct from Burkitt lymphomas

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Blood 2018年第21期132卷 2280-2285页

作者： Rabea Wagener Cristina López Kortine Kleinheinz Julia Bausinger Sietse M Aukema Inga Nagel Umut H Toprak Julian Seufert Janine Altmüller Holger Thiele Christof Schneider Julia Kolarova Jeongbin Park Daniel Hübschmann Eva M Murga Penas Hans G Drexler Andishe Attarbaschi Randi Hovland Eigil Kjeldsen Michael Kneba Udo Kontny Laurence de Leval Peter Nürnberg Ilske Oschlies David Oscier Brigitte Schlegelberger Stephan Stilgenbauer Wilhelm Wössmann Matthias Schlesner Birgit Burkhardt Wolfram Klapper Elaine S Jaffe Ralf Küppers Reiner Siebert Institute of Human Genetics Ulm University and Ulm University Medical Center Ulm Germany. Institute of Human Genetics Christian-Albrechts University Kiel & University Hospital Schleswig-Holstein Campus Kiel Kiel Germany. Division of Theoretical Bioinformatics German Cancer Research Center (DKFZ) Heidelberg Germany. Institute of Pharmacy and Molecular Biotechnology and Bioquant University of Heidelberg Heidelberg Germany. Institute of Pharmacology Christian-Albrechts University Kiel Germany. Bioinformatics and Omics Data Analytics DKFZ Heidelberg Germany. Faculty of Biosciences Heidelberg University Heidelberg Germany. Cologne Center for Genomics Center for Molecular Medicine Cologne (CMMC) University of Cologne Cologne Germany. Cologne Center for Genomics University of Cologne Cologne Germany. Department of Internal Medicine III University of Ulm Ulm Germany. Pediatric Immunology Hematology and Oncology University Hospital Heidelberg Heidelberg Germany. German Collection of Microorganisms and Cell Cultures Leibniz Institute Braunschweig Germany. Department of Pediatric Hematology and Oncology St Anna Children's Hospital Medical University of Vienna Vienna Austria. Department for Medical Genetics Haukeland University Hospital Bergen Norway. Cancer Cytogenetics Section Hemodiagnostic Laboratory Department of Haematology Cancer and Inflammation Center Aarhus University Hospital Aarhus Denmark. Department of Hematology University Hospital Schleswig-Holstein Kiel Germany. Division of Pediatric Hematology Oncology and Stem Cell Transplantation Medical Faculty RWTH Aachen University Aachen Germany. Institute of Pathology Lausanne University Hospital Lausanne Switzerland. Hematopathology Section Christian-Albrechts University Kiel Germany. Royal Bournemouth and Christchurch NHS Foundation Trust Bournemouth United Kingdom. Department of Human Genetics Hannover Medical School Hannover Germany. Department of Pediatric Hematology and Oncology Justus-Lieb

The notes instances of Burkitt lymphoma/leukemia (BL) with IG- rearrangement displaying a B-cell precursor immunophenotype (termed herein "preBLL"). To characterize the molecular pathogenesis of preBLL, we investigated 13 preBLL cases (including 1 cell line), of which 12 were analyzable using genome, exome, and targeted sequencing, imbalance mapping, and DNA methylation profiling. In 5 patients with reads across the IG- breakpoint junctions, we found evidence that the translocation derived from an aberrant VDJ recombination, as is typical for IG translocations arising in B-cell precursors. Genomic changes like biallelic IGH translocations or VDJ rearrangements combined with translocation into the VDJ region on the second allele, potentially preventing expression of a productive immunoglobulin, were detected in 6 of 13 cases. We did not detect mutations in genes frequently altered in BL, but instead found activating and/or mutations in 7 of 12 preBLLs. Gains on 1q, recurrent in BL and preB lymphoblastic leukemia/lymphoma (pB-ALL/LBL), were detected in 7 of 12 preBLLs. DNA methylation profiling showed preBLL to cluster with precursor B cells and pB-ALL/LBL, but apart from BL. We conclude that preBLL genetically and epigenetically resembles pB-ALL/LBL rather than BL. Therefore, we propose that preBLL be considered as a pB-ALL/LBL with recurrent genetic abnormalities.

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