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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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Genomics and epidemiology for gastric adenocarcinomas (GE4GAC): a Brazilian initiative to study gastric cancer

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Applied Cancer research 2019年第1期39卷 1-4页

作者： Bartelli, Thais F. Senda de Abrantes, Lais L. Freitas, Helano C. Thomas, Andrew M. Silva, Jordana M. Albuquerque, Gabriela E. Araújo, Luiza F. Branco, Gabriela P. de Amorim, Maria G. Serpa, Marianna S. Takenaka, Isabella K. T. M. Souza, Deborah T. Monção, Lucas O. Moda, Bruno S. Valieris, Renan Defelicibus, Alexandre Borges, Rodrigo Drummond, Rodrigo D. Alves, Francisco I. A. Santos, Monize N. P. Bobrovnitchaia, Irina G. Elhaik, Eran Coelho, Luiz G. V. Khayat, André Demachki, Samia Assumpção, Paulo P. Santiago, Karina M. Torrezan, Giovana T. Carraro, Dirce M. Peres, Stela V. Calsavara, Vinícius F. Burbano, Rommel Nóbrega, Calebe R. Baladão, Graziela P. P. Pereira, Ana C. C. Gatti, Camila M. Fagundes, Marcela A. Araújo, Marília S. Miranda, Tayana V. Barbosa, Monica S. Cardoso, Daniela M. M. Carneiro, Lilian C. Brito, Alexandre M. Ramos, Amanda F. P. L. Silva, Lucas L. L. Pontes, Jaqueline C. Tiengo, Tatiane Arantes, Paola E. Santana, Vilma Cordeiro, Milena Sant’Ana, Rosane O. Andrade, Hanna B. Anaissi, Ana K. M. Sampaio, Sara V. Abdallah, Emne A. Chinen, Ludmilla T. D. Braun, Alexcia C. Flores, Bianca C. T. Mello, Celso A. L. Claro, Laura C. L. Sztokfisz, Claudia Z. Altamirano, Carlos C. Carter, David R. F. Jesus, Victor H. F. Riechelmann, Rachel Medina, Tiago Gollob, Kenneth J. Martins, Vilma R. Setúbal, João C. Pelosof, Adriane G. Coimbra, Felipe J. Costa-Jr, Wilson L. Silva, Israel T. Nunes, Diana N. Curado, Maria P. Dias-Neto, Emmanuel Lab of Medical Genomics A.C.Camargo Cancer Center Sao Paulo Brazil International Research Center A.C.Camargo Cancer Center Sao Paulo Brazil Clinical Oncology Department A.C. Camargo Cancer Center São Paulo Brazil Department CIBIO University of Trento Trento Italy Biochemistry Department Chemistry Institute Universidade de São Paulo São Paulo Brazil Lab. of Bioinformatics and Computational Biology A.C.Camargo Cancer Center Sao Paulo Brazil Data Science group International Research Center A.C.Camargo Cancer Center Sao Paulo Brazil Department of Animal & Plant Sciences University of Sheffield Sheffield UK Instituto Alfa de Gastroenterologia Hospital das Clínicas Universidade Federal de Minas Gerais Belo Horizonte Brazil Instituto de Ciências Biológicas Universidade Federal do Pará Belém Brazil Núcleo de Pesquisas em Oncologia Universidade Federal do Pará Belém Brazil Lab. de Genômica e Biologia Molecular A.C.Camargo Cancer Center Sao Paulo Brazil Epidemiology and Statistics Group A.C.Camargo Cancer Center Sao Paulo Brazil Laboratório de Biologia Molecular Hospital Ophir Loyola Belém Brazil Universidade Federal de Goiás IPTESP – Instituto de Patologia Tropical e Saúde Pública Goiânia Brazil Department of Abdominal Surgery Hospital Araujo Jorge Goiânia Brazil Instituto de Saúde Coletiva da Universidade Federal da Bahia Salvador Brazil Instituto do Cancer do Ceará Fortaleza Brazil Department of Pathology A.C.Camargo Cancer Center São Paulo Brazil Endoscopy sector A.C.Camargo Cancer Center São Paulo Brazil Instituto Nacional de Enfermedades Neoplásicas Surquillo Peru Dept. of Biological and Medical Sciences Faculty of Health and Life Sciences Oxford Brookes University Oxford UK Translational Immuno-oncology Group A.C.Camargo Cancer Center Sao Paulo Brazil Tumor Biology and Biomarkers Group A.C.Camargo Cancer Center Sao Paulo Brazil Department of Abdominal Surgery A.C.Camargo Cancer Center São Paulo Brazil

Gastric cancer (GC) is the fifth most common type of cancer worldwide with high incidences in Asia, Central, and South American countries. This patchy distribution means that GC studies are neglected by large research centers from developed countries. The need for further understanding of this complex disease, including the local importance of epidemiological factors and the rich ancestral admixture found in Brazil, stimulated the implementation of the GE4GAC project. GE4GAC aims to embrace epidemiological, clinical, molecular and microbiological data from Brazilian controls and patients with malignant and pre-malignant gastric disease. In this letter, we summarize the main goals of the project, including subject and sample accrual and current findings.

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Nanopublications: A Growing Resource of Provenance-Centric Scientific Linked data

Nanopublications: A Growing Resource of Provenance-Centric S...

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IEEE International Conference on e-science and Grid Computing

作者： Tobias Kuhn Albert Meroño-Peñuela Alexander Malic Jorrit H. Poelen Allen H. Hurlbert Emilio Centeno Ortiz Laura I. Furlong Núria Queralt-Rosinach Christine Chichester Juan M. Banda Egon Willighagen Friederike Ehrhart Chris Evelo Tareq B. Malas Michel Dumontier Department of Computer Science Vrije Universiteit Amsterdam Amsterdam Netherlands Vrije Universiteit Amsterdam Amsterdam Noord-Holland NL Institute of Data Science Maastricht University Netherlands 400 Perkins St Oakland California USA Department of Biology University of North Carolina Chapel Hill USA Research Programme on Biomedical Informatics Universitat Pompeu Fabra Barcelona Spain Department of Integrative Structural and Computational Biology The Scripps Research Institute La Jolla USA Datafair.xyz Geneva Switzerland Department of Computer Science Georgia State University USA Department of Bioinformatics BiGCaT NUTRIM Maastricht University The Netherlands Department of Human Genetics Leiden University Medical Center Netherlands

Nanopublications are a Linked data format for scholarly data publishing that has received considerable uptake in the last few years. In contrast to the common Linked data publishing practice, nanopublications work at the granular level of atomic information snippets and provide a consistent container format to attach provenance and metadata at this atomic level. While the nanopublications format is domain-independent, the datasets that have become available in this format are mostly from Life science domains, including data about diseases, genes, proteins, drugs, biological pathways, and biotic interactions. More than 10 million such nanopublications have been published, which now form a valuable resource for studies on the domain level of the given Life science domains as well as on the more technical levels of provenance modeling and heterogeneous Linked data. We provide here an overview of this combined nanopublication dataset, show the results of some overarching analyses, and describe how it can be accessed and queried.

关键词： Nanobioscience Diseases Linked data Proteins bioinformatics Publishing databases

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A second update on mapping the human genetic architecture of COVID-19

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Nature 2023年第7977期621卷 E7-E26页

作者： Masahiro Kanai Christine Stevens Benjamin M. Neale Mark Daly Andrea Ganna Amy Trankiem Mary K. Balaconis Samuli Ripatti Lindo Nkambul Mark J. Daly Sam Bryant Matthew Solomonson Shea J. Andrews Mattia Cordioli Juha Karjalainen Juha Mehtonen Matti Pirinen Andrea Corbetta Bradley Jermy Kati Donner Katja Kivinen Aarno Palotie Mari Kaunisto Kumar Veerapen Konrad J. Karczewski Alicia R. Martin Elizabeth G. Atkinson Kristin Tsuo Nikolas Baya Rahul Gupta Raymond K. Walters Duncan S. Palmer Gopal Sarma Nathan Cheng Wenhan Lu Claire Churchhouse Jacqueline I. Goldstein Daniel King Wei Zhou Cotton Seed Hilary Finucane F. Kyle Satterstrom Gita A. Pathak Akiko Iwasaki Karolina Chwialkowska Karolina Chwiałkowska Brooke N. Wolford Hajar Fauzan Ahmad Shea Andrews Kathrin Aprile von Hohenstaufen Puoti Palwende R. Boua Guillaume Butler-Laporte Celia M. T. Greenwood Bartha M. Knoppers Mark Lathrop Carmen L. Cadilla Francesca Colombo Nicole Dueker Chloe Kirk Atanu Kumar Dutta Yasser M. El-Sherbiny Jehan J. El-Jawhari Doaa Shahin Ahmed Elzeiny Tamer A. Mansour Madonna M. Eltoukhy Attia A. S. Mohamed Sahar Esmaeeli Annika Faucon Israel Fernández Cadenas Israel Fernandez-Cadenas Laia Llucià-Carol Natalia Cullell Elena Muiño Jara Cárcel-Márquez Margherita Francescatto Laurent Francioli Lindokuhle Nkambule Jatin Arora Soumya Raychaudhuri Caroline Cusick Lude Franke Macarena Fuentes Macarena Fuentes-Guajardo David Gómez Cabrero Emi N. Harry Philip Jansen József L. Szentpéteri Réka Várnai Elżbieta Kaja Athanasios Kousathanas Dorote Pasko Mark J. Caulfield Alex Stuckey Christopher A. Odhams Susan Walker Daniel Rhodes Richard H. Scott Loukas Moutsianas Afshan Siddiq Peter Goddard Sally Donovan Tala Zainy Fiona Maleady-Crowe Linda Todd Shahla Salehi Greg Elgar Georgia Chan Prabhu Arumugam Christine Patch Augusto Rendon Tom A. Fowler Jose E. Krieger Sanjay K. Patel Audrey Lemaçon Sophie Limou Pietro Lió Eirini Marouli Charles Hinds Minttu M. Marttila Carolina Medina-Gómez Isabelle Migeotte Soumyajit Mondal Andrés Moreno-Estrada Leire Moya Tomok Broad Institute of MIT and Harvard Cambridge MA USA Analytic and Translational Genetics Unit Massachusetts General Hospital Boston MA USA Program in Medical and Population Genetics Broad Institute of MIT and Harvard Cambridge MA USA Department of Biomedical Informatics Harvard Medical School Boston MA USA Program in Bioinformatics and Integrative Genomics Harvard Medical School Boston MA USA Institute for Molecular Medicine Finland (FIMM) University of Helsinki Helsinki Finland Institute for Molecular Medicine Finland University of Helsinki Helsinki Finland Institute for Molecular Medicine Finland (FIMM) HiLIFE University of Helsinki Helsinki Finland Public Health Faculty of Medicine University of Helsinki Helsinki Finland Analytic & Translational Genetics Unit Massachusetts General Hospital Boston MA USA Stanley Center for Psychiatric Research & Program in Medical and Population Genetics Cambridge UK Institute for Molecular Medicine Finland (FIMM) Univerisity of Helsinki Helsinki Finland University of California San Francisco San Francisco CA USA Department of Molecular and Human Genetics Baylor College of Medicine Houston TX USA Program in Biological and Biomedical Sciences Harvard Medical School Boston MA USA Department of Psychiatry School of Medicine Yale University New Haven CT USA Veteran Affairs Connecticut Healthcare System West Haven CT USA Yale University New Haven CT USA Centre for Bioinformatics and Data Analysis Medical University of Bialystok Bialystok Poland Department of Computational Medicine and Bioinformatics University of Michigan Ann Arbor MI USA Faculty of Industrial Sciences and Technology Universiti Malaysia Pahang Pahang Malaysia Icahn School of Medicine at Mount Sinai New York NY USA Genolier Innovation Network and Hub Swiss Medical Network Genolier Healthcare Campus Genolier Switzerland Immediate Independent Multidisciplinary Med & Biotech Research Association Milan Italy Clinical Research Unit of Nanor

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Author Correction: High p16 expression and heterozygous RB1 loss are biomarkers for CDK4/6 inhibitor resistance in ER+ breast cancer

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Nature communications 2022年第1期13卷 6928页

作者： Marta Palafox Laia Monserrat Meritxell Bellet Guillermo Villacampa Abel Gonzalez-Perez Mafalda Oliveira Fara Brasó-Maristany Nusaibah Ibrahimi Srinivasaraghavan Kannan Leonardo Mina Maria Teresa Herrera-Abreu Andreu Òdena Mònica Sánchez-Guixé Marta Capelán Analía Azaro Alejandra Bruna Olga Rodríguez Marta Guzmán Judit Grueso Cristina Viaplana Javier Hernández Faye Su Kui Lin Robert B Clarke Carlos Caldas Joaquín Arribas Stefan Michiels Alicia García-Sanz Nicholas C Turner Aleix Prat Paolo Nuciforo Rodrigo Dienstmann Chandra S Verma Nuria Lopez-Bigas Maurizio Scaltriti Monica Arnedos Cristina Saura Violeta Serra Experimental Therapeutics Group Vall d'Hebron Institute of Oncology Barcelona Spain. Breast Cancer and Melanoma Group Vall d'Hebron Institute of Oncology Barcelona Spain. Department of Medical Oncology Hospital Vall d'Hebron Barcelona Spain. Oncology Data Science Group Vall d'Hebron Institute of Oncology Barcelona Spain. Institute for Research in Biomedicine (IRB Barcelona) Barcelona Spain. Research Program on Biomedical Informatics Universitat Pompeu Fabra Barcelona Spain. Translational Genomics and Targeted Therapies in Solid Tumors August Pi i Sunyer Biomedical Research Institute (IDIBAPS) Barcelona Spain. Service de Biostatistique et d'Epidémiologie Gustave Roussy Villejuif France. Oncostat U1018 Inserm University Paris-Saclay Villejuif France. Bioinformatics Institute (A*STAR) Singapore Singapore. Medica Scientia Innovation Research (MedSIR) Barcelona Spain. The Breast Cancer Now Research Centre London UK. Preclinical Modelling of Pediatric Cancer Evolution Group The Institute of Cancer Research London UK. Translational Molecular Pathology Vall d'Hebron Institute of Research (VHIR) Barcelona Spain. Novartis Pharmaceuticals East Hanover NJ USA. Genentech Inc. South San Francisco California USA. Breast Biology Group Manchester Breast Centre Manchester UK. Cancer Research UK Cambridge UK. CIBERONC Vall d'Hebron Institute of Oncology Barcelona Spain. Growth Factors Laboratory Vall d'Hebron Institute of Oncology Barcelona Spain. Department of Biochemistry and Molecular Biology Universitat Autònoma de Barcelona Barcelona Spain. IMIM (Hospital del Mar Medical Research Institute) Barcelona Spain. Institució Catalana de Recerca i Estudis Avançats (ICREA) Barcelona Spain. University of Barcelona Barcelona Spain. Department of Medical Oncology Hospital Clinic Barcelona Spain. SOLTI Breast Cancer Research Group Barcelona Spain. Department of Oncology IOB Institute of Oncology Barcelona Spain. Molecular Oncology Group Vall d'Hebron Institute of On

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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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Genetic analysis of over 1 million people identifies 535 new loci associated with blood pressure traits (vol 50, pg 1412, 2018)

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NATURE GENETICS 2018年第12期50卷 1755-1755页

作者： Evangelou, Evangelos Warren, Helen R. Mosen-Ansorena, David Mifsud, Borbala Pazoki, Raha Gao, He Ntritsos, Georgios Dimou, Niki Cabrera, Claudia P. Karaman, Ibrahim Fu Liang Ng Evangelou, Marina Witkowska, Katarzyna Tzanis, Evan Hellwege, Jacklyn N. Giri, Ayush Edwards, Digna R. Velez Sun, Yan V. Cho, Kelly Gaziano, J. Michael Wilson, Peter W. F. Tsao, Philip S. Kovesdy, Csaba P. Esko, Tonu Magi, Reedik Milani, Lili Almgren, Peter Boutin, Thibaud Debette, Stephanie Ding, Jun Giulianini, Franco Holliday, Elizabeth G. Jackson, Anne U. Li-Gao, Ruifang Lin, Wei-Yu Luan, Jian'an Mangino, Massimo Oldmeadow, Christopher Prins, Bram Peter Qian, Yong Sargurupremraj, Muralidharan Shah, Nabi Surendran, Praveen Theriault, Sebastien Verweij, Niek Willems, Sara M. Zhao, Jing-Hua Amouyel, Philippe Connell, John de Mutsert, Renee Doney, Alex S. F. Farrall, Martin Menni, Cristina Morris, Andrew D. Noordam, Raymond Pare, Guillaume Poulter, Neil R. Shields, Denis C. Stanton, Alice Thom, Simon Abecasis, Goncalo Amin, Najaf Arking, Dan E. Ayers, Kristin L. Barbieri, Caterina M. Batini, Chiara Bis, Joshua C. Blake, Tineka Bochud, Murielle Boehnke, Michael Boerwinkle, Eric Boomsma, Dorret I. Bottinger, Erwin P. Braund, Peter S. Brumat, Marco Campbell, Archie Campbell, Harry Chakravarti, Aravinda Chambers, John C. Chauhan, Ganesh Ciullo, Marina Cocca, Massimiliano Collins, Francis Cordell, Heather J. Davies, Gail de Borst, Martin H. de Geus, Eco J. Deary, Ian J. Deelen, Joris Del Greco, Fabiola M. Demirkale, Cumhur Yusuf Dorr, Marcus Ehret, Georg B. Elosua, Roberto Enroth, Stefan Erzurumluoglu, A. Mesut Ferreira, Teresa Franberg, Mattias Franco, Oscar H. Gandin, Ilaria Gasparini, Paolo Giedraitis, Vilmantas Gieger, Christian Girotto, Giorgia Goel, Anuj Gow, Alan J. Gudnason, Vilmundur Guo, Xiuqing Gyllensten, Ulf Hamsten, Anders Harris, Tamara B. Harris, Sarah E. Hartman, Catharina A. Havulinna, Aki S. Hicks, Andrew A. Hofer, Edith Hofman, Albert Hottenga, Jouke-Jan Huffman, Jennifer E. Hwang, Shih-Jen Ingelsson, Erik James, Alan Jansen Department of Epidemiology and Biostatistics Imperial College London London UK Department of Hygiene and Epidemiology University of Ioannina Medical School Ioannina Greece William Harvey Research Institute Barts and The London School of Medicine and Dentistry Queen Mary University of London London UK National Institute for Health Research Barts Cardiovascular Biomedical Research Center Queen Mary University of London London UK MRC-PHE Centre for Environment and Health Imperial College London London UK Department of Mathematics Imperial College London London UK Division of Epidemiology Department of Medicine Institute for Medicine and Public Health Vanderbilt Genetics Institute Vanderbilt University Medical Center Tennessee Valley Healthcare System (626)/Vanderbilt University Nashville TN USA Vanderbilt Genetics Institute Vanderbilt Epidemiology Center Department of Obstetrics and Gynecology Vanderbilt University Medical Center Tennessee Valley Health Systems VA Nashville TN USA Department of Epidemiology Emory University Rollins School of Public Health Atlanta GA USA Department of Biomedical Informatics Emory University School of Medicine Atlanta GA USA Massachusetts Veterans Epidemiology Research and Information Center (MAVERIC) VA Boston Healthcare System Boston MA USA Division of Aging Department of Medicine Brigham and Women’s Hospital Department of Medicine Harvard Medical School Boston MA USA Atlanta VAMC and Emory Clinical Cardiovascular Research Institute Atlanta GA USA VA Palo Alto Health Care System Division of Cardiovascular Medicine Stanford University School of Medicine Stanford CA USA Nephrology Section Memphis VA Medical Center and University of Tennessee Health Science Center Memphis TN USA Estonian Genome Center University of Tartu Tartu Estonia Program in Medical and Population Genetics Broad Institute of Harvard and MIT Cambridge MA USA Department Clinical Sciences Malmö Lund University Malmö Sweden MRC Human Genetics Un

High blood pressure is a highly heritable and modifiable risk factor for cardiovascular disease. We report the largest genetic association study of blood pressure traits (systolic, diastolic and pulse pressure) to date in over 1 million people of European ancestry. We identify 535 novel blood pressure loci that not only offer new biological insights into blood pressure regulation but also highlight shared genetic architecture between blood pressure and lifestyle exposures. Our findings identify new biological pathways for blood pressure regulation with potential for improved cardiovascular disease prevention in the future.

关键词： Cardiovascular diseases Genome informatics Genome-wide association studies

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Dense sampling of bird diversity increases power of comparative genomics (vol 587, pg 252, 2020)

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NATURE 2021年第7856期592卷 E24-E24页

作者： Feng, Shaohong Stiller, Josefin Deng, Yuan Armstrong, Joel Fang, Qi Reeve, Andrew Hart Xie, Duo Chen, Guangji Guo, Chunxue Faircloth, Brant C. Petersen, Bent Wang, Zongji Zhou, Qi Diekhans, Mark Chen, Wanjun Andreu-Sanchez, Sergio Margaryan, Ashot Howard, Jason Travis Parent, Carole Pacheco, George Sinding, Mikkel-Holger S. Puetz, Lara Cavill, Emily Ribeiro, Angela M. Eckhart, Leopold Fjeldsa, Jon Hosner, Peter A. Brumfield, Robb T. Christidis, Les Bertelsen, Mads F. Sicheritz-Ponten, Thomas Tietze, Dieter Thomas Robertson, Bruce C. Song, Gang Borgia, Gerald Claramunt, Santiago Lovette, Irby J. Cowen, Saul J. Njoroge, Peter Dumbacher, John Philip Ryder, Oliver A. Fuchs, Jerome Bunce, Michael Burt, David W. Cracraft, Joel Meng, Guanliang Hackett, Shannon J. Ryan, Peter G. Jonsson, Knud Andreas Jamieson, Ian G. da Fonseca, Rute R. Braun, Edward L. Houde, Peter Mirarab, Siavash Suh, Alexander Hansson, Bengt Ponnikas, Suvi Sigeman, Hanna Stervander, Martin Frandsen, Paul B. van der Zwan, Henriette van der Sluis, Rencia Visser, Carina Balakrishnan, Christopher N. Clark, Andrew G. Fitzpatrick, John W. Bowman, Reed Chen, Nancy Cloutier, Alison Sackton, Timothy B. Edwards, Scott V. Foote, Dustin J. Shakya, Subir B. Sheldon, Frederick H. Vignal, Alain Soares, Andre E. R. Shapiro, Beth Gonzalez-Solis, Jacob Ferrer-Obiol, Joan Rozas, Julio Riutort, Marta Tigano, Anna Friesen, Vicki Dalen, Love Urrutia, Araxi O. Szekely, Tamas Liu, Yang Campana, Michael G. Corvelo, Andre Fleischer, Robert C. Rutherford, Kim M. Gemmell, Neil J. Dussex, Nicolas Mouritsen, Henrik Thiele, Nadine Delmore, Kira Liedvogel, Miriam Franke, Andre Hoeppner, Marc P. Krone, Oliver Fudickar, Adam M. Mila, Borja Ketterson, Ellen D. Fidler, Andrew Eric Friis, Guillermo Parody-Merino, Angela M. Battley, Phil F. Cox, Murray P. Lima, Nicholas Costa Barroso Prosdocimi, Francisco Parchman, Thomas Lee Schlinger, Barney A. Loiselle, Bette A. Blake, John G. Lim, Haw Chuan Day, Lainy B. Fuxjager, Matthew J. Baldwin, Maude W. Braun, Michael J. Wirthlin, Morgan Dikow, China National GeneBank BGI-Shenzhen Shenzhen China State Key Laboratory of Genetic Resources and Evolution Kunming Institute of Zoology Chinese Academy of Sciences Kunming China BGI-Shenzhen Shenzhen China Villum Centre for Biodiversity Genomics Section for Ecology and Evolution Department of Biology University of Copenhagen Copenhagen Denmark BGI Education Center University of Chinese Academy of Sciences Shenzhen China MOE Laboratory of Biosystems Homeostasis and Protection Life Sciences Institute Zhejiang University Hangzhou China Department of Neuroscience and Developmental Biology University of Vienna Vienna Austria Center for Excellence in Animal Evolution and Genetics Chinese Academy of Sciences Kunming China James D. Watson Institute of Genome Sciences Hangzhou China UC Santa Cruz Genomics Institute UC Santa Cruz Santa Cruz CA USA Natural History Museum of Denmark University of Copenhagen Copenhagen Denmark Center for Macroecology Evolution and Climate GLOBE Institute University of Copenhagen Copenhagen Denmark Department of Biological Sciences Louisiana State University Baton Rouge LA USA Museum of Natural Science Louisiana State University Baton Rouge LA USA Centre of Excellence for Omics-Driven Computational Biodiscovery (COMBio) Faculty of Applied Sciences AIMST University Kedah Malaysia Section for Evolutionary Genomics The GLOBE Institute Faculty of Health and Medical Sciences University of Copenhagen Copenhagen Denmark Institute of Molecular Biology National Academy of Sciences Yerevan Armenia University Museum Norwegian University of Science and Technology Trondheim Norway Center for Reproductive Medicine The 2nd Affiliated Hospital School of Medicine Zhejiang University Hangzhou China Novogene Durham NC USA Duke University Medical Center Durham NC USA The Rockefeller University New York NY USA Howard Hughes Medical Institute Chevy Chase MD USA Department of Dermatology Medical University of Vienna Vienna Austria

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Correction to: An autosomal dominant neurological disorder caused by de novo variants in FAR1 resulting in uncontrolled synthesis of ether lipids

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Genetics in medicine : official journal of the American College of Medical Genetics 2021年第12期23卷 2467页

作者： Sacha Ferdinandusse Kirsty McWalter Heleen Te Brinke Lodewijk IJlst Petra M Mooijer Jos P N Ruiter Alida E M van Lint Mia Pras-Raves Eric Wever Francisca Millan Maria J Guillen Sacoto Amber Begtrup Mark Tarnopolsky Lauren Brady Roger L Ladda Susan L Sell Catherine B Nowak Jessica Douglas Cuixia Tian Elizabeth Ulm Seth Perlman Arlene V Drack Karen Chong Nicole Martin Jennifer Brault Elly Brokamp Camilo Toro William A Gahl Ellen F Macnamara Lynne Wolfe Quinten Waisfisz Petra J G Zwijnenburg Alban Ziegler Magalie Barth Rosemarie Smith Sara Ellingwood Deborah Gaebler-Spira Somayeh Bakhtiari Michael C Kruer Antoine H C van Kampen Ronald J A Wanders Hans R Waterham David Cassiman Frédéric M Vaz Laboratory Genetic Metabolic Diseases Amsterdam UMC University of Amsterdam Department of Clinical Chemistry Amsterdam Gastroenterology Endocrinology Metabolism Amsterdam The Netherlands. s.ferdinandusse@amsterdamumc.nl. GeneDx Gaithersburg MD USA. Laboratory Genetic Metabolic Diseases Amsterdam UMC University of Amsterdam Department of Clinical Chemistry Amsterdam Gastroenterology Endocrinology Metabolism Amsterdam The Netherlands. Core Facility Metabolomics Amsterdam UMC Amsterdam The Netherlands. Bioinformatics Laboratory Department of Epidemiology and Data Science Amsterdam Public Health Research Institute Amsterdam UMC University of Amsterdam Amsterdam The Netherlands. Department of Pediatrics McMaster University Children's Hospital Hamilton ON Canada. Department of Pediatrics Penn State Children's Hospital Hershey PA USA. The Feingold Center for Children Division of Genetics and Genomics Boston Children's Hospital Boston MA USA. Division of Neurology Cincinnati Children's Hospital Medical Center Department of Pediatrics University of Cincinnati College of Medicine Cincinnati OH USA. Division of Human Genetics Cincinnati Children's Hospital Medical Center Cincinnati OH USA. Department of Neurology University of Iowa Hospitals and Clinics Iowa City IA USA. Department of Ophthalmology and Visual Sciences University of Iowa Iowa City IA USA. Mount Sinai Hospital Department of Obstetrics and Gynecology Prenatal Diagnosis and Medical Genetics Program Toronto ON Canada. Vanderbilt University Medical Center Department of Pediatrics Nashville TN USA. NIH Undiagnosed Diseases Program Office of the Clinical Director National Human Genome Research Institute NIH Bethesda MD USA. Department of Clinical Genetics Amsterdam UMC Vrije Universiteit Amsterdam Amsterdam The Netherlands. Genetic department University Hospital Angers Angers France. Division of Genetics Department of Pediatrics Maine Medical Center Portland ME USA. Feinberg Northwest

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Genome-wide association study of long COVID

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Nature Genetics 2025年 1-16页

作者： Lammi, Vilma Nakanishi, Tomoko Jones, Samuel E. Andrews, Shea J. Karjalainen, Juha Cortés, Beatriz O’Brien, Heath E. Ochoa-Guzman, Ana Fulton-Howard, Brian E. Broberg, Martin Haapaniemi, Hele H. Kanai, Masahiro Pirinen, Matti Schmidt, Axel Mitchell, Ruth E. Mousas, Abdou Mangino, Massimo Huerta-Chagoya, Alicia Sinnott-Armstrong, Nasa Cirulli, Elizabeth T. Vaudel, Marc Kwong, Alex S. F. Maiti, Amit K. Marttila, Minttu M. Posner, Daniel C. Rodriguez, Alexis A. Batini, Chiara Minnai, Francesca Dearman, Anna R. Warmerdam, C. A. Robert Sequeros, Celia B. Winkler, Thomas W. Jordan, Daniel M. Rešcenko, Raimonds Miano, Lorenzo Lane, Jacqueline M. Chung, Ryan K. Guillen-Guio, Beatriz Leavy, Olivia C. Carvajal-Silva, Laura Aguilar-Valdés, Kevin Frangione, Erika Guare, Lindsay Vergasova, Ekaterina Marouli, Eirini Striano, Pasquale Zainulabid, Ummu Afeera Kumar, Ashutosh Ahmad, Hajar Fauzan Edahiro, Ryuya Azekawa, Shuhei Maj, Carlo Pensel, Max C. Miller, Abigail Nöthen, Markus M. Behzad, Pari Schultz, Sonja Heggemann, Julia Balla, Daniella Morrison, David R. Mooser, Vincent Perley, Danielle Ragoussis, Jiannis Rousseau, Simon Shi, Fangyi Lathrop, G. Mark Yanishevsky, Solomia Laurent, Laetitia Auld, Daniel Bertrand, Mylene Boisclair, Ariane Bourque, Guillaume Bujold, David Durand, Madeleine Adra, Darin St-Cyr, Janick Niemi, Mari E. K. Iyengar, Sudha K. Cai, Tianxi Cho, Kelly Sarvadhavabhatla, Sannidhi Donaire, Maria Sophia Valenzuela-Jorquera, Héctor Lamoza, Eduardo Arévalo, Tamara V. Retamales-Ortega, Rocío Sanhueza, Sergio Selman, Carolina S. Silva, Andrea X. Alarcon, Teresa A. Martínez, Matías F. Quiroga, Romina Zuñiga-Pacheco, Paula Zapata-Contreras, Daniela Yáñez, Cristian E. Quiñones, Luis A. Tobar-Calfucoy, Eduardo A. Monardes-Ramírez, Virginia A. Signore, Iskra A. Guajardo, Lissette G. Figueroa, Alvaro Oróstica, Karen Y. Muñoz, Christian A. Fuentes-Guajardo, Macarena Bocchieri, Pamela Cabrera, Camilo Echeverria, Cesar A. Cerpa, Leslie C. Donoso, Gerardo Gutiérrez-Richards, Scarlett Nova-Lamperti, Estefania Saez Hidalgo Institute for Molecular Medicine Finland (FIMM) Helsinki Institute of Life Science (HiLIFE) University of Helsinki Helsinki Finland University of Helsinki Helsinki Finland Department of Human Genetics McGill University Montreal QC Canada Centre for Clinical Epidemiology Department of Medicine Lady Davis Institute Jewish General Hospital McGill University Montreal QC Canada Kyoto-McGill International Collaborative Program in Genomic Medicine Graduate School of Medicine Kyoto University Kyoto Japan Department of Genome Informatics Graduate School of Medicine the University of Tokyo Tokyo Japan Research Fellow Japan Society for the Promotion of Science Tokyo Japan Lady Davis Institute Jewish General Hospital McGill University Montreal QC Canada Department of Psychiatry and Behavioral Sciences University of California San Francisco San Francisco CA United States Program in Medical and Population Genetics Broad Institute of Harvard and MIT Cambridge MA United States Stanley Center for Psychiatric Research Broad Institute of Harvard and MIT Cambridge MA United States Analytic and Translational Genetics Unit Massachusetts General Hospital Boston MA United States Genomes for Life-GCAT Lab CORE Program Germans Trias i Pujol Research Institute (IGTP) Badalona Spain Grup de REcerca en Impacte de les Malalties Cròniques i les seves Trajectòries (GRIMTra) Barcelona Spain Germans Trias i Pujol Research Institute (IGTP) Badalona Spain Sano Genetics Limited London United Kingdom Unidad de Biología Molecular y Medicina Genómica Instituto Nacional de Ciencias Médicas y Nutrición Salvador Zubirán Mexico City Mexico Instituto Nacional de Ciencias Médicas y Nutrición Salvador Zubirán Mexico City Mexico Genetics and Genomic Sciences Icahn School of Medicine at Mount Sinai New York City NY United States Broad Institute Cambridge MA United States Analytical and Translational Genetics Unit Massachusetts General Hospital Harvard Medical School Boston MA United Sta

Infections can lead to persistent symptoms and diseases such as shingles after varicella zoster or rheumatic fever after streptococcal infections. Similarly, severe acute respiratory syndrome coronavirus 2 (SARS‑CoV‑2) infection can result in long coronavirus disease (COVID), typically manifesting as fatigue, pulmonary symptoms and cognitive dysfunction. The biological mechanisms behind long COVID remain unclear. We performed a genome-wide association study for long COVID including up to 6,450 long COVID cases and 1,093,995 population controls from 24 studies across 16 countries. We discovered an association of FOXP4 with long COVID, independent of its previously identified association with severe COVID-19. The signal was replicated in 9,500 long COVID cases and 798,835 population controls. Given the transcription factor FOXP4’s role in lung physiology and pathology, our findings highlight the importance of lung function in the pathophysiology of long COVID. © The Author(s) 2025.

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