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LifeTime and improving European healthcare through cell-based interceptive medicine (vol 587, pg 377, 2020)

NATURE 2021年第7852期592卷 E8-E8页

作者： Rajewsky, Nikolaus Almouzni, Genevieve Gorski, Stanislaw A. Aerts, Stein Amit, Ido Bertero, Michela G. Bock, Christoph Bredenoord, Annelien L. Cavalli, Giacomo Chiocca, Susanna Clevers, Hans De Strooper, Bart Eggert, Angelika Ellenberg, Jan Fernandez, Xose M. Figlerowicz, Marek Gasser, Susan M. Hubner, Norbert Kjems, Jorgen Knoblich, Jurgen A. Krabbe, Grietje Lichter, Peter Linnarsson, Sten Marine, Jean-Christophe Marioni, John C. Marti-Renom, Marc A. Netea, Mihai G. Nickel, Dorthe Nollmann, Marcelo Novak, Halina R. Parkinson, Helen Piccolo, Stefano Pinheiro, Ines Pombo, Ana Popp, Christian Reik, Wolf Roman-Roman, Sergio Rosenstiel, Philip Schultze, Joachim L. Stegle, Oliver Tanay, Amos Testa, Giuseppe Thanos, Dimitris Theis, Fabian J. Torres-Padilla, Maria-Elena Valencia, Alfonso Vallot, Celine van Oudenaarden, Alexander Vidal, Marie Voet, Thierry Berlin Institute for Medical Systems Biology Max Delbrück Center for Molecular Medicine in the Helmholtz Association Berlin Germany Charité-Universitätsmedizin Berlin Germany Berlin Institute of Health (BIH) Berlin Germany German Center for Cardiovascular Research (DZHK) Partner Site Berlin Berlin Germany Institute for Biology Humboldt University of Berlin Berlin Germany Cardiovascular and Metabolic Sciences Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC) Berlin Germany Department of Pediatric Oncology/Hematology Charité-Universitätsmedizin Berlin Berlin Germany Institut Curie CNRS PSL Research University Sorbonne Université Nuclear Dynamics Unit Equipe Labellisée Ligue contre le cancer Paris France VIB Center for Brain and Disease Research Leuven Belgium Department of Human Genetics KU Leuven Leuven Belgium Department of Neurosciences KU Leuven Leuven Belgium UK Dementia Research Institute at UCL University College London London UK Wellcome Sanger Institute Wellcome Genome Campus Cambridge UK Department of Immunology Weizmann Institute of Science Rehovot Israel Centre for Genomic Regulation (CRG) Barcelona Institute of Science and Technology Barcelona Spain CNAG-CRG Centre for Genomic Regulation Barcelona Institute of Science and Technology Barcelona Spain Universitat Pompeu Fabra Barcelona Spain ICREA Barcelona Spain CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences Vienna Austria Department of Laboratory Medicine Medical University of Vienna Vienna Austria Ludwig Boltzmann Institute for Rare and Undiagnosed Diseases Vienna Austria Department of Medical Humanities Julius Center for Health Sciences and Primary Care University Medical Center Utrecht Utrecht The Netherlands Institute of Human Genetics UMR 9002 CNRS and University of Montpellier Montpellier France Department of Experimental Oncology IEO European Institute of Oncology IRCCS Milan Italy Department of Oncology and Hemato

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

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

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

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

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

npj biodiversity

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npj biodiversity 2024年第1期3卷 31页

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

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Publisher Correction: Genome-wide association study reveals mechanisms underlying dilated cardiomyopathy and myocardial resilience

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Nature genetics 2024年第12期56卷 2843页

作者： Sean J Jurgens Joel T Rämö Daria R Kramarenko Leonoor F J M Wijdeveld Jan Haas Mark D Chaffin Sophie Garnier Liam Gaziano Lu-Chen Weng Alex Lipov Sean L Zheng Albert Henry Jennifer E Huffman Saketh Challa Frank Rühle Carmen Diaz Verdugo Christian Krijger Juárez Shinwan Kany Constance A van Orsouw Kiran Biddinger Edwin Poel Amanda L Elliott Xin Wang Catherine Francis Richard Ruan Satoshi Koyama Leander Beekman Dominic S Zimmerman Jean-François Deleuze Eric Villard David-Alexandre Trégouët Richard Isnard Dorret I Boomsma Eco J C de Geus Rafik Tadros Yigal M Pinto Arthur A M Wilde Jouke-Jan Hottenga Juha Sinisalo Teemu Niiranen Roddy Walsh Amand F Schmidt Seung Hoan Choi Kyong-Mi Chang Philip S Tsao Paul M Matthews James S Ware R Thomas Lumbers Saskia van der Crabben Jari Laukkanen Aarno Palotie Ahmad S Amin Philippe Charron Benjamin Meder Patrick T Ellinor Mark Daly Krishna G Aragam Connie R Bezzina Department of Experimental Cardiology Amsterdam Cardiovascular Sciences Heart Failure & Arrhythmias Amsterdam UMC location University of Amsterdam Amsterdam the Netherlands. Cardiovascular Disease Initiative Broad Institute of MIT and Harvard Cambridge MA USA. Cardiovascular Research Center Massachusetts General Hospital Boston MA USA. Institute for Molecular Medicine Finland (FIMM) Helsinki Institute of Life Science (HiLIFE) University of Helsinki Helsinki Finland. European Reference Network for rare low prevalence and complex diseases of the heart: ERN GUARD-Heart Amsterdam the Netherlands. Department of Physiology Amsterdam UMC location Vrije Universiteit Amsterdam the Netherlands. Department of Medicine III Institute for Cardiomyopathies Heidelberg (ICH) University Hospital Heidelberg Heidelberg Germany. Site Heidelberg/Mannheim DZHK Heidelberg Germany. Research Unit on Cardiovascular Disorders Metabolism and Nutrition Team Genomics and Pathophysiology of Cardiovascular Disease Sorbone Université INSERM Paris France. ICAN Institute for Cardiometabolism and Nutrition Paris France. National Heart and Lung Institute Imperial College London London UK. MRC Laboratory of Medical Sciences Imperial College London London UK. Royal Brompton and Harefield Hospitals Guy's and St. Thomas' NHS Foundation Trust London UK. Institute of Cardiovascular Science University College London London UK. Institute of Health Informatics University College London London UK. Massachusetts Veterans Epidemiology Research and Information Center (MAVERIC) VA Boston Healthcare System Boston MA USA. Palo Alto Veterans Institute for Research (PAVIR) Palo Alto Health Care System Palo Alto CA USA. Harvard Medical School Boston MA USA. Bioinformatics Core Facility Institute of Molecular Biology gGmbH (IMB) Mainz Germany. Department of Genetic Epidemiology Institute of Human Genetics University of Münster Münster Germany. Department of Cardiology University Heart and Vascular

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Comprehensive evaluation of coding region point mutations in microsatellite-unstable colorectal cancer

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EMBO Molecular medicine 2018年第9期10卷 e8552-e8552页

作者： Kondelin, Johanna Salokas, Kari Saarinen, Lilli Ovaska, Kristian Rauanheimo, Heli Plaketti, Roosa-Maria Hamberg, Jiri Liu, Xiaonan Yadav, Leena Gylfe, Alexandra E Cajuso, Tatiana Hänninen, Ulrika A Palin, Kimmo Ristolainen, Heikki Katainen, Riku Kaasinen, Eevi Tanskanen, Tomas Aavikko, Mervi Taipale, Minna Taipale, Jussi Renkonen-Sinisalo, Laura Lepistö, Anna Koskensalo, Selja Böhm, Jan Mecklin, Jukka-Pekka Ongen, Halit Dermitzakis, Emmanouil T Kilpivaara, Outi Vahteristo, Pia Turunen, Mikko Hautaniemi, Sampsa Tuupanen, Sari Karhu, Auli Välimäki, Niko Varjosalo, Markku Pitkänen, Esa Aaltonen, Lauri A Medicum/Department of Medical and Clinical Genetics University of Helsinki Helsinki Finland Genome-Scale Biology Research Program Research Programs Unit University of Helsinki Helsinki Finland Institute of Biotechnology University of Helsinki Helsinki Finland Helsinki Institute of Life Science University of Helsinki Helsinki Finland Division of Functional Genomics Department of Medical Biochemistry and Biophysics (MBB) Karolinska Institutet Stockholm Sweden Department of Biosciences and Nutrition Karolinska Institutet Huddinge Sweden Science for Life Center Huddinge Sweden Department of Surgery Helsinki University Central Hospital Hospital District of Helsinki and Uusimaa Helsinki Finland The HUCH Gastrointestinal Clinic Helsinki University Central Hospital Helsinki Finland Department of Pathology Jyväskylä Central Hospital Jyväskylä Finland Department of Surgery Jyväskylä Central Hospital University of Eastern Finland Jyväskylä Finland Department Sport and Health Sciences University of Jyväskylä Jyväskylä Finland Department of Genetic Medicine and Development University of Geneva Medical School Geneva Switzerland Institute for Genetics and Genomics in Geneva (iGE3) University of Geneva Geneva Switzerland Swiss Institute of Bioinformatics Geneva Switzerland

Microsatellite instability (MSI) leads to accumulation of an excessive number of mutations in the genome, mostly small insertions and deletions. MSI colorectal cancers (CRCs), however, also contain more point mutations than microsatellite-stable (MSS) tumors, yet they have not been as comprehensively studied. To identify candidate driver genes affected by point mutations in MSI CRC, we ranked genes based on mutation significance while correcting for replication timing and gene expression utilizing an algorithm, MutSigCV. Somatic point mutation data from the exome kit-targeted area from 24 exome-sequenced sporadic MSI CRCs and respective normals, and 12 whole-genome-sequenced sporadic MSI CRCs and respective normals were utilized. The top 73 genes were validated in 93 additional MSI CRCs. The MutSigCV ranking identified several well-established MSI CRC driver genes and provided additional evidence for previously proposed CRC candidate genes as well as shortlisted genes that have to our knowledge not been linked to CRC before. Two genes, SMARCB1 and STK38L, were also functionally scrutinized, providing evidence of a tumorigenic role, for SMARCB1 mutations in particular. © 2018 The Authors. Published under the terms of the CC BY 4.0 license

关键词： cancer genetics colorectal cancer microsatellite instability

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Author Correction: Genotypic characterization of multiple drug resistant Escherichia coli isolates from a pediatric cancer hospital in Egypt

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Scientific reports 2020年第1期10卷 7415页

作者： Reem Hassan Marwa Tantawy Nouran A Gouda Mariam G Elzayat Sara Gabra Amena Nabih Aya A Diab Mohamed El-Hadidi Usama Bakry Mohamed R Shoeb Mervat Elanany Lobna Shalaby Ahmed A Sayed Molecular Microbiology Unit Children's cancer hospital Egypt 57357 Cairo Egypt. Department of clinical pathology Faculty of Medicine Cairo University Cairo Egypt. Genomics Program Children's cancer hospital Egypt 57357 Cairo Egypt. Bioinformatics Group Center of Informatics Sciences (CIS) Nile University Giza Egypt. Microbiology Unit Children's cancer hospital Egypt 57357 Cairo Egypt. Infectious disease unit Children's cancer hospital Egypt 57357 Cairo Egypt. Department of pediatric oncology National cancer Institute Cairo University Cairo Egypt. Genomics Program Children's cancer hospital Egypt 57357 Cairo Egypt. ahmad.sayed@***. Department of Biochemistry Faculty of Science Ain Shams University Cairo Egypt. ahmad.sayed@***.

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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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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Author Correction: Genome-wide association study identifies Sjögren's risk loci with functional implications in immune and glandular cells

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Nature communications 2022年第1期13卷 6519页

作者： Bhuwan Khatri Kandice L Tessneer Astrid Rasmussen Farhang Aghakhanian Tove Ragna Reksten Adam Adler Ilias Alevizos Juan-Manuel Anaya Lara A Aqrawi Eva Baecklund Johan G Brun Sara Magnusson Bucher Maija-Leena Eloranta Fiona Engelke Helena Forsblad-d'Elia Stuart B Glenn Daniel Hammenfors Juliana Imgenberg-Kreuz Janicke Liaaen Jensen Svein Joar Auglænd Johnsen Malin V Jonsson Marika Kvarnström Jennifer A Kelly He Li Thomas Mandl Javier Martín Gaétane Nocturne Katrine Brække Norheim Øyvind Palm Kathrine Skarstein Anna M Stolarczyk Kimberly E Taylor Maria Teruel Elke Theander Swamy Venuturupalli Daniel J Wallace Kiely M Grundahl Kimberly S Hefner Lida Radfar David M Lewis Donald U Stone C Erick Kaufman Michael T Brennan Joel M Guthridge Judith A James R Hal Scofield Patrick M Gaffney Lindsey A Criswell Roland Jonsson Per Eriksson Simon J Bowman Roald Omdal Lars Rönnblom Blake Warner Maureen Rischmueller Torsten Witte A Darise Farris Xavier Mariette Marta E Alarcon-Riquelme Caroline H Shiboski Marie Wahren-Herlenius Wan-Fai Ng Kathy L Sivils Indra Adrianto Gunnel Nordmark Christopher J Lessard Genes and Human Disease Research Program Oklahoma Medical Research Foundation Oklahoma City OK USA. Arthritis and Clinical Immunology Research Program Oklahoma Medical Research Foundation Oklahoma City OK USA. Department of Clinical Science University of Bergen Bergen Norway. NGS Core Laboratory Oklahoma Medical Research Foundation Oklahoma City OK USA. Salivary Disorder Unit National Institute of Dental and Craniofacial Research Bethesda MD USA. Center for Autoimmune Diseases Research (CREA) Universidad del Rosario Bogotá Colombia. Department of Oral Surgery and Oral Medicine Faculty of Dentistry University of Oslo Oslo Norway. Department of Health Sciences Kristiania University College Oslo Norway. Department of Medical Sciences Rheumatology and Science for Life Laboratory Uppsala University Uppsala Sweden. Department of Rheumatology Faculty of Medicine and Health Örebro University Örebro Sweden. Department of Rheumatology and Immunology Hannover Medical School Hannover Germany. Department of Rheumatology and Inflammation Research Sahlgrenska Academy at University of Gothenburg Gothenburg Sweden. Department of Rheumatology Haukeland University Hospital Bergen Norway. Department of Internal Medicine Clinical Immunology Unit Stavanger University Hospital Stavanger Norway. Section for Oral and Maxillofacial Radiology Department of Clinical Dentistry Medical Faculty University of Bergen Bergen Norway. Rheumatology Unity Department of Medicine Karolinska University Hospital Karolinska Institutet Stockholm Sweden. Academic Specialist Center Center for Rheumatology and Studieenheten Stockholm Health Services Region Stockholm Sweden. Translational Sciences The Janssen Pharmaceutical Companies of Johnson & Johnson Spring House PA USA. Rheumatology Department of Clinical Sciences Malmö Lund University Malmö Sweden. Instituto de Biomedicina y Parasitología López-Neyra Consejo Superior de Investigaciones Científicas (CSIC) Granada Spain. Université

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Data integration of bulk and single-cell transcriptomics from cerebral organoids and post-mortem brains to identify cell types and cell type specific driver genes in autism

Research Square

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Research Square 2020年

作者： Lim, Elaine T. Chan, Yingleong Burns, Mannix J. Guo, Xiaoge Erdin, Serkan Tai, Derek J.C. Reichert, Julia M. Chan, Ying Kai Chiang, Jessica J. Meyers, Katharina Zhang, Xiaochang Walsh, Christopher A. Yankner, Bruce A. Raychaudhuri, Soumya Hirschhorn, Joel N. Gusella, James F. Talkowski, Michael E. Church, George M. DZNE Germany Program in Bioinformatics and Integrative Biology Departments of Neurology and Molecular Cell and Cancer Biology University of Massachusetts Medical School WorcesterMA01605 United States Department of Genetics Harvard Medical School BostonMA02115 United States Wyss Institute for Biologically Inspired Engineering Harvard University BostonMA02115 United States Stanley Center for Psychiatric Research Broad Institute of MIT and Harvard CambridgeMA02115 United States Center for Genomic Medicine Massachusetts General Hospital BostonMA02115 United States Department of Neurology Massachusetts General Hospital BostonMA02115 United States Department of Human Genetics The Grossman Institute for Neuroscience Quantitative Biology and Human Behavior The University of Chicago ChicagoIL60637 United States Division of Genetics and Genomics Manton Center for Orphan Disease Research Howard Hughes Medical Institute Boston Children’s Hospital BostonMA02115 United States Departments of Pediatrics and Neurology Harvard Medical School BostonMA02115 United States Divisions of Genetics and Rheumatology Brigham and Women's Hospital Harvard Medical School BostonMA02115 United States Partners Center for Personalized Genetic Medicine BostonMA02115 United States Faculty of Medical and Human Sciences University of Manchester ManchesterM13 9PL United Kingdom Division of Endocrinology Boston Children's Hospital BostonMA02115 United States Center for Basic and Translational Obesity Research Boston Children's Hospital BostonMA02115 United States

Human-derived cerebral organoids demonstrate great promise for identifying cell types and cell type specific molecular processes perturbed by genetic variants associated with neuropsychiatric and neurodevelopmental disorders, which are notoriously challenging to study using animal models. However, considerable challenges remain in achieving robust, scalable and generalizable phenotyping of organoids to discover cell types and cell type specific genes. We perform RNA sequencing on 71 samples comprising 1,420 cerebral organoids from 25 donors, and describe a framework (Orgo-Seq) to integrate bulk RNA and single-cell RNA sequence data from human post-mortem brains and cerebral organoids, for the identification of cell types and cell type specific individual genes. We apply Orgo-Seq for two autism-associated loci: 16p11.2 deletions and 15q11-13 duplications, and identify neuroepithelial cells as critical cell types for 16p11.2 deletions, and discover novel and previously reported cell type specific driver genes. Finally, we validated our results that mutations in the KCTD13 gene in the 16p11.2 locus lead to imbalances in the proportion of neuroepithelial cells, using CRISPR/Cas9-edited mosaic organoids. Our work presents a quantitative technological framework to integrate multiple transcriptomics datasets to identify cell types and cell type specific driver genes associated with complex diseases using cerebral organoids. © 2020, CC BY.

关键词： Genes

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