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arXiv 2023年

作者： Callahan, Tiffany J. Tripodi, Ignacio J. Stefanski, Adrianne L. Cappelletti, Luca Taneja, Sanya B. Wyrwa, Jordan M. Casiraghi, Elena Matentzoglu, Nicolas A. Reese, Justin Silverstein, Jonathan C. Hoyt, Charles Tapley Boyce, Richard D. Malec, Scott A. Unni, Deepak R. Joachimiak, Marcin P. Robinson, Peter N. Mungall, Christopher J. Cavalleri, Emanuele Fontana, Tommaso Valentini, Giorgio Mesiti, Marco Gillenwater, Lucas A. Santangelo, Brook Vasilevsky, Nicole A. Hoehndorf, Robert Bennett, Tellen D. Ryan, Patrick B. Hripcsak, George Kahn, Michael G. Bada, Michael Baumgartner, William A. Hunter, Lawrence E. Computational Bioscience Program University of Colorado Anschutz Medical Campus AuroraCO80045 United States Department of Biomedical Informatics Columbia University Irving Medical Center New YorkNY10032 United States Computer Science Department Interdisciplinary Quantitative Biology University of Colorado Boulder BoulderCO80301 United States AnacletoLab Computer Science Department University of Milan 20122 Italy Intelligent Systems Program University of Pittsburgh PittsburghPA15260 United States Department of Physical Medicine and Rehabilitation School of Medicine University of Colorado Anschutz Medical Campus AuroraCO80045 United States Division of Environmental Genomics and Systems Biology Lawrence Berkeley National Laboratory BerkeleyCA94720 United States Semanticly Ltd Athens Greece Department of Biomedical Informatics University of Pittsburgh School of Medicine PittsburghPA15206 United States Laboratory of Systems Pharmacology Harvard Medical School BostonMA02115 United States Division of Translational Informatics University of New Mexico School of Medicine AlbuquerqueNM87131 United States SIB Swiss Institute of Bioinformatics Basel Switzerland Berlin Institute of Health at Charité-Universitatsmedizin Berlin10117 Germany ELLIS European Laboratory for Learning and Intelligent Systems Germany Department of Biomedical Informatics University of Colorado School of Medicine AuroraCO80045 United States Data Collaboration Center Critical Path Institute 1840 E River Rd. Suite 100 TucsonAZ85718 United States Computer Electrical and Mathematical Sciences & Engineering Division Computational Bioscience Research Center King Abdullah University of Science and Technology Thuwal23955-6900 Saudi Arabia Department of Pediatrics University of Colorado School of Medicine AuroraCO80045 United States Janssen Research and Development RaritanNJ08869 United States Division of General Internal Medicine University of Colorado School of Medicine A

Translational research requires data at multiple scales of biological organization. Advancements in sequencing and multi-omics technologies have increased the availability of these data, but researchers face significant integration challenges. Knowledge graphs (KGs) are used to model complex phenomena, and methods exist to construct them automatically. However, tackling complex biomedical integration problems requires flexibility in the way knowledge is modeled. Moreover, existing KG construction methods provide robust tooling at the cost of fixed or limited choices among knowledge representation models. PheKnowLator (Phenotype Knowledge Translator) is a semantic ecosystem for automating the FAIR (Findable, Accessible, Interoperable, and Reusable) construction of ontologically grounded KGs with fully customizable knowledge representation. The ecosystem includes KG construction resources (e.g., data preparation APIs), analysis tools (e.g., SPARQL endpoints and abstraction algorithms), and benchmarks (e.g., prebuilt KGs and embeddings). We evaluated the ecosystem by systematically comparing it to existing open-source KG construction methods and by analyzing its computational performance when used to construct 12 large-scale KGs. With flexible knowledge representation, PheKnowLator enables fully customizable KGs without compromising performance or usability. © 2023, CC BY.

关键词： Ecosystems

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γ-Linolenic acid in maternal milk drives cardiac metabolic maturation (vol 618, pg 365, 2023)

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NATURE 2023年第7968期619卷 E24-E24页

作者： Paredes, Ana Justo-Mendez, Raquel Jimenez-Blasco, Daniel Nunez, Vanessa Calero, Irene Villalba-Orero, Maria Alegre-Marti, Andrea Fischer, Thierry Gradillas, Ana Sant'Anna, Viviane Aparecida Rodrigues Were, Felipe Huang, Zhiqiang Hernansanz-Agustin, Pablo Contreras, Carmen Martinez, Fernando Camafeita, Emilio Vazquez, Jesus Ruiz-Cabello, Jesus Area-Gomez, Estela Sanchez-Cabo, Fatima Treuter, Eckardt Bolanos, Juan Pedro Estebanez-Perpina, Eva Ruperez, Francisco Javier Barbas, Coral Enriquez, Jose Antonio Ricote, Mercedes Cardiovascular Regeneration Program Centro Nacional de Investigaciones Cardiovasculares (CNIC) Madrid Spain Departamento de Medicina y Cirugía Animal Universidad Complutense de Madrid (UCM) Madrid Spain CIBER de Fragilidad y Envejecimiento Saludable (CIBERFES) Madrid Spain Institute of Functional Biology and Genomics (IBFG) University of Salamanca CSIC Salamanca Spain Institute for Biomedical Research of Salamanca (IBSAL) Salamanca Spain Department of Biochemistry and Molecular Biomedicine Institute of Biomedicine (IBUB) of the University of Barcelona (UB) Barcelona Spain Department of Immunology and Oncology Centro Nacional de Biotecnología-Consejo Superior de Investigaciones Científicas (CNB/CSIC) Campus Universidad Autónoma de Madrid (UAM) Madrid Spain Centro de Metabolómica y Bioanálisis (CEMBIO) Facultad de Farmacia Universidad San Pablo-CEU CEU Universities Madrid Spain Bioinformatics Unit Centro Nacional de Investigaciones Cardiovasculares (CNIC) Madrid Spain CIBER de Enfermedades Cardiovasculares (CIBERCV) Madrid Spain Department of Biosciences and Nutrition Karolinska Institutet Huddinge Sweden Proteomics Unit Centro Nacional de Investigaciones Cardiovasculares (CNIC) Madrid Spain CIC biomaGUNE Basque Research and Technology Alliance (BRTA) San Sebastian Spain Ikerbasque Basque Foundation for Science Bilbao Spain CIBER de Enfermedades Respiratorias (CIBERES) Madrid Spain Departamento de Ciencias Farmacéuticas Facultad de Farmacia Universidad Complutense Madrid (UCM) Madrid Spain Departament of Cellular and Molecular Biology Centro de Investigaciones Biológicas Margarita Salas-CSIC Madrid Spain Department of Neurology Columbia University Medical Campus New York NY USA

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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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Genome-wide analyses identify 30 loci associated with obsessive–compulsive disorder

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Nature Genetics 2025年 1-13页

作者： Strom, Nora I. Gerring, Zachary F. Galimberti, Marco Yu, Dongmei Halvorsen, Matthew W. Abdellaoui, Abdel Rodriguez-Fontenla, Cristina Sealock, Julia M. Bigdeli, Tim Coleman, Jonathan R. Mahjani, Behrang Thorp, Jackson G. Bey, Katharina Burton, Christie L. Luykx, Jurjen J. Zai, Gwyneth Alemany, Silvia Andre, Christine Askland, Kathleen D. Bäckman, Julia Banaj, Nerisa Barlassina, Cristina Nissen, Judith Becker Bienvenu, O. Joseph Black, Donald Bloch, Michael H. Børte, Sigrid Bosch, Rosa Breen, Michael Brennan, Brian P. Brentani, Helena Buxbaum, Joseph D. Bybjerg-Grauholm, Jonas Byrne, Enda M. Cabana-Dominguez, Judit Camarena, Beatriz Camarena, Adrian Cappi, Carolina Carracedo, Angel Casas, Miguel Cavallini, Maria Cristina Ciullo, Valentina Cook, Edwin H. Crosby, Jesse Cullen, Bernadette A. De Schipper, Elles J. Delorme, Richard Djurovic, Srdjan Elias, Jason A. Estivill, Xavier Falkenstein, Martha J. Fundin, Bengt T. Garner, Lauryn Gironda, Christina Goes, Fernando S. Grados, Marco A. Grove, Jakob Guo, Wei Haavik, Jan Hagen, Kristen Harrington, Kelly Havdahl, Alexandra Höffler, Kira D. Hounie, Ana G. Hucks, Donald Hultman, Christina Janecka, Magdalena Jenike, Eric Karlsson, Elinor K. Kelley, Kara Klawohn, Julia Krasnow, Janice E. Krebs, Kristi Lange, Christoph Lanzagorta, Nuria Levey, Daniel Lindblad-Toh, Kerstin Macciardi, Fabio Maher, Brion Mathes, Brittany McArthur, Evonne McGregor, Nathaniel McLaughlin, Nicole C. Meier, Sandra Miguel, Euripedes C. Mulhern, Maureen Nestadt, Paul S. Nurmi, Erika L. O’Connell, Kevin S. Osiecki, Lisa Ousdal, Olga Therese Palviainen, Teemu Pedersen, Nancy L. Piras, Federica Potluri, Sriramya Rabionet, Raquel Ramirez, Alfredo Rauch, Scott Reichenberg, Abraham Riddle, Mark A. Ripke, Stephan Rosário, Maria C. Sampaio, Aline S. Schiele, Miriam A. Skogholt, Anne Heidi Sloofman, Laura G. Smit, Jan Artigas, María Soler Thomas, Laurent F. Tifft, Eric Vallada, Homero van Kirk, Nathanial Veenstra-VanderWeele, Jeremy Vulink, Nienke N. Walker, Christopher P. Wang, Ying Wendland, Jens R. Winsvold Department of Psychology Humboldt-Universität zu Berlin Berlin Germany Department of Psychiatric Phenomics and Genomics (IPPG) Ludwig-Maximilians University Munich Munich Germany Centre for Psychiatry Research Department of Clinical Neuroscience Karolinska Institutet and Stockholm Health Services Region Stockholm Stockholm Sweden Department of Biomedicine Aarhus University Aarhus Denmark University Hospital of Psychiatry and Psychotherapy University of Bern Bern Switzerland Department of Mental Health and Neuroscience Translational Neurogenomics QIMR Berghofer Medical Research Institute Brisbane QLD Australia Department of Population Health and Immunity Healthy Development and Ageing Walter and Eliza Hall Institute of Medical Research Melbourne VIC Australia Department of Psychiatry Human Genetics Yale University New Haven CT United States VA Connecticut Healthcare System West Haven CT United States Department of Center for Genomic Medicine Psychiatric and Neurodevelopmental Genetics Unit Massachusetts General Hospital Boston MA United States Stanley Center for Psychiatric Research Broad Institute of MIT and Harvard Cambridge MA United States Department of Genetics University of North Carolina at Chapel Hill Chapel Hill NC United States Department of Psychiatry Amsterdam University Medical Centers University of Amsterdam Amsterdam Netherlands Center for Research in Molecular Medicine and Chronic Diseases (CiMUS) Genomics and Bioinformatics University of Santiago de Compostela Santiago de Compostela Spain Grupo de Medicina Xenómica Genetics Instituto de Investigación Sanitaria de Santiago de Compostela (FIDIS) Santiago de Compostela Spain Vanderbilt Genetics Institute Vanderbilt University Nashville TN United States Department of Psychiatry and Behavioral Sciences SUNY Downstate Health Sciences University Brooklyn NY United States VA NY Harbor Healthcare System Brooklyn NY United States Social Genetic and Developmental Psychiatry Centre Insti

Obsessive–compulsive disorder (OCD) affects ~1% of children and adults and is partly caused by genetic factors. We conducted a genome-wide association study (GWAS) meta-analysis combining 53,660 OCD cases and 2,044,417 controls and identified 30 independent genome-wide significant loci. Gene-based approaches identified 249 potential effector genes for OCD, with 25 of these classified as the most likely causal candidates, including WDR6, DALRD3 and CTNND1 and multiple genes in the major histocompatibility complex (MHC) region. We estimated that ~11,500 genetic variants explained 90% of OCD genetic heritability. OCD genetic risk was associated with excitatory neurons in the hippocampus and the cortex, along with D₁ and D₂ type dopamine receptor-containing medium spiny neurons. OCD genetic risk was shared with 65 of 112 additional phenotypes, including all the psychiatric disorders we examined. In particular, OCD shared genetic risk with anxiety, depression, anorexia nervosa and Tourette syndrome and was negatively associated with inflammatory bowel diseases, educational attainment and body mass index. © The Author(s) 2025.

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

NPJ Biodiversity

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NPJ Biodiversity 2024年第1期3卷 1-17页

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

A genomic database of all Earth’s eukaryotic species could contribute to many scientific discoveries;however, only a tiny fraction of species have genomic information available. In 2018, scientists across the world united under the Earth BioGenome Project (EBP), aiming to produce a database of highquality reference genomes containing all ~1.5 million recognized eukaryotic species. As the European node of the EBP, the European Reference Genome Atlas (ERGA) sought to implement a new decentralised, equitable and inclusive model for producing reference genomes. For this, ERGA launched a Pilot Project establishing the first distributed reference genome production infrastructure and testing it on 98 eukaryotic species from 33 European countries. Here we outline the infrastructure and explore its effectiveness for scaling high-quality reference genome production, whilst considering equity and inclusion. The outcomes and lessons learned provide a solid foundation for ERGA while offering key learnings to other transnational, national genomic resource projects and the EBP. © The Author(s) 2024, corrected publication 2024.

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Author Correction: Antibodies from dengue patients with prior exposure to Japanese encephalitis virus are broadly neutralizing against Zika virus

Communications biology

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Communications biology 2024年第1期7卷 252页

作者： Gielenny M Salem Jedhan Ucat Galula Shang-Rung Wu Jyung-Hurng Liu Yen-Hsu Chen Wen-Hung Wang Sheng-Fan Wang Cheng-Sheng Song Fan-Chi Chen Adrian B Abarientos Guan-Wen Chen Cheng-I Wang Day-Yu Chao Graduate Institute of Microbiology and Public Health College of Veterinary Medicine National Chung Hsing University Taichung City 402 Taiwan. Institute of Oral Medicine School of Dentistry College of Medicine National Cheng Kung University Tainan City 701 Taiwan. Institute of Basic Medical Sciences College of Medicine National Cheng Kung University Tainan City 701 Taiwan. Graduate Institute of Genomics and Bioinformatics College of Life Sciences National Chung Hsing University Taichung City 40227 Taiwan. School of Medicine College of Medicine National Sun Yat-Sen University Kaohsiung City 80424 Taiwan. Center for Tropical Medicine and Infectious Disease Research Kaohsiung Medical University Kaohsiung City 80708 Taiwan. Division of Infectious Diseases Department of Internal Medicine Kaohsiung Medical University Hospital Kaohsiung Medical University Kaohsiung City 80708 Taiwan. Department of Medical Laboratory Science and Biotechnology Kaohsiung Medical University Kaohsiung City 80708 Taiwan. Doctoral Program in Microbial Genomics National Chung Hsing University and Academia Sinica Taichung City 402 Taiwan. Singapore Immunology Network Agency for Science Technology and Research (A*STAR) 8A Biomedical Grove Immunos Singapore 138648 Singapore. Graduate Institute of Microbiology and Public Health College of Veterinary Medicine National Chung Hsing University Taichung City 402 Taiwan. dychao@nchu.edu.tw. Doctoral Program in Microbial Genomics National Chung Hsing University and Academia Sinica Taichung City 402 Taiwan. dychao@nchu.edu.tw. Department of Post-Baccalaureate Medicine College of Medicine National Chung Hsing University Taichung City 402 Taiwan. dychao@nchu.edu.tw.

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Patterns of somatic structural variation in human cancer genomes (vol 578, pg 112, 2020)

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NATURE 2023年第7948期614卷 E38-E38页

作者： Li, Yilong Roberts, Nicola D. Wala, Jeremiah A. Shapira, Ofer Schumacher, Steven E. Kumar, Kiran Khurana, Ekta Waszak, Sebastian Korbel, Jan O. Haber, James E. Imielinski, Marcin Weischenfeldt, Joachim Beroukhim, Rameen Campbell, Peter J. Cancer Genome Project Wellcome Trust Sanger Institute Hinxton UK Totient Inc Cambridge MA USA Wellcome Sanger Institute Wellcome Genome Campus Hinxton UK Department of Haematology University of Cambridge Cambridge UK Cambridge University Hospitals NHS Foundation Trust Cambridge UK Korea Advanced Institute of Science and Technology Daejeon South Korea Department of Zoology Genetics and Physical Anthropology University of Santiago de Compostela Santiago de Compostela Spain Centre for Research in Molecular Medicine and Chronic Diseases (CIMUS) University of Santiago de Compostela Santiago de Compostela Spain The Biomedical Research Centre (CINBIO) University of Vigo Vigo Spain Centre for Research in Molecular Medicine and Chronic Diseases (CiMUS) Universidade de Santiago de Compostela Santiago de Compostela Spain Department of Zoology Genetics and Physical Anthropology (CiMUS) Universidade de Santiago de Compostela Santiago de Compostela Spain The Biomedical Research Centre (CINBIO) Universidade de Vigo Vigo Spain The Broad Institute of Harvard and MIT Cambridge MA USA Bioinformatics and Integrative Genomics Harvard University Cambridge MA USA Department of Cancer Biology Dana-Farber Cancer Institute Boston MA USA Broad Institute of MIT and Harvard Cambridge MA USA Department of Medical Oncology Dana-Farber Cancer Institute Boston MA USA Harvard Medical School Boston MA USA Massachusetts General Hospital Center for Cancer Research Charlestown MA USA Dana-Farber Cancer Institute Boston MA USA Department of Biostatistics and Computational Biology Dana-Farber Cancer Institute and Harvard Medical School Boston MA USA Weill Cornell Medical College New York NY USA Department of Physiology and Biophysics Weill Cornell Medicine New York NY USA Institute for Computational Biomedicine Weill Cornell Medicine New York NY USA Controlled Department and Institution New York NY USA Englander Institute for Precision Medicine Weill Cornell Medicine Ne

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Author Correction: The landscape of viral associations in human cancers

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Nature genetics 2023年第6期55卷 1077页

作者： Marc Zapatka Ivan Borozan Daniel S Brewer Murat Iskar Adam Grundhoff Malik Alawi Nikita Desai Holger Sültmann Holger Moch Colin S Cooper Roland Eils Vincent Ferretti Peter Lichter Division of Molecular Genetics German Cancer Research Center (DKFZ) Heidelberg Germany. Informatics and Bio-computing Program Ontario Institute for Cancer Research Toronto Ontario Canada. Norwich Medical School University of East Anglia Norwich UK. Earlham Institute Norwich UK. Heinrich-Pette-Institute Leibniz Institute for Experimental Virology Hamburg Germany. German Center for Infection Research (DZIF) Partner Site Hamburg-Borstel-Lübeck-Riems Hamburg Germany. Bioinformatics Core University Medical Center Hamburg-Eppendorf Hamburg Germany. Bioinformatics Group Department of Computer Science University College London London UK. Biomedical Data Science Laboratory Francis Crick Institute London UK. National Center for Tumor Diseases (NCT) Heidelberg Heidelberg Germany. Division of Cancer Genome Research German Cancer Research Center (DKFZ) Heidelberg Germany. German Cancer Consortium (DKTK) Heidelberg Germany. Department of Pathology and Molecular Pathology University and University Hospital Zürich Zurich Switzerland. Institute of Cancer Research London UK. University of East Anglia Norwich UK. Division of Theoretical Bioinformatics German Cancer Research Center (DKFZ) Heidelberg Germany. Department of Bioinformatics and Functional Genomics Institute of Pharmacy and Molecular Biotechnology Heidelberg University and BioQuant Center Heidelberg Germany. Center for Digital Health Berlin Institute of Health and Charité Universitätsmedizin Berlin Berlin Germany. Ontario Institute for Cancer Research MaRS Centre Toronto Ontario Canada. Department of Biochemistry and Molecular Medicine University of Montreal Montreal Québec Canada. Division of Molecular Genetics German Cancer Research Center (DKFZ) Heidelberg Germany. peter.lichter@dkfz-heidelberg.de. German Cancer Consortium (DKTK) Heidelberg Germany. peter.lichter@dkfz-heidelberg.de.

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Author Correction: Pathway and network analysis of more than 2500 whole cancer genomes

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Nature communications 2022年第1期13卷 7566页

作者： Matthew A Reyna David Haan Marta Paczkowska Lieven P C Verbeke Miguel Vazquez Abdullah Kahraman Sergio Pulido-Tamayo Jonathan Barenboim Lina Wadi Priyanka Dhingra Raunak Shrestha Gad Getz Michael S Lawrence Jakob Skou Pedersen Mark A Rubin David A Wheeler Søren Brunak Jose M G Izarzugaza Ekta Khurana Kathleen Marchal Christian von Mering S Cenk Sahinalp Alfonso Valencia Jüri Reimand Joshua M Stuart Benjamin J Raphael Department of Computer Science Princeton University Princeton NJ 08540 USA. Department of Biomedical Informatics Emory University Atlanta GA 30322 USA. Department of Biomolecular Engineering and UC Santa Cruz Genomics Institute University of California Santa Cruz Santa Cruz CA 95060 USA. Computational Biology Program Ontario Institute for Cancer Research Toronto Ontario Canada. Department of Information Technology IDLab Ghent University IMEC Ghent the Netherlands. Department of Plant Biotechnology and Bioinformatics Ghent University Ghent the Netherlands. Barcelona Supercomputing Center (BSC) Barcelona 08034 Spain. Department of Clinical and Molecular Medicine Faculty of Medicine and Health Sciences Norwegian University of Science and Technology Trondheim Norway. Institute of Molecular Life Sciences and Swiss Institute of Bioinformatics University of Zurich CH-8057 Zurich Switzerland. Department of Pathology and Molecular Pathology University Hospital Zurich CH-8091 Zurich Switzerland. Department of Physiology and Biophysics Weill Cornell Medicine New York NY 10065 USA. Vancouver Prostate Centre 2660 Oak Street Vancouver BC V6H 3Z6 Canada. The Broad Institute of MIT and Harvard Cambridge MA 02124 USA. Massachusetts General Hospital Center for Cancer Research Charlestown MA 02129 USA. Harvard Medical School 250 Longwood Avenue Boston MA 02115 USA. Massachusetts General Hospital Department of Pathology Boston MA 02114 USA. Department of Molecular Medicine (MOMA) Aarhus University Hospital Aarhus Denmark. Bioinformatics Research Centre (BiRC) Aarhus University Aarhus Denmark. Human Genome Sequencing Center Baylor College of Medicine Houston TX 77030 USA. DTU Bioinformatics Department of Bio and Health Informatics Technical University of Denmark Kemitorvet 2800 Kongens Lyngby Denmark. Novo Nordisk Foundation Center for Protein Research Faculty of Health and Medical Sciences University of Copenhagen 2200 Copenhagen Denmark. De

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Characterization and expression of the microtubule associated protein tau gene isoforms and their impact on clinical outcomes in glioma patients

Computational and Structural Biotechnology Reports

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Computational and Structural Biotechnology Reports 2024年 1卷

作者： Axel M. Hidalgo Vipin Singh Thenral Mangadu Deblina Guha Enrique I. Ramos Chandrima Das Shrikanth S. Gadad Bioinformatics Program The University of Texas at El Paso USA Center of Emphasis in Cancer Department of Molecular and Translational Medicine Texas Tech University Health Sciences Center El Paso 130 Rick Francis st. El Paso TX 79905 USA Biophysics and Structural Genomics Division Saha Institute of Nuclear Physics 1/AF Bidhannagar Kolkata 700064 India Minority AIDS Research Center Department of Health Sciences The University of Texas at El Paso TX 79968 USA The University of Texas at El Paso TX 79968 USA HomiBhaba National Institute Mumbai 400094 India L. Frederick Francis Graduate School of Biomedical Sciences Texas Tech University Health Sciences Center El Paso 130 Rick Francis st. El Paso TX 79905 USA Mays Cancer Center UT Health San Antonio MD Anderson Cancer Center San Antonio TX 78229 USA

Gliomas are the most common tumors found in the central nervous system. They are classified based on their histopathological malignancy. Low-grade gliomas (LGG) can turn into glioblastomas (GBM), the most aggressive form of brain cancer with the worst prognosis. Previous studies have shown that microtubule-associated protein tau ( MAPT ) is increased in GBM and that reducing it can improve survival in animal models. On the other hand, elevated MAPT expression has been linked to increased survival in LGG, indicating its potential as a survival biomarker. However, previous studies have primarily focused on the canonical protein-coding transcripts and gene-level expression of MAPT , disregarding the diversity of its many isoforms. Many diseases in almost every tissue have been associated with a dysregulation of alternative splicing, either through an altered ratio of the expressed isoforms or by expressing aberrant transcripts with different alternative transcription start and termination sites. This study investigates the association of specific MAPT transcripts with survival in LGG and GBM using publicly available genomic datasets and performing statistical analyses. The results of the study indicated coding and several non-coding isoforms associated with overall survival (OS), disease-specific survival (DSS), and progression-free interval (PFI). After including the relevant predictors as covariates, it was observed that among the protein-coding isoforms, MAPT-205 and MAPT-201 were significantly associated with clinical survival endpoints, but with opposite trends. These findings highlight the importance of studying the role of MAPT isoforms in glioma cellular phenotypes, aggressiveness, and patient survival.

关键词： Transcription Gene expression Differential exon usage Isoforms

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