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Systemic analysis of osteoblast-specific DNA methylation marks reveals novel epigenetic basis of osteoblast differentiation

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Bone Reports 2017年 6卷 109-119页

作者： Yu, Fangtang Shen, Hui Deng, Hong-Wen Center for Bioinformatics and Genomics Department of Global Biostatistics and Data Science School of Public Health and Tropical Medicine Tulane University New Orleans 70112 LA United States College of Life Sciences Hunan Normal University Changsha 410081 Hunan China College of Life Sciences and Bioengineering Beijing Jiaotong University Beijing 100044 China

DNA methylation is an important epigenetic modification that contributes to the lineage commitment and specific functions of different cell types. In this study, we compared ENCODE-generated genome-wide DNA methylation profiles of human osteoblast with 21 other types of human cells in order to identify osteoblast-specific methylation events. For most of the cell strains, data from two isogenic replicates were included, resulting in a total of 51 DNA methylation datasets. We identified 852 significant osteoblast-specific differentially methylated CpGs (DMCs) and 295 significant differentially methylated regions (DMRs). Significant DMCs/DMRs were not enriched in CpG islands (CGIs) and promoters, but more strongly enriched in CGI shores/shelves and in gene body and intergenic regions. The genes associated with significant DMRs were highly enriched in biological processes related to transcriptional regulation and critical for regulating bone metabolism and skeletal development under physiologic and pathologic conditions. By integrating the DMR data with the extensive gene expression and chromatin epigenomics data, we observed complex, context-dependent relationships between DNA methylation, chromatin states, and gene expression, suggesting diverse DNA methylation-mediated regulatory mechanisms. Our results also highlighted a number of novel osteoblast-relevant genes. For example, the integrated evidences from DMR analysis, histone modification and RNA-seq data strongly support that there is a novel isoform of neurexin-2 (NRXN2) gene specifically expressed in osteoblast. NRXN2 was known to function as a cell adhesion molecule in the vertebrate nervous system, but its functional role in bone is completely unknown and thus worth further investigation. In summary, we reported a comprehensive analysis of osteoblast-specific DNA methylation profiles and revealed novel insights into the epigenetic basis of osteoblast differentiation and activity. © 2017 The Authors

关键词： Alternative splicing Cell-specific Differential methylation analysis Methylation Osteoblast Transcription

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Declaración PRISMA 2020: una guía actualizada para la publicación de revisiones sistemáticas

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Revista Española de Cardiología (English Edition) 2021年第9期74卷 790-799页

作者： Matthew J. Page Joanne E. McKenzie Patrick M. Bossuyt Isabelle Boutron Tammy C. Hoffmann Cynthia D. Mulrow Larissa Shamseer Jennifer M. Tetzlaff Elie A. Akl Sue E. Brennan Roger Chou Julie Glanville Jeremy M. Grimshaw Asbjørn Hróbjartsson Manoj M. Lalu Tianjing Li Elizabeth W. Loder Evan Mayo-Wilson David Moher School of Public Health and Preventive Medicine Monash University Melbourne Australia Department of Clinical Epidemiology Biostatistics and Bioinformatics Amsterdam University Medical Centres University of Amsterdam Amsterdam Países Bajos Université de Paris Centre of Epidemiology and Statistics (CRESS) Inserm F 75004 Paris Francia Institute for Evidence-Based Healthcare Faculty of Health Sciences and Medicine Bond University Gold Coast Australia University of Texas Health Science Center at San Antonio San Antonio Texas Estados Unidos Annals of Internal Medicine Knowledge Translation Program Li Ka Shing Knowledge Institute Toronto Canadá School of Epidemiology and Public Health Faculty of Medicine University of Ottawa Ottawa Canada Evidence Partners Ottawa Canadá Clinical Research Institute American University of Beirut Beirut Líbano Department of Health Research Methods Evidence and Impact McMaster University Hamilton Ontario Canadá Department of Medical Informatics and Clinical Epidemiology Oregon Health & Science University Portland Oregón Estados Unidos York Health Economics Consortium (YHEC Ltd) University of York York Reino Unido Clinical Epidemiology Program Ottawa Hospital Research Institute Ottawa Canadá School of Epidemiology and Public Health University of Ottawa Ottawa Canadá Department of Medicine University of Ottawa Ottawa Canadá Centre for Evidence-Based Medicine Odense Odense University Hospital Odense Dinamarca Department of Clinical Research University of Southern Denmark Odense Dinamarca Open Patient data Explorative Network Odense University Hospital Odense Dinamarca Department of Anesthesiology and Pain Medicine The Ottawa Hospital Ottawa Canadá Clinical Epidemiology Program Blueprint Translational Research Group Ottawa Hospital Research Institute Ottawa Canadá Regenerative Medicine Program Ottawa Hospital Research Institute Ottawa Canadá Department of Ophthalmology School of Medicine University of Colorado Denver Den

La declaración PRISMA ( Preferred Reporting Items for Systematic reviews and Meta-Analyses ), publicada en 2009, se diseñó para ayudar a los autores de revisiones sistemáticas a documentar de manera transparente el porqué de la revisión, qué hicieron los autores y qué encontraron. Durante la última década, ha habido muchos avances en la metodología y terminología de las revisiones sistemáticas, lo que ha requerido una actualización de esta guía. La declaración prisma 2020 sustituye a la declaración de 2009 e incluye una nueva guía de presentación de las publicaciones que refleja los avances en los métodos para identificar, seleccionar, evaluar y sintetizar estudios. La estructura y la presentación de los ítems ha sido modificada para facilitar su implementación. En este artículo, presentamos la lista de verificación PRISMA 2020 con 27 ítems, y una lista de verificación ampliada que detalla las recomendaciones en la publicación de cada ítem, la lista de verificación del resumen estructurado PRISMA 2020 y el diagrama de flujo revisado para revisiones sistemáticas. The Preferred Reporting Items for Systematic reviews and Meta-Analyses (PRISMA) statement, published in 2009, was designed to help systematic reviewers transparently report why the review was done, what the authors did, and what they found. Over the past decade, advances in systematic review methodology and terminology have necessitated an update to the guideline. The PRISMA 2020 statement replaces the 2009 statement and includes new reporting guidance that reflects advances in methods to identify, select, appraise, and synthesise studies. The structure and presentation of the items have been modified to facilitate implementation. In this article, we present the PRISMA 2020 27-item checklist, an expanded checklist that details reporting recommendations for each item, the PRISMA 2020 abstract checklist, and the revised flow diagrams for original and updated reviews. Full English text available from : ***

关键词： Guía de publicación Revisión sistemática Metanálisis Escritura médica Publishing guide Systematic review Meta-analysis Medical writing

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Author Correction: PNPO-PLP axis senses prolonged hypoxia in macrophages by regulating lysosomal activity

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Nature metabolism 2024年第12期6卷 2391页

作者： Hiroki Sekine Haruna Takeda Norihiko Takeda Akihiro Kishino Hayato Anzawa Takayuki Isagawa Nao Ohta Shohei Murakami Hideya Iwaki Nobufumi Kato Shu Kimura Zun Liu Koichiro Kato Fumiki Katsuoka Masayuki Yamamoto Fumihito Miura Takashi Ito Masatomo Takahashi Yoshihiro Izumi Hiroyuki Fujita Hitoshi Yamagata Takeshi Bamba Takaaki Akaike Norio Suzuki Kengo Kinoshita Hozumi Motohashi Department of Medical Biochemistry Tohoku University Graduate School of Medicine Sendai Japan. hiroki.sekine.c2@tohoku.ac.jp. Department of Medical Biochemistry Tohoku University Graduate School of Medicine Sendai Japan. Division of Cardiology and Metabolism Center for Molecular Medicine Jichi Medical University Shimotsuke Japan. Department of Cardiovascular Medicine Graduate School of Medicine The University of Tokyo Tokyo Japan. Department of Gene Expression Regulation IDAC Tohoku University Sendai Japan. Department of System Bioinformatics Graduate School of Information Sciences Tohoku University Sendai Japan. Department of Integrative Genomics Tohoku Medical Megabank Organization Tohoku University Sendai Japan. Data Science Center Jichi Medical University Shimotsuke Japan. Division of Oxygen Biology United Centers for Advanced Research and Translational Medicine Tohoku University Graduate School of Medicine Sendai Japan. Department of Biochemistry and Molecular Biology Tohoku Medical Megabank Organization Tohoku University Sendai Japan. Department of Biochemistry Kyushu University Graduate School of Medical Sciences Fukuoka Japan. Division of Metabolomics Medical Institute of Bioregulation Kyushu University Fukuoka Japan. Advanced Research Laboratory Canon Medical Systems Corporation Otawara Japan. Department of Environmental Medicine and Molecular Toxicology Tohoku University Graduate School of Medicine Sendai Japan. Department of Medical Biochemistry Tohoku University Graduate School of Medicine Sendai Japan. hozumi.motohashi.a7@tohoku.ac.jp. Department of Gene Expression Regulation IDAC Tohoku University Sendai Japan. hozumi.motohashi.a7@tohoku.ac.jp.

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66O Association of a blood T cell fitness gene signature with clinical benefit from ImmTAC bispecific T cell engagers

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Annals of Oncology 2024年 35卷 S239-S240页

作者： J.J. Sacco R.D. Carvajal O. Hamid P.B. Kirk L. Collins M.O. Butler A.N. Shoushtari J.C. Hassel A.P. Ikeguchi L. Hernandez-Aya P. Nathan J.M. Piulats Rodriguez H. Shaw D. Davar C. Han M.R. Middleton F. Thistlethwaite F. Peck K. Ranade T. Sato Medical Oncology Department The Clatterbridge Cancer Centre and University of Liverpool Wirral UK Medical Oncology Northwell Health Cancer Institute New York NY USA Melanoma Center and Phase I Immuno-Oncology Program The Angeles Clinic and Research Institute a Cedars-Sinai Affiliate Los Angeles CA USA Translational Medicine Immunocore Limited Abingdon-on-Thames UK Bioinformatics and Data Science Immunocore Limited Abingdon-on-Thames UK Department of Medical Oncology and Hematology Princess Margaret Cancer Center Toronto ON Canada Medical Oncology Memorial Sloan Kettering Cancer Center New York NY USA Department of Dermatology and National Center for Tumor Diseases University Hospital Heidelberg Heidelberg Germany Department of Medicine Stephenson Cancer Center/University of Oklahoma Oklahoma City OK USA Cutaneous Oncology University of Miami Sylvester Comprehensive Cancer Center Miami Beach FL USA Medical Oncology Department Mount Vernon Cancer Centre Northwood UK Medical Oncology Department ICO - Institut Català d'Oncologia l'Hospitalet (Hospital Duran i Reynals) Barcelona Spain Medical Oncology UCLH - University College London Hospitals NHS Foundation Trust London UK Medical Oncology University of Pittsburgh Cancer Institute Pittsburgh PA USA Faculty of Medical & Health Sciences University of Auckland Auckland New Zealand Department of Oncology University of Oxford Oxford UK Medical Oncology Department The Christie NHS Foundation Trust Manchester UK Clinical Development Immunocore Limited Abingdon-on-Thames UK Translational Medicine Department Immunocore LLC Rockville MD USA Sidney Kimmel Cancer Center Jefferson University Philadelphia PA USA

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High-depth African genomes inform human migration and health (vol 586, pg 741, 2020)

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NATURE 2021年第7856期592卷 E26-E26页

作者： Choudhury, Ananyo Aron, Shaun Botigue, Laura R. Sengupta, Dhriti Botha, Gerrit Bensellak, Taoufik Wells, Gordon Kumuthini, Judit Shriner, Daniel Fakim, Yasmina J. Ghoorah, Anisah W. Dareng, Eileen Odia, Trust Falola, Oluwadamilare Adebiyi, Ezekiel Hazelhurst, Scott Mazandu, Gaston Nyangiri, Oscar A. Mbiyavanga, Mamana Benkahla, Alia Kassim, Samar K. Mulder, Nicola Adebamowo, Sally N. Chimusa, Emile R. Muzny, Donna Metcalf, Ginger Gibbs, Richard A. Matovu, Enock Bucheton, Bruno Hertz-Fowler, Christiane Koffi, Mathurin Macleod, Annette Mumba-Ngoyi, Dieudonne Noyes, Harry Nyangiri, Oscar A. Simo, Gustave Simuunza, Martin Rotimi, Charles Ramsay, Michele Choudhury, Ananyo Choudhury, Ananyo Aron, Shaun Botigue, Laura Sengupta, Dhriti Botha, Gerrit Bensellak, Taoufik Wells, Gordon Kumuthini, Judit Shriner, Daniel Fakim, Yasmina J. Ghoorah, Anisah W. Dareng, Eileen Odia, Trust Falola, Oluwadamilare Adebiyi, Ezekiel Hazelhurst, Scott Mazandu, Gaston Nyangiri, Oscar A. Mbiyavanga, Mamana Benkahla, Alia Kassim, Samar K. Mulder, Nicola Adebamowo, Sally N. Chimusa, Emile R. Rotimi, Charles Ramsay, Michele Adeyemo, Adebowale A. Lombard, Zane Hanchard, Neil A. Adebamowo, Clement Agongo, Godfred Boua, Romuald P. Oduro, Abraham Sorgho, Hermann Landoure, Guida Cisse, Lassana Diarra, Salimata Samassekou, Oumar Anabwani, Gabriel Matshaba, Mogomotsi Joloba, Moses Kekitiinwa, Adeodata Mardon, Graeme Mpoloka, Sununguko W. Kyobe, Samuel Mlotshwa, Busisiwe Mwesigwa, Savannah Retshabile, Gaone Williams, Lesedi Wonkam, Ambroise Moussa, Ahmed Adu, Dwomoa Ojo, Akinlolu Burke, David Salako, Babatunde O. Matovu, Enock Bucheton, Bruno Hertz-Fowler, Christiane Koffi, Mathurin Macleod, Annette Mumba-Ngoyi, Dieudonne Noyes, Harry Nyangiri, Oscar A. Simo, Gustave Simuunza, Martin Awadalla, Philip Bruat, Vanessa Gbeha, Elias Adeyemo, Adebowale A. Lombard, Zane Hanchard, Neil A. Sydney Brenner Institute for Molecular Bioscience Faculty of Health Sciences University of the Witwatersrand Johannesburg South Africa School of Electrical and Information Engineering University of the Witwatersrand Johannesburg South Africa Division of Human Genetics National Health Laboratory Service and School of Pathology Faculty of Health Sciences University of the Witwatersrand Johannesburg South Africa Navrongo Health Research Centre Navrongo Ghana Clinical Research Unit of Nanoro Institut de Recherche en Sciences de la Sante Bobo-Dioulasso Burkina Faso Center for Research in Agricultural Genomics (CRAG) Plant and Animal Genomics Program CSIC-IRTA-UAB-UB Barcelona Spain Computational Biology Division and H3ABioNet Department of Integrative Biomedical Sciences IDM University of Cape Town Cape Town South Africa System and Data Engineering Team Abdelmalek Essaadi University ENSA Tangier Morocco Centre for Proteomic and Genomic Research (CPGR) Cape Town South Africa South African National Bioinformatics Institute University of the Western Cape Bellville South Africa Africa Health Research Institute Durban South Africa Center for Research on Genomics and Global Health National Human Genome Research Institute National Institutes of Health Bethesda MD USA Department of Agriculture and Food Science Faculty of Agriculture University of Mauritius Reduit Mauritius Department of Digital Technologies Faculty of Information Communication & Digital Technologies University of Mauritius Reduit Mauritius Department of Public Health and Primary Care University of Cambridge Cambridge UK Institute of Human Virology Nigeria Abuja Nigeria Department of Epidemiology and Public Health University of Maryland School of Medicine University of Maryland Baltimore Baltimore MD USA University of Maryland Greenebaum Comprehensive Cancer Center University of Maryland School of Medicine University of Maryland Baltimore Baltimore MD USA Institute of Human Virology and Greeneba

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Modeling the causal regulatory network by integrating chromatin accessibility and transcriptome data

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National science Review 2016年第2期3卷 240-251页

作者： Yong Wang Rui Jiang Wing Hung Wong Department of Statistics Department of Biomedical Data ScienceBio-X ProgramStanford University Academy of Mathematics and Systems Science National Center for Mathematics and Interdisciplinary SciencesChinese Academy of Sciences MOE Key Laboratory of Bioinformatics Bioinformatics Division and Center for Synthetic and Systems BiologyTNLISTDepartment of AutomationTsinghua University

Cell packs a lot of genetic and regulatory information through a structure known as chromatin,*** is wrapped around histone proteins and is tightly packed in a remarkable *** express a gene in a specific coding region,the chromatin would open up and DNA loop may be formed by interacting enhancers and ***,the mediator and cohesion complexes,sequence-specific transcription factors,and RNA polymerase Ⅱ are recruited and work together to elaborately regulate the expression *** is in pressing need to understand how the information,about when,where,and to what degree genes should be expressed,is embedded into chromatin structure and gene regulatory *** to large consortia such as Encyclopedia of DNA Elements(ENCODE) and Roadmap Epigenomic projects,extensive data on chromatin accessibility and transcript abundance are available across many tissues and cell *** rich data offer an exciting opportunity to model the causal regulatory ***,we will review the current experimental approaches,foundational data,computational problems,interpretive frameworks,and integrative models that will enable the accurate interpretation of regulatory ***,we will discuss the efforts to organize,analyze,model,and integrate the DNA accessibility data,transcriptional data,and functional genomic regions *** believe that these efforts will eventually help us understand the information flow within the cell and will influence research directions across many fields.

关键词： gene regulatory network open chromatin DNA accessibility transcription factor colocalization statistical model data integration

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Correction to: Effect of early tumor response on the health-related quality of life among patients on second-line chemotherapy for advanced gastric cancer in the ABSOLUTE trial

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Gastric cancer : official journal of the International Gastric Cancer Association and the Japanese Gastric Cancer Association 2021年第2期24卷 477-478页

作者： Kazumasa Fujitani Kohei Shitara Atsuo Takashima Keisuke Koeda Hiroki Hara Norisuke Nakayama Shuichi Hironaka Kazuhiro Nishikawa Yutaka Kimura Kenji Amagai Hisashi Hosaka Yoshito Komatsu Ken Shimada Ryohei Kawabata Hideki Ohdan Yasuhiro Kodera Masato Nakamura Takako Eguchi Nakajima Yoshinori Miyata Toshikazu Moriwaki Tetsuya Kusumoto Kazuo Nishikawa Kazuhiro Ogata Masashi Shimura Satoshi Morita Wasaburo Koizumi Department of Surgery Osaka General Medical Center 3-1-56 Bandaihigashi Sumiyoshi-ku Osaka 558-0056 Japan. fujitani@gh.opho.jp. Department of Gastrointestinal Oncology National Cancer Center Hospital East Kashiwa Japan. Gastrointestinal Medical Oncology Division National Cancer Center Hospital Tokyo Japan. Department of Medical Safety Science Iwate Medical University Morioka Japan. Department of Gastroenterology Saitama Cancer Center Ina-machi Japan. Department of Gastroenterology Kanagawa Cancer Center Yokohama Japan. Clinical Trial Promotion Department Chiba Cancer Center Chiba Japan. Department of Medical Oncology and Hematology Faculty of Medicine Oita University Oita Japan. Department of Surgery National Hospital Organization Osaka National Hospital Osaka Japan. Department of Surgery Sakai City Medical Center Sakai Japan. Department of Gastroenterology Ibaraki Prefectural Central Hospital Kasama Japan. Division of Gastroenterology Gunma Prefectural Cancer Center Ohta Japan. Division of Cancer Chemotherapy Hokkaido University Hospital Cancer Center Sapporo Japan. Division of Medical Oncology Department of Internal Medicine Showa University Northern Yokohama Hospital Yokohama Japan. Department of Surgery Osaka Rosai Hospital Osaka Japan. Department of Gastroenterological and Transplant Surgery Graduate School of Biomedical and Health Sciences Hiroshima University Hiroshima Japan. Department of Gastroenterological Surgery Nagoya University Graduate School of Medicine Nagoya Japan. Aizawa Comprehensive Cancer Center Aizawa Hospital Nagano Japan. Department of Clinical Oncology St. Marianna University School of Medicine Kawasaki Japan. Kyoto Innovation Center for Next Generation Clinical Trials and iPS Cell Therapy Kyoto University Hospital Kyoto Japan. Department of Medical Oncology Saku Central Hospital Advanced Care Center Saku Japan. Division of Gastroenterology Faculty of Medicine University of Tsukuba Tsukuba Japan. Department of Gast

The article Effect of early tumor response on the health-related quality of life among patients.

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

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Nature genetics 2023年第6期55卷 1080页

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

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A genome-wide association study with 1,126,563 individuals identifies new risk loci for Alzheimer's disease (Sep, 10.1038/s41588-021-00921-z, 2021)

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NATURE GENETICS 2022年第7期54卷 1062-1062页

作者： Wightman, Douglas P. Jansen, Iris E. Savage, Jeanne E. Shadrin, Alexey A. Bahrami, Shahram Holland, Dominic Rongve, Arvid Borte, Sigrid Winsvold, Bendik S. Drange, Ole Kristian Martinsen, Amy E. Skogholt, Anne Heidi Willer, Cristen Brathen, Geir Bosnes, Ingunn Nielsen, Jonas Bille Fritsche, Lars G. Thomas, Laurent F. Pedersen, Linda M. Gabrielsen, Maiken E. Johnsen, Marianne Bakke Meisingset, Tore Wergeland Zhou, Wei Proitsi, Petroula Hodges, Angela Dobson, Richard Velayudhan, Latha Heilbron, Karl Auton, Adam Sealock, Julia M. Davis, Lea K. Pedersen, Nancy L. Reynolds, Chandra A. Karlsson, Ida K. Magnusson, Sigurdur Stefansson, Hreinn Thordardottir, Steinunn Jonsson, Palmi V. Snaedal, Jon Zettergren, Anna Skoog, Ingmar Kern, Silke Waern, Margda Zetterberg, Henrik Blennow, Kaj Stordal, Eystein Hveem, Kristian Zwart, John-Anker Athanasiu, Lavinia Selnes, Per Saltvedt, Ingvild Sando, Sigrid B. Ulstein, Ingun Djurovic, Srdjan Fladby, Tormod Aarsland, Dag Selbaek, Geir Ripke, Stephan Stefansson, Kari Andreassen, Ole A. Posthuma, Danielle Department of Complex Trait Genetics Center for Neurogenomics and Cognitive Research Amsterdam Neuroscience VU Amsterdam Amsterdam the Netherlands Department of Child and Adolescent Psychiatry and Pediatric Psychology Section Complex Trait Genetics Amsterdam Neuroscience Vrije Universiteit Medical Center Amsterdam University Medical Center Amsterdam the Netherlands NORMENT Centre University of Oslo Oslo Norway Institute of Clinical Medicine University of Oslo Oslo Norway Division of Mental Health and Addiction Oslo University Hospital Oslo Norway Research and Communication Unit for Musculoskeletal Health (FORMI) Department of Research Innovation and Education Division of Clinical Neuroscience Oslo University Hospital Oslo Norway K. G. Jebsen Center for Genetic Epidemiology Department of Public Health and Nursing Faculty of Medicine and Health Sciences Norwegian University of Science and Technology Trondheim Norway Department of Research Innovation and Education Division of Clinical Neuroscience Oslo University Hospital Oslo Norway Department of Neurology Akershus University Hospital Lørenskog Norway Department of Geriatric Medicine Oslo University Hospital Oslo Norway Norwegian National Advisory Unit on Ageing and Health Vestfold Hospital Trust Tønsberg Norway Department of Neurosciences University of California San Diego La Jolla CA USA Department of Research and Innovation Helse Fonna Haugesund Hospital Haugesund Norway The University of Bergen Institute of Clinical Medicine (K1) Bergen Norway Department of Neurology Oslo University Hospital Oslo Norway Department of Clinical and Molecular Medicine Norwegian University of Science and Technology Trondheim Norway Department of Internal Medicine Division of Cardiovascular Medicine University of Michigan Ann Arbor MI USA Department of Epidemiology Research Statens Serum Institut Copenhagen Denmark HUNT Research Center Department of Public Health and Nursing Faculty of Medicine and Health Scien

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Essential guidelines for computational method benchmarking

arXiv

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arXiv 2018年

作者： Weber, Lukas M. Saelens, Wouter Cannoodt, Robrecht Soneson, Charlotte Hapfelmeier, Alexander Gardner, Paul P. Boulesteix, Anne-Laure Saeys, Yvan Robinson, Mark D. Institute of Molecular Life Sciences University of Zurich Zurich Switzerland SIB Swiss Institute of Bioinformatics University of Zurich Zurich Switzerland Data Mining and Modelling for Biomedicine VIB Center for Inflammation Research Ghent Belgium Department of Applied Mathematics Computer Science and Statistics Ghent University Ghent Belgium Institute of Medical Informatics Statistics and Epidemiology Technical University of Munich Munich Germany Department of Biochemistry University of Otago Dunedin New Zealand Institute for Medical Information Processing Biometry and Epidemiology Ludwig-Maximilians-University Munich Germany Friedrich Miescher Institute for Biomedical Research SIB Swiss Institute of Bioinformatics Basel Switzerland

In computational biology and other sciences, researchers are frequently faced with a choice between several computational methods for performing data analyses. Benchmarking studies aim to rigorously compare the performance of different methods using well-characterized benchmark datasets, to determine the strengths of each method or to provide recommendations regarding suitable choices of methods for an analysis. However, benchmarking studies must be carefully designed and implemented to provide accurate, unbiased, and informative results. Here, we summarize key practical guidelines and recommendations for performing high-quality benchmarking analyses, based on our experiences in computational biology. Copyright © 2018, The Authors. All rights reserved.

关键词： Benchmarking

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