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Correction to: Genes associated with survival of female bovine blastocysts produced in vivo

Cell and tissue research 2020年第3期382卷 679页

作者： A M Zolini J Block M B Rabaglino G Rincon M Hoelker J J Bromfield D Salilew-Wondim P J Hansen Department of Animal Sciences D.H. Barron Reproductive and Perinatal Biology Research Program and Genetics Institute University of Florida PO Box 110910 Gainesville FL 32611-0910 USA. Zoetis Inc. Kalamazoo MI 49007 USA. Instituto de Investigación en Ciencias de La Salud CONICET Córdoba Argentina. Quantitative Genetics Bioinformatics and Computational Biology Group Department of Applied Mathematics and Computer Science Technical University of Denmark Kemitorvet 2800 Kgs. Lyngby Denmark. Institute of Animal Science Animal Breeding and Husbandry University of Bonn Bonn Germany. Teaching and Research Station Frankenforst Faculty of Agriculture University of Bonn Königswinter Germany. Center of Integrated Dairy Research University of Bonn Bonn Germany. Department of Animal Sciences D.H. Barron Reproductive and Perinatal Biology Research Program and Genetics Institute University of Florida PO Box 110910 Gainesville FL 32611-0910 USA. pjhansen@ufl.edu.

The first error is on page 5. A sentence lists two genes as SCNA1A and SCNA2A but they should be SCN1A and SCN2A.

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A systems biology approach uncovers novel disease mechanisms in age-related macular degeneration

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Cell Genomics 2023年第6期3卷 100302-100302页

作者： Orozco, Luz D. Owen, Leah A. Hofmann, Jeffrey Stockwell, Amy D. Tao, Jianhua Haller, Susan Mukundan, Vineeth T. Clarke, Christine Lund, Jessica Sridhar, Akshayalakshmi Mayba, Oleg Barr, Julie L. Zavala, Rylee A. Graves, Elijah C. Zhang, Charles Husami, Nadine Finley, Robert Au, Elizabeth Lillvis, John H. Farkas, Michael H. Shakoor, Akbar Sherva, Richard Kim, Ivana K. Kaminker, Joshua S. Townsend, Michael J. Farrer, Lindsay A. Yaspan, Brian L. Chen, Hsu-Hsin DeAngelis, Margaret M. Department of Bioinformatics and Computational Biology Genentech South San Francisco 94080 CA United States Department of Ophthalmology and Visual Sciences University of Utah School of Medicine The University of Utah Salt Lake City 84132 UT United States Department of Population Health Sciences University of Utah School of Medicine The University of Utah Salt Lake City 84132 UT United States Department of Obstetrics and Gynecology University of Utah School of Medicine The University of Utah Salt Lake City 84132 UT United States Department of Ophthalmology Ross Eye Institute Jacobs School of Medicine and Biomedical Sciences State University of New York University at Buffalo Buffalo 14203 NY United States Department of Pathology Genentech South San Francisco 94080 CA United States Department of Human Genetics Genentech South San Francisco 94080 CA United States Departments of Microchemistry Proteomics and Lipidomics Genentech South San Francisco 94080 CA United States Department of Human Pathobiology & OMNI Reverse Translation Genentech South San Francisco 94080 CA United States Neuroscience Graduate Program Jacobs School of Medicine and Biomedical Sciences State University of New York University at Buffalo Buffalo 14203 NY United States Department of Biochemistry Jacobs School of Medicine and Biomedical Sciences State University of New York University at Buffalo Buffalo 14203 NY United States Veterans Administration Western New York Healthcare System Buffalo 14212 NY United States Department of Medicine Biomedical Genetics Boston University School of Medicine Boston 02118 MA United States Retina Service Massachusetts Eye & Ear Department of Ophthalmology Harvard Medical School Boston 02114 MA United States Genetics Genomics and Bioinformatics Graduate Program Jacobs School of Medicine and Biomedical Sciences State University of New York University at Buffalo Buffalo 14203 NY United States

Age-related macular degeneration (AMD) is a leading cause of blindness, affecting 200 million people worldwide. To identify genes that could be targeted for treatment, we created a molecular atlas at different stages of AMD. Our resource is comprised of RNA sequencing (RNA-seq) and DNA methylation microarrays from bulk macular retinal pigment epithelium (RPE)/choroid of clinically phenotyped normal and AMD donor eyes (n = 85), single-nucleus RNA-seq (164,399 cells), and single-nucleus assay for transposase-accessible chromatin (ATAC)-seq (125,822 cells) from the retina, RPE, and choroid of 6 AMD and 7 control donors. We identified 23 genome-wide significant loci differentially methylated in AMD, over 1,000 differentially expressed genes across different disease stages, and an AMD Müller state distinct from normal or gliosis. Chromatin accessibility peaks in genome-wide association study (GWAS) loci revealed putative causal genes for AMD, including HTRA1 and C6orf223. Our systems biology approach uncovered molecular mechanisms underlying AMD, including regulators of WNT signaling, FRZB and TLE2, as mechanistic players in disease. © 2023 The Authors

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Publisher Correction: Integrating yeast chemical genomics and mammalian cell pathway analysis

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Acta pharmacologica Sinica 2020年第5期41卷 729页

作者： Fu-Lai Zhou Sheena C Li Yue Zhu Wan-Jing Guo Li-Jun Shao Justin Nelson Scott Simpkins De-Hua Yang Qing Liu Yoko Yashiroda Jin-Biao Xu Yao-Yue Fan Jian-Min Yue Minoru Yoshida Tian Xia Chad L Myers Charles Boone Ming-Wei Wang The National Center for Drug Screening and the CAS Key Laboratory of Receptor Research Shanghai Institute of Materia Medica Chinese Academy of Sciences (CAS) Shanghai 201203 China. University of Chinese Academy of Sciences Beijing 100049 China. RIKEN Center for Sustainable Resource Science Wako Saitama 3510198 Japan. Bioinformatics and Computational Biology Program University of Minnesota-Twin Cities Minneapolis Minnesota 55455 USA. The State Key Laboratory of Drug Research Shanghai Institute of Materia Medica Chinese Academy of Sciences Shanghai 201203 China. Department of Biology The University of Tokyo Bunkyo-ku Tokyo 1138657 Japan. Collaborative Research for Innovative Microbiology The University of Tokyo Bunkyo-ku Tokyo 1138657 Japan. Department of Electronics and Information Engineering Huazhong University of Science and Technology Wuhan 430074 China. Bioinformatics and Computational Biology Program University of Minnesota-Twin Cities Minneapolis Minnesota 55455 USA. chadm@umn.edu. RIKEN Center for Sustainable Resource Science Wako Saitama 3510198 Japan. charlie.boone@utoronto.ca. Donnelly Centre and Department of Molecular Genetics University of Toronto Ontario M5S 3E1 Canada. charlie.boone@utoronto.ca. The National Center for Drug Screening and the CAS Key Laboratory of Receptor Research Shanghai Institute of Materia Medica Chinese Academy of Sciences (CAS) Shanghai 201203 China. mwwang@***. University of Chinese Academy of Sciences Beijing 100049 China. mwwang@***.

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: Genomic analysis of a large set of currently-and historically-important human adenovirus pathogens

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Emerging microbes & infections 2018年第1期7卷 208页

作者： Ashrafali M Ismail Tiange Cui Kalpana Dommaraju Gurdeep Singh Shoaleh Dehghan Jason Seto Susmita Shrivastava Nadia B Fedorova Neha Gupta Timothy B Stockwell Rebecca Halpin Ramana Madupu Albert Heim Adriana E Kajon Eric G Romanowski Regis P Kowalski Jambulingam Malathi Kuzhanthai L Therese Hajib Narahari Madhavan Qiwei Zhang Leonardo J Ferreyra Morris S Jones Jaya Rajaiya David W Dyer James Chodosh Donald Seto Department of Ophthalmology Howe Laboratory Massachusetts Eye and Ear Infirmary Harvard Medical School Boston MA 02114 USA. Bioinformatics and Computational Biology Program School of Systems Biology George Mason University Manassas VA 20110 USA. Chemistry Department American University Washington DC 20016 USA. J. Craig Venter Institute Rockville MD 20850 USA. Institut für Virologie Medizinische Hochschule Hannover Hannover 30625 Germany. Lovelace Respiratory Research Institute Albuquerque NM 87108 USA. Charles T. Campbell Ophthalmic Microbiology Laboratory Ear and Eye Institute School of Medicine University of Pittsburgh Pittsburgh PA 15213 USA. L & T Microbiology Research Center Kamalnayan Bajaj Research Center Sankara Nethralaya No. 41 College Road Chennai Tamil Nadu 600006 India. Biosafety Level-3 Laboratory School of Public Health Southern Medical University 510515 Guangzhou China. Institute of Virology "J. M. Vanella" Enfermera Gordillo Gómez s/n Agencia 4 Ciudad Universitaria CP 5016 Córdoba Argentina. School of Public Health University of California Berkeley Berkeley CA 94704 USA. Department of Microbiology and Immunology University of Oklahoma Health Sciences Center Oklahoma City OK 73104 USA. Department of Ophthalmology Howe Laboratory Massachusetts Eye and Ear Infirmary Harvard Medical School Boston MA 02114 USA. james_chodosh@meei.harvard.edu. Bioinformatics and Computational Biology Program School of Systems Biology George Mason University Manassas VA 20110 USA. dseto@gmu.edu.

The original publication of this article [1] was missing the below author that made contributions to the research and the published article.

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Development and Validation Of a Highly Sensitive and Specific Gene Expression Classifier To Prospectively Screen and Identify B-Precursor Acute Lymphoblastic Leukemia (ALL) Patients With a Philadelphia Chromosome-Like ("Ph-like" or "BCR-ABL1-Like") Signature For Therapeutic Targeting and Clinical Intervention

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BLOOD 2013年第21期122卷 826-826页

作者： Harvey, Richard C. Kang, Huining Roberts, Kathryn G. Chen, I-Ming L. Atlas, Susan R. Bedrick, Edward J. Gastier-Foster, Julie M. Zhang, Jinghui Gerhard, Daniels S. Smith, Malcolm A. Larsen, Eric C. Raetz, Elizabeth A. Winick, Naomi J. Carroll, William L. Stonerock, Eileen Heerema, Nyla A. Carroll, Andrew J. Chen, Shann-Ching Song, Guangchun Becksfort, Jared Rusch, Michael Li, Yongjin Ma, Jing Ell, Denise Reshmi, Shalini C. Loh, Mignon L. Davidas, Meenakshi Hunger, Stephen P. Mullighan, Charles G. Willman, Cheryl L. Pathology University of New Mexico Albuquerque NM USA Cancer Center University of New Mexico Albuquerque NM USA Pathology St. Jude Children's Research Hospital Memphis TN USA Cancer Center/Pathology University of New Mexico Albuquerque NM USA Physics and Astronomy University of New Mexico Albuquerque NM USA Internal Medicine University of New Mexico Cancer Center Albuquerque NM USA Ohio State University Laboratory Medicine/Pathology Nationwide Childrens Hospital Columbus OH USA Computational Biology St Jude Children's Research Hospital Memphis TN USA Office of Cancer Genomics National Cancer Institute Bethesda MD USA Maine Children's Cancer Program Scarborough ME USA Pedatrics New York University Langone Medical Center New York NY USA Department of Pediatrics University of Texas Southwestern Medical Center Dallas TX USA Cancer Institute New York University New York NY USA Nationwide Childrens Hospital Columbus OH USA Department of Pathology Wexner Medical Center at Ohio State University Columbus OH USA Department of Genetics University of Alabama at Birmingham Birmingham AL USA Department of Pathology St Jude Children's Research Hospital Memphis TN USA Information Sciences Research Informatics Bioinformatics St. Jude Children's Research Hospital Memphis TN USA

826

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The ABCs of Experimental Evolution

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International Scholarly Research Notices 2013年第1期2013卷

作者： Zaid Abdo Mathew Stein Andrzej Wojtowicz Kim M. Pepin Departments of Statistics University of Idaho Moscow ID 83844 USAuidaho.edu Department of Mathematics University of Idaho Moscow ID 83844 USAuidaho.edu Program of Bioinformatics and Computational Biology (BCB) University of Idaho Moscow ID 83844 USAuidaho.edu USDA-ARS South Atlantic Area 950 College Station Road Athens GA 30605-2720 USA Department of Computer Engineering University of Idaho Moscow ID 83844 USAuidaho.edu Micron Technology Inc. Boise ID 83716 *** Department of Animal Sciences Washington State University Pullman WA 99164 USAwsu.edu Fogarty International Center National Institutes of Health 31 Center Drive MSC 2220 Bethesda MD 20892-2220 USAfic.nih.gov Department of Biology Colorado State University Campus Delivery 1878 Fort Collins CO 80523 USAcolostate.edu

Microbial evolution is complex and is influenced by many sources of variation. Experimental evolution is no exception, although it is more controlled, easily replicated, and typically devoid of interactions between species. Mathematical modeling of the evolutionary process can help in understanding the underlying mechanisms that drive outcome of such experiments. These models can be complex and parameter rich, limiting their feasibility for statistical inference. In this paper, we introduce the use of Approximate Bayesian Computation (ABC) as a tool for statistical inference in the study of experimental evolution. ABC is a fast and simple method for fitting complex models to data. We utilize this method, coupled with a mechanistic model of experimental evolution, to study the evolution process of bacteriophage ϕ X174 under benign selection pressure. Our results highlight three mutation-selection scenarios that could explain this process: high mutation/low selection pressure, low mutation/high selection pressure, and low mutation/low selection pressure, with posterior support of 19%, 9.5%, and 71.5% for each of these scenarios, respectively. Sequence data support the first candidate. Though surprising, this scenario was not improbable based on our analysis.

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Author Correction: Comprehensive molecular characterization of mitochondrial genomes in human cancers

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Nature genetics 2023年第6期55卷 1078页

作者： Yuan Yuan Young Seok Ju Youngwook Kim Jun Li Yumeng Wang Christopher J Yoon Yang Yang Inigo Martincorena Chad J Creighton John N Weinstein Yanxun Xu Leng Han Hyung-Lae Kim Hidewaki Nakagawa Keunchil Park Peter J Campbell Han Liang Department of Bioinformatics and Computational Biology The University of Texas MD Anderson Cancer Center Houston TX USA. Cancer Genome Project Wellcome Trust Sanger Institute Hinxton UK. Graduate School of Medical Science and Engineering Korea Advanced Institute of Science and Technology Daejeon Korea. Department of Health Science and Technology Samsung Advanced Institute for Health Science and Technology Sungkyunkwan University School of Medicine Seoul Korea. Samsung Genome Institute Samsung Medical Center Seoul Korea. Quantitative and Computational Biosciences Graduate Program Baylor College of Medicine Houston TX USA. Division of Biostatistics The University of Texas Health Science Center at Houston School of Public Health Houston TX USA. Department of Medicine and Dan L. Duncan Cancer Center Division of Biostatistics Baylor College of Medicine Houston TX USA. Department of Systems Biology The University of Texas MD Anderson Cancer Center Houston TX USA. Department of Applied Mathematics and Statistics Johns Hopkins University Baltimore MD USA. Department of Biochemistry and Molecular Biology The University of Texas Health Science Center at Houston McGovern Medical School Houston TX USA. Department of Biochemistry Ewha Womans University School of Medicine Seoul Korea. Laboratory for Cancer Genomics RIKEN Center for Integrative Medical Sciences Yokohama Japan. Division of Hematology/Oncology Samsung Medical Center Sungkyunkwan University School of Medicine Seoul Korea. kpark@skku.edu. Samsung Advanced Institute for Health Sciences and Technology Sungkyunkwan University School of Medicine Seoul South Korea. kpark@skku.edu. Cancer Genome Project Wellcome Trust Sanger Institute Hinxton UK. pc8@sanger.ac.uk. Department of Haematology University of Cambridge Cambridge UK. pc8@sanger.ac.uk. Department of Bioinformatics and Computational Biology The University of Texas MD Anderson Cancer Center Houston TX USA. hliang1@mdanderson.org. Quantitative and Comp

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Polygenic enrichment distinguishes disease associations of individual cells in single-cell RNA-seq data

Research Square

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Research Square 2021年

作者： Zhang, Martin Jinye Hou, Kangcheng Pasaniuc, Bogdan Price, Alkes L. Dey, Kushal K. Jagadeesh, Karthik A. Weinand, Kathryn Sakaue, Saori Taychameekiatchai, Aris Rao, Poorvi Pisco, Angela Oliveira Zou, James Wang, Bruce Gandal, Michael Raychaudhuri, Soumya Harvard University United States Osaka University Japan Department of Epidemiology Harvard T.H. Chan School of Public Health BostonMA United States Program in Medical and Population Genetics Broad Institute of MIT and Harvard CambridgeMA United States Bioinformatics Interdepartmental Program University of California Los Angeles Los AngelesCA United States Department of Pathology and Laboratory Medicine David Geffen School of Medicine University of California Los Angeles Los AngelesCA United States Department of Computational Medicine David Geffen School of Medicine University of California Los Angeles Los AngelesCA United States Center for Data Sciences Brigham and Women’s Hospital BostonMA United States Division of Genetics Department of Medicine Brigham and Women’s Hospital Harvard Medical School BostonMA United States Division of Rheumatology Inflammation and Immunity Department of Medicine Brigham and Women’s Hospital Harvard Medical School BostonMA United States Department of Biomedical Informatics Harvard Medical School BostonMA United States Department of Medicine and Liver Center University of California San Francisco San FranciscoCA United States Developmental and Stem Cell Biology Graduate Program University of California San Francisco San FranciscoCA United States Chan Zuckerberg Biohub San FranciscoCA United States Department of Electrical Engineering Stanford University Palo AltoCA United States Department of Biomedical Data Science Stanford University Palo AltoCA United States Department of Psychiatry David Geffen School of Medicine University of California Los Angeles Los AngelesCA United States Department of Human Genetics David Geffen School of Medicine University of California Los Angeles Los AngelesCA United States Program in Neurobehavioral Genetics Semel Institute David Geffen School of Medicine University of California Los Angeles Los AngelesCA United States Versus Arthritis Centre for Genetics and Genomic

Gene expression at the individual cell-level resolution, as quantified by single-cell RNA-sequencing (scRNA-seq), can provide unique insights into the pathology and cellular origin of diseases and complex traits. Here, we introduce single-cell Disease Relevance Score (scDRS), an approach that links scRNA-seq with polygenic risk of disease at individual cell resolution;scDRS identifies individual cells that show excess expression levels for genes in a disease-specific gene set constructed from GWAS data. We determined via simulations that scDRS is well-calibrated and powerful in identifying individual cells associated to disease. We applied scDRS to GWAS data from 74 diseases and complex traits (average N =341K) in conjunction with 16 scRNA-seq data sets spanning 1.3 million cells from 31 tissues and organs. At the cell type level, scDRS broadly recapitulated known links between classical cell types and disease, and also produced novel biologically plausible findings. At the individual cell level, scDRS identified subpopulations of disease-associated cells that are not captured by existing cell type labels, including subpopulations of CD4+ T cells associated with inflammatory bowel disease, partially characterized by their effector-like states;subpopulations of hippocampal CA1 pyramidal neurons associated with schizophrenia, partially characterized by their spatial location at the proximal part of the hippocampal CA1 region;and subpopulations of hepatocytes associated with triglyceride levels, partially characterized by their higher ploidy levels. At the gene level, we determined that genes whose expression across individual cells was correlated with the scDRS score (thus reflecting co-expression with GWAS disease genes) were strongly enriched for gold-standard drug target and Mendelian disease genes. © 2021, CC BY.

关键词： RNA

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40. Genomic profiling of lung adenocarcinomas with increased MET copy numbers

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Cancer Genetics 2018年 226卷 51-51页

作者： Liu, Ching-Hua (Ruby) Chen, Hui Fang, Lianghua Hu, Peter C. Gu, Jun Zhao, Jin Abraham, Ronald Yao, Hui Singh, Rajesh R. Jeffrey Medeiros, L. Luthra, Rajyalakshimi Lu, Xinyan Department of Hematopathology University of Texas MD Anderson Cancer Center Houston TX United States Master of Science in Diagnostic Genetics Program School of Health Professions University of Texas MD Anderson Cancer Center Houston TX United States Department of Pathology Northwestern University Feinberg School of Medicine Chicago IL United States Department of Pathology University of Texas MD Anderson Cancer Center Houston TX United States Department of Oncology Jiangsu Hospital of Traditional Chinese Medicine Nanjing Jiangsu China Department of Clinical Laboratory Hunan Cancer Hospital and The Affiliated Cancer Hospital of Xiangya School of Medicine Central South University Shangsha Hunan China Department of Bioinformatics and Computational Biology University of Texas MD Anderson Cancer Center Houston TX United States

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Author Correction: Myeloid lineage enhancers drive oncogene synergy in CEBPA/CSF3R mutant acute myeloid leukemia

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Nature communications 2022年第1期13卷 3471页

作者： Theodore P Braun Mariam Okhovat Cody Coblentz Sarah A Carratt Amy Foley Zachary Schonrock Brittany M Curtiss Kimberly Nevonen Brett Davis Brianna Garcia Dorian LaTocha Benjamin R Weeder Michal R Grzadkowski Joey C Estabrook Hannah G Manning Kevin Watanabe-Smith Sophia Jeng Jenny L Smith Amanda R Leonti Rhonda E Ries Shannon McWeeney Cristina Di Genua Roy Drissen Claus Nerlov Soheil Meshinchi Lucia Carbone Brian J Druker Julia E Maxson Knight Cancer Institute Oregon Health & Science University Portland OR 97239 USA. Division of Hematology and Medical Oncology Oregon Health & Science University Portland OR 97239 USA. Knight Cardiovascular Institute Oregon Health & Science University Portland OR 97239 USA. Program in Molecular and Cellular Biology Oregon Health & Science University Portland OR 97239 USA. Computational Biology Program Oregon Health & Science University Portland OR 97239 USA. Division of Bioinformatics and Computational Biology Oregon Health & Science University Portland OR 97239 USA. Clinical Research Division Fred Hutchinson Cancer Research Center 1100 Fairview Ave N Seattle WA 98109 USA. MRC Molecular Haematology Unit MRC Weatherall Institute of Molecular Medicine John Radcliffe Hospital Headley Way Oxford OX3 9DS UK. Division of Pediatric Hematology/Oncology University of Washington Seattle WA 98195 USA. Department of Molecular and Medical Genetics Oregon Health & Science University Portland OR 97239 USA. Howard Hughes Medical Institute Portland OR USA. Knight Cancer Institute Oregon Health & Science University Portland OR 97239 USA. maxsonj@ohsu.edu. Division of Hematology and Medical Oncology Oregon Health & Science University Portland OR 97239 USA. maxsonj@ohsu.edu.

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