Zobrazeno 1 - 10
of 3 985
pro vyhledávání: '"Wold BJ"'
Autor:
Loving R; Division of Biology and Biological Engineering, California Institute of Technology, USA., Sullivan DK; Division of Biology and Biological Engineering, California Institute of Technology, USA.; UCLA-Caltech Medical Scientist Training Program, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, 90095, USA., Reese F; Developmental and Cell Biology, University of California Irvine, Irvine, USA.; Center for Complex Biological Systems, University of California Irvine, Irvine, USA., Rebboah E; Developmental and Cell Biology, University of California Irvine, Irvine, USA.; Center for Complex Biological Systems, University of California Irvine, Irvine, USA., Sakr J; Developmental and Cell Biology, University of California Irvine, Irvine, USA.; Center for Complex Biological Systems, University of California Irvine, Irvine, USA., Rezaie N; Developmental and Cell Biology, University of California Irvine, Irvine, USA.; Center for Complex Biological Systems, University of California Irvine, Irvine, USA., Liang HY; Developmental and Cell Biology, University of California Irvine, Irvine, USA.; Center for Complex Biological Systems, University of California Irvine, Irvine, USA., Filimban G; Developmental and Cell Biology, University of California Irvine, Irvine, USA.; Center for Complex Biological Systems, University of California Irvine, Irvine, USA., Kawauchi S; Developmental and Cell Biology, University of California Irvine, Irvine, USA., Oakes C; Division of Biology and Biological Engineering, California Institute of Technology, USA., Trout D; Division of Biology and Biological Engineering, California Institute of Technology, USA., Williams BA; Division of Biology and Biological Engineering, California Institute of Technology, USA., MacGregor G; Developmental and Cell Biology, University of California Irvine, Irvine, USA., Wold BJ; Division of Biology and Biological Engineering, California Institute of Technology, USA., Mortazavi A; Developmental and Cell Biology, University of California Irvine, Irvine, USA.; Center for Complex Biological Systems, University of California Irvine, Irvine, USA., Pachter L; Division of Biology and Biological Engineering, California Institute of Technology, USA.; Department of Computing and Mathematical Sciences, California Institute of Technology, Pasadena, USA.
Publikováno v:
BioRxiv : the preprint server for biology [bioRxiv] 2024 Jul 19. Date of Electronic Publication: 2024 Jul 19.
Systematic assessment of long-read RNA-seq methods for transcript identification and quantification.
Autor:
Pardo-Palacios FJ; Institute for Integrative Systems Biology, Spanish National Research Council (CSIC), Paterna, Spain., Wang D; Department of Biomedical Informatics, The Ohio State University, Columbus, OH, USA.; Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI, USA., Reese F; Department of Developmental and Cell Biology, University of California, Irvine, Irvine, CA, USA.; Center for Complex Biological Systems, University of California, Irvine, Irvine, CA, USA., Diekhans M; UC Santa Cruz Genomics Institute, University of California, Santa Cruz, Santa Cruz, CA, USA., Carbonell-Sala S; Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona, Spain., Williams B; Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA., Loveland JE; European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus Hinxton, Cambridge, UK., De María M; Department of Physiological Sciences, College of Veterinary Medicine, Gainesville, FL, USA.; Cherokee Nation System Solutions, contractor to the US Geological Survey-Wetland and Aquatic Research Center, Gainesville, FL, USA., Adams MS; Department of Molecular Cell and Developmental Biology, University of California, Santa Cruz, Santa Cruz, CA, USA., Balderrama-Gutierrez G; Department of Developmental and Cell Biology, University of California, Irvine, Irvine, CA, USA.; Center for Complex Biological Systems, University of California, Irvine, Irvine, CA, USA., Behera AK; Department of Biomolecular Engineering, University of California, Santa Cruz, Santa Cruz, CA, USA., Gonzalez Martinez JM; European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus Hinxton, Cambridge, UK., Hunt T; European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus Hinxton, Cambridge, UK., Lagarde J; Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona, Spain.; Flomics Biotech, SL, Barcelona, Spain., Liang CE; Department of Molecular Cell and Developmental Biology, University of California, Santa Cruz, Santa Cruz, CA, USA., Li H; Department of Biomedical Informatics, The Ohio State University, Columbus, OH, USA.; Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI, USA., Meade MJ; Department of Molecular Physiology and Biological Physics, University of Virginia, Charlottesville, VA, USA., Moraga Amador DA; Interdisciplinary Center for Biotechnology Research, University of Florida, Gainesville, FL, USA., Prjibelski AD; Department of Computer Science, University of Helsinki, Helsinki, Finland.; Center for Bioinformatics and Algorithmic Biotechnology, Institute of Translational Biomedicine, St. Petersburg State University, St. Petersburg, Russia., Birol I; Canada's Michael Smith Genome Sciences Centre, BC Cancer, Vancouver, British Columbia, Canada., Bostan H; Biostatistics and Computational Biology Branch, National Institute of Environmental Health Sciences, Durham, NC, USA., Brooks AM; Biostatistics and Computational Biology Branch, National Institute of Environmental Health Sciences, Durham, NC, USA., Çelik MH; Department of Developmental and Cell Biology, University of California, Irvine, Irvine, CA, USA.; Center for Complex Biological Systems, University of California, Irvine, Irvine, CA, USA., Chen Y; Genome Institute of Singapore (GIS), Agency for Science, Technology and Research (A*STAR), Singapore, Singapore., Du MRM; Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, Australia., Felton C; Department of Biomolecular Engineering, University of California, Santa Cruz, Santa Cruz, CA, USA., Göke J; Genome Institute of Singapore (GIS), Agency for Science, Technology and Research (A*STAR), Singapore, Singapore.; Department of Statistics and Data Science, National University of Singapore, Singapore, Singapore., Hafezqorani S; Canada's Michael Smith Genome Sciences Centre, BC Cancer, Vancouver, British Columbia, Canada., Herwig R; Department Computational Molecular Biology, Max-Planck-Institute for Molecular Genetics, Berlin, Germany., Kawaji H; Research Center for Genome & Medical Sciences, Tokyo Metropolitan Institute of Medical Science, Tokyo, Japan., Lee J; Genome Institute of Singapore (GIS), Agency for Science, Technology and Research (A*STAR), Singapore, Singapore., Li JL; Biostatistics and Computational Biology Branch, National Institute of Environmental Health Sciences, Durham, NC, USA., Lienhard M; Department Computational Molecular Biology, Max-Planck-Institute for Molecular Genetics, Berlin, Germany., Mikheenko A; Department of Neuromuscular Diseases, UCL Queen Square Institute of Neurology, London, UK., Mulligan D; Department of Biomolecular Engineering, University of California, Santa Cruz, Santa Cruz, CA, USA., Nip KM; Canada's Michael Smith Genome Sciences Centre, BC Cancer, Vancouver, British Columbia, Canada., Pertea M; Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD, USA.; Center for Computational Biology, Johns Hopkins University, Baltimore, MD, USA., Ritchie ME; Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, Australia.; Department of Medical Biology, The University of Melbourne, Parkville, Victoria, Australia., Sim AD; Genome Institute of Singapore (GIS), Agency for Science, Technology and Research (A*STAR), Singapore, Singapore., Tang AD; Department of Biomolecular Engineering, University of California, Santa Cruz, Santa Cruz, CA, USA., Wan YK; Genome Institute of Singapore (GIS), Agency for Science, Technology and Research (A*STAR), Singapore, Singapore.; Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore., Wang C; Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, Australia., Wong BY; Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD, USA.; Center for Computational Biology, Johns Hopkins University, Baltimore, MD, USA., Yang C; Canada's Michael Smith Genome Sciences Centre, BC Cancer, Vancouver, British Columbia, Canada., Barnes I; European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus Hinxton, Cambridge, UK., Berry AE; European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus Hinxton, Cambridge, UK., Capella-Gutierrez S; Barcelona Supercomputing Center, Barcelona, Spain., Cousineau A; Program in Molecular Medicine, Diabetes Center of Excellence, University of Massachusetts Chan Medical School, Worcester, MA, USA., Dhillon N; Department of Biomolecular Engineering, University of California, Santa Cruz, Santa Cruz, CA, USA., Fernandez-Gonzalez JM; Barcelona Supercomputing Center, Barcelona, Spain., Ferrández-Peral L; Institute for Integrative Systems Biology, Spanish National Research Council (CSIC), Paterna, Spain., Garcia-Reyero N; Energy, Installations & Environment, Office of the Assistant Secretary of Defense, Washington, DC, USA., Götz S; Biobam Bioinformatics, Valencia, Spain., Hernández-Ferrer C; Barcelona Supercomputing Center, Barcelona, Spain., Kondratova L; Genetics Institute, University of Florida, Gainesville, FL, USA., Liu T; Cardiff University, Cardiff, UK., Martinez-Martin A; Institute for Integrative Systems Biology, Spanish National Research Council (CSIC), Paterna, Spain., Menor C; Biobam Bioinformatics, Valencia, Spain., Mestre-Tomás J; Institute for Integrative Systems Biology, Spanish National Research Council (CSIC), Paterna, Spain., Mudge JM; European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus Hinxton, Cambridge, UK., Panayotova NG; Interdisciplinary Center for Biotechnology Research, University of Florida, Gainesville, FL, USA., Paniagua A; Institute for Integrative Systems Biology, Spanish National Research Council (CSIC), Paterna, Spain., Repchevsky D; Barcelona Supercomputing Center, Barcelona, Spain., Ren X; Institute for Human Genetics, University of California, San Francisco, San Francisco, CA, USA., Rouchka E; Department of Biochemistry & Molecular Genetics, University of Louisville, Louisville, KY, USA., Saint-John B; Department of Biomolecular Engineering, University of California, Santa Cruz, Santa Cruz, CA, USA., Sapena E; European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK., Sheynkman L; Department of Molecular Physiology and Biological Physics, University of Virginia, Charlottesville, VA, USA., Smith ML; Department of Biochemistry & Molecular Genetics, University of Louisville, Louisville, KY, USA., Suner MM; European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus Hinxton, Cambridge, UK., Takahashi H; Center for Integrative Medical Sciences, Laboratory for Transcriptome Technology, RIKEN, Yokohama, Japan., Youngworth IA; Department of Genetics, Stanford University, Palo Alto, CA, USA., Carninci P; Center for Integrative Medical Sciences, Laboratory for Transcriptome Technology, RIKEN, Yokohama, Japan.; Human Technopole, Milano, Italy., Denslow ND; Department of Physiological Sciences, College of Veterinary Medicine, Gainesville, FL, USA.; Center for Environmental and Human Toxicology, Department of Physiological Sciences, University of Florida, Gainesville, FL, USA., Guigó R; Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona, Spain.; Universitat Pompeu Fabra (UPF), Barcelona, Spain., Hunter ME; US Geological Survey, Wetland and Aquatic Research Center, Gainesville, FL, USA., Maehr R; Program in Molecular Medicine, Diabetes Center of Excellence, University of Massachusetts Chan Medical School, Worcester, MA, USA., Shen Y; Institute for Human Genetics, Department of Neurology, University of California, San Francisco, San Francisco, CA, USA., Tilgner HU; Brain and Mind Research Institute and Center for Neurogenetics, Weill Cornell Medicine, New York City, NY, USA., Wold BJ; Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA., Vollmers C; Department of Biomolecular Engineering, University of California, Santa Cruz, Santa Cruz, CA, USA. vollmers@ucsc.edu., Frankish A; European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus Hinxton, Cambridge, UK. frankish@ebi.ac.uk., Au KF; Department of Biomedical Informatics, The Ohio State University, Columbus, OH, USA. kinfai@med.umich.edu.; Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI, USA. kinfai@med.umich.edu., Sheynkman GM; Department of Molecular Physiology and Biological Physics, University of Virginia, Charlottesville, VA, USA. gs9yr@virginia.edu.; Center for Public Health Genomics, University of Virginia, Charlottesville, VA, USA. gs9yr@virginia.edu.; UVA Cancer Center, University of Virginia, Charlottesville, VA, USA. gs9yr@virginia.edu., Mortazavi A; Department of Developmental and Cell Biology, University of California, Irvine, Irvine, CA, USA. ali.mortazavi@uci.edu.; Center for Complex Biological Systems, University of California, Irvine, Irvine, CA, USA. ali.mortazavi@uci.edu., Conesa A; Institute for Integrative Systems Biology, Spanish National Research Council (CSIC), Paterna, Spain. ana.conesa@csic.es.; Microbiology and Cell Science Department, Institute for Food and Agricultural Sciences, University of Florida, Gainesville, FL, USA. ana.conesa@csic.es., Brooks AN; UC Santa Cruz Genomics Institute, University of California, Santa Cruz, Santa Cruz, CA, USA. anbrooks@ucsc.edu.; Department of Biomolecular Engineering, University of California, Santa Cruz, Santa Cruz, CA, USA. anbrooks@ucsc.edu.
Publikováno v:
Nature methods [Nat Methods] 2024 Jul; Vol. 21 (7), pp. 1349-1363. Date of Electronic Publication: 2024 Jun 07.
Autor:
Rebboah E; Developmental and Cell Biology, University of California Irvine, Irvine, USA.; Center for Complex Biological Systems, University of California Irvine, Irvine, USA., Rezaie N; Developmental and Cell Biology, University of California Irvine, Irvine, USA.; Center for Complex Biological Systems, University of California Irvine, Irvine, USA., Williams BA; Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, USA., Weimer AK; Novo Nordisk Foundation Center for Genomic Mechanisms of Disease, Broad Institute of MIT and Harvard, Cambridge, USA., Shi M; Department of Next Generation Sequencing and Microchemistry, Proteomics and Lipidomics, Genentech, San Francisco, USA., Yang X; Department of Genetics, Stanford University School of Medicine, Palo Alto, USA., Liang HY; Developmental and Cell Biology, University of California Irvine, Irvine, USA., Dionne LA; The Jackson Laboratory, Bar Harbor, USA., Reese F; Developmental and Cell Biology, University of California Irvine, Irvine, USA., Trout D; Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, USA., Jou J; Department of Genetics, Stanford University School of Medicine, Palo Alto, USA., Youngworth I; Department of Genetics, Stanford University School of Medicine, Palo Alto, USA., Reinholdt L; The Jackson Laboratory, Bar Harbor, USA., Morabito S; Developmental and Cell Biology, University of California Irvine, Irvine, USA.; Center for Complex Biological Systems, University of California Irvine, Irvine, USA., Snyder MP; Department of Genetics, Stanford University School of Medicine, Palo Alto, USA., Wold BJ; Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, USA., Mortazavi A; Developmental and Cell Biology, University of California Irvine, Irvine, USA.; Center for Complex Biological Systems, University of California Irvine, Irvine, USA.
Publikováno v:
BioRxiv : the preprint server for biology [bioRxiv] 2024 Jun 14. Date of Electronic Publication: 2024 Jun 14.
Autor:
Rezaie N; Department of Developmental and Cell Biology, University of California, Irvine, CA, USA.; Center for Complex Biological Systems, University of California, Irvine, CA, USA., Rebboah E; Department of Developmental and Cell Biology, University of California, Irvine, CA, USA.; Center for Complex Biological Systems, University of California, Irvine, CA, USA., Williams BA; Division of Biology, California Institute of Technology, Pasadena, CA, USA., Liang HY; Department of Developmental and Cell Biology, University of California, Irvine, CA, USA.; Center for Complex Biological Systems, University of California, Irvine, CA, USA., Reese F; Department of Developmental and Cell Biology, University of California, Irvine, CA, USA.; Center for Complex Biological Systems, University of California, Irvine, CA, USA., Balderrama-Gutierrez G; Department of Developmental and Cell Biology, University of California, Irvine, CA, USA.; Center for Complex Biological Systems, University of California, Irvine, CA, USA., Dionne LA; The Jackson Laboratory, Bar Harbor, ME, USA., Reinholdt L; The Jackson Laboratory, Bar Harbor, ME, USA., Trout D; Division of Biology, California Institute of Technology, Pasadena, CA, USA., Wold BJ; Division of Biology, California Institute of Technology, Pasadena, CA, USA., Mortazavi A; Department of Developmental and Cell Biology, University of California, Irvine, CA, USA.; Center for Complex Biological Systems, University of California, Irvine, CA, USA.
Publikováno v:
BioRxiv : the preprint server for biology [bioRxiv] 2024 Feb 29. Date of Electronic Publication: 2024 Feb 29.
Autor:
Zhang B; The Key Laboratory for Stem Cells and Tissue Engineering, Ministry of Education, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, China., He P; European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, UK.; Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, UK., Lawrence JEG; Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, UK.; Department of Trauma and Orthopaedics, Cambridge University Hospitals NHS Foundation Trust, Addenbrooke's Hospital, Cambridge, UK., Wang S; The Key Laboratory for Stem Cells and Tissue Engineering, Ministry of Education, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, China.; Department of Obstetrics, Guangzhou Institute of Pediatrics, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangzhou, China., Tuck E; Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, UK., Williams BA; Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA., Roberts K; Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, UK., Kleshchevnikov V; Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, UK., Mamanova L; Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, UK.; Enhanc3D Genomics Ltd, Cambridge, UK., Bolt L; Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, UK.; Genomics England, London, UK., Polanski K; Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, UK., Li T; Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, UK., Elmentaite R; Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, UK., Fasouli ES; Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, UK.; Basic Research Center, Biomedical Research Foundation, Academy of Athens, Athens, Greece., Prete M; Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, UK., He X; John van Geest Centre for Brain Repair, Department of Clinical Neurosciences, University of Cambridge, Cambridge, UK.; Wellcome-MRC Cambridge Stem Cell Institute, University of Cambridge, Cambridge, UK., Yayon N; European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, UK.; Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, UK., Fu Y; The Key Laboratory for Stem Cells and Tissue Engineering, Ministry of Education, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, China., Yang H; The Key Laboratory for Stem Cells and Tissue Engineering, Ministry of Education, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, China., Liang C; The Key Laboratory for Stem Cells and Tissue Engineering, Ministry of Education, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, China., Zhang H; Institute of Human Virology, Key Laboratory of Tropical Disease Control of Ministry of Education, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, China., Blain R; Sorbonne Université, INSERM, CNRS, Institut de la Vision, Paris, France., Chedotal A; Sorbonne Université, INSERM, CNRS, Institut de la Vision, Paris, France.; Institut de pathologie, groupe hospitalier Est, hospices civils de Lyon, Lyon, France.; University Claude Bernard Lyon 1, MeLiS, CNRS UMR5284, INSERM U1314, Lyon, France., FitzPatrick DR; MRC Human Genetics Unit, IGC, University of Edinburgh, WGH, Edinburgh, UK., Firth H; Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, UK., Dean A; Department of Clinical Neurosciences, Cambridge University Hospitals NHS Foundation, Cambridge, UK., Bayraktar OA; Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, UK., Marioni JC; European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, UK.; Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, UK., Barker RA; John van Geest Centre for Brain Repair, Department of Clinical Neurosciences, University of Cambridge, Cambridge, UK.; Wellcome-MRC Cambridge Stem Cell Institute, University of Cambridge, Cambridge, UK., Storer MA; Wellcome-MRC Cambridge Stem Cell Institute, University of Cambridge, Cambridge, UK., Wold BJ; Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA., Zhang H; The Key Laboratory for Stem Cells and Tissue Engineering, Ministry of Education, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, China. zhanghongbo@mail.sysu.edu.cn.; Advanced Medical Technology Center, the First Affiliated Hospital, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, China. zhanghongbo@mail.sysu.edu.cn.; Department of Histology and Embryology, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, China. zhanghongbo@mail.sysu.edu.cn., Teichmann SA; Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, UK. st9@sanger.ac.uk.; Theory of Condensed Matter Group, Department of Physics, Cavendish Laboratory, University of Cambridge, Cambridge, UK. st9@sanger.ac.uk.
Publikováno v:
Nature [Nature] 2023 Dec 06. Date of Electronic Publication: 2023 Dec 06.
Autor:
Moyers BA; HudsonAlpha Institute for Biotechnology, Huntsville, Alabama 35806, USA., Partridge EC; HudsonAlpha Institute for Biotechnology, Huntsville, Alabama 35806, USA., Mackiewicz M; HudsonAlpha Institute for Biotechnology, Huntsville, Alabama 35806, USA., Betti MJ; Vanderbilt University Medical Center, Nashville, Tennessee 37232, USA., Darji R; HudsonAlpha Institute for Biotechnology, Huntsville, Alabama 35806, USA., Meadows SK; HudsonAlpha Institute for Biotechnology, Huntsville, Alabama 35806, USA., Newberry KM; HudsonAlpha Institute for Biotechnology, Huntsville, Alabama 35806, USA., Brandsmeier LA; HudsonAlpha Institute for Biotechnology, Huntsville, Alabama 35806, USA., Wold BJ; Merkin Institute for Translational Research, California Institute of Technology, Pasadena, California 91125, USA., Mendenhall EM; HudsonAlpha Institute for Biotechnology, Huntsville, Alabama 35806, USA; rmyers@hudsonalpha.org emendenhall@hudsonalpha.org., Myers RM; HudsonAlpha Institute for Biotechnology, Huntsville, Alabama 35806, USA; rmyers@hudsonalpha.org emendenhall@hudsonalpha.org.
Publikováno v:
Genome research [Genome Res] 2023 Dec 01; Vol. 33 (11), pp. 1879-1892. Date of Electronic Publication: 2023 Dec 01.
Systematic assessment of long-read RNA-seq methods for transcript identification and quantification.
Autor:
Pardo-Palacios FJ; Institute for Integrative Systems Biology, Spanish National Research Council (CSIC), Paterna, Spain.; These authors contributed equally to this work., Wang D; Department of Biomedical Informatics, The Ohio State University, Columbus, USA.; Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, USA.; These authors contributed equally to this work., Reese F; Developmental and Cell Biology, University of California, Irvine, Irvine, USA.; Center for Complex Biological Systems, University of California, Irvine, Irvine, USA.; These authors contributed equally to this work., Diekhans M; UC Santa Cruz Genomics Institute, University of California, Santa Cruz, Santa Cruz, USA.; These authors contributed equally to this work., Carbonell-Sala S; Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr. Aiguader 88, Barcelona 08003, Catalonia, Spain.; These authors contributed equally to this work., Williams B; Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, USA.; These authors contributed equally to this work., Loveland JE; European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK.; These authors contributed equally to this work., De María M; Department of Physiological Sciences, College of Veterinary Medicine, University of Florida, Gainesville, USA.; Center for Environmental and Human Toxicology, University of Florida, Gainesville, USA.; These authors contributed equally to this work., Adams MS; Molecular Cell and Developmental Biology, University of California, Santa Cruz, Santa Cruz, USA.; These authors contributed equally to this work., Balderrama-Gutierrez G; Developmental and Cell Biology, University of California, Irvine, Irvine, USA.; Center for Complex Biological Systems, University of California, Irvine, Irvine, USA.; These authors contributed equally to this work., Behera AK; Department of Biomolecular Engineering, University of California, Santa Cruz, Santa Cruz, USA.; These authors contributed equally to this work., Gonzalez JM; European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK.; These authors contributed equally to this work., Hunt T; European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK.; These authors contributed equally to this work., Lagarde J; Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr. Aiguader 88, Barcelona 08003, Catalonia, Spain.; Flomics Biotech, Dr Aiguader 88, Barcelona 08003, Spain.; These authors contributed equally to this work., Liang CE; Molecular Cell and Developmental Biology, University of California, Santa Cruz, Santa Cruz, USA.; These authors contributed equally to this work., Li H; Department of Biomedical Informatics, The Ohio State University, Columbus, USA.; Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, USA.; These authors contributed equally to this work., Jerryd Meade M; Department of Molecular Physiology and Biological Physics, University of Virginia, Charlottesville, USA.; These authors contributed equally to this work., Moraga Amador DA; Interdisciplinary Center for Biotechnology Research, University of Florida, Gainesville, USA.; These authors contributed equally to this work., Prjibelski AD; Department of Computer Science, University of Helsinki, Helsinki, Finland.; Center for Bioinformatics and Algorithmic Biotechnology, Institute of Translational Biomedicine, St. Petersburg State University, St. Petersburg, Russia.; These authors contributed equally to this work., Birol I; Canada's Michael Smith Genome Sciences Centre, BC Cancer, Vancouver, Canada., Bostan H; Biostatistics and Computational Biology Branch, National Institute of Environmental Health Sciences, Durham, USA., Brooks AM; Biostatistics and Computational Biology Branch, National Institute of Environmental Health Sciences, Durham, USA., Hasan Çelik M; Developmental and Cell Biology, University of California, Irvine, Irvine, USA.; Center for Complex Biological Systems, University of California, Irvine, Irvine, USA., Chen Y; Genome Institute of Singapore (GIS), Agency for Science, Technology and Research (A*STAR), Singapore, Singapore., Du MRM; Walter and Eliza Hall Institute of Medical Research, Parkville, Australia., Felton C; Department of Biomolecular Engineering, University of California, Santa Cruz, Santa Cruz, USA., Göke J; Genome Institute of Singapore (GIS), Agency for Science, Technology and Research (A*STAR), Singapore, Singapore.; Department of Statistics and Data Science, National University of Singapore, Singapore, Singapore., Hafezqorani S; Canada's Michael Smith Genome Sciences Centre, BC Cancer, Vancouver, Canada., Herwig R; Department Computational Molecular Biology, Max-Planck-Institute for Molecular Genetics, Berlin, Germany., Kawaji H; Research Center for Genome & Medical Sciences, Tokyo Metropolitan Institute of Medical Science, Tokyo, Japan., Lee J; Genome Institute of Singapore (GIS), Agency for Science, Technology and Research (A*STAR), Singapore, Singapore., Liang Li J; Biostatistics and Computational Biology Branch, National Institute of Environmental Health Sciences, Durham, USA., Lienhard M; Department Computational Molecular Biology, Max-Planck-Institute for Molecular Genetics, Berlin, Germany., Mikheenko A; Department of Neuromuscular Diseases, UCL Queen Square Institute of Neurology, London, UK., Mulligan D; Department of Biomolecular Engineering, University of California, Santa Cruz, Santa Cruz, USA., Ming Nip K; Canada's Michael Smith Genome Sciences Centre, BC Cancer, Vancouver, Canada., Pertea M; Department of Biomedical Engineering, Johns Hopkins University, Baltimore, USA.; Center for Computational Biology, Johns Hopkins University, Baltimore, USA., Ritchie ME; Walter and Eliza Hall Institute of Medical Research, Parkville, Australia.; Department of Medical Biology, The University of Melbourne, Parkville, Australia., Sim AD; Genome Institute of Singapore (GIS), Agency for Science, Technology and Research (A*STAR), Singapore, Singapore., Tang AD; Department of Biomolecular Engineering, University of California, Santa Cruz, Santa Cruz, USA., Kei Wan Y; Genome Institute of Singapore (GIS), Agency for Science, Technology and Research (A*STAR), Singapore, Singapore.; Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore., Wang C; Walter and Eliza Hall Institute of Medical Research, Parkville, Australia., Wong BY; Department of Biomedical Engineering, Johns Hopkins University, Baltimore, USA.; Center for Computational Biology, Johns Hopkins University, Baltimore, USA., Yang C; Canada's Michael Smith Genome Sciences Centre, BC Cancer, Vancouver, Canada., Barnes I; European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK., Berry A; European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK., Capella S; Barcelona Supercomputing Cente, Barcelona, Spain., Dhillon N; Department of Biomolecular Engineering, University of California, Santa Cruz, Santa Cruz, USA., Fernandez-Gonzalez JM; Barcelona Supercomputing Cente, Barcelona, Spain., Ferrández-Peral L; Institute for Integrative Systems Biology, Spanish National Research Council (CSIC), Paterna, Spain., Garcia-Reyero N; Environmental Laboratory, US Army Engineer Research & Development Center, Vicksburg, USA., Goetz S; Biobam Bioinformatics SL, Valencia, Spain., Hernández-Ferrer C; Barcelona Supercomputing Cente, Barcelona, Spain., Kondratova L; Genetics Institute, University of Florida, Gainesville, USA., Liu T; Cardiff University, Cardiff, UK., Martinez-Martin A; Institute for Integrative Systems Biology, Spanish National Research Council (CSIC), Paterna, Spain., Menor C; Biobam Bioinformatics SL, Valencia, Spain., Mestre-Tomás J; Institute for Integrative Systems Biology, Spanish National Research Council (CSIC), Paterna, Spain., Mudge JM; European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK., Panayotova NG; Interdisciplinary Center for Biotechnology Research, University of Florida, Gainesville, USA., Paniagua A; Institute for Integrative Systems Biology, Spanish National Research Council (CSIC), Paterna, Spain., Repchevsky D; Barcelona Supercomputing Cente, Barcelona, Spain., Rouchka E; Department of Biochemistry & Molecular Genetics, University of Louisville, Louisville, USA., Saint-John B; Department of Biomolecular Engineering, University of California, Santa Cruz, Santa Cruz, USA., Sapena E; European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK, UK., Sheynkman L; Department of Molecular Physiology and Biological Physics, University of Virginia, Charlottesville, USA., Laird Smith M; Department of Biochemistry & Molecular Genetics, University of Louisville, Louisville, USA., Suner MM; European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK., Takahashi H; Center for Integrative Medical Sciences, Laboratory for Transcriptome Technology, RIKEN, Yokohama, Japan., Youngworth IA; Department of Genetics, Stanford University, Palo Alto, USA., Carninci P; Center for Integrative Medical Sciences, Laboratory for Transcriptome Technology, RIKEN, Yokohama, Japan.; Human Technopole, Milano, Italy., Denslow ND; Department of Physiological Sciences, College of Veterinary Medicine, University of Florida, Gainesville, USA.; Center for Environmental and Human Toxicology, Department of Physiological Sciences,, University of Florida, Gainesville, USA., Guigó R; Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr. Aiguader 88, Barcelona 08003, Catalonia, Spain.; Universitat Pompeu Fabra (UPF), Barcelona, Catalonia, Spain., Hunter ME; U.S. Geological Survey, Wetland and Aquatic Research Center, Gainesville, USA., Tilgner HU; Brain and Mind Research Institute and Center for Neurogenetics, Weill Cornell Medicine, New York City, USA., Wold BJ; Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, USA., Vollmers C; Department of Biomolecular Engineering, University of California, Santa Cruz, Santa Cruz, USA., Frankish A; European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK., Fai Au K; Department of Biomedical Informatics, The Ohio State University, Columbus, USA.; Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, USA., Sheynkman GM; Department of Molecular Physiology and Biological Physics, University of Virginia, Charlottesville, USA.; Center for Public Health Genomics.; UVA Cancer Center, University of Virginia, Charlottesville, USA., Mortazavi A; Developmental and Cell Biology, University of California, Irvine, Irvine, USA.; Center for Complex Biological Systems, University of California, Irvine, Irvine, USA., Conesa A; Institute for Integrative Systems Biology, Spanish National Research Council (CSIC), Paterna, Spain.; Microbiology and Cell Science Department, Institute for Food and Agricultural Sciences, University of Florida, Gainesville, USA., Brooks AN; UC Santa Cruz Genomics Institute, University of California, Santa Cruz, Santa Cruz, USA.; Department of Biomolecular Engineering, University of California, Santa Cruz, Santa Cruz, USA.
Publikováno v:
BioRxiv : the preprint server for biology [bioRxiv] 2023 Jul 27. Date of Electronic Publication: 2023 Jul 27.
The ENCODE4 long-read RNA-seq collection reveals distinct classes of transcript structure diversity.
Autor:
Reese F; Developmental and Cell Biology, University of California, Irvine, Irvine, USA.; Center for Complex Biological Systems, University of California, Irvine, Irvine, USA., Williams B; Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, USA., Balderrama-Gutierrez G; Developmental and Cell Biology, University of California, Irvine, Irvine, USA.; Center for Complex Biological Systems, University of California, Irvine, Irvine, USA., Wyman D; Center for Complex Biological Systems, University of California, Irvine, Irvine, USA., Çelik MH; Center for Complex Biological Systems, University of California, Irvine, Irvine, USA., Rebboah E; Center for Complex Biological Systems, University of California, Irvine, Irvine, USA., Rezaie N; Center for Complex Biological Systems, University of California, Irvine, Irvine, USA., Trout D; Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, USA., Razavi-Mohseni M; Department of Biomedical Engineering, Johns Hopkins University, Baltimore, USA.; McKusick-Nathans Department of Genetic Medicine, Johns Hopkins University, Baltimore, USA., Jiang Y; Program in Computational Biology and Bioinformatics, Yale University, New Haven, USA.; Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, USA., Borsari B; Program in Computational Biology and Bioinformatics, Yale University, New Haven, USA.; Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, USA.; Centre for Genomic Regulation, The Barcelona Institute of Science and Technology, Barcelona, Spain., Morabito S; Center for Complex Biological Systems, University of California, Irvine, Irvine, USA., Liang HY; Center for Complex Biological Systems, University of California, Irvine, Irvine, USA., McGill CJ; Developmental and Cell Biology, University of California, Irvine, Irvine, USA.; Center for Complex Biological Systems, University of California, Irvine, Irvine, USA., Rahmanian S; Center for Complex Biological Systems, University of California, Irvine, Irvine, USA., Sakr J; Center for Complex Biological Systems, University of California, Irvine, Irvine, USA.; Department of Pharmaceutical Sciences, University of California, Irvine, Irvine, USA., Jiang S; Developmental and Cell Biology, University of California, Irvine, Irvine, USA.; Center for Complex Biological Systems, University of California, Irvine, Irvine, USA., Zeng W; Developmental and Cell Biology, University of California, Irvine, Irvine, USA.; Center for Complex Biological Systems, University of California, Irvine, Irvine, USA., Carvalho K; Center for Complex Biological Systems, University of California, Irvine, Irvine, USA., Weimer AK; Department of Genetics, Stanford University School of Medicine, Palo Alto, USA., Dionne LA; The Jackson Laboratory, The Jackson Laboratory, Bar Harbor, USA., McShane A; Cellular and Molecular Biology Program, University of Michigan, Ann Arbor, USA.; Department of Radiation Oncology, University of Michigan, Ann Arbor, USA., Bedi K; Department of Biostatistics, University of Michigan, Ann Arbor, USA.; Center for RNA Biomedicine and Rogel Cancer Center, University of Michigan, Ann Arbor, USA., Elhajjajy SI; Program in Bioinformatics and Integrative Biology, University of Massachusetts Chan Medical School, Worcester, USA., Upchurch S; Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, USA., Jou J; Department of Genetics, Stanford University School of Medicine, Palo Alto, USA., Youngworth I; Department of Genetics, Stanford University School of Medicine, Palo Alto, USA., Gabdank I; Department of Genetics, Stanford University School of Medicine, Palo Alto, USA., Sud P; Department of Genetics, Stanford University School of Medicine, Palo Alto, USA., Jolanki O; Department of Genetics, Stanford University School of Medicine, Palo Alto, USA., Strattan JS; Department of Genetics, Stanford University School of Medicine, Palo Alto, USA., Kagda MS; Department of Genetics, Stanford University School of Medicine, Palo Alto, USA., Snyder MP; Department of Genetics, Stanford University School of Medicine, Palo Alto, USA., Hitz BC; Department of Genetics, Stanford University School of Medicine, Palo Alto, USA., Moore JE; Program in Bioinformatics and Integrative Biology, University of Massachusetts Chan Medical School, Worcester, USA., Weng Z; Program in Bioinformatics and Integrative Biology, University of Massachusetts Chan Medical School, Worcester, USA., Bennett D; Rush Alzheimer's Disease Center, Rush University Medical Center, Chicago, USA.; Department of Neurological Sciences, Rush University Medical Center, Chicago, USA., Reinholdt L; The Jackson Laboratory, The Jackson Laboratory, Bar Harbor, USA., Ljungman M; Center for RNA Biomedicine and Rogel Cancer Center, University of Michigan, Ann Arbor, USA.; Departments of Radiation Oncology and Environmental Health Sciences, University of Michigan, Ann Arbor, USA., Beer MA; Department of Biomedical Engineering, Johns Hopkins University, Baltimore, USA.; McKusick-Nathans Department of Genetic Medicine, Johns Hopkins University, Baltimore, USA., Gerstein MB; Program in Computational Biology and Bioinformatics, Yale University, New Haven, USA.; Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, USA.; Section on Biomedical Informatics and Data Science, Yale University, New Haven, USA.; Department of Statistics and Data Science, Yale University, New Haven, USA.; Department of Computer Science, Yale University, New Haven, USA., Pachter L; Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, USA.; Department of Computing and Mathematical Sciences, California Institute of Technology, Pasadena, USA., Guigó R; Centre for Genomic Regulation, The Barcelona Institute of Science and Technology, Barcelona, Spain.; Department of Medicine and Life Sciences, Universitat Pompeu Fabra, Barcelona, Spain., Wold BJ; Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, USA., Mortazavi A; Developmental and Cell Biology, University of California, Irvine, Irvine, USA.; Center for Complex Biological Systems, University of California, Irvine, Irvine, USA.
Publikováno v:
BioRxiv : the preprint server for biology [bioRxiv] 2023 May 16. Date of Electronic Publication: 2023 May 16.
Autor:
Upchurch S; Biology and Biomedical Engineering, California Institute of Technology, Pasadena, CA 91125, United States., Palumbo E; Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona, Catalonia 08003, Spain., Adams J; Ontario Institute for Cancer Research, Toronto, ON M5G 0A3, Canada., Bujold D; Department of Human Genetics, McGill University, Montreal, QC H3A 0G4, Canada., Bourque G; Department of Human Genetics, McGill University, Montreal, QC H3A 0G4, Canada., Nedzel J; Broad Institute, Cambridge, MA 02142, United States., Graham K; Department of Genetics, Stanford University, Stanford, CA 94305, United States., Kagda MS; Department of Genetics, Stanford University, Stanford, CA 94305, United States., Assis P; Department of Genetics, Stanford University, Stanford, CA 94305, United States., Hitz B; Department of Genetics, Stanford University, Stanford, CA 94305, United States., Righi E; Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona, Catalonia 08003, Spain., Guigó R; Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona, Catalonia 08003, Spain.; Department of Medicine and Life Sciences, Universitat Pompeu Fabra (UPF), Barcelona, Catalonia 08002, Spain., Wold BJ; Biology and Biomedical Engineering, California Institute of Technology, Pasadena, CA 91125, United States.
Publikováno v:
Bioinformatics (Oxford, England) [Bioinformatics] 2023 Apr 03; Vol. 39 (4).
Autor:
Regev, A, Teichmann, SA, Lander, ES, Amit, I, Benoist, C, Birney, E, Bodenmiller, B, Campbell, PJ, Carninci, P, Clatworthy, M, Clevers, H, Deplancke, B, Dunham, I, Eberwine, J, Eils, R, Enard, W, Farmer, A, Fugger, L, Göttgens, B, Hacohen, N, Haniffa, M, Hemberg, M, Kim, SK, Klenerman, P, Kriegstein, A, Lein, E, Linnarsson, S, Lundberg, E, Lundeberg, J, Majumder, P, Marioni, JC, Merad, M, Mhlanga, M, Nawijn, M, Netea, M, Nolan, G, Pe'er, D, Phillipakis, A, Ponting, CP, Quake, SR, Reik, W, Rozenblatt-Rosen, O, Sanes, JR, Satija, R, Schumacher, TN, Shalek, AK, Shapiro, E, Sharma, P, Shin, JW, Stegle, O, Stratton, MR, Stubbington, MJT, Theis, FJ, Uhlen, M, van Oudenaarden, A, Wagner, A, Watt, FM, Weissman, JS, Wold, BJ, Xavier, RJ, Yosef, N
The recent advent of methods for high-throughput single-cell molecular profiling has catalyzed a growing sense in the scientific community that the time is ripe to complete the 150-year-old effort to identify all cell types in the human body. The Hum
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https://explore.openaire.eu/search/publication?articleId=dedup_wf_001::f30a0e14d984ce1edece507acc572dcd
https://ora.ox.ac.uk/objects/uuid:4f6fd5b8-a1d7-48ba-8391-2877bb870300
https://ora.ox.ac.uk/objects/uuid:4f6fd5b8-a1d7-48ba-8391-2877bb870300