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.

Characterization of protein isoform diversity in human umbilical vein endothelial cells via long-read proteogenomics.

Autor: Mehlferber MM; Department of Biochemistry and Molecular Genetics, University of Virginia, Charlottesville, VA, USA.; Department of Molecular Physiology and Biological Physics, University of Virginia, Charlottesville, Virginia, USA., Jeffery ED; Department of Molecular Physiology and Biological Physics, University of Virginia, Charlottesville, Virginia, USA., Saquing J; Department of Molecular Physiology and Biological Physics, University of Virginia, Charlottesville, Virginia, USA., Jordan BT; Department of Molecular Physiology and Biological Physics, University of Virginia, Charlottesville, Virginia, USA., Sheynkman L; Department of Molecular Physiology and Biological Physics, University of Virginia, Charlottesville, Virginia, USA., Murali M; Department of Molecular Physiology and Biological Physics, University of Virginia, Charlottesville, Virginia, USA., Genet G; Department of Cell Biology, University of Virginia School of Medicine, Charlottesville, VA, USA., Acharya BR; Department of Cell Biology, University of Virginia School of Medicine, Charlottesville, VA, USA.; Cardiovascular Research Center, University of Virginia, Charlottesville, VA, USA.; Wellcome Centre for Cell-Matrix Research, Faculty of Biology, Medicine and Health, the University of Manchester, UK., Hirschi KK; Department of Cell Biology, University of Virginia School of Medicine, Charlottesville, VA, USA.; Cardiovascular Research Center, University of Virginia, Charlottesville, VA, USA., Sheynkman GM; Department of Biochemistry and Molecular Genetics, University of Virginia, Charlottesville, VA, USA.; Department of Molecular Physiology and Biological Physics, University of Virginia, Charlottesville, Virginia, USA.; Center for Public Health Genomics, University of Virginia, Charlottesville, VA, USA.; UVA Comprehensive Cancer Center, University of Virginia, Charlottesville, Virginia, USA.

Publikováno v: RNA biology [RNA Biol] 2022 Jan; Vol. 19 (1), pp. 1228-1243.

SUsPECT: a pipeline for variant effect prediction based on custom long-read transcriptomes for improved clinical variant annotation.

Autor: Salz, Renee¹ (AUTHOR), Saraiva-Agostinho, Nuno² (AUTHOR), Vorsteveld, Emil³ (AUTHOR), van der Made, Caspar I.^3,4 (AUTHOR), Kersten, Simone³ (AUTHOR), Stemerdink, Merel⁵ (AUTHOR), Allen, Jamie² (AUTHOR), Volders, Pieter-Jan^6,7 (AUTHOR), Hunt, Sarah E.² (AUTHOR), Hoischen, Alexander^3,4 (AUTHOR), 't Hoen, Peter A.C.¹ (AUTHOR) peter-bram.thoen@radboudumc.nl

Publikováno v: BMC Genomics. 6/6/2023, Vol. 24 Issue 1, p1-10. 10p.

Transcription Factors and Splice Factors—Interconnected Regulators of Stem Cell Differentiation.

Autor: Mehlferber, Madison M., Kuyumcu-Martinez, Muge, Miller, Clint L., Sheynkman, Gloria M.

Publikováno v: Current Stem Cell Reports; Jun2023, Vol. 9 Issue 2, p31-41, 11p