换一批
换一批Systematic assessment of long-read RNA-seq methods for transcript identification and quantification.
作者：
Francisco J,Pardo-Palacios [1]
;
Dingjie,Wang [2]
;
Fairlie,Reese [3]
;
Mark,Diekhans [4]
;
Sílvia,Carbonell-Sala [5]
;
Brian,Williams [6]
;
Jane E,Loveland [7]
;
Maite,De María [8]
;
Matthew S,Adams [9]
;
Gabriela,Balderrama-Gutierrez [3]
;
Amit K,Behera [10]
;
Jose M,Gonzalez Martinez [7]
;
Toby,Hunt [7]
;
Julien,Lagarde [11]
;
Cindy E,Liang [9]
;
Haoran,Li [2]
;
Marcus Jerryd,Meade [12]
;
David A,Moraga Amador [13]
;
Andrey D,Prjibelski [14]
;
Inanc,Birol [15]
;
Hamed,Bostan [16]
;
Ashley M,Brooks [16]
;
Muhammed Hasan,Çelik [3]
;
Ying,Chen [17]
;
Mei R M,Du [18]
;
Colette,Felton [10]
;
Jonathan,Göke [19]
;
Saber,Hafezqorani [15]
;
Ralf,Herwig [20]
;
Hideya,Kawaji [21]
;
Joseph,Lee [17]
;
Jian-Liang,Li [16]
;
Matthias,Lienhard [20]
;
Alla,Mikheenko [22]
;
Dennis,Mulligan [10]
;
Ka Ming,Nip [15]
;
Mihaela,Pertea [23]
;
Matthew E,Ritchie [24]
;
Andre D,Sim [17]
;
Alison D,Tang [10]
;
Yuk Kei,Wan [25]
;
Changqing,Wang [18]
;
Brandon Y,Wong [23]
;
Chen,Yang [15]
;
If,Barnes [7]
;
Andrew E,Berry [7]
;
Salvador,Capella-Gutierrez [26]
;
Alyssa,Cousineau [27]
;
Namrita,Dhillon [10]
;
Jose M,Fernandez-Gonzalez [26]
;
Luis,Ferrández-Peral [1]
;
Natàlia,Garcia-Reyero [28]
;
Stefan,Götz [29]
;
Carles,Hernández-Ferrer [26]
;
Liudmyla,Kondratova [30]
;
Tianyuan,Liu [31]
;
Alessandra,Martinez-Martin [1]
;
Carlos,Menor [29]
;
Jorge,Mestre-Tomás [1]
;
Jonathan M,Mudge [7]
;
Nedka G,Panayotova [13]
;
Alejandro,Paniagua [1]
;
Dmitry,Repchevsky [26]
;
Xingjie,Ren [32]
;
Eric,Rouchka [33]
;
Brandon,Saint-John [10]
;
Enrique,Sapena [34]
;
Leon,Sheynkman [12]
;
Melissa Laird,Smith [33]
;
Marie-Marthe,Suner [7]
;
Hazuki,Takahashi [35]
;
Ingrid A,Youngworth [36]
;
Piero,Carninci [37]
;
Nancy D,Denslow [38]
;
Roderic,Guigó [39]
;
Margaret E,Hunter [40]
;
Rene,Maehr [27]
;
Yin,Shen [41]
;
Hagen U,Tilgner [42]
;
Barbara J,Wold [6]
;
Christopher,Vollmers [43]
;
Adam,Frankish [44]
;
Kin Fai,Au [45]
;
Gloria M,Sheynkman [46]
;
Ali,Mortazavi [47]
;
Ana,Conesa [48]
;
Angela N,Brooks [49]
作者单位：
Institute for Integrative Systems Biology, Spanish National Research Council (CSIC), Paterna, Spain.
[1]
Department of Biomedical Informatics, The Ohio State University, Columbus, OH, USA.;Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI, USA.
[2]
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.
[3]
UC Santa Cruz Genomics Institute, University of California, Santa Cruz, Santa Cruz, CA, USA.
[4]
Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona, Spain.
[5]
Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA.
[6]
European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus Hinxton, Cambridge, UK.
[7]
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.
[8]
Department of Molecular Cell and Developmental Biology, University of California, Santa Cruz, Santa Cruz, CA, USA.
[9]
Department of Biomolecular Engineering, University of California, Santa Cruz, Santa Cruz, CA, USA.
[10]
Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona, Spain.;Flomics Biotech, SL, Barcelona, Spain.
[11]
Department of Molecular Physiology and Biological Physics, University of Virginia, Charlottesville, VA, USA.
[12]
Interdisciplinary Center for Biotechnology Research, University of Florida, Gainesville, FL, USA.
[13]
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.
[14]
Canada's Michael Smith Genome Sciences Centre, BC Cancer, Vancouver, British Columbia, Canada.
[15]
Biostatistics and Computational Biology Branch, National Institute of Environmental Health Sciences, Durham, NC, USA.
[16]
Genome Institute of Singapore (GIS), Agency for Science, Technology and Research (A*STAR), Singapore, Singapore.
[17]
Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, Australia.
[18]
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.
[19]
Department Computational Molecular Biology, Max-Planck-Institute for Molecular Genetics, Berlin, Germany.
[20]
Research Center for Genome & Medical Sciences, Tokyo Metropolitan Institute of Medical Science, Tokyo, Japan.
[21]
Department of Neuromuscular Diseases, UCL Queen Square Institute of Neurology, London, UK.
[22]
Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD, USA.;Center for Computational Biology, Johns Hopkins University, Baltimore, MD, USA.
[23]
Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, Australia.;Department of Medical Biology, The University of Melbourne, Parkville, Victoria, Australia.
[24]
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.
[25]
Barcelona Supercomputing Center, Barcelona, Spain.
[26]
Program in Molecular Medicine, Diabetes Center of Excellence, University of Massachusetts Chan Medical School, Worcester, MA, USA.
[27]
Energy, Installations & Environment, Office of the Assistant Secretary of Defense, Washington, DC, USA.
[28]
Biobam Bioinformatics, Valencia, Spain.
[29]
Genetics Institute, University of Florida, Gainesville, FL, USA.
[30]
Cardiff University, Cardiff, UK.
[31]
Institute for Human Genetics, University of California, San Francisco, San Francisco, CA, USA.
[32]
Department of Biochemistry & Molecular Genetics, University of Louisville, Louisville, KY, USA.
[33]
European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK.
[34]
Center for Integrative Medical Sciences, Laboratory for Transcriptome Technology, RIKEN, Yokohama, Japan.
[35]
Department of Genetics, Stanford University, Palo Alto, CA, USA.
[36]
Center for Integrative Medical Sciences, Laboratory for Transcriptome Technology, RIKEN, Yokohama, Japan.;Human Technopole, Milano, Italy.
[37]
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.
[38]
Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona, Spain.;Universitat Pompeu Fabra (UPF), Barcelona, Spain.
[39]
US Geological Survey, Wetland and Aquatic Research Center, Gainesville, FL, USA.
[40]
Institute for Human Genetics, Department of Neurology, University of California, San Francisco, San Francisco, CA, USA.
[41]
Brain and Mind Research Institute and Center for Neurogenetics, Weill Cornell Medicine, New York City, NY, USA.
[42]
Department of Biomolecular Engineering, University of California, Santa Cruz, Santa Cruz, CA, USA. vollmers@ucsc.edu.
[43]
European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus Hinxton, Cambridge, UK. frankish@ebi.ac.uk.
[44]
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.
[45]
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.
[46]
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.
[47]
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.
[48]
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.
[49]
主题词
人类(Humans);动物(Animals);小鼠(Mice);基因表达谱(Gene Expression Profiling);序列分析, RNA(Sequence Analysis, RNA);分子序列注释(Molecular Sequence Annotation)
DOI
10.1038/s41592-024-02298-3
PMID
38849569
发布时间
2024-11-10
- 浏览0
Nature methods
Nature methods
1349-1363页
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