DNABERT-based explainable lncRNA identification in plant genome assemblies

Autor: Danilevicz, Monica F., Gill, Mitchell, Fernandez, Cassandria G. Tay, Petereit, Jakob, Upadhyaya, Shriprabha R., Batley, Jacqueline, Bennamoun, Mohammed, Edwards, David, Bayer, Philipp E.

Publikováno v: In Computational and Structural Biotechnology Journal 2023 21:5676-5685

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Global Genotype by Environment Prediction Competition Reveals That Diverse Modeling Strategies Can Deliver Satisfactory Maize Yield Estimates.

Autor: Washburn JD; USDA-ARS-MWA-PGRU, 302-A Curtis Hall, U. of MO., Columbia, MO, 65211, USA., Varela JI; Department of Plant and Agroecosystem Sciences, University of Wisconsin - Madison, 1575 Linden Drive, Madison, WI, 53706, USA.; Corteva Agrisciences, 8305 NW 62nd Ave, Johnston, IA, 50131, USA., Xavier A; Corteva Agrisciences, 8305 NW 62nd Ave, Johnston, IA, 50131, USA.; Department of Agronomy, Purdue University, 915 Mitch Daniels Blvd, West Lafayette, IN 47907, United States., Chen Q; Department of Crop and Soil Sciences, North Carolina State University, Raleigh, NC, 27695, USA., Ertl D; Iowa Corn Promotion Board, Johnston, IA, 50131, USA., Gage JL; Department of Crop and Soil Sciences, North Carolina State University, Raleigh, NC, 27695, USA., Holland JB; Department of Crop and Soil Sciences, North Carolina State University, Raleigh, NC, 27695, USA.; USDA-ARS Plant Science Research Unit, Raleigh, NC, 27695, USA., Lima DC; Department of Plant and Agroecosystem Sciences, University of Wisconsin - Madison, 1575 Linden Drive, Madison, WI, 53706, USA., Romay MC; Institute for Genomic Diversity, Cornell University, Ithaca, NY, 14853, USA., Lopez-Cruz M; Departments of Epidemiology & Biostatistics and Statistics & Probability, and Institute for Quantitative Health Science and Engineering, Michigan State University, 775 Woodlot Dr., East Lansing, MI, 48823, USA., de Los Campos G; Departments of Epidemiology & Biostatistics and Statistics & Probability, and Institute for Quantitative Health Science and Engineering, Michigan State University, 775 Woodlot Dr., East Lansing, MI, 48823, USA., Barber W; Corteva Agrisciences, 8305 NW 62nd Ave, Johnston, IA, 50131, USA., Zimmer C; Corteva Agrisciences, 8305 NW 62nd Ave, Johnston, IA, 50131, USA., Silva IT; Corteva Agrisciences, 8305 NW 62nd Ave, Johnston, IA, 50131, USA., Rocha F; Corteva Agrisciences, 8305 NW 62nd Ave, Johnston, IA, 50131, USA., Rincent R; Université Paris-Saclay, INRAE, CNRS, AgroParisTech, GQE - Le Moulon, 91190 Gif-sur-Yvette, France., Ali B; Université Paris-Saclay, INRAE, CNRS, AgroParisTech, GQE - Le Moulon, 91190 Gif-sur-Yvette, France., Hu H; Department of Plant Sciences, University of California Davis, One Shield Drive, Davis, CA, 95616, USA., Runcie DE; Department of Plant Sciences, University of California Davis, One Shield Drive, Davis, CA, 95616, USA., Gusev K; Smart Agri Labs, 2055 Limestone Rd STE 200-C, Wilmington, DE, 19808, USA., Slabodkin A; Smart Agri Labs, 2055 Limestone Rd STE 200-C, Wilmington, DE, 19808, USA., Bax P; Smart Agri Labs, 2055 Limestone Rd STE 200-C, Wilmington, DE, 19808, USA., Aubert J; Université Paris-Saclay, AgroParisTech, INRAE, UMR MIA Paris-Saclay, 91120, Palaiseau, France., Gangloff H; Université Paris-Saclay, AgroParisTech, INRAE, UMR MIA Paris-Saclay, 91120, Palaiseau, France., Mary-Huard T; Université Paris-Saclay, INRAE, CNRS, AgroParisTech, GQE - Le Moulon, 91190 Gif-sur-Yvette, France.; Université Paris-Saclay, AgroParisTech, INRAE, UMR MIA Paris-Saclay, 91120, Palaiseau, France., Vanrenterghem T; Université Paris-Saclay, AgroParisTech, INRAE, UMR MIA Paris-Saclay, 91120, Palaiseau, France., Quesada-Traver C; Molecular Plant Breeding, Institute of Agricultural Sciences, ETH Zurich, Universitätstrasse 2, CH-8092 Zurich, Switzerland., Yates S; Molecular Plant Breeding, Institute of Agricultural Sciences, ETH Zurich, Universitätstrasse 2, CH-8092 Zurich, Switzerland., Ariza-Suárez D; Molecular Plant Breeding, Institute of Agricultural Sciences, ETH Zurich, Universitätstrasse 2, CH-8092 Zurich, Switzerland., Ulrich A; Puregene AG, Etzmatt 273, CH-4314 Zeiningen, Switzerland.; Institute of Agricultural Sciences, ETH Zurich, Universitätstrasse 2, CH-8092 Zürich, Switzerland., Wyler M; MWSchmid GmbH, Hauptstrasse 34, CH-8750 Glarus, Switzerland., Kick DR; USDA-ARS-MWA-PGRU, 302-A Curtis Hall, U. of MO., Columbia, MO, 65211, USA., Bellis ES; Department of Computer Science, Arkansas State University, 2105 E. Aggie Rd., Jonesboro, AR, 72401, USA., Causey JL; Department of Computer Science, Arkansas State University, 2105 E. Aggie Rd., Jonesboro, AR, 72401, USA., Chavez ES; Department of Computer Science, Arkansas State University, 2105 E. Aggie Rd., Jonesboro, AR, 72401, USA., Wang Y; Department of Computer Science, Arkansas State University, 2105 E. Aggie Rd., Jonesboro, AR, 72401, USA., Piyush V; Department of Statistics, University of Nebraska - Lincoln, 340 Hardin Hall North Wing, Lincoln, NE, 68583, USA., Fernando GD; Department of Statistics, University of Nebraska - Lincoln, 340 Hardin Hall North Wing, Lincoln, NE, 68583, USA., Hu RK; Genomics and Computational Biology, Perelman School of Medicine at the University of Pennsylvania, 3700 Hamilton Walk, Philadelphia, PA, 19104, USA., Kumar R; Genomics and Computational Biology, Perelman School of Medicine at the University of Pennsylvania, 3700 Hamilton Walk, Philadelphia, PA, 19104, USA.; Medical Scientist Training Program, Perelman School of Medicine at the University of Pennsylvania, 3400 Civic Center Blvd., Philadelphia, PA, 19104, USA., Timon AJ; Genomics and Computational Biology, Perelman School of Medicine at the University of Pennsylvania, 3700 Hamilton Walk, Philadelphia, PA, 19104, USA., Venkatesh R; Genomics and Computational Biology, Perelman School of Medicine at the University of Pennsylvania, 3700 Hamilton Walk, Philadelphia, PA, 19104, USA., Abá KS; DOE Great Lakes Bioenergy Research Center, Michigan State University, East Lansing, MI, 48824, USA.; Genetics and Genome Sciences Graduate Program, Michigan State University, East Lansing, MI, 48824, USA., Chen H; Genetics and Genome Sciences Graduate Program, Michigan State University, East Lansing, MI, 48824, USA., Ranaweera T; DOE Great Lakes Bioenergy Research Center, Michigan State University, East Lansing, MI, 48824, USA.; Department of Plant Biology, Michigan State University, East Lansing, MI, 48824, USA., Shiu SH; DOE Great Lakes Bioenergy Research Center, Michigan State University, East Lansing, MI, 48824, USA.; Department of Plant Biology, Michigan State University, East Lansing, MI, 48824, USA.; Department of Computational Mathematics, Science, and Engineering, Michigan State University, East Lansing, MI, 48824, USA., Wang P; NC Plant Science Initiative, North Carolina State University, 840 Oval Drive, Raleigh, NC, 27606, USA.; Department of Electrical and Computer Engineering, North Carolina State University, 890 Oval Dr, Raleigh, NC, 27606, USA., Gordon MJ; NC Plant Science Initiative, North Carolina State University, 840 Oval Drive, Raleigh, NC, 27606, USA.; Department of Electrical and Computer Engineering, North Carolina State University, 890 Oval Dr, Raleigh, NC, 27606, USA., Amos BK; NC Plant Science Initiative, North Carolina State University, 840 Oval Drive, Raleigh, NC, 27606, USA.; Department of Electrical and Computer Engineering, North Carolina State University, 890 Oval Dr, Raleigh, NC, 27606, USA., Busato S; NC Plant Science Initiative, North Carolina State University, 840 Oval Drive, Raleigh, NC, 27606, USA.; Department of Electrical and Computer Engineering, North Carolina State University, 890 Oval Dr, Raleigh, NC, 27606, USA., Perondi D; NC Plant Science Initiative, North Carolina State University, 840 Oval Drive, Raleigh, NC, 27606, USA.; Department of Electrical and Computer Engineering, North Carolina State University, 890 Oval Dr, Raleigh, NC, 27606, USA., Gogna A; Department of Breeding Research, Leibniz-Institut für Pflanzengenetik und Kulturpflanzenforschung, Corrensstraße 3, Gatersleben, 6466, Germany., Psaroudakis D; Department of Molecular Genetics, Leibniz-Institut für Pflanzengenetik und Kulturpflanzenforschung, Corrensstraße 3, Gatersleben, 6466, Germany., Chen CPJ; School of Animal Sciences, Virginia Tech, Blacksburg, VA, 24061, USA., Al-Mamun HA; School of Biological Sciences and Centre of Applied Bioinformatics, University of Western Australia, Perth, WA, Australia., Danilevicz MF; School of Biological Sciences and Centre of Applied Bioinformatics, University of Western Australia, Perth, WA, Australia., Upadhyaya SR; School of Biological Sciences and Centre of Applied Bioinformatics, University of Western Australia, Perth, WA, Australia., Edwards D; School of Biological Sciences and Centre of Applied Bioinformatics, University of Western Australia, Perth, WA, Australia., de Leon N; Department of Plant and Agroecosystem Sciences, University of Wisconsin - Madison, 1575 Linden Drive, Madison, WI, 53706, USA.

Publikováno v: BioRxiv : the preprint server for biology [bioRxiv] 2024 Sep 19. Date of Electronic Publication: 2024 Sep 19.