Cross-species modeling of plant genomes at single nucleotide resolution using a pre-trained DNA language model.

Autor: Zhai J; Institute for Genomic Diversity, Cornell University, Ithaca, NY USA 14853., Gokaslan A; Department of Computer Science, Cornell University, Ithaca, NY, USA 14853., Schiff Y; Department of Computer Science, Cornell University, Ithaca, NY, USA 14853., Berthel A; Institute for Genomic Diversity, Cornell University, Ithaca, NY USA 14853., Liu ZY; Section of Plant Breeding and Genetics, Cornell University, Ithaca, NY USA 14853., Lai WY; Institute for Genomic Diversity, Cornell University, Ithaca, NY USA 14853., Miller ZR; Institute for Genomic Diversity, Cornell University, Ithaca, NY USA 14853., Scheben A; Simons Center for Quantitative Biology, Cold Spring Harbor Laboratory, 1 Bungtown Road, Cold Spring Harbor, NY USA 11724., Stitzer MC; Institute for Genomic Diversity, Cornell University, Ithaca, NY USA 14853., Romay MC; Institute for Genomic Diversity, Cornell University, Ithaca, NY USA 14853., Buckler ES; Institute for Genomic Diversity, Cornell University, Ithaca, NY USA 14853.; Section of Plant Breeding and Genetics, Cornell University, Ithaca, NY USA 14853.; USDA-ARS; Ithaca, NY, USA 14853., Kuleshov V; Department of Computer Science, Cornell University, Ithaca, NY, USA 14853.

Publikováno v: BioRxiv : the preprint server for biology [bioRxiv] 2024 Aug 22. Date of Electronic Publication: 2024 Aug 22.

Coexistence of many species under a random competition-colonization trade-off.

Autor: Miller ZR; Department of Ecology & Evolution, University of Chicago, Chicago, IL 60637.; Department of Plant Biology, University of Illinois, Urbana, IL, 61801., Clenet M; Laboratoire d'Informatique Gaspard-Monge, UMR 8049, CNRS, Université Gustave Eiffel, Marne-la-Vallée 77454, France., Della Libera K; Department of Ecology & Evolution, University of Chicago, Chicago, IL 60637., Massol F; Université Lille, CNRS, INSERM, CHU Lille, Institut Pasteur de Lille, U1019-UMR 9017-Center for Infection and Immunity of Lille, Lille F-59000, France., Allesina S; Department of Ecology & Evolution, University of Chicago, Chicago, IL 60637.

Publikováno v: Proceedings of the National Academy of Sciences of the United States of America [Proc Natl Acad Sci U S A] 2024 Jan 30; Vol. 121 (5), pp. e2314215121. Date of Electronic Publication: 2024 Jan 23.

Reduced Hippocampal Volumes in Children with History of Hypoxic Ischemic Encephalopathy after Therapeutic Hypothermia.

Autor: Pfister KM; Department of Pediatrics, University of Minnesota, 2450 Riverside Ave., AO-401, Minneapolis, MN 55454, USA., Stoyell SM; Institute of Child Development, University of Minnesota, Campbell Hall, 51 E River Rd., Minneapolis, MN 55455, USA., Miller ZR; Institute of Child Development, University of Minnesota, Campbell Hall, 51 E River Rd., Minneapolis, MN 55455, USA., Hunt RH; Institute of Child Development, University of Minnesota, Campbell Hall, 51 E River Rd., Minneapolis, MN 55455, USA., Zorn EP; Department of Pediatrics, University of Minnesota, 2450 Riverside Ave., AO-401, Minneapolis, MN 55454, USA., Thomas KM; Institute of Child Development, University of Minnesota, Campbell Hall, 51 E River Rd., Minneapolis, MN 55455, USA.

Publikováno v: Children (Basel, Switzerland) [Children (Basel)] 2023 Jun 02; Vol. 10 (6). Date of Electronic Publication: 2023 Jun 02.

The Practical Haplotype Graph, a platform for storing and using pangenomes for imputation.

Autor: Bradbury PJ; United States Department of Agriculture-Agricultural Research Service, Robert W. Holley Center, Ithaca, NY 14853, USA., Casstevens T; Institute for Genomic Diversity, Cornell University, Ithaca, NY 14853, USA., Jensen SE; Plant Breeding and Genetics Section, School of Integrative Plant Science, Cornell University, Ithaca, NY 14853, USA., Johnson LC; Institute for Genomic Diversity, Cornell University, Ithaca, NY 14853, USA., Miller ZR; Institute for Genomic Diversity, Cornell University, Ithaca, NY 14853, USA., Monier B; Institute for Genomic Diversity, Cornell University, Ithaca, NY 14853, USA., Romay MC; Institute for Genomic Diversity, Cornell University, Ithaca, NY 14853, USA., Song B; Institute for Genomic Diversity, Cornell University, Ithaca, NY 14853, USA., Buckler ES; United States Department of Agriculture-Agricultural Research Service, Robert W. Holley Center, Ithaca, NY 14853, USA.; Institute for Genomic Diversity, Cornell University, Ithaca, NY 14853, USA.; Plant Breeding and Genetics Section, School of Integrative Plant Science, Cornell University, Ithaca, NY 14853, USA.

Publikováno v: Bioinformatics (Oxford, England) [Bioinformatics] 2022 Aug 02; Vol. 38 (15), pp. 3698-3702.

Development of the Wheat Practical Haplotype Graph database as a resource for genotyping data storage and genotype imputation.

Autor: Jordan KW; Department of Plant Pathology, Kansas State University, Manhattan, KS 66506, USA.; USDA-ARS, Hard Winter Wheat Genetics Research Unit, Manhattan, KS 66502, USA., Bradbury PJ; USDA-ARS, Plant Soil and Nutrition Research Unit, Ithaca, NY 14853, USA., Miller ZR; Institute for Genomic Diversity, Cornell University, Ithaca, NY 14853, USA., Nyine M; Department of Plant Pathology, Kansas State University, Manhattan, KS 66506, USA., He F; Department of Plant Pathology, Kansas State University, Manhattan, KS 66506, USA., Fraser M; Department of Agronomy and Plant Genetics, University of Minnesota, St. Paul, MN 55108, USA., Anderson J; Department of Agronomy and Plant Genetics, University of Minnesota, St. Paul, MN 55108, USA., Mason E; Department of Soil and Crop Sciences, Colorado State University, Fort Collins, CO 80521, USA., Katz A; Department of Soil and Crop Sciences, Colorado State University, Fort Collins, CO 80521, USA., Pearce S; Department of Soil and Crop Sciences, Colorado State University, Fort Collins, CO 80521, USA., Carter AH; Department of Crop and Soil Sciences, Washington State University, Pullman, WA 99164, USA., Prather S; Department of Crop and Soil Sciences, Washington State University, Pullman, WA 99164, USA., Pumphrey M; Department of Crop and Soil Sciences, Washington State University, Pullman, WA 99164, USA., Chen J; Department of Plant Sciences, University of Idaho, Aberdeen, ID 83210, USA., Cook J; Department of Plant Sciences and Plant Pathology, Montana State University, Bozeman, MT 59717, USA., Liu S; Department of Soil and Crop Sciences, Texas A&M AgriLife Research, Amarillo, TX 79106, USA., Rudd JC; Department of Soil and Crop Sciences, Texas A&M AgriLife Research, Amarillo, TX 79106, USA., Wang Z; Department of Soil and Crop Sciences, Texas A&M AgriLife Research, Amarillo, TX 79106, USA., Chu C; Department of Soil and Crop Sciences, Texas A&M AgriLife Research, Amarillo, TX 79106, USA., Ibrahim AMH; Department of Soil and Crop Sciences, Texas A&M AgriLife Research, Amarillo, TX 79106, USA., Turkus J; Department of Plant, Soil and Microbial Sciences, Michigan State University, East Lansing, MI 48824, USA., Olson E; Department of Plant, Soil and Microbial Sciences, Michigan State University, East Lansing, MI 48824, USA., Nagarajan R; Department of Plant and Soil Sciences, Oklahoma State University, Stillwater, OK 74075, USA., Carver B; Department of Plant and Soil Sciences, Oklahoma State University, Stillwater, OK 74075, USA., Yan L; Department of Plant and Soil Sciences, Oklahoma State University, Stillwater, OK 74075, USA., Taagen E; Institute for Genomic Diversity, Cornell University, Ithaca, NY 14853, USA., Sorrells M; Institute for Genomic Diversity, Cornell University, Ithaca, NY 14853, USA., Ward B; USDA-ARS, Plant Science Research Unit, Raleigh, NC 27695, USA., Ren J; Department of Plant Pathology, Kansas State University, Manhattan, KS 66506, USA.; Integrative Genomics Facility, Kansas State University, Manhattan, KS 66506, USA., Akhunova A; Department of Plant Pathology, Kansas State University, Manhattan, KS 66506, USA.; Integrative Genomics Facility, Kansas State University, Manhattan, KS 66506, USA., Bai G; USDA-ARS, Hard Winter Wheat Genetics Research Unit, Manhattan, KS 66502, USA., Bowden R; USDA-ARS, Hard Winter Wheat Genetics Research Unit, Manhattan, KS 66502, USA., Fiedler J; USDA-ARS, Cereal Crops Research Unit, Fargo, ND 58102, USA., Faris J; USDA-ARS, Cereal Crops Research Unit, Fargo, ND 58102, USA., Dubcovsky J; Department of Plant Sciences, University of California-Davis, Davis, CA 95616, USA., Guttieri M; USDA-ARS, Hard Winter Wheat Genetics Research Unit, Manhattan, KS 66502, USA., Brown-Guedira G; USDA-ARS, Plant Science Research Unit, Raleigh, NC 27695, USA., Buckler E; USDA-ARS, Plant Soil and Nutrition Research Unit, Ithaca, NY 14853, USA., Jannink JL; USDA-ARS, Plant Soil and Nutrition Research Unit, Ithaca, NY 14853, USA., Akhunov ED; Department of Plant Pathology, Kansas State University, Manhattan, KS 66506, USA.

Publikováno v: G3 (Bethesda, Md.) [G3 (Bethesda)] 2022 Feb 04; Vol. 12 (2).