119,433 research outputs found
No.349, Joseph Morrell, interview by Newell Bringhurst
No full textTranscript (26 pages) of interview by Newell Bringhurst with Joseph Morrell, a cousin of Fawn Brodie, on January 8, 1988. This interview is no. 349 in the Everett L. Cooley Oral History Project, and tape no. U-1387In an interview with Newell Bringhurst, Morrell (a cousin of Fawn Brodie) talks about the family in Huntsville, Utah, and his memories of Fawn. He also describes the reaction of various family members to
Letters from Francis C. Kelly and Mrs. L.D. Morrell to Hagan
No full textHolograph letters from Francis [C. Kelly] (Rome), and 1921 from Mrs. L.[D.] Morrell, Rome, to Hagan, concerning an act of charity towards Fr. Laws from a fund which both Hagan and Archbishop Mannix have control over. Hagan sends Lire 100 which Mrs. Morrell passes on. ([Kelly]'s letter carries Philadelphia ad- dress on the envelope.
SNP Genotyping Data from the Barley Experimental Population from "Two Genomic Regions Contribute Disproportionately to Geographic Differentiation in Wild Barley"
No full textThe 318 sampled wild barley accensions, known as the Wild Barley Diversity Collection (WBDC), were genotyped using the Illumina Golden Gate Genotyping Assay with two Barley Oligo Pool assay chips (BOPA1 and BOPA2). The genotype calls were based on machine-scored data using the program ALCHEMY and the SNPs were annotated using the program SNPMeta. The BOPA1 & 2 files contains the output of the ALCHEMY program.
Finally the original individual SSR for barley are publicly available at the website called GrainGenes and the sample used in this dataset are included as a txt file. All three files (tsv and txt) can be opened by text editors.Two Barley Oligo Pool Assay chips (BOPA 1 and 2) were genotyped from the Wild Barley Diversity Collection. Due to its broad geographic distribution and ecological adaptation, this collection is a valuable source of potentially useful genes.USDA NIFA 2011-68002-30029University of Minnesota Doctoral Dissertation FellowshipLieberman-Okinow Endowment at the University of MinnesotaUSAID-funded Cereals Comparative Genomics InitiativeFang, Zhou; Gonzales, Ana M; Clegg, Michael T; Smith, Kevin P; Muehlbauer, Gary J; Steffenson, Brian J; Morrell, Peter L. (2016). SNP Genotyping Data from the Barley Experimental Population from "Two Genomic Regions Contribute Disproportionately to Geographic Differentiation in Wild Barley". Retrieved from the University Digital Conservancy, http://doi.org/10.13020/D6B59N
Comparative genomics approaches accurately predict deleterious variants in plants
No full textThe genes and mutations information in this table were downloaded from UniProt/Swiss-Prot database (http://www.uniprot.org/) and http://www.arabidopsis.org. Single nucleotide polymorphisms (SNPs) without any known phenotype were obtained from a set of 80 sequenced A. thaliana strains (Ensembl, version 81, “Cao_SNPs”, Cao, et al., 2011). We used six approaches: LRT, PolyPhen2, SIFT 4G, Provean, MAPP, Gerp++ to predict deleterious varaints. The details can be avaible in Kono, et al., 2017 (http://www.biorxiv.org/content/early/2017/02/27/112318)Recent advances in genome resequencing have led to increased interest in prediction of the functional consequences of genetic variants. Variants at phylogenetically conserved sites are of particular interest, because they are more likely than variants at phylogenetically variable sites to have deleterious effects on fitness and contribute to phenotypic variation. Numerous comparative genomic approaches have been developed to predict deleterious variants, but they are nearly always judged based on their ability to identify known disease-causing mutations in humans. Determining the accuracy of deleterious variant predictions in nonhuman species is important to understanding evolution, domestication, and potentially to improving crop quality and yield. To examine our ability to predict deleterious variants in plants we generated a curated database of 2,910 Arabidopsis thaliana mutants with known phenotypes. We evaluated seven approaches and found that while all performed well, the single best-performing approach was a likelihood ratio test applied to homologs identified in 42 plant genomes. Although the approaches did not always agree, we found only slight differences in performance when comparing mutations with gross versus biochemical phenotypes, duplicated versus single copy genes, and when using a single approach versus ensemble predictions. We conclude that deleterious mutations can be reliably predicted in A. thaliana and likely other plant species, but that the relative performance of various approaches can depend on the organism to which they are applied.US National Science Foundation Plant Genome Program grant (DBI-1339393 to JCF and PLM)US Department of Agriculture Biotechnology Risk Assessment Research Grants Program (BRAG) (USDA BRAG 2015-06504 to PLM)University of Minnesota Doctoral Dissertation Fellowship (to TJYK)Kono, Thomas John Y; Lei, Li; Shih, Ching-Hua; Hoffman, Paul J; Morrell, Peter L; Fay, Justin C. (2018). Comparative genomics approaches accurately predict deleterious variants in plants. Retrieved from the University Digital Conservancy, https://doi.org/10.13020/D6N69S
Writers Talk with L. E. Modesitt, Jr., and Alex Bledsoe
No full textSpeculative fiction convention Context 25 will take place in Columbus on September 28-30. Guest of Honor L. E. Modesitt, Jr. gives the sci-fi lowdown to OSU student Alyssa Morrell, and Fantasy Guest of Honor Alex Bledsoe discusses his writing with OSU student Anna Shvets. Also, OSU student Samantha Demmerle reviews Liz Free or Die.The media can be accessed here: http://streaming.osu.edu/knowledgebank/WritersTalk-Audio/WT_WCRS_2012-9-17.mp3Ohio State University. Center for the Study and Teaching of Writin
Identification of genetic variation associated with high-temperature tolerance in cowpea
No full text1. File List
A. Filename: Cowpea_enviormental_ancest_822
Short description: Dataset related to environmental ancestry analysis in cowpea lines.
B. Filename: Partner_Favorites.vcf.gz
Short description: VCF file of variants from selected partner-preferred cowpea lines.
C. Filename: README.md
Short description: Markdown-formatted readme containing project metadata and notes.
D. Filename: README_WIP_Roland_Cowpea.txt
Short description: In-progress readme draft with additional annotation and format testing notes.
E. Filename: Readme_published_V5.txt
Short description: Final published version of the project readme with all required metadata.
F. Filename: VIGNA_rate6_ANCEST.bed
Short description: Ancestral state inference output using rate6 model in BED format.
G. Filename: VIGNA_rate6_ANCEST_ESTSFS.bed
Short description: BED file with ancestral states inferred using EST-SFS for comparison.
H. Filename: all_hits_MAF 3.bed.numbers
Short description: BED file annotated with allele frequency hit counts.
I. Filename: cowpea_490_stats_AA_rename.vcf.gz
Short description: VCF file with ancestral allele statistics for 490 cowpea samples.
J. Filename: cowpea_490_stats_AA_rename.vcf.gz.csi
Short description: Index file for the cowpea_490_stats_AA_rename VCF.
K. Filename: iSelect_ancestral.bed
Short description: Ancestral state calls for iSelect SNP array loci in BED format.This dataset includes filtered and unfiltered variant call files (VCFs), structural variant data (BEDPE), callable and uncallable region masks (BED), and phenotype data collected from mutagenized barley lines and control hybrids. It incorporates sequencing results from 10x Genomics, Oxford Nanopore, PacBio, and Illumina platforms.This study was funded by the Foundation for Food & Agriculture Research (Award# ICRC20-0000000032) to EFR, KJB, MA-M, OB, and PLM. The authors thank Tchamba Marimagne (IITA Genebank, Nigeria) for his valuable input during passport data curation, and Fiona Todd (University of Minnesota, USA) for the curation of materials associated with the manuscript. This research was carried out with software and hardware support provided by the Minnesota Supercomputing Institute (MSI) at the University of Minnesota. This research benefited from the advice and guidance of Timothy J. Close (U. of California Riverside, USA).Akakpo, Roland; Morrell, Peter; Lee, Elaine; Pacheco, Jacob; Rios, Esteban; Kantar, Michael; Boukar, Ousmane; Volz, Kevin; Akinmade, Habib; Alonso, Luis; Boote, Kenneth; Muñoz-Amatriaín, María. (2025). Identification of genetic variation associated with high-temperature tolerance in cowpea. Retrieved from the Data Repository for the University of Minnesota (DRUM), https://doi.org/10.13020/XXPS-Q694
Barley Genotyping SNPs Annotated using SNPMeta
No full textThese are SNPs on two Illumina GoldenGate genotyping arrays and one 9k iSelect genotyping array. The ascertainment scheme for the SNPs is available in Close, Timothy J., et al. "Development and implementation of high-throughput SNP genotyping in barley." BMC genomics 10.1 (2009): 1.SNPs annotations were derived from publicly available DNA sequences in GenBank using BLAST. Gene name, functional impact, and other information are returned using the program SNPMeta available for download at https://github.com/MorrellLAB/SNPMeta.US National Institute for Food and Agriculture (NIFA) (2011-68002-30029)USDA National Needs Fellowship (USDA NIFA 2011-38420-20068)USDA - Agricultural Research Service (Appropriation No. 5430-21000-006-00D)Kansas State UniversityKono, Thomas J Y; Kiran, Seth; Poland, Jesse A; Morrell, Peter L. (2016). Barley Genotyping SNPs Annotated using SNPMeta. Retrieved from the University Digital Conservancy, http://doi.org/10.13020/D63K53
Going Beyond Counting First Authors in Author Co-citation Analysis
No full textThe present study examines one of the fundamental aspects of author co-citation analysis (ACA) - the way co-citation
counts are defined. Co-citation counting provides the data on which all subsequent statistical analyses and mappings
are based, and we compare ACA results based on two different types of co-citation counting - the traditional type that
only counts the first one among a cited work's authors on the one hand and a non-traditional type that takes into
account the first 5 authors of a cited work on the other hand. Results indicate that the picture produced through this non-traditional author co-citation counting contains more coherent author groups and is therefore considerably clearer. However, this picture represents fewer specialties in the research field being studied than that produced through the traditional first-author co-citation counting when the same number of top-ranked authors is selected and analyzed. Reasons for these effects are discussed
Reclaiming fatherhood after disrupted intergenerational transmission of father roles: indigenous men in Canada and African men in the new South Africa
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