Bioinformatics Research Center

Works Published in 2021

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Displaying all 7 works

Sorted by most recent date added to the index first, which may not be the same as publication date order.

2021 article

Measuring Phylogenetic Information of Incomplete Sequence Data

Seo, T.-K., Gascuel, O., & Thorne, J. L. (2021, September 1). SYSTEMATIC BIOLOGY.

MeSH headings : Evolution, Molecular; INDEL Mutation; Models, Genetic; Models, Statistical; Phylogeny; Sequence Alignment
TL;DR: A new test for model adequacy is developed by comparing the Fisher information of actual and simulated sequences and identifying which alignment sites and tree branches are most affected by gaps and model misspecification. (via Semantic Scholar)
Source: Web Of Science
Added: March 14, 2022

2021 journal article

Quantitative Trait Locus Mapping for Common Scab Resistance in a Tetraploid Potato Full-Sib Population

PLANT DISEASE, 105(10), 3048–3054.

By: G. Pereira*, M. Mollinari n, X. Qu*, C. Thill*, Z. Zeng n, K. Haynes*, G. Yencho n

author keywords: disease resistance; polyploid QTL model; single-nucleotide polymorphism; Solanum tuberosum; Streptomyces spp
MeSH headings : Chromosome Mapping; Plant Tubers / genetics; Quantitative Trait Loci / genetics; Solanum tuberosum / genetics; Tetraploidy
UN Sustainable Development Goal Categories
2. Zero Hunger (Web of Science)
13. Climate Action (Web of Science)
15. Life on Land (Web of Science)
Source: Web Of Science
Added: January 18, 2022

2021 journal article

Genome and transcriptome sequencing of the green bottle fly, Lucilia sericata, reveals underlying factors of sheep flystrike and maggot debridement therapy

GENOMICS, 113(6), 3978–3988.

author keywords: Lucilia sericata; Maggot debridement therapy; Whole genome; Salivary gland; Malpighian tubule; Heat shock
MeSH headings : Animals; Calliphoridae; Debridement; Diptera / genetics; Humans; Larva / genetics; Larva / metabolism; Sheep / genetics; Transcriptome
TL;DR: The assembly of a 565.3 Mb genome from long read PacBio DNA sequencing of genomic DNA is reported, which will underpin future genetic studies and in development of engineered strains for genetic control of L. sericata and for biotechnology-enhanced maggot therapy. (via Semantic Scholar)
Source: Web Of Science
Added: October 26, 2021

2021 article

Pedigree-based and phylogenetic methods support surprising patterns of mutation rate and spectrum in the gray mouse lemur

Campbell, C. R., Tiley, G. P., Poelstra, J. W., Hunnicutt, K. E., Larsen, P. A., Lee, H.-J., … Yoder, A. D. (2021, July 16). HEREDITY.

By: C. Campbell*, G. Tiley*, J. Poelstra*, K. Hunnicutt*, P. Larsen*, H. Lee*, J. Thorne n, M. Reis*, A. Yoder*

MeSH headings : Animals; Cheirogaleidae / genetics; Genome; Mice; Mutation Rate; Pedigree; Phylogeny
TL;DR: This study provides the first direct mutation-rate estimate for a strepsirrhine (i.e., the lemurs and lorises), which comprises nearly half of the primate clade, and finds both the rate and spectrum to be robust to the manipulation of a wide range of computational filtering criteria. (via Semantic Scholar)
UN Sustainable Development Goal Categories
15. Life on Land (OpenAlex)
Source: Web Of Science
Added: August 2, 2021

2021 article

High-resolution characterization of the structural features and genetic variation of six feline leukocyte antigen class I loci via single molecule, real-time (SMRT) sequencing

Holmes, J. C., Scholl, E. H., Dickey, A. N., & Hess, P. R. (2021, June 27). IMMUNOGENETICS.

By: J. Holmes n, E. Scholl n, A. Dickey n & P. Hess n

author keywords: Cats; Class I genes; High-throughput DNA sequencing; Major histocompatibility complex; Polymorphism
MeSH headings : Animals; Cats; Exons; Genes, MHC Class I / genetics; Genetic Variation; Haplotypes; High-Throughput Nucleotide Sequencing; Histocompatibility Antigens Class I / chemistry; Histocompatibility Antigens Class I / genetics; Sequence Analysis, DNA / methods
TL;DR: A targeted approach to FLAI genotyping, using the single-molecule real-time (SMRT) platform, which allows full-length (3.4-kb) reads without assembly, is developed, which could allow highly accurate allele surveys in large cat cohorts. (via Semantic Scholar)
UN Sustainable Development Goal Categories
Source: Web Of Science
Added: July 6, 2021

2021 journal article

Discovery of a major QTL for root-knot nematode (Meloidogyne incognita) resistance in cultivated sweetpotato (Ipomoea batatas)

THEORETICAL AND APPLIED GENETICS, 134(7), 1945–1955.

MeSH headings : Animals; Chromosome Mapping; Disease Resistance / genetics; Genetic Linkage; Genotype; Ipomoea batatas / genetics; Ipomoea batatas / parasitology; Plant Diseases / genetics; Plant Diseases / parasitology; Polymorphism, Single Nucleotide; Quantitative Trait Loci; Tylenchoidea / pathogenicity
TL;DR: A major dominant QTL for root-knot nematode (RKN) resistance is discovered using a high-density integrated genetic linkage map of hexaploid sweetpotato, which represents a significant step forward in understanding of the genetic architecture of RKN resistance and sets the stage for future utilization of genomics-assisted breeding inSweetpotato breeding programs. (via Semantic Scholar)
UN Sustainable Development Goal Categories
2. Zero Hunger (Web of Science)
13. Climate Action (Web of Science)
Source: Web Of Science
Added: April 26, 2021

2021 journal article

The recombination landscape and multiple QTL mapping in a Solanum tuberosum cv. 'Atlantic'-derived F-1 population

HEREDITY, 126(5), 817–830.

By: G. Pereira n, M. Mollinari n, M. Schumann n, M. Clough n, Z. Zeng n & G. Yencho n

MeSH headings : Phenotype; Plant Breeding; Plant Tubers; Quantitative Trait Loci; Recombination, Genetic; Solanum tuberosum / genetics
TL;DR: Genetic analyses of an F1 population derived from a cross involving ‘Atlantic’, a widely grown chipping variety in the USA, find those on chromosome 5 that have been previously implicated in maturity (StCDF1) and tuber formation (POTH1). (via Semantic Scholar)
UN Sustainable Development Goal Categories
2. Zero Hunger (Web of Science)
13. Climate Action (Web of Science)
14. Life Below Water (OpenAlex)
15. Life on Land (Web of Science)
Source: Web Of Science
Added: March 29, 2021

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