Bioinformatics Research Center

Works Published in 2020

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Displaying all 6 works

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

2020 journal article

Complete Genome Sequences of Six Lactobacilli Isolated from American Quarter Horses

MICROBIOLOGY RESOURCE ANNOUNCEMENTS, 9(47).

By: R. Meinders n, M. Mendoza n, A. Dickey n, E. Scholl n & H. Hassan n

TL;DR: The complete circular genome sequences of six Lactobacillus strains and their plasmids, if any, from the fecal material of quarter horses at different ages are reported. (via Semantic Scholar)
UN Sustainable Development Goal Categories
15. Life on Land (Web of Science)
Source: Web Of Science
Added: January 4, 2021

2020 journal article

Assembly of whole-chromosome pseudomolecules for polyploid plant genomes using outbred mapping populations

NATURE GENETICS, 52(11), 1256-+.

MeSH headings : Algorithms; Chromosomes, Plant; Computer Simulation; Genetic Linkage; Genome, Plant; Genotype; Ipomoea / genetics; Plant Breeding; Poaceae / genetics; Polyploidy; Protein Array Analysis; Solanum tuberosum / genetics
TL;DR: PolyGembler, a method for grouping and ordering contigs into complete pseudomolecules by combining long-read sequencing and genotype information from an outbred mapping population, improves the accuracy for assembly of polyploidy plant genomes. (via Semantic Scholar)
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: November 24, 2020

2020 journal article

Sequencing depth and genotype quality: accuracy and breeding operation considerations for genomic selection applications in autopolyploid crops

THEORETICAL AND APPLIED GENETICS, 133(12), 3345–3363.

MeSH headings : Crops, Agricultural / genetics; Crops, Agricultural / growth & development; Genotype; Ipomoea batatas / genetics; Ipomoea batatas / growth & development; Phenotype; Plant Breeding; Polymorphism, Single Nucleotide; Polyploidy; Quantitative Trait Loci; Selection, Genetic; Sequence Analysis, DNA
TL;DR: It is concluded that genomic selection can help accelerate the rate of genetic gains in potato and sweetpotato, however, application of genomic selection should be considered as part of optimizing the entire breeding program. (via Semantic Scholar)
Source: Web Of Science
Added: September 21, 2020

2020 journal article

A novel vision-based real-time method for evaluating postural risk factors associated with musculoskeletal disorders

APPLIED ERGONOMICS, 87.

By: L. Li n, T. Martin n & X. Xu n

author keywords: RULA; Deep learning; MSD risk assessment
MeSH headings : Adult; Deep Learning; Ergonomics / methods; Female; Humans; Image Processing, Computer-Assisted / methods; Lifting; Male; Musculoskeletal Diseases / diagnostic imaging; Musculoskeletal Diseases / etiology; Occupational Diseases / diagnostic imaging; Occupational Diseases / etiology; Photography / methods; Posture; Risk Assessment; Risk Factors; Upper Extremity / diagnostic imaging
TL;DR: This document examines a novel end-to-end implementation of a deep learning-based algorithm for rapid upper limb assessment (RULA) and indicates that using data augmentation (a strategy to diversify the training data) can significantly improve the robustness of the model. (via Semantic Scholar)
UN Sustainable Development Goal Categories
Source: Web Of Science
Added: June 22, 2020

2020 journal article

Incorporating Nearest-Neighbor Site Dependence into Protein Evolution Models

JOURNAL OF COMPUTATIONAL BIOLOGY, 27(3), 361–375.

By: G. Larson*, J. Thorne n & S. Schmidler*

author keywords: diffusion process; dynamic programming; evolution; phylogeny; protein structure
MeSH headings : Computational Biology / methods; Evolution, Molecular; Models, Statistical; Proteins / chemistry; Proteins / metabolism; Sequence Alignment; Sequence Analysis, Protein; Structural Homology, Protein
TL;DR: This work develops a simple model of site-dependent sequence evolution, which is used to demonstrate the bias resulting from the application of standard site-independent sequence evolution models and yields a significant reduction of bias in estimated evolutionary distances. (via Semantic Scholar)
UN Sustainable Development Goal Categories
15. Life on Land (Web of Science)
Source: Web Of Science
Added: April 20, 2020

2020 journal article

Improving Cancer Drug Discovery by Studying Cancer across the Tree of Life

MOLECULAR BIOLOGY AND EVOLUTION, 37(1), 11–17.

By: J. Somarelli*, A. Boddy*, H. Gardner*, S. DeWitt*, J. Tuohy*, K. Megquier*, M. Sheth*, S. Hsu* ...

author keywords: veterinary oncology; cross-species studies; cancer drug discovery; evolutionary biology
MeSH headings : Animals; Drug Discovery; Humans; Neoplasms / drug therapy; Neoplasms / veterinary
TL;DR: Clinical trials in veterinary patients with cancer provide an opportunity to evaluate a novel therapeutic in a setting that recapitulates many of the key features of human cancers, including key genomic aberrations that underly tumor development, response and resistance to treatment, and the presence of comorbidities that can affect outcomes. (via Semantic Scholar)
Source: Web Of Science
Added: March 10, 2020

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