Bioinformatics Research Center

Works Published in 2018

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

2018 article

Modeling Dependence in Evolutionary Inference for Proteins


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

author keywords: Protein structure; Evolution; Dynamic programming; Phylogeny; Diffusion process
TL;DR: It is demonstrated that this extended, site-dependent model (SDM), extended to account for correlated evolutionary drift among neighboring amino acid positions, yields a significant reduction of bias in estimated evolutionary distances and helps further improve phylogenetic tree reconstruction. (via Semantic Scholar)
UN Sustainable Development Goal Categories
15. Life on Land (Web of Science)
Source: Web Of Science
Added: March 18, 2019

2018 journal article

Polyphasic characterization of four soil-derived phenanthrene-degrading Acidovorax strains and proposal of Acidovorax carolinensis sp nov.


By: D. Singleton*, J. Lee*, A. Dickey n, A. Stroud*, E. Scholl n, F. Wright n, M. Aitken*

author keywords: Acidovorax; Phenanthrene; Polycyclic aromatic hydrocarbons
MeSH headings : Biodegradation, Environmental; Comamonadaceae / chemistry; Comamonadaceae / classification; Comamonadaceae / genetics; Comamonadaceae / physiology; DNA, Bacterial; Genes, Bacterial; Genome, Bacterial / genetics; Metabolic Networks and Pathways / genetics; North Carolina; Phenanthrenes / metabolism; Phylogeny; RNA, Ribosomal, 16S; Sequence Analysis, DNA; Soil Microbiology; Soil Pollutants / metabolism
TL;DR: Four bacterial strains identified as members of the Acidovorax genus were isolated from two geographically distinct but similarly contaminated soils in North Carolina, USA, characterized, and their genomes sequenced, indicating that they likely represent a single species within the genus. (via Semantic Scholar)
UN Sustainable Development Goal Categories
15. Life on Land (OpenAlex)
Source: Web Of Science
Added: October 16, 2018

2018 journal article

Confirmation of high-throughput screening data and novel mechanistic insights into VDR-xenobiotic interactions by orthogonal assays

Scientific Reports, 8.

By: D. Mahapatra, J. Franzosa, K. Roell, M. Kuenemann, K. Houck, D. Reif, D. Fourches, S. Kullman

Source: NC State University Libraries
Added: August 6, 2018

2018 journal article

Improving wood properties for wood utilization through multi-omics integration in lignin biosynthesis


By: J. Wang n, M. Matthews n, C. Williams n, R. Shi n, C. Yang n, S. Tunlaya-Anukit n, H. Chen n, Q. Li* ...

MeSH headings : Gene Expression Regulation, Plant; Lignin / biosynthesis; Lignin / genetics; Plants, Genetically Modified / genetics; Populus / genetics; Populus / metabolism; Transcriptome / genetics; Trees / genetics; Trees / metabolism; Wood / chemistry; Wood / physiology; Xylem / metabolism
TL;DR: A multi-omics quantitative integrative analysis of lignin biosynthesis can advance the strategic engineering of wood for timber, pulp, and biofuels and may lead to greater understanding of other pathways for improved growth and adaptation. (via Semantic Scholar)
Source: Web Of Science
Added: August 6, 2018

2018 journal article

On the substructure controls in rare variant analysis: Principal components or variance components?


author keywords: population substructure; principal components analysis; rare variant association tests; variance components
MeSH headings : Computer Simulation; Confounding Factors, Epidemiologic; Genetic Association Studies; Genetic Variation; Humans; Models, Genetic; Principal Component Analysis
TL;DR: Evaluating the performance of SKAT coupling with principal components (PC) or variance components (VC) based PS correction methods found that PC‐based methods can account for confounding effects in most scenarios except for admixture, although the number of sufficient PCs depends on the PS complexity and the type of variants used. (via Semantic Scholar)
UN Sustainable Development Goal Categories
Source: Web Of Science
Added: August 6, 2018

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