Works Published in 2017
Displaying all 17 works
Sorted by most recent date added to the index first, which may not be the same as publication date order.
2017 journal article
Genetic effects on gene expression across human tissues
Nature, 550(7675), 204–213.
Ed(s): A. Battle *, C. Brown *, B. Engelhardt * & S. Montgomery *
MeSH headings : Alleles; Chromosomes, Human / genetics; Disease / genetics; Female; Gene Expression Profiling; Gene Expression Regulation / genetics; Genetic Variation; Genome, Human / genetics; Genotype; Humans; Male; Organ Specificity / genetics; Quantitative Trait Loci / genetics
TL;DR:
It is found that local genetic variation affects gene expression levels for the majority of genes, and inter-chromosomal genetic effects for 93 genes and 112 loci are identified, enabling a mechanistic interpretation of gene regulation and the genetic basis of disease.
(via Semantic Scholar)
www.nature.com (publisher PDF)
UN Sustainable Development Goal Categories
3. Good Health and Well-being
(Web of Science)
Sources: Crossref, NC State University Libraries
Added: December 19, 2020
2017 journal article
Landscape of X chromosome inactivation across human tissues
Nature, 550(7675), 244–248.
MeSH headings : Chromosomes, Human, X / genetics; Female; Genes, X-Linked / genetics; Genome, Human / genetics; Genomics; Humans; Male; Organ Specificity / genetics; Phenotype; Sequence Analysis, RNA; Single-Cell Analysis; Transcriptome / genetics; X Chromosome Inactivation / genetics
TL;DR:
It is shown that incomplete XCI affects at least 23% of X-chromosomal genes, identified seven genes that escape XCI with support from multiple lines of evidence and demonstrated that escape from XCI results in sex biases in gene expression, establishing incomplete X CI as a mechanism that is likely to introduce phenotypic diversity.
(via Semantic Scholar)
Source: Crossref
Added: December 19, 2020
2017 journal article
Changes in vaginal community state types reflect major shifts in the microbiome
Microbial Ecology in Health and Disease, 28(1), 1303265.
TL;DR:
The results show that the CST concept is useful for studying microbiome dynamics, with healthy subjects persist in a CST for two to three weeks or more on average, while those with evidence of dysbiosis tend to change more often.
(via Semantic Scholar)
UN Sustainable Development Goal Categories
15. Life on Land
(OpenAlex)
Source: Crossref
Added: February 5, 2020
2017 journal article
The impact of rare variation on gene expression across tissues
Nature, 550(7675), 239–243.
MeSH headings : Bayes Theorem; Female; Gene Expression Profiling; Genetic Variation / genetics; Genome, Human / genetics; Genomics; Genotype; Humans; Male; Models, Genetic; Organ Specificity / genetics; Sequence Analysis, RNA
TL;DR:
It is demonstrated that rare variants contribute to large gene expression changes across tissues and provide an integrative method for interpretation of rare variants in individual genomes.
(via Semantic Scholar)
Sources: Crossref, NC State University Libraries
Added: January 25, 2020
2017 journal article
Dynamic landscape and regulation of RNA editing in mammals
Nature, 550(7675), 249–254.
MeSH headings : Adenosine Deaminase / genetics; Adenosine Deaminase / metabolism; Animals; Female; Genotype; HEK293 Cells; Humans; Male; Mice; Muscles / metabolism; Nuclear Proteins / metabolism; Organ Specificity / genetics; Primates / genetics; Proteolysis; RNA Editing / genetics; RNA-Binding Proteins / genetics; RNA-Binding Proteins / metabolism; Spatio-Temporal Analysis; Species Specificity; Transcriptome / genetics
TL;DR:
This work curated an extensive set of ADAR1 and ADAR2 targets and showed that many editing sites display distinct tissue-specific regulation by the ADAR enzymes in vivo, suggesting stronger cis-directed regulation of RNA editing for most sites, although the small set of conserved coding sites is under stronger trans-regulation.
(via Semantic Scholar)
UN Sustainable Development Goal Categories
15. Life on Land
(OpenAlex)
Sources: Crossref, NC State University Libraries
Added: January 25, 2020
2017 journal article
A Two-Stage Hidden Markov Model Design for Biomarker Detection, with Application to Microbiome Research
Statistics in Biosciences, 10(1), 41–58.
author keywords: Biomarker; False discovery rates; Hidden Markov model; Metagenomics; Metatranscriptomics; PCR
TL;DR:
This paper studies an efficient HMM–FDR-based two-stage design, using a simple integrated analysis procedure across the stages, and proposes a power analysis method that shows excellent performance when compared to available methods.
(via Semantic Scholar)
UN Sustainable Development Goal Categories
3. Good Health and Well-being
(Web of Science)
Sources: Crossref, NC State University Libraries
Added: January 25, 2020
2017 journal article
Changes in vaginal community state types reflect major shifts in the microbiome
Microbial Ecology in Health and Disease, 28(1), 1303265.
Source: ORCID
Added: October 7, 2019
2017 journal article
A Pipeline for High-Throughput Concentration Response Modeling of Gene Expression for Toxicogenomics
Frontiers in Genetics, 8, 168.
Sources: NC State University Libraries, ORCID
Added: August 6, 2018
2017 journal article
Genetic effects on gene expression across human tissues
Nature, 550(7675), 204-.
Source: NC State University Libraries
Added: August 6, 2018
2017 journal article
Editor's Highlight: Comparative Dose-Response Analysis of Liver and Kidney Transcriptomic Effects of Trichloroethylene and Tetrachloroethylene in B6C3F1 Mouse
TOXICOLOGICAL SCIENCES, 160(1), 95–110.
author keywords: volatile organic compounds; agents; toxicogenomics; methods; dose-response; risk assessment; kidney; systems toxicology; liver; systems toxicology
MeSH headings : Animals; Dose-Response Relationship, Drug; Environmental Pollutants / toxicity; Gene Expression Profiling / methods; Gene Expression Regulation; Gene Regulatory Networks; Kidney / drug effects; Kidney / metabolism; Liver / drug effects; Liver / metabolism; Male; Mice; Risk Assessment; Sequence Analysis, RNA; Tetrachloroethylene / toxicity; Transcriptome; Trichloroethylene / toxicity
TL;DR:
D dose-response modeling of the transcriptomic data was performed and the resulting points of departure (PODs) were compared to those for apical endpoints derived from long-term studies with these chemicals in rats, mice, and humans, converting to human equivalent doses using tissue-specific dosimetry models.
(via Semantic Scholar)
UN Sustainable Development Goal Categories
3. Good Health and Well-being
(Web of Science)
Sources: Web Of Science, ORCID
Added: August 6, 2018
2017 journal article
Adrenal-derived stress hormones modulate ozone-induced lung injury and inflammation
TOXICOLOGY AND APPLIED PHARMACOLOGY, 329, 249–258.
author keywords: Ozone; Lung; Stress hormones; Adrenalectomy; RNAseq
MeSH headings : Adrenal Cortex / metabolism; Adrenal Cortex / surgery; Adrenal Medulla / metabolism; Adrenal Medulla / surgery; Adrenalectomy; Animals; Corticosterone / blood; Cytokines / metabolism; Disease Models, Animal; Epinephrine / blood; Gene Expression Regulation; Inflammation Mediators / metabolism; Lung / metabolism; Lung / pathology; Lung Injury / blood; Lung Injury / chemically induced; Lung Injury / genetics; Lung Injury / prevention & control; Male; Neutrophils / metabolism; Oxidative Stress; Ozone; Pneumonia / blood; Pneumonia / chemically induced; Pneumonia / genetics; Pneumonia / pathology; Pneumonia / prevention & control; RNA, Messenger / genetics; RNA, Messenger / metabolism; Rats, Inbred WKY; Signal Transduction; Stress, Physiological / genetics; Transcription, Genetic
TL;DR:
It is demonstrated that ozone‐induced lung injury and neutrophilic inflammation require the presence of circulating epinephrine and corticosterone, which transcriptionally regulates signaling mechanisms involved in this response.
(via Semantic Scholar)
UN Sustainable Development Goal Categories
3. Good Health and Well-being
(Web of Science; OpenAlex)
11. Sustainable Cities and Communities
(Web of Science)
Source: Web Of Science
Added: August 6, 2018
2017 journal article
Editor's Highlight: Collaborative Cross Mouse Population Enables Refinements to Characterization of the Variability in Toxicokinetics of Trichloroethylene and Provides Genetic Evidence for the Role of PPAR Pathway in Its Oxidative Metabolism
TOXICOLOGICAL SCIENCES, 158(1), 48–62.
author keywords: population; trichloroethylene; mouse
MeSH headings : Alcohol Dehydrogenase / biosynthesis; Aldehyde Dehydrogenase / biosynthesis; Animals; Dose-Response Relationship, Drug; Enzyme Induction; Female; Gene-Environment Interaction; Kidney / drug effects; Liver / drug effects; Liver / enzymology; Liver / metabolism; Male; Mice; Oxidation-Reduction; Peroxisome Proliferator-Activated Receptors / genetics; Peroxisome Proliferator-Activated Receptors / metabolism; Quantitative Trait Loci; Species Specificity; Toxicokinetics; Trichloroethylene / blood; Trichloroethylene / pharmacokinetics; Trichloroethylene / toxicity
TL;DR:
This study shows that CC mouse population is a valuable tool to quantitatively evaluate inter-individual variability in chemical metabolism and to identify genes and pathways that may underpin population differences.
(via Semantic Scholar)
UN Sustainable Development Goal Categories
3. Good Health and Well-being
(Web of Science)
Source: Web Of Science
Added: August 6, 2018
2017 journal article
A tiered, Bayesian approach to estimating population variability for regulatory decision-making
Altex-Alternatives to Animal Experimentation, 34(3), 377–388.
Source: NC State University Libraries
Added: August 6, 2018
2017 journal article
A procedure to detect general association based on concentration of ranks
Stat, 6(1), 88–101.
Sources: NC State University Libraries, ORCID
Added: August 6, 2018
2017 journal article
An improved and explicit surrogate variable analysis procedure by coefficient adjustment
BIOMETRIKA, 104(2), 303–316.
author keywords: Batch effect; High-dimensional data; Principal component analysis; Surrogate variable analysis
TL;DR:
This paper proposes an improved surrogate variable analysis, using all measured features, that has anatural connection with restricted least squares, which allows for study of its theoretical properties and shows that the method is competitive with state‐of‐the‐art methods.
(via Semantic Scholar)
UN Sustainable Development Goal Categories
3. Good Health and Well-being
(Web of Science)
15. Life on Land
(OpenAlex)
Source: Web Of Science
Added: August 6, 2018
2017 journal article
Functional Architectures of Local and Distal Regulation of Gene Expression in Multiple Human Tissues
AMERICAN JOURNAL OF HUMAN GENETICS, 100(4), 605–616.
MeSH headings : Anxiety / genetics; Computer Simulation; Depression / genetics; Gene Expression Regulation; Humans; Linkage Disequilibrium; Organ Specificity; Quantitative Trait Loci; Regression Analysis; Twins / genetics
TL;DR:
This work leveraged all variants (not just those that pass stringent significance thresholds) to analyze the functional architecture of local and distal regulation of gene expression in 15 human tissues by employing an extension of stratified LD-score regression that produces robust results in simulations.
(via Semantic Scholar)
UN Sustainable Development Goal Categories
3. Good Health and Well-being
(Web of Science)
Source: Web Of Science
Added: August 6, 2018
2017 journal article
Conditional eQTL analysis reveals allelic heterogeneity of gene expression
HUMAN MOLECULAR GENETICS, 26(8), 1444–1451.
MeSH headings : Alleles; Blood; Gene Expression Profiling; Gene Expression Regulation; Genetic Heterogeneity; Genome-Wide Association Study; Humans; Phenotype; Polymorphism, Single Nucleotide / genetics; Quantitative Trait Loci / genetics; Transcriptome / genetics
TL;DR:
An online conditional cis eZTL mapping catalog for whole blood is provided, which can be used to lookup eQTLs more accurately than in standard unconditional whole blood eQ TL databases.
(via Semantic Scholar)
UN Sustainable Development Goal Categories
3. Good Health and Well-being
(Web of Science)
Source: Web Of Science
Added: August 6, 2018
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