Fred Andrew Wright
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Works (131)
Updated: November 14th, 2024 05:02
2024 journal article
Characterizing PFAS hazards and risks: a human population-based in vitro cardiotoxicity assessment strategy
HUMAN GENOMICS, 18(1).
open access via doi.org (publisher)
Sources: Web Of Science, NC State University Libraries
Added: September 9, 2024
2024 journal article
Control of false discoveries in grouped hypothesis testing for eQTL data
BMC BIOINFORMATICS, 25(1).
author keywords: eQTL; Grouped hypothesis testing; False discovery rate; Empirical Bayes
UN Sustainable Development Goal Categories
3. Good Health and Well-being
(Web of Science)
Sources: Web Of Science, NC State University Libraries
Added: April 22, 2024
2024 article
Genetic variation in severe cystic fibrosis liver disease is associated with novel mechanisms for disease pathogenesis
Stonebraker, J., Pace, R., Gallins, P., Dang, H., Aksit, M., Faino, A., … Knowles, M. (2024, March 27). HEPATOLOGY, Vol. 3.
author keywords: MAIT cells; whole genome sequencing; GWAS; TWAS; CFLD
UN Sustainable Development Goal Categories
3. Good Health and Well-being
(Web of Science; OpenAlex)
Sources: Web Of Science, NC State University Libraries
Added: April 15, 2024
2024 journal article
Hazard and risk characterization of 56 structurally diverse PFAS using a targeted battery of broad coverage assays using six human cell types
TOXICOLOGY, 503.
author keywords: PFAS; In vitro; Grouping; Risk characterization; Margin of exposure
UN Sustainable Development Goal Categories
3. Good Health and Well-being
(Web of Science)
6. Clean Water and Sanitation
(Web of Science)
Sources: Web Of Science, NC State University Libraries
Added: May 7, 2024
2024 article
Informing Hazard Identification and Risk Characterization of Environmental Chemicals by Combining Transcriptomic and Functional Data from Human-Induced Pluripotent Stem-Cell-Derived Cardiomyocytes
Tsai, H.-H. D., Ford, L. C., Burnett, S. D., Dickey, A. N., Wright, F. A., Chiu, W. A., & Rusyn, I. (2024, July 24). CHEMICAL RESEARCH IN TOXICOLOGY.
UN Sustainable Development Goal Categories
3. Good Health and Well-being
(Web of Science)
11. Sustainable Cities and Communities
(Web of Science)
Source: Web Of Science
Added: August 5, 2024
2024 journal article
Liver eQTL meta-analysis illuminates potential molecular mechanisms of cardiometabolic traits
AMERICAN JOURNAL OF HUMAN GENETICS, 111(9).
Sources: Web Of Science, NC State University Libraries
Added: September 23, 2024
2024 journal article
Risk-Based Prioritization of PFAS Using Phenotypic and Transcriptomic Data from Human Induced Pluripotent Stem Cell-Derived Hepatocytes and Cardiomyocytes
ALTEX-ALTERNATIVES TO ANIMAL EXPERIMENTATION, 41(3), 363–381.
Source: Web Of Science
Added: September 23, 2024
2024 article
Time for CHANGE: system-level interventions for bringing forward the date of effective use of NAMs in regulatory toxicology
Mathisen, G. H., Bearth, A., Jones, L. B., Hoffmann, S., Vist, G. E., Ames, H. M., … Whaley, P. (2024, June 14). ARCHIVES OF TOXICOLOGY.
UN Sustainable Development Goal Categories
3. Good Health and Well-being
(Web of Science)
11. Sustainable Cities and Communities
(Web of Science)
Source: Web Of Science
Added: July 1, 2024
2024 article
To Accept or Not To Accept a Read-Across Adaptation: A Systematic Analysis of 15 Years of Testing Proposal Decisions by the European Chemicals Agency
Roe, H. M., Ball, N., Wright, F. A., Chiu, W. A., & Rusyn, I. (2024, September). TOXICOLOGY LETTERS, Vol. 399, pp. S63–S63.
Source: Web Of Science
Added: November 12, 2024
2024 article
Two-Stage Machine Learning-Based Approach to Predict Points of Departure for Human Noncancer and Developmental/Reproductive Effects
Kvasnicka, J., Aurisano, N., Borries, K., Lu, E.-H., Fantke, P., Jolliet, O., … Chiu, W. A. (2024, May 2). ENVIRONMENTAL SCIENCE & TECHNOLOGY.
author keywords: QSAR model; machine learning; toxicity prediction; chemical risk assessment; high-throughput screening; life cycle impact assessment (LCIA)
UN Sustainable Development Goal Categories
3. Good Health and Well-being
(Web of Science)
11. Sustainable Cities and Communities
(Web of Science)
Source: Web Of Science
Added: June 17, 2024
2023 article
A tiered testing strategy based on in vitro phenotypic and transcriptomic data for selecting representative petroleum UVCBs for toxicity evaluation in vivo
Tsai, H.-H. D., House, J. S., Wright, F. A., Chiu, W. A., & Rusyn, I. (2023, April 20). TOXICOLOGICAL SCIENCES.
author keywords: transcriptomic; petroleum; grouping; dose-response; HTTr; NAMs
MeSH headings : Humans; Transcriptome; Petroleum / toxicity; Endothelial Cells; Gene Expression Profiling; Cell Line
TL;DR:
This study found that two cell types-iPSC-derived-hepatocytes and -cardiomyocytes-contributed the most informative and protective PODs and may be used to inform selection of representative petroleum UVCBs for further toxicity evaluation in vivo.
(via Semantic Scholar)
UN Sustainable Development Goal Categories
3. Good Health and Well-being
(Web of Science)
11. Sustainable Cities and Communities
(Web of Science)
Sources: Web Of Science, ORCID
Added: May 22, 2023
2023 journal article
Analysis of reproducibility and robustness of a renal proximal tubule microphysiological system OrganoPlate 3-lane 40 for in vitro studies of drug transport and toxicity
TOXICOLOGICAL SCIENCES.
author keywords: kidney; in vitro models; validation
UN Sustainable Development Goal Categories
3. Good Health and Well-being
(Web of Science; OpenAlex)
Source: Web Of Science
Added: September 5, 2023
2023 article
Application of Ion Mobility Spectrometry-Mass Spectrometry for Compositional Characterization and Fingerprinting of a Library of Diverse Crude Oil Samples
Cordova, A. C., Dodds, J. N., Tsai, H.-H. D., Lloyd, D. T., Roman-Hubers, A. T., Wright, F. A., … Rusyn, I. (2023, August 22). ENVIRONMENTAL TOXICOLOGY AND CHEMISTRY.
author keywords: Analytical chemistry; Environmental chemistry; Hazard; risk assessment; Mixtures; Oil spills
TL;DR:
It is found that IMS-MS data has complementary advantages for fingerprinting and characterization of diverse crude oils and that the proposed polycyclic aromatic hydrocarbon (PAH) biomarkers can be used for rapid exposure characterization.
(via Semantic Scholar)
Source: Web Of Science
Added: September 5, 2023
2023 journal article
Genetic Modifiers of Cystic Fibrosis Lung Disease Severity
AMERICAN JOURNAL OF RESPIRATORY AND CRITICAL CARE MEDICINE, 207(10), 1324–1333.
author keywords: cystic fibrosis; whole-genome sequencing; lung disease severity; GWAS/TWAS; pathway analyses
MeSH headings : Humans; Cystic Fibrosis / genetics; Genome-Wide Association Study / methods; Cystic Fibrosis Transmembrane Conductance Regulator / genetics; Patient Acuity; Lung; Microtubule-Associated Proteins / genetics
TL;DR:
This pre- modulator genomic, transcriptomic, and pathway association study of 7,840 pwCF will facilitate mechanistic and post-modulator genetic studies and, development of novel therapeutics for CF lung disease.
(via Semantic Scholar)
UN Sustainable Development Goal Categories
3. Good Health and Well-being
(Web of Science; OpenAlex)
Sources: Web Of Science, ORCID, NC State University Libraries
Added: May 16, 2023
2023 journal article
Integrative Chemical-Biological Grouping of Complex High Production Volume Substances from Lower Olefin Manufacturing Streams
TOXICS, 11(7).
author keywords: UVCB; petroleum; regulatory risk assessment; read-across; ion mobility spectrometry
UN Sustainable Development Goal Categories
3. Good Health and Well-being
(Web of Science)
11. Sustainable Cities and Communities
(Web of Science)
Sources: Web Of Science, ORCID, NC State University Libraries
Added: July 6, 2023
2023 article
Simultaneous modeling of multivariate heterogeneous responses and heteroskedasticity via a two-stage composite likelihood
Ting, B. W. W., Wright, F. A., & Zhou, Y.-H. (2023, May 22). BIOMETRICAL JOURNAL.
author keywords: heterogeneity; heteroskedasticity; multivariate statistics; precision medicine; prediction
TL;DR:
A previous method for multivariate probit estimation is built upon using a two‐stage composite likelihood that exhibits favorable computational time while retaining attractive parameter estimation properties and has the potential to better leverage genomics data and provide interpretable inference for pleiotropy.
(via Semantic Scholar)
UN Sustainable Development Goal Categories
3. Good Health and Well-being
(Web of Science)
Sources: Web Of Science, ORCID
Added: May 23, 2023
2023 article
Ten years of using key characteristics of human carcinogens to organize and evaluate mechanistic evidence in IARC Monographs on the identification of carcinogenic hazards to humans: Patterns and associations
Rusyn, I., & Wright, F. A. (2023, December 23). TOXICOLOGICAL SCIENCES.
author keywords: cancer risk assessment; risk assessment; safety evaluation
TL;DR:
Increased availability of systemized data streams, such as human in vitro data, would provide the basis for confident conclusions about both positive and negative associations and constitute relative contributions of various sources of weight in expert judgments.
(via Semantic Scholar)
UN Sustainable Development Goal Categories
3. Good Health and Well-being
(Web of Science)
11. Sustainable Cities and Communities
(Web of Science)
16. Peace, Justice and Strong Institutions
(OpenAlex)
Source: Web Of Science
Added: January 29, 2024
2022 journal article
A Population-Based Human In Vitro Approach to Quantify Inter-Individual Variability in Responses to Chemical Mixtures
TOXICS, 10(8).
author keywords: population-wide; inter-individual variability; toxicodynamics; chemical mixtures; defined mixtures; human health risk assessment; uncertainty factors; genome-wide association study
TL;DR:
The data show that population variability of the mixtures is unlikely to exceed that of the most variable component, and that similarity in genome-wide associations among components may be used to accrue additional evidence for grouping of constituents in a mixture for cumulative assessments.
(via Semantic Scholar)
UN Sustainable Development Goal Categories
3. Good Health and Well-being
(Web of Science)
11. Sustainable Cities and Communities
(Web of Science)
Sources: Web Of Science, ORCID, NC State University Libraries
Added: August 2, 2022
2022 journal article
A resource for integrated genomic analysis of the human liver
SCIENTIFIC REPORTS, 12(1).
MeSH headings : Bayes Theorem; Genome-Wide Association Study / methods; Genomics; Humans; Liver; Polymorphism, Single Nucleotide; Quantitative Trait Loci
TL;DR:
This study generated whole-transcriptome RNA-Seq from genotyped liver samples and used existing data from the GTEx Project and previous liver eQTL studies to create an enhanced transcriptomic sequence resource in the human liver, finding that MHC genes, and especially class II genes, are enriched for liver-specific eZTL patterns.
(via Semantic Scholar)
UN Sustainable Development Goal Categories
3. Good Health and Well-being
(Web of Science)
Sources: Web Of Science, ORCID, NC State University Libraries
Added: September 8, 2022
2022 journal article
Characterization of compositional variability in petroleum substances
FUEL, 317.
author keywords: UVCB; Registration; Variability; IMS-MS
Sources: Web Of Science, NC State University Libraries
Added: May 10, 2022
2022 journal article
Characterization of population variability of 1,3-butadiene derived protein adducts in humans and mice
REGULATORY TOXICOLOGY AND PHARMACOLOGY, 132.
MeSH headings : Animals; Biomarkers; Butadienes / chemistry; Butadienes / metabolism; Butadienes / toxicity; Carcinogens / metabolism; Carcinogens / toxicity; Hemoglobins / metabolism; Humans; Mice
TL;DR:
Quantitative estimated from this study can be used to reduce uncertainties in the parameter estimates used in the models to derive the inhalation unit risk, as well as to address possible differences in variability in 1,3-butadiene metabolism that may be dose-related.
(via Semantic Scholar)
UN Sustainable Development Goal Categories
3. Good Health and Well-being
(Web of Science)
Source: Web Of Science
Added: June 6, 2022
2022 journal article
Correlation Analysis of Variables From the Atherosclerosis Risk in Communities Study
FRONTIERS IN PHARMACOLOGY, 13.
author keywords: cluster analysis; systems biology; meta-analysis as topic; ARIC; cardiovascular disease
TL;DR:
The data-driven approach can facilitate data harmonization and curation efforts by providing human annotators with groups of related variables reflecting the themes present in the data.
(via Semantic Scholar)
UN Sustainable Development Goal Categories
3. Good Health and Well-being
(Web of Science)
4. Quality Education
(OpenAlex)
11. Sustainable Cities and Communities
(Web of Science)
Source: Web Of Science
Added: August 8, 2022
2022 article
Fast Multivariate Probit Estimation via a Two-Stage Composite Likelihood
Ting, B., Wright, F., & Zhou, Y.-H. (2022, February 15). STATISTICS IN BIOSCIENCES, Vol. 2.
author keywords: Composite; Likelihood; Multivariate; Probit; Two-stage; Two-step
TL;DR:
This work proposes a fast method for multivariate probit estimation via a two-stage composite likelihood, and notes that the approach sets the stage for extensions beyond the purely binary setting.
(via Semantic Scholar)
UN Sustainable Development Goal Categories
3. Good Health and Well-being
(Web of Science)
Sources: Web Of Science, ORCID, NC State University Libraries
Added: February 15, 2022
2022 article
Genomic map of candidate human imprint control regions: the imprintome
Jima, D. D., Skaar, D. A., Planchart, A., Motsinger-Reif, A., Cevik, S. E., Park, S. S., … Hoyo, C. (2022, June 25). EPIGENETICS, Vol. 6.
author keywords: Epigenetics; genomic imprinting; foetal origins; whole genome; methylation; imprint control regions
MeSH headings : Adult; Humans; Genomic Imprinting; DNA Methylation; Chromosome Mapping; Alleles; Genomics
TL;DR:
This draft of the human imprintome will allow for the systematic determination of the role of early-acquired imprinting dysregulation in the pathogenesis of human diseases and developmental and behavioural disorders.
(via Semantic Scholar)
UN Sustainable Development Goal Categories
3. Good Health and Well-being
(Web of Science)
Sources: Web Of Science, NC State University Libraries, ORCID
Added: July 11, 2022
2022 journal article
Grouping of UVCB Substances with Dose-Response Transcriptomics Data from Human Cell-Based Assays
ALTEX-ALTERNATIVES TO ANIMAL EXPERIMENTATION, 39(3), 388–404.
MeSH headings : Biological Assay; Endothelial Cells; Humans; Induced Pluripotent Stem Cells; Petroleum; Transcriptome
TL;DR:
The results further demonstrate the value of NAMs for grouping of UVCBs, identify informative cell lines, and provide data that could be used for justifying selection of substances for further testing that may be required for registration.
(via Semantic Scholar)
UN Sustainable Development Goal Categories
3. Good Health and Well-being
(Web of Science)
11. Sustainable Cities and Communities
(Web of Science)
Sources: Web Of Science, NC State University Libraries
Added: August 29, 2022
2022 journal article
Identification and single-base gene-editing functional validation of a cis-EPO variant as a genetic predictor for EPO-increasing therapies
AMERICAN JOURNAL OF HUMAN GENETICS, 109(9), 1638–1652.
MeSH headings : Anemia / drug therapy; Anemia / genetics; Coronary Artery Disease / genetics; Genome-Wide Association Study; Humans; Mendelian Randomization Analysis; Myocardial Infarction / genetics; Renal Insufficiency, Chronic / genetics
TL;DR:
A combination of genetic and functional studies provides a powerful approach to investigate the potential therapeutic profile of EPO-increasing therapies for treating anemia in CKD.
(via Semantic Scholar)
UN Sustainable Development Goal Categories
3. Good Health and Well-being
(Web of Science; OpenAlex)
Source: Web Of Science
Added: November 21, 2022
2022 journal article
Leveraging TOPMed imputation server and constructing a cohort-specific imputation reference panel to enhance genotype imputation among cystic fibrosis patients
HUMAN GENETICS AND GENOMICS ADVANCES, 3(2).
TL;DR:
It is demonstrated that despite having ∼3% the sample size of TOPMed, the CFGP reference panel can still outperform TOPMed when imputing some CF disease-causing variants, likely due to allele and haplotype differences between CF patients and general populations.
(via Semantic Scholar)
UN Sustainable Development Goal Categories
3. Good Health and Well-being
(Web of Science)
Sources: Web Of Science, NC State University Libraries
Added: May 10, 2022
2022 journal article
MagicalRsq: Machine-learning-based genotype imputation quality calibration
AMERICAN JOURNAL OF HUMAN GENETICS, 109(11), 1986–1997.
MeSH headings : Humans; Genome-Wide Association Study / methods; Polymorphism, Single Nucleotide / genetics; Calibration; Genotype; Machine Learning
TL;DR:
MagicalRsq is proposed, a machine-learning-based method that integrates variant-level imputation and population genetics statistics, to provide a better calibrated imputation quality metric and will benefit downstream analysis by better distinguishing well-imputed variants from those poorly imputed.
(via Semantic Scholar)
UN Sustainable Development Goal Categories
3. Good Health and Well-being
(Web of Science)
Sources: Web Of Science, NC State University Libraries
Added: January 17, 2023
2022 journal article
Model systems and organisms for addressing inter- and intra-species variability in risk assessment
REGULATORY TOXICOLOGY AND PHARMACOLOGY, 132.
MeSH headings : Animals; Mice; Models, Theoretical; Risk Assessment; Toxicokinetics; Uncertainty
TL;DR:
It is concluded that population-based models are now beginning to realize their potential to address long-standing data gaps in inter- and intra-species variability.
(via Semantic Scholar)
UN Sustainable Development Goal Categories
3. Good Health and Well-being
(Web of Science)
11. Sustainable Cities and Communities
(Web of Science)
Source: Web Of Science
Added: August 15, 2022
2022 journal article
Pleiotropic modifiers of age-related diabetes and neonatal intestinal obstruction in cystic fibrosis
AMERICAN JOURNAL OF HUMAN GENETICS, 109(10), 1894–1908.
MeSH headings : Cystic Fibrosis / complications; Cystic Fibrosis / genetics; Cystic Fibrosis Transmembrane Conductance Regulator / genetics; Diabetes Mellitus / genetics; Genome-Wide Association Study; Humans; Infant, Newborn; Infant, Newborn, Diseases; Intestinal Obstruction / complications; Intestinal Obstruction / genetics
TL;DR:
Different loci modify risk of CFRD and MI; however, a subset exhibit pleiotropic effects indicating etiologic and mechanistic overlap between these two otherwise distinct complications of CF.
(via Semantic Scholar)
UN Sustainable Development Goal Categories
3. Good Health and Well-being
(Web of Science; OpenAlex)
Sources: Web Of Science, NC State University Libraries
Added: November 21, 2022
2022 journal article
Spatial and Temporal Analysis of Impacts of Hurricane Florence on Criteria Air Pollutants and Air Toxics in Eastern North Carolina
INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH, 19(3).
author keywords: air pollution; geospatial analyses; criteria pollutants; volatile organic compounds
MeSH headings : Air Pollutants / analysis; Air Pollution / analysis; Cyclonic Storms; Environmental Monitoring; North Carolina; Vehicle Emissions / analysis
UN Sustainable Development Goal Categories
3. Good Health and Well-being
(Web of Science)
11. Sustainable Cities and Communities
(Web of Science)
13. Climate Action
(OpenAlex)
Source: Web Of Science
Added: March 7, 2022
2022 article
TwinEQTL: ultrafast and powerful association analysis for eQTL and GWAS in twin studies
Xia, K., Shabalin, A. A., Yin, Z., Chung, W., Sullivan, P. F., Wright, F. A., … Zou, F. (2022, June 11). GENETICS.
author keywords: Twin; eQTL; GWAS
MeSH headings : Humans; Gene Frequency; Genome-Wide Association Study / methods; Linear Models; Polymorphism, Single Nucleotide; Quantitative Trait Loci
UN Sustainable Development Goal Categories
3. Good Health and Well-being
(Web of Science)
Source: Web Of Science
Added: July 11, 2022
2021 journal article
Application of Edible Montmorillonite Clays for the Adsorption and Detoxification of Microcystin
ACS APPLIED BIO MATERIALS, 4(9), 7254–7265.
Contributors: M. Wang *, K. Rivenbark *, J. Gong n , n & T. Phillips*
author keywords: adsorption isotherm; Hydra vulgaris; Lemna minor; Caenorhabditis elegans; molecular model; dietary sorbent
MeSH headings : Adsorption; Animals; Bentonite / chemistry; Caenorhabditis elegans; Charcoal / pharmacology; Clay / chemistry; Hydra; Microcystins / chemistry
TL;DR:
Edible montmorillonite clays were characterized for their ability to bind MC containing leucine and arginine under conditions simulating the gastrointestinal tract and compared with a medical-grade activated carbon and validated in a battery of living organisms, suggesting that edible montMorillonites are safe and efficacious binders for MC-LR.
(via Semantic Scholar)
UN Sustainable Development Goal Categories
6. Clean Water and Sanitation
(OpenAlex)
Sources: Web Of Science, NC State University Libraries, ORCID
Added: October 12, 2021
2021 journal article
Data Processing Workflow to Identify Structurally Related Compounds in Petroleum Substances Using Ion Mobility Spectrometry-Mass Spectrometry
ENERGY & FUELS, 35(13), 10529–10539.
TL;DR:
This work demonstrates how rapid untargeted IMS-MS analysis and the proposed data processing workflow can be used to provide confident compositional characterization of hydrocarbon-containing substances.
(via Semantic Scholar)
Sources: Web Of Science, NC State University Libraries
Added: July 26, 2021
2021 journal article
Environmental impacts of Hurricane Florence flooding in eastern North Carolina: temporal analysis of contaminant distribution and potential human health risks
JOURNAL OF EXPOSURE SCIENCE AND ENVIRONMENTAL EPIDEMIOLOGY, 31(5), 810–822.
author keywords: Disaster research response; Superfund; Chemical contaminants
MeSH headings : Cyclonic Storms; Environmental Monitoring; Gas Chromatography-Mass Spectrometry; Humans; Metals; North Carolina / epidemiology; Soil
TL;DR:
PAH and metals detected downstream from the coal ash storage pond that leaked were detected and were indicative of a pyrogenic source of contamination and PAH at these sites were of human health concern because cancer risk values exceeded 1 × 10−6 threshold.
(via Semantic Scholar)
UN Sustainable Development Goal Categories
3. Good Health and Well-being
(Web of Science)
Source: Web Of Science
Added: May 24, 2021
2021 journal article
Intra- and Inter-Species Variability in Urinary N7-(1-Hydroxy-3-buten-2-yl)guanine Adducts Following Inhalation Exposure to 1,3-Butadiene
CHEMICAL RESEARCH IN TOXICOLOGY, 34(11), 2375–2383.
MeSH headings : Animals; Butadienes / administration & dosage; Butadienes / metabolism; Butadienes / urine; Chromatography, Liquid; DNA Adducts / administration & dosage; DNA Adducts / metabolism; DNA Adducts / urine; Female; Inhalation Exposure; Male; Mice; Mice, Inbred Strains; Nanotechnology; Spectrometry, Mass, Electrospray Ionization
TL;DR:
Urinary EB-GII levels, particularly from human studies, may be useful for quantitative characterization of human variability in cancer risks to butadiene, and are largely consistent with UFH estimates for other chemicals based on human data for non-cancer endpoints.
(via Semantic Scholar)
UN Sustainable Development Goal Categories
3. Good Health and Well-being
(Web of Science)
Source: Web Of Science
Added: November 29, 2021
2021 journal article
Potential Human Health Hazard of Post-Hurricane Harvey Sediments in Galveston Bay and Houston Ship Channel: A Case Study of Using In Vitro Bioactivity Data to Inform Risk Management Decisions
INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH, 18(24).
author keywords: new approach methods (NAMs); environmental mixtures; disaster research
MeSH headings : Bays; Cyclonic Storms; Disasters; Environmental Monitoring; Geologic Sediments; Humans; Polycyclic Aromatic Hydrocarbons / analysis; Risk Management; Water Pollutants, Chemical / analysis; Water Pollutants, Chemical / toxicity
TL;DR:
It is found that in vitro bioactivity can be used as a comprehensive indicator of potential hazards and is an example of a new approach method (NAM) to inform risk management decisions on site cleanup.
(via Semantic Scholar)
UN Sustainable Development Goal Categories
3. Good Health and Well-being
(Web of Science)
11. Sustainable Cities and Communities
(Web of Science)
13. Climate Action
(OpenAlex)
Sources: Web Of Science, ORCID, NC State University Libraries
Added: December 20, 2021
2021 journal article
Relationships between constituents of energy drinks and beating parameters in human induced pluripotent stem cell (iPSC)-Derived cardiomyocytes
FOOD AND CHEMICAL TOXICOLOGY, 149.
author keywords: Cardiovascular; Heart rate; QT interval; Theophylline; Adenine; Azelate
MeSH headings : Calcium / metabolism; Cell Differentiation; Cell Survival / drug effects; Drug-Related Side Effects and Adverse Reactions; Energy Drinks / analysis; Heart Diseases / chemically induced; Humans; Induced Pluripotent Stem Cells / drug effects; Myocytes, Cardiac / drug effects; Risk Assessment
TL;DR:
It was found that some of the energy drinks elicited adverse effects on the cardiomyocytes with the most common being an increase in the beat rate, while QT prolongation was also observed at the lowest concentrations.
(via Semantic Scholar)
UN Sustainable Development Goal Categories
3. Good Health and Well-being
(Web of Science)
7. Affordable and Clean Energy
(OpenAlex)
Sources: Web Of Science, ORCID, NC State University Libraries
Added: February 4, 2021
2021 personal communication
The COVID-19 Pandemic Vulnerability Index (PVI) Dashboard: Monitoring County-Level Vulnerability Using Visualization, Statistical Modeling, and Machine Learning
Marvel, S. W., House, J. S., Wheeler, M., Song, K., Zhou, Y.-H., Wright, F. A., … Reif, D. M. (2021, January).
Contributors: S. Marvel n, J. House* , M. Wheeler *, K. Song n, Y. Zhou n , n, W. Chiu *, I. Rusyn *, A. Motsinger-Reif*, D. Reif n
MeSH headings : COVID-19 / epidemiology; Data Visualization; Health Status Indicators; Humans; Machine Learning; Models, Statistical; Vulnerable Populations
UN Sustainable Development Goal Categories
3. Good Health and Well-being
(Web of Science)
Sources: Web Of Science, NC State University Libraries, ORCID
Added: March 22, 2021
2020 journal article
Classification of estrogenic compounds by coupling high content analysis and machine learning algorithms
PLOS COMPUTATIONAL BIOLOGY, 16(9).
MeSH headings : Algorithms; Cell Line; Estrogens / classification; Estrogens / metabolism; Humans; Machine Learning; Receptors, Estrogen / metabolism
TL;DR:
A machine learning pipeline for rapid, accurate, and sensitive assessment of the endocrine-disrupting potential of benchmark chemicals based on data generated from high content analysis showed that highly accurate and generalized classification models with a minimum number of features can be constructed without loss of generality.
(via Semantic Scholar)
UN Sustainable Development Goal Categories
3. Good Health and Well-being
(Web of Science)
11. Sustainable Cities and Communities
(Web of Science)
Source: Web Of Science
Added: October 26, 2020
2020 journal article
Grouping of UVCB Substances with New Approach Methodologies (NAMs) Data
ALTEX-ALTERNATIVES TO ANIMAL EXPERIMENTATION, 38(1), 123–137.
Contributors: J. House n , F. Grimm, W. Klaren, A. Dalzell, S. Kuchi, S. Zhang, K. Lenz, P. Boogaard
MeSH headings : Animal Testing Alternatives / methods; Hazardous Substances / chemistry; Hazardous Substances / toxicity; Humans; Induced Pluripotent Stem Cells / drug effects; Petroleum / analysis; Petroleum / toxicity; Toxicity Tests / methods
TL;DR:
It is demonstrated that in vitro test-derived biological activity signatures, including bioactivity from human induced pluripotent stem cell and primary cells, can be used to inform groupings of UVCBs, to assist in identification of representative substances in each group for testing when needed, and to fill data gaps by read-across.
(via Semantic Scholar)
UN Sustainable Development Goal Categories
3. Good Health and Well-being
(Web of Science)
11. Sustainable Cities and Communities
(Web of Science)
Sources: Web Of Science, ORCID, NC State University Libraries
Added: March 15, 2021
2020 journal article
Low-Dose Silver Nanoparticle Surface Chemistry and Temporal Effects on Gene Expression in Human Liver Cells
SMALL, 16(21).
Contributors: J. House n , E. Bouzos*, K. Fahy *, V. Francisco*, D. Lloyd n, n, A. Motsinger-Reif*, P. Asuri *, K. Wheeler *
author keywords: nanotoxicity; silver nanoparticles; transcriptomics
MeSH headings : Gene Expression / drug effects; Hepatocytes / drug effects; Humans; Metal Nanoparticles / chemistry; Silver; Surface Properties; Time Factors
TL;DR:
Universal to all surface coatings, AgNP-treated cells responded by inactivating proliferation and enabling cell cycle checkpoints, which provide a foundation for understanding hepatic response to low-dose AgNPs for future risk assessment.
(via Semantic Scholar)
UN Sustainable Development Goal Categories
3. Good Health and Well-being
(Web of Science)
Sources: Web Of Science, ORCID, NC State University Libraries
Added: April 14, 2020
2020 personal communication
Questioning Existing Cancer Hazard Evaluation Standards in the Name of Statistics
Rusyn, I., Chiu, W. A., & Wright, F. A. (2020, October).
MeSH headings : Biological Assay; Glycine / analogs & derivatives; Humans; Neoplasms / epidemiology; Reference Standards
TL;DR:
This argument sets a potentially far-reaching precedent to revisit decades of standard practice of cancer hazard evaluation performed by national and international agencies, and proposes a very high bar to classify a chemical as positive in a rodent bioassay.
(via Semantic Scholar)
UN Sustainable Development Goal Categories
3. Good Health and Well-being
(Web of Science)
11. Sustainable Cities and Communities
(Web of Science)
Source: Web Of Science
Added: December 14, 2020
2020 journal article
Rapid Hazard Characterization of Environmental Chemicals Using a Compendium of Human Cell Lines from Different Organs
ALTEX-ALTERNATIVES TO ANIMAL EXPERIMENTATION, 37(4), 623–638.
TL;DR:
The potential of this in vitro screening model for rapidly evaluating potential hazards of chemicals using a small number of human cells is demonstrated to inform rapid risk-based decision-making through ranking, clustering, and assessment of both hazard and risks of diverse environmental chemicals.
(via Semantic Scholar)
UN Sustainable Development Goal Categories
3. Good Health and Well-being
(Web of Science)
11. Sustainable Cities and Communities
(Web of Science)
Source: Web Of Science
Added: February 15, 2021
2020 journal article
Risk Characterization of Environmental Samples Using In Vitro Bioactivity and Polycyclic Aromatic Hydrocarbon Concentrations Data
TOXICOLOGICAL SCIENCES, 179(1), 108–120.
author keywords: polycyclic aromatic hydrocarbons; mixtures toxicology; in vitro models; iPSC; humanized models; human risk assessment; risk assessment; new approach methods; bioactivity; spatial analysis
MeSH headings : Cyclonic Storms; Endothelial Cells; Environmental Exposure / adverse effects; Environmental Monitoring; Humans; Polycyclic Aromatic Hydrocarbons / toxicity
TL;DR:
This work sets the stage for identification of the areas of concern and direct quantitative risk characterization based on bioactivity data, thereby providing an important supplement to traditional individual chemical analyses by shedding light on constituents that may be missed from targeted chemical monitoring.
(via Semantic Scholar)
UN Sustainable Development Goal Categories
3. Good Health and Well-being
(Web of Science)
11. Sustainable Cities and Communities
(Web of Science)
Source: Web Of Science
Added: March 15, 2021
2020 journal article
Systematic Comparisons for Composition Profiles, Taxonomic Levels, and Machine Learning Methods for Microbiome-Based Disease Prediction
FRONTIERS IN MOLECULAR BIOSCIENCES, 7.
author keywords: phenotype prediction; machine learning method; k-mers; operational taxonomic unit (OTU); amplicon sequence variant (ASV); phylogenetic analysis
TL;DR:
The use of short k-mers, which have computational advantages and conceptual simplicity, is shown to be effective as a source for microbiome-based prediction, among machine-learning approaches, and tree-based methods show consistent, though modest, advantages in prediction accuracy.
(via Semantic Scholar)
UN Sustainable Development Goal Categories
3. Good Health and Well-being
(Web of Science)
Sources: Web Of Science, NC State University Libraries
Added: January 19, 2021
2020 journal article
The GTEx Consortium atlas of genetic regulatory effects across human tissues
SCIENCE, 369(6509), 1318–1330.
MeSH headings : Datasets as Topic; Disease / genetics; Female; Gene Expression Regulation; Genome-Wide Association Study; Humans; Male; Organ Specificity; Quantitative Trait Loci; Sequence Analysis, RNA
TL;DR:
Leveraging the large diversity of tissues, insights are provided into the tissue specificity of genetic effects and it is shown that cell type composition is a key factor in understanding gene regulatory mechanisms in human tissues.
(via Semantic Scholar)
UN Sustainable Development Goal Categories
3. Good Health and Well-being
(Web of Science)
Source: Web Of Science
Added: November 16, 2020
2019 journal article
A New Liver Expression Quantitative Trait Locus Map From 1,183 Individuals Provides Evidence for Novel Expression Quantitative Trait Loci of Drug Response, Metabolic, and Sex-Biased Phenotypes
CLINICAL PHARMACOLOGY & THERAPEUTICS, 107(6), 1383–1393.
MeSH headings : Adolescent; Adult; Aged; Aged, 80 and over; Antineoplastic Agents / adverse effects; Antineoplastic Agents / pharmacology; Child; Child, Preschool; Female; Gene Expression Regulation / genetics; Genetic Variation; Genome-Wide Association Study; Genotype; Humans; Hypolipidemic Agents / pharmacology; Infant; Liver / metabolism; Male; Middle Aged; Phenotype; Proprotein Convertase 9 / genetics; Quantitative Trait Loci / genetics; Receptors, G-Protein-Coupled / genetics; Sex Factors; Young Adult
TL;DR:
Translational relevance of these results is evidenced by linking DPYD eQTLs to differences in safety of chemotherapy, linking the sex‐biased regulation of PCSK9 expression to anti‐lipid therapy, and identifying the G‐protein coupled receptor GPR180 as a novel drug target for hypertriglyceridemia.
(via Semantic Scholar)
UN Sustainable Development Goal Categories
3. Good Health and Well-being
(Web of Science; OpenAlex)
Sources: Web Of Science, NC State University Libraries
Added: February 10, 2020
2019 article
Development of the Texas A&M Superfund Research Program Computational Platform for Data Integration, Visualization, and Analysis
29TH EUROPEAN SYMPOSIUM ON COMPUTER AIDED PROCESS ENGINEERING, PT A, Vol. 46, pp. 967–972.
author keywords: Data analytics; data integration; statistical analysis; collaborative networks
TL;DR:
The Texas A&M Superfund Research Program computational platform is demonstrated, which houses and integrates large-scale, diverse datasets generated across the Center, provides basic visualization service to facilitate interpretation, monitors data quality, and finally implements a variety of state-of-the-art statistical analysis for model/tool development.
(via Semantic Scholar)
UN Sustainable Development Goal Categories
3. Good Health and Well-being
(Web of Science)
11. Sustainable Cities and Communities
(Web of Science)
Source: Web Of Science
Added: November 25, 2019
2019 journal article
Grouping of complex substances using analytical chemistry data: A framework for quantitative evaluation and visualization
PLOS ONE, 14(10).
Contributors: M. Onel*, B. Beykal *, K. Ferguson *, W. Chiu *, T. McDonald *, L. Zhou *, J. House n , n
MeSH headings : Chemistry Techniques, Analytical / methods; Gas Chromatography-Mass Spectrometry; Petroleum / analysis; Principal Component Analysis; Reference Standards; Sample Size
TL;DR:
A framework with unsupervised and supervised analyses to optimally group complex substances based on their analytical features is proposed and a quantitative comparative assessment of clustering results via Fowlkes–Mallows index, and classification results via model accuracies in predicting the group of an unknown complex substance is presented.
(via Semantic Scholar)
UN Sustainable Development Goal Categories
3. Good Health and Well-being
(Web of Science)
11. Sustainable Cities and Communities
(Web of Science)
Sources: Web Of Science, ORCID, NC State University Libraries
Added: June 1, 2020
2019 journal article
Population-Based Analysis of DNA Damage and Epigenetic Effects of 1,3-Butadiene in the Mouse
CHEMICAL RESEARCH IN TOXICOLOGY, 32(5), 887–898.
MeSH headings : Animals; Butadienes / toxicity; Carcinogens, Environmental / toxicity; DNA Adducts / chemistry; DNA Adducts / genetics; DNA Adducts / metabolism; DNA Methylation / drug effects; Epigenesis, Genetic / drug effects; Guanine / analogs & derivatives; Guanine / chemistry; Histones / metabolism; Kidney / drug effects; Liver / drug effects; Lung / drug effects; Male; Mice; Mutagens / toxicity
TL;DR:
1,3-butadiene is used to demonstrate how the Collaborative Cross mouse population can be used to identify the mechanisms for and quantify the degree of interindividual variability in tissue-specific effects that are relevant to chemically induced carcinogenesis.
(via Semantic Scholar)
UN Sustainable Development Goal Categories
3. Good Health and Well-being
(Web of Science; OpenAlex)
Source: Web Of Science
Added: June 17, 2019
2019 journal article
Using Collaborative Cross Mouse Population to Fill Data Gaps in Risk Assessment: A Case Study of Population-Based Analysis of Toxicokinetics and Kidney Toxicodynamics of Tetrachloroethylene
ENVIRONMENTAL HEALTH PERSPECTIVES, 127(6).
MeSH headings : Animals; Collaborative Cross Mice; Glutathione / analogs & derivatives; Glutathione / metabolism; Hepatitis A Virus Cellular Receptor 1 / genetics; Hepatitis A Virus Cellular Receptor 1 / metabolism; Kidney / drug effects; Kidney Diseases / chemically induced; Kidney Diseases / metabolism; Liver / drug effects; Male; Risk Assessment / methods; Species Specificity; Tetrachloroethylene / metabolism; Tetrachloroethylene / pharmacokinetics; Tetrachloroethylene / toxicity; Toxicokinetics
TL;DR:
The utility of the CC mouse population is demonstrated in characterizing metabolism–toxicity interactions and quantifying interindividual variability and the default uncertainty factor for human variability may be marginally adequate to protect 95%, but not more, of the population for kidney toxicity mediated by PERC.
(via Semantic Scholar)
UN Sustainable Development Goal Categories
3. Good Health and Well-being
(Web of Science)
Source: Web Of Science
Added: July 29, 2019
2018 journal article
A Human Population-Based Organotypic In Vitro Model for Cardiotoxicity Screening
ALTEX-ALTERNATIVES TO ANIMAL EXPERIMENTATION, 35(4), 441–452.
Contributors: F. Grimm *, A. Blanchette, J. House , K. Ferguson, N. Hsieh, C. Dalaijamts, A. Wright, B. Anson
MeSH headings : Cardiotoxicity / genetics; Cardiovascular Agents / pharmacology; Cardiovascular Agents / toxicity; Cell Differentiation / drug effects; Cell Differentiation / genetics; Female; Healthy Volunteers; Humans; In Vitro Techniques; Induced Pluripotent Stem Cells / cytology; Induced Pluripotent Stem Cells / drug effects; Male; Myocytes, Cardiac / drug effects; Myocytes, Cardiac / physiology; Phenotype; Reproducibility of Results
TL;DR:
iPSC-derived cardiomyocytes exhibited reproducible donor-specific differences in baseline function and drug-induced effects, demonstrating the feasibility of using a panel of population-based organotypic cells from healthy donors as an animal replacement experimental model to quantify inter-individual variability in xenobiotic responses.
(via Semantic Scholar)
UN Sustainable Development Goal Categories
3. Good Health and Well-being
(Web of Science)
Sources: Web Of Science, ORCID, NC State University Libraries
Added: December 10, 2018
2018 journal article
A common allele in FGF21 associated with sugar intake is associated with body shape, lower total body-fat percentage, and higher blood pressure
Cell Reports, 23(2), 327–336.
Source: NC State University Libraries
Added: August 6, 2018
2018 journal article
Airway mucosal host defense is key to genomic regulation of cystic fibrosis lung disease severity
American Journal of Respiratory and Critical Care Medicine, 197(1), 79–93.
Source: NC State University Libraries
Added: August 6, 2018
2018 journal article
HT-eQTL: integrative expression quantitative trait loci analysis in a large number of human tissues
BMC Bioinformatics, 19.
Source: NC State University Libraries
Added: August 6, 2018
2018 journal article
Multi-dimensional in vitro bioactivity profiling for grouping of glycol ethers
REGULATORY TOXICOLOGY AND PHARMACOLOGY, 101, 91–102.
Contributors: F. Grimm *, J. House n , M. Wilson*, O. Sirenko*, Y. Iwata*, n, N. Ball, I. Rusyn *
author keywords: New assessment methodologies; Glycol ethers; In vitro; ToxPi; Read-across; Safety assessment
MeSH headings : Animals; Cell Line; Ethers / classification; Ethers / toxicity; Glycols / classification; Glycols / toxicity; Humans; Risk Assessment; Solvents / classification; Solvents / toxicity; Toxicity Tests
TL;DR:
In this study, a suite of organotypic and population‐based in vitro models are applied for comprehensive bioactivity profiling of twenty E‐Series and P‐Series glycol ethers, solvents with a broad variation in toxicity ranging from relatively non‐toxic to reproductive and hematopoetic system toxicants.
(via Semantic Scholar)
UN Sustainable Development Goal Categories
3. Good Health and Well-being
(Web of Science)
11. Sustainable Cities and Communities
(Web of Science)
Sources: Web Of Science, ORCID, NC State University Libraries
Added: April 22, 2019
2018 journal article
Periconceptional maternal mediterranean diet is associated with favorable offspring behaviors and altered CpG methylation of imprinted genes
Frontiers in Cell and Developmental Biology, 6(SEP), 107.
Contributors: J. House n , M. Mendez*, R. Maguire n, S. Gonzalez-Nahm *, Z. Huang *, J. Daniels *, S. Murphy *, B. Fuemmeler *, n, C. Hoyo n
TL;DR:
In this ethnically diverse cohort, maternal adherence to a Mediterranean diet in early pregnancy was associated with favorable neurobehavioral outcomes in early childhood and with sex-dependent methylation differences of MEG3, IGF2, and SGCE/PEG10 DMRs.
(via Semantic Scholar)
UN Sustainable Development Goal Categories
3. Good Health and Well-being
(Web of Science)
Sources: NC State University Libraries, ORCID, NC State University Libraries
Added: January 21, 2019
2018 journal article
Polyphasic characterization of four soil-derived phenanthrene-degrading Acidovorax strains and proposal of Acidovorax carolinensis sp nov.
SYSTEMATIC AND APPLIED MICROBIOLOGY, 41(5), 460–472.
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
Population-based dose-response analysis of liver transcriptional response to trichloroethylene in mouse
MAMMALIAN GENOME, 29(1-2), 168–181.
Contributors: A. Venkatratnam*, J. House n , K. Konganti*, C. McKenney n, D. Threadgill *, W. Chiu *, D. Aylor n, n, I. Rusyn *
MeSH headings : Animals; Dose-Response Relationship, Drug; Genetics, Population; Kidney / drug effects; Kidney / metabolism; Liver / drug effects; Liver / metabolism; Mice; Transcription, Genetic / drug effects; Transcriptome / genetics; Trichloroacetic Acid / metabolism; Trichloroethylene / toxicity
TL;DR:
The usefulness of mouse population-based studies in assessing inter-individual variation in toxicological responses is highlighted, but it is cautioned that genetic mapping may be challenging because of the complexity in gene exposure–dose relationships.
(via Semantic Scholar)
UN Sustainable Development Goal Categories
3. Good Health and Well-being
(Web of Science; OpenAlex)
Sources: Web Of Science, ORCID, NC State University Libraries
Added: August 6, 2018
2018 journal article
ToxPi Graphical User Interface 2.0: Dynamic exploration, visualization, and sharing of integrated data models
BMC Bioinformatics, 19.
Source: NC State University Libraries
Added: August 6, 2018
2017 journal article
A Pipeline for high-throughput concentration response modeling of gene expression for toxicogenomics
Frontiers in Genetics, 8.
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.
Source: NC State University Libraries
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
Adrenal-derived stress hormones modulate ozone-induced lung injury and inflammation
TOXICOLOGY AND APPLIED PHARMACOLOGY, 329, 249–258.
Contributors: A. Henriquez *, J. House n , D. Miller*, S. Snow *, A. Fisher*, H. Ren*, M. Schladweiler *, A. Ledbetter*, n, U. Kodavanti *
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)
Sources: Web Of Science, ORCID
Added: August 6, 2018
2017 journal article
An empirical Bayes approach for multiple tissue eQTL analysis
Biostatistics (Oxford, England), 19(3), 391–406.
MeSH headings : Bayes Theorem; Biostatistics / methods; Gene Expression; Genomics / methods; Genotyping Techniques / methods; Humans; Models, Statistical; Quantitative Trait Loci
TL;DR:
A hierarchical Bayesian model (MT‐eQTL) for multi‐tissue eQTL analysis that explicitly captures patterns of variation in the presence or absence of eQ TL, as well as the heterogeneity of effect sizes across tissues is developed.
(via Semantic Scholar)
UN Sustainable Development Goal Categories
3. Good Health and Well-being
(Web of Science)
Source: NC State University Libraries
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
Computation of ancestry scores with mixed families and unrelated individuals
BIOMETRICS, 74(1), 155–164.
author keywords: Genetic association; Population stratification; Principal components
MeSH headings : Cystic Fibrosis / genetics; Family; Genome; Genotype; Humans; Models, Genetic; Pedigree; Principal Component Analysis
TL;DR:
Two main novel strategies are considered: matrix substitution based on decomposition of a target family‐orthogonalized covariance matrix, and using family‐averaged data to obtain loadings using the family‐average method, which shows superior performance.
(via Semantic Scholar)
UN Sustainable Development Goal Categories
3. Good Health and Well-being
(Web of Science)
Sources: Web Of Science, ORCID, NC State University Libraries
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
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
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
Estimation of cis-eQTL effect sizes using a log of linear model
BIOMETRICS, 74(2), 616–625.
author keywords: eQTL analyses; EQTL effect size; Multiple testing; Nonlinear regression
MeSH headings : Algorithms; Alleles; Gene Expression; Humans; Linear Models; Quantitative Trait Loci; Statistics as Topic
TL;DR:
A new, log‐of‐linear model for eQTL action is proposed, termed ACME, that captures allelic contributions to cis‐acting eZTLs in an additive fashion, yielding effect size estimates that correspond to a biologically coherent model of cis‐eQTLs.
(via Semantic Scholar)
UN Sustainable Development Goal Categories
3. Good Health and Well-being
(Web of Science)
Sources: Web Of Science, ORCID, NC State University Libraries
Added: October 16, 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
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)
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
Genetic effects on gene expression across human tissues
Nature, 550(7675), 204-.
Source: NC State University Libraries
Added: August 6, 2018
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
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
2016 journal article
A chemical-biological similarity-based grouping of complex substances as a prototype approach for evaluating chemical alternatives
GREEN CHEMISTRY, 18(16), 4407–4419.
Contributors: F. Grimm *, Y. Iwata*, O. Sirenko*, G. Chappell *, n, D. Reif n , J. Braisted *, D. Gerhold *
TL;DR:
An experimental and computational approach to categorizing UVCBs according to chemical and biological similarities is presented.
(via Semantic Scholar)
UN Sustainable Development Goal Categories
3. Good Health and Well-being
(Web of Science)
11. Sustainable Cities and Communities
(Web of Science)
Sources: Web Of Science, ORCID, NC State University Libraries
Added: August 6, 2018
2016 journal article
Erratum: Corrigendum: Synchronized age-related gene expression changes across multiple tissues in human and the link to complex diseases
Scientific Reports, 6(1), 19384.
TL;DR:
This work catalogueed age-related gene expression changes in nine tissues from nearly two hundred individuals collected by the Genotype-Tissue Expression (GTEx) project, finding the aging gene expression signatures are very tissue specific and enrichment for some well-known aging components such as mitochondrial biology is observed in many tissues.
(via Semantic Scholar)
Source: Crossref
Added: January 4, 2021
2016 journal article
Gene expression in major depressive disorder
Molecular Psychiatry, 21(3), 339–347.
Source: NC State University Libraries
Added: August 6, 2018
2016 journal article
Homologous recombination and translesion DNA synthesis play critical roles on tolerating DNA damage caused by trace levels of hexavalent chromium
PLoS One, 11(12).
Source: NC State University Libraries
Added: August 6, 2018
2016 journal article
Integrative approaches for large-scale transcriptome-wide association studies
Nature Genetics, 48(3), 245–252.
MeSH headings : Animals; Gene Expression Regulation / genetics; Genetic Predisposition to Disease; Genome-Wide Association Study; Genotype; Humans; Mice; Obesity / genetics; Obesity / pathology; Phenotype; Quantitative Trait Loci / genetics; Transcriptome / genetics
UN Sustainable Development Goal Categories
3. Good Health and Well-being
(Web of Science)
Source: Crossref
Added: February 24, 2020
2016 journal article
Integrative approaches for large-scale transcriptome-wide association studies
Nature Genetics, 48(3), 245–252.
Source: NC State University Libraries
Added: August 6, 2018
2016 conference paper
Poster: risk-based attack surface approximation
Symposium and Bootcamp on the Science of Security, 121–123.
Source: NC State University Libraries
Added: August 6, 2018
2016 journal article
The projack: a resampling approach to correct for ranking bias in high-throughput studies
Biostatistics (Oxford, England), 17(1), 54–64.
Source: NC State University Libraries
Added: August 6, 2018
2015 journal article
Consistent testing for recurrent genomic aberrations
BIOMETRIKA, 102(4), 783–796.
author keywords: Consistency; DNA copy number; DNA methylation; Genome-wide association study; Hypothesis testing
TL;DR:
The analysis establishes the consistency of cyclic shift values for datasets with a fixed set of samples as the number of observed variables tends to infinity, under the assumption that each sample is an independent realization of a stationary Markov chain.
(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
2015 journal article
Erratum: Gene expression in major depressive disorder
Molecular Psychiatry, 21(3), 444–444.
TL;DR:
The authors noticed that the Supplementary Figure legends were not published with the paper, and the legends accompany this erratum.
(via Semantic Scholar)
Source: Crossref
Added: August 28, 2020
2015 journal article
Erratum: Prediction of human population responses to toxic compounds by a collaborative competition
Nature Biotechnology, 33(10), 1109–1109.
TL;DR:
The authors have added 12 additional authors to the list of “Other participants in the NIEHS-NCATS-UNC DREAM Toxicogenetics Collaboration,” including Alok Jaiswal, Antti Poso, Himanshu Chheda, Ismeet Kaur, Jing Tang, John-Patrick Mpindi, Krister Wennerberg, Natalio Krasnogor, Samuel Kaski and Tero Aittokallio.
(via Semantic Scholar)
Source: Crossref
Added: February 24, 2020
2015 journal article
Gene Expression in Transformed Lymphocytes Reveals Variation in Endomembrane and HLA Pathways Modifying Cystic Fibrosis Pulmonary Phenotypes
The American Journal of Human Genetics, 96(2), 318–328.
MeSH headings : Cystic Fibrosis / genetics; Cystic Fibrosis / pathology; Endoplasmic Reticulum Stress / genetics; Gene Expression Profiling; Genes, MHC Class I / genetics; Genetic Variation; Humans; Linear Models; Phenotype; Receptors, Lysophosphatidic Acid / genetics; Sequence Deletion / genetics
TL;DR:
Gene expression provided a powerful tool to identify unrecognized heritable variation, complementing ongoing GWASs in this rare disease and enriched for heritable genetic variation and expression quantitative traits.
(via Semantic Scholar)
UN Sustainable Development Goal Categories
3. Good Health and Well-being
(Web of Science; OpenAlex)
Sources: Crossref, NC State University Libraries
Added: August 6, 2018
2015 journal article
Gene expression in major depressive disorder
Molecular Psychiatry, 21(3), 339–347.
MeSH headings : Adult; Anxiety Disorders / genetics; Cross-Sectional Studies; Depressive Disorder, Major / diagnosis; Depressive Disorder, Major / genetics; Female; Gene Expression / genetics; Gene Expression Regulation / genetics; Genetic Predisposition to Disease / genetics; Genome-Wide Association Study; Humans; Interleukin-6 / genetics; Interleukin-6 / metabolism; Killer Cells, Natural / metabolism; Longitudinal Studies; Male; Middle Aged; Polymorphism, Single Nucleotide / genetics; Signal Transduction / genetics
TL;DR:
Multiple gene expression associations with MDD were identified and a measurable impact of current MDD state on gene expression is suggested, in line with the immune suppression and immune activation hypothesis of MDD.
(via Semantic Scholar)
UN Sustainable Development Goal Categories
3. Good Health and Well-being
(Web of Science; OpenAlex)
Source: Crossref
Added: August 28, 2020
2015 journal article
Genome-wide association meta-analysis identifies five modifier loci of lung disease severity in cystic fibrosis
Nature Communications, 6(1).
MeSH headings : Adolescent; Adult; Amino Acid Transport Systems; Amino Acid Transport Systems, Neutral / genetics; Child; Cystic Fibrosis / genetics; Cystic Fibrosis / metabolism; Cystic Fibrosis / pathology; Female; Genome-Wide Association Study; Humans; Lung / metabolism; Lung / pathology; Male; Middle Aged; Mucin-4 / genetics; Mucins / genetics; Severity of Illness Index; Transcription Factors / genetics; Young Adult
UN Sustainable Development Goal Categories
3. Good Health and Well-being
(Web of Science; OpenAlex)
Source: Crossref
Added: February 5, 2020
2015 journal article
Genome-wide association meta-analysis identifies five modifier loci of lung disease severity in cystic fibrosis
Nature Communications, 6.
Source: NC State University Libraries
Added: August 6, 2018
2015 journal article
Hypothesis testing at the extremes: fast and robust association for high-throughput data
BIOSTATISTICS, 16(3), 611–625.
author keywords: Density approximation; Exact testing; Permutation
MeSH headings : Biostatistics; Breast Neoplasms / genetics; Computer Simulation; Cystic Fibrosis / genetics; Databases, Nucleic Acid / statistics & numerical data; Female; High-Throughput Nucleotide Sequencing / statistics & numerical data; High-Throughput Screening Assays / statistics & numerical data; Humans; Likelihood Functions; Linear Models; Polymorphism, Single Nucleotide; Sample Size; Software
TL;DR:
An approximation to exact association tests of trend that is accurate and fast enough for standard use in high-throughput settings, and can easily provide standard two-sided or doubled [Formula: see text]-values is presented.
(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
2015 journal article
Identification of Novel Gene Targets and Putative Regulators of Arsenic-Associated DNA Methylation in Human Urothelial Cells and Bladder Cancer
Chemical Research in Toxicology, 28(6), 1144–1155.
MeSH headings : Adult; Aged; Arsenic / metabolism; Arsenic / toxicity; Cell Transformation, Neoplastic / chemically induced; DNA Methylation / drug effects; DNA Methylation / genetics; Female; Humans; Middle Aged; Urinary Bladder Neoplasms / chemically induced; Urinary Bladder Neoplasms / genetics; Urinary Bladder Neoplasms / pathology; Urothelium / cytology; Urothelium / drug effects; Young Adult
TL;DR:
Both the arsenic- and cancer-associated genes are enriched for the binding sites of common transcription factors known to play roles in carcinogenesis, demonstrating a novel potential mechanistic link between iAs exposure and bladder cancer.
(via Semantic Scholar)
UN Sustainable Development Goal Categories
3. Good Health and Well-being
(Web of Science; OpenAlex)
6. Clean Water and Sanitation
(Web of Science)
Source: Crossref
Added: February 5, 2020
2015 journal article
Identification of novel gene targets and putative regulators of arsenic-associated DNA methylation in human urothelial cells and bladder cancer
Chemical Research in Toxicology, 28(6), 1144–1155.
Source: NC State University Libraries
Added: August 6, 2018
2015 journal article
In vitro screening for population variability in toxicity of pesticide-containing mixtures
ENVIRONMENT INTERNATIONAL, 85, 147–155.
Contributors: N. Abdo *, B. Wetmore *, G. Chappell *, D. Shea n , n & I. Rusyn *
author keywords: Pesticide; Mixture; Population
MeSH headings : Black People / genetics; Cell Culture Techniques; Cell Line; Cell Survival / drug effects; Cell Survival / genetics; Complex Mixtures / analysis; Complex Mixtures / toxicity; Dose-Response Relationship, Drug; Genome-Wide Association Study; Genotype; Hazardous Substances / analysis; Hazardous Substances / toxicity; Humans; Hydrocarbons, Chlorinated / analysis; Hydrocarbons, Chlorinated / toxicity; Multivariate Analysis; Pesticides / analysis; Pesticides / toxicity; Polymorphism, Genetic; Reproducibility of Results; White People / genetics
TL;DR:
A combination of in vitro human population-based cytotoxicity screening followed by dosimetric adjustment and comparative population genomics analyses enables quantitative evaluation of human health hazard from complex environmental mixtures.
(via Semantic Scholar)
UN Sustainable Development Goal Categories
3. Good Health and Well-being
(Web of Science)
6. Clean Water and Sanitation
(OpenAlex)
11. Sustainable Cities and Communities
(Web of Science)
Sources: Web Of Science, ORCID, NC State University Libraries
Added: August 6, 2018
2015 journal article
Population-Based in Vitro Hazard and Concentration-Response Assessment of Chemicals: The 1000 Genomes High-Throughput Screening Study
ENVIRONMENTAL HEALTH PERSPECTIVES, 123(5), 458–466.
MeSH headings : Cell Line, Tumor; Genome-Wide Association Study / methods; Genotype; Humans; Risk Assessment; Toxicity Tests / methods
TL;DR:
This experimental approach fills critical gaps unaddressed by recent large-scale toxicity testing programs, providing quantitative, experimentally based estimates of human toxicodynamic variability, and also testable hypotheses about mechanisms contributing to interindividual variation.
(via Semantic Scholar)
UN Sustainable Development Goal Categories
3. Good Health and Well-being
(Web of Science)
11. Sustainable Cities and Communities
(Web of Science)
Source: Web Of Science
Added: August 6, 2018
2015 journal article
Prediction of human population responses to toxic compounds by a collaborative competition
Nature Biotechnology, 33(9), 933–940.
MeSH headings : Computer Simulation; Dose-Response Relationship, Drug; Genetic Predisposition to Disease / genetics; Genetics, Population; Hazardous Substances / toxicity; High-Throughput Screening Assays / methods; Humans; Incidence; Lymphocytes / cytology; Lymphocytes / drug effects; Lymphocytes / physiology; Models, Genetic; Risk Assessment / methods; Toxicity Tests / methods
TL;DR:
The results from a community-based DREAM challenge to predict toxicities of environmental compounds with potential adverse health effects for human populations highlight the possibility of predicting health risks associated with unknown compounds, although risk estimation accuracy remains suboptimal.
(via Semantic Scholar)
UN Sustainable Development Goal Categories
3. Good Health and Well-being
(Web of Science)
11. Sustainable Cities and Communities
(Web of Science)
Source: Crossref
Added: February 24, 2020
2015 journal article
Prediction of human population responses to toxic compounds by a collaborative competition
Nature Biotechnology, 33(9), 933–172.
Source: NC State University Libraries
Added: August 6, 2018
2015 journal article
Synchronized age-related gene expression changes across multiple tissues in human and the link to complex diseases
Scientific Reports, 5(1), 15145.
MeSH headings : Adult; Aged; Aging / genetics; Animals; Cluster Analysis; Computational Biology / methods; Female; Gene Expression; Gene Expression Profiling; Gene Expression Regulation; Genetic Association Studies; Humans; Male; Mice; Middle Aged; Molecular Sequence Annotation; Mutation; Organ Specificity / genetics; Young Adult
TL;DR:
This work catalogueed age-related gene expression changes in nine tissues from nearly two hundred individuals collected by the Genotype-Tissue Expression (GTEx) project, finding the aging gene expression signatures are very tissue specific and enrichment for some well-known aging components such as mitochondria biology is observed in many tissues.
(via Semantic Scholar)
Source: Crossref
Added: January 4, 2021
2015 journal article
The human transcriptome across tissues and individuals
Science, 348(6235), 660–665.
Source: NC State University Libraries
Added: August 6, 2018
2014 journal article
Convergence of sample eigenvalues, eigenvectors, and principal component scores for ultra-high dimensional data
BIOMETRIKA, 101(2), 484–490.
author keywords: High-dimension low sample size data; Principal component analysis; Random matrix
TL;DR:
This paper investigates principal component analysis under the ultra-high dimensional regime, where both the number of features and the sample size increase as the ratio of the two quantities also increases.
(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
2014 journal article
Heritability and genomics of gene expression in peripheral blood
Nature Genetics, 46(5), 430–437.
MeSH headings : Blood / metabolism; Gene Expression Profiling; Gene Expression Regulation / genetics; Genotype; Humans; Inheritance Patterns / genetics; Likelihood Functions; Netherlands; Polymorphism, Single Nucleotide / genetics; Quantitative Trait Loci / genetics
TL;DR:
Gen expression profiles in 2,752 twins were assessed, using a classic twin design, to quantify expression heritability and quantitative trait loci (eQTLs) in peripheral blood, providing a new resource toward understanding the genetic control of transcription.
(via Semantic Scholar)
UN Sustainable Development Goal Categories
1. No Poverty
(OpenAlex)
3. Good Health and Well-being
(Web of Science)
Source: Crossref
Added: February 5, 2020
2014 journal article
Heritability and genomics of gene expression in peripheral blood
Nature Genetics, 46(5), 430–437.
Source: NC State University Libraries
Added: August 6, 2018
2014 journal article
Physiologically Based Pharmacokinetic (PBPK) Modeling of Interstrain Variability in Trichloroethylene Metabolism in the Mouse
ENVIRONMENTAL HEALTH PERSPECTIVES, 122(5), 456–463.
MeSH headings : Animals; Bayes Theorem; Dichloroacetic Acid / metabolism; Humans; Male; Mice; Trichloroethylene / metabolism; Trichloroethylene / pharmacokinetics
TL;DR:
When extrapolated to lower doses more relevant to environmental exposures, mouse population-derived variability estimates for TCE metabolism closely matched population variability estimates previously derived from human toxicokinetic studies with TCE, highlighting the utility of mouse interstrain metabolism studies for addressing toxicokinetics variability.
(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
2014 journal article
Whole-Exome Sequencing Identifies Rare and Low-Frequency Coding Variants Associated with LDL Cholesterol
The American Journal of Human Genetics, 94(2), 233–245.
MeSH headings : Adult; Aged; Apolipoproteins E / blood; Apolipoproteins E / genetics; Cholesterol, LDL / genetics; Cohort Studies; Dyslipidemias / blood; Dyslipidemias / genetics; Exome; Female; Follow-Up Studies; Gene Frequency; Genetic Code; Genome-Wide Association Study; Genotype; Humans; Lipase / genetics; Male; Middle Aged; Phenotype; Polymorphism, Single Nucleotide; Proprotein Convertase 9; Proprotein Convertases / genetics; Receptors, LDL / genetics; Sequence Analysis, DNA; Serine Endopeptidases / genetics
TL;DR:
This large whole-exome-sequencing study for LDL-C identified a gene not known to be implicated in LDL- C and provides unique insight into the design and analysis of similar experiments.
(via Semantic Scholar)
UN Sustainable Development Goal Categories
3. Good Health and Well-being
(OpenAlex)
Source: Crossref
Added: August 28, 2020
2013 journal article
Assessment of beating parameters in human induced pluripotent stem cells enables quantitative in vitro screening for cardiotoxicity
Toxicology and Applied Pharmacology, 273(3), 500–507.
author keywords: iPSC; Calcium flux; Cardiotoxicity; hERG; Phenotypic screening; Predictive toxicology
MeSH headings : Area Under Curve; Cardiotoxins / pharmacology; Cell Survival / drug effects; Cells, Cultured; Drug Evaluation, Preclinical / methods; Drug-Related Side Effects and Adverse Reactions / diagnosis; Heart Diseases / chemically induced; Heart Diseases / diagnosis; Heart Diseases / pathology; High-Throughput Screening Assays; Humans; Induced Pluripotent Stem Cells / drug effects; Induced Pluripotent Stem Cells / metabolism; Myocytes, Cardiac / drug effects; Myocytes, Cardiac / metabolism; Myocytes, Cardiac / physiology; Phenotype; Risk Assessment
TL;DR:
Multi-parameter screening of beating profiles allows for cardiotoxicity risk assessment and identification of specific patterns defining mechanism-specific effects, and may be used widely for compound screening and early safety evaluation in drug development.
(via Semantic Scholar)
UN Sustainable Development Goal Categories
3. Good Health and Well-being
(OpenAlex)
Source: Crossref
Added: August 28, 2020
2013 journal article
Space-time clustering and the permutation moments of quadratic forms
Stat, 2(1), 292–302.
author keywords: exact testing; resampling; statistical computing
TL;DR:
The extension of this work to quadratic forms greatly expands the utility of density approximations for these problems, including for high-dimensional applications, where the statistics must be extreme in order to exceed stringent testing thresholds.
(via Semantic Scholar)
UN Sustainable Development Goal Categories
1. No Poverty
(OpenAlex)
3. Good Health and Well-being
(Web of Science)
Source: Crossref
Added: February 5, 2020
2013 journal article
The Genotype-Tissue Expression (GTEx) project
Nature Genetics, 45(6), 580–585.
MeSH headings : Consensus Development Conferences, NIH as Topic; Gene Expression; Gene Expression Profiling; Genome-Wide Association Study; Government Programs / ethics; Government Programs / legislation & jurisprudence; Humans; Molecular Sequence Annotation; Organ Specificity; Quantitative Trait Loci; Tissue Banks; United States
TL;DR:
The Genotype-Tissue Expression (GTEx) project is described, which will establish a resource database and associated tissue bank for the scientific community to study the relationship between genetic variation and gene expression in human tissues.
(via Semantic Scholar)
Source: Crossref
Added: August 28, 2020
2013 journal article
The Value of Statistical or Bioinformatics Annotation for Rare Variant Association With Quantitative Trait
Genetic Epidemiology, 37(7), 666–674.
author keywords: rare variants; association; weighting; variable selection; variant annotation
MeSH headings : Computational Biology; Genetic Variation / genetics; Genome-Wide Association Study; Genomics; Genotype; Humans; Models, Genetic; Molecular Sequence Annotation; Phenotype; Polymorphism, Single Nucleotide / genetics; Quantitative Trait Loci
TL;DR:
A systematic evaluation of multiple weighting schemes through a series of simulations intended to mimic large sequencing studies of a quantitative trait finds that the difference in power between phenotype‐dependent schemes is negligible when high‐quality functional annotations are available.
(via Semantic Scholar)
Source: Crossref
Added: August 28, 2020
2013 journal article
Unified Analysis of Secondary Traits in Case–Control Association Studies
Journal of the American Statistical Association, 108(502), 566–576.
author keywords: GWAS; Profile likelihood; Pseudo-likelihood; Retrospective study; Secondary phenotype; Semiparametric method
TL;DR:
A general retrospective likelihood framework is presented to perform association testing for both binary and continuous secondary traits, which respects marginal models and incorporates the interaction term and an alternative pseudo-likelihood method for handling covariates is presented.
(via Semantic Scholar)
Source: Crossref
Added: August 28, 2020
2012 journal article
Exome sequencing of extreme phenotypes identifies DCTN4 as a modifier of chronic Pseudomonas aeruginosa infection in cystic fibrosis
Nature Genetics, 44(8), 886–889.
MeSH headings : Adolescent; Age of Onset; Child; Child, Preschool; Cystic Fibrosis / complications; Cystic Fibrosis / genetics; Dynactin Complex; Exome; Gene Frequency; Humans; Infant; Infant, Newborn; Linkage Disequilibrium; Microtubule-Associated Proteins / genetics; Phenotype; Polymorphism, Single Nucleotide; Pseudomonas Infections / etiology; Pseudomonas Infections / genetics; Pseudomonas aeruginosa
TL;DR:
An extreme phenotype study design is used to discover that variants in DCTN4, encoding a dynactin protein, are associated with time to first P. aeruginosa airway infection, chronic P.aerug inosa infection and mucoid P. AerugInosa in individuals with cystic fibrosis.
(via Semantic Scholar)
Source: Crossref
Added: August 28, 2020
2012 journal article
Multiple apical plasma membrane constituents are associated with susceptibility to meconium ileus in individuals with cystic fibrosis
Nature Genetics, 44(5), 562–569.
MeSH headings : Amino Acid Transport Systems; Amino Acid Transport Systems, Neutral / genetics; Antiporters / genetics; Cell Membrane / metabolism; Cystic Fibrosis / genetics; Cystic Fibrosis Transmembrane Conductance Regulator / genetics; Genetic Predisposition to Disease; Genome-Wide Association Study; Genotype; Humans; Ileus / genetics; Intestinal Obstruction / etiology; Meconium; Polymorphism, Single Nucleotide / genetics; Sodium-Hydrogen Exchanger 3; Sodium-Hydrogen Exchangers / genetics; Sulfate Transporters
TL;DR:
It is suggested that modulating activities of apical membrane constituents could complement current therapeutic paradigms for cystic fibrosis and provide evidence of association between meconium ileus and multiple genes encoding constituents of the apical plasma membrane where CFTR resides.
(via Semantic Scholar)
Source: Crossref
Added: August 28, 2020
2011 journal article
A novel lung disease phenotype adjusted for mortality attrition for cystic fibrosis Genetic modifier studies
Pediatric Pulmonology, 46(9), 857–869.
author keywords: forced expiratory volume; age effects; severity of illness index
MeSH headings : Adolescent; Child; Chronic Disease; Clinical Trials as Topic; Cystic Fibrosis / genetics; Cystic Fibrosis / mortality; Female; Humans; Male; Multicenter Studies as Topic; Phenotype; Respiratory Function Tests; Severity of Illness Index; Survival Analysis
TL;DR:
Genetic studies of lung disease in cystic fibrosis are hampered by the lack of a severity measure that accounts for chronic disease progression and mortality attrition and combining analyses across studies requires common phenotypes that are robust to study design and patient ascertainment.
(via Semantic Scholar)
UN Sustainable Development Goal Categories
3. Good Health and Well-being
(OpenAlex)
Source: Crossref
Added: August 28, 2020
2011 journal article
Genome-wide association and linkage identify modifier loci of lung disease severity in cystic fibrosis at 11p13 and 20q13.2
Nature Genetics, 43(6), 539–546.
MeSH headings : Adolescent; Adult; Child; Chromosomes, Human, Pair 11; Chromosomes, Human, Pair 20; Cystic Fibrosis / genetics; Female; Genetic Linkage; Genome-Wide Association Study; Humans; Lung Diseases / genetics; Male; Phenotype; Quantitative Trait Loci
TL;DR:
The authors' findings provide insight into the causes of variation in lung disease severity in cystic fibrosis and suggest new therapeutic targets for this life-limiting disorder.
(via Semantic Scholar)
UN Sustainable Development Goal Categories
3. Good Health and Well-being
(OpenAlex)
Source: Crossref
Added: August 28, 2020
2011 journal article
MicroRNA expression in the livers of inbred mice
Mutation Research/Fundamental and Molecular Mechanisms of Mutagenesis, 714(1-2), 126–133.
author keywords: MicroRNA; Liver; Mouse; Gene expression
MeSH headings : Animals; Gene Expression; Liver / metabolism; Mice; Mice, Inbred Strains / genetics; MicroRNAs / metabolism; Polymorphism, Single Nucleotide
TL;DR:
The stability of mouse liver miRNA expression in a genetically diverse population suggests that treatment-induced disruptions in liver mi RNA expression may indicate an important mechanism for the disturbance of normal liver function, and may prove to be a useful genetic background-independent biomarker of toxicant effect.
(via Semantic Scholar)
UN Sustainable Development Goal Categories
3. Good Health and Well-being
(Web of Science; OpenAlex)
Sources: Crossref, Web Of Science
Added: August 6, 2018
2010 journal article
Interactome analysis of longitudinal pharyngeal infection of cynomolgus macaques by group A Streptococcus
Proceedings of the National Academy of Sciences, 107(10), 4693–4698.
author keywords: epithelial growth factor receptor; host pathogen; microarray; Streptococcus pyogenes; transcriptome
MeSH headings : Animals; Bacterial Proteins / genetics; Bacterial Proteins / metabolism; Clathrin-Coated Vesicles / metabolism; Cytokines / metabolism; GTP Phosphohydrolases / genetics; GTP Phosphohydrolases / metabolism; Gene Expression Profiling; Host-Pathogen Interactions; Hyaluronic Acid / metabolism; Macaca fascicularis / genetics; Macaca fascicularis / metabolism; Macaca fascicularis / microbiology; Neutrophils / metabolism; Neutrophils / microbiology; Neutrophils / pathology; Oligonucleotide Array Sequence Analysis; Pharyngitis / genetics; Pharyngitis / microbiology; Pharynx / metabolism; Pharynx / microbiology; Pharynx / pathology; Reverse Transcriptase Polymerase Chain Reaction; Streptococcus pyogenes / genetics; Streptococcus pyogenes / metabolism; Streptococcus pyogenes / physiology
TL;DR:
These results are unique in providing a comprehensive understanding of the host–pathogen interactome during mucosal infection by a bacterial pathogen.
(via Semantic Scholar)
Source: Crossref
Added: August 28, 2020
2010 journal article
Nuclear Factor κ-Light Chain-Enhancer of Activated B Cells is Activated by Radiotherapy and is Prognostic for Overall Survival in Patients With Rectal Cancer Treated With Preoperative Fluorouracil-Based Chemoradiotheraphy
International Journal of Radiation Oncology*Biology*Physics, 80(3), 705–711.
author keywords: Chemoradiotherapy; NF-kappa B; rectal cancer; prognostic markers; inducible resistance genes; TRAF1; Bcl-2; cIAP-2; interleukin 8
MeSH headings : Adult; Aged; Aged, 80 and over; Combined Modality Therapy / methods; Female; Genes, bcl-2 / genetics; Humans; Inhibitor of Apoptosis Proteins / genetics; Interleukin-8 / genetics; Male; Middle Aged; NF-kappa B / metabolism; Neoplasm Proteins / metabolism; Prognosis; Prospective Studies; Radiation Tolerance / genetics; Rectal Neoplasms / drug therapy; Rectal Neoplasms / genetics; Rectal Neoplasms / metabolism; Rectal Neoplasms / mortality; Rectal Neoplasms / radiotherapy; Retrospective Studies; TNF Receptor-Associated Factor 1 / genetics; Treatment Outcome
TL;DR:
NF-κB might play an important role in tumor metastasis but not to the resistance to chemoradiotherapy, and nuclear expression at baseline in rectal cancer was prognostic for overall survival but not predictive of the response to RT.
(via Semantic Scholar)
UN Sustainable Development Goal Categories
3. Good Health and Well-being
(OpenAlex)
Source: Crossref
Added: January 4, 2021
2010 journal article
Use of Pharmaco-Metabonomics for Early Prediction of Acetaminophen-Induced Hepatotoxicity in Humans
Clinical Pharmacology & Therapeutics, 88(1), 45–51.
MeSH headings : Acetaminophen / adverse effects; Acetaminophen / metabolism; Acetaminophen / pharmacology; Adolescent; Adult; Alanine Transaminase / blood; Analgesics, Non-Narcotic / adverse effects; Analgesics, Non-Narcotic / metabolism; Analgesics, Non-Narcotic / pharmacology; Biotransformation; Chemical and Drug Induced Liver Injury / diagnosis; Chemical and Drug Induced Liver Injury / genetics; Chemical and Drug Induced Liver Injury / urine; Cohort Studies; Data Interpretation, Statistical; Female; Humans; Least-Squares Analysis; Liver Function Tests; Magnetic Resonance Spectroscopy; Male; Middle Aged; Multivariate Analysis; Predictive Value of Tests; Young Adult
TL;DR:
It is demonstrated that the pattern of endogenous metabolites in urine could predict susceptibility to acetaminophen‐induced liver injury in rats, and this “early‐intervention pharmaco‐metabonomics” approach should now be tested in clinical trials of other potentially hepatotoxic drugs.
(via Semantic Scholar)
UN Sustainable Development Goal Categories
3. Good Health and Well-being
(OpenAlex)
Source: Crossref
Added: August 28, 2020
2009 journal article
A susceptibility gene for type 2 diabetes confers substantial risk for diabetes complicating cystic fibrosis
Diabetologia, 52(9), 1858–1865.
author keywords: Association; CFRD; Corticosteroid; Cystic fibrosis; Diabetes; Genetics; Glucocorticoid; Modifier gene; TCF7L2
TL;DR:
A genetic variant conferring risk for type 2 diabetes in the general population is a modifier of risk for diabetes in CF.
(via Semantic Scholar)
UN Sustainable Development Goal Categories
3. Good Health and Well-being
(OpenAlex)
Source: Crossref
Added: August 28, 2020
2009 journal article
An approximate Bayesian approach for quantitative trait loci estimation
Computational Statistics & Data Analysis, 54(2), 565–574.
TL;DR:
This paper presents a Bayesian linkage model that offers directly interpretable posterior densities or Bayes factors for linkage, and employs the Laplace approximation for integration over nuisance parameters in backcross (BC) and F2 intercross designs.
(via Semantic Scholar)
Source: Crossref
Added: August 28, 2020
2009 journal article
Erratum: Genomewide association for schizophrenia in the CATIE study: results of stage 1
Molecular Psychiatry, 14(12), 1144–1144.
Source: Crossref
Added: February 24, 2020
2009 journal article
Genetic Modifiers of Liver Disease in Cystic Fibrosis
JAMA, 302(10), 1076–1083.
MeSH headings : Adolescent; Adult; Age Factors; Child; Child, Preschool; Cystic Fibrosis / complications; Cystic Fibrosis / genetics; Female; Glutathione S-Transferase pi / genetics; Humans; Hypertension, Portal / etiology; Hypertension, Portal / genetics; Infant; Liver Cirrhosis / etiology; Liver Cirrhosis / genetics; Liver Diseases / etiology; Liver Diseases / genetics; Logistic Models; Male; Mannose-Binding Lectin / genetics; Peptidyl-Dipeptidase A / genetics; Polymorphism, Genetic; Risk; Transforming Growth Factor beta1 / genetics; Young Adult; alpha 1-Antitrypsin / genetics
TL;DR:
The SERPINA1 Z allele is a risk factor for liver disease in CF and patients who carry the Z allele are at greater risk of developing severe liver disease with portal hypertension.
(via Semantic Scholar)
UN Sustainable Development Goal Categories
3. Good Health and Well-being
(OpenAlex)
Source: Crossref
Added: January 17, 2021
2009 journal article
Replication and narrowing of gene expression quantitative trait loci using inbred mice
Mammalian Genome, 20(7), 437–446.
MeSH headings : Animals; Chromosome Mapping / methods; DNA Replication; Female; Gene Expression Profiling / methods; Linkage Disequilibrium; Male; Mice / classification; Mice / genetics; Mice, Inbred Strains; Phylogeny; Quantitative Trait Loci
TL;DR:
EQTL mapping in inbred strains is best carried out in combination with an eQTL linkage study, and the shorter linkage disequilibrium in the MDP strains allowed us to considerably narrow the locus and limit the number of candidate genes to a cluster of Serpin genes, which code for extracellular proteases.
(via Semantic Scholar)
Source: Crossref
Added: August 28, 2020
2008 journal article
A robust QTL mapping procedure
Journal of Statistical Planning and Inference, 139(3), 978–989.
author keywords: GEE; Generalized least squares estimate; Quantitative trait; Weighted least squares estimate; Wilcoxon-Mann-Whitney statistic
TL;DR:
This work generalizes the mapping problem to a genuine nonparametric setup and provides a robust estimation procedure for the situation where the underlying phenotype distributions are completely unspecified, in quantitative-trait linkage studies using experimental crosses.
(via Semantic Scholar)
Source: Crossref
Added: August 28, 2020
2008 journal article
Comment on a Simple and Improved Correction for Population Stratification
The American Journal of Human Genetics, 82(2), 524–526.
MeSH headings : Case-Control Studies; Genetic Markers; Genetics, Population; Genotype; Humans; Polymorphism, Single Nucleotide; Regression Analysis; Research Design
TL;DR:
To the Editor: In the May 2007 issue of the American Journal of Human Genetics, Epstein, Allen, and Satten1 (hereafter referred to as EAS) introduced a new method for controlling population stratification in case-control association studies.
(via Semantic Scholar)
Source: Crossref
Added: August 28, 2020
2008 journal article
Estimating Odds Ratios in Genome Scans: An Approximate Conditional Likelihood Approach
The American Journal of Human Genetics, 82(5), 1064–1074.
MeSH headings : Genome, Human; Haplotypes; Humans; Likelihood Functions; Models, Genetic; Odds Ratio; Software
TL;DR:
This work introduces a method, based on the estimate of genetic effect and its standard error as reported by standard statistical software, to correct for this bias in case-control association studies and develops a principled method to construct confidence intervals for the genetic effect that acknowledges the conditioning on statistical significance.
(via Semantic Scholar)
Source: Crossref
Added: August 28, 2020
2008 journal article
Estimating Odds Ratios in Genome Scans: An Approximate Conditional Likelihood Approach
The American Journal of Human Genetics, 82(5), 1224.
Source: Crossref
Added: August 28, 2020
2008 journal article
Genomewide association for schizophrenia in the CATIE study: results of stage 1
Molecular Psychiatry, 13(6), 570–584.
author keywords: schizophrenia; genomewide association; CATIE
MeSH headings : Antipsychotic Agents / therapeutic use; Case-Control Studies; Computational Biology; DNA / genetics; DNA / isolation & purification; Genetic Markers; Genetic Variation; Genome, Human; Genotype; Humans; National Institute of Mental Health (U.S.); Polymorphism, Single Nucleotide; Schizophrenia / drug therapy; Schizophrenia / genetics; United States
TL;DR:
These data do not provide evidence for the involvement of any genomic region with schizophrenia detectable with moderate sample size, however, a planned genomewide association study for response phenotypes and inclusion of individual phenotype and genotype data from this study in meta-analyses hold promise for eventual identification of susceptibility and protective variants.
(via Semantic Scholar)
UN Sustainable Development Goal Categories
3. Good Health and Well-being
(Web of Science)
Sources: Crossref, Web Of Science
Added: August 6, 2018
2005 journal article
Genetic Modifiers of Lung Disease in Cystic Fibrosis
New England Journal of Medicine, 353(14), 1443–1453.
MeSH headings : Adolescent; Adult; Child; Cystic Fibrosis / classification; Cystic Fibrosis / genetics; Cystic Fibrosis Transmembrane Conductance Regulator / genetics; DNA Replication; Female; Forced Expiratory Volume; Genotype; Humans; Linkage Disequilibrium; Logistic Models; Lung Diseases / classification; Lung Diseases / genetics; Lung Diseases / physiopathology; Male; Middle Aged; Phenotype; Polymorphism, Genetic; Severity of Illness Index; Transforming Growth Factor beta / genetics
TL;DR:
Genetic variation in the 5' end of TGFbeta1 or a nearby upstream region modifies disease severity in cystic fibrosis.
(via Semantic Scholar)
UN Sustainable Development Goal Categories
3. Good Health and Well-being
(OpenAlex)
Source: Crossref
Added: August 28, 2020
2005 journal article
Group A Streptococcus Transcriptome Dynamics during Growth in Human Blood Reveals Bacterial Adaptive and Survival Strategies
The American Journal of Pathology, 166(2), 455–465.
MeSH headings : DNA, Complementary / metabolism; Female; Flow Cytometry; Gene Expression Regulation, Bacterial; Humans; Male; Models, Biological; Mutation; Nucleic Acid Hybridization; Oligonucleotide Array Sequence Analysis; RNA / metabolism; RNA, Messenger / metabolism; Reverse Transcriptase Polymerase Chain Reaction; Streptococcal Infections / blood; Streptococcal Infections / metabolism; Streptococcus / metabolism; Time Factors
TL;DR:
Investigation of the transcriptome of a wild-type serotype M1 GAS strain in human blood reinforced the hypothesis that CovR-CovS has an important role linking key biosynthetic, catabolic, and virulence functions during transcriptome restructuring.
(via Semantic Scholar)
Source: Crossref
Added: August 28, 2020
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