High-dimensional Integration of Biological Systems

Works Published in 2022

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Displaying works 1 - 20 of 27 in total

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

2022 journal article

MagicalRsq: Machine-learning-based genotype imputation quality calibration

AMERICAN JOURNAL OF HUMAN GENETICS, 109(11), 1986–1997.

By: Q. Sun *, Y. Yang *, J. Rosen *, M. Jiang *, J. Chen *, W. Liu *, J. Wen *, L. Raffield * ...

MeSH headings : Humans; Genome-Wide Association Study / methods; Polymorphism, Single Nucleotide / genetics; Calibration; Genotype; Machine Learning
topics (OpenAlex): Cystic Fibrosis Research Advances; Genetic Associations and Epidemiology; Genomics and Rare Diseases
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)
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Sources: Web Of Science, NC State University Libraries
Added: January 17, 2023

2022 journal article

Ontogeny of cellular organization and LGR5 expression in porcine cochlea revealed using tissue clearing and 3D imaging

ISCIENCE, 25(8).

By: A. Moatti n , C. Li n, S. Sivadanam  n, Y. Cai n, J. Ranta n, J. Piedrahita n , A. Cheng *, F. Ligler n, A. Greenbaum n

topics (OpenAlex): Hearing, Cochlea, Tinnitus, Genetics; Molecular Biology Techniques and Applications; Bat Biology and Ecology Studies
TL;DR: Data reveal that hair cell organization, inner ear morphology, cellular cartography in the organ of Corti, and spatiotemporal expression of LGR5 are dynamic over developmental stages in a pattern not previously documented. (via Semantic Scholar)
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Source: Web Of Science
Added: December 19, 2022

2022 journal article

A Double Penalty Model for Ensemble Learning

MATHEMATICS, 10(23).

By: W. Wang * & Y. Zhou  n

author keywords: double penalty model; interpretability; partially linear model; separability
topics (OpenAlex): Machine Learning and Data Classification; Gaussian Processes and Bayesian Inference; Explainable Artificial Intelligence (XAI)
TL;DR: By considering ensemble learning for two learning ensemble components as a double penalty model, this work provides a framework to better understand the relative convergence and identifiability of the two components. (via Semantic Scholar)
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Sources: ORCID, Web Of Science, NC State University Libraries
Added: December 1, 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.

By: C. Harlow *, J. Gandawijaya *, R. Bamford *, E. Martin*, A. Wood *, P. Most *, T. Tanaka *, H. Leonard * ...

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
topics (OpenAlex): Erythropoietin and Anemia Treatment; Cancer, Hypoxia, and Metabolism; Adenosine and Purinergic Signaling
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)
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Source: Web Of Science
Added: November 21, 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.

By: M. Aksit, H. Ling, R. Pace, K. Raraigh, F. Onchiri, A. Faino, K. Pagel, E. Pugh ...

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
topics (OpenAlex): Neonatal Respiratory Health Research; Cystic Fibrosis Research Advances; Infant Nutrition and Health
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)
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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

C3NA: correlation and consensus-based cross-taxonomy network analysis for compositional microbial data

BMC BIOINFORMATICS, 23(1).

By: K. Song n & Y. Zhou  n

author keywords: Co-occurrence network analysis; Microbiome; R package; Consensus clustering; Module preservation analysis
MeSH headings : Phylogeny; Consensus
topics (OpenAlex): Bioinformatics and Genomic Networks; Gut microbiota and health; Metabolomics and Mass Spectrometry Studies
TL;DR: C3NA is presented, a user-friendly R package for investigating compositional microbial sequencing data to identify and compare co-occurrence patterns across different taxonomic levels and discovered clusters of study and disease-dependent taxa that overlap with known functional taxa studied by other discovery studies and differential abundance analyses. (via Semantic Scholar)
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Sources: Web Of Science, NC State University Libraries
Added: November 21, 2022

2022 journal article

Inhalable dry powder mRNA vaccines based on extracellular vesicles

Matter, 5(9), 2960–2974.

By: K. Popowski n , A. Moatti n , G. Scull n, D. Silkstone n, H. Lutz  n, B. Abad  n, A. George n , E. Belcher  n ...

topics (OpenAlex): Extracellular vesicles in disease; RNA Interference and Gene Delivery; Inhalation and Respiratory Drug Delivery
TL;DR: The results suggest that extracellular vesicles can serve as an inhaled mRNA drug-delivery system that is superior to synthetic liposomes. (via Semantic Scholar)
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3. Good Health and Well-being (Web of Science; OpenAlex)
Source: Web Of Science
Added: October 17, 2022

2022 journal article

A resource for integrated genomic analysis of the human liver

SCIENTIFIC REPORTS, 12(1).

By: Y. Zhou, P. Gallins, A. Etheridge, D. Jima, E. Scholl, F. Wright, F. Innocenti

MeSH headings : Bayes Theorem; Genome-Wide Association Study / methods; Genomics; Humans; Liver; Polymorphism, Single Nucleotide; Quantitative Trait Loci
topics (OpenAlex): Hepatitis C virus research; Liver Disease Diagnosis and Treatment; Cancer-related molecular mechanisms research
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)
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Sources: Web Of Science, ORCID, NC State University Libraries
Added: September 8, 2022

2022 journal article

Improve the Colorectal Cancer Diagnosis Using Gut Microbiome Data

FRONTIERS IN MOLECULAR BIOSCIENCES, 9.

By: Y. Zhou & G. Sun

author keywords: machine learning; prediction; feature engineering; colorectal cancer; mediation analysis; 16S rRNA
topics (OpenAlex): Gut microbiota and health; Colorectal Cancer Screening and Detection; Machine Learning in Healthcare
TL;DR: A machine learning method for gut microbiome data to assist in diagnosing colorectal cancer, which shows an 8.7% higher prediction accuracy and 13% higher area under the receiver operator characteristic curve than other published work. (via Semantic Scholar)
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3. Good Health and Well-being (Web of Science; OpenAlex)
Sources: Web Of Science, NC State University Libraries
Added: September 6, 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.

By: J. House n , F. Grimm *, W. Klaren *, A. Dalzell*, S. Kuchi*, S. Zhang *, K. Lenz*, P. Boogaard * ...

MeSH headings : Biological Assay; Endothelial Cells; Humans; Induced Pluripotent Stem Cells; Petroleum; Transcriptome
topics (OpenAlex): Animal testing and alternatives; Molecular Biology Techniques and Applications; Effects and risks of endocrine disrupting chemicals
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)
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Source: Web Of Science
Added: August 29, 2022

2022 journal article

Model systems and organisms for addressing inter- and intra-species variability in risk assessment

REGULATORY TOXICOLOGY AND PHARMACOLOGY, 132.

By: I. Rusyn *, W. Chiu * & F. Wright n

MeSH headings : Animals; Mice; Models, Theoretical; Risk Assessment; Toxicokinetics; Uncertainty
topics (OpenAlex): Animal testing and alternatives; Effects and risks of endocrine disrupting chemicals; Computational Drug Discovery Methods
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)
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Source: Web Of Science
Added: August 15, 2022

2022 journal article

Correlation Analysis of Variables From the Atherosclerosis Risk in Communities Study

FRONTIERS IN PHARMACOLOGY, 13.

By: M. Mandal *, J. Levy*, C. Ives *, S. Hwang *, Y. Zhou, A. Motsinger-Reif*, H. Pan *, W. Huggins * ...

author keywords: cluster analysis; systems biology; meta-analysis as topic; ARIC; cardiovascular disease
topics (OpenAlex): Health, Environment, Cognitive Aging; Computational Drug Discovery Methods; Health Systems, Economic Evaluations, Quality of Life
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)
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Source: Web Of Science
Added: August 8, 2022

2022 journal article

A Population-Based Human In Vitro Approach to Quantify Inter-Individual Variability in Responses to Chemical Mixtures

TOXICS, 10(8).

By: L. Ford *, S. Jang *, Z. Chen *, Y. Zhou  n, P. Gallins n, F. Wright n, W. Chiu *, I. Rusyn *

author keywords: population-wide; inter-individual variability; toxicodynamics; chemical mixtures; defined mixtures; human health risk assessment; uncertainty factors; genome-wide association study
topics (OpenAlex): Carcinogens and Genotoxicity Assessment; Effects and risks of endocrine disrupting chemicals; Gene expression and cancer classification
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)
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Sources: Web Of Science, ORCID, NC State University Libraries
Added: August 2, 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.

By: K. Xia *, A. Shabalin *, Z. Yin*, W. Chung *, P. Sullivan *, F. Wright n, M. Styner *, J. Gilmore *, R. Santelli*, F. Zou *

author keywords: Twin; eQTL; GWAS
MeSH headings : Humans; Gene Frequency; Genome-Wide Association Study / methods; Linear Models; Polymorphism, Single Nucleotide; Quantitative Trait Loci
topics (OpenAlex): Genetic Associations and Epidemiology; Genetic Mapping and Diversity in Plants and Animals; Genetic Syndromes and Imprinting
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Source: Web Of Science
Added: July 11, 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.

By: D. Jima n, D. Skaar n , A. Planchart n , A. Motsinger-Reif n, S. Cevik  n, S. Park n, M. Cowley n , F. Wright n ...

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
topics (OpenAlex): Genetic Syndromes and Imprinting; Epigenetics and DNA Methylation; Genetics and Neurodevelopmental Disorders
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)
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Source: Web Of Science
Added: July 11, 2022

2022 journal article

Complete CFTR gene sequencing in 5,058 individuals with cystic fibrosis informs variant-specific treatment

JOURNAL OF CYSTIC FIBROSIS, 21(1), 463–470.

By: K. Raraigh *, M. Aksit *, K. Hetrick*, R. Pace *, H. Ling *, W. O'Neal *, E. Blue *, Y. Zhou  n ...

author keywords: Whole genome sequencing; CFTR; Modulator therapy; Variant identification; Variant annotation
MeSH headings : Alleles; Cohort Studies; Cystic Fibrosis / diagnosis; Cystic Fibrosis / genetics; Cystic Fibrosis Transmembrane Conductance Regulator / genetics; Genotype; Humans; Mutation
topics (OpenAlex): Cystic Fibrosis Research Advances; Neonatal Respiratory Health Research; Child Nutrition and Feeding Issues
TL;DR: Complete CFTR gene sequencing in 5,058 individuals with CF identified at least one DNA variant in 99.6% of the cohort that is targetable by current molecular or emerging gene-based therapeutic technologies. (via Semantic Scholar)
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Sources: Web Of Science, NC State University Libraries
Added: July 5, 2022

2022 journal article

Accounting for population structure in genetic studies of cystic fibrosis

HUMAN GENETICS AND GENOMICS ADVANCES, 3(3).

By: H. Kingston *, A. Stilp *, W. Gordon *, J. Broome *, S. Gogarten *, H. Ling *, J. Barnard *, S. Dugan-Perez * ...

topics (OpenAlex): Cystic Fibrosis Research Advances
TL;DR: The results suggest that PC adjustment can adequately prevent spurious associations between genetic variants and CF-related traits and are therefore effective tools to control for population structure even when population structure is confounded with disease severity and a common pathogenic variant. (via Semantic Scholar)
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Sources: Web Of Science, NC State University Libraries
Added: June 27, 2022

2022 journal article

Characterization of population variability of 1,3-butadiene derived protein adducts in humans and mice

REGULATORY TOXICOLOGY AND PHARMACOLOGY, 132.

By: G. Boysen, I. Rusyn, W. Chiu & F. Wright

MeSH headings : Animals; Biomarkers; Butadienes / chemistry; Butadienes / metabolism; Butadienes / toxicity; Carcinogens / metabolism; Carcinogens / toxicity; Hemoglobins / metabolism; Humans; Mice
topics (OpenAlex): Carcinogens and Genotoxicity Assessment; Air Quality and Health Impacts; Effects and risks of endocrine disrupting chemicals
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)
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Source: Web Of Science
Added: June 6, 2022

2022 journal article

Quantitative analysis of illumination and detection corrections in adaptive light sheet fluorescence microscopy

BIOMEDICAL OPTICS EXPRESS, 13(5), 2960–2974.

By: M. Rai, C. Li n & A. Greenbaum n

topics (OpenAlex): Advanced Fluorescence Microscopy Techniques; Cell Image Analysis Techniques; Photoacoustic and Ultrasonic Imaging
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Source: Web Of Science
Added: May 31, 2022

2022 journal article

A Machine Learning Pipeline for Mortality Prediction in the ICU

International Journal of Digital Health, 2(1).

By: Y. Sun n & Y. Zhou  n

topics (OpenAlex): Machine Learning in Healthcare; Sepsis Diagnosis and Treatment; Medical Coding and Health Information
TL;DR: This paper proposes a cohort study that builds a pipeline that extracts ICD-9 codes and laboratory tests from public available electronic ICU databases, and improves the in-hospital mortality prediction accuracy using a combination of neural network missing data imputation approach and decision tree based outcome prediction algorithm. (via Semantic Scholar)
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Source: ORCID
Added: May 13, 2022

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