Works (49)

Updated: April 3rd, 2024 20:23

2022 article

Assessing the Nucleotide-Level Impact of Spaceflight Stress using RNA-Sequencing Data

Knight, M. S., Doherty, C. J., & Nielsen, D. M. (2022, December 2).

By: M. Knight n, C. Doherty n & D. Nielsen n

TL;DR: GeneLab data is used to examine DNA sequence variants linked to spaceflight stress exposure and provides a baseline for the types of mutations that could be detected, demonstrating that RNA-Seq data is a useful resource for evaluating DNA damage from spaceflight. (via Semantic Scholar)
Source: ORCID
Added: December 3, 2022

2019 journal article

Interferon-λ3 Promotes Epithelial Defense and Barrier Function Against Cryptosporidium parvum Infection

Cellular and Molecular Gastroenterology and Hepatology, 8(1), 1–20.

By: S. Ferguson n, D. Foster n, B. Sherry n, S. Magness n, D. Nielsen n & J. Gookin n

author keywords: Cryptosporidiosis; Cytokine; Enterocyte; Protozoa
MeSH headings : Animals; Cell Line; Cryptosporidiosis / genetics; Cryptosporidiosis / immunology; Cryptosporidiosis / parasitology; Cryptosporidium parvum / physiology; Cytokines / genetics; Cytokines / metabolism; Disease Models, Animal; Gene Expression Profiling; Intestinal Mucosa / immunology; Mice; Mice, Inbred C57BL; Oligonucleotide Array Sequence Analysis; Swine; Up-Regulation
TL;DR: These studies identify IFN-λ2/3 as a key epithelial defense mechanism against C parvum infection and Priming of IECs with recombinant human IFn-λ3 promoted cellular defense against CParvum infections and abrogated C parVum–induced loss of barrier function by decreasing paracellular permeability to sodium. (via Semantic Scholar)
Sources: Web Of Science, NC State University Libraries, Crossref, ORCID
Added: July 15, 2019

2017 journal article

Genetics of Hereditary Ataxia in Scottish Terriers

Journal of Veterinary Internal Medicine, 31(4), 1132–1139.

By: G. Urkasemsin n, D. Nielsen n, A. Singleton*, S. Arepalli*, D. Hernandez*, C. Agler n, N. Olby n

author keywords: Canine; Cerebellar abiotrophy; Cerebellar ataxia; Neurodegeneration
MeSH headings : Animals; Brain / diagnostic imaging; Dog Diseases / diagnostic imaging; Dog Diseases / genetics; Dogs; Female; Genetic Linkage / genetics; Genome-Wide Association Study / veterinary; Homozygote; Magnetic Resonance Imaging / veterinary; Male; Neuroimaging / veterinary; Pedigree; Spinocerebellar Degenerations / diagnostic imaging; Spinocerebellar Degenerations / genetics; Spinocerebellar Degenerations / veterinary
TL;DR: This finding suggests that further genetic investigation of the potential region of interest on CFA X should be considered in order to identify the causal mutation as well as develop a genetic test to eliminate the disease from this breed. (via Semantic Scholar)
UN Sustainable Development Goal Categories
Sources: Crossref, NC State University Libraries, Web Of Science
Added: August 6, 2018

2017 journal article

Networks Underpinning Symbiosis Revealed Through Cross-Species eQTL Mapping

Genetics, 206(4), 2175–2184.

By: Y. Guo n, S. Fudali n, J. Gimeno n, P. DiGennaro n, S. Chang n, V. Williamson*, D. Bird n, D. Nielsen n

Contributors: Y. Guo n, S. Fudali n, J. Gimeno n, P. Digennaro n, S. Chang n, V. Williamson*, D. Bird n, D. Nielsen n

author keywords: transspecies; trans-eQTL; host-pathogen interaction; symbiosis; RNA-Seq
MeSH headings : Animals; Chromosome Mapping / methods; Gene Regulatory Networks; Genetic Pleiotropy; Helminth Proteins / genetics; Helminth Proteins / metabolism; Medicago / genetics; Medicago / parasitology; Plant Proteins / genetics; Plant Proteins / metabolism; Polymorphism, Genetic; Quantitative Trait Loci; Symbiosis / genetics; Transcription Factors / genetics; Transcription Factors / metabolism; Tylenchoidea / genetics; Tylenchoidea / pathogenicity
TL;DR: An expression quantitative trait locus (eQTL) mapping-based approach to identify cause-and-effect relationships between genes from two partners engaged in an interspecific interaction is developed and applied to data from a Salmonella infection study, successfully identifying polymorphisms in the human genome affecting bacterial expression. (via Semantic Scholar)
UN Sustainable Development Goal Categories
2. Zero Hunger (Web of Science)
13. Climate Action (Web of Science)
15. Life on Land (OpenAlex)
Sources: Web Of Science, NC State University Libraries, ORCID
Added: August 6, 2018

2015 journal article

Increased exposure to acute thermal stress is associated with a non-linear increase in recombination frequency and an independent linear decrease in fitness in Drosophila

BMC EVOLUTIONARY BIOLOGY, 15.

By: S. Jackson n, D. Nielsen n & N. Singh n

MeSH headings : Animals; Biological Evolution; Drosophila melanogaster / cytology; Drosophila melanogaster / genetics; Drosophila melanogaster / physiology; Heat-Shock Response; Meiosis; Recombination, Genetic
TL;DR: It is found that increased exposure to heat shock conditions is associated with a non-linear increase in meiotic recombination frequency, and an independent effect of heat shock on organismal fitness, with fitness decreasing with increased duration of thermal stress. (via Semantic Scholar)
Sources: Web Of Science, NC State University Libraries
Added: August 6, 2018

2015 journal article

Maize Homologs of Hydroxycinnamoyltransferase, a Key Enzyme in Lignin Biosynthesis, Bind the Nucleotide Binding Leucine-Rich Repeat Rp1 Proteins to Modulate the Defense Response

Plant Physiol, 169(3), 2230–2243.

By: G. Wang, Y. He, R. Strauch, B. Olukolu, D. Nielsen, X. Li, P. Balint-Kurti

Sources: NC State University Libraries, ORCID
Added: August 6, 2018

2014 journal article

A Genome-Wide Association Study of the Maize Hypersensitive Defense Response Identifies Genes That Cluster in Related Pathways

PLoS Genetics, 10(8), e1004562.

By: B. Olukolu n, G. Wang n, V. Vontimitta*, B. Venkata*, S. Marla*, J. Ji*, E. Gachomo*, K. Chu* ...

Contributors: B. Olukolu n, G. Wang n, V. Vontimitta*, B. Venkata*, S. Marla*, J. Ji*, E. Gachomo*, K. Chu* ...

Ed(s): J. McDowell

MeSH headings : Chromosome Mapping; Disease Resistance / genetics; Genome-Wide Association Study; Linkage Disequilibrium; Plant Diseases / genetics; Plant Proteins / genetics; Polymorphism, Single Nucleotide; Quantitative Trait Loci / genetics; Zea mays / genetics
TL;DR: This study provides the first system-wide analysis of natural variation that modulates the HR response in plants with low but significant correlations between HR-related traits and several previously-measured disease resistance traits. (via Semantic Scholar)
UN Sustainable Development Goal Categories
2. Zero Hunger (Web of Science)
13. Climate Action (Web of Science)
Sources: Crossref, NC State University Libraries, ORCID
Added: October 23, 2019

2014 journal article

Aspergillus flavus infection induces transcriptional and physical changes in developing maize kernels

Frontiers in Microbiology, 5.

By: A. Dolezal*, X. Shu n, G. OBrian n, D. Nielsen n, C. Woloshuk*, R. Boston n, G. Payne n

author keywords: Aspergillus flavus; maize; transcription; genetic; aflatoxins; pathogenesis
TL;DR: Data indicate that infection of the maize kernel by A. flavus induced metabolic changes in the kernel, including the production of a defense response, as well as a disruption in kernel development, which indicates host response to infection by the fungus. (via Semantic Scholar)
Sources: Crossref, NC State University Libraries, NC State University Libraries
Added: August 6, 2018

2014 journal article

Canine hereditary ataxia in old english sheepdogs and gordon setters is associated with a defect in the autophagy gene encoding RAB24

PLoS Genet, 10(2), e1003991.

By: C. Agler, D. Nielsen, G. Urkasemsin, A. Singleton, N. Tonomura, S. Sigurdsson, R. Tang, K. Linder ...

Sources: NC State University Libraries, ORCID
Added: August 6, 2018

2014 journal article

Improved structural annotation of protein-coding genes in the Meloidogyne hapla genome using RNA-Seq

Worm, 3(1), e29158.

By: Y. Guo n, D. Bird n & D. Nielsen n

TL;DR: The current genome annotation for the Meloidogyne hapla genome utilizing RNA-Seq data is refined, and in silico predictions of trans-splicing were validated by comparison with earlier results derived from an independent cDNA library constructed to capture trans- spliced transcripts. (via Semantic Scholar)
Sources: Crossref, NC State University Libraries
Added: January 7, 2020

2013 journal article

A method for detecting hidden additivity in two-factor unreplicated experiments

Computational Statistics & Data Analysis, 67, 95–104.

author keywords: Interaction effects; Latent variables; Non-additivity
TL;DR: A multiplicity-adjusted all-configurations maximum interaction F (ACMIF) test to detect hidden additivity is developed and is illustrated using two data sets taken from the literature and a third taken from a recent study of copy number variation due to lymphoma. (via Semantic Scholar)
UN Sustainable Development Goal Categories
2. Zero Hunger (Web of Science)
13. Climate Action (Web of Science)
Sources: Crossref, NC State University Libraries, Web Of Science
Added: August 6, 2018

2013 journal article

Gene Profiling of Canine B-Cell Lymphoma Reveals Germinal Center and Postgerminal Center Subtypes with Different Survival Times, Modeling Human DLBCL

Cancer Research, 73(16), 5029–5039.

By: K. Richards n, A. Motsinger-Reif n, H. Chen n, Y. Fedoriw n, C. Fan n, D. Nielsen n, G. Small n, R. Thomas n ...

MeSH headings : Adolescent; Animals; Child; Child, Preschool; DNA-Binding Proteins / genetics; DNA-Binding Proteins / metabolism; Disease Models, Animal; Dogs; Female; Gene Expression Profiling / methods; Germinal Center / metabolism; Germinal Center / pathology; Humans; Immunoglobulin Heavy Chains / genetics; Immunoglobulin Heavy Chains / metabolism; Interferon Regulatory Factors / genetics; Interferon Regulatory Factors / metabolism; Lymph Nodes / metabolism; Lymph Nodes / pathology; Lymphoma, B-Cell / genetics; Lymphoma, B-Cell / metabolism; Lymphoma, B-Cell / pathology; Lymphoma, Large B-Cell, Diffuse / genetics; Lymphoma, Large B-Cell, Diffuse / metabolism; Lymphoma, Large B-Cell, Diffuse / pathology; Male; Mutation; NF-kappa B / genetics; NF-kappa B / metabolism; Proto-Oncogene Proteins c-bcl-6; Transcriptome
TL;DR: These studies identify molecular similarities to h DLBCL that introduce pet dogs as a representative model of hDLBCL for future studies, including therapeutic clinical trials. (via Semantic Scholar)
Sources: Web Of Science, NC State University Libraries, Crossref
Added: August 6, 2018

2013 journal article

Gene selection and cancer type classification of diffuse large-B-cell lymphoma using a bivariate mixture model for two-species data

Hum Genomics, 7, 2.

By: Y. Su, D. Nielsen, L. Zhu, K. Richards, S. Suter, M. Breen, A. Motsinger-Reif, J. Osborne

Sources: NC State University Libraries, ORCID
Added: August 6, 2018

2013 journal article

Genomic architecture of adaptive color pattern divergence and convergence in Heliconius butterflies

GENOME RESEARCH, 23(8), 1248–1257.

MeSH headings : Adaptation, Biological / genetics; Animal Distribution; Animals; Base Sequence; Bayes Theorem; Butterflies / genetics; Conserved Sequence; Evolution, Molecular; Genetic Speciation; Genome, Insect; Genotype; Haplotypes; High-Throughput Nucleotide Sequencing; Likelihood Functions; Models, Genetic; Molecular Sequence Annotation; Molecular Sequence Data; Panama; Phenotype; Phylogeny; Pigmentation / genetics; Sequence Analysis, DNA; South America; Synteny; Transcriptome; Wings, Animal / physiology
TL;DR: A combination of techniques are used to annotate the genomic interval modulating red color pattern variation, identify a narrow region responsible for adaptive divergence and convergence in Heliconius wing color patterns, and explore the evolutionary history of these adaptive alleles. (via Semantic Scholar)
UN Sustainable Development Goal Categories
15. Life on Land (Web of Science; OpenAlex)
Sources: Web Of Science, NC State University Libraries
Added: August 6, 2018

2013 journal article

Localization, morphology and transcriptional profile of Aspergillus flavus during seed colonization

MOLECULAR PLANT PATHOLOGY, 14(9), 898–909.

By: A. Dolezal n, G. Obrian n, D. Nielsen n, C. Woloshuk*, R. Boston n & G. Payne n

MeSH headings : Aspergillus flavus / genetics; Aspergillus flavus / growth & development; Aspergillus flavus / pathogenicity; Chromosomes, Fungal / genetics; Colony Count, Microbial; DNA, Fungal / isolation & purification; Electrophoresis, Agar Gel; Endosperm / microbiology; Gene Expression Profiling; Gene Expression Regulation, Fungal; Genes, Fungal / genetics; Humans; Seeds / cytology; Seeds / microbiology; Transcription Factors / metabolism; Transcription, Genetic; Zea mays / cytology; Zea mays / microbiology
TL;DR: Results from these studies indicate that A. flavus is capable of infecting all tissues of the immature kernel by 96 h after infection and will aid in the development of strategies aimed at preventing or slowing down A. flavus colonization of the maize kernel. (via Semantic Scholar)
UN Sustainable Development Goal Categories
2. Zero Hunger (OpenAlex)
Sources: Web Of Science, NC State University Libraries
Added: August 6, 2018

2011 journal article

Characterization of Canine Osteosarcoma by Array Comparative Genomic Hybridization and RT-qPCR: Signatures of Genomic Imbalance in Canine Osteosarcoma Parallel the Human Counterpart

GENES CHROMOSOMES & CANCER, 50(11), 859–874.

MeSH headings : Animals; Bone Neoplasms / genetics; Bone Neoplasms / veterinary; Comparative Genomic Hybridization; Core Binding Factor Alpha 1 Subunit / genetics; DNA Copy Number Variations; Dog Diseases / genetics; Dogs; Female; Gene Dosage; Genomic Instability; Humans; In Situ Hybridization, Fluorescence; Male; Membrane Proteins / genetics; Osteosarcoma / genetics; Osteosarcoma / veterinary; PTEN Phosphohydrolase / genetics; Real-Time Polymerase Chain Reaction; Reproducibility of Results; Tumor Suppressor Proteins / genetics
TL;DR: Large scale screening of genomic imbalance in canine OS further validates the use of the dog as a suitable model for human cancers, supporting the idea that dysregulation discovered in canine cancers will provide an avenue for complementary study in human counterparts. (via Semantic Scholar)
UN Sustainable Development Goal Categories
Sources: Web Of Science, NC State University Libraries
Added: August 6, 2018

2011 journal article

Gene Expression profile and response to maize kernels by Aspergillus flavus

Phytopathology, 101(7), 797–804.

By: B. Reese, G. Payne*, D. Nielsen* & C. Woloshuk

MeSH headings : 6-Phytase / genetics; 6-Phytase / metabolism; Aflatoxins / biosynthesis; Aspergillus flavus / enzymology; Aspergillus flavus / genetics; Aspergillus flavus / growth & development; Aspergillus flavus / pathogenicity; Down-Regulation; Gene Expression Profiling / methods; Gene Expression Regulation, Fungal / genetics; Oligonucleotide Array Sequence Analysis / methods; Reverse Transcriptase Polymerase Chain Reaction; Seeds / microbiology; Sequence Deletion; Transformation, Genetic; Up-Regulation; Virulence; Zea mays / growth & development; Zea mays / microbiology
TL;DR: The study revealed the genome-wide effects of immature maize kernels on A. flavus and suggest that phytase has a role in pathogenesis, and the fungal response to the kernel environment during colonization. (via Semantic Scholar)
Sources: Web Of Science, NC State University Libraries
Added: August 6, 2018

2011 journal article

Genome-wide linkage study of atopic dermatitis in West Highland White Terriers

BMC Genetics, 12(1), 37.

By: C. Salzmann n, T. Olivry n, D. Nielsen n, J. Paps n, T. Harris n & N. Olby n

Contributors: C. Salzmann n, T. Olivry n, D. Nielsen n, J. Paps n, T. Harris n & N. Olby n

MeSH headings : Animals; Chromosome Mapping; Dermatitis, Atopic / genetics; Dermatitis, Atopic / veterinary; Dog Diseases / genetics; Dogs; Genetic Linkage; Genotype
TL;DR: The study was unable to detect any chromosomal regions significantly linked to canine AD, and a genome-wide SNP association study in a larger cohort of WHWTs may prove more successful by providing higher density coverage and higher statistical power. (via Semantic Scholar)
Sources: Crossref, NC State University Libraries, ORCID
Added: August 29, 2019

2010 journal article

Genomic Hotspots for Adaptation: The Population Genetics of Müllerian Mimicry in Heliconius erato

PLoS Genetics, 6(2), e1000796.

By: B. Counterman n, F. Araujo-Perez*, H. Hines n, S. Baxter*, C. Morrison*, D. Lindstrom n, R. Papa*, L. Ferguson* ...

Ed(s): M. Nachman

MeSH headings : Adaptation, Physiological / genetics; Animals; Butterflies / genetics; Chromosomes, Artificial, Bacterial / genetics; Gene Expression Regulation; Genetic Loci / genetics; Genetic Variation; Genetics, Population; Genome / genetics; Genotype; Hybridization, Genetic; Linkage Disequilibrium / genetics; Open Reading Frames / genetics; Peru; Phenotype; Physical Chromosome Mapping; Pigmentation / genetics; Polymorphism, Single Nucleotide / genetics; Sequence Analysis, DNA
TL;DR: Detailed characterize nucleotide variation, genotype-by-phenotype associations, linkage disequilibrium (LD), and candidate gene expression patterns across two unlinked genomic intervals that control yellow and red wing pattern variation among mimetic forms of Heliconius erato and provides convincing evidence for parallel changes in gene regulation across co-mimetic lineages. (via Semantic Scholar)
UN Sustainable Development Goal Categories
15. Life on Land (Web of Science)
Sources: Crossref, NC State University Libraries
Added: September 5, 2020

2009 journal article

Functional and geographical differentiation of candidate balanced polymorphisms in Arabidopsis thaliana

MOLECULAR ECOLOGY, 18(13), 2844–2855.

By: J. Reininga n, D. Nielsen n & M. Purugganan*

author keywords: adaptation; balancing selection; population genetics
MeSH headings : Alleles; Arabidopsis / genetics; Arabidopsis Proteins / genetics; DNA, Plant / genetics; Gene Expression Regulation, Plant; Genes, Plant; Genetics, Population; Genome, Plant; Polymorphism, Genetic; Selection, Genetic
TL;DR: The data support a hypothesis of balancing selection at all three candidate loci and provide a basis for more detailed functional work by identifying possible functional differences that might be selectively maintained. (via Semantic Scholar)
UN Sustainable Development Goal Categories
15. Life on Land (Web of Science)
Sources: Web Of Science, NC State University Libraries
Added: August 6, 2018

2009 journal article

Proceedings of the First International Conference on Toxicogenomics Integrated with Environmental Sciences (TIES-2007)

BMC Proceedings, 3(S2).

By: P. Bushel*, D. Nielsen n & W. Tong*

TL;DR: A collection of articles as proceedings of the conference and an in-depth topical review of the utility of bioinformatics in the fields of toxicogenomics and environmental genomics are compiled. (via Semantic Scholar)
Sources: Crossref, NC State University Libraries
Added: September 5, 2020

2008 journal article

Does strong linkage disequilibrium guarantee redundant association results?

Genetic Epidemiology, 32(6), 546–552.

author keywords: linkage disequilibrium; association mapping; negative correlation; case control; transmission disequilibrium
MeSH headings : Computer Simulation; Gene Frequency; Genetic Markers; Genome, Human; Haplotypes; Humans; Linkage Disequilibrium; Models, Genetic; Models, Statistical; Phenotype; Polymorphism, Single Nucleotide; Quantitative Trait, Heritable
TL;DR: This work finds that in the null hypothesis situation, where there is no association between the markers and the phenotype, the relationship between LD and the correlation between association test outcomes is clear, though it is not always ideal. (via Semantic Scholar)
UN Sustainable Development Goal Categories
3. Good Health and Well-being (Web of Science; OpenAlex)
Sources: Crossref, NC State University Libraries, Web Of Science
Added: August 6, 2018

2008 conference paper

Linkage Analysis in American Staffordshire Terriers with Hereditary Cerebellar Cortical Degeneration

Journal of Veterinary Internal Medicine, 22(3), 723–724.

By: N. Olby, T. Harris, P. Mehta, M. Breen, R. Thomas, R. Myers, D. Nielsen

Event: 26th Annual American College of Veterinary Internal Medicine Forum at San Antonio, TX on June 4-7, 2008

Source: NC State University Libraries
Added: March 19, 2021

2008 journal article

The effect of temperature on Natural Antisense Transcript (NAT) expression in Aspergillus flavus

Current Genetics, 54(5), 241–269.

By: C. Smith*, D. Robertson n, B. Yates*, D. Nielsen n, D. Brown n, R. Dean n, G. Payne n

author keywords: Aspergillus flavus; Natural antisense transcripts (NATs); Temperature; Gene expression
MeSH headings : Aspergillus flavus / genetics; Aspergillus flavus / metabolism; Expressed Sequence Tags; Fungal Proteins / genetics; Fungal Proteins / metabolism; Gene Expression Regulation, Fungal; Genome, Fungal; RNA Precursors / metabolism; RNA, Antisense / metabolism; Temperature; Transcription, Genetic / genetics
TL;DR: RNA expression analysis showed that 32 NATs and 2,709 genes were differentially expressed between 37°C and 28°C, the conducive temperature for the biosynthesis of aflatoxin (AF) and many other secondary metabolites. (via Semantic Scholar)
Sources: Crossref, NC State University Libraries, Web Of Science
Added: August 6, 2018

2007 journal article

Comprehensive Transcriptome Profiling in Tomato Reveals a Role for Glycosyltransferase in Mi-Mediated Nematode Resistance

Plant Physiology, 144(2), 1079–1092.

Contributors: J. Schaff n, D. Nielsen n, C. Smith n, E. Scholl n & D. Bird n

MeSH headings : Animals; Feeding Behavior / physiology; Gene Expression; Gene Expression Profiling; Gene Expression Regulation, Plant; Gene Silencing; Genomics; Glycosyltransferases / metabolism; Host-Parasite Interactions / physiology; Solanum lycopersicum / enzymology; Solanum lycopersicum / genetics; Solanum lycopersicum / parasitology; Oligonucleotide Array Sequence Analysis; Plant Roots / enzymology; Plant Roots / metabolism; Plant Roots / parasitology; Reproduction / physiology; Tylenchoidea / physiology
TL;DR: The root transcriptome of the resistant and susceptible cultivars ‘Motelle’ and ‘Moneymaker’ is interrogated, providing a picture of global gene expression changes in roots during compatible and incompatible associations with RKN, and point to candidates for further investigation. (via Semantic Scholar)
UN Sustainable Development Goal Categories
2. Zero Hunger (Web of Science)
13. Climate Action (Web of Science)
15. Life on Land (OpenAlex)
Sources: Crossref, Web Of Science, ORCID, NC State University Libraries
Added: August 6, 2018

2007 journal article

Elucidation of veA-dependent genes associated with aflatoxin and sclerotial production in Aspergillus flavus by functional genomics

Applied Microbiology and Biotechnology, 76(5), 1107–1118.

author keywords: Aspergillus flavus; veA; aflatoxin; sclerotia; microarray
MeSH headings : Aflatoxins / biosynthesis; Anthraquinones / metabolism; Aspergillus flavus / genetics; Aspergillus flavus / growth & development; Aspergillus flavus / metabolism; Fungal Proteins / genetics; Fungal Proteins / metabolism; Gene Expression Profiling; Gene Expression Regulation, Fungal; Gene Library; Genomics; Oligonucleotide Array Sequence Analysis / methods
TL;DR: Microarray technology was used to identify a subgroup of veA-dependent genes that exhibited time-dependent expression profiles similar to those of known aflatoxin biosynthetic genes or that were candidates for involvement in sclerotial production in the wild type. (via Semantic Scholar)
Sources: Crossref, NC State University Libraries, Web Of Science
Added: August 6, 2018

2006 journal article

A unified mixed-model method for association mapping that accounts for multiple levels of relatedness

Nature Genetics, 38(2), 203–208.

By: J. Yu*, G. Pressoir*, W. Briggs*, I. Vroh Bi*, M. Yamasaki*, J. Doebley*, M. McMullen*, B. Gaut* ...

Contributors: J. Yu*, G. Pressoir*, W. Briggs*, I. Bi*, M. Yamasaki*, J. Doebley*, M. McMullen*, B. Gaut* ...

MeSH headings : Gene Expression; Genetic Techniques; Genetic Variation; Heredity / genetics; Humans; Models, Genetic; Phenotype; Quantitative Trait, Heritable; Research Design; Zea mays / genetics
TL;DR: A unified mixed-model approach to account for multiple levels of relatedness simultaneously as detected by random genetic markers is developed and provides a powerful complement to currently available methods for association mapping. (via Semantic Scholar)
UN Sustainable Development Goal Categories
2. Zero Hunger (Web of Science)
13. Climate Action (Web of Science)
15. Life on Land (Web of Science)
Sources: Crossref, Web Of Science, ORCID
Added: August 6, 2018

2005 journal article

Association of genetic polymorphisms with risk of renal injury after coronary bypass graft surgery

American Journal of Kidney Diseases, 45(3), 519–530.

By: M. Stafford-Smith*, M. Podgoreanu*, M. Swaminathan*, B. Phillips-Bute*, J. Mathew*, E. Hauser*, M. Winn*, C. Milano* ...

author keywords: acute renal failure (ARF); polymorphism; genetic; postoperative; intensive care; cardiopulmonary bypass (CPB); heart surgery; cardiac surgery; human; angiotensin-converting enzyme (ACE); associate study; candidate genes
MeSH headings : Acute Kidney Injury / blood; Acute Kidney Injury / epidemiology; Acute Kidney Injury / ethnology; Acute Kidney Injury / genetics; Black or African American / genetics; Aged; Alleles; Angiotensins / genetics; Apolipoproteins E / genetics; Cardiovascular Diseases / epidemiology; Cardiovascular Diseases / surgery; Coronary Artery Bypass; Creatinine / blood; Cytokines / genetics; DNA Mutational Analysis; Female; Follow-Up Studies; Genetic Predisposition to Disease; Humans; Male; Middle Aged; Nitric Oxide Synthase / genetics; Nitric Oxide Synthase Type III; North Carolina / epidemiology; Polymorphism, Genetic; Postoperative Complications / epidemiology; Prospective Studies; Pulmonary Disease, Chronic Obstructive / epidemiology; Receptor, Angiotensin, Type 1 / genetics; Risk; White People / genetics
TL;DR: It is identified that genetic polymorphisms that collectively provide 2- to 4-fold improvement over preoperative clinical factors alone in explaining post-cardiac surgery renal dysfunction are associated with increased renal inflammatory and/or vasoconstrictor responses. (via Semantic Scholar)
UN Sustainable Development Goal Categories
3. Good Health and Well-being (Web of Science; OpenAlex)
Sources: Crossref, NC State University Libraries, Web Of Science
Added: August 6, 2018

2005 journal article

Genetic Polymorphisms and the Risk of Stroke After Cardiac Surgery

Stroke, 36(9), 1854–1858.

author keywords: cardiac surgical procedures; C-reactive protein; interleukin-6; polymorphism; stroke
MeSH headings : Aged; Alleles; C-Reactive Protein / genetics; Cardiopulmonary Bypass; Female; Genetic Predisposition to Disease; Genetic Variation; Humans; Inflammation; Interleukin-6 / genetics; Male; Middle Aged; Models, Genetic; Multivariate Analysis; Mutation; Odds Ratio; Polymorphism, Genetic; Polymorphism, Single Nucleotide; Postoperative Complications; Risk; Sex Factors; Stroke / genetics; Thoracic Surgery
TL;DR: It is demonstrated that common genetic variants of CRP (3′UTR 1846C/T) and IL-6 (−174G/C) are significantly associated with the risk of stroke after cardiac surgery, suggesting a pivotal role of inflammation in post–cardiac surgery stroke. (via Semantic Scholar)
Sources: Crossref, NC State University Libraries, Web Of Science
Added: August 6, 2018

2005 journal article

Measures of human population structure show heterogeneity among genomic regions

Genome Research, 15(11), 1468–1476.

By: B. Weir n, L. Cardon*, A. Anderson n, D. Nelson & W. Hill*

MeSH headings : Chromosomes, Human / genetics; Ethnicity / genetics; Genetic Heterogeneity; Genetics, Population; Genome, Human / genetics; Genomics / methods; Haplotypes / genetics; Humans; Linkage Disequilibrium / genetics; Polymorphism, Single Nucleotide / genetics; United States
TL;DR: Estimates of genetic population structure (F(ST) were constructed from all autosomes in two large SNP data sets, and it is shown that individual-marker estimates are too variable to be useful. (via Semantic Scholar)
Sources: Crossref, Web Of Science
Added: August 6, 2018

2005 journal article

Measures of human population structure show heterogeneity among genomic regions

Genome Res, 15(11), 1468–1476.

By: B. Weir, L. Cardon, A. Anderson, D. Nielsen & W. Hill

Source: ORCID
Added: January 25, 2021

2004 journal article

Effect of Two- and Three-Locus Linkage Disequilibrium on the Power to Detect Marker/Phenotype Associations

Genetics, 168(2), 1029–1040.

By: D. Nielsen n, M. Ehm*, D. Zaykin* & B. Weir n

MeSH headings : Case-Control Studies; Computational Biology / methods; Computational Biology / statistics & numerical data; Genetic Markers / genetics; Genetic Variation / genetics; Genotype; Haplotypes; Humans; Linkage Disequilibrium / genetics; Phenotype; Polymorphism, Genetic / genetics; Quantitative Trait, Heritable
TL;DR: This work examines many different patterns of LD defined by both pairwise and joint multilocus LD terms, and examines how changes in these patterns affect the power to detect association when performing single-marker and haplotype-based case-control tests. (via Semantic Scholar)
Sources: Crossref, NC State University Libraries, Web Of Science
Added: August 6, 2018

2004 conference paper

Multi-locus Linkage Disequilibrium and Haplotype-Based Tests of Association

Computational Methods for SNPs and Haplotype Inference, 139–139.

By: D. Nielsen n

Event: DIMACS/RECOMB Satellite Workshop at Piscataway, New Jersey, USA on November 21-22, 2002

TL;DR: Several tests of haplotype association are presented here, along with a comparison of these tests within different LD contexts, and there is no longer a simple relationship with recombination. (via Semantic Scholar)
Sources: Crossref, NC State University Libraries
Added: March 5, 2021

2004 journal article

The Splicing Graph – A Tool for Visualising Gene Structure and Alternative Splicing

Future Drug Discovery, 62–65.

By: J. Leipzig, D. Nielsen & S. Heber

Source: NC State University Libraries
Added: March 19, 2021

2001 journal article

Applying Data Mining Techniques to the Mapping of Complex Disease Genes

Genetic Epidemiology, 21(S1), S435–S440.

By: W. Czika n, B. Weir n, S. Edwards n, R. Thompson n, D. Nielsen n, J. Brocklebank n, C. Zinkus n, E. Martin*, K. Nobler

MeSH headings : Chromosome Mapping / statistics & numerical data; Data Collection / statistics & numerical data; Decision Trees; Gene Frequency; Genetic Markers / genetics; Genetic Predisposition to Disease / genetics; Genotype; Humans; Models, Genetic; Polymorphism, Single Nucleotide / genetics; Regression Analysis
TL;DR: The result of incorporating data mining techniques with more classical methods is an improvement in the analysis, both by correctly classifying the affection status of more individuals and by locating more single nucleotide polymorphisms related to the disease, relative to analyses that use classical methods alone. (via Semantic Scholar)
UN Sustainable Development Goal Categories
Sources: Crossref, NC State University Libraries, ORCID
Added: August 6, 2018

2001 journal article

Association Studies under General Disease Models

Theoretical Population Biology, 60(3), 253–263.

By: D. Nielsen n & B. Weir n

MeSH headings : Alleles; Apolipoproteins E / genetics; Chromosome Mapping / methods; Cytochrome P-450 CYP2D6 / genetics; Genetic Markers; Genetic Predisposition to Disease; Genotype; Haplotypes; Humans; Linkage Disequilibrium; Models, Genetic; Phenotype
TL;DR: A general framework to examine association mapping methods is adopted which helps to clarify the nature of case-control and transmission/disequilibrium-type tests and reveals the relationship between measures of association and coefficients of linkage disequilibrium. (via Semantic Scholar)
UN Sustainable Development Goal Categories
Sources: Crossref, NC State University Libraries, Web Of Science
Added: August 6, 2018

2001 journal article

Association mapping: where we’ve been, where we’re going

Expert Review of Molecular Diagnostics, 1(3), 334–342.

By: D. Nielsen n & D. Zaykin n

MeSH headings : Analysis of Variance; Case-Control Studies; Chromosome Mapping; Family Health; Genetic Markers; Genotype; Haplotypes; Humans; Linkage Disequilibrium; Molecular Diagnostic Techniques; Phenotype; Quantitative Trait, Heritable
TL;DR: The basis of association mapping is described, and a number of the commonly used techniques used for localizing – or mapping – genes affecting a trait of interest are discussed. (via Semantic Scholar)
Sources: NC State University Libraries, ORCID
Added: January 25, 2021

2001 journal article

Dwarf8 polymorphisms associate with variation in flowering time

Nature Genetics, 28(3), 286–289.

By: J. Thornsberry n, M. Goodman n, J. Doebley*, S. Kresovich*, D. Nielsen n & E. Buckler n

MeSH headings : Genes, Plant; Linkage Disequilibrium; Phenotype; Plant Proteins / genetics; Plant Shoots / genetics; Plant Shoots / growth & development; Polymorphism, Genetic; Quantitative Trait, Heritable; Reproduction / genetics; Zea mays / genetics; Zea mays / growth & development
UN Sustainable Development Goal Categories
2. Zero Hunger (Web of Science)
13. Climate Action (Web of Science)
15. Life on Land (Web of Science)
Sources: Crossref, Web Of Science, ORCID
Added: August 6, 2018

2001 journal article

Evolution of the Simulated Data Problem

Genetic Epidemiology, 21(S1), S325–S331.

By: D. Thomas*, I. Borecki*, G. Thomson*, K. Weiss*, L. Almasy*, J. Blangero*, D. Nielsen n, J. Terwilliger n, D. Zaykin n, J. MacCluer*

author keywords: complex diseases; linkage disequilibrium; pedigree data; population genetics; simulation
MeSH headings : Chromosome Mapping; Computer Simulation; Genetics, Population; Genotype; Humans; Phenotype
TL;DR: The simulated data problem was designed via an interactive process by the Simulation Problem Organizing Committee and the selected data simulators and a population genetics model was used to generate the simulated genes. (via Semantic Scholar)
UN Sustainable Development Goal Categories
Sources: Crossref, Web Of Science, ORCID
Added: August 6, 2018

2001 journal article

GAW12: Simulated Genome Scan, Sequence, and Family Data for a Common Disease

Genetic Epidemiology, 21(S1), S332–S338.

By: L. Almasy*, J. Terwilliger*, D. Nielsen n, T. Dyer*, D. Zaykin n & J. Blangero*

author keywords: population isolate; quantitative trait; simulation
MeSH headings : Adolescent; Adult; Aged; Child; Chromosome Mapping / statistics & numerical data; Female; Genetic Markers / genetics; Genetic Variation / genetics; Genetics, Population; Genome, Human; Humans; Lod Score; Male; Microsatellite Repeats; Middle Aged; Models, Genetic; Phenotype; Polymorphism, Genetic; Quantitative Trait, Heritable; Recombination, Genetic
TL;DR: The Genetic Analysis Workshop (GAW) 12 simulated data involves a common disease defined by imposing a threshold on a quantitative liability distribution Associated with the disease are five quantitative risk factors, a quantitative environmental exposure, and a dichotomous environmental variable. (via Semantic Scholar)
UN Sustainable Development Goal Categories
Sources: Crossref, NC State University Libraries, Web Of Science
Added: August 6, 2018

1999 journal article

A classical setting for associations between markers and loci affecting quantitative traits

Genetical Research, 74(3), 271–277.

By: D. Nielsen n & B. Weir n

MeSH headings : Animals; Genetic Markers; Humans; Mathematical Computing; Models, Genetic; Quantitative Trait, Heritable
TL;DR: It is considered that this greater-than-usual level of generality leads to additional insights, in a way reminiscent of Cockerham's decomposition of genetic variance into five terms: three terms in addition to the usual additive and dominance terms. (via Semantic Scholar)
UN Sustainable Development Goal Categories
Sources: Crossref, NC State University Libraries, Web Of Science
Added: August 6, 2018

1999 journal article

Localization of the locus causing Spider Lamb Syndrome to the distal end of ovine Chromosome 6

Mammalian Genome, 10(1), 35–38.

By: N. Cockett*, T. Shay*, J. Beever*, D. Nielsen n, J. Albretsen*, M. Georges*, K. Peterson*, A. Stephens* ...

MeSH headings : Animal Diseases / genetics; Animals; Chromosome Mapping; Female; Genetic Linkage; Genetic Markers; Inbreeding; Male; Osteochondrodysplasias / genetics; Pedigree; Polymorphism, Single-Stranded Conformational; Protein-Tyrosine Kinases; Receptor, Fibroblast Growth Factor, Type 3; Receptors, Fibroblast Growth Factor / genetics; Sheep / genetics
TL;DR: Two large pedigrees segregating for the SLS mutation were established, and a genome scan with genetic markers from previously published genome maps of cattle and sheep was used to map the locus causing SLS. (via Semantic Scholar)
UN Sustainable Development Goal Categories
2. Zero Hunger (OpenAlex)
Sources: Crossref, Web Of Science, ORCID
Added: August 6, 2018

1999 journal article

Novel tests for marker-disease association using the collaborative study on the genetics of alcoholism data

Genetic Epidemiology, 17(S1), S265–S270.

By: D. Nielsen n & D. Zaykin n

MeSH headings : Alcoholism / genetics; Algorithms; Bayes Theorem; Black People / genetics; Chromosome Mapping; Genetic Linkage; Genetic Markers; Genetic Testing; Genome; Humans; Linkage Disequilibrium; White People / genetics
TL;DR: Several novel tests for association and linkage in the presence of association to the Genetic Analysis Workshop 11 Problem 1 data set included a Hardy‐Weinberg test for association between a marker and a disease susceptibility locus, a Bayesian transmission/disequilibrium test, and aBayesian case‐control test. (via Semantic Scholar)
UN Sustainable Development Goal Categories
3. Good Health and Well-being (OpenAlex)
Sources: Crossref, NC State University Libraries
Added: September 5, 2020

1998 journal article

Detecting Marker-Disease Association by Testing for Hardy-Weinberg Disequilibrium at a Marker Locus

The American Journal of Human Genetics, 63(5), 1531–1540.

By: D. Nielsen n, M. Ehm* & B. Weir n

MeSH headings : Alleles; Genes, Recessive; Genetic Diseases, Inborn / genetics; Genetic Markers; Genetic Predisposition to Disease; Heterozygote; Humans; Linkage Disequilibrium; Models, Genetic; Models, Statistical
TL;DR: It does not follow that the usual measures of linkage disequilibrium are zero, given disease heterogeneity, and care is needed in the drawing of inferences from marker Hardy-Weinberg disequilibria for disease-susceptibility loci with more than two alleles. (via Semantic Scholar)
Sources: Crossref, NC State University Libraries, Web Of Science
Added: August 6, 2018

1996 journal article

Polar Overdominance at the Ovine callipyge Locus

Science, 273(5272), 236–238.

By: N. Cockett*, S. Jackson*, T. Shay*, F. Farnir*, S. Berghmans*, G. Snowder*, D. Nielsen*, M. Georges*

MeSH headings : Animals; Chromosome Mapping; Crosses, Genetic; Female; Genes, Dominant; Genomic Imprinting; Genotype; Heterozygote; Lod Score; Male; Models, Genetic; Muscle, Skeletal / anatomy & histology; Mutation; Phenotype; Sheep / anatomy & histology; Sheep / genetics
TL;DR: The callipYge phenotype was found to be characterized by a nonmendelian inheritance pattern, referred to as polar overdominance, where only heterozygous individuals having inherited the callipyge mutation from their sire express the phenotype. (via Semantic Scholar)
Sources: Crossref, ORCID
Added: January 25, 2021

1995 journal article

Mapping Quantitative Trait Loci Controlling Milk Production in Dairy Cattle by Exploiting Progeny Testing

Genetics, 139(2), 907–920.

By: M. Georges, D. Nielsen*, M. Mackinnon, A. Mishra, R. Okimoto, A. Pasquino, L. Sargeant, A. Sorensen ...

MeSH headings : Animals; Cattle / genetics; Chromosome Mapping / methods; Female; Genetic Markers; Lactation / genetics; Lod Score; Male; Pedigree
Sources: NC State University Libraries, ORCID
Added: January 25, 2021

1994 journal article

Chromosomal localization of the callipyge gene in sheep (Ovis aries) using bovine DNA markers.

Proceedings of the National Academy of Sciences, 91(8), 3019–3023.

By: N. Cockett*, S. Jackson*, T. Shay*, D. Nielsen*, S. Moore*, M. Steele*, W. Barendse*, R. Green*, M. Georges*

MeSH headings : Animals; Base Sequence; Cattle; Chromosome Mapping; DNA Primers / chemistry; Genes; Genetic Linkage; Genetic Markers; Meat; Molecular Sequence Data; Muscles / anatomy & histology; Sheep / genetics
TL;DR: Chromosomal localization of the ovine callipyge locus is the first step toward positional cloning of the corresponding gene in Bovidae. (via Semantic Scholar)
UN Sustainable Development Goal Categories
15. Life on Land (OpenAlex)
Sources: Crossref, NC State University Libraries
Added: September 5, 2020

1993 journal article

Microsatellite mapping of a gene affecting horn development in Bos taurus

Nature Genetics, 4(2), 206–210.

By: M. Georges, R. Drinkwater*, T. King*, A. Mishra*, S. Moore*, D. Nielsen*, L. Sargeant*, A. Sorensen* ...

MeSH headings : Alleles; Animals; Breeding; Cattle / anatomy & histology; Cattle / genetics; Chromosome Mapping; DNA, Satellite / genetics; Female; Genes; Genetic Markers; Horns / growth & development; Hybrid Cells; Lod Score; Male; Pedigree; Phenotype; Rodentia; Selection, Genetic
TL;DR: The existence of the postulated polled locus and the hypothesized inheritance pattern will allow marker assisted selection for the polledness trait in breeding programs and is a first step towards positional cloning and molecular study of a gene that has been subjected to both natural and artificial selection. (via Semantic Scholar)
Sources: Crossref, ORCID
Added: January 25, 2021

1993 journal article

Microsatellite mapping of the gene causing weaver disease in cattle will allow the study of an associated quantitative trait locus.

Proceedings of the National Academy of Sciences, 90(3), 1058–1062.

By: M. Georges, A. Dietz, A. Mishra, D. Nielsen*, L. Sargeant, A. Sorensen, M. Steele, X. Zhao, H. Leipold, J. Womack

author keywords: ATAXIA; LINKAGE; QTL
MeSH headings : Animals; Base Sequence; Cattle; Cattle Diseases / etiology; Cattle Diseases / genetics; Chromosome Mapping; DNA, Satellite / genetics; Encephalomyelitis / etiology; Encephalomyelitis / genetics; Encephalomyelitis / veterinary; Genetic Linkage; Genetic Markers / genetics; Milk / metabolism; Molecular Sequence Data; Pedigree; Statistics as Topic
TL;DR: This microsatellite can be used to identify weaver carriers, to select against this genetic defect, and to study the effect of the corresponding chromosomal region on milk production in Brown Swiss and other breeds of cattle. (via Semantic Scholar)
Sources: Crossref, ORCID
Added: January 25, 2021

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