D. M. Nielsen

Works (20)

Updated: July 5th, 2023 16:03

2013 journal article

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

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

By: C. Franck *, D. Nielsen n  & J. Osborne n

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)
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Sources: Web Of Science, Crossref, 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.

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

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

2010 journal article

Genomic hotspots for adaptation: The population genetics of Mullerian mimicry in Heliconius erato

PLoS Genetics, 6(4).

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

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

2008 journal article

Does strong linkage disequilibrium guarantee redundant association results?

Genetic Epidemiology, 32(6), 546–552.

By: D. Nielsen n , S. Suchindran n & C. Smith n

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)
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Sources: Web Of Science, Crossref, NC State University Libraries
Added: August 6, 2018

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: Web Of Science, Crossref, NC State University Libraries
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.

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

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)
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15. Life on Land (OpenAlex)
Sources: Web Of Science, ORCID, NC State University Libraries, Crossref
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.

By: J. Cary *, G. OBrian n, D. Nielsen n , W. Nierman*, P. Harris-Coward*, J. Yu*, D. Bhatnagar*, T. Cleveland *, G. Payne n, A. Calvo *

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: Web Of Science, Crossref, NC State University Libraries
Added: August 6, 2018

2005 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)
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Sources: Web Of Science, ORCID, Crossref
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)
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Sources: Web Of Science, Crossref, NC State University Libraries
Added: August 6, 2018

2005 journal article

Genetic Polymorphisms and the Risk of Stroke After Cardiac Surgery

Stroke, 36(9), 1854–1858.

By: H. Grocott  n, W. White  n, R. Morris  n, M. Podgoreanu  n, J. Mathew  n, D. Nielsen n , D. Schwinn  n, M. Newman  n

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)
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3. Good Health and Well-being (Web of Science; OpenAlex)
Sources: Web Of Science, Crossref, NC State University Libraries
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)
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Sources: Web Of Science, Crossref
Added: August 6, 2018

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)
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Sources: Web Of Science, Crossref, NC State University Libraries
Added: August 6, 2018

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 n

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)
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Sources: NC State University Libraries, Crossref
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)
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Sources: Web Of Science, Crossref, NC State University Libraries
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)
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Sources: Web Of Science, Crossref, NC State University Libraries
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)
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2. Zero Hunger (OpenAlex)
Sources: Web Of Science, Crossref
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(Suppl.1), S265–270.

By: D. Nielsen & D. Zaykin

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

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)
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Sources: Web Of Science, Crossref, NC State University Libraries
Added: August 6, 2018

1987 book

Virginia's forest and wildlife resources: Present and future

Blacksburg: School of Forestry and Wildlife Resources, Virginia Polytechnic Institute & State University.

By: O. Hall, R. McElwee, L. H. W., N. F. M. & L. Nielsen

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

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