Works Published in 2008
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.
2008 journal article
Hemochromatosis Gene Polymorphisms, Mitochondrial Haplogroups, and Peripheral Lipoatrophy during Antiretroviral Therapy
The Journal of Infectious Diseases, 197(6), 858–866.
TL;DR:
HFE 187C>G and, possibly, mitochondrial haplogroup J gave relative protection against lipoatrophy during ART in A5005s and these associations should be replicated in other studies.
(via Semantic Scholar)
academic.oup.com (publisher PDF)
UN Sustainable Development Goal Categories
3. Good Health and Well-being
(OpenAlex)
Source: Crossref
Added: October 29, 2021
2008 conference paper
Linkage Analysis in American Staffordshire Terriers with Hereditary Cerebellar Cortical Degeneration
Journal of Veterinary Internal Medicine, 22(3), 723–724.
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.
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
Added: September 5, 2020
2008 journal article
Critical Assessment of QSAR Models of Environmental Toxicity against Tetrahymena pyriformis: Focusing on Applicability Domain and Overfitting by Variable Selection
Journal of Chemical Information and Modeling, 48(9), 1733–1746.
MeSH headings : Animals; Computer Simulation; Databases, Factual; Environmental Pollutants / chemistry; Environmental Pollutants / toxicity; Models, Biological; Models, Statistical; Normal Distribution; Predictive Value of Tests; Quantitative Structure-Activity Relationship; Reproducibility of Results; Tetrahymena pyriformis / drug effects; Toxicity Tests / standards
TL;DR:
It is shown that incorrect validation of a model may result in the wrong estimation of its performance and suggested how this problem could be circumvented and the distance to model metric could also be used to augment mechanistic QSAR models by estimating their prediction errors.
(via Semantic Scholar)
UN Sustainable Development Goal Categories
10. Reduced Inequalities
(OpenAlex)
Source: Crossref
Added: August 28, 2020
2008 journal article
Combinatorial QSAR Modeling of Chemical Toxicants Tested against Tetrahymena pyriformis
Journal of Chemical Information and Modeling, 48(4), 766–784.
MeSH headings : Animals; Combinatorial Chemistry Techniques; Quantitative Structure-Activity Relationship; Tetrahymena pyriformis / drug effects; Toxicity Tests
TL;DR:
An international virtual collaboratory consisting of six independent groups with shared interests in computational chemical toxicology develops 15 different types of QSAR models of aquatic toxicity and finds that consensus models afford higher prediction accuracy for the external validation data sets with the highest space coverage as compared to individual constituent models.
(via Semantic Scholar)
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)
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
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
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
262: Molecular signatures of preeclampsia in human term placentas
American Journal of Obstetrics and Gynecology, 199(6), S84.
UN Sustainable Development Goal Categories
2. Zero Hunger
(OpenAlex)
Source: Crossref
Added: February 24, 2020
2008 journal article
SILIP: A novel stable isotope labeling method for in planta quantitative proteomic analysis
Plant Journal, 56(5), 840–854.
Contributors: J. Schaff n, F. Mbeunkui n, K. Blackburn n, D. Bird n & M. Goshe n
author keywords: plant proteomics; quantitative analysis; mass spectrometry; liquid chromatography; isotope-coded; isotope ratio
MeSH headings : Chromatography, Liquid; Isotope Labeling / methods; Solanum lycopersicum / metabolism; Nitrogen / metabolism; Nitrogen Isotopes / metabolism; Phenotype; Plant Proteins / metabolism; Proteomics / methods; Soil; Tandem Mass Spectrometry
TL;DR:
SILIP (stable isotope labeling in planta) is developed using tomato plants as a method that allows soil-grown plants to be efficiently labeled using a 14N/15N isotope coding strategy, and thus provides a new quantitative proteomics tool to study both plant and plant-microorganism systems.
(via Semantic Scholar)
UN Sustainable Development Goal Categories
3. Good Health and Well-being
(Web of Science)
Source: ORCID
Added: January 30, 2020
2008 journal article
Genetic basis for adverse events after smallpox vaccination (Journal of Infectious Diseases (2008) 198, (16-22))
Journal of Infectious Diseases, 198(5).
Contributors: D. Reif , B. McKinney & A. Motsinger
UN Sustainable Development Goal Categories
3. Good Health and Well-being
(OpenAlex)
Source: ORCID
Added: May 14, 2019
2008 journal article
Genetic Basis for Adverse Events after Smallpox Vaccination
The Journal of Infectious Diseases, 198(1), 16–22.
Contributors: D. Reif* , B. McKinney *, A. Motsinger*, S. Chanock *, K. Edwards *, M. Rock*, J. Moore, J. Crowe Jr.
MeSH headings : Adult; Female; Genetic Predisposition to Disease; Genotype; Humans; Interferon Regulatory Factor-1 / genetics; Interleukin-4 / genetics; Male; Methylenetetrahydrofolate Reductase (NADPH2) / genetics; Polymorphism, Single Nucleotide; Smallpox Vaccine / adverse effects; Vaccination / adverse effects
TL;DR:
Genetic polymorphisms in genes expressing an enzyme previously associated with adverse reactions to a variety of pharmacologic agents (MTHFR) and an immunological transcription factor (IRF1) were associated with AEs after smallpox vaccination in 2 independent study samples.
(via Semantic Scholar)
UN Sustainable Development Goal Categories
3. Good Health and Well-being
(OpenAlex)
Sources: Crossref, ORCID
Added: May 14, 2019
2008 conference paper
A balanced accuracy fitness function leads to robust analysis using grammatical evolution neural networks in the case of class imbalance
Proceedings of the 10th annual conference on Genetic and evolutionary computation - GECCO '08, 353–354.
Contributors: N. Hardison n, D. Reif* , T. Fanelli*, M. Ritchie *, S. Dudek * & A. Motsinger-Reif n
TL;DR:
It is shown that when using classification error, class imbalance greatly decreases the power of GENN, and balanced error has replaced classification error in the GENN algorithm.
(via Semantic Scholar)
UN Sustainable Development Goal Categories
3. Good Health and Well-being
(OpenAlex)
Source: ORCID
Added: May 14, 2019
2008 journal article
A Comparison of Analytical Methods for Genetic Association Studies
GENETIC EPIDEMIOLOGY, 32(8), 767–778.
Contributors: A. Motsinger-Reif n, D. Reif* , T. Fanelli* & M. Ritchie *
author keywords: genetic association study; epistasis; multifactor dimensionality reduction; grammatical evolution neural networks; focused interaction testing framework
MeSH headings : Data Interpretation, Statistical; Epistasis, Genetic; Genetic Linkage; Genetic Techniques; Genome; Humans; Models, Genetic; Models, Statistical; Models, Theoretical; Neural Networks, Computer; Phenotype; Probability; Regression Analysis; Software
TL;DR:
This study compares the performance of six analytical approaches to detect both main effects and gene‐gene interactions in a range of genetic models and demonstrates the strengths and weaknesses of each and illustrates the importance of continued methods development.
(via Semantic Scholar)
UN Sustainable Development Goal Categories
3. Good Health and Well-being
(Web of Science)
15. Life on Land
(OpenAlex)
Sources: Web Of Science, ORCID
Added: August 6, 2018
2008 journal article
Basing population genetic inferences and models of molecular evolution upon desired stationary distributions of DNA or protein sequences
PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES, 363(1512), 3931–3939.
author keywords: variable-length Markov model; profile hidden Markov model; insertion-deletion model; scaled selection coefficient; fitness; Pfam
MeSH headings : Computer Simulation; DNA / genetics; Evolution, Molecular; Genetics, Population; INDEL Mutation / genetics; Markov Chains; Models, Genetic; Population Density; Proteins / genetics; Selection, Genetic
TL;DR:
This work explores how to construct time-reversible evolutionary models that yield stationary distributions of sequences that match given target distributions, and introduces an insertion–deletion model that describes selectively neutral evolutionary changes to DNA.
(via Semantic Scholar)
UN Sustainable Development Goal Categories
15. Life on Land
(Web of Science)
Source: Web Of Science
Added: August 6, 2018
2008 journal article
A sequence-anchored genetic linkage map for the moss, Physcomitrella patens
Plant Journal, 56(5), 840–854.
Source: NC State University Libraries
Added: August 6, 2018
2008 journal article
Sequence and genetic map of Meloidogyne hapla: A compact nematode genome for plant parasitism
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 105(39), 14802–14807.
Contributors: C. Opperman n, D. Bird n , V. Williamson *, D. Rokhsar *, M. Burke n, J. Cohn n, J. Cromer n, S. Diener n
author keywords: compaction; dauer; development; horizontal gene transfer; gene
MeSH headings : Animals; Base Sequence; Caenorhabditis elegans / genetics; Chromosome Mapping; Evolution, Molecular; Gene Duplication; Gene Transfer, Horizontal; Genome, Helminth; Host-Parasite Interactions / genetics; Molecular Sequence Data; Multigene Family; Operon; Phylogeny; Plants / parasitology; Synteny; Tylenchoidea / genetics
TL;DR:
Meloidogyne hapla is established as a tractable model plant-parasitic nematode amenable to forward and reverse genetics, and a complete genome sequence is presented that defines a platform to elucidate mechanisms of parasitism by what is the largest uncontrolled group of plant pathogens worldwide.
(via Semantic Scholar)
UN Sustainable Development Goal Categories
Sources: Web Of Science, ORCID, NC State University Libraries
Added: August 6, 2018
2008 journal article
Selection shapes malaria genomes and drives divergence between pathogens infecting hominids versus rodents
BMC Evolutionary Biology, 8.
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.
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: Web Of Science, Crossref, NC State University Libraries
Added: August 6, 2018
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