Works Published in 2006
Displaying works 1 - 20 of 21 in total
Sorted by most recent date added to the index first, which may not be the same as publication date order.
2006 journal article
Immunogenetics of CD4 Lymphocyte Count Recovery during Antiretroviral Therapy: An AIDS Clinical Trials Group Study
The Journal of Infectious Diseases, 194(8), 1098–1107.
MeSH headings : Adult; Antiretroviral Therapy, Highly Active; Apoptosis Regulatory Proteins / genetics; CD4 Lymphocyte Count; CD4-Positive T-Lymphocytes / cytology; Female; HIV Infections / blood; HIV Infections / drug therapy; HIV Infections / epidemiology; HIV Infections / genetics; Humans; Interleukin-2 / genetics; Male; Membrane Glycoproteins / genetics; Polymorphism, Genetic; Puerto Rico / epidemiology; Receptors, Interleukin-15; Receptors, Interleukin-2 / genetics; Retrospective Studies; TNF-Related Apoptosis-Inducing Ligand; Tumor Necrosis Factor-alpha / genetics; United States / epidemiology
academic.oup.com (publisher PDF)
UN Sustainable Development Goal Categories
3. Good Health and Well-being
(OpenAlex)
Source: Crossref
Added: October 29, 2021
2006 journal article
Drug Transporter and Metabolizing Enzyme Gene Variants and Nonnucleoside Reverse-Transcriptase Inhibitor Hepatotoxicity
Clinical Infectious Diseases, 43(6), 779–782.
MeSH headings : Adult; Alkynes; Anti-HIV Agents / adverse effects; Anti-HIV Agents / metabolism; Anti-HIV Agents / therapeutic use; Aryl Hydrocarbon Hydroxylases / genetics; Benzoxazines; Case-Control Studies; Chemical and Drug Induced Liver Injury; Cyclopropanes; Cytochrome P-450 CYP2B6; Cytochrome P-450 CYP3A; Cytochrome P-450 Enzyme System / genetics; Female; Genes, MDR; Genetic Variation; Genotype; HIV Infections / drug therapy; HIV-1; Humans; Liver / drug effects; Liver Diseases / genetics; Liver Diseases / virology; Male; Nevirapine / adverse effects; Nevirapine / metabolism; Nevirapine / therapeutic use; Oxazines / adverse effects; Oxazines / metabolism; Oxazines / therapeutic use; Oxidoreductases, N-Demethylating / genetics; Reverse Transcriptase Inhibitors / adverse effects; Reverse Transcriptase Inhibitors / metabolism; Reverse Transcriptase Inhibitors / therapeutic use
TL;DR:
This nested case-control study examined relationships between MDR1, CYP2B6, and CYP3A4 variants and hepatotoxicity during antiretroviral therapy with either efavirenz- or nevirapine-containing regimens.
(via Semantic Scholar)
UN Sustainable Development Goal Categories
3. Good Health and Well-being
(OpenAlex)
Source: Crossref
Added: October 29, 2021
2006 journal article
Multifactor dimensionality reduction reveals gene–gene interactions associated with multiple sclerosis susceptibility in African Americans
Genes & Immunity, 7(4), 310–315.
MeSH headings : Black or African American / genetics; Case-Control Studies; Epistasis, Genetic; Female; Gene Deletion; Genetic Predisposition to Disease; Genotype; Humans; Interleukin-5 Receptor alpha Subunit; Lipopolysaccharide Receptors / genetics; Male; Multifactorial Inheritance; Multiple Sclerosis / genetics; Multiple Sclerosis / immunology; Polymorphism, Genetic; Polymorphism, Single Nucleotide; Receptors, Interleukin / genetics; Receptors, Interleukin-4 / genetics
TL;DR:
A highly efficient multilocus genotyping assay representing variation in 34 genes associated with inflammatory pathways is used to explore gene–gene interactions and disease susceptibility in a well-characterized African-American case–control MS data set, and the multifactor dimensionality reduction (MDR) test is applied to detect epistasis.
(via Semantic Scholar)
Source: Crossref
Added: October 29, 2021
2006 chapter
Comparison of Neural Network Optimization Approaches for Studies of Human Genetics
In F. Rothlauf (Ed.), Applications of Evolutionary Computing. EvoWorkshops 2006 (pp. 103–114).
Ed(s): F. Rothlauf
TL;DR:
This study demonstrates the utility of using GE to evolve NN in studies of complex human disease and compares the performance of GENN to GPNN, a traditional back-propagation neural network (BPNN) and a random search algorithm.
(via Semantic Scholar)
Source: Crossref
Added: October 29, 2021
2006 journal article
The effect of reduction in cross-validation intervals on the performance of multifactor dimensionality reduction
Genetic Epidemiology, 30(6), 546–555.
author keywords: model validation; MDR; epistasis; gene-gene interactions
MeSH headings : Alzheimer Disease / genetics; Genetic Predisposition to Disease / genetics; Genotype; Humans; Models, Genetic; Multifactorial Inheritance; Polymorphism, Genetic; Risk Assessment / statistics & numerical data
TL;DR:
It was found that eliminating CV made final model selection impossible, but that reducing the number of CV intervals from ten to five caused no loss of power, thereby reducing the computation time of the algorithm by half.
(via Semantic Scholar)
UN Sustainable Development Goal Categories
3. Good Health and Well-being
(OpenAlex)
Source: Crossref
Added: October 29, 2021
2006 journal article
A unified mixed-model method for association mapping that accounts for multiple levels of relatedness
Nature Genetics, 38(2), 203–208.
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, ORCID
Added: January 25, 2021
2006 journal article
Benchmarking of Linear and Nonlinear Approaches for Quantitative Structure−Property Relationship Studies of Metal Complexation with Ionophores
Journal of Chemical Information and Modeling, 46(2), 808–819.
MeSH headings : Algorithms; Europium / chemistry; Ionophores / chemistry; Linear Models; Models, Theoretical; Nonlinear Dynamics; Organometallic Compounds / chemistry; Quantitative Structure-Activity Relationship; Silver / chemistry; Software Validation
TL;DR:
Individual structure-complexation property models obtained with nonlinear methods demonstrated a significantly better performance than the models built using multilinear regression analysis (MLRA), however, the averaging of several MLRA models based on SMF descriptors provided as good of a prediction as the most efficient nonlinear techniques.
(via Semantic Scholar)
Source: Crossref
Added: August 28, 2020
2006 journal article
Detection of putative secreted proteins in the plant-parasitic nematode Heterodera schachtii
Parasitology Research, 98(5), 414–424.
Contributors: B. Vanholme *, M. Mitreva *, W. Van Criekinge *, M. Logghe*, D. Bird n , J. McCarter*, G. Gheysen *
MeSH headings : Animals; Computational Biology / methods; Contig Mapping; DNA, Helminth / chemistry; DNA, Helminth / genetics; Expressed Sequence Tags; Gene Library; Glycoside Hydrolases / chemistry; Glycoside Hydrolases / genetics; Helminth Proteins / genetics; Plants / parasitology; Protein Sorting Signals / genetics; Protein Structure, Tertiary / genetics; Tylenchoidea / genetics
TL;DR:
The in silico approach described here is an effective way to identify putative secreted proteins and prioritize candidates for further studies and provides the first report of an arabinogalactan endo-1,4-β-galactosidase enzyme in animals.
(via Semantic Scholar)
UN Sustainable Development Goal Categories
2. Zero Hunger
(Web of Science)
13. Climate Action
(Web of Science)
Source: ORCID
Added: January 30, 2020
2006 journal article
Visual analysis of statistical results from microarray studies of human breast cancer.
Oncology Reports, c, 1043–1047. http://europepmc.org/abstract/med/16525698
Source: ORCID
Added: May 14, 2019
2006 article
Integrated analysis of genetic and proteomic data.
http://europepmc.org/theses/ETH/7299
Source: ORCID
Added: May 14, 2019
2006 journal article
Visual analysis of statistical results from microarray studies of human breast cancer
Oncol Rep, 4(4), 1043–1047.
Contributors: D. Reif* & J. Moore
MeSH headings : Antineoplastic Agents / therapeutic use; Breast Neoplasms / drug therapy; Breast Neoplasms / genetics; Data Interpretation, Statistical; Databases, Genetic; Female; Gene Expression Profiling; Humans; Oligonucleotide Array Sequence Analysis; Software
TL;DR:
Using a publicly available microarray dataset of gene expression response to chemotherapeutic agents in human breast cancer cell lines, it is demonstrated the usefulness of the EVA system for interpreting statistical results.
(via Semantic Scholar)
Source: ORCID
Added: May 14, 2019
2006 conference paper
Understanding the evolutionary process of grammatical evolution neural networks for feature selection in genetic epidemiology
Proceedings of the 2006 IEEE Symposium on Computational Intelligence in Bioinformatics and Computational Biology, CIBCB'06, 263–270.
Contributors: A. Motsinger*, D. Reif* , S. Dudek * & M. Ritchie *
TL;DR:
The evolutionary characteristics of GENN are compared to that of a random search neural network strategy to better understand the benefits provided by the evolutionary learning process - including advantages with respect to chromosome size and the representation of functional versus non-functional features within the models generated by the two approaches.
(via Semantic Scholar)
UN Sustainable Development Goal Categories
3. Good Health and Well-being
(OpenAlex)
Source: ORCID
Added: May 14, 2019
2006 journal article
Machine Learning for Detecting Gene-Gene Interactions
Applied Bioinformatics, 5(2), 77â88.
Contributors: B. McKinney *, D. Reif* , M. Ritchie* & J. Moore *
MeSH headings : Algorithms; Animals; Artificial Intelligence; Genome, Human; Genomics / methods; Genotype; Humans; Models, Genetic; Models, Statistical; Neural Networks, Computer; Polymorphism, Single Nucleotide
TL;DR:
This review discusses machine-learning models and algorithms for identifying and characterising susceptibility genes in common, complex, multifactorial human diseases and focuses on the following machine- learning methods that have been used to detect gene-gene interactions: neural networks, cellular automata, random forests, and multifactor dimensionality reduction.
(via Semantic Scholar)
UN Sustainable Development Goal Categories
15. Life on Land
(OpenAlex)
Source: ORCID
Added: May 14, 2019
2006 conference paper
Feature selection using a random forests classifier for the integrated analysis of multiple data types
Proceedings of the 2006 IEEE Symposium on Computational Intelligence in Bioinformatics and Computational Biology, CIBCB'06, 171–178.
Contributors: D. Reif* , A. Motsinger*, B. McKinney *, J. Crowe Jr. & J. Moore
TL;DR:
The results indicate that utilizing multiple data types is beneficial when the disease model is complex and the phenotypic outcome-associated data type is unknown, and RF is adept at identifying relevant features in high-dimensional data with small main effects and low heritability.
(via Semantic Scholar)
UN Sustainable Development Goal Categories
15. Life on Land
(OpenAlex)
Source: ORCID
Added: May 14, 2019
2006 journal article
Cytokine expression patterns associated with systemic adverse events following smallpox immunization.
Journal of Infectious Diseases, 194(4), 444–453.
Contributors: B. McKinney *, D. Reif* , M. Rock*, K. Edwards *, S. Kingsmore *, J. Moore, J. Crowe Jr.
MeSH headings : Adolescent; Adult; Chemokine CCL11; Chemokines, CC / blood; Chemokines, CC / immunology; Cytokines / blood; Cytokines / immunology; Decision Trees; Female; Granulocyte Colony-Stimulating Factor / blood; Granulocyte Colony-Stimulating Factor / immunology; Humans; Intercellular Adhesion Molecule-1 / blood; Intercellular Adhesion Molecule-1 / immunology; Male; Skin Diseases, Vesiculobullous / chemically induced; Skin Diseases, Vesiculobullous / pathology; Skin Diseases, Vesiculobullous / prevention & control; Smallpox / prevention & control; Smallpox Vaccine / adverse effects; Tissue Inhibitor of Metalloproteinase-2 / blood; Tissue Inhibitor of Metalloproteinase-2 / immunology; Vaccinia virus / immunology
TL;DR:
This cytokine signature is characteristic of particular inflammatory response pathways and suggests that the secretion of cytokines by fibroblasts plays a central role in systemic adverse events.
(via Semantic Scholar)
Source: ORCID
Added: May 14, 2019
2006 journal article
Predicting Shine-Dalgarno sequence locations exposes genome annotation errors
PLOS COMPUTATIONAL BIOLOGY, 2(5), 454–466.
MeSH headings : Base Sequence; Codon, Initiator / genetics; Computational Biology; Escherichia coli / genetics; Gene Expression Regulation, Bacterial / genetics; Genome, Bacterial / genetics; Hydrogen Bonding; Models, Genetic; Peptide Chain Initiation, Translational / genetics; RNA, Messenger / genetics; RNA, Messenger / metabolism; RNA, Ribosomal / genetics; RNA, Ribosomal / metabolism; Research Design
TL;DR:
A new metric, relative spacing (RS), is created to identify both the location and the hybridization potential of SD sequences by simulating the binding between mRNAs and single-stranded 16S rRNA 3′ tails and provides a new way to explore the role of rRNA–mRNA nucleotide hybridization in translation initiation.
(via Semantic Scholar)
UN Sustainable Development Goal Categories
3. Good Health and Well-being
(Web of Science)
7. Affordable and Clean Energy
(OpenAlex)
Source: Web Of Science
Added: August 6, 2018
2006 journal article
A murine specific expansion of the Rhox cluster involved in embryonic stem cell biology is under natural selection
BMC Genomics, 7.
Source: NC State University Libraries
Added: August 6, 2018
2006 journal article
A method for isolation of Pasteuria penetrans endospores for bioassay and genomic studies
Journal of Nematology, 38(1), 165–167. http://www.scopus.com/inward/record.url?eid=2-s2.0-34248330929&partnerID=MN8TOARS
Contributors: J. Waterman, D. Bird & C. Opperman
Sources: NC State University Libraries, ORCID
Added: August 6, 2018
2006 journal article
A method for generating Meloidogyne incognita males
Journal of Nematology, 38(2), 192–194. http://www.scopus.com/inward/record.url?eid=2-s2.0-33750134280&partnerID=MN8TOARS
Contributors: D. Snyder, C. Opperman & D. Bird
Sources: NC State University Libraries, ORCID
Added: August 6, 2018
2006 journal article
Nematode gene sequences: Update for December 2005
Journal of Nematology, 37(4), 417–421.
Source: NC State University Libraries
Added: August 6, 2018
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