Works Published in 2013
Displaying works 1 - 20 of 48 in total
Sorted by most recent date added to the index first, which may not be the same as publication date order.
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
Added: September 5, 2020
2013 journal article
Integrative Chemical–Biological Read-Across Approach for Chemical Hazard Classification
Chemical Research in Toxicology, 26(8), 1199–1208.
MeSH headings : Animals; Anti-Bacterial Agents / chemistry; Anti-Bacterial Agents / toxicity; Anticonvulsants / chemistry; Anticonvulsants / toxicity; Bacteria / metabolism; Benzbromarone / chemistry; Benzbromarone / toxicity; Carbamazepine / chemistry; Carbamazepine / toxicity; Chloramphenicol / chemistry; Chloramphenicol / toxicity; Databases, Chemical; Gout Suppressants / chemistry; Gout Suppressants / toxicity; Hazardous Substances / classification; Hazardous Substances / toxicity; Liver / drug effects; Quantitative Structure-Activity Relationship; Rats; Transcriptome / drug effects
TL;DR:
A hazard classification and visualization method that draws upon both chemical structural similarity and comparisons of biological responses to chemicals measured in multiple short-term assays ("biological" similarity) to predict chemical toxicity.
(via Semantic Scholar)
citeseerx.ist.psu.edu (repository)
Source: Crossref
Added: August 28, 2020
2013 journal article
Predicting Binding Affinity of CSAR Ligands Using Both Structure-Based and Ligand-Based Approaches
Journal of Chemical Information and Modeling, 53(8), 1915–1922.
MeSH headings : Databases, Pharmaceutical; Drug Discovery / methods; Ligands; Molecular Docking Simulation; Protein Binding; Quantitative Structure-Activity Relationship; Support Vector Machine
TL;DR:
This study shows that externally validated 2D QSAR models were capable of ranking CSAR ligands at least as accurately as more computationally intensive structure-based approaches used both by us and by other groups and ligand-based QSar models can complement structure- based approaches by boosting the prediction performances when used in consensus.
(via Semantic Scholar)
Source: Crossref
Added: August 28, 2020
2013 journal article
Discovery of Novel Antimalarial Compounds Enabled by QSAR-Based Virtual Screening
Journal of Chemical Information and Modeling, 53(2), 475–492.
MeSH headings : Antimalarials / chemistry; Antimalarials / pharmacology; Drug Discovery / methods; Humans; Malaria, Falciparum / drug therapy; Models, Biological; Plasmodium falciparum / drug effects; Quantitative Structure-Activity Relationship
TL;DR:
Quantitative structure-activity relationship models developed for a data set of 3133 compounds defined as either active or inactive against P. falciparum revealed novel chemical scaffolds which could be employed as starting points to discover novel antimalarial agents.
(via Semantic Scholar)
Source: Crossref
Added: August 28, 2020
2013 journal article
Using Graph Indices for the Analysis and Comparison of Chemical Datasets
Molecular Informatics, 32(9-10), 827–842.
author keywords: Chemical dataset graph; Graph indices; QSAR; ADDAGRA
TL;DR:
It is demonstrated that chemical datasets can be effectively characterized and compared by computing simple graph indices such as the average vertex degree or Randic connectivity index.
(via Semantic Scholar)
Source: Crossref
Added: August 28, 2020
2013 journal article
Unified Analysis of Secondary Traits in Case–Control Association Studies
Journal of the American Statistical Association, 108(502), 566–576.
author keywords: GWAS; Profile likelihood; Pseudo-likelihood; Retrospective study; Secondary phenotype; Semiparametric method
TL;DR:
A general retrospective likelihood framework is presented to perform association testing for both binary and continuous secondary traits, which respects marginal models and incorporates the interaction term and an alternative pseudo-likelihood method for handling covariates is presented.
(via Semantic Scholar)
Source: Crossref
Added: August 28, 2020
2013 journal article
The Genotype-Tissue Expression (GTEx) project
Nature Genetics, 45(6), 580–585.
MeSH headings : Consensus Development Conferences, NIH as Topic; Gene Expression; Gene Expression Profiling; Genome-Wide Association Study; Government Programs / ethics; Government Programs / legislation & jurisprudence; Humans; Molecular Sequence Annotation; Organ Specificity; Quantitative Trait Loci; Tissue Banks; United States
TL;DR:
The Genotype-Tissue Expression (GTEx) project is described, which will establish a resource database and associated tissue bank for the scientific community to study the relationship between genetic variation and gene expression in human tissues.
(via Semantic Scholar)
Source: Crossref
Added: August 28, 2020
2013 journal article
Assessment of beating parameters in human induced pluripotent stem cells enables quantitative in vitro screening for cardiotoxicity
Toxicology and Applied Pharmacology, 273(3), 500–507.
author keywords: iPSC; Calcium flux; Cardiotoxicity; hERG; Phenotypic screening; Predictive toxicology
MeSH headings : Area Under Curve; Cardiotoxins / pharmacology; Cell Survival / drug effects; Cells, Cultured; Drug Evaluation, Preclinical / methods; Drug-Related Side Effects and Adverse Reactions / diagnosis; Heart Diseases / chemically induced; Heart Diseases / diagnosis; Heart Diseases / pathology; High-Throughput Screening Assays; Humans; Induced Pluripotent Stem Cells / drug effects; Induced Pluripotent Stem Cells / metabolism; Myocytes, Cardiac / drug effects; Myocytes, Cardiac / metabolism; Myocytes, Cardiac / physiology; Phenotype; Risk Assessment
TL;DR:
Multi-parameter screening of beating profiles allows for cardiotoxicity risk assessment and identification of specific patterns defining mechanism-specific effects, and may be used widely for compound screening and early safety evaluation in drug development.
(via Semantic Scholar)
UN Sustainable Development Goal Categories
3. Good Health and Well-being
(OpenAlex)
Source: Crossref
Added: August 28, 2020
2013 journal article
Space-time clustering and the permutation moments of quadratic forms
Stat, 2(1), 292–302.
author keywords: exact testing; resampling; statistical computing
TL;DR:
The extension of this work to quadratic forms greatly expands the utility of density approximations for these problems, including for high-dimensional applications, where the statistics must be extreme in order to exceed stringent testing thresholds.
(via Semantic Scholar)
UN Sustainable Development Goal Categories
1. No Poverty
(OpenAlex)
3. Good Health and Well-being
(Web of Science)
Source: Crossref
Added: August 28, 2020
2013 journal article
The Value of Statistical or Bioinformatics Annotation for Rare Variant Association With Quantitative Trait
Genetic Epidemiology, 37(7), 666–674.
author keywords: rare variants; association; weighting; variable selection; variant annotation
MeSH headings : Computational Biology; Genetic Variation / genetics; Genome-Wide Association Study; Genomics; Genotype; Humans; Models, Genetic; Molecular Sequence Annotation; Phenotype; Polymorphism, Single Nucleotide / genetics; Quantitative Trait Loci
TL;DR:
A systematic evaluation of multiple weighting schemes through a series of simulations intended to mimic large sequencing studies of a quantitative trait finds that the difference in power between phenotype‐dependent schemes is negligible when high‐quality functional annotations are available.
(via Semantic Scholar)
Source: Crossref
Added: August 28, 2020
2013 journal article
Using the emerging Collaborative Cross to probe the immune system
Genes & Immunity, 15(1), 38–46.
author keywords: Collaborative Cross; Fc epsilon R; QTL
MeSH headings : Animals; B-Lymphocytes / physiology; CD11c Antigen / metabolism; CD8-Positive T-Lymphocytes / physiology; Genetic Variation; Genome-Wide Association Study; Haplotypes; Immunogenetics / methods; Lymphocyte Subsets / physiology; Mice; Mice, Inbred Strains / genetics; Mice, Inbred Strains / immunology; Quantitative Trait Loci; Receptors, IgE / metabolism; T-Lymphocytes / physiology
TL;DR:
Comparison of overall strain effects in the CC founders with strain effects at QTL in the pre-CC revealed sharp contrasts in the genetic architecture of two traits with significant loci: variation in CD23 can be explained largely by additive genetics at one locus, whereas variation in B-to-T ratio has a more complex etiology.
(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)
Source: Crossref
Added: August 28, 2020
2013 journal article
Genetically Determined Severity of Anti-Myeloperoxidase Glomerulonephritis
The American Journal of Pathology, 182(4), 1219–1226.
MeSH headings : Animals; Antibodies, Antineutrophil Cytoplasmic / immunology; Bone Marrow Cells / pathology; Chimera; Crosses, Genetic; Female; Genetic Linkage; Genome / genetics; Genotype; Glomerulonephritis / genetics; Glomerulonephritis / immunology; Glomerulonephritis / pathology; Immunoglobulin G / immunology; Male; Mice; Mice, Inbred Strains; Neutrophil Activation / genetics; Peroxidase / genetics; Peroxidase / immunology; Polymorphism, Single Nucleotide / genetics
UN Sustainable Development Goal Categories
3. Good Health and Well-being
(OpenAlex)
Source: Crossref
Added: August 28, 2020
2013 journal article
Solution NMR studies of the plant peptide hormone CEP inform function
FEBS Letters, 587(24), 3979–3985.
Contributors: B. Bobay, P. Digennaro, E. Scholl, N. Imin, M. Djordjevic & D. McK Bird
author keywords: NMR; Molecular dynamic; CEP; Root-knot nematode; Peptide; CLE; Meloidogyne
MeSH headings : Amino Acid Sequence; Animals; Genome, Plant / physiology; Host-Parasite Interactions / physiology; Models, Molecular; Molecular Dynamics Simulation; Molecular Mimicry / physiology; Molecular Sequence Data; Nuclear Magnetic Resonance, Biomolecular; Plant Diseases / genetics; Plant Diseases / parasitology; Plant Growth Regulators / chemistry; Plant Growth Regulators / physiology; Plants / genetics; Plants / metabolism; Root Nodules, Plant / metabolism; Root Nodules, Plant / parasitology; Sequence Homology, Amino Acid; Tylenchoidea / genetics; Tylenchoidea / metabolism
TL;DR:
The first NMR structures of CEP are presented and it is shown that root‐knot nematode also encodes CEP, presumably to mimic plant CEP as part of their stereotypic, parasitic interaction with vascular plants.
(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
2013 journal article
Using in vitro high throughput screening assays to identify potential endocrine-disrupting chemicals.
Environmental Health Perspectives, 121(1), 7–14.
Contributors: D. Rotroff *, D. Dix, K. Houck, T. Knudsen, M. Martin, K. McLaurin, D. Reif* , K. Crofton*
author keywords: androgen; endocrine; estrogen; high throughput; in vitro; ToxCast
MeSH headings : Androgens / analysis; Endocrine Disruptors / analysis; Estrogens / analysis; High-Throughput Screening Assays / methods; United States; United States Environmental Protection Agency
TL;DR:
Overall, results suggest that current ToxCast assays can accurately identify chemicals with potential to interact with the estrogenic and androgenic pathways, and could help prioritize chemicals for EDSP T1S assays.
(via Semantic Scholar)
Source: ORCID
Added: May 14, 2019
2013 journal article
ToxPi GUI: an interactive visualization tool for transparent integration of data from diverse sources of evidence.
Bioinformatics, 29(3), 402–403.
Contributors: D. Reif* , M. Sypa*, E. Lock *, F. Wright*, A. Wilson *, T. Cathey*, R. Judson *, I. Rusyn *
MeSH headings : Computer Graphics; Software; Toxicity Tests / methods; User-Computer Interface
TL;DR:
The Toxicological Prioritization Index (ToxPi) was developed to enable integration of multiple sources of evidence on exposure and/or safety, transformed into transparent visual rankings to facilitate decision making.
(via Semantic Scholar)
Source: ORCID
Added: May 14, 2019
2013 journal article
Real-time growth kinetics measuring hormone mimicry for ToxCast chemicals in T-47D human ductal carcinoma cells.
Chemical Research in Toxicology, 26(7), 1097–1107.
Contributors: D. Rotroff *, D. Dix*, K. Houck *, R. Kavlock*, T. Knudsen *, M. Martin*, D. Reif* , A. Richard *
MeSH headings : Breast Neoplasms / metabolism; Breast Neoplasms / pathology; Carcinoma, Ductal, Breast / metabolism; Carcinoma, Ductal, Breast / pathology; Cell Line, Tumor; Cell Proliferation / drug effects; Environmental Pollutants / toxicity; Female; High-Throughput Screening Assays; Hormones / metabolism; Humans; Kinetics; Molecular Mimicry; Receptors, Estrogen / metabolism; Time Factors; Toxicity Tests
TL;DR:
This cell-based assay rapidly detects chemical effects on T-47D growth and shows potential, in combination with other HTS assays, to detect environmentally relevant chemicals with potential estrogenic activity.
(via Semantic Scholar)
Source: ORCID
Added: May 14, 2019
2013 journal article
Perspectives on validation of high-throughput assays supporting 21st century toxicity testing.
Altex, 30(1), 51–66. http://europepmc.org/abstract/med/23338806
Contributors: R. Judson, R. Kavlock, M. Martin, D. Reif , K. Houck, T. Knudsen, A. Richard, R. Tice
Source: ORCID
Added: May 14, 2019
2013 journal article
In vitro perturbations of targets in cancer hallmark processes predict rodent chemical carcinogenesis.
Toxicological Sciences, 131(1), 40–55.
Contributors: N. Kleinstreuer *, D. Dix*, K. Houck *, R. Kavlock*, T. Knudsen *, M. Martin*, K. Paul*, D. Reif*
author keywords: cancer hallmarks; carcinogenesis; predictive toxicology; in vitro and alternatives; bioinformatics
MeSH headings : Animals; Biomarkers, Tumor / analysis; Biomarkers, Tumor / genetics; Carcinogenicity Tests; Carcinogens / chemistry; Carcinogens / toxicity; Databases, Factual; Endpoint Determination; High-Throughput Screening Assays; In Vitro Techniques; Mice; Neoplasms / chemically induced; Neoplasms / genetics; Predictive Value of Tests; Rats; Species Specificity; Thyroid Neoplasms / chemically induced; Thyroid Neoplasms / genetics
TL;DR:
A model was developed in which genes/pathways function as hypothetical enhancers or promoters of rat thyroid tumors, acting secondary to the key initiating event of thyroid hormone disruption, which represents a chemical carcinogenicity prioritization tool supporting targeted testing and functional validation of cancer pathways.
(via Semantic Scholar)
Source: ORCID
Added: May 14, 2019
2013 journal article
Decision tree-based method for integrating gene expression, demographic, and clinical data to determine disease endotypes.
BMC Systems Biology, 7, 119.
Contributors: C. Williams-DeVane *, D. Reif* , E. Cohen Hubal*, P. Bushel*, E. Hudgens*, J. Gallagher*, S. Edwards*
author keywords: Asthma; Endotypes; Gene Expression; Integrated analysis
MeSH headings : Adolescent; Asthma / blood; Asthma / genetics; Child; Cluster Analysis; Computational Biology / methods; Decision Trees; Demography; Gene Expression Profiling; Genome-Wide Association Study; Humans
TL;DR:
A multi-step decision tree-based method is described for defining endotypes based on gene expression, clinical covariates, and disease indicators using childhood asthma as a case study and it gives the best segregation of asthmatics and non-asthmatics.
(via Semantic Scholar)
UN Sustainable Development Goal Categories
16. Peace, Justice and Strong Institutions
(OpenAlex)
Source: ORCID
Added: May 14, 2019
2013 journal article
Comparing metabolomic and pathologic biomarkers alone and in combination for discriminating Alzheimer’s disease from normal cognitive aging
Acta Neuropathologica Communications, 1(1), 28.
author keywords: Alzheimer's disease; Dementias; Metabolomics; Cerebrospinal fluid biomarkers; Stepwise logistic regression
MeSH headings : Aged; Aging / cerebrospinal fluid; Aging / drug effects; Aging / pathology; Alzheimer Disease / cerebrospinal fluid; Alzheimer Disease / diagnosis; Alzheimer Disease / drug therapy; Alzheimer Disease / pathology; Amyloid beta-Peptides / cerebrospinal fluid; Area Under Curve; Biomarkers / cerebrospinal fluid; Chromatography, Liquid; Cognition; Diagnosis, Differential; Female; Gas Chromatography-Mass Spectrometry; Humans; Logistic Models; Male; Metabolomics / methods; Neuropsychological Tests; tau Proteins / cerebrospinal fluid
TL;DR:
Several CSF small-molecule metabolites that discriminated especially well between clinically diagnosed AD and control groups appear to be suitable for further confirmatory and validation studies, and show the potential to provide predictive performance for AD.
(via Semantic Scholar)
UN Sustainable Development Goal Categories
3. Good Health and Well-being
(Web of Science)
10. Reduced Inequalities
(OpenAlex)
Source: ORCID
Added: May 14, 2019
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