Works Published in 2012
Displaying works 1 - 20 of 36 in total
Sorted by most recent date added to the index first, which may not be the same as publication date order.
2012 journal article
Human Intestinal Transporter Database: QSAR Modeling and Virtual Profiling of Drug Uptake, Efflux and Interactions
Pharmaceutical Research, 30(4), 996–1007.
author keywords: ADMET; drug transport; efflux; membrane transport proteins; permeability
MeSH headings : Artificial Intelligence; Biological Transport, Active; Computer Simulation; Databases, Pharmaceutical; Databases, Protein; Humans; Intestinal Mucosa / metabolism; Membrane Transport Proteins / chemistry; Membrane Transport Proteins / metabolism; Models, Biological; Pharmaceutical Preparations / chemistry; Pharmaceutical Preparations / metabolism; Pharmacokinetics; Quantitative Structure-Activity Relationship
TL;DR:
The compendium of predictive QSAR models developed in this study can be used for virtual profiling of drug candidates and/or environmental agents with the optimal transporter profiles with high prediction accuracies in the virtual screening of DrugBank compounds.
(via Semantic Scholar)
europepmc.org (repository)
Source: Crossref
Added: January 21, 2021
2012 journal article
Exome sequencing of extreme phenotypes identifies DCTN4 as a modifier of chronic Pseudomonas aeruginosa infection in cystic fibrosis
Nature Genetics, 44(8), 886–889.
MeSH headings : Adolescent; Age of Onset; Child; Child, Preschool; Cystic Fibrosis / complications; Cystic Fibrosis / genetics; Dynactin Complex; Exome; Gene Frequency; Humans; Infant; Infant, Newborn; Linkage Disequilibrium; Microtubule-Associated Proteins / genetics; Phenotype; Polymorphism, Single Nucleotide; Pseudomonas Infections / etiology; Pseudomonas Infections / genetics; Pseudomonas aeruginosa
TL;DR:
An extreme phenotype study design is used to discover that variants in DCTN4, encoding a dynactin protein, are associated with time to first P. aeruginosa airway infection, chronic P.aerug inosa infection and mucoid P. AerugInosa in individuals with cystic fibrosis.
(via Semantic Scholar)
Source: Crossref
Added: August 28, 2020
2012 journal article
Multiple apical plasma membrane constituents are associated with susceptibility to meconium ileus in individuals with cystic fibrosis
Nature Genetics, 44(5), 562–569.
MeSH headings : Amino Acid Transport Systems; Amino Acid Transport Systems, Neutral / genetics; Antiporters / genetics; Cell Membrane / metabolism; Cystic Fibrosis / genetics; Cystic Fibrosis Transmembrane Conductance Regulator / genetics; Genetic Predisposition to Disease; Genome-Wide Association Study; Genotype; Humans; Ileus / genetics; Intestinal Obstruction / etiology; Meconium; Polymorphism, Single Nucleotide / genetics; Sodium-Hydrogen Exchanger 3; Sodium-Hydrogen Exchangers / genetics; Sulfate Transporters
TL;DR:
It is suggested that modulating activities of apical membrane constituents could complement current therapeutic paradigms for cystic fibrosis and provide evidence of association between meconium ileus and multiple genes encoding constituents of the apical plasma membrane where CFTR resides.
(via Semantic Scholar)
Source: Crossref
Added: August 28, 2020
2012 journal article
Loss of Power in Two-Stage Residual-Outcome Regression Analysis in Genetic Association Studies
Genetic Epidemiology, n/a-n/a.
author keywords: loss of power; two-stage regression; degrees of freedom
MeSH headings : Bias; Female; Genetic Association Studies; Humans; Male; Regression Analysis
TL;DR:
While there may be some potential advantages with the 2SR approach in both ease of use and computational and data management efficiency, some issues, such as the bias of estimates, power, and type I error, need to be thoroughly investigated.
(via Semantic Scholar)
UN Sustainable Development Goal Categories
3. Good Health and Well-being
(Web of Science; OpenAlex)
Source: Crossref
Added: February 24, 2020
2012 journal article
A sequence-anchored linkage map of the plant-parasitic nematode meloidogyne hapla reveals exceptionally high genome-wide recombination
G3: Genes, Genomes, Genetics, 2(7), 815–824.
Contributors: V. Thomas*, S. Fudali*, J. Schaff*, Q. Liu*, E. Scholl*, C. Opperman *, D. Bird n , V. Williamson *
author keywords: root-knot nematode; SNP; integrated map
MeSH headings : Amplified Fragment Length Polymorphism Analysis; Animals; Cellulase / classification; Chromosome Mapping; Contig Mapping; Crosses, Genetic; Genetic Linkage; Genetic Variation; Genome, Helminth; Genome, Plant; Genotype; Meiosis; Phylogeny; Plants / genetics; Plants / parasitology; Polymorphism, Single Nucleotide; Polysaccharide-Lyases / classification; Recombination, Genetic; Tylenchoidea / genetics
TL;DR:
This work presents the most comprehensive linkage map of a parasitic nematode to date and, together with genomic and transcript sequence resources, empowers M. hapla as a tractable model for analyses of genome organization and the inheritance of phenotypic traits.
(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
2012 journal article
Aggregating Data for Computational Toxicology Applications: The U.S. Environmental Protection Agency (EPA) Aggregated Computational Toxicology Resource (ACToR) System.
International Journal of Molecular Sciences, 13(2), 1805–1831.
Contributors: R. Judson *, M. Martin*, P. Egeghy *, S. Gangwal*, D. Reif* , P. Kothiya *, M. Wolf*, T. Cathey*
author keywords: computational toxicology; database; hazard; exposure; high-throughput screening; ACToR; ToxCastDB; ExpoCastDB; ToxRefDB; DSSTox
MeSH headings : Algorithms; Computational Biology / methods; Databases, Factual / standards; Databases, Factual / supply & distribution; Ecotoxicology / methods; Ecotoxicology / organization & administration; Environmental Pollutants / toxicity; Humans; Software; United States; United States Environmental Protection Agency / organization & administration
TL;DR:
The organization of the ACToR data repository is described and selected examples of use cases are provided, including links to underlying biological information related to genes and pathways.
(via Semantic Scholar)
Source: ORCID
Added: May 14, 2019
2012 journal article
Zebrafish developmental screening of the ToxCast™ Phase I chemical library.
Reproductive Toxicology, 33(2), 174–187.
Contributors: S. Padilla *, D. Corum*, B. Padnos*, D. Hunter *, A. Beam *, K. Houck *, N. Sipes *, N. Kleinstreuer *
author keywords: Zebrafish; Development; Concentration-response; ToxCast (TM); Octanol-water partition coefficient; Chemical class
MeSH headings : Animals; Embryo, Nonmammalian / drug effects; Environmental Pollutants / toxicity; Models, Animal; Pesticides / toxicity; Small Molecule Libraries; Teratogens / toxicity; Toxicity Tests / methods; Zebrafish
TL;DR:
The zebrafish embryo screen, by providing an integrated model of the developing vertebrate, compliments the ToxCast assay portfolio and has the potential to provide information relative to overt and organismal toxicity.
(via Semantic Scholar)
Source: ORCID
Added: May 14, 2019
2012 journal article
Update on EPA’s ToxCast Program: Providing High Throughput Decision Support Tools for Chemical Risk Management
Chem. Res. Toxicol., 25(7), 1287â1302.
Contributors: R. Kavlock*, K. Chandler*, K. Houck *, S. Hunter*, R. Judson *, N. Kleinstreuer *, T. Knudsen *, M. Martin*
MeSH headings : Biological Assay; Decision Support Techniques; Environmental Pollutants / chemistry; Environmental Pollutants / toxicity; Humans; Program Development; Risk Management; United States; United States Environmental Protection Agency
TL;DR:
A summary of the initial, proof of concept, Phase I of ToxCast that has laid the groundwork for the next phases and future directions of the program is provided.
(via Semantic Scholar)
Source: ORCID
Added: May 14, 2019
2012 journal article
Incorporating exposure information into the toxicological prioritization index decision support framework
Science of The Total Environment, 435-436, 316â325.
Contributors: S. Gangwal*, D. Reif* , S. Mosher*, P. Egeghy *, J. Wambaugh *, R. Judson *, E. Hubal *
author keywords: ExpoCast; Exposure assessment; ToxCast; Exposure metrics; Exposure prioritization; Pesticides
MeSH headings : Adolescent; Adult; Child; Child, Preschool; Decision Support Techniques; Environmental Exposure; Fruit / chemistry; Hazardous Substances / analysis; Humans; Infant; Male; Middle Aged; Models, Biological; Nutrition Surveys / statistics & numerical data; Pesticide Residues / adverse effects; Pesticide Residues / analysis; Risk Assessment / methods; Vegetables / chemistry; Young Adult
TL;DR:
The goal of this analysis is to demonstrate the utility of the ToxPi framework for incorporating exposure information to rank chemicals and improve understanding of key exposure surrogates and build confidence in exposure-based chemical prioritization.
(via Semantic Scholar)
Source: ORCID
Added: May 14, 2019
2012 journal article
Incorporating biological, chemical, and toxicological knowledge into predictive models of toxicity.
Toxicological Sciences, 130(2), 440–441.
Contributors: D. Dix*, K. Houck *, R. Judson *, N. Kleinstreuer *, T. Knudsen *, M. Martin*, D. Reif* , A. Richard *
MeSH headings : Animals; Hazardous Substances / toxicity
TL;DR:
An evaluation of statistical models for classifying in vivo toxicity endpoints from ToxRefDB using ToxCast in vitro bioactivity data and chemical structure descriptors concluded that the current Tox cast phase I assays and chemicals have limited applicability for predicting in vivo chemical hazards.
(via Semantic Scholar)
Source: ORCID
Added: May 14, 2019
2012 journal article
A comparison of internal model validation methods for multifactor dimensionality reduction in the case of genetic heterogeneity
BMC Research Notes, 5(1), 623.
Contributors: J. Gory n, H. Sweeney n, D. Reif n & A. Motsinger-Reif n
MeSH headings : Algorithms; Computer Simulation; Epistasis, Genetic; Genetic Heterogeneity; Humans; Models, Genetic; Multifactor Dimensionality Reduction / standards; Research Design; Validation Studies as Topic
TL;DR:
Results show that the cross-validation approach greatly outperformed the three-way split approach in detecting heterogeneity and emphasize the challenge of detecting heterogeneity models and the need for further methods development.
(via Semantic Scholar)
UN Sustainable Development Goal Categories
1. No Poverty
(OpenAlex)
Source: ORCID
Added: May 14, 2019
2012 conference paper
A comparison of GE optimized neural networks and decision trees
Proceedings of the fourteenth international conference on Genetic and evolutionary computation conference companion - GECCO Companion '12, 611–614.
Contributors: K. Hoover, D. Reif n , R. Marceau n, T. Harris n & A. Motsinger-Reif n
TL;DR:
Grammatical evolution of decision trees (GEDT) is shown to be not as effective as GENN at detecting disease causing polymorphisms especially in more difficult to detect models, but this power trade off may be worth it for interpretability.
(via Semantic Scholar)
UN Sustainable Development Goal Categories
16. Peace, Justice and Strong Institutions
(OpenAlex)
Source: ORCID
Added: May 14, 2019
2012 journal article
Multivariate methods and software for association mapping in dose-response genome-wide association studies
Biodata Mining, 5.
Source: NC State University Libraries
Added: August 6, 2018
2012 article
BioCreative-2012 Virtual Issue
Wu, C. H., Arighi, C. N., Cohen, K. B., Hirschman, L., Krallinger, M., Lu, Z., … Wilbur, W. J. (2012, December 5). DATABASE-THE JOURNAL OF BIOLOGICAL DATABASES AND CURATION.
MeSH headings : Congresses as Topic; Cooperative Behavior; Data Mining; Databases, Genetic; Periodicals as Topic; Workflow
TL;DR:
This DATABASE virtual issue captures the major results from the BioCreative-2012 Workshop on Interactive Text Mining in the Biocuration Workflow and is the fifth special issue devoted to Biocreative.
(via Semantic Scholar)
UN Sustainable Development Goal Categories
3. Good Health and Well-being
(Web of Science)
Source: Web Of Science
Added: August 6, 2018
2012 journal article
Targeted journal curation as a method to improve data currency at the Comparative Toxicogenomics Database
Database-The Journal of Biological Databases and Curation.
Source: NC State University Libraries
Added: August 6, 2018
2012 personal communication
Loss of power in two-stage residual-outcome regression analysis in genetic association studies
Source: NC State University Libraries
Added: August 6, 2018
2012 journal article
Collaborative biocuration-text-mining development task for document prioritization for curation
DATABASE-THE JOURNAL OF BIOLOGICAL DATABASES AND CURATION.
MeSH headings : Cooperative Behavior; Data Mining / methods; Databases, Genetic; Disease; Documentation / methods; Genes; Humans; Internet; Toxicogenetics; User-Computer Interface
TL;DR:
A detailed description of the Critical Assessment of Information Extraction systems in Biology (BioCreAtIvE) challenge evaluation is presented and a summary of the results are presented.
(via Semantic Scholar)
UN Sustainable Development Goal Categories
3. Good Health and Well-being
(Web of Science)
Source: Web Of Science
Added: August 6, 2018
2012 journal article
The biogeography and filtering of woody plant functional diversity in North and South America
Global Ecology and Biogeography, 21(8), 798–808.
Source: NC State University Libraries
Added: August 6, 2018
2012 journal article
OSA: a fast and accurate alignment tool for RNA-Seq
Bioinformatics, 28(14), 1933–1934.
Source: NC State University Libraries
Added: August 6, 2018
2012 journal article
A genome-wide association analysis of temozolomide response using lymphoblastoid cell lines shows a clinically relevant association with MGMT
PHARMACOGENETICS AND GENOMICS, 22(11), 796–802.
author keywords: genome-wide association studies; lymphoblastoid cell lines; MGMT; pharmacogenetics; temozolomide
MeSH headings : Antineoplastic Agents, Alkylating / pharmacology; Cell Line, Tumor; DNA Methylation; DNA Modification Methylases / genetics; DNA Repair Enzymes / genetics; Dacarbazine / analogs & derivatives; Dacarbazine / pharmacology; Gene Expression Regulation, Neoplastic; Genome, Human; Genome-Wide Association Study; Humans; Polymorphism, Single Nucleotide; Precursor Cell Lymphoblastic Leukemia-Lymphoma / drug therapy; Precursor Cell Lymphoblastic Leukemia-Lymphoma / genetics; Precursor Cell Lymphoblastic Leukemia-Lymphoma / pathology; Temozolomide; Tumor Suppressor Proteins / genetics
TL;DR:
Genome-wide association analysis using ∼2.1 million quality-controlled single-nucleotide polymorphisms (SNPs) identified a statistically significant association (P<10−8) with SNPs in the O6-methylguanine-DNA methyltransferase (MGMT) gene.
(via Semantic Scholar)
UN Sustainable Development Goal Categories
3. Good Health and Well-being
(Web of Science)
Source: Web Of Science
Added: August 6, 2018
Citation Index includes data from a number of different sources. If you have questions about the sources of data in the Citation Index or need a set of data which is free to re-distribute, please contact us.
Certain data included herein are derived from the Web of Science© and InCites© (2024) of Clarivate Analytics. All rights reserved. You may not copy or re-distribute this material in whole or in part without the prior written consent of Clarivate Analytics.
