Works (67)
Updated: November 6th, 2024 14:10
2024 article
Comparative toxicogenomics database's 20th anniversary: update 2025
Davis, A. P., Wiegers, T. C., Sciaky, D., Barkalow, F., Strong, M., Wyatt, B., … Mattingly, C. J. (2024, October 10). NUCLEIC ACIDS RESEARCH, Vol. 10.
open access via doi.org (publisher)
Sources: Web Of Science, NC State University Libraries
Added: October 21, 2024
2024 journal article
Transforming environmental health datasets from the comparative toxicogenomics database into chord diagrams to visualize molecular mechanisms
FRONTIERS IN TOXICOLOGY, 6.
author keywords: data visualization; chord diagram; r; molecular mechanisms; environmental health; database; tetramers
UN Sustainable Development Goal Categories
3. Good Health and Well-being
(Web of Science)
Sources: Web Of Science, NC State University Libraries
Added: August 19, 2024
2023 journal article
CTD tetramers: a new online tool that computationally links curated chemicals, genes, phenotypes, and diseases to inform molecular mechanisms for environmental health
TOXICOLOGICAL SCIENCES, 195(2), 155–168.
author keywords: database tool; chemical-disease pathway; molecular mechanisms; environmental health; knowledge gaps; adverse outcome pathway
UN Sustainable Development Goal Categories
3. Good Health and Well-being
(Web of Science)
6. Clean Water and Sanitation
(Web of Science)
Sources: Web Of Science, NC State University Libraries
Added: April 1, 2024
2023 journal article
Developmental cadmium exposure disrupts zebrafish vestibular calcium channels interfering with otolith formation and inner ear function
NEUROTOXICOLOGY, 96, 129–139.
author keywords: Cadmium; Developmental toxicology; Behavior; Vestibular system; P2X receptor; Zebrafish
MeSH headings : Animals; Zebrafish; Cadmium / toxicity; Otolithic Membrane; Vestibule, Labyrinth; Vestibular Diseases
TL;DR:
Cadmium-induced ototoxicity is linked to vestibular-based behavioral abnormalities and auditory sensitivity following developmental exposure, and calcium ion channel function is associated with these defects.
(via Semantic Scholar)
UN Sustainable Development Goal Categories
3. Good Health and Well-being
(Web of Science)
Sources: Web Of Science, NC State University Libraries
Added: June 12, 2023
2022 article
Comparative Toxicogenomics Database (CTD): update 2023
Davis, A. P., Wiegers, T. C., Johnson, R. J., Sciaky, D., Wiegers, J., & Mattingly, C. J. (2022, September 28). NUCLEIC ACIDS RESEARCH, Vol. 9.
MeSH headings : Humans; Toxicogenetics; Databases, Factual; Phenotype
TL;DR:
A 20% increase in overall CTD content is reported and CTD Tetramers, a novel tool that computationally generates four-unit information blocks connecting a chemical, gene, phenotype, and disease to construct potential molecular mechanistic pathways are presented.
(via Semantic Scholar)
UN Sustainable Development Goal Categories
3. Good Health and Well-being
(Web of Science)
Sources: Web Of Science, NC State University Libraries
Added: October 11, 2022
2021 journal article
CTD anatomy: Analyzing chemical-induced phenotypes and exposures from an anatomical perspective, with implications for environmental health studies
CURRENT RESEARCH IN TOXICOLOGY, 2, 128–139.
author keywords: Anatomy; Chemical; Phenotype; Disease; Environmental health; Database
UN Sustainable Development Goal Categories
3. Good Health and Well-being
(Web of Science)
Sources: Web Of Science, NC State University Libraries
Added: January 3, 2022
2021 journal article
Predicting molecular mechanisms, pathways, and health outcomes induced by Juul e-cigarette aerosol chemicals using the Comparative Toxicogenomics Database
CURRENT RESEARCH IN TOXICOLOGY, 2, 272–281.
author keywords: E-cigarettes; Vaping; Juul; Respiratory disease; Database; Environmental exposure
UN Sustainable Development Goal Categories
3. Good Health and Well-being
(Web of Science; OpenAlex)
Sources: Web Of Science, NC State University Libraries
Added: January 3, 2022
2021 journal article
Regulatory status of pesticide residues in cannabis: Implications to medical use in neurological diseases
CURRENT RESEARCH IN TOXICOLOGY, 2, 140–148.
author keywords: Cannabis; Pesticide; Database; Regulation; Seizure; Contaminant
TL;DR:
Network analysis reveals potential interactions of insecticides, cannabinoids, and seizure at a functional level in cannabis.
(via Semantic Scholar)
UN Sustainable Development Goal Categories
3. Good Health and Well-being
(Web of Science)
Sources: Web Of Science, NC State University Libraries
Added: January 3, 2022
2020 review
Beyond the looking glass: recent advances in understanding the impact of environmental exposures on neuropsychiatric disease
[Review of ]. NEUROPSYCHOPHARMACOLOGY, 45(7), 1086–1096.
MeSH headings : Environmental Exposure / adverse effects; Humans; Mental Disorders / etiology
UN Sustainable Development Goal Categories
3. Good Health and Well-being
(Web of Science)
Sources: Web Of Science, NC State University Libraries
Added: March 30, 2020
2020 journal article
Comparative Toxicogenomics Database (CTD): update 2021
NUCLEIC ACIDS RESEARCH, 49(D1), D1138–D1143.
MeSH headings : Databases, Chemical; Databases, Factual; Databases, Genetic; Gene-Environment Interaction; Genome, Human / drug effects; Genomics / methods; Genotype; Humans; Internet; Knowledge Bases; Organ Specificity; Phenotype; Prescription Drugs / chemistry; Prescription Drugs / pharmacology; Software; Toxicogenetics / methods; Xenobiotics / chemistry; Xenobiotics / toxicity
TL;DR:
This biennial update of the public Comparative Toxicogenomics Database (CTD) reports a 20% increase in CTD curated content and provides 45 million toxicogenomic relationships and introduces new CTD Anatomy pages that allow users to uniquely explore and analyze chemical–phenotype interactions from an anatomical perspective.
(via Semantic Scholar)
UN Sustainable Development Goal Categories
3. Good Health and Well-being
(Web of Science)
Sources: Web Of Science, NC State University Libraries
Added: February 8, 2021
2020 journal article
Leveraging the Comparative Toxicogenomics Database to Fill in Knowledge Gaps for Environmental Health: A Test Case for Air Pollution-induced Cardiovascular Disease
TOXICOLOGICAL SCIENCES, 177(2), 392–404.
author keywords: environmental health; chemical-induced pathways; air pollution; cardiovascular disease; database
MeSH headings : Air Pollutants / toxicity; Air Pollution; Cardiovascular Diseases / chemically induced; Environmental Exposure; Environmental Health; Humans; Toxicogenetics
TL;DR:
This paper systematically compute the genes, molecular mechanisms, and biological events for the environmental health association linking air pollution toxicants with two cardiovascular diseases as a test case and identifies 19 genes and 96 phenotypes shared between these two air pollutant-induced outcomes.
(via Semantic Scholar)
UN Sustainable Development Goal Categories
3. Good Health and Well-being
(Web of Science)
11. Sustainable Cities and Communities
(Web of Science)
Sources: Web Of Science, NC State University Libraries
Added: December 14, 2020
2018 journal article
Accessing an Expanded Exposure Science Module at the Comparative Toxicogenomics Database
ENVIRONMENTAL HEALTH PERSPECTIVES, 126(1).
MeSH headings : Databases, Factual; Environmental Exposure / adverse effects; Gene Ontology; Humans; Phenotype; Toxicogenetics
UN Sustainable Development Goal Categories
3. Good Health and Well-being
(Web of Science)
Sources: Web Of Science, NC State University Libraries
Added: August 6, 2018
2018 journal article
Cadmium exposure increases the risk of juvenile obesity: a human and zebrafish comparative study
International Journal of Obesity, 42(7), 1285–1295.
Contributors: A. Green n, C. Hoyo n, n , Y. Luo n, J. Tzeng n, S. Murphy *, D. Buchwalter n , A. Planchart n
MeSH headings : Adipogenesis / drug effects; Animals; Cadmium / adverse effects; Cadmium / analysis; Cadmium / blood; Disease Models, Animal; Environmental Exposure / adverse effects; Environmental Exposure / analysis; Female; Humans; Infant, Newborn; Male; Maternal Exposure / adverse effects; Metals, Heavy / adverse effects; Metals, Heavy / analysis; Pediatric Obesity / blood; Pediatric Obesity / chemically induced; Pediatric Obesity / epidemiology; Pregnancy; Pregnant Women; Prenatal Exposure Delayed Effects / blood; Prenatal Exposure Delayed Effects / chemically induced; Prenatal Exposure Delayed Effects / epidemiology; Prospective Studies; Socioeconomic Factors; United States / epidemiology; Zebrafish / metabolism
TL;DR:
The findings identify Cd as a potential human obesogen, suggesting that the underlying mechanisms may be evolutionarily conserved, and that zebrafish may be a valuable model for uncovering pathways leading to Cd-mediated obesity in human populations.
(via Semantic Scholar)
UN Sustainable Development Goal Categories
3. Good Health and Well-being
(Web of Science; OpenAlex)
Sources: Crossref, NC State University Libraries, ORCID
Added: August 7, 2019
2018 journal article
Chemical-Induced Phenotypes at CTD Help Inform the Predisease State and Construct Adverse Outcome Pathways
TOXICOLOGICAL SCIENCES, 165(1), 145–156.
author keywords: phenotype; database; curation; chemical; disease; adverse outcome pathway
MeSH headings : Adverse Outcome Pathways; Animals; Databases, Factual; Drug-Related Side Effects and Adverse Reactions / genetics; Gene Ontology; Gene-Environment Interaction; Humans; Phenotype; Toxicogenetics / methods
TL;DR:
This work introduces a new chemical-phenotype module that describes how chemicals can affect molecular, cellular, and physiological phenotypes, and presents 3 diverse case studies discerning the effect of vehicle emissions on altered leukocyte migration, the role of cadmium in influencing phenotypes preceding Alzheimer disease, and the connection of arsenic-induced glucose metabolic phenotypes with diabetes.
(via Semantic Scholar)
UN Sustainable Development Goal Categories
3. Good Health and Well-being
(Web of Science)
Sources: Web Of Science, NC State University Libraries
Added: October 16, 2018
2018 journal article
Heavy Metal Exposure and Metabolic Syndrome: Evidence from Human and Model System Studies
Current Environmental Health Reports, 5(1), 110–124.
author keywords: Metabolic syndrome; Diabetes; Heavy metals; Cadmium; Pb; Mercury
MeSH headings : Animals; Cadmium / adverse effects; Disease Models, Animal; Humans; Lead / adverse effects; Mercury / adverse effects; Metabolic Syndrome / chemically induced; Metals, Heavy / adverse effects
TL;DR:
Assessment of potential causal links between heavy metal exposure and metabolic syndrome remains challenging as epidemiological data are largely cross-sectional; and variation in study design, including samples used for heavy metal measurements, age of subjects at which MS outcomes are measured, and the population demographics vary widely.
(via Semantic Scholar)
UN Sustainable Development Goal Categories
3. Good Health and Well-being
(Web of Science; OpenAlex)
Sources: Crossref, NC State University Libraries, ORCID
Added: August 7, 2019
2018 journal article
The Comparative Toxicogenomics Database: update 2019
NUCLEIC ACIDS RESEARCH, 47(D1), D948–D954.
MeSH headings : Databases, Pharmaceutical; Disease / genetics; Environmental Exposure; Humans; Phenotype; Toxicogenetics; Vocabulary, Controlled
TL;DR:
This biennial update presents a new chemical–phenotype module that codes chemical-induced effects on phenotypes, curated using controlled vocabularies for chemicals, phenotype, taxa, and anatomical descriptors, and describes new querying and display features for the enhanced chemical–exposure science module, providing greater scope of content and utility.
(via Semantic Scholar)
UN Sustainable Development Goal Categories
3. Good Health and Well-being
(Web of Science)
9. Industry, Innovation and Infrastructure
(OpenAlex)
Sources: Web Of Science, NC State University Libraries
Added: April 9, 2019
2017 review
Applying evolutionary genetics to developmental toxicology and risk assessment
[Review of ]. REPRODUCTIVE TOXICOLOGY, 69, 174–186.
author keywords: Evolutionary genetics; Developmental toxicology; Systems toxicology; Birth defects; Signaling pathways; High-throughput screening; Evo-Devo
MeSH headings : Animals; Computational Biology; Evolution, Molecular; Humans; Phylogeny; Risk Assessment; Systems Biology; Teratology
TL;DR:
This synthesis can lead to novel applications in developmental toxicity and risk assessment, but also can pave the way for applying an evo-devo perspective to the study of developmental origins of health and disease.
(via Semantic Scholar)
UN Sustainable Development Goal Categories
3. Good Health and Well-being
(Web of Science)
11. Sustainable Cities and Communities
(Web of Science)
Sources: Web Of Science, NC State University Libraries
Added: August 6, 2018
2017 article
Informatics and Data Analytics to Support Exposome-Based Discovery for Public Health
ANNUAL REVIEW OF PUBLIC HEALTH, VOL 38, Vol. 38, pp. 279–294.
author keywords: exposures; bioinformatics; genomics; environment-wide association studies; data standards
MeSH headings : Biomedical Research; Computational Biology; Ecosystem; Environmental Exposure / adverse effects; Humans; Public Health; Risk Factors
TL;DR:
If an exposome data ecosystem is brought to fruition, it will likely play a role as central as genomic science has had in molding the current and new generations of biomedical researchers, computational scientists, and public health research programs.
(via Semantic Scholar)
UN Sustainable Development Goal Categories
3. Good Health and Well-being
(Web of Science)
Sources: Web Of Science, NC State University Libraries
Added: August 6, 2018
2016 journal article
Advancing Exposure Science through Chemical Data Curation and Integration in the Comparative Toxicogenomics Database
Environmental Health Perspectives, 124(10), 1592–1599.
Contributors: C. Grondin n, A. Davis n, T. Wiegers n, B. King *, J. Wiegers n, D. Reif n , J. Hoppin n , n
TL;DR:
Curation and integration of exposure data within the CTD provides researchers with new opportunities to correlate exposures with human health outcomes, to identify underlying potential molecular mechanisms, and to improve understanding about the exposome.
(via Semantic Scholar)
UN Sustainable Development Goal Categories
3. Good Health and Well-being
(Web of Science)
Sources: Web Of Science, NC State University Libraries, ORCID, Crossref
Added: August 6, 2018
2016 journal article
Advancing toxicology research using in vivo high throughput toxicology with small fish models
Altex-Alternatives to Animal Experimentation, 33(4), 435–452.
Source: NC State University Libraries
Added: August 6, 2018
2016 journal article
Assessing the state of the art in biomedical relation extraction: overview of the BioCreative V chemical-disease relation (CDR) task
DATABASE-THE JOURNAL OF BIOLOGICAL DATABASES AND CURATION.
MeSH headings : Biomedical Research; Data Mining / methods; Databases, Factual; Disease; Humans; Statistics as Topic; Time Factors
TL;DR:
This task was found to be successful in engaging the text-mining research community, producing a large annotated corpus and improving the results of automatic disease recognition and CDR extraction.
(via Semantic Scholar)
UN Sustainable Development Goal Categories
3. Good Health and Well-being
(Web of Science)
Sources: Web Of Science, NC State University Libraries
Added: August 6, 2018
2016 journal article
BioCreative V CDR task corpus: a resource for chemical disease relation extraction
DATABASE-THE JOURNAL OF BIOLOGICAL DATABASES AND CURATION.
MeSH headings : Computational Biology / methods; Data Mining / methods; Databases, Factual; Disease; Humans; Toxicogenetics / methods
TL;DR:
The BC5CDR corpus was successfully used for the BioCreative V challenge tasks and should serve as a valuable resource for the text-mining research community.
(via Semantic Scholar)
UN Sustainable Development Goal Categories
3. Good Health and Well-being
(Web of Science)
Sources: Web Of Science, NC State University Libraries
Added: August 6, 2018
2016 journal article
From the Cover: Embryonic Exposure to TCDD Impacts Osteogenesis of the Axial Skeleton in Japanese medaka,Oryzias latipes
Toxicological Sciences, 155(2), 485–496.
Contributors: A. Watson, A. Planchart n , n , C. Winkler *, D. Reif n & S. Kullman n
author keywords: receptor, aryl hydrocarbon; gene expression/regulation, bone; transgenic models; methods, developmental/teratology; reproductive and developmental toxicology
MeSH headings : Animals; Calcification, Physiologic / drug effects; Down-Regulation / drug effects; Microscopy, Confocal; Musculoskeletal Diseases / metabolism; Oryzias / embryology; Osteogenesis / drug effects; Polychlorinated Dibenzodioxins / toxicity; Real-Time Polymerase Chain Reaction; Skeleton / drug effects; Skeleton / metabolism; Trans-Activators / drug effects
TL;DR:
It is suggested that TCDD exposure inhibits axial bone formation through dysregulation of osteoblast differentiation.
(via Semantic Scholar)
UN Sustainable Development Goal Categories
3. Good Health and Well-being
(Web of Science)
14. Life Below Water
(OpenAlex)
Sources: Web Of Science, NC State University Libraries, ORCID, Crossref
Added: August 6, 2018
2016 journal article
Generating Gene Ontology-Disease Inferences to Explore Mechanisms of Human Disease at the Comparative Toxicogenomics Database
PLOS ONE, 11(5).
MeSH headings : Computational Biology; Databases, Genetic; Disease / genetics; Drug Repositioning; Gene Ontology; Humans; Toxicogenetics
TL;DR:
This inference set should aid researchers, bioinformaticists, and pharmaceutical drug makers in finding commonalities in disease mechanisms, which in turn could help identify new therapeutics, new indications for existing pharmaceuticals, potential disease comorbidities, and alerts for side effects.
(via Semantic Scholar)
UN Sustainable Development Goal Categories
3. Good Health and Well-being
(Web of Science)
Sources: Web Of Science, NC State University Libraries
Added: August 6, 2018
2016 review
Laying a Community-Based Foundation for Data-Driven Semantic Standards in Environmental Health Sciences
[Review of ]. ENVIRONMENTAL HEALTH PERSPECTIVES, 124(8), 1136–1140.
MeSH headings : Cooperative Behavior; Environmental Exposure / standards; Environmental Exposure / statistics & numerical data; Environmental Health / standards; Humans; Internet; National Institute of Environmental Health Sciences (U.S.); United States
TL;DR:
A foundation for enabling the development of community-based and data-driven semantic standards that will ultimately improve standardization, sharing, and interoperability of EHS information is developed.
(via Semantic Scholar)
UN Sustainable Development Goal Categories
3. Good Health and Well-being
(Web of Science)
Sources: Web Of Science, NC State University Libraries
Added: August 6, 2018
2016 journal article
The Comparative Toxicogenomics Database: update 2017
NUCLEIC ACIDS RESEARCH, 45(D1), D972–D978.
MeSH headings : Computational Biology / methods; Databases, Chemical; Databases, Genetic; Gene Ontology; Humans; Search Engine; Signal Transduction; Toxicogenetics / methods; User-Computer Interface; Web Browser
TL;DR:
This update describes the new exposure module (that harmonizes exposure science information with core toxicogenomic data) and introduces a novel dataset of GO-disease inferences (that identify common molecular underpinnings for seemingly unrelated pathologies).
(via Semantic Scholar)
UN Sustainable Development Goal Categories
3. Good Health and Well-being
(Web of Science)
Sources: Web Of Science, NC State University Libraries
Added: August 6, 2018
2016 journal article
ToxEvaluator: an integrated computational platform to aid the interpretation of toxicology study-related findings
DATABASE-THE JOURNAL OF BIOLOGICAL DATABASES AND CURATION.
MeSH headings : Animals; Computational Biology / methods; Computer Simulation; Database Management Systems; Databases, Factual; Humans; Mice; Toxicogenetics / methods; User-Computer Interface
TL;DR:
ToxEvaluator was developed jointly by Pfizer and the Comparative Toxicogenomics Database as an in silico platform to facilitate interpretation of toxicity findings in light of prior knowledge and rapidly identified direct and indirect linkages between cerivastatin and myopathy.
(via Semantic Scholar)
UN Sustainable Development Goal Categories
3. Good Health and Well-being
(Web of Science)
Sources: Web Of Science, NC State University Libraries
Added: August 6, 2018
2015 conference paper
Integrating literature-based curated data to predict mechanisms of toxicity
Presented at the OpenTox USA 2015, Baltimore, MD.
Event: OpenTox USA 2015 at Baltimore, MD on February 10-12, 2015
Source: NC State University Libraries
Added: August 10, 2019
2014 journal article
BioC interoperability track overview
DATABASE-THE JOURNAL OF BIOLOGICAL DATABASES AND CURATION.
MeSH headings : Biomedical Research; Computational Biology; Data Mining; Database Management Systems; Databases, Factual; Internet; Natural Language Processing; Software
TL;DR:
The interoperability track at the BioCreative IV workshop featured contributions using or highlighting the BioC format, which included additional implementations of BioC, many new corpora in the format, biomedical NLP tools consuming and producing the format and online services using the format.
(via Semantic Scholar)
UN Sustainable Development Goal Categories
3. Good Health and Well-being
(Web of Science)
4. Quality Education
(OpenAlex)
Sources: Web Of Science, NC State University Libraries
Added: August 6, 2018
2014 journal article
The Comparative Toxicogenomics Database's 10th year anniversary: update 2015
NUCLEIC ACIDS RESEARCH, 43(D1), D914–D920.
MeSH headings : Databases, Chemical / history; Disease / etiology; Disease / genetics; Genomics / history; History, 21st Century; Internet; Phenotype; Toxicogenetics / history
TL;DR:
The prototype database originally described in its first report has transformed into a sophisticated resource used actively today to help scientists develop and test hypotheses about the etiologies of environmentally influenced diseases.
(via Semantic Scholar)
UN Sustainable Development Goal Categories
3. Good Health and Well-being
(Web of Science)
Sources: Web Of Science, NC State University Libraries
Added: August 6, 2018
2014 journal article
Web services-based text-mining demonstrates broad impacts for interoperability and process simplification
DATABASE-THE JOURNAL OF BIOLOGICAL DATABASES AND CURATION.
MeSH headings : Data Mining / methods; Databases, Chemical; Databases, Genetic; Disease / genetics; Genes; Internet; Time Factors; Toxicogenetics
TL;DR:
A description of the challenge and summary of results are presented, demonstrating how curation groups can effectively use interoperable NER technologies to simplify text-mining pipeline implementation.
(via Semantic Scholar)
UN Sustainable Development Goal Categories
3. Good Health and Well-being
(Web of Science)
Sources: Web Of Science, NC State University Libraries
Added: August 6, 2018
2013 journal article
A CTD-Pfizer collaboration: manual curation of 88 000 scientific articles text mined for drug-disease and drug-phenotype interactions
DATABASE-THE JOURNAL OF BIOLOGICAL DATABASES AND CURATION.
MeSH headings : Cooperative Behavior; Data Mining; Databases, Factual; Disease; Drug Industry; Humans; Pharmaceutical Preparations / metabolism; Phenotype; Publications; Toxicogenetics
TL;DR:
A collaboration between safety researchers at Pfizer and the research team at the Comparative Toxicogenomics Database (CTD) to text mine and manually review a collection of 88 629 articles relating over 1 200 pharmaceutical drugs to their potential involvement in cardiovascular, neurological, renal and hepatic toxicity.
(via Semantic Scholar)
UN Sustainable Development Goal Categories
3. Good Health and Well-being
(Web of Science)
Sources: Web Of Science, NC State University Libraries
Added: August 6, 2018
2013 journal article
Text Mining Effectively Scores and Ranks the Literature for Improving Chemical-Gene-Disease Curation at the Comparative Toxicogenomics Database
PLOS ONE, 8(4).
MeSH headings : Algorithms; Data Mining / methods; Databases, Factual; Disease / genetics; Documentation; Humans; Metals, Heavy / toxicity; Molecular Sequence Annotation; Publications; Reproducibility of Results; Toxicogenetics
TL;DR:
It is demonstrated how fully incorporating text mining-based DRS scoring into the curation pipeline enhances manual curation by prioritizing more relevant articles, thereby increasing data content, productivity, and efficiency.
(via Semantic Scholar)
UN Sustainable Development Goal Categories
3. Good Health and Well-being
(Web of Science)
Sources: Web Of Science, 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. Y., … al. (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)
Sources: Web Of Science, NC State University Libraries
Added: August 6, 2018
2012 journal article
Collaborative biocuration--text-mining development task for document prioritization for curation
Database, 2012(0), bas037–bas037.
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)
Sources: Crossref, NC State University Libraries, Web Of Science
Added: August 6, 2018
2012 journal article
Computation of Neutron Multiplicity Statistics Using Deterministic Transport
IEEE TRANSACTIONS ON NUCLEAR SCIENCE, 59(2), 314–322.
author keywords: Coincidence techniques; neutron detectors; inverse problems; simulation
UN Sustainable Development Goal Categories
11. Sustainable Cities and Communities
(Web of Science)
Sources: Web Of Science, NC State University Libraries
Added: August 6, 2018
2012 journal article
Disease model curation improvements at Mouse Genome Informatics
Database, 2012(0), bar063–bar063.
MeSH headings : Animals; Database Management Systems; Databases, Factual; Disease Models, Animal; Genome; Humans; Mice / genetics; Molecular Sequence Annotation; User-Computer Interface
TL;DR:
The merged Medical Subject Headings (MeSH) and OMIM disease vocabulary created by the Comparative Toxicogenomics Database (CTD) project is evaluated and an extended version of the vocabulary is created to meet the genetic disease-specific curation needs at MGI.
(via Semantic Scholar)
Sources: Crossref, NC State University Libraries
Added: August 7, 2019
2012 journal article
MEDIC: a practical disease vocabulary used at the Comparative Toxicogenomics Database
Database, 2012(0), bar065–bar065.
MeSH headings : Databases, Factual; Disease / classification; Humans; Subject Headings; Toxicogenetics
TL;DR:
The construction, implementation, maintenance and use of MEDIC is described to raise awareness of this resource and to offer it as a putative scaffold in the formal construction of an official disease ontology.
(via Semantic Scholar)
Sources: Crossref, NC State University Libraries
Added: August 7, 2019
2012 journal article
Providing the Missing Link: the Exposure Science Ontology ExO
ENVIRONMENTAL SCIENCE & TECHNOLOGY, 46(6), 3046–3053.
MeSH headings : Environmental Exposure / analysis; Environmental Health; Environmental Pollutants; Humans; Models, Theoretical
TL;DR:
Development of an Exposure Ontology, ExO, designed to address this information gap by facilitating centralization and integration of exposure data and intended to link exposure science and diverse environmental health disciplines including toxicology, epidemiology, disease surveillance, and epigenetics.
(via Semantic Scholar)
UN Sustainable Development Goal Categories
3. Good Health and Well-being
(Web of Science)
Sources: Web Of Science, NC State University Libraries
Added: August 6, 2018
2012 journal article
Ranking Transitive Chemical-Disease Inferences Using Local Network Topology in the Comparative Toxicogenomics Database
PLOS ONE, 7(11).
MeSH headings : Cluster Analysis; Databases, Factual; Drug-Related Side Effects and Adverse Reactions / genetics; Gene Regulatory Networks; Humans; Protein Interaction Mapping; Toxicogenetics / methods
TL;DR:
A statistic to score and rank inferences based on the topology of the local network consisting of the chemical, disease and each of the genes used to make an inference is implemented, which uniquely takes into account the number of common neighbors and the connectivity of each entity involved.
(via Semantic Scholar)
UN Sustainable Development Goal Categories
3. Good Health and Well-being
(Web of Science)
Sources: Web Of Science, NC State University Libraries
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 journal article
The Comparative Toxicogenomics Database: update 2013
Nucleic Acids Research, 41(D1), D1104–D1114.
MeSH headings : Computer Graphics; Databases, Chemical; Disease / genetics; Internet; Software; Toxicogenetics
UN Sustainable Development Goal Categories
3. Good Health and Well-being
(Web of Science)
14. Life Below Water
(OpenAlex)
Sources: Crossref, NC State University Libraries, Web Of Science
Added: August 6, 2018
2011 journal article
Aquatic models, genomics and chemical risk management
Comparative Biochemistry and Physiology Part C: Toxicology & Pharmacology, 155(1), 169–173.
Contributors: K. Cheng *, D. Hinton *, * & A. Planchart*
author keywords: Aquatic toxicology; Phenome project; Zebrafish; Genomics; Atlas
MeSH headings : Animals; Computational Biology / methods; Databases, Factual; Ecotoxicology; Environmental Exposure / analysis; Environmental Monitoring / methods; Fishes / anatomy & histology; Fishes / genetics; Fishes / physiology; Gene-Environment Interaction; Genomics / methods; Internet; Models, Animal; Risk Factors; User-Computer Interface
TL;DR:
It is concluded that automation, database generation, and web-based accessibility, facilitated by genomic/transcriptomic data and high-performance and cloud computing, will potentiate the unique and potentially key roles that aquatic models play in advancing systems biology, drug development, and environmental risk management.
(via Semantic Scholar)
Sources: Crossref, NC State University Libraries, ORCID
Added: August 7, 2019
2011 journal article
DiseaseComps: a metric that discovers similar diseases based upon common toxicogenomic profiles at CTD
Bioinformation, 7(4), 154–156.
TL;DR:
This work leveraged curated datasets to compute similarity indices that can be used to produce lists of comparable diseases (“DiseaseComps”) based upon shared toxicogenomic profiles, which now classifies diseases with common molecular characteristics, instead of the traditional approach of using histology or tissue of origin to define the disorder.
(via Semantic Scholar)
Sources: Crossref, NC State University Libraries
Added: August 7, 2019
2011 journal article
The curation paradigm and application tool used for manual curation of the scientific literature at the Comparative Toxicogenomics Database
Database, 2011(0), bar034–bar034.
MeSH headings : Database Management Systems; Databases, Factual; Disease; Humans; Internet; Pharmaceutical Preparations; Toxicogenetics; User-Computer Interface; Vocabulary, Controlled
TL;DR:
This approach to manual curation that uses a powerful and efficient paradigm involving mnemonic codes is incorporated into a web-based curation tool to further increase efficiency and productivity, implement quality control in real-time and accommodate biocurators working remotely.
(via Semantic Scholar)
Sources: Crossref, NC State University Libraries
Added: August 7, 2019
2010 journal article
2,3,7,8-Tetrachlorodibenzo-p-dioxin Upregulates FoxQ1b in Zebrafish Jaw Primordium
Chemical Research in Toxicology, 23(3), 480–487.
Contributors: A. Planchart* & *
MeSH headings : Animals; Embryo, Nonmammalian / metabolism; Enhancer Elements, Genetic; Environmental Pollutants / pharmacology; Forkhead Transcription Factors / genetics; Gene Expression Regulation, Developmental / drug effects; Jaw / metabolism; Jaw / pathology; Jaw Abnormalities / chemically induced; Polychlorinated Dibenzodioxins / pharmacology; Receptors, Aryl Hydrocarbon / metabolism; Up-Regulation / drug effects; Zebrafish / genetics; Zebrafish / metabolism; Zebrafish Proteins / genetics; Zebrafish Proteins / metabolism
TL;DR:
FoxQ1b is specifically expressed in the jaw primordium where it discretely outlines a developing jaw structure known as Meckel's cartilage--a conserved structure in all jawed vertebrates that develops abnormally in the presence of TCDD.
(via Semantic Scholar)
UN Sustainable Development Goal Categories
14. Life Below Water
(OpenAlex)
Sources: Crossref, NC State University Libraries, ORCID
Added: August 10, 2019
2010 journal article
The Comparative Toxicogenomics Database: update 2011
Nucleic Acids Research, 39(Database), D1067–D1072.
MeSH headings : Databases, Factual; Disease / etiology; Disease / genetics; Environmental Exposure; Gene Regulatory Networks; Genes; Hazardous Substances / toxicity; Humans; Software; Toxicogenetics
TL;DR:
Since 2009, the content of CTD has dramatically increased the content to 1.4 million chemical–gene–disease data points and added many features, statistical analyses and analytical tools, including GeneComps and ChemComps, to help users generate testable hypotheses about the molecular mechanisms of environmental diseases.
(via Semantic Scholar)
Sources: Crossref, NC State University Libraries
Added: August 7, 2019
2010 chapter
Understanding environment-disease connections: An introduction to the comparative toxicogenomics database (ctd)
In Nature Pathway Interaction Database.
Source: NC State University Libraries
Added: August 10, 2019
2009 journal article
GeneComps and ChemComps: a new CTD metric to identify genes and chemicals with shared toxicogenomic profiles
Bioinformation, 4(4), 173–174.
author keywords: gene; chemical; toxicogenomic; database; curation
TL;DR:
GeneComps and ChemComps are now provided for every curated gene and chemical in CTD and provide a novel way to view and classify genes and chemicals and will help advance testable hypotheses about environmental chemical-genedisease networks.
(via Semantic Scholar)
Sources: Crossref, NC State University Libraries
Added: August 10, 2019
2009 journal article
Genetic and environmental pathways to complex diseases
BMC Systems Biology, 3(1), 46.
MeSH headings : Databases, Genetic; Disease / genetics; Environment; Evolution, Molecular; Gene Expression Regulation; Genome-Wide Association Study; Genotype; Humans; Mental Disorders / etiology; Mental Disorders / genetics; Mental Disorders / metabolism; Mental Disorders / pathology; Metabolic Diseases / etiology; Metabolic Diseases / genetics; Metabolic Diseases / metabolism; Metabolic Diseases / pathology; Phenotype; Transcription, Genetic
TL;DR:
This analysis identifies natural and synthetic retinoids, antipsychotic medications, Omega 3 fatty acids, and pyrethroid pesticides as potential environmental modulators of metabolic syndrome phenotypes through PPAR and adipocytokine signaling and organophosphate pesticides as potential environmental modulators of neuropsychiatric phenotypes.
(via Semantic Scholar)
Sources: Crossref, NC State University Libraries
Added: August 10, 2019
2009 journal article
Perturbation of Defense Pathways by Low-Dose Arsenic Exposure in Zebrafish Embryos
Environmental Health Perspectives, 117(6), 981–987.
Contributors: * , T. Hampton *, K. Brothers *, N. Griffin* & A. Planchart*
author keywords: arsenic; Comparative Toxicogenomics Database; embryonic development; gene regulatory networks; immunity; microarray; toxicogenomics; transcriptional profiling; zebrafish
MeSH headings : Animals; Arsenic / toxicity; Embryo, Nonmammalian; Gene Expression / drug effects; Oligonucleotide Array Sequence Analysis; Reverse Transcriptase Polymerase Chain Reaction; Water Pollutants, Chemical / toxicity; Zebrafish / metabolism
TL;DR:
It is demonstrated that arsenic significantly down-regulates expression levels of multiple genes potentially critical for regulating the establishment of an immune response, and provides molecular evidence consistent with phenotypic observations reported in other model systems.
(via Semantic Scholar)
Sources: Crossref, NC State University Libraries, ORCID
Added: August 10, 2019
2009 journal article
Text mining and manual curation of chemical-gene-disease networks for the Comparative Toxicogenomics Database (CTD)
BMC Bioinformatics, 10(1).
MeSH headings : Computational Biology / methods; Databases, Factual; Gene Regulatory Networks; Information Storage and Retrieval / methods; Toxicogenetics
TL;DR:
This text-mining project is unique in its integration of existing tools into a single workflow with direct application to CTD, which allowed us to measure the potential of these integrated tools to improve prioritization of journal articles for manual curation.
(via Semantic Scholar)
Sources: Crossref, NC State University Libraries
Added: August 10, 2019
2008 journal article
An Evaluation of Information Content as a Metric for the Inference of Putative Conserved Noncoding Regions in DNA Sequences Using a Genetic Algorithms Approach
IEEE/ACM Transactions on Computational Biology and Bioinformatics, 5(1), 1–14.
author keywords: evolutionary computing; genetic algorithms; biology; genetics
MeSH headings : Algorithms; Animals; Base Sequence; Computational Biology / methods; Confidence Intervals; Conserved Sequence / genetics; Cystic Fibrosis Transmembrane Conductance Regulator / genetics; Enhancer Elements, Genetic / genetics; Glutathione Transferase / genetics; Humans; Models, Genetic; Regulatory Sequences, Nucleic Acid / genetics; Sequence Alignment; Sequence Analysis, DNA / methods; Sex-Determining Region Y Protein / genetics
TL;DR:
Results indicate that IC does not identify highly conserved regions and, thus, is not the appropriate metric for this task, whereas variations on IC, as well as the original metric, succeed in identifying putative Conserved regions.
(via Semantic Scholar)
Sources: Crossref, NC State University Libraries
Added: August 10, 2019
2008 journal article
Chemical databases for environmental health and clinical research
Toxicology Letters, 186(1), 62–65.
author keywords: Chemical; Drug; Database; Toxicogenomics
MeSH headings : Animals; Databases, Factual; Drug-Related Side Effects and Adverse Reactions; Environmental Exposure; Environmental Health; Environmental Medicine; Environmental Pollutants / toxicity; Humans; Toxicogenetics
TL;DR:
These databases and their associated resources are incrementally strengthening the expanding field of toxicogenomics-based research by providing centralized sources of manually and computationally curated datasets and highly sophisticated tools for the meta-analysis of continually increasing environmental chemical, drug and small-molecule datasets.
(via Semantic Scholar)
Sources: Crossref, NC State University Libraries
Added: August 10, 2019
2008 journal article
Comparative Toxicogenomics Database: a knowledgebase and discovery tool for chemical-gene-disease networks
Nucleic Acids Research, 37(Database), D786–D792.
MeSH headings : Databases, Factual; Disease / etiology; Disease / genetics; Environmental Exposure; Genes; Genomics; Hazardous Substances / toxicity; Humans; Models, Biological; Proteins / drug effects; Proteins / genetics; Systems Integration; Toxicogenetics
TL;DR:
The Comparative Toxicogenomics Database is a curated database that promotes understanding about the effects of environmental chemicals on human health by integrating data to be integrated to construct chemical–gene–disease networks.
(via Semantic Scholar)
Sources: Crossref, NC State University Libraries
Added: August 10, 2019
2008 journal article
The Comparative Toxicogenomics Database facilitates identification and understanding of chemical-gene-disease associations: arsenic as a case study
BMC Medical Genomics, 1(1).
TL;DR:
Analysis of curated data for the chemical arsenic provides insight into the biological functions and molecular networks affected by exposure to arsenic, including stress response, apoptosis, cell cycle, and specific protein signaling pathways.
(via Semantic Scholar)
Sources: Crossref, NC State University Libraries
Added: August 10, 2019
2007 conference paper
Towards Interactive Visualization for Exploring Conserved Motifs in Noncoding DNA Sequence
2007 Frontiers in the Convergence of Bioscience and Information Technologies. Presented at the 2007 Frontiers in the Convergence of Bioscience and Information Technologies.
Event: 2007 Frontiers in the Convergence of Bioscience and Information Technologies
TL;DR:
The work presented here describes initial efforts toward interactive visualization of putative functional elements specifically for work with conserved elements.
(via Semantic Scholar)
Sources: Crossref, NC State University Libraries
Added: August 10, 2019
2006 journal article
The Comparative Toxicogenomics Database (CTD): a resource for comparative toxicological studies
Journal of Experimental Zoology Part A: Comparative Experimental Biology, 305A(9), 689–692.
MeSH headings : Animals; Databases, Factual; Humans; Toxicogenetics; Xenobiotics / toxicity
TL;DR:
The publicly available Comparative Toxicogenomics Database (CTD) is developed to promote understanding about the effects of environmental chemicals on human health and identifies interactions between chemicals and genes and facilitates cross-species comparative studies of these genes.
(via Semantic Scholar)
Sources: Crossref, NC State University Libraries
Added: August 10, 2019
2006 journal article
The Comparative Toxicogenomics Database: A Cross-Species Resource for Building Chemical-Gene Interaction Networks
Toxicological Sciences, 92(2), 587–595.
author keywords: CTD; chemicals; environment; GO; toxicology; pathways; interactions
MeSH headings : Animals; Databases, Factual; Environmental Health; Humans; Toxicogenetics
TL;DR:
New CTD features include integrated cross-links to microarray data from chemicals, genes, and sequences in CTD, a reference set related to chemical-gene and protein interactions identified by an information retrieval system, and a "Chemicals in the News" initiative that provides links from CTD chemicals to environmental health articles from the popular press.
(via Semantic Scholar)
UN Sustainable Development Goal Categories
15. Life on Land
(OpenAlex)
Sources: Crossref, NC State University Libraries
Added: August 10, 2019
2005 conference paper
Preliminary Results for GAMI: A Genetic Algorithms Approach to Motif Inference
2005 IEEE Symposium on Computational Intelligence in Bioinformatics and Computational Biology. Presented at the 2005 IEEE Symposium on Computational Intelligence in Bioinformatics and Computational Biology.
Event: 2005 IEEE Symposium on Computational Intelligence in Bioinformatics and Computational Biology
TL;DR:
GAMI is able to find a host of putative conserved patterns; possible approaches for validating the utility of the conserved regions are discussed.
(via Semantic Scholar)
Sources: Crossref, NC State University Libraries
Added: August 10, 2019
2004 journal article
Cell and Molecular Biology of Marine Elasmobranchs: Squalus acanthias and Raja erinacea
Zebrafish, 1(2), 111–120.
TL;DR:
It appears that sharks have tissue regenerative capability beyond what is commonly seen in mammals, and these comparative vertebrate models may play an increasing role in the larger picture of human biomedical research.
(via Semantic Scholar)
UN Sustainable Development Goal Categories
14. Life Below Water
(OpenAlex)
Sources: Crossref, NC State University Libraries
Added: August 10, 2019
2004 journal article
Marine Organism Cell Biology and Regulatory Sequence Discoveryin Comparative Functional Genomics
Cytotechnology, 46(2-3), 123–137.
TL;DR:
Data and tools resulting from comparative studies will contribute to understanding transcriptional regulation of biomedically important genes and provide new avenues for medical therapeutics and disease prevention.
(via Semantic Scholar)
UN Sustainable Development Goal Categories
14. Life Below Water
(OpenAlex)
Sources: Crossref, NC State University Libraries
Added: August 10, 2019
2004 journal article
Promoting comparative molecular studies in environmental health research: an overview of the comparative toxicogenomics database (CTD)
The Pharmacogenomics Journal, 4(1), 5–8.
MeSH headings : Animals; Databases, Genetic / trends; Environmental Health / trends; Humans; Toxicogenetics / trends
TL;DR:
An overview of the comparative toxicogenomics database (CTD) and promoting comparative molecular studies in environmental health research is presented.
(via Semantic Scholar)
Sources: Crossref, NC State University Libraries
Added: August 10, 2019
2003 journal article
The Comparative Toxicogenomics Database (CTD).
Environmental Health Perspectives, 111(6), 793–795.
author keywords: aquatic; comparative; database; environmental health; fishes; genomic; health; toxicogenomics; toxicology
MeSH headings : Animals; Databases, Factual; Environmental Health; Environmental Pollutants / adverse effects; Genetic Predisposition to Disease; Humans; Pharmacogenetics / statistics & numerical data; Pharmacogenetics / trends; Research / trends; Toxicology / trends
TL;DR:
The intent of this report is to invite community participation in the development of CTD to ensure that it will be a valuable resource for environmental health, molecular biology, and toxicology research.
(via Semantic Scholar)
Sources: Crossref, NC State University Libraries
Added: August 10, 2019
2001 journal article
Green fluorescent protein (GFP) as a marker of aryl hydrocarbon receptor (AhR) function in developing zebrafish (Danio rerio).
Environmental Health Perspectives, 109(8), 845–849.
MeSH headings : Animals; Biomarkers / analysis; Cytochrome P-450 CYP1A1 / genetics; Eye Abnormalities / chemically induced; Green Fluorescent Proteins; Luminescent Proteins / biosynthesis; Models, Animal; Morphogenesis / drug effects; Polychlorinated Dibenzodioxins / toxicity; Receptors, Aryl Hydrocarbon / genetics; Spine / abnormalities; Transcription, Genetic; Transfection; Zebrafish / embryology
TL;DR:
An inducible in vivo reporter system to examine expression of the aryl hydrocarbon receptor (AhR) during development in zebrafish (Danio rerio) and whether AhR-regulated GFP expression correlated with sites of TCDD toxicity is developed.
(via Semantic Scholar)
UN Sustainable Development Goal Categories
14. Life Below Water
(OpenAlex)
Sources: Crossref, NC State University Libraries
Added: August 10, 2019
2001 journal article
Posttranscriptional silencing of cytochrome P4501A1 (CYP1A1) during zebrafish (Danio rerio) development
Developmental Dynamics, 222(4), 645–654.
author keywords: cytochrome P450; monooxygenase; zebrafish; Ah receptor; dioxin
MeSH headings : Aging / metabolism; Animals; Base Sequence / genetics; Cloning, Molecular; Cytochrome P-450 CYP1A1 / genetics; Cytochrome P-450 CYP1A1 / metabolism; Embryo, Nonmammalian / drug effects; Embryo, Nonmammalian / physiology; Environmental Pollutants / poisoning; Gene Expression Regulation; Gene Expression Regulation, Developmental; Gene Silencing; Molecular Sequence Data; Polychlorinated Dibenzodioxins / poisoning; RNA, Messenger / metabolism; Transcription, Genetic; Zebrafish / embryology; Zebrafish / genetics; Zebrafish / metabolism
TL;DR:
The data suggest that TCDD‐mediated induction of CYP1A1 activity is regulated differentially in developing and mature systems.
(via Semantic Scholar)
Sources: Crossref, NC State University Libraries
Added: August 10, 2019
1999 journal article
Estrogen Receptor Reduces CYP1A1 Induction in Cultured Human Endometrial Cells
Journal of Biological Chemistry, 274(6), 3430–3438.
MeSH headings : Cell Line; Cytochrome P-450 CYP1A1 / biosynthesis; Cytochrome P-450 CYP1A1 / genetics; Endometrium / cytology; Endometrium / drug effects; Endometrium / enzymology; Enzyme Induction; Estradiol / pharmacology; Female; Humans; Polychlorinated Dibenzodioxins / pharmacology; RNA, Messenger / genetics; Receptors, Estrogen / physiology; Transcription, Genetic / drug effects
TL;DR:
The data suggest that 17β-estradiol reduced CYP1A1 expression at the transcriptional level by squelching available nuclear factor-1, a transcription factor that interacts with both Ah and estrogen receptors.
(via Semantic Scholar)
UN Sustainable Development Goal Categories
3. Good Health and Well-being
(OpenAlex)
Sources: Crossref, NC State University Libraries
Added: August 10, 2019
Employment
Updated: September 9th, 2019 21:21
2019 - present
NC State University Raleigh, NC, US
Professor
Biological Sciences
2018 - present
NC State University Raleigh, NC, US
Interim Head
Biological Sciences
2012 - 2019
NC State University Raleigh, NC, US
Associate Professor
Biological Sciences
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