Recent Works

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Sorted by most recent date added to the index first, which may not be the same as publication date order.

2025 article

A workflow for human health hazard evaluation using transcriptomic data and Key Characteristics-based gene sets

Tsai, H.-H. D., Oware, K. D., Wright, F. A., Chiu, W. A., & Rusyn, I. (2025, April 3). TOXICOLOGICAL SCIENCES.

By: H. Tsai, K. Oware, F. Wright, W. Chiu & I. Rusyn

author keywords: transcriptomics; key characteristics; gene set enrichment; gene expression
topics (OpenAlex): Computational Drug Discovery Methods; Carcinogens and Genotoxicity Assessment; Gene expression and cancer classification
Source: Web Of Science
Added: April 14, 2025

2025 article

Co-occurrence drives horizontal gene transfer among marine prokaryotes

Douglas, G. M., Tromas, N., Gaudin, M., Lypaczewksi, P., Bobay, L.-M., Shapiro, B. J., & Chaffron, S. (2025, March 28).

By: G. Douglas, N. Tromas, M. Gaudin, P. Lypaczewksi, L. Bobay*, B. Shapiro, S. Chaffron

topics (OpenAlex): Microbial Community Ecology and Physiology; Bacteriophages and microbial interactions; Polar Research and Ecology
Source: ORCID
Added: April 1, 2025

2025 journal article

Integrating AI-powered text mining from PubTator into the manual curation workflow at the Comparative Toxicogenomics Database

DATABASE-THE JOURNAL OF BIOLOGICAL DATABASES AND CURATION, 2025.

MeSH headings : Toxicogenetics; Data Mining / methods; Data Curation / methods; Humans; Databases, Factual; Workflow; Databases, Genetic
topics (OpenAlex): Biomedical Text Mining and Ontologies; Genetics, Bioinformatics, and Biomedical Research; Bioinformatics and Genomic Networks
Sources: Web Of Science, NC State University Libraries
Added: March 10, 2025

2025 article

Connected Chromatin Amplifies Acetylation-Modulated Nucleosome Interactions

Li, R., & Lin, X. (2025, March 3). BIOCHEMISTRY, Vol. 3.

By: R. Li & X. Lin

co-author countries: Japan 🇯🇵
MeSH headings : Nucleosomes / metabolism; Nucleosomes / chemistry; Acetylation; Histones / metabolism; Histones / chemistry; Chromatin / metabolism; Chromatin / chemistry; Protein Processing, Post-Translational; DNA / metabolism; DNA / chemistry; Molecular Dynamics Simulation; Humans; Chromatin Assembly and Disassembly
topics (OpenAlex): Genomics and Chromatin Dynamics; RNA Research and Splicing; DNA and Nucleic Acid Chemistry
Sources: ORCID, Web Of Science, NC State University Libraries
Added: March 3, 2025

2025 journal article

Zebrafish Cyp1b1 knockout alters eye and brain metabolomic profiles, affecting ocular and neurobehavioral function

TOXICOLOGY AND APPLIED PHARMACOLOGY, 496.

By: D. Perone, A. Annalora, J. Goldstone, A. Dickey, M. Salanga, R. Francolini, F. Wright, C. Marcus, R. Tanguay, M. Garcia-Jaramillo

author keywords: Cytochrome P450; Untargeted metabolomics; Mutliomics; Zebrafish; Eye disorders
MeSH headings : Animals; Zebrafish / genetics; Cytochrome P-450 CYP1B1 / genetics; Cytochrome P-450 CYP1B1 / metabolism; Brain / metabolism; Behavior, Animal; Eye / metabolism; Metabolomics; Zebrafish Proteins / genetics; Zebrafish Proteins / metabolism; Larva; Gene Knockout Techniques; Reflex, Startle; Metabolome
topics (OpenAlex): Zebrafish Biomedical Research Applications; Metabolomics and Mass Spectrometry Studies; Eicosanoids and Hypertension Pharmacology
Source: Web Of Science
Added: March 3, 2025

2025 article

Examining risk assessment implications of genetic and dose-dependent dynamics of lead exposure in breastfeeding using the collaborative cross mouse population

Cuomo, D., Song, Z., Nitcher, M., Lynch, R., Barba, E., Feinberg, A. P., … Threadgill, D. W. (2025, February 11). TOXICOLOGICAL SCIENCES.

By: D. Cuomo, Z. Song, M. Nitcher, R. Lynch, E. Barba, A. Feinberg, I. Rusyn, F. Wright, W. Chiu, D. Threadgill

author keywords: lead; risk assessment; mouse model; maternal exposure
MeSH headings : Animals; Female; Risk Assessment; Lead / toxicity; Lead / blood; Dose-Response Relationship, Drug; Breast Feeding; Collaborative Cross Mice; Lactation; Mice; Pregnancy; Maternal Exposure / adverse effects; Male
topics (OpenAlex): Effects and risks of endocrine disrupting chemicals; Animal Behavior and Welfare Studies
Source: Web Of Science
Added: February 24, 2025

2025 article

Interpretable Protein-DNA Interactions Captured by Structure-Sequence Optimization

Zhang, Y., Silvernail, I., Lin, Z., & Lin, X. (2025, February 7).

By: Y. Zhang n, I. Silvernail n, Z. Lin n & X. Lin n

topics (OpenAlex): RNA and protein synthesis mechanisms; Genomics and Chromatin Dynamics; Protein Structure and Dynamics
UN Sustainable Development Goals Color Wheel
UN Sustainable Development Goal Categories
7. Affordable and Clean Energy (OpenAlex)
Source: ORCID
Added: February 7, 2025

2025 article

Interpretable Protein-DNA Interactions Captured by Structure-Sequence Optimization

Zhang, Y., Silvernail, I., Lin, Z., & Lin, X. (2025, February 7).

By: Y. Zhang n, I. Silvernail n, Z. Lin n & X. Lin n

topics (OpenAlex): RNA and protein synthesis mechanisms; Genomics and Chromatin Dynamics; Protein Structure and Dynamics
UN Sustainable Development Goals Color Wheel
UN Sustainable Development Goal Categories
7. Affordable and Clean Energy (OpenAlex)
Source: ORCID
Added: February 7, 2025

2025 article

Updated Guidance for Communicating PFAS Identification Confidence with Ion Mobility Spectrometry

Boatman, A. K., Chappel, J. R., Kirkwood-Donelson, K. I., Fleming, J. F., Reif, D. M., Schymanski, E. L., … Baker, E. S. (2025, January 28).

By: A. Boatman*, J. Chappel*, K. Kirkwood-Donelson, J. Fleming, D. Reif*, E. Schymanski*, J. Rager*, E. Baker*

co-author countries: Luxembourg 🇱🇺
topics (OpenAlex): Per- and polyfluoroalkyl substances research; Hemoglobin structure and function; Methemoglobinemia and Tumor Lysis Syndrome; Health, Environment, Cognitive Aging
Source: ORCID
Added: January 28, 2025

2025 journal article

Bayesian analysis of the rate of spontaneous malignant mesothelioma among <i>BAP1</i> mutant mice in the absence of asbestos exposure

SCIENTIFIC REPORTS, 15(1).

By: D. Nielsen, M. Hsu, M. Zapata III, G. Ciavarra & L. Zyl

author keywords: Mesothelioma; Asbestos; BAP1; Mouse studies; Historical control data; Bayesian statistics
MeSH headings : Animals; Ubiquitin Thiolesterase / genetics; Mice; Asbestos / toxicity; Asbestos / adverse effects; Bayes Theorem; Mesothelioma, Malignant / genetics; Mesothelioma, Malignant / pathology; Tumor Suppressor Proteins / genetics; Germ-Line Mutation; Lung Neoplasms / genetics; Lung Neoplasms / pathology; Lung Neoplasms / chemically induced
topics (OpenAlex): Occupational and environmental lung diseases; Carcinogens and Genotoxicity Assessment
Sources: Web Of Science, NC State University Libraries
Added: January 13, 2025

2024 journal article

Bayesian gene set benchmark dose estimation for “omic” responses

Bioinformatics.

By: D. Zilber, K. Messier, J. House, F. Parham, S. Auerbach & M. Wheeler

Ed(s): C. Kendziorski

MeSH headings : Animals; Rats; Bayes Theorem; Benchmarking; Gene Expression Profiling / methods; Transcriptome
topics (OpenAlex): Animal testing and alternatives; Computational Drug Discovery Methods; Carcinogens and Genotoxicity Assessment
Source: ORCID
Added: January 7, 2025

2025 journal article

A Systematic Analysis of Read-Across Adaptations in Testing Proposal Evaluations by the European Chemicals Agency

ALTEX-ALTERNATIVES TO ANIMAL EXPERIMENTATION, 42(1), 22–38.

By: H. Roe, H. Tsai, N. Ball, F. Wright, W. Chiu & I. Rusyn

MeSH headings : Animal Testing Alternatives / methods; Toxicity Tests / methods; European Union; Hazardous Substances / toxicity; Risk Assessment / methods; Humans; Europe
topics (OpenAlex): Recycling and Waste Management Techniques; Chemical Safety and Risk Management; Nuclear and radioactivity studies
Source: Web Of Science
Added: February 17, 2025

2025 journal article

Comparative analysis of the physiological and transport functions of various sources of renal proximal tubule cells under static and fl uidic conditions in PhysioMimix T12 platform

DRUG METABOLISM AND DISPOSITION, 53(1).

By: C. Sakolish, H. Moyer, H. Tsai, L. Ford, A. Dickey, P. Bajaj, R. Villenave, P. Hewitt ...

co-author countries: Switzerland 🇨🇭 Germany 🇩🇪
author keywords: Kidney; Toxicity; Pharmacokinetics; Organ-on-chip
MeSH headings : Humans; Kidney Tubules, Proximal / metabolism; Kidney Tubules, Proximal / cytology; Epithelial Cells / metabolism; Biological Transport / physiology; Organic Anion Transport Protein 1 / metabolism; Organic Anion Transport Protein 1 / genetics; Organic Cation Transporter 2 / metabolism; Organic Cation Transporter 2 / genetics; Cells, Cultured; Organic Anion Transporters, Sodium-Independent / metabolism; Organic Anion Transporters, Sodium-Independent / genetics; Lab-On-A-Chip Devices; Cell Line; Telomerase / metabolism
topics (OpenAlex): Renal and related cancers; Organ Donation and Transplantation; Genetic and Kidney Cyst Diseases; Birth, Development, and Health; Chronic Kidney Disease and Diabetes; Dialysis and Renal Disease Management
Source: Web Of Science
Added: January 27, 2025

2024 journal article

Is increased mutation driving genetic diversity in dogs within the Chornobyl exclusion zone?

PLOS ONE, 19(12).

MeSH headings : Animals; Dogs / genetics; Chernobyl Nuclear Accident; Genetic Variation; Mutation; Microsatellite Repeats / genetics; Ukraine; Alleles
topics (OpenAlex): Human-Animal Interaction Studies; Forensic and Genetic Research; Genetic diversity and population structure
Sources: Web Of Science, NC State University Libraries
Added: January 13, 2025

2025 journal article

Phenotype variability in diet-induced obesity and response to (−)-epigallocatechin gallate supplementation in a Diversity Outbred mouse cohort: A model for exploring gene x diet interactions for dietary bioactives

Nutrition Research, 133, 78–93.

By: M. Sweet, L. Iglesias-Carres, P. Ellsworth, J. Carter, D. Nielsen, D. Aylor, J. Tessem, A. Neilson

author keywords: EGCG; Diversity Outbred; Gene x environment; Phenotype; Genetic polymorphism
MeSH headings : Animals; Catechin / analogs & derivatives; Catechin / pharmacology; Catechin / administration & dosage; Obesity / genetics; Diet, High-Fat; Phenotype; Male; Mice; Body Composition / drug effects; Dietary Supplements; Gene-Environment Interaction; Disease Models, Animal; Animals, Outbred Strains; Longitudinal Studies
topics (OpenAlex): Tea Polyphenols and Effects; Nutrition, Genetics, and Disease; Phytochemicals and Antioxidant Activities
UN Sustainable Development Goals Color Wheel
UN Sustainable Development Goal Categories
2. Zero Hunger (OpenAlex)
Sources: Web Of Science, NC State University Libraries, ORCID, Crossref
Added: January 13, 2025

2024 journal article

Co-evolution and Gene Transfers Drive Speciation Patterns in Host-Associated Bacteria

MOLECULAR BIOLOGY AND EVOLUTION, 41(12).

By: C. Stott, A. Diop, K. Raymann & L. Bobay

Ed(s): H. Hendrickson

author keywords: speciation; bacteria; symbiosis; horizontal gene transfer; honeybee
MeSH headings : Gene Transfer, Horizontal; Animals; Bees / microbiology; Bees / genetics; Genetic Speciation; Bacteria / genetics; Gastrointestinal Microbiome; Host Microbial Interactions / genetics; Symbiosis; Homologous Recombination; Evolution, Molecular
topics (OpenAlex): Plant and animal studies; Insect and Pesticide Research; Insect and Arachnid Ecology and Behavior
UN Sustainable Development Goals Color Wheel
UN Sustainable Development Goal Categories
15. Life on Land (OpenAlex)
Sources: ORCID, Web Of Science, NC State University Libraries
Added: December 13, 2024

2025 journal article

Homologous recombination shapes the architecture and evolution of bacterial genomes

Nucleic Acids Research.

By: E. Torrance, A. Diop & L. Bobay

MeSH headings : Genome, Bacterial / genetics; Evolution, Molecular; Homologous Recombination / genetics; Base Composition / genetics; Bacteria / genetics; Bacteria / classification; Bayes Theorem; Selection, Genetic; Phylogeny; Genomics / methods
topics (OpenAlex): Genomics and Phylogenetic Studies; Evolution and Genetic Dynamics; Escherichia coli research studies
UN Sustainable Development Goals Color Wheel
UN Sustainable Development Goal Categories
15. Life on Land (OpenAlex)
Source: ORCID
Added: December 11, 2024

2024 article

Nucleosome condensate and linker DNA alter chromatin folding pathways and rates

Qiu, Y., Liu, S., Lin, X., Unarta, I. C., Huang, X., & Zhang, B. (2024, November 16).

topics (OpenAlex): Genomics and Chromatin Dynamics; DNA Repair Mechanisms; DNA and Nucleic Acid Chemistry
UN Sustainable Development Goals Color Wheel
UN Sustainable Development Goal Categories
7. Affordable and Clean Energy (OpenAlex)
Source: ORCID
Added: November 17, 2024

2024 article

To Accept or Not To Accept a Read-Across Adaptation: A Systematic Analysis of 15 Years of Testing Proposal Decisions by the European Chemicals Agency

Roe, H. M., Ball, N., Wright, F. A., Chiu, W. A., & Rusyn, I. (2024, September). TOXICOLOGY LETTERS, Vol. 399, pp. S63–S63.

By: H. Roe*, N. Ball, F. Wright n, W. Chiu* & I. Rusyn*

topics (OpenAlex): Chemistry and Chemical Engineering
Source: Web Of Science
Added: November 12, 2024

2024 article

Profiling the cancer-prone microenvironment in a zebrafish model for MPNST

Cero, C., House, J. S., Verdi, V., Ferguson, J. L., Jima, D. D., Selmek, A. A., … Shive, H. R. (2024, November 7). ONCOGENE, Vol. 11.

By: C. Cero, J. House, V. Verdi, J. Ferguson, D. Jima, A. Selmek, O. Patania, J. Dwyer ...

MeSH headings : Animals; Zebrafish / genetics; Tumor Microenvironment / genetics; Disease Models, Animal; Humans; Gene Expression Regulation, Neoplastic; Neurofibrosarcoma / genetics; Neurofibrosarcoma / pathology; Neurofibrosarcoma / metabolism; Zebrafish Proteins / genetics; Zebrafish Proteins / metabolism; Transcriptome; Gene Expression Profiling; Cell Adhesion Molecules / genetics; Cell Adhesion Molecules / metabolism
topics (OpenAlex): Aquaculture disease management and microbiota; Cancer, Hypoxia, and Metabolism; Zebrafish Biomedical Research Applications
UN Sustainable Development Goals Color Wheel
UN Sustainable Development Goal Categories
10. Reduced Inequalities (OpenAlex)
Sources: ORCID, Web Of Science, NC State University Libraries
Added: November 7, 2024

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.

MeSH headings : Toxicogenetics; Humans; Software; Databases, Genetic; Anniversaries and Special Events; Databases, Factual; Data Curation
topics (OpenAlex): Biomedical Text Mining and Ontologies; Bioinformatics and Genomic Networks; Gene expression and cancer classification
Sources: Web Of Science, NC State University Libraries
Added: October 21, 2024

2024 article

Connected Chromatin Amplifies Acetylation-modulated Nucleosome Interactions

Li, R., & Lin, X. (2024, October 13).

By: R. Li n & X. Lin n

topics (OpenAlex): Genomics and Chromatin Dynamics; DNA and Nucleic Acid Chemistry; RNA Research and Splicing
Source: ORCID
Added: October 15, 2024

2024 article

Prevalence and Dynamics of Genome Rearrangements in Bacteria and Archaea

Martinez-Gutierrez, C. A., & Bobay, L.-M. (2024, October 5).

By: C. Martinez-Gutierrez & L. Bobay*

topics (OpenAlex): Chromosomal and Genetic Variations; Genomics and Phylogenetic Studies; Genomic variations and chromosomal abnormalities
Source: ORCID
Added: October 8, 2024

2024 article

The GeoTox Package: Open-source software for connecting spatiotemporal exposure to individual and population-level risk

Messier, K. P., Reif, D. M., & Marvel, S. W. (2024, September 24).

By: K. Messier, D. Reif* & S. Marvel

topics (OpenAlex): Health, Environment, Cognitive Aging; Climate Change and Health Impacts; Nutritional Studies and Diet
Source: ORCID
Added: October 1, 2024

2024 article

Streamlining Phenotype Classification and Highlighting Feature Candidates: A Screening Method for Non-Targeted Ion Mobility Spectrometry-Mass Spectrometry (IMS-MS) Data

Chappel, J. R., Kirkwood-Donelson, K. I., Dodds, J. N., Fleming, J., Reif, D. M., & Baker, E. S. (2024, September 18). ANALYTICAL CHEMISTRY, Vol. 9.

By: J. Chappel, K. Kirkwood-Donelson, J. Dodds, J. Fleming, D. Reif & E. Baker

MeSH headings : Ion Mobility Spectrometry / methods; Mass Spectrometry / methods; Phenotype; Chromatography, Liquid / methods; Support Vector Machine; Humans
topics (OpenAlex): Metabolomics and Mass Spectrometry Studies; Mass Spectrometry Techniques and Applications; Isotope Analysis in Ecology
Sources: Web Of Science, NC State University Libraries
Added: September 30, 2024

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