David Michael Reif

Aggregated Molecular Phenotype Scores: Enhancing Assessment and Visualization of Mass Spectrometry Imaging Data for Tissue-Based Diagnostics

Chappel, J. R., King, M. E., Fleming, J., Eberlin, L. S., Reif, D. M., & Baker, E. S. (2023, August 14). ANALYTICAL CHEMISTRY, Vol. 8.

Bayesian matrix completion for hypothesis testing

Jin, B., Dunson, D. B., Rager, J. E., Reif, D. M., Engel, S. M., & Herring, A. H. (2023, March 15). JOURNAL OF THE ROYAL STATISTICAL SOCIETY SERIES C-APPLIED STATISTICS, Vol. 3.

Deep autoencoder-based behavioral pattern recognition outperforms standard statistical methods in high-dimensional zebrafish studies

Green, A. J., Truong, L., Thunga, P., Leong, C., Hancock, M., Tanguay, R. L., & Reif, D. M. (2023, September 17).

Legacy and emerging per- and polyfluoroalkyl substances suppress the neutrophil respiratory burst

JOURNAL OF IMMUNOTOXICOLOGY, 20(1).

MKX-AS1 Gene Expression Associated with Variation in Drug Response to Oxaliplatin and Clinical Outcomes in Colorectal Cancer Patients

PHARMACEUTICALS, 16(5).

Pharmacogenomic Analyses Implicate B Cell Developmental Status and MKL1 as Determinants of Sensitivity toward Anti-CD20 Monoclonal Antibody Therapy

CELLS, 12(12).

RYK Gene Expression Associated with Drug Response Variation of Temozolomide and Clinical Outcomes in Glioma Patients

PHARMACEUTICALS, 16(5).

Utilizing Aggregated Molecular Phenotype (AMP) Scores to Visualize Simultaneous Molecular Changes in Mass Spectrometry Imaging Data

Chappel, J. R., King, M. E., Fleming, J., Eberlin, L. S., Reif, D. M., & Baker, E. S. (2023, June 5).

Comparison of National Vulnerability Indices Used by the Centers for Disease Control and Prevention for the COVID-19 Response

Public Health Reports, 137(4), 803–812.

Demonstrating a systems approach for integrating disparate data streams to inform decisions on children's environmental health

BMC PUBLIC HEALTH, 22(1).

Systematic developmental toxicity assessment of a structurally diverse library of PFAS in zebrafish

JOURNAL OF HAZARDOUS MATERIALS, 431.

TCDD alters essential transcriptional regulators of osteogenic differentiation in multipotent mesenchymal stem cells

Watson, A. L. T. D., Carmona Baez, A., Jima, D., Reif, D., Ding, J., Roberts, R., & Kullman, S. W. (2022, November 12). TOXICOLOGICAL SCIENCES, Vol. 11.

The Ahr2-Dependent wfikkn1 Gene Influences Zebrafish Transcriptome, Proteome, and Behavior

Shankar, P., Garcia, G. R., LaDu, J. K., Sullivan, C. M., Dunham, C. L., Goodale, B. C., … Tanguay, R. L. (2022, April 4). TOXICOLOGICAL SCIENCES, Vol. 4.

ToxPi*GIS Toolkit: creating, viewing, and sharing integrative visualizations for geospatial data using ArcGIS

Fleming, J., Marvel, S. W., Supak, S., Motsinger-Reif, A. A., & Reif, D. M. (2022, April 26). JOURNAL OF EXPOSURE SCIENCE AND ENVIRONMENTAL EPIDEMIOLOGY, Vol. 4.

Utilizing Pine Needles to Temporally and Spatially Profile Per- and Polyfluoroalkyl Substances (PFAS)

ENVIRONMENTAL SCIENCE & TECHNOLOGY, 56(6), 3441–3451.

Utilizing a Population-Genetic Framework to Test for Gene-Environment Interactions between Zebrafish Behavior and Chemical Exposure

TOXICS, 10(12).

Wildfires and extracellular vesicles: Exosomal MicroRNAs as mediators of cross-tissue cardiopulmonary responses to biomass smoke

ENVIRONMENT INTERNATIONAL, 167.

Concurrent Evaluation of Mortality and Behavioral Responses: A Fast and Efficient Testing Approach for High-Throughput Chemical Hazard Identification

Frontiers in Toxicology, 3.

Development of a Pandemic Awareness STEM Outreach Curriculum: Utilizing a Computational Thinking Taxonomy Framework

EDUCATION SCIENCES, 11(3).

Extending the lymphoblastoid cell line model for drug combination pharmacogenomics

Green, A. J., Anchang, B., Akhtari, F. S., Reif, D. M., & Motsinger-Reif, A. (2021, May 28). PHARMACOGENOMICS, Vol. 22.

High-throughput screening and genome-wide analyses of 44 anticancer drugs in the 1000 Genomes cell lines reveals an association of the NQO1 gene with the response of multiple anticancer drugs

PLOS GENETICS, 17(8).

Leveraging high-throughput screening data, deep neural networks, and conditional generative adversarial networks to advance predictive toxicology

PLOS COMPUTATIONAL BIOLOGY, 17(7).

Multiomic Big Data Analysis Challenges: Increasing Confidence in the Interpretation of Artificial Intelligence Assessments

ANALYTICAL CHEMISTRY, 93(22), 7763–7773.

The COVID-19 Pandemic Vulnerability Index (PVI) Dashboard: Monitoring County-Level Vulnerability Using Visualization, Statistical Modeling, and Machine Learning

Marvel, S. W., House, J. S., Wheeler, M., Song, K., Zhou, Y.-H., Wright, F. A., … Reif, D. M. (2021, January).

ToxPi*GIS Toolkit: Creating, viewing, and sharing integrative visualizations for geospatial data using ArcGIS

Fleming, J., Marvel, S. W., Motsinger-Reif, A. A., & Reif, D. M. (2021, October 11). (Vol. 10). Vol. 10.

Uncovering Evidence for Endocrine-Disrupting Chemicals That Elicit Differential Susceptibility through Gene-Environment Interactions

[Review of ]. TOXICS, 9(4).

Utilizing Pine Needles to Temporally and Spatially Profile Per- and Polyfluoroalkyl Substances

Kirkwood, K. I., Fleming, J., Nguyen, H., Reif, D. M., Baker, E. S., & Belcher, S. M. (2021, August 26). (Vol. 8). Vol. 8.

Bayesian Matrix Completion for Hypothesis Testing

(2020, September 17).

Children’s Environmental Health: A Systems Approach for Anticipating Impacts from Chemicals

International Journal of Environmental Research and Public Health, 17(22), 8337.

Concentration-response evaluation of ToxCast compounds for multivariate activity patterns of neural network function

ARCHIVES OF TOXICOLOGY, 94(2), 469–484.

HGBEnviroScreen: Enabling Community Action through Data Integration in the Houston–Galveston–Brazoria Region

International Journal of Environmental Research and Public Health, 17(4), 1130.

In vivo assessment of respiratory burst inhibition by xenobiotic exposure using larval zebrafish

Journal of Immunotoxicology, 17(1), 94–104.

Inappropriate Citation of Vaccine Article

The Journal of Infectious Diseases, 222(8), 1413–1414.

Structural-based connectivity and omic phenotype evaluations (SCOPE): a cheminformatics toolbox for investigating lipidomic changes in complex systems

ANALYST, 145(22), 7197–7209.

The COVID-19 Pandemic Vulnerability Index (PVI) Dashboard: monitoring county level vulnerability

Marvel, S. W., House, J. S., Wheeler, M., Song, K., Zhou, Y., Wright, F. A., … Reif, D. M. (2020, August 13). MedRxiv, Vol. 8.

The multi-dimensional embryonic zebrafish platform predicts flame retardant bioactivity

REPRODUCTIVE TOXICOLOGY, 96, 359–369.

Associations between access to healthcare, environmental quality, and end-stage renal disease survival time: Proportional-hazards models of over 1,000,000 people over 14 years

PLOS ONE, 14(3).

Determination of chemical-disease risk values to prioritize connections between environmental factors, genetic variants, and human diseases

Toxicology and Applied Pharmacology, 379, 114674.

Integration of curated and high-throughput screening data to elucidate environmental influences on disease pathways

Computational Toxicology, 12, 100094.

Multivariate modeling of engineered nanomaterial features associated with developmental toxicity

NanoImpact, 16.

Population-based toxicity screening in human induced pluripotent stem cell-derived cardiomyocytes

Toxicology and Applied Pharmacology, 381.

Sex-specific effects of perinatal FireMaster® 550 (FM 550) exposure on socioemotional behavior in prairie voles

Neurotoxicology and Teratology, 79, 106840.

Synergistic Chemotherapy Drug Response Is a Genetic Trait in Lymphoblastoid Cell Lines

FRONTIERS IN GENETICS, 10.

Systematic determination of the relationship between nanoparticle core diameter and toxicity for a series of structurally analogous gold nanoparticles in zebrafish

Nanotoxicology, 4, 1—15.

Characterizing the effects of missing data and evaluating imputation methods for chemical prioritization applications using ToxPi

BIODATA MINING, 11(1).

Confirmation of high-throughput screening data and novel mechanistic insights into VDR-xenobiotic interactions by orthogonal assays

Scientific Reports, 8(1).

Elucidating Gene-by-Environment Interactions Associated with Differential Susceptibility to Chemical Exposure.

Environmental Health Perspectives, 6(6).

Neonatal mice exposed to a high-fat diet in utero influence the behaviour of their nursing dam

Proceedings of the Royal Society B: Biological Sciences, 285(1891), 20181237.

Population genetic diversity in zebrafish lines

MAMMALIAN GENOME, 29(1-2), 90–100.

ToxPi Graphical User Interface 2.0: Dynamic exploration, visualization, and sharing of integrated data models.

BMC Bioinformatics, 3(1).

Use of high-throughput in vitro toxicity screening data in cancer hazard evaluations by IARC Monograph Working Groups.

ALTEX, 35(1), 51–64.

A New Statistical Approach to Characterize Chemical-Elicited Behavioral Effects in High-Throughput Studies Using Zebrafish

PLOS ONE, 12(1).

A data-driven weighting scheme for multivariate phenotypic endpoints recapitulates zebrafish developmental cascades

TOXICOLOGY AND APPLIED PHARMACOLOGY, 314, 109–117.

An introduction to terminology and methodology of chemical synergy-perspectives from across disciplines

Frontiers in Pharmacology, 8(APR).

An introduction to terminology and methodology of chemical synergy-perspectives from across disciplines

[Review of ]. Frontiers in Pharmacology, 8.

Incorporating ToxCast and Tox21 datasets to rank biological activity of chemicals at Superfund sites in North Carolina

ENVIRONMENT INTERNATIONAL, 101, 19–26.

Integrating Morphological and Behavioral Phenotypes in Developing Zebrafish

The Rights and Wrongs of Zebrafish: Behavioral Phenotyping of Zebrafish, pp. 259–272.

Transgenerational inheritance of neurobehavioral and physiological deficits from developmental exposure to benzo[a]pyrene in zebrafish

TOXICOLOGY AND APPLIED PHARMACOLOGY, 329, 148–157.

A chemical-biological similarity-based grouping of complex substances as a prototype approach for evaluating chemical alternatives

GREEN CHEMISTRY, 18(16), 4407–4419.

Advancing Exposure Science through Chemical Data Curation and Integration in the Comparative Toxicogenomics Database

Environmental Health Perspectives, 124(10), 1592–1599.

Advancing Exposure Science through Chemical Data Curation and Integration in the Comparative Toxicogenomics Database.

Environmental Health Perspectives, 10. http://europepmc.org/abstract/med/27170236

Advancing toxicology research using in vivo high throughput toxicology with small fish models

ALTEX, 33(4), 435–452.

Aggregate entropy scoring for quantifying activity across endpoints with irregular correlation structure

REPRODUCTIVE TOXICOLOGY, 62, 92–99.

Analysis of the Effects of Cell Stress and Cytotoxicity on In Vitro Assay Activity Across a Diverse Chemical and Assay Space.

Toxicological Sciences : an Official Journal of the Society of Toxicology, 10(2), 409–409.

Decoupling of a neutron interferometer from temperature gradients

Review of Scientific Instruments, 87(12), 123507.

Editor's Highlight: Analysis of the Effects of Cell Stress and Cytotoxicity on In Vitro Assay Activity Across a Diverse Chemical and Assay Space.

Toxicological Sciences : an Official Journal of the Society of Toxicology, 8(2), 323–339.

Eigenvector metabolite analysis reveals dietary effects on the association among metabolite correlation patterns, gene expression, and phenotypes

METABOLOMICS, 12(11).

Evolutionary and Functional Diversification of the Vitamin D Receptor-Lithocholic Acid Partnership

PLOS ONE, 11(12).

From the Cover: Embryonic Exposure to TCDD Impacts Osteogenesis of the Axial Skeleton in Japanese medaka,Oryzias latipes

Toxicological Sciences, 155(2), 485–496.

High-throughput characterization of chemical-associated embryonic behavioral changes predicts teratogenic outcomes

ARCHIVES OF TOXICOLOGY, 90(6), 1459–1470.

Lifetime substance use as a predictor of postpartum mental health

Archives of Women's Mental Health, 20(1), 189–199.

Prioritizing Environmental Chemicals for Obesity and Diabetes Outcomes Research: A Screening Approach Using ToxCast (TM) High-Throughput Data

[Review of ]. ENVIRONMENTAL HEALTH PERSPECTIVES, 124(8), 1141–1154.

Using toxcast™ data to reconstruct dynamic cell state trajectories and estimate toxicological points of departure

Environmental Health Perspectives, 124(7), 910–919.

Carcinogenicity of lindane, DDT, and 2,4-dichlorophenoxyacetic acid.

The Lancet. Oncology, 8.

Comparison of toxicity values across zebrafish early life stages and mammalian studies: Implications for chemical testing

Reproductive Toxicology, 55, 3–10.

Computational Methods Used in Systems Biology

In Systems Biology in Toxicology and Environmental Health (pp. 85–115).

Data-driven asthma endotypes defined from blood biomarker and gene expression data

PLoS ONE, 10(2).

Embracing complexity: Searching for gene-gene and gene environment interactions in genetic epidemiology

In Genomics and Proteomics: Principles, Technologies, and Applications (pp. 19–58).

Food for Thought...: Toxicity testing in the 21st century beyond environmental chemicals

Altex, 32(3), 171–181.

Impact of Low-Dose Oral Exposure to Bisphenol A (BPA) on Juvenile and Adult Rat Exploratory and Anxiety Behavior: A CLARITY-BPA Consortium Study

TOXICOLOGICAL SCIENCES, 148(2), 341–354.

Molecular Cloning, Functional Characterization, and Evolutionary Analysis of Vitamin D Receptors Isolated from Basal Vertebrates

PLOS ONE, 10(4).

Comparing metabolomic and pathologic biomarkers alone and in combination for discriminating Alzheimer's disease from normal cognitive aging

Acta Neuropathologica Communications, 2(1), 28.

Erratum to Incorporating human dosimetry and exposure into High-throughput in Vitro Toxicity Screening [Toxicological sciences 137, 2, (2014), 499]

Toxicological Sciences, 137(2).

Hierarchical Dose-Response Modeling for High-Throughput Toxicity Screening of Environmental Chemicals

BIOMETRICS, 70(1), 237–246.

Multidimensional in vivo hazard assessment using zebrafish.

Toxicological Sciences, 137(1), 212–233.

Phenotypic screening of the ToxCast chemical library to classify toxic and therapeutic mechanisms

Nature Biotechnology, 32(6), 583–591.

Predictive endocrine testing in the 21st century using in vitro assays of estrogen receptor signaling responses

Environmental Science and Technology, 48(15), 8706–8716.

Profiling of the Tox21 10K compound library for agonists and antagonists of the estrogen receptor alpha signaling pathway

Scientific Reports, 4.

Test driving ToxCast: endocrine profiling for 1858 chemicals included in phase II

CURRENT OPINION IN PHARMACOLOGY, 19, 145–152.

ToxiFly: Can fruit flies be used to identify toxicity pathways for airborne chemicals?

Neurotoxicology and Teratology, 43, 89.

A Computational Model Predicting Disruption of Blood Vessel Development

PLoS Comput Biol, 9(4), e1002996.

Decision tree-based method for integrating gene expression, demographic, and clinical data to determine disease endotypes.

BMC Systems Biology, 7, 119.

Dosimetric anchoring of in vivo and in vitro studies for perfluorooctanoate and perfluorooctanesulfonate.

Toxicological Sciences, 136(2), 308–327.