Bioinformatics - 2023

Davis, A. P., Wiegers, T. C., Wiegers, J., Wyatt, B., Johnson, R. J., Sciaky, D., … Mattingly, C. J. (2023). 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. https://doi.org/10.1093/toxsci/kfad069

Rusyn, I., & Wright, F. A. (2023, December 23). Ten years of using key characteristics of human carcinogens to organize and evaluate mechanistic evidence in IARC Monographs on the identification of carcinogenic hazards to humans: Patterns and associations. TOXICOLOGICAL SCIENCES. https://doi.org/10.1093/toxsci/kfad134

Marinello, W. P., Gillera, S. E. A., Huang, L., Rollman, J., Reif, D. M., & Patisaul, H. B. (2023). Uncovering the common factors of chemical exposure and behavior: Evaluating behavioral effects across a testing battery using factor analysis. NEUROTOXICOLOGY, 99, 264–273. https://doi.org/10.1016/j.neuro.2023.10.012

Chappel, J. R., Kirkwood-Donelson, K. I., Reif, D. M., & Baker, E. S. (2023, October 25). From big data to big insights: statistical and bioinformatic approaches for exploring the lipidome. ANALYTICAL AND BIOANALYTICAL CHEMISTRY, Vol. 10. https://doi.org/10.1007/s00216-023-04991-2

Wallis, D. J., Kotlarz, N., Knappe, D. R. U., Collier, D. N., Lea, C. S., Reif, D., … Hoppin, J. A. (2023). Estimation of the Half-Lives of Recently Detected Per- and Polyfluorinated Alkyl Ethers in an Exposed Community. ENVIRONMENTAL SCIENCE & TECHNOLOGY, 57(41), 15348–15355. https://doi.org/10.1021/acs.est.2c08241

Green, A. J., Truong, L., Thunga, P., Leong, C., Hancock, M., Tanguay, R. L., & Reif, D. M. (2023, September 17). Deep autoencoder-based behavioral pattern recognition outperforms standard statistical methods in high-dimensional zebrafish studies. https://doi.org/10.1101/2023.09.13.557544

Cordova, A. C., Dodds, J. N., Tsai, H.-H. D., Lloyd, D. T., Roman-Hubers, A. T., Wright, F. A., … Rusyn, I. (2023, August 22). Application of Ion Mobility Spectrometry-Mass Spectrometry for Compositional Characterization and Fingerprinting of a Library of Diverse Crude Oil Samples. ENVIRONMENTAL TOXICOLOGY AND CHEMISTRY. https://doi.org/10.1002/etc.5727

Sakolish, C., Moyer, H. L., Tsai, H.-H. D., Ford, L. C., Dickey, A. N., Wright, F. A., … Rusyn, I. (2023). Analysis of reproducibility and robustness of a renal proximal tubule microphysiological system OrganoPlate 3-lane 40 for in vitro studies of drug transport and toxicity. TOXICOLOGICAL SCIENCES. https://doi.org/10.1093/toxsci/kfad080

Chappel, J. R., King, M. E., Fleming, J., Eberlin, L. S., Reif, D. M., & Baker, E. S. (2023, August 14). Aggregated Molecular Phenotype Scores: Enhancing Assessment and Visualization of Mass Spectrometry Imaging Data for Tissue-Based Diagnostics. ANALYTICAL CHEMISTRY, Vol. 8. https://doi.org/10.1021/acs.analchem.3c02389

Cordova, A. C., Klaren, W. D., Ford, L. C., Grimm, F. A., Baker, E. S., Zhou, Y.-H., … Rusyn, I. (2023). Integrative Chemical-Biological Grouping of Complex High Production Volume Substances from Lower Olefin Manufacturing Streams. TOXICS, 11(7). https://doi.org/10.3390/toxics11070586

Ting, B. W. W., Wright, F. A., & Zhou, Y.-H. (2023, May 22). Simultaneous modeling of multivariate heterogeneous responses and heteroskedasticity via a two-stage composite likelihood. BIOMETRICAL JOURNAL. https://doi.org/10.1002/bimj.202200029

Zhou, Y.-H., Gallins, P. J., Pace, R. G., Dang, H., Aksit, M. A., Blue, E. E., … Knowles, M. R. (2023). Genetic Modifiers of Cystic Fibrosis Lung Disease Severity. AMERICAN JOURNAL OF RESPIRATORY AND CRITICAL CARE MEDICINE, 207(10), 1324–1333. https://doi.org/10.1164/rccm.202209-1653OC

Small, G. W., Akhtari, F. S., Green, A. J., Havener, T. M., Sikes, M., Quintanhila, J., … Wiltshire, T. (2023). Pharmacogenomic Analyses Implicate B Cell Developmental Status and MKL1 as Determinants of Sensitivity toward Anti-CD20 Monoclonal Antibody Therapy. CELLS, 12(12). https://doi.org/10.3390/cells12121574

Chappel, J. R., King, M. E., Fleming, J., Eberlin, L. S., Reif, D. M., & Baker, E. S. (2023, June 5). Utilizing Aggregated Molecular Phenotype (AMP) Scores to Visualize Simultaneous Molecular Changes in Mass Spectrometry Imaging Data. https://doi.org/10.1101/2023.06.01.543306

Tsai, H.-H. D., House, J. S., Wright, F. A., Chiu, W. A., & Rusyn, I. (2023, April 20). A tiered testing strategy based on in vitro phenotypic and transcriptomic data for selecting representative petroleum UVCBs for toxicity evaluation in vivo. TOXICOLOGICAL SCIENCES. https://doi.org/10.1093/toxsci/kfad041

Gonzalez, R. D., Small, G. W., Green, A. J., Akhtari, F. S., Motsinger-Reif, A. A., Quintanilha, J. C. F., … Wiltshire, T. (2023). MKX-AS1 Gene Expression Associated with Variation in Drug Response to Oxaliplatin and Clinical Outcomes in Colorectal Cancer Patients. PHARMACEUTICALS, 16(5). https://doi.org/10.3390/ph16050757

Gonzalez, R. D., Small, G. W., Green, A. J., Akhtari, F. S., Havener, T. M., Quintanilha, J. C. F., … Wiltshire, T. (2023). RYK Gene Expression Associated with Drug Response Variation of Temozolomide and Clinical Outcomes in Glioma Patients. PHARMACEUTICALS, 16(5). https://doi.org/10.3390/ph16050726

Phelps, D. W., Palekar, A. I., Conley, H. E., Ferrero, G., Driggers, J. H., Linder, K. E., … Yoder, J. A. (2023). Legacy and emerging per- and polyfluoroalkyl substances suppress the neutrophil respiratory burst. JOURNAL OF IMMUNOTOXICOLOGY, 20(1). https://doi.org/10.1080/1547691X.2023.2176953

Jin, B., Dunson, D. B., Rager, J. E., Reif, D. M., Engel, S. M., & Herring, A. H. (2023, March 15). Bayesian matrix completion for hypothesis testing. JOURNAL OF THE ROYAL STATISTICAL SOCIETY SERIES C-APPLIED STATISTICS, Vol. 3. https://doi.org/10.1093/jrsssc/qlac005

Watson, A. L. T. D., Baez, A. C., Jima, D., Reif, D., Ding, J., Roberts, R., & Kullman, S. W. (2023). TCDD alters essential transcriptional regulators of osteogenic differentiation in multipotent mesenchymal stem cells. Toxicological Sciences. https://doi.org/10.1093/toxsci/kfac120