Bioinformatics - 2021

Chen, Z., Jang, S., Kaihatu, J. M., Zhou, Y.-H., Wright, F. A., Chiu, W. A., & Rusyn, I. (2021). Potential Human Health Hazard of Post-Hurricane Harvey Sediments in Galveston Bay and Houston Ship Channel: A Case Study of Using In Vitro Bioactivity Data to Inform Risk Management Decisions. INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH, 18(24). https://doi.org/10.3390/ijerph182413378

Pinkhasova, D. V., Jameson, L. E., Conrow, K. D., Simeone, M. P., Davis, A. P., Wiegers, T. C., … Leung, M. C. K. (2021). Regulatory status of pesticide residues in cannabis: Implications to medical use in neurological diseases. CURRENT RESEARCH IN TOXICOLOGY, 2, 140–148. https://doi.org/10.1016/j.crtox.2021.02.007

Grondin, C. J., Davis, A. P., Wiegers, J. A., Wiegers, T. C., Sciaky, D., Johnson, R. J., & Mattingly, C. J. (2021). 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. https://doi.org/10.1016/j.crtox.2021.08.001

Davis, A. P., Wiegers, T. C., Wiegers, J., Grondin, C. J., Johnson, R. J., Sciaky, D., & Mattingly, C. J. (2021). 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. https://doi.org/10.1016/j.crtox.2021.03.001

Erber, L., Goodman, S., Wright, F. A., Chiu, W. A., Tretyakova, N. Y., & Rusyn, I. (2021). Intra- and Inter-Species Variability in Urinary N7-(1-Hydroxy-3-buten-2-yl)guanine Adducts Following Inhalation Exposure to 1,3-Butadiene. CHEMICAL RESEARCH IN TOXICOLOGY, 34(11), 2375–2383. https://doi.org/10.1021/acs.chemrestox.1c00291

Ma, J., & Motsinger-Reif, A. (2021). Prediction of synergistic drug combinations using PCA-initialized deep learning. BIODATA MINING, 14(1). https://doi.org/10.1186/s13040-021-00278-3

Fleming, J., Marvel, S. W., Motsinger-Reif, A. A., & Reif, D. M. (2021, October 11). ToxPi*GIS Toolkit: Creating, viewing, and sharing integrative visualizations for geospatial data using ArcGIS (Vol. 10). Vol. 10. https://doi.org/10.1101/2021.10.08.21264756

Wang, M., Rivenbark, K., Gong, J., Wright, F. A., & Phillips, T. D. (2021). Application of Edible Montmorillonite Clays for the Adsorption and Detoxification of Microcystin. ACS APPLIED BIO MATERIALS, 4(9), 7254–7265. https://doi.org/10.1021/acsabm.1c00779

Lee, H. K., Wetzel-Strong, S. E., Aylor, D. L., & Marchuk, D. A. (2021). A Neuroprotective Locus Modulates Ischemic Stroke Infarction Independent of Collateral Vessel Anatomy. FRONTIERS IN NEUROSCIENCE, 15. https://doi.org/10.3389/fnins.2021.705160

Kirkwood, K. I., Fleming, J., Nguyen, H., Reif, D. M., Baker, E. S., & Belcher, S. M. (2021, August 26). Utilizing Pine Needles to Temporally and Spatially Profile Per- and Polyfluoroalkyl Substances (Vol. 8). Vol. 8. https://doi.org/10.1101/2021.08.24.457570

Akhtari, F. S., Green, A. J., Small, G. W., Havener, T. M., House, J. S., Roell, K. R., … Motsinger-Reif, A. A. (2021). 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). https://doi.org/10.1371/journal.pgen.1009732

McDonough, C. W., Warren, H. R., Jack, J. R., Motsinger-Reif, A. A., Armstrong, N. D., Bis, J. C., … Cooper-DeHoff, R. M. (2021, August 15). Adverse Cardiovascular Outcomes and Antihypertensive Treatment: A Genome-Wide Interaction Meta-Analysis in the International Consortium for Antihypertensive Pharmacogenomics Studies. CLINICAL PHARMACOLOGY & THERAPEUTICS. https://doi.org/10.1002/cpt.2355

Muratov, E. N., Amaro, R., Andrade, C. H., Brown, N., Ekins, S., Fourches, D., … Tropsha, A. (2021, July 2). A critical overview of computational approaches employed for COVID-19 drug discovery. CHEMICAL SOCIETY REVIEWS. https://doi.org/10.1039/d0cs01065k

Roman-Hubers, A. T., Cordova, A. C., Aly, N. A., McDonald, T. J., Lloyd, D. T., Wright, F. A., … Rusyn, I. (2021). Data Processing Workflow to Identify Structurally Related Compounds in Petroleum Substances Using Ion Mobility Spectrometry-Mass Spectrometry. ENERGY & FUELS, 35(13), 10529–10539. https://doi.org/10.1021/acs.energyfuels.1c00892

Odenkirk, M. T., Reif, D. M., & Baker, E. S. (2021). Multiomic Big Data Analysis Challenges: Increasing Confidence in the Interpretation of Artificial Intelligence Assessments. ANALYTICAL CHEMISTRY, 93(22), 7763–7773. https://doi.org/10.1021/acs.analchem.0c04850

Green, A. J., Mohlenkamp, M. J., Das, J., Chaudhari, M., Truong, L., Tanguay, R. L., & Reif, D. M. (2021). Leveraging high-throughput screening data, deep neural networks, and conditional generative adversarial networks to advance predictive toxicology. PLOS COMPUTATIONAL BIOLOGY, 17(7). https://doi.org/10.1371/journal.pcbi.1009135

Mansouri, K., Karmaus, A. L., Fitzpatrick, J., Patlewicz, G., Pradeep, P., Alberga, D., … Kleinstreuer, N. C. (2021). CATMoS: Collaborative Acute Toxicity Modeling Suite. ENVIRONMENTAL HEALTH PERSPECTIVES, 129(4). https://doi.org/10.1289/EHP8495

Thunga, P., Truong, L., Tanguay, R. L., & Reif, D. M. (2021). Concurrent Evaluation of Mortality and Behavioral Responses: A Fast and Efficient Testing Approach for High-Throughput Chemical Hazard Identification. Frontiers in Toxicology, 3. https://doi.org/10.3389/ftox.2021.670496

Jiang, T., Li, Y., & Motsinger-Reif, A. A. (2021). Knockoff boosted tree for model-free variable selection. BIOINFORMATICS, 37(7), 976–983. https://doi.org/10.1093/bioinformatics/btaa770

Kranse, O., Beasley, H., Adams, S., Pires-daSilva, A., Bell, C., Lilley, C. J., … Akker, S. (2021). Toward genetic modification of plant-parasitic nematodes: delivery of macromolecules to adults and expression of exogenous mRNA in second stage juveniles. G3-GENES GENOMES GENETICS, 11(2). https://doi.org/10.1093/g3journal/jkaa058

Green, A. J., Anchang, B., Akhtari, F. S., Reif, D. M., & Motsinger-Reif, A. (2021, May 28). Extending the lymphoblastoid cell line model for drug combination pharmacogenomics. PHARMACOGENOMICS, Vol. 22. https://doi.org/10.2217/pgs-2020-0160

Aly, N. A., Casillas, G., Luo, Y.-S., McDonald, T. J., Wade, T. L., Zhu, R., … Rusyn, I. (2021). Environmental impacts of Hurricane Florence flooding in eastern North Carolina: temporal analysis of contaminant distribution and potential human health risks. JOURNAL OF EXPOSURE SCIENCE AND ENVIRONMENTAL EPIDEMIOLOGY, 31(5), 810–822. https://doi.org/10.1038/s41370-021-00325-5

Li, X., & Fourches, D. (2021). SMILES Pair Encoding: A Data-Driven Substructure Tokenization Algorithm for Deep Learning. JOURNAL OF CHEMICAL INFORMATION AND MODELING, 61(4), 1560–1569. https://doi.org/10.1021/acs.jcim.0c01127

Akhtari, F. S., Havener, T. M., Hertz, D. L., Ash, J., Larson, A., Carey, L. A., … Motsinger-Reif, A. A. (2021). Race and smoking status associated with paclitaxel drug response in patient-derived lymphoblastoid cell lines. PHARMACOGENETICS AND GENOMICS, 31(2), 48–52. https://doi.org/10.1097/FPC.0000000000000419

Takeda, K., Ikenaka, Y., Fourches, D., Tanaka, K. D., Nakayama, S. M. M., Triki, D., … Ishizuka, M. (2021). The VKORC1 ER-luminal loop mutation (Leu76Pro) leads to a significant resistance to warfarin in black rats (Rattus rattus). PESTICIDE BIOCHEMISTRY AND PHYSIOLOGY, 173. https://doi.org/10.1016/j.pestbp.2021.104774

Wallis, D. J., Truong, L., La Du, J., Tanguay, R. L., & Reif, D. M. (2021). [Review of Uncovering Evidence for Endocrine-Disrupting Chemicals That Elicit Differential Susceptibility through Gene-Environment Interactions]. TOXICS, 9(4). https://doi.org/10.3390/toxics9040077

Luo, Y.-S., Chen, Z., Blanchette, A. D., Zhou, Y.-H., Wright, F. A., Baker, E. S., … Rusyn, I. (2021). Relationships between constituents of energy drinks and beating parameters in human induced pluripotent stem cell (iPSC)-Derived cardiomyocytes. FOOD AND CHEMICAL TOXICOLOGY, 149. https://doi.org/10.1016/j.fct.2021.111979

Marvel, S. W., House, J. S., Wheeler, M., Song, K., Zhou, Y.-H., Wright, F. A., … Reif, D. M. (2021, January). The COVID-19 Pandemic Vulnerability Index (PVI) Dashboard: Monitoring County-Level Vulnerability Using Visualization, Statistical Modeling, and Machine Learning. https://doi.org/10.1289/EHP8690

House, J. S., Grimm, F. A., Klaren, W. D., Dalzell, A., Kuchi, S., Zhang, S.-D., … Rusyn, I. (2021). Grouping of UVCB Substances with New Approach Methodologies (NAMs) Data. ALTEX-ALTERNATIVES TO ANIMAL EXPERIMENTATION, 38(1), 123–137. https://doi.org/10.14573/altex.2006262

Chen, Z., Lloyd, D., Zhou, Y.-H., Chiu, W. A., Wright, F. A., & Rusyn, I. (2021). Risk Characterization of Environmental Samples Using In Vitro Bioactivity and Polycyclic Aromatic Hydrocarbon Concentrations Data. TOXICOLOGICAL SCIENCES, 179(1), 108–120. https://doi.org/10.1093/toxsci/kfaa166

Gilchrist, P. O., Alexander, A. B., Green, A. J., Sanders, F. E., Hooker, A. Q., & Reif, D. M. (2021). Development of a Pandemic Awareness STEM Outreach Curriculum: Utilizing a Computational Thinking Taxonomy Framework. EDUCATION SCIENCES, 11(3). https://doi.org/10.3390/educsci11030109

Davis, A. P., Grondin, C. J., Johnson, R. J., Sciaky, D., Wiegers, J., Wiegers, T. C., & Mattingly, C. J. (2021). Comparative Toxicogenomics Database (CTD): update 2021. NUCLEIC ACIDS RESEARCH, 49(D1), D1138–D1143. https://doi.org/10.1093/nar/gkaa891

Borrel, A., Melander, C., & Fourches, D. (2021). Cheminformatics Analysis of Fluoroquinolones and Their Inhibition Potency Against Four Pathogens. MOLECULAR INFORMATICS, 40(5). https://doi.org/10.1002/minf.202000215

Weeks, J. M., Motsinger-Reif, A. A., & Reems, M. M. (2021). In vitro iatrogenic hemolysis of canine packed red blood cells during various rapid transfusion techniques. JOURNAL OF VETERINARY EMERGENCY AND CRITICAL CARE, 31(1), 25–31. https://doi.org/10.1111/vec.13020