Bioinformatics - 2020

Reich, B. J., Guan, Y., Fourches, D., Warren, J. L., Sarnat, S. E., & Chang, H. H. (2020). INTEGRATIVE STATISTICAL METHODS FOR EXPOSURE MIXTURES AND HEALTH. ANNALS OF APPLIED STATISTICS, 14(4), 1945–1963. https://doi.org/10.1214/20-AOAS1364

Chen, Z., Liu, Y., Wright, F. A., Chiu, W. A., & Rusyn, I. (2020). Rapid Hazard Characterization of Environmental Chemicals Using a Compendium of Human Cell Lines from Different Organs. ALTEX-ALTERNATIVES TO ANIMAL EXPERIMENTATION, 37(4), 623–638. https://doi.org/10.14573/altex.2002291

Song, K., Wright, F. A., & Zhou, Y.-H. (2020). Systematic Comparisons for Composition Profiles, Taxonomic Levels, and Machine Learning Methods for Microbiome-Based Disease Prediction. FRONTIERS IN MOLECULAR BIOSCIENCES, 7. https://doi.org/10.3389/fmolb.2020.610845

Odenkirk, M. T., Stratton, K. G., Gritsenko, M. A., Bramer, L. M., Webb-Robertson, B.-J. M., Bloodsworth, K. J., … Baker, E. S. (2020). Unveiling molecular signatures of preeclampsia and gestational diabetes mellitus with multi-omics and innovative cheminformatics visualization tools. MOLECULAR OMICS, 16(6). https://doi.org/10.1039/d0mo00074d

Rusyn, I., Chiu, W. A., & Wright, F. A. (2020, October). Questioning Existing Cancer Hazard Evaluation Standards in the Name of Statistics. https://doi.org/10.1093/toxsci/kfaa077

Davis, A. P., Wiegers, T. C., Grondin, C. J., Johnson, R. J., Sciaky, D., Wiegers, J., & Mattingly, C. J. (2020). 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. https://doi.org/10.1093/toxsci/kfaa113

Truong, L., Marvel, S., Reif, D. M., Thomas, D. G., Pande, P., Dasgupta, S., … Tanguay, R. L. (2020). The multi-dimensional embryonic zebrafish platform predicts flame retardant bioactivity. REPRODUCTIVE TOXICOLOGY, 96, 359–369. https://doi.org/10.1016/j.reprotox.2020.08.007

Gallins, P., Saghapour, E., & Zhou, Y.-H. (2020). Exploring the Limits of Combined Image/'omics Analysis for Non-cancer Histological Phenotypes. FRONTIERS IN GENETICS, 11. https://doi.org/10.3389/fgene.2020.555886

Odenkirk, M. T., Zin, P. P. K., Ash, J. R., Reif, D. M., Fourches, D., & Baker, E. S. (2020). Structural-based connectivity and omic phenotype evaluations (SCOPE): a cheminformatics toolbox for investigating lipidomic changes in complex systems. ANALYST, 145(22), 7197–7209. https://doi.org/10.1039/d0an01638a

Aguet, F., Barbeira, A. N., Bonazzola, R., Brown, A., Castel, S. E., Jo, B., … Volpi, S. (2020). The GTEx Consortium atlas of genetic regulatory effects across human tissues. SCIENCE, 369(6509), 1318–1330. https://doi.org/10.1126/science.aaz1776

Hubal, E. A. C., Reif, D. M., Slover, R., Mullikin, A., & Little, J. C. (2020). Children’s Environmental Health: A Systems Approach for Anticipating Impacts from Chemicals. International Journal of Environmental Research and Public Health, 17(22), 8337. https://doi.org/10.3390/ijerph17228337

Singam, E. R. A., Tachachartvanich, P., Fourches, D., Soshilov, A., Hsieh, J. C. Y., La Merrill, M. A., … Durkin, K. A. (2020). Structure-based virtual screening of perfluoroalkyl and polyfluoroalkyl substances (PFASs) as endocrine disruptors of androgen receptor activity using molecular docking and machine learning. ENVIRONMENTAL RESEARCH, 190. https://doi.org/10.1016/j.envres.2020.109920

Widmayer, S. J., Handel, M. A., & Aylor, D. L. (2020). Age and Genetic Background Modify Hybrid Male Sterility in House Mice. GENETICS, 216(2), 585–597. https://doi.org/10.1534/genetics.120.303474

Mukherjee, R., Beykal, B., Szafran, A. T., Onel, M., Stossi, F., Mancini, M. G., … Pistikopoulos, E. N. (2020). Classification of estrogenic compounds by coupling high content analysis and machine learning algorithms. PLOS COMPUTATIONAL BIOLOGY, 16(9). https://doi.org/10.1371/journal.pcbi.1008191

Garbutt, T. A., Konganti, K., Konneker, T., Hillhouse, A., Phelps, D., Jones, A., … Threadgill, D. W. (2020). Derivation of stable embryonic stem cell-like, but transcriptionally heterogenous, induced pluripotent stem cells from non-permissive mouse strains. MAMMALIAN GENOME, 31(9-12), 263–286. https://doi.org/10.1007/s00335-020-09849-x

Yergaliyev, T. M., Alexander-Shani, R., Dimerets, H., Pivonia, S., Bird, D. M. K., Rachmilevitch, S., & Szitenberg, A. (2020). Bacterial Community Structure Dynamics in Meloidogyne incognita-Infected Roots and Its Role in Worm-Microbiome Interactions. MSPHERE, 5(4). https://doi.org/10.1128/mSphere.00306-20

Bayesian Matrix Completion for Hypothesis Testing. (2020, September 17).

Day, K., Schneible, J. D., Young, A. T., Pozdin, V. A., Driessche, G., Gaffney, L. A., … Menegatti, S. (2020). Photoinduced reconfiguration to control the protein-binding affinity of azobenzene-cyclized peptides. JOURNAL OF MATERIALS CHEMISTRY B, 8(33), 7413–7427. https://doi.org/10.1039/d0tb01189d

Cools, F., Triki, D., Geerts, N., Delputte, P., Fourches, D., & Cos, P. (2020). In vitroandin vivoEvaluation ofin silicoPredicted Pneumococcal UDPG:PP Inhibitors. FRONTIERS IN MICROBIOLOGY, 11. https://doi.org/10.3389/fmicb.2020.01596

Zin, P. P. K., Borrel, A., & Fourches, D. (2020). Benchmarking 2D/3D/MD-QSAR Models for Imatinib Derivatives: How Far Can We Predict? JOURNAL OF CHEMICAL INFORMATION AND MODELING, 60(7), 3342–3360. https://doi.org/10.1021/acs.jcim.0c00200

Marvel, S. W., House, J. S., Wheeler, M., Song, K., Zhou, Y., Wright, F. A., … Reif, D. M. (2020, August 13). The COVID-19 Pandemic Vulnerability Index (PVI) Dashboard: monitoring county level vulnerability (Vol. 8). Vol. 8. https://doi.org/10.1101/2020.08.10.20169649

Reese, H. R., Xiao, X., Shanahan, C. C., Driessche, G. A., Fourches, D., Carbonell, R. G., … Menegatti, S. (2020). Novel peptide ligands for antibody purification provide superior clearance of host cell protein impurities. JOURNAL OF CHROMATOGRAPHY A, 1625. https://doi.org/10.1016/j.chroma.2020.461237

Craun, K., Ekena, J., Sacco, J., Jiang, T., Motsinger-Reif, A., & Trepanier, L. A. (2020). Genetic and environmental risk for lymphoma in boxer dogs. JOURNAL OF VETERINARY INTERNAL MEDICINE, 34(5), 2068–2077. https://doi.org/10.1111/jvim.15849

Levin, K. A., Tucker, M. R., Bird, D. M., & Mather, D. E. (2020). Infection by cyst nematodes induces rapid remodelling of developing xylem vessels in wheat roots. SCIENTIFIC REPORTS, 10(1). https://doi.org/10.1038/s41598-020-66080-z

Wise, C. F., Hammel, S. C., Herkert, N., Ma, J., Motsinger-Reif, A., Stapleton, H. M., & Breen, M. (2020). Comparative Exposure Assessment Using Silicone Passive Samplers Indicates That Domestic Dogs Are Sentinels To Support Human Health Research. ENVIRONMENTAL SCIENCE & TECHNOLOGY, 54(12), 7409–7419. https://doi.org/10.1021/acs.est.9b06605

Lynch, A. M., Ruterbories, L., Jack, J., Motsinger-Reif, A. A., & Hanel, R. (2020). The influence of packed cell volume versus plasma proteins on thromboelastographic variables in canine blood. JOURNAL OF VETERINARY EMERGENCY AND CRITICAL CARE, 30(4), 418–425. https://doi.org/10.1111/vec.12979

Muratov, E. N., Bajorath, J., Sheridan, R. P., Tetko, I. V., Filimonov, D., Poroikov, V., … Tropsha, A. (2020, June 7). QSAR without borders (vol 10, pg 531, 2020). CHEMICAL SOCIETY REVIEWS, Vol. 49, pp. 3716–3716. https://doi.org/10.1039/d0cs90041a

Muratov, E. N., Bajorath, J., Sheridan, R. P., Tetko, I. V., Filimonov, D., Poroikov, V., … Tropsha, A. (2020). [Review of QSAR without borders]. CHEMICAL SOCIETY REVIEWS, 49(11), 3525–3564. https://doi.org/10.1039/d0cs00098a

Ma, J., Bair, E., & Motsinger-Reif, A. (2020). Nonlinear Dose-Response Modeling of High-Throughput Screening Data Using an Evolutionary Algorithm. DOSE-RESPONSE, 18(2). https://doi.org/10.1177/1559325820926734

Li, X., & Fourches, D. (2020). Inductive transfer learning for molecular activity prediction: Next-Gen QSAR Models with MolPMoFiT. JOURNAL OF CHEMINFORMATICS, 12(1). https://doi.org/10.1186/s13321-020-00430-x

Phelps, D. W., Fletcher, A. A., Rodriguez-Nunez, I., Balik-Meisner, M. R., Tokarz, D. A., Reif, D. M., … Yoder, J. A. (2020). In vivo assessment of respiratory burst inhibition by xenobiotic exposure using larval zebrafish. Journal of Immunotoxicology, 17(1), 94–104. https://doi.org/10.1080/1547691X.2020.1748772

Crestani, E., Harb, H., Charbonnier, L.-M., Leirer, J., Motsinger-Reif, A., Rachid, R., … Chatila, T. A. (2020). Untargeted metabolomic profiling identifies disease-specific signatures in food allergy and asthma. JOURNAL OF ALLERGY AND CLINICAL IMMUNOLOGY, 145(3), 897–906. https://doi.org/10.1016/j.jaci.2019.10.014

Zin, P. P. K., Williams, G., & Fourches, D. (2020). SIME: synthetic insight-based macrolide enumerator to generate the V1B library of 1 billion macrolides. JOURNAL OF CHEMINFORMATICS, 12(1). https://doi.org/10.1186/s13321-020-00427-6

House, J. S., Bouzos, E., Fahy, K. M., Francisco, V. M., Lloyd, D. T., Wright, F. A., … Wheeler, K. E. (2020). Low-Dose Silver Nanoparticle Surface Chemistry and Temporal Effects on Gene Expression in Human Liver Cells. SMALL, 16(21). https://doi.org/10.1002/smll.202000299

Mansouri, K., Kleinstreuer, N., Abdelaziz, A. M., Alberga, D., Alves, V. M., Andersson, P. L., … Judson, R. S. (2020). CoMPARA: Collaborative Modeling Project for Androgen Receptor Activity. ENVIRONMENTAL HEALTH PERSPECTIVES, 128(2). https://doi.org/10.1289/EHP5580

Kosnik, M. B., Strickland, J. D., Marvel, S. W., Wallis, D. J., Wallace, K., Richard, A. M., … Shafer, T. J. (2020). Concentration-response evaluation of ToxCast compounds for multivariate activity patterns of neural network function. ARCHIVES OF TOXICOLOGY, 94(2), 469–484. https://doi.org/10.1007/s00204-019-02636-x

Li, X., Kleinstreuer, N. C., & Fourches, D. (2020). Hierarchical Quantitative Structure-Activity Relationship Modeling Approach for Integrating Binary, Multiclass, and Regression Models of Acute Oral Systemic Toxicity. CHEMICAL RESEARCH IN TOXICOLOGY, 33(2), 353–366. https://doi.org/10.1021/acs.chemrestox.9b00259

Bhandari, S., Lewis, P. G. T., Craft, E., Marvel, S. W., Reif, D. M., & Chiu, W. A. (2020). HGBEnviroScreen: Enabling Community Action through Data Integration in the Houston–Galveston–Brazoria Region. International Journal of Environmental Research and Public Health, 17(4), 1130. https://doi.org/10.3390/ijerph17041130

Etheridge, A. S., Gallins, P. J., Jima, D., Broadaway, K. A., Ratain, M. J., Schuetz, E., … Innocenti, F. (2020). A New Liver Expression Quantitative Trait Locus Map From 1,183 Individuals Provides Evidence for Novel Expression Quantitative Trait Loci of Drug Response, Metabolic, and Sex-Biased Phenotypes. CLINICAL PHARMACOLOGY & THERAPEUTICS, 107(6), 1383–1393. https://doi.org/10.1002/cpt.1751

Schoonmaker, A., Hao, Y., Bird, D. M. K., & Conant, G. C. (2020). A Single, Shared Triploidy in Three Species of Parasitic Nematodes. G3-GENES GENOMES GENETICS, 10(1), 225–233. https://doi.org/10.1534/g3.119.400650

Reif, D. M., Chanock, S. J., Edwards, K. M., & Crowe, J. E. (2020). Inappropriate Citation of Vaccine Article. The Journal of Infectious Diseases, 222(8), 1413–1414. https://doi.org/10.1093/infdis/jiz287