Superfund Research Program
This page provides a bibliography of data science and data sharing publications from SRP grant recipients.
2024
- Bramer L, Dixon HM, Degnan D, Rohlman D, Herbstman JB, Anderson KA, Waters KM. 2024. Expanding the access of wearable silicone wristbands in community-engaged research through best practices in data analysis and integration. Pac Symp Biocomput 29:170-186. PMID:38160278 PMCID:PMC10766083
- Gentry E, Collins S, Panitchpakdi M, Belda-Ferre P, Stewart AK, Carrillo Terrazas M, Lu H, Zuffa S, Yan T, Avila-Pacheco J, Plichta D, Aron A, Wang M, Jarmusch A, Hao F, Syrkin-Nikolau M, Vlamakis H, Ananthakrishnan AN, Boland BS, Hemperly A, Vande Casteele N, Gonzalez FJ, Clish C, Xavier R, Chu H, Baker ES, Patterson A, Knight R, Siegel D, Dorrestein PC. 2024. Reverse metabolomics for the discovery of chemical structures from humans. Nature 626(7998):419-426. doi:10.1038/s41586-023-06906-8 PMID:38052229
- Koh J, Ng CH, Nah B, Tan D, Loomba R, Huang DQ. 2024. NASH is the leading cause of hepatocellular carcinoma in liver transplant candidates. Clin Gastroenterol Hepatol 22(1):197-199. doi:10.1016/j.cgh.2023.05.019 PMID:37245718
- Reder G, Bjurstrom E, Brunnsaker D, Kronstrom F, Lasin P, Tiukova I, Savolainen O, Dodds J, May J, Wikswo J, McLean J, King R. 2024. AutonoMS: Automated ion mobility metabolomic fingerprinting. J Am Soc Mass Spectrom doi:10.1021/jasms.3c00396 PMID:38310603
2023
- Aghayev Z, Szafran AT, Tran A, Ganesh HS, Stossi F, Zhou L, Mancini MA, Pistikopoulos EN, Beykal B. 2023. Machine learning methods for endocrine disrupting potential identification based on single-cell data. Chem Eng Sci 281:119086. doi:10.1016/j.ces.2023.119086 PMID:37637227 PMCID:PMC10448728
- Aghayev Z, Walker GF, Iseri F, Ali M, Szafran AT, Stossi F, Mancini MA, Pistikopoulos EN, Beykal B. 2023. Binary classification of the endocrine disrupting chemicals by artificial neural networks. ESCAPE 52:2631-2636. doi:10.1016/b978-0-443-15274-0.50418-2 PMID:37575176 PMCID:PMC1041341
- Anderson L, Kanneganti D, Houk MB, Holm RH, Smith T. 2023. Generative AI as a tool for environmental health research translation. Geohealth 7. doi:10.1029/2023GH000875 PMID:37502196 PMCID:PMC10369501
- Baker ES, Hoang C, Uritboonthai W, Heyman HM, Pratt BS, MacCoss MJ, MacLean BX, Plumb R, Aisporna A, Siuzdak G. 2023. METLIN-CCS: an ion mobility spectrometry collision cross section database. Nat Methods doi:10.1038/s41592-023-02078-5 PMID:37932399
- Chappel JR, Kirkwood-Donelson KI, Reif DM, Baker ES. 2023. From big data to big insights: statistical and bioinformatic approaches for exploring the lipidome. Anal Bioanal Chem doi:10.1007/s00216-023-04991-2 PMID:37875675
- Eaves LA, Lanier P, Enggasser AE, Chung G, Turla T, Rager JE, Fry RC. 2023. Generation of the Chemical and Social Stressors Integration Technique (CASS-IT) to identify areas of holistic public health concern: an application to North Carolina. Sci Total Environ 862:160409. doi:10.1016/j.scitotenv.2022.160409 PMID:36436630
- Efromson J, Ferrero G, Begue A, Doman TJ, Dugo C, Barker A, Saliu V, Reamey P, Kim K, Harfouche M, Yoder J. 2023. Automated, high-throughput quantification of EGFP-expressing neutrophils in zebrafish by machine learning and a highly-parallelized microscope. PLoS One 18(12):e0295711. doi:10.1371/journal.pone.0295711 PMID:38060605 PMCID:PMC10703246
- Gosline S, Kim DN, Pande P, Thomas DG, Truong L, Hoffman PD, Barton ML, Loftus J, Moran A, Hampton S, Dowson S, Franklin L, Degnan D, Anderson LN, Thessen AE, Tanguay RL, Anderson KA, Waters KM. 2023. The Superfund Research Program Analytics Portal: linking environmental chemical exposure to biological phenotypes. Sci Data 10(1):151. doi:10.1038/s41597-023-02021-5 PMID:36944655 PMCID:PMC1003089
- Gourronc FA, Chimenti MS, Lehmler H, Ankrum J, Klingelhutz AJ. 2023. Updating Dataset of transcriptomic changes that occur in human preadipocytes over a 3-day course of exposure to 3,3',4,4',5-pentachlorobiphenyl (PCB126) with additional data on exposure to 2,2',5,5'-tetrachlorobiphenyl (PCB52) or its 4-hydroxy metabolite (4-OH-PCB52). Data Brief 49:109415. doi:10.1016/j.dib.2023.109415 PMID:37520642 PMCID:PMC10375549
- Hejazi NS, Boileau P, van der Laan MJ, Hubbard AE. 2023. A generalization of moderated statistics to data adaptive semiparametric estimation in high-dimensional biology. Stat Methods Med Res 32(3):539-554. doi:10.1177/09622802221146313 PMID:36573044
- Huang DQ, Tan DJ, Ng CH, Amangurbanova M, Sutter N, Tay PW, Lim WH, Yong JN, Tang A, Syn N, Muthiah M, Tan EX, Dave S, Tay B, Majzoub AM, Gerberi D, Kim BK, Loomba R. 2023. Hepatocellular carcinoma incidence in alcohol-associated cirrhosis: systematic review and meta-analysis. Clin Gastroenterol Hepatol 21(5):1169-1177. doi:10.1016/j.cgh.2022.06.032 PMID:35940513
- Huckvale ED, Powell CD, Jin H, Moseley HN. 2023. Benchmark dataset for training machine learning models to predict the pathway involvement of metabolites. Metabolites 13(11):1120. doi:10.3390/metabo13111120 PMID:37999216 PMCID:PMC10673125
- Jiang M, Hu CJ, Rowe CL, Kang H, Gong X, Dagucon CP, Wang J, Lin Y, Sood A, Guo Y, Zhu Y, Alexis N, Gilliland FD, Belinsky SA, Yu X, Leng S. 2023. Application of artificial intelligence in quantifying lung deposition dose of black carbon in people with exposure to ambient combustion particles. J Expo Sci Environ Epidemiol doi:10.1038/s41370-023-00607-0 PMID:37848612
- Ju Y, Neumann O, Bajomo MM, Zhao Y, Nordlander P, Halas N, Patel AB. 2023. Identifying surface-enhanced Raman spectra with a Raman library using machine learning. ACS Nano 17(21):21251-21261. doi:10.1021/acsnano.3c05510 PMID:37910670
- McCoy D, Hubbard AE, van der Laan MJ. 2023. CVtreeMLE: efficient estimation of mixed exposures using data adaptive decision trees and cross-validated targeted maximum likelihood estimation in R. J Open Source Softw 8(82):4181. doi:10.21105/joss.04181 PMID:37398941 PMCID:PMC10312067
- McCoy D, Schuler A, Hubbard AE, van der Laan MJ. 2023. SuperNOVA: semi-parametric identification and estimation of interaction and effect modification in mixed exposure using stochastic interventions in R. J Open Source Softw 8(91):5422. doi:10.21105/joss.05422
- Nault R, Cave MC, Ludewig G, Moseley HN, Pennell KG, Zacharewski TR. 2023. A case for accelerating standards to achieve the FAIR principles of environmental health research experimental data. Environ Health Perspect 131(6):65001. doi:10.1289/EHP11484 PMID:37352010 PMCID:PMC10289218
- Powell CD, Moseley HN. 2023. The metabolomics workbench file status website: a metadata repository promoting FAIR principles of metabolomics data. BMC Bioinformatics 24(1):299. doi:10.1186/s12859-023-05423-9 PMID:37482620 PMCID:PMC10364356
- Roostaei J, Wager YZ, Shi W, Dittrich T, Miller CJ, Gopalakrishnan K. 2023. IoT-based edge computing (IoTEC) for improved environmental monitoring. Sustain Comput 38:100870. doi:10.1016/j.suscom.2023.100870 PMID:37234690 PMCID:PMC10206678
- Shen Y, Kioumourtzoglou M, Wu H, Vokonas PS, Spiro, III A, Navas-Acien A, Baccarelli A, Gao F. 2023. Cohort network: A knowledge graph toward data dissemination and knowledge-driven discovery for cohort studies. Environ Sci Technol 57(22):8236-8244. doi:10.1021/acs.est.2c08174 PMID:37224396
- Teimoori S, Olya MH, Miller CJ. 2023. Groundwater level monitoring network design with machine learning methods. J Hydrol 625(PartB):130145. doi:10.1016/j.jhydrol.2023.130145
- Thompson PT, Moseley HN. 2023. MESSES: Software for transforming messy research datasets into clean submissions to metabolomics workbench for public sharing. Metabolites 13(7):842. doi:10.3390/metabo13070842 PMID:37512549 PMCID:PMC10386444
- Thompson PT, Ojha S, Powell CD, Pennell KG, Moseley HN. 2023. A proposed FAIR approach for disseminating geospatial information system maps. Sci Data 10(1):389. doi:10.1038/s41597-023-02281-1 PMID:37328607 PMCID:PMC10275873
- Zeng RW, Yong JN, Tan DJ, Fu CE, Lim WH, Xiao J, Chan KE, Tan C, Goh XL, Chee D, Syn N, Tan EX, Muthiah M, Ng CH, Tamaki N, Lee SW, Kim BK, Nguyen MH, Loomba R, Huang DQ. 2023. Meta-analysis: chemoprevention of hepatocellular carcinoma with statins, aspirin and metformin. Aliment Pharmacol Ther 57(6):600-609. doi:10.1111/apt.17371 PMID:36625733
2022
- Armstrong MD, Vickers R, Coronell Nieto O. 2022. Dataset of reverse osmosis membrane transport properties calculated with and without assumptions about concentration polarization and solute rejection and the errors associated with each assumption. Data Brief 44:108538. doi:10.1016/j.dib.2022.108538 PMID:36060824 PMCID:PMC9436753
- Bajomo MM, Ju Y, Zhou J, Elefterescu S, Farr C, Zhao Y, Neumann O, Nordlander P, Patel AB, Halas N. 2022. Computational chromatography: a machine learning strategy for demixing individual chemical components in complex mixtures. Proc Natl Acad Sci U S A 119(52):e2211406119. doi:10.1073/pnas.2211406119 PMID:36534806
- Beykal B, Diangelakis NA, Pistikopoulos EN. 2022. Continuous-time surrogate models for data-driven dynamic optimization. ESCAPE 51:205-210. doi:10.1016/b978-0-323-95879-0.50035-7 PMID:36622647 PMCID:PMC9823268
- Bhattacharyya A, Pal S, Mitra R, Rai SN. 2022. Applications of Bayesian shrinkage prior models in clinical research with categorical responses. BMC Med Res Methodol doi:10.1186/s12874-022-01560-6 PMID:35484507 PMCID:PMC9046716
- Bilbao A, Gibbons BC, Stow SM, Kyle AD, Bloodsworth KJ, Payne SH, Smith RD, Ibrahim YM, Baker ES, Fjeldsted JC. 2022. A preprocessing tool for enhanced ion mobility-mass spectrometry-based omics workflows. J Proteome Res 21:798-807. doi:10.1021/acs.jproteome.1c00425 PMID:34382401 PMCID:PMC8837709
- Carpenito T, Manjourides J. 2022. MISL: Multiple imputation by super learning. Stat Methods Med Res 12. doi:10.1177/09622802221104238 PMID:35658622
- Chiu WA, Lynch MT, Lay CR, Antezana A, Malek P, Sokolinski S, Rogers RD. 2022. Bayesian estimation of human population toxicokinetics of PFOA, PFOS, PFHxS, and PFNA from studies of contaminated drinking water. Environ Health Perspect 130(12):127001. doi:10.1289/EHP10103 PMID:36454223 PMCID:PMC9714558
- Cohen Hubal EA, DeLuca NM, Mullikin A, Slover R, Little JC, Reif DM. 2022. Demonstrating a systems approach for integrating disparate data streams to inform decisions on children's environmental health. BMC Public Health 22(1):313. doi:10.1186/s12889-022-12682-3 PMID:35168583 PMCID:PMC8845296
- Ewald JM, Schnoor JL, Mattes TE. 2022. Combined read- and assembly-based metagenomics to reconstruct a Dehalococcoides mccartyi genome from PCB-contaminated sediments and evaluate functional differences among organohalide-respiring consortia in the presence of different halogenated contaminants. FEMS Microbiol Ecol 98(7). doi:10.1093/femsec/fiac067 PMID:35665806
- Ewald JM, Schnoor JL, Mattes TE. 2022. Metagenomes, metagenome-assembled genomes, and metatranscriptomes from polychlorinated biphenyl-contaminated sediment microcosms. Microbiol Resour Ann 4. doi:10.1128/mra.01126-21 PMID:35766865
- Foster MR, Rainey M, Watson C, Dodds J, Kirkwood KI, Fernandez FM, Baker ES. 2022. Uncovering PFAS and other xenobiotics in the dark metabolome using ion mobility spectrometry, mass defect analysis, and machine learning. Environ Sci Technol 56. doi:10.1021/acs.est.2c00201 PMID:35653285 PMCID:PMC9474714
- Gourronc FA, Helm BK, Robertson LW, Chimenti MS, Lehmler H, Ankrum J, Klingelhutz AJ. 2022. Dataset of transcriptomic changes that occur in human preadipocytes over a 3-day course of exposure to 3,3',4,4',5-Pentachlorobiphenyl (PCB126). Data Brief 45:108571. doi:10.1016/j.dib.2022.108571 PMID:36131953 PMCID:PMC9483567
- Howe CG, Nozadi S, Garcia E, O'Connor TG, Starling AP, Farzan SF, Jackson BP, Madan J, Alshawabkeh AN, Cordero JF, Bastain TM, Meeker JD, Breton CV, Karagas MR. 2022. Prenatal metal(loid) mixtures and birth weight for gestational age: A pooled analysis of three cohorts participating in the ECHO program. Environ Int 161. doi:10.1016/j.envint.2022.107102 PMID:35081493 PMCID:PMC8891091
- Hu XC, Dai M, Sun JM, Sunderland EM. 2022. The utility of machine learning models for predicting chemical contaminants in drinking water: promise, challenges, and opportunities. Curr Environ Health Rep doi:10.1007/s40572-022-00389-x PMID:36527604
- Kirkwood KI, Fleming J, Nguyen H, Reif DM, Baker ES, Belcher SM. 2022. Utilizing pine needles to temporally and spatially profile per- and polyfluoroalkyl substances (PFAS). Environ Sci Technol 56:3441-3451. doi:10.1021/acs.est.1c06483 PMID:35175744
- Kirkwood KI, Pratt BS, Shulman N, Tamura K, MacCoss MJ, MacLean BX, Baker ES. 2022. Utilizing Skyline to analyze lipidomics data containing liquid chromatography, ion mobility spectrometry and mass spectrometry dimensions. Nat Protoc doi:10.1038/s41596-022-00714-6 PMID:35831612
- Koval L, Dionisio KL, Friedman KP, Isaacs KK, Rager JE. 2022. Environmental mixtures and breast cancer: identifying co-exposure patterns between understudied vs breast cancer-associated chemicals using chemical inventory informatics. J Expo Sci Environ Epidemiol doi:10.1038/s41370-022-00451-8 PMID:35710593
- Kowalczewski A, Sakolish C, Hoang P, Liu X, Jacquir S, Rusyn I, Ma Z. 2022. Integrating nonlinear analysis and machine learning for human induced pluripotent stem cell-based drug cardiotoxicity testing. J Tissue Eng Regen Med doi:10.1002/term.3325 PMID:35621199
- Pammi M, Aghaeepour N, Neu J. 2022. Multiomics, artificial intelligence, and precision medicine in perinatology. Pediatric Research 8. doi:10.1038/s41390-022-02181-x PMID:35804156
- Rahman SM, Lan J, Kaeli D, Dy J, Alshawabkeh AN, Gu AZ. 2022. Machine learning-based biomarkers identification from toxicogenomics - bridging to regulatory relevant phenotypic endpoints. J Hazard Mater 423. doi:10.1016/j.jhazmat.2021.127141 PMID:34560480
- Rainey M, Watson C, Asef CK, Foster MR, Baker ES, Fernandez FM. 2022. CCS predictor 2.0: an open-source Jupyter notebook tool for filtering out false positives in metabolomics. Anal Chem 94(50):17456-17466. doi:10.1021/acs.analchem.2c03491 PMID:36473057 PMCID:PMC9772062
- Ramaprasad AS, Smith MT, McCoy D, Hubbard AE, La Merrill MA, Durkin KA. 2022. Predicting the binding of small molecules to nuclear receptors using machine learning. Brief Bioinform 23(3). doi:10.1093/bib/bbac114 PMID:35383362 PMCID:PMC9116378
- Reed JR, Guidry JJ, Backes WL. 2022. Proteomic and bioinformatics analysis of membrane lipid domains after Brij 98 solubilization of uninduced and phenobarbital-induced rat liver microsomes: Defining the membrane localization of the P450 enzyme system. Drug Metab Dispos 50(4):374-385. doi:10.1124/dmd.121.000752 PMID:35094979
- Rivera BN, Ghetu CC, Chang Y, Truong L, Tanguay RL, Anderson KA, Tilton SC. 2022. Leveraging multiple data streams for prioritization of mixtures for hazard characterization. Toxics 10(11):651. doi:10.3390/toxics10110651 PMID:36355943
- Roell K, Koval L, Boyles R, Patlewicz G, Ring C, Rider CV, Ward-Caviness C, Reif DM, Jaspers I, Fry RC, Rager JE. 2022. Development of the InTelligence and Machine LEarning (TAME) Toolkit for introductory data science, chemical-biological analyses, predictive modeling, and database mining for environmental health research. Front Toxicol 4. doi:10.3389/ftox.2022.893924 PMID:35812168 PMCID:PMC9257219
- Rusyn I, Chiu WA. 2022. Decision-Making with New Approach Methodologies: Time to Replace Default Uncertainty Factors with Data. Toxicol Sci doi:10.1093/toxsci/kfac033 PMID:35404442
- Saie AE, Fu C, Grimm SL, Robertson M, Hoffman K, Putluri V, Ambati CS, Putluri N, Shivanna B, Coarfa C, Pammi M. 2022. Metabolome and microbiome multi-omics integration from a murine lung inflammation model of bronchopulmonary dysplasia. Pediatric Research 10. doi:10.1038/s41390-022-02002-1 PMID:35338351
- Shao K, Ji C, Chiu WA. 2022. Using prior toxicological data to support dose-response assessment-identifying plausible prior distributions for dichotomous dose-response models. Environ Sci Technol 56(22):16506-16516. doi:10.1021/acs.est.2c05872 PMID:36279400
- Thaiparambil J, Dong J, Grimm SL, Perera D, Ambati CS, Putluri V, Robertson M, Patel TD, Mistretta B, Gunaratne PH, Kim MP, Yustein JT, Putluri N, Coarfa C, El-Zein R. 2022. Integrative metabolomics and transcriptomics analysis reveals novel therapeutic vulnerabilities in lung cancer. Cancer Med doi:10.1002/cam4.4933 PMID:35676822
- Thompson PT, Powell CD, Moseley HN. 2022. Academic tracker: software for tracking and reporting publications associated with authors and grants. PLoS One 17(11):e0277834. doi:10.1371/journal.pone.0277834 PMID:36399468 PMCID:PMC9674155
- Todero JE, Koch-Laskowski K, Shi Q, Kanke M, Hung Y, Beck R, Styblo M, Sethupathy P. 2022. Candidate master microRNA regulator of arsenic-induced pancreatic beta cell impairment revealed by multi-omics analysis. Arch Toxicol 96(6):1685-1699. doi:10.1007/s00204-022-03263-9 PMID:35314868 PMCID:PMC9095563
- Varner PM, Gunsch C. 2022. Complete genome sequence of NAH7-harboring pseudomonas putida strain G7. Microbiol Resour Ann doi:10.1128/mra.00394-22 PMID:36129275 PMCID:PMC9584282
- Wambaugh J, Rager JE. 2022. Exposure forecasting - ExpoCast - for data-poor chemicals in commerce and the environment. J Expo Sci Environ Epidemiol doi:10.1038/s41370-022-00492-z PMID:36347934
- Welch BM, Keil AP, Buckley JP, Calafat AM, Christenbury KE, Engel SM, O'Brien KM, Rosen EM, James-Todd T, Zota AR, Ferguson KK, Alshawabkeh AN, Cordero JF, Meeker JD, Barrett ES, Bush NR, Nguyen RH, Sathyanarayana S, Swan SH, Cantonwine DE, Aalborg J, Dabelea D, Starling AP, Hauser R, Messerlian C, Zhang Y, Bradman A, Eskenazi B, Charley PH, Holland NT, Bloom MS, Newman RB, Wenzel AG, Braun JM, Lanphear BP, Yolton K, Factor-Litvak P, Herbstman JB, Rauh VA, Drobnis EZ, Sparks AE, Redmon JB, Wang C, Binder AM, Michels KB, Baird DD, Jukic AM, Weinberg CR, Wilcox AJ, Rich DQ, Weinberger B, Padmanabhan V, Watkins DJ, Hertz-Picciotto I, Schmidt RJ. 2022. Associations between prenatal urinary biomarkers of phthalate exposure and preterm birth: A pooled study at 16 US cohorts. JAMA Pediatr doi:10.1001/jamapediatrics.2022.2252 PMID:35816333 PMCID:PMC9274448
- Youn J, Rai N, Tagkopoulos I. 2022. Knowledge integration and decision support for accelerated discovery of antibiotic resistance genes. Nat Commun doi:10.1038/s41467-022-29993-z PMID:35487919 PMCID:PMC9055065
- Zhabotynsky V, Huang L, Little P, Hu Y, Pardo-Manuel de Villena F, Zou F, Sun W. 2022. eQTL mapping using allele-specific count data is computationally feasible, powerful, and provides individual-specific estimates of genetic effects. PLoS Genet 18. doi:10.1371/journal.pgen.1010076 PMID:35286297 PMCID:PMC8947591
- Zhang C, Li X, Stietz KP, Sethi S, Yang W, Marek RF, Ding X, Lein PJ, Hornbuckle KC, Joachim-Lehmler H. 2022. Machine learning-assisted identification and quantification of hydroxylated metabolites of polychlorinated biphenyls in animal samples. Environ Sci Technol 56(18):13169-13178. doi:10.1021/acs.est.2c02027 PMID:36047920
- Zhou Y, Gallins P, Etheridge AS, Jima DD, Scholl EH, Wright FA, Innocenti F. 2022. A resource for integrated genomic analysis of the human liver. Sci Rep 12(1):15151. doi:10.1038/s41598-022-18506-z PMID:36071064 PMCID:PMC9452507
2021
- Aryal A, Harmon AC, Dugas TR. 2021. Particulate matter air pollutants and cardiovascular disease: Strategies for intervention. Pharmacol Ther 223:107890. doi:10.1016/j.pharmthera.2021.107890 PMID:33992684 PMCID:PMC8216045
- Chen Z, Lloyd D, Zhou Y, Chiu WA, Wright FA, Rusyn I. 2021. Risk characterization of environmental samples using in vitro bioactivity and polycyclic aromatic hydrocarbon (PAH) concentrations data. Toxicol Sci 179(1):108-120. doi:10.1093/toxsci/kfaa166 PMID:33165562 PMCID:PMC7797768
- Eaves LA, Keil A, Rager JE, George A, Fry RC. 2021. Analysis of the novel NCWELL database highlights two decades of co-occurrence of toxic metals in North Carolina private well water: Public health and environmental justice implications. Sci Total Environ 812:151479. doi:10.1016/j.scitotenv.2021.151479 PMID:34767890 (ahead of print)
- Ganesh HS, Beykal B, Szafran AT, Stossi F, Zhou L, Mancini MA, Pistikopoulos EN. 2021. Predicting the estrogen receptor activity of environmental chemicals by single-cell image analysis and data-driven modeling. ESCAPE 50:481-486. doi:10.1016/b978-0-323-88506-5.50076-0 PMID:34355221 PMCID:PMC8331057
- House JS, Grimm FA, Klaren WD, Dalzell A, Kuchi S, Zhang S, Lenz K, Boogaard PJ, Ketelslegers HB, Gant TW, Wright FA, Rusyn I. 2021. Grouping of UVCB substances with new approach methodologies (NAMs) data. ALTEX 38:123-137. doi:10.14573/altex.2006262 PMID:33086383 PMCID:PMC7900923
- Marvel S, House JS, Wheeler M, Song K, Zhou Y, Wright FA, Chiu WA, Rusyn I, Motsinger-Reif A, Reif DM. 2021. The COVID-19 Pandemic Vulnerability Index (PVI) dashboard: Monitoring county-level vulnerability using visualization, statistical modeling, and machine learning. Environ Health Perspect 129:17701. doi:10.1289/EHP8690 PMID:33400596 PMCID:PMC7785295
- Newman G, Malecha M, Atoba K. 2021. Integrating ToxPi outputs with ArcGIS Dashboards to identify neighborhood threat levels of contaminant transferal during flood events. J of Spa Sci 13. doi:10.1080/14498596.2021.1891149
- Orr AA, Wang M, Beykal B, Ganesh HS, Hearon S, Pistikopoulos EN, Phillips TD, Tamamis P. 2021. Combining experimental isotherms, minimalistic simulations, and a model to understand and predict chemical adsorption onto montmorillonite clays. ACS Omega 6(22):14090-14103. doi:10.1021/acsomega.1c00481 PMID:34124432 PMCID:PMC8190805
- Powell CD, Moseley HN. 2021. The mwtab python library for RESTful Access and enhanced quality control, deposition, and curation of the metabolomics workbench data repository. Metabolites 11(3). doi:10.3390/metabo11030163 PMID:33808985 PMCID:PMC8000456
- Roman-Hubers AT, Cordova AC, Aly NA, McDonald TJ, Lloyd D, Wright FA, Baker ES, Chiu WA, Rusyn I. 2021. Data processing workflow to identify structurally related compounds in petroleum substances using ion mobility spectrometry-mass spectrometry. Energy Fuels 35:10529-10539. doi:10.1021/acs.energyfuels.1c00892 PMID:34366560 PMCID:PMC8341389
- Shaw JL, Semmens E, Okihiro M, Lewis JL, Hirschfeld M, VanWagoner TM, Stephens L, Easa D, Ross JL, Graham N, Watson SE, Szyld EG, Dillard DA, Pyles LA, Darden PM, Carlson JC, McCulloh RJ, Snowden JN, Adeky SH, Singleton R, Smith PG. 2021. Best practices for conducting clinical trials with Indigenous children in the United States. Am J Public Health 111. doi:10.2105/AJPH.2021.306372 PMID:34436921 PMCID:PMC8494399
- Stingone JA, Triantafillou S, Larsen A, Kitt JP, Shaw GM, Marsillach J. 2021. Interdisciplinary data science to advance environmental health research and improve birth outcomes. Environ Res 197. doi:10.1016/j.envres.2021.111019 PMID:33737076 PMCID:PMC8187296
2020
- Bhandari S, Lewis PT, Craft ES, Marvel S, Reif DM, Chiu WA. 2020. HGBEnviroScreen: Enabling community action through data integration in the Houston-Galveston-Brazoria region. Int J Environ Res Public Health 17. doi:10.3390/ijerph17041130 PMID:32053902
- Chen Z, Liu Y, Wright FA, Chiu WA, Rusyn I. 2020. Rapid hazard characterization of environmental chemicals using a compendium of human cell lines from different organs. ALTEX 37:623-638. doi:10.14573/altex.2002291 PMID:32521033
- House JS, Bouzos E, Fahy K, Francisco VM, Lloyd D, Wright FA, Motsinger-Reif A, Asuri P, Wheeler K. 2020. Low dose silver nanoparticle surface chemistry and temporal effects on gene expression in human liver cells. Wiley Interdiscip Rev Nanomed Nanobiotechnol doi:10.1002/smll.202000299 PMID:32227433 PMCID:PMC7446734
- Malecha M, Kirsch KR, Karaye I, Horney JA, Newman G. 2020. Advancing the toxics mobility inventory: Development and application of a toxics mobility vulnerability index to Harris County, Texas. Sustainability 13(6):282-291. doi:10.1089/sus.2020.0067
- Mukherjee R, Beykal B, Szafran AT, Onel M, Stossi F, Mancini MG, Lloyd D, Wright FA, Zhou L, Mancini MA, Pistikopoulos EN. 2020. Classification of estrogenic compounds by coupling high content analysis and machine learning algorithms. PLoS Comput Biol 16:24. doi:10.1371/journal.pcbi.1008191 PMID:32970665 PMCID:PMC7538107
- Wilson LB, Truong L, Simonich MT, Tanguay RL. 2020. Systematic Assessment of Exposure Variations on Observed Bioactivity in Zebrafish Chemical Screening. Toxics 8. doi:10.3390/toxics8040087 PMID:33066419 PMCID:PMC7712973
2019
- Brown J, Phillips AR, Lewis DA, Mans M, Chang Y, Tanguay RL, Peterson ES, Waters KM, Tilton SC. 2019. Bioinformatics Resource Manager: a systems biology web tool for microRNA and omics data integration. BMC Bioinformatics 20:255. doi:10.1186/s12859-019-2805-6 PMID:31101000
- Byrd D, Chen J, Vogtmann E, Hullings A, Song S, Amir A, Kibriya MG, Ahsan H, Chen Y, Nelson H, Knight R, Shi J, Chia N, Sinha R. 2019. Reproducibility, stability, and accuracy of microbial profiles by fecal sample collection method in three distinct populations. PLoS One doi:10.1371/journal.pone.0224757 PMID:31738775 PMCID:PMC6860998
- Mukherjee R, Onel M, Beykal B, Szafran AT, Stossi F, Mancini MA, Zhou L, Wright FA, Pistikopoulos EN. 2019. Development of the Texas A&M Superfund Research Program computational platform for data integration, visualization, and analysis. Computer Aided Chemical Engineering 46:967-972. doi:10.1016/B978-0-12-818634-3.50162-4 PMID:31612156 PMCID:PMC6791821
- Sandhaus S, Kaufmann D, Ramirez-Andreotta M. 2019. Public participation, trust and data sharing: gardens as hubs for citizen science and environmental health literacy efforts. Int J Sci Educ B Commun Public Engagem 9:54-71. doi:10.1080/21548455.2018.1542752 PMID:31485378 PMCID:PMC6726431
2018
- Grimm FA, Blanchette A, House JS, Ferguson K, Hsieh N, Dalaijamts C, Wright AA, Anson B, Wright FA, Chiu WA, Rusyn I. 2018. A human population-based organotypic in vitro model for cardiotoxicity screening. ALTEX 35:441-452. doi:10.14573/altex.1805301 PMID:29999168 PMCID:PMC6231908
- Marvel S, To K, Grimm FA, Wright FA, Rusyn I, Reif DM. 2018. ToxPi Graphical User Interface 2.0: dynamic exploration, visualization, and sharing of integrated data models. BMC Bioinformatics 19(1):80. doi:10.1186/s12859-018-2089-2 PMID:29506467 PMCID:PMC5838926
- Venkatratnam A, House JS, Konganti K, McKenney C, Threadgill DW, Chiu WA, Aylor DL, Wright FA, Rusyn I. 2018. Population-based dose-response analysis of liver transcriptional response to trichloroethylene in mouse. Mamm Genome 29:168-181. doi:10.1007/s00335-018-9734-y PMID:29353386 PMCID:PMC6094947
2017
- Edmands WM, Petrick L, Barupal D, Scalbert A, Wilson MJ, Wickliffe JK, Rappaport SM. 2017. compMS2Miner: an automatable metabolite identification, visualization, and data-sharing R package for high-resolution LC-MS data sets. Anal Chem 89(7):3919-3928. doi:10.1021/acs.analchem.6b02394 PMID:28225587 PMCID:PMC6338221
- House JS, Grimm FA, Jima DD, Zhou Y, Rusyn I, Wright FA. 2017. A pipeline for high-throughput concentration response modeling of gene expression for toxicogenomics. Front Genet 8:168. doi:10.3389/fgene.2017.00168 PMID:29163636 PMCID:PMC5672545
2016
- McIntosh S, Perez-Ramos J, Demment MM, Velez Vega CM, Avendano E, Ossip DJ, Dye TD. 2016. Development and implementation of culturally tailored offline mobile health surveys. JMIR Public Health Surveill 2(1):e28. doi:10.2196/publichealth.5408 PMID:27256208 PMCID:PMC4911512
- Ramirez-Andreotta M, Brody JG, Lothrop N, Loh M, Beamer P, Brown P. 2016. Improving environmental health literacy and justice through environmental exposure results communication. Int J Environ Health Res 13(7):690. doi:10.3390/ijerph13070690 PMID:27399755 PMCID:PMC4962231
- Rohlman D, Frey G, Kile ML, Harper B, Harris S, Motorykin O, Simonich SL, Harding A. 2016. Communicating results of a dietary exposure study following consumption of traditionally smoked salmon. Environ Justice 9(3):85-92. doi:10.1089/env.2016.0006 PMID:28804531 PMCID:PMC4981151
2014
- Lewis RC, Cantonwine DE, Anzalota del Toro LV, Calafat AM, Valentin-Blasini L, Davis MD, Baker SE, Alshawabkeh AN, Cordero JF, Meeker JD. 2014. Urinary biomarkers of exposure to insecticides, herbicides, and one insect repellent among pregnant women in Puerto Rico. Environ Health 13:97. doi:10.1186/1476-069X-13-97 PMID:25409771 PMCID:PMC4258050
- Park S, Tao Y, Meeker JD, Harlow SD, Mukherjee B. 2014. Environmental risk score as a new tool to examine multi-pollutants in epidemiologic research: an example from the NHANES study using serum lipid levels. PLoS One 9(6):e98632. doi:10.1371/journal.pone.0098632 PMID:24901996 PMCID:PMC4047033
2012
- Harding A, Harper B, Stone D, O'Neill C, Berger P, Harris S, Donatuto J. 2012. Conducting research with tribal communities: sovereignty, ethics, and data-sharing issues. Environ Health Perspect 120(1):6-10. doi:10.1289/ehp.1103904 PMID:21890450 PMCID:PMC3261947
- Hobbie KA, Peterson ES, Barton ML, Waters KM, Anderson KA. 2012. Integration of data systems and technology improves research and collaboration for a Superfund Research Center. J Lab Autom 17(4):275-283. doi:10.1177/2211068212448428 PMID:22651935 PMCID:PMC3460553
- Slusky DA, Metayer C, Aldrich MC, Ward MH, Lea CS, Selvin S, Buffler PA. 2012. Reliability of maternal-reports regarding the use of household pesticides: Experience from a case-control study of childhood leukemia. Cancer Epidemiol 36(4):375-380. doi:10.1016/j.canep.2011.12.009 PMID:22277328 PMCID:PMC4140525
- Tilton SC, Tal TL, Scroggins SM, Franzosa JA, Peterson ES, Tanguay RL, Waters KM. 2012. Bioinformatics resource manager v2.3: an integrated software environment for systems biology with microRNA and cross-species analysis tools. BMC Bioinformatics 13(1):311. doi:10.1186/1471-2105-13-311 PMID:23174015 PMCID:PMC3534564
2010
- Chen Y, Christiani DC, Su HJ, Hsueh Y, Smith TJ, Ryan LM, Chao S, Lee J, Guo YL. 2010. Early-life or lifetime sun exposure, sun reaction, and the risk of squamous cell carcinoma in an Asian population. Cancer Causes Control 21(5):771-6. doi:10.1007/s10552-010-9505-x PMID:20084542 PMCID:PMC3816003
2009
- Zhu H, Martin T, Ye L, Sedykh A, Young D, Tropsha A. 2009. Quantitative structure-activity relationship modeling of rat acute toxicity by oral exposure. Chem Res Toxicol 22(12):1913-1921. doi:10.1021/tx900189p PMID:19845371 PMCID:PMC2796713
2006
- Burgoon LD, Boutros PC, Dere E, Zacharewski TR. 2006. dbZach: A MIAME-compliant toxicogenomic supportive relational database. Toxicol Sci 90(2):558-68. PMID:16403854