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Project Publications: Texas A&M University: Novel Analytical and Computational Strategies for Exposure Assessment of Complex Mixtures

Superfund Research Program

Novel Analytical and Computational Strategies for Exposure Assessment of Complex Mixtures

Project Leader: Erin S. Baker (University of North Carolina-Chapel Hill)
Grant Number: P42ES027704
Funding Period: 2022-2027
View this project in the NIH Research Portfolio Online Reporting Tools (RePORT)

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Publications

2024

  • 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
  • Odenkirk MT, Zheng X, Kyle JE, Stratton KG, Nicora CD, Bloodsworth KJ, Mclean C, Masters C, Monroe ME, Doecke J, Smith RD, Burnum-Johnson KE, Roberts BR, Baker ES. 2024. Deciphering ApoE genotype-driven proteomic and lipidomic alterations in Alzheimer's disease across distinct brain regions. J Proteome Res doi:10.1021/acs.jproteome.3c00604 PMID:38236019

2023

  • Baker ES. 2023. Assessing how chemical exposures affect human health. LC GC Eur 36:7-10. PMID:37900911 PMCID:PMC10611144
  • 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, King ME, Fleming J, Eberlin LS, Reif DM, Baker ES. 2023. Aggregated molecular phenotype scores: Enhancing assessment and visualization of mass spectrometry imaging data for tissue-based diagnostics. Anal Chem 95(34):12913-12922. doi:10.1021/acs.analchem.3c02389 PMID:37579019
  • 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
  • Cordova AC, Klaren WD, Ford L, Grimm FA, Baker ES, Zhou Y, Wright FA, Rusyn I. 2023. Integrative chemical-biological grouping of complex high production volume substances from lower olefin manufacturing streams. Toxics 11(7):586. doi:10.3390/toxics11070586 PMID:37505552 PMCID:PMC10385386
  • Foley MH, Walker ME, Stewart AK, O'Flaherty S, Gentry E, Patel S, Beaty VV, Allen G, Pan M, Simpson JB, Perkins C, Vanhoy ME, Dougherty MK, McGill SK, Gulati AS, Dorrestein PC, Baker ES, Redinbo MR, Barrangou R, Theriot CM. 2023. Bile salt hydrolases shape the bile acid landscape and restrict clostridioides difficile growth in the murine gut. Nat Microbiol doi:10.1038/s41564-023-01337-7 PMID:36914755 PMCID:PMC10066039
  • Kirkwood-Donelson KI, Dodds J, Schnetzer A, Hall N, Baker ES. 2023. Uncovering per- and polyfluoroalkyl substances (PFAS) with nontargeted ion mobility spectrometry-mass spectrometry analyses. Sci Adv 9(43):eadj7048. doi:10.1126/sciadv.adj7048 PMID:37878714 PMCID:PMC10599621
  • Sakolish C, Moyer HL, Tsai H, Ford L, Dickey AN, Wright FA, Han G, Bajaj P, Baltazar MT, Carmichael PL, Stanko JP, Ferguson SS, 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. Toxicol Sci doi:10.1093/toxsci/kfad080 PMID:37555834
  • Stewart AK, Foley MH, Dougherty MK, McGill SK, Gulati AS, Gentry E, Hagey LR, Dorrestein PC, Theriot CM, Dodds J, Baker ES. 2023. Using multidimensional separations to distinguish isomeric amino acid-bile acid conjugates and assess their presence and perturbations in model systems. Anal Chem 95(41):15357-15366. doi:10.1021/acs.analchem.3c03057 PMID:37796494

2022

  • Bilbao A, Munoz N, Kim J, Orton DJ, Gao Y, Poorey K, Pomraning KR, Weitz KK, Burnet MC, Nicora CD, Wilton R, Deng S, Dai Z, Oksen E, Gee A, Fasani RA, Tsalenko A, Tanjore D, Gardner J, Smith RD, Michener JK, Gladden JM, Baker ES, Petzold CJ, Kim Y, Apffel A, Magnuson JK, Burnum-Johnson KE. 2022. PeakDecoder: A machine learning-based identification algorithm for multidimensional mass spectrometry measurements and its application for synthetic biology. Nat Commun
  • Butler KE, Baker ES. 2022. A high-throughput ion mobility spectrometry-mass spectrometry screening method for opioid profiling. J Am Soc Mass Spectrom 33(10):1904-1913. doi:10.1021/jasms.2c00186 PMID:36136315
  • Doyle MG, Odenkirk MT, Stewart AK, Nelson JP, Baker ES, De La Cruz F. 2022. Assessing the fate of dissolved organic compounds in landfill leachate and wastewater treatment systems. ACS ES&T Wat doi:10.1021/acsestwater.2c00320
  • Gentry E, Collins S, Panitchpakdi M, Belda-Ferre P, Stewart AK, Wang M, Jarmusch A, Avila-Pacheco J, Plichta D, Aron A, Vlamakis H, Ananthakrishnan AN, Clish C, Xavier R, Baker ES, Patterson A, Knight R, Siegel D. 2022. Synthesis-based reverse metabolomics approach for the discovery of chemical structures from humans and animals. Nature PMID:38052229
  • Kirkwood KI, Dodds J, Baker ES. 2022. An investigation into the presence and migration of perfluoroalkyl substances in nonstick cookware advertised as PFAS-free. Environ Sci Technol
  • 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
  • Roman-Hubers AT, Aeppli C, Dodds J, Baker ES, McFarlin KM, Letinski DJ, Zhao L, Mitchell DA, Parkerton TF, Prince RC, Nedwed T, Rusyn I. 2022. Temporal chemical composition changes in water below a crude oil slick irradiated with natural sunlight. Mar Pollut Bull 185:114360. doi:10.1016/j.marpolbul.2022.114360 PMID:36413931
  • Valdiviezo A, Kato Y, Baker ES, Chiu WA, Rusyn I. 2022. Evaluation of metabolism of a defined pesticide mixture through multiple in vitro liver models. Toxics 10(10):566. doi:10.3390/toxics10100566 PMID:36287846 PMCID:PMC9609317
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