Grantee Research Project Results
Publications Details for Grant Number R840032
Integrating tissue chips, rapid untargeted analytical methods and molecular modeling for toxicokinetic screening of chemicals, their metabolites and mixtures
RFA:
Advancing Toxicokinetics for Efficient and Robust Chemical Evaluations (2019)
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| Reference Type | Citation | Progress Report Year | Document Sources |
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| Abstract | Bilbao A, Gibbons B, Stow S, Kyle J, Bloodsworth K, Payne S, Smith R, Ibrahim Y, Baker E, Fjeldsted J. A Preprocessing Tool for Enhanced Ion Mobility-Mass Spectrometry-Based Omics Workflows. JOURNAL OF PROTEOME RESEARCH 2021;21(3):798-807 |
R840032 (2022) |
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| Abstract | Butler K, Baker E. A High-Throughput Ion Mobility Spectrometry-Mass Spectrometry Screening Method for Opioid Profiling. JOURNAL OF THE AMERICAN SOCIETY OF MASS SPECTROMETRY 2022;23(10):1904-1913 |
R840032 (2022) |
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| Abstract | Witchey S, Doyle M, Fredenburg J, St. Armour G, Horman B, Odenkirk M, Aulor D, Baker E, Patisaul H. Impacts of Gestational FireMaster 550 (FM 550) Exposure on the Neonatal Cortex are Sex Specific and Largely Attributable to the Organophosphate Esters. NEUROINDOCRINOLOGY 2022;10(1159) |
R840032 (2022) |
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| Abstract | Baker ES, Hoang C, Uritboonthai W, Heyman HM, Pratt B, MacCoss M, MacLean B, Plumb R, Aisporna A, Siuzdak G. METLIN-CCS:an ion mobility spectrometry collision cross section database. Nature Methods 2023;20(12):1836-1837. |
R840032 (2024) |
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| Abstract | Baker ES, Uritboonthai W, Aisporna A, Hoang C, Heyman HM, Connell L, Olivier-Jimenez D, Giera M, Siuzdak G. METLIN-CCS lipid database:an authentic standards resource for lipid classification and identification. Nature Metabolism 2024:1-2. |
R840032 (2024) |
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| Journal Article | Aly N, Dodds J, Luo Y, Grimm F, Foster M, Rusyn I, Baker E. Utilizing ion mobility spectrometry-mass spectrometry for the characterization and detection of persistent organic pollutants and their metabolites. ANALYTICAL AND BIOANALYTICAL CHEMISTRY 2021;414(3):1245-1258 |
R840032 (2022) |
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| Journal Article | Baker E, Hoang C, Uritboonthai W, Heyman H, Pratt B, MacCross M, MacLean B, Plumb R, Aisporna A, Siuzdak G. METLIN-CCS:an ion mobility spectrometry collision cross section database. NATURE METHODS 2023;1-2. |
R840032 (2023) |
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| Journal Article | Boatman A, Chappel J, Polera M, Dodds J, Belcher S, Baker E. Assessing Per- and Polyfluoroalkyl Substances in Fish Fillet Using Non-Targeted Analyses. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2024; |
R840032 (2023) |
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| Journal Article | Chappel J, King M, Fleming J, Eberlin L, Reif D, Baker E. Aggregated Molecular Phenotype Scores: Enhancing Assessment and Visualization of Mass Spectrometry Imaging Data for Tissue-Based Diagnostics. ANALYTICAL CHEMISTRY 2023;Online ahead of print |
R840032 (2023) |
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| Journal Article | Chappel J, Kirkwood-Donelson K, Reif D, Baker E. From big data to big insights: statistical and bioinformatic approaches for exploring the lipidome. ANALYTICAL AND BIOANALYTICAL CHEMISTRY 2023; |
R840032 (2023) |
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| Journal Article | Chappel J, Kirkwood-Donelson K, Dodds J, Fleming J, Reif D, Baker E. Streamlining Phenotype Classification and Highlighting Feature Candidates: A Screening Method for Non-Targeted Ion Mobility Spectrometry-Mass Spectrometry (IMS-MS) Data. ANALYTICAL CHEMISTRY 2024; |
R840032 (2023) |
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| Journal Article | Dodds J, Baker E. Improving the Speed and Selectivity of Newborn Screening Using Ion Mobility SpectrometryâMass Spectrometry. ANALYTICAL CHEMISTRY 2021;93(51):17094-17102 |
R840032 (2022) |
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| Journal Article | Dodds J, Kirkwood-Donelson K, Boatman A, Knappe D, Hall N, Schnetzer A, Baker E. Evaluating Solid Phase Adsorption Toxin Tracking (SPATT) for passive monitoring of per-and polyfluoroalkyl substances (PFAS) with Ion Mobility Spectrometry-Mass Spectrometry (IMS-MS). SCIENCE OF THE TOTAL ENVIRONMENT 2024;947. |
R840032 (2023) |
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| Journal Article | Foley M, Walker M, Stewart A, O'Flaherty S, Gentry E, Patel S, Beaty V, Allen G, Pan M, Simpson J, Perkins C, Vanoy M, Doughtery M, McGill S, Gulati A, Dorrenstein P, Baker E, Redinbo M, Barrangou R, Theriot C. Bile salt hydrolases shape the bile acid landscape and restrict Clostridioides difficile growth in the murine gut. NATURE MICROBIOLOGY 2023;8(4):611-628 |
R840032 (2022) |
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| Journal Article | Foster M, Rainey M, Watson C, Dodds J, Kirkwood K, Fernandez F, Baker E. Uncovering PFAS and Other Xenobiotics in the Dark Metabolome Using Ion Mobility Spectrometry, Mass Defect Analysis, and Machine Learning. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2022;56(12):9133-9143 |
R840032 (2022) |
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| Journal Article | Kirkwood K, Fleming J, Nguyn F, Reif D, Baker E, Belcher S. Utilizing Pine Needles to Temporally and Spatially Profile Per- and Polyfluoroalkyl Substances (PFAS). ENVIRONMENTAL SCIENCE & TECHNOLOGY 2022;56(6):3441-3451 |
R840032 (2022) |
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| Journal Article | Lin H, Chiu W. Development of a Physiologically Based Gut Absorption Model for Probabilistic Prediction of Environmental Chemical Bioavailability. ALTEX-ALTERNATIVES TO ANIMAL EXPERIMENTATION 2023;40(3):471-484 |
R840032 (2023) |
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| Journal Article | Mirfazaelian A, Kim K-B, Anand SS, Kim HJ, Tornero-Velez R, Bruckner JV, Fisher JW. Development of a physiologically based pharmacokinetic model for deltamethrin in the adult male Sprague-Dawley rat. Toxicological Sciences 2006;93(2):432-442. |
R830800 (2005) R830800 (2006) R830800 (Final) R840032 (2023) |
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| Journal Article | Odenkirk M, Zheng X, Kyle J, Stratton K, Niorca C, Bloodsworth K, Mclean C, Masters C, Monroe M, Doecke J, Smith R, Burnum-Johnson K, Roberts B, Baker E. Deciphering ApoE Genotype-Driven Proteomic and Lipidomic Alterations in Alzheimer's Disease Across Distinct Brain Regions. JOURNAL OF PROTEOME RESEARCH 2024; |
R840032 (2023) |
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| Journal Article | Sakolish C, Reese CE, Luo YS, Valdiviezo A, Schurdak ME, Gough A, Taylor DL, Chiu WA, Venetti LA, Rusyn I. Analysis of reproducibility and robustness of a human microfluidic four-cell liver acinus microphysiology system (LAMPS). Toxicology 2021;448. |
R835736 (Final) R840032 (2021) |
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| Journal Article | Solosky A, Claudio I, Chapel J, Kirkwood-Donelson K, Janech M, Bland A, Gulland F, Neely B, Baker E. Proteomic and Lipidomic Plasma Evaluations Reveal Biomarkers for Domoic Acid Toxicosis in California Sea Lions. JOURNAL OF PROTEOME RESEARCH 2024;23(12):5577-5585 |
R840032 (2023) |
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| Journal Article | Stewart AK, Foley MH, Doughetry MK,. McGill, SK, Gulati AS, Gentry EC, Hagey LR, Dorrenstein PC, Theirot CM, Dodds JN, Baker ES. Using Multidimensional Separations to Distinguish Isomeric Amino Acid-Bile Acid Conjugates and Assess Their Presence and Perturbations in Model Systems.ANALYTICAL CHEMISTRY 2023;95(41):15357-15366. |
R840032 (2023) |
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| Journal Article | Dodds JN, Alexander NL, Kirkwood KI, Foster MR, Hopkins ZR, Knappe DR, Baker ES. From Pesticides to Per-and Polyfluoroalkyl Substances:An Evaluation of Recent Targeted and Untargeted Mass Spectrometry Methods for Xenobiotics. Analytical chemistry 2020;93(1):641-56. |
R840032 (2021) |
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| Journal Article | Odenkirk MT, Reif DM, Baker ES. Multiomic Big Data Analysis Challenges:Increasing Confidence in the Interpretation of Artificial Intelligence Assessments. Analytical Chemistry 2021. |
R840032 (2021) R840032 (2022) |
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| Journal Article | Chappel JR, King ME, Fleming J, Eberlin LS, Reif DM, Baker ES. Aggregated molecular phenotype scores:enhancing assessment and visualization of mass spectrometry imaging data for tissue-based diagnostics. Analytical Chemistry 2023;95(34):12913-12922. |
R840032 (2024) |
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| Journal Article | Sakolish C, Moyer HL, Tsai HH, Ford LC, Dickey AN, Wright FA, Han G, Bajaj P, Baltazar MT, Carmichael PL, Stanko JP. 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 2023;196(1):52-70. |
R840032 (2024) |
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| Journal Article | Lim AY, Kato Y, Sakolish C, Valdiviezo A, Han G, Bajaj P, Stanko J, Ferguson SS, Villenave R, Hewitt P, Hardwick RN. Reproducibility and robustness of a liver microphysiological system PhysioMimix LC12 under varying culture conditions and cell type combinations. Bioengineering 2023;10(10):1195. |
R840032 (2024) |
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| Journal Article | Kirkwood-Donelson KI, Dodds JN, Schnetzer A, Hall N, Baker ES. Uncovering per-and polyfluoroalkyl substances (PFAS) with nontargeted ion mobility spectrometry–mass spectrometry analyses. Science Advances 2023;9(43):eadj7048. |
R840032 (2024) |
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| Journal Article | Stewart AK, Foley MH, Dougherty MK, McGill SK, Gulati AS, Gentry EC, Hagey LR, Dorrestein PC, Theriot CM, Dodds JN, Baker ES. Using multidimensional separations to distinguish isomeric amino acid–bile acid conjugates and assess their presence and perturbations in model systems. Analytical Chemistry 2023;95(41):15357-15366. |
R840032 (2024) |
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| Journal Article | Lin HC, Sakolish C, Moyer HL, Carmichael PL, Baltazar MT, Ferguson SS, Stanko JP, Hewitt P, Rusyn I, Chiu WA. An in vitro-in silico workflow for predicting renal clearance of PFAS. Toxicology and Applied Pharmacology 2024;489:117015. |
R840032 (2024) |
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| Journal Article | Vidal MS, Richardson LS, Kammala AK, Kim S, Lam PY, Cherukuri R, Thomas TJ, Bettayeb M, Han A, Rusyn I, Menon R. Endocrine-disrupting compounds and their impact on human placental function:evidence from placenta organ-on-chip studies. Lab on a Chip 2024;24(6):1727-1749. |
R840032 (2024) |
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| Journal Article | Chappel JR, Kirkwood-Donelson KI, Reif DM, Baker ES. From big data to big insights:statistical and bioinformatic approaches for exploring the lipidome. Analytical and Bioanalytical Chemistry 2024;416(9):2189-2202. |
R840032 (2024) |
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| Journal Article | Kirkwood-Donelson KI, Chappel J, Tobin E, Dodds JN, Reif DM, DeWitt JC, Baker ES. Investigating mouse hepatic lipidome dysregulation following exposure to emerging per-and polyfluoroalkyl substances (PFAS). Chemosphere 2024;354:141654. |
R840032 (2024) |
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| Journal Article | Sakolish C, Moyer HL, Tsai HH, Ford LC, Dickey AN, Bajaj P, Villenave R, Hewitt P, Ferguson SS, Stanko J, Rusyn I. Comparative analysis of the physiological and transport functions of various sources of renal proximal tubule cells under static and fluidic conditions in PhysioMimix T12 platform. Drug Metabolism and Disposition 2024:100001. |
R840032 (2024) |
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| Journal Article | Rusyn I, Roth A. Editorial overview of the special issue on application of tissue chips in toxicology. Toxicology 2021:152687-. |
R840032 (2021) |
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| Journal Article | Solosky AM, Kirkwood-Donelson KI, Odenkirk MT, Baker ES. Recent additions and access to a multidimensional lipidomic database containing liquid chromatography, ion mobility spectrometry, and tandem mass spectrometry information. Analytical and Bioanalytical Chemistry 2024:1-7. |
R840032 (2024) |
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| Presentation | Baker ES. IMS now and tomorrow. Presented at the 72nd American Society for Mass Spectrometry Annual Conference, June 2-6, 2024, Anaheim, CA. |
R840032 (2024) |
not available |
| Presentation | Baker ES, Kirkwood-Donelson KI, Dodds JN, Boatman A, Chappel K, Kudzin G, Solosky AM. Linking chemical exposure to human health with novel multidimensional analyses and informatics approaches. Presented at the 40th Annual Meeting of the Swiss Group of Mass Spectrometry, October 25-27, 2023, Beatenburg, Switzerland. |
R840032 (2024) |
not available |
| Presentation | Rusyn I. Microphysiological systems:TEX-VAL Consortium's experience with evaluating academic and commercial tissue chips. Presented at the Society of Toxicology (SOT) Annual Meeting, March 10-14, Salt Lake City, UT. |
R840032 (2024) |
not available |
| Presentation | Baker ES, Kirkwood-Donelson KI, Dodds JN, Boatman A, Chappel K, Solosky A, Fallas A, Kudzin G. Multidimensional non-targeted screening and size-dependent fragmentation. Presented at the International Conference on Non-Target Screening, October 16-19, 2023, Erding, Germany. |
R840032 (2024) |
not available |
The perspectives, information and conclusions conveyed in research project abstracts, progress reports, final reports, journal abstracts and journal publications convey the viewpoints of the principal investigator and may not represent the views and policies of ORD and EPA. Conclusions drawn by the principal investigators have not been reviewed by the Agency.