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Journal Article (31)
Reference Type Reference Title Journal Author Citation Progress Report Year Document Sources
Journal Article Utilizing ion mobility spectrometry-mass spectrometry for the characterization and detection of persistent organic pollutants and their metabolites. ANALYTICAL AND BIOANALYTICAL CHEMISTRY Aly N, Dodds J, Luo Y, Grimm F, Foster M, Rusyn I, Baker E 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)
Journal Article METLIN-CCS: an ion mobility spectrometry collision cross section database NATURE METHODS Baker E, Hoang C, Uritboonthai W, Heyman H, Pratt B, MacCross M, MacLean B, Plumb R, Aisporna A, Siuzdak G 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)
Journal Article Assessing Per- and Polyfluoroalkyl Substances in Fish Fillet Using Non-Targeted Analyses ENVIRONMENTAL SCIENCE & TECHNOLOGY Boatman A, Chappel J, Polera M, Dodds J, Belcher S, Baker E 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)
Journal Article Aggregated Molecular Phenotype Scores: Enhancing Assessment and Visualization of Mass Spectrometry Imaging Data for Tissue-Based Diagnostics ANALYTICAL CHEMISTRY Chappel J, King M, Fleming J, Eberlin L, Reif D, Baker E 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)
Journal Article From big data to big insights: statistical and bioinformatic approaches for exploring the lipidome ANALYTICAL AND BIOANALYTICAL CHEMISTRY Chappel J, Kirkwood-Donelson K, Reif D, Baker E 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)
Journal Article Streamlining Phenotype Classification and Highlighting Feature Candidates: A Screening Method for Non-Targeted Ion Mobility Spectrometry-Mass Spectrometry (IMS-MS) Data ANALYTICAL CHEMISTRY Chappel J, Kirkwood-Donelson K, Dodds J, Fleming J, Reif D, Baker E 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)
Journal Article Improving the Speed and Selectivity of Newborn Screening Using Ion Mobility Spectrometry–Mass Spectrometry ANALYTICAL CHEMISTRY Dodds J, Baker E Dodds J, Baker E. Improving the Speed and Selectivity of Newborn Screening Using Ion Mobility Spectrometry–Mass Spectrometry. ANALYTICAL CHEMISTRY 2021;93(51):17094-17102 R840032 (2022)
Journal Article 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 Dodds J, Kirkwood-Donelson K, Boatman A, Knappe D, Hall N, Schnetzer A, Baker E 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)
Journal Article Bile salt hydrolases shape the bile acid landscape and restrict Clostridioides difficile growth in the murine gut. NATURE MICROBIOLOGY 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 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)
Journal Article Uncovering PFAS and Other Xenobiotics in the Dark Metabolome Using Ion Mobility Spectrometry, Mass Defect Analysis, and Machine Learning. ENVIRONMENTAL SCIENCE & TECHNOLOGY Foster M, Rainey M, Watson C, Dodds J, Kirkwood K, Fernandez F, Baker E 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)
Journal Article Utilizing Pine Needles to Temporally and Spatially Profile Per- and Polyfluoroalkyl Substances (PFAS) ENVIRONMENTAL SCIENCE & TECHNOLOGY Kirkwood K, Fleming J, Nguyn F, Reif D, Baker E, Belcher S 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)
Journal Article Development of a Physiologically Based Gut Absorption Model for Probabilistic Prediction of Environmental Chemical Bioavailability ALTEX-ALTERNATIVES TO ANIMAL EXPERIMENTATION Lin H, Chiu W 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)
Journal Article Development of a physiologically based pharmacokinetic model for deltamethrin in the adult male Sprague-Dawley rat. None Mirfazaelian A, Kim K-B, Anand SS, Kim HJ, Tornero-Velez R, Bruckner JV, Fisher JW 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)
Journal Article Deciphering ApoE Genotype-Driven Proteomic and Lipidomic Alterations in Alzheimer's Disease Across Distinct Brain Regions JOURNAL OF PROTEOME RESEARCH 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 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)
Journal Article Analysis of reproducibility and robustness of a human microfluidic four-cell liver acinus microphysiology system (LAMPS) None Sakolish C, Reese CE, Luo YS, Valdiviezo A, Schurdak ME, Gough A, Taylor DL, Chiu WA, Venetti LA, Rusyn I 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)
Journal Article Proteomic and Lipidomic Plasma Evaluations Reveal Biomarkers for Domoic Acid Toxicosis in California Sea Lions JOURNAL OF PROTEOME RESEARCH Solosky A, Claudio I, Chapel J, Kirkwood-Donelson K, Janech M, Bland A, Gulland F, Neely B, Baker E 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)
Journal Article McGill, SK, Gulati AS, Gentry EC, Hagey LR, Dorrenstein PC, Theirot CM, Dodds JN, Baker ES. ANALYTICAL CHEMISTRY Stewart AK, Foley MH, Doughetry MK 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)
Journal Article From Pesticides to Per-and Polyfluoroalkyl Substances:An Evaluation of Recent Targeted and Untargeted Mass Spectrometry Methods for Xenobiotics. ANALYTICAL CHEMISTRY Dodds JN, Alexander NL, Kirkwood KI, Foster MR, Hopkins ZR, Knappe DR, Baker ES 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)
Journal Article Multiomic Big Data Analysis Challenges:Increasing Confidence in the Interpretation of Artificial Intelligence Assessments. None Odenkirk MT, Reif DM, Baker ES 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)
Journal Article Aggregated molecular phenotype scores:enhancing assessment and visualization of mass spectrometry imaging data for tissue-based diagnostics. ANALYTICAL CHEMISTRY Chappel JR, King ME, Fleming J, Eberlin LS, Reif DM, Baker ES 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)
Journal Article 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 Sakolish C, Moyer HL, Tsai HH, Ford LC, Dickey AN, Wright FA, Han G, Bajaj P, Baltazar MT, Carmichael PL, Stanko JP 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)
Journal Article Reproducibility and robustness of a liver microphysiological system PhysioMimix LC12 under varying culture conditions and cell type combinations. BIOENGINEERING Lim AY, Kato Y, Sakolish C, Valdiviezo A, Han G, Bajaj P, Stanko J, Ferguson SS, Villenave R, Hewitt P, Hardwick RN 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)
Journal Article Uncovering per-and polyfluoroalkyl substances (PFAS) with nontargeted ion mobility spectrometry–mass spectrometry analyses. SCIENCE ADVANCES Kirkwood-Donelson KI, Dodds JN, Schnetzer A, Hall N, Baker ES 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)
Journal Article Using multidimensional separations to distinguish isomeric amino acid–bile acid conjugates and assess their presence and perturbations in model systems. ANALYTICAL CHEMISTRY Stewart AK, Foley MH, Dougherty MK, McGill SK, Gulati AS, Gentry EC, Hagey LR, Dorrestein PC, Theriot CM, Dodds JN, Baker ES 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)
Journal Article An in vitro-in silico workflow for predicting renal clearance of PFAS. TOXICOLOGY AND APPLIED PHARMACOLOGY Lin HC, Sakolish C, Moyer HL, Carmichael PL, Baltazar MT, Ferguson SS, Stanko JP, Hewitt P, Rusyn I, Chiu WA 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)
Journal Article Endocrine-disrupting compounds and their impact on human placental function:evidence from placenta organ-on-chip studies. LAB ON A CHIP Vidal MS, Richardson LS, Kammala AK, Kim S, Lam PY, Cherukuri R, Thomas TJ, Bettayeb M, Han A, Rusyn I, Menon R 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)
Journal Article From big data to big insights:statistical and bioinformatic approaches for exploring the lipidome. ANALYTICAL AND BIOANALYTICAL CHEMISTRY Chappel JR, Kirkwood-Donelson KI, Reif DM, Baker ES 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)
Journal Article Investigating mouse hepatic lipidome dysregulation following exposure to emerging per-and polyfluoroalkyl substances (PFAS). CHEMOSPHERE Kirkwood-Donelson KI, Chappel J, Tobin E, Dodds JN, Reif DM, DeWitt JC, Baker ES 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)
Journal Article 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 Sakolish C, Moyer HL, Tsai HH, Ford LC, Dickey AN, Bajaj P, Villenave R, Hewitt P, Ferguson SS, Stanko J, Rusyn I 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)
Journal Article Editorial overview of the special issue on application of tissue chips in toxicology. TOXICOLOGY Rusyn I, Roth A Rusyn I, Roth A. Editorial overview of the special issue on application of tissue chips in toxicology. Toxicology 2021:152687-. R840032 (2021)
Journal Article Recent additions and access to a multidimensional lipidomic database containing liquid chromatography, ion mobility spectrometry, and tandem mass spectrometry information. ANALYTICAL AND BIOANALYTICAL CHEMISTRY Solosky AM, Kirkwood-Donelson KI, Odenkirk MT, Baker ES 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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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.

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