Richard D Beger

Summary

Affiliation: Food and Drug Administration
Country: USA

Publications

  1. ncbi request reprint Cambridge Healthtech Institute's 7th Annual, identifying and validating metabolic markers for drug development and clinical studies
    Richard D Beger
    National Center for Toxicological Research, Jefferson, AR 72079, USA
    Expert Rev Mol Diagn 7:113-5. 2007
  2. ncbi request reprint Computational modeling of biologically active molecules using NMR spectra
    Richard D Beger
    Division of Systems Toxicology, National Center for Toxicological Research, Food and Drug Administration, Jefferson, AR 72079, USA
    Drug Discov Today 11:429-35. 2006
  3. doi request reprint Metabolomics approaches for discovering biomarkers of drug-induced hepatotoxicity and nephrotoxicity
    Richard D Beger
    Division of Systems Toxicology, National Center for Toxicological Research, Food and Drug Administration, Jefferson, AR 72079 9502, USA
    Toxicol Appl Pharmacol 243:154-66. 2010
  4. doi request reprint Metabonomics of acute kidney injury in children after cardiac surgery
    Richard D Beger
    Division of Systems Toxicology, United States Food and Drug Administration, National Center for Toxicological Research, Jefferson, AR 72079, USA
    Pediatr Nephrol 23:977-84. 2008
  5. doi request reprint Evaluations of the trans-sulfuration pathway in multiple liver toxicity studies
    Laura K Schnackenberg
    Division of Systems Toxicology, National Center for Toxicological Research, Food and Drug Administration, FDA, Jefferson, AR 72079, USA
    Toxicol Appl Pharmacol 235:25-32. 2009
  6. ncbi request reprint Modeling and assaying dioxin-like biological effects for both dioxin-like and certain non-dioxin-like compounds
    Jon G Wilkes
    Division of Systems Toxicology, Department of Biostatistics, University of Arkansas for Medical Sciences, Little Rock 72205 7199, USA
    Toxicol Sci 102:187-95. 2008
  7. ncbi request reprint Studies of acetaminophen and metabolites in urine and their correlations with toxicity using metabolomics
    Jinchun Sun
    Division of Systems Toxicology, National Center for Toxicological Research, Food and Drug Administration, Jefferson, AR 72079, USA
    Drug Metab Lett 3:130-6. 2009
  8. ncbi request reprint Predicting toxic equivalence factors from 13C nuclear magnetic resonance spectra for dioxins, furans, and polychlorinated biphenyls using linear and nonlinear pattern recognition methods
    Dan A Buzatu
    Division of Chemistry, National Center for Toxicological Research, U S Food and Drug Administration, Jefferson, Arkansas 72079, USA
    Environ Toxicol Chem 23:24-31. 2004
  9. doi request reprint Metabonomics evaluation of urine from rats given acute and chronic doses of acetaminophen using NMR and UPLC/MS
    Jinchun Sun
    Division of Systems Toxicology, National Center for Toxicological Research, Food and Drug Administration, Jefferson, AR 72079, USA
    J Chromatogr B Analyt Technol Biomed Life Sci 871:328-40. 2008
  10. ncbi request reprint Combining NMR spectral and structural data to form models of polychlorinated dibenzodioxins, dibenzofurans, and biphenyls binding to the AhR
    Richard D Beger
    Division of Chemistry, National Center for Toxicological Research, Food and Drug Administration, Jefferson, AR 72079, USA
    J Comput Aided Mol Des 16:727-40. 2002

Collaborators

Detail Information

Publications37

  1. ncbi request reprint Cambridge Healthtech Institute's 7th Annual, identifying and validating metabolic markers for drug development and clinical studies
    Richard D Beger
    National Center for Toxicological Research, Jefferson, AR 72079, USA
    Expert Rev Mol Diagn 7:113-5. 2007
  2. ncbi request reprint Computational modeling of biologically active molecules using NMR spectra
    Richard D Beger
    Division of Systems Toxicology, National Center for Toxicological Research, Food and Drug Administration, Jefferson, AR 72079, USA
    Drug Discov Today 11:429-35. 2006
    ..3D-QSDAR modeling could be useful for estimating chemical toxicity, risk assessment of environmental contaminants and drug lead-compound identifications...
  3. doi request reprint Metabolomics approaches for discovering biomarkers of drug-induced hepatotoxicity and nephrotoxicity
    Richard D Beger
    Division of Systems Toxicology, National Center for Toxicological Research, Food and Drug Administration, Jefferson, AR 72079 9502, USA
    Toxicol Appl Pharmacol 243:154-66. 2010
    ..Analytical platforms for metabolomics, chemometrics for mining metabolomics data and the applications of the metabolomics technologies are covered in detail with emphasis on recent work in the field...
  4. doi request reprint Metabonomics of acute kidney injury in children after cardiac surgery
    Richard D Beger
    Division of Systems Toxicology, United States Food and Drug Administration, National Center for Toxicological Research, Jefferson, AR 72079, USA
    Pediatr Nephrol 23:977-84. 2008
    ..90 and specificity was 0.95 for a cut-off value of 24 ng/microl for HVA-SO4 at 12 h after surgery. We concluded that urinary HVA-SO4 represents a novel, sensitive, and predictive early biomarker of AKI after pediatric cardiac surgery...
  5. doi request reprint Evaluations of the trans-sulfuration pathway in multiple liver toxicity studies
    Laura K Schnackenberg
    Division of Systems Toxicology, National Center for Toxicological Research, Food and Drug Administration, FDA, Jefferson, AR 72079, USA
    Toxicol Appl Pharmacol 235:25-32. 2009
    ..The metabolic and transcriptomic results show that the trans-sulfuration pathway from SAMe to glutathione was disturbed due to the administration of heptatotoxicants...
  6. ncbi request reprint Modeling and assaying dioxin-like biological effects for both dioxin-like and certain non-dioxin-like compounds
    Jon G Wilkes
    Division of Systems Toxicology, Department of Biostatistics, University of Arkansas for Medical Sciences, Little Rock 72205 7199, USA
    Toxicol Sci 102:187-95. 2008
    ..It suggested that in silico and in vitro nomination protocols may facilitate practical risk assessment when chemical family members exhibit different degrees of toxicity operating via a common mechanism...
  7. ncbi request reprint Studies of acetaminophen and metabolites in urine and their correlations with toxicity using metabolomics
    Jinchun Sun
    Division of Systems Toxicology, National Center for Toxicological Research, Food and Drug Administration, Jefferson, AR 72079, USA
    Drug Metab Lett 3:130-6. 2009
    ..The potential toxicity of a drug can be assessed through the study of the drug's metabolite profiles...
  8. ncbi request reprint Predicting toxic equivalence factors from 13C nuclear magnetic resonance spectra for dioxins, furans, and polychlorinated biphenyls using linear and nonlinear pattern recognition methods
    Dan A Buzatu
    Division of Chemistry, National Center for Toxicological Research, U S Food and Drug Administration, Jefferson, Arkansas 72079, USA
    Environ Toxicol Chem 23:24-31. 2004
    ..The QSDAR models provide a rapid, simple way to model the toxicity of dioxin and dioxin-like compounds...
  9. doi request reprint Metabonomics evaluation of urine from rats given acute and chronic doses of acetaminophen using NMR and UPLC/MS
    Jinchun Sun
    Division of Systems Toxicology, National Center for Toxicological Research, Food and Drug Administration, Jefferson, AR 72079, USA
    J Chromatogr B Analyt Technol Biomed Life Sci 871:328-40. 2008
    ..Similar patterns of metabolic changes in response to acute or chronic dosing suggest similar detoxification and recovery mechanisms following APAP administration...
  10. ncbi request reprint Combining NMR spectral and structural data to form models of polychlorinated dibenzodioxins, dibenzofurans, and biphenyls binding to the AhR
    Richard D Beger
    Division of Chemistry, National Center for Toxicological Research, Food and Drug Administration, Jefferson, AR 72079, USA
    J Comput Aided Mol Des 16:727-40. 2002
    ..80. Another CoSCoSA model for all 52 compounds had an r2 of 0.85 and an average q(2)2 of 0.52. Major benefits of CoSCoSA modeling include ease of development since the technique does not use molecular docking routines...
  11. ncbi request reprint Comparative structural connectivity spectra analysis (CoSCoSA) models of steroid binding to the corticosteroid binding globulin
    Richard D Beger
    Division of Chemistry, National Center for Toxicological Research, Food and Drug Administration, Jefferson, Arkansas 72079 9502, USA
    J Chem Inf Comput Sci 42:1123-31. 2002
    ....
  12. ncbi request reprint Models of steroid binding based on the minimum deviation of structurally assigned 13C NMR spectra analysis (MiDSASA)
    Richard D Beger
    Division of Chemistry, National Center for Toxicological Research, Food and Drug Administration, Jefferson, Arkansas 72079 9502, USA
    J Chem Inf Comput Sci 44:1489-96. 2004
    ..88. A MiDSASA template model for 50 steroids binding the aromatse enzyme based on the average activity of the four nearest compounds had a correlation of 0.71...
  13. pmc Metabonomics evaluations of age-related changes in the urinary compositions of male Sprague Dawley rats and effects of data normalization methods on statistical and quantitative analysis
    Laura K Schnackenberg
    National Center for Toxicological Research NCTR, Jefferson, AR 72079, USA
    BMC Bioinformatics 8:S3. 2007
    ..Additionally, the effects of age on the metabolic profiles were examined by both NMR and UPLC/MS analyses...
  14. doi request reprint Study of valproic acid-induced endogenous and exogenous metabolite alterations using LC-MS-based metabolomics
    Jinchun Sun
    Division of Systems Toxicology, National Center for Toxicological Research, US FDA, Jefferson, AR, USA
    Bioanalysis 2:207-16. 2010
    ..An LC-MS-based metabolomics approach was undertaken in order to detect urinary VPA metabolites and to discover early biomarkers of the adverse effects induced by VPA...
  15. ncbi request reprint Age-related differences in susceptibility to toxic effects of valproic acid in rats
    Parvaneh Espandiari
    FDA, Center for Drug Evaluation and Research, Silver Spring, MD 20993, USA
    J Appl Toxicol 28:628-37. 2008
    ..In conclusion, this study showed that the vulnerability profile of each age group was different indicating that a multi-age pediatric animal model is appropriate to assess more completely age-dependent changes in drug toxicity...
  16. ncbi request reprint In vitro cytotoxicity of nonpolar constituents from different parts of kava plant (Piper methysticum)
    Jin Woo Jhoo
    National Center for Toxicological Research, U S Food and Drug Administration, HFT 230, 3900 NCTR Road, Jefferson, Arkansas 72079, USA
    J Agric Food Chem 54:3157-62. 2006
    ..The identity of the compound was confirmed by (1)H and (13) C NMR and MS techniques...
  17. doi request reprint Metabolomics evaluation of hydroxyproline as a potential marker of melamine and cyanuric acid nephrotoxicity in male and female Fischer F344 rats
    Laura K Schnackenberg
    Division of Systems Biology, National Center for Toxicological Research, US FDA, Jefferson Laboratories, Jefferson, AR 72079, USA
    Food Chem Toxicol 50:3978-83. 2012
    ..Hydroxyproline may be a noninvasive urinary biomarker for detection of acute kidney injury potentially associated with kidney fibrosis...
  18. pmc Serum metabolomic profiles from patients with acute kidney injury: a pilot study
    Jinchun Sun
    Division of Systems Biology, National Center for Toxicological Research, US FDA, Jefferson, AR 72079, USA
    J Chromatogr B Analyt Technol Biomed Life Sci 893:107-13. 2012
    ..The results of this pilot study demonstrate the utility of metabolomics in the discovery of novel serum biomarkers that can facilitate the diagnosis and determine prognosis of AKI in hospitalized patients...
  19. doi request reprint (13)C NMR-Distance Matrix Descriptors: Optimal Abstract 3D Space Granularity for Predicting Estrogen Binding
    Svetoslav H Slavov
    Division of Systems Biology, National Center for Toxicological Research, U S Food and Drug Administration, 3900 NCTR Rd, Jefferson, Arkansas 72079, United States
    J Chem Inf Model 52:1854-64. 2012
    ..The highest ranked bins from partial least-squares weights were found to be associated with structural features known to be essential for binding to the estrogen receptor. ..
  20. doi request reprint Metabolomics techniques in nanotoxicology studies
    Laura K Schnackenberg
    Division of Systems Biology, National Center for Toxicological Research, US Food and Drug Administration, Jefferson, AR, USA
    Methods Mol Biol 926:141-56. 2012
    ..Furthermore, metabolomics can provide mechanistic insight into nanotoxicity. This chapter focuses on the application of both LC/MS and NMR-based metabolomics approaches to study the potential toxicity of nanoparticles...
  21. doi request reprint Assessment of usnic acid toxicity in rat primary hepatocytes using ¹³C isotopomer distribution analysis of lactate, glutamate and glucose
    Bakary J Sonko
    Division of Systems Biology, National Center for Toxicological Research, US FDA, Jefferson, AR 72079, USA
    Food Chem Toxicol 49:2968-74. 2011
    ..Augmented oxidative phosphorylation at the lower UA concentrations may be an adaptive response by the cells to compensate for diminished mitochondrial function...
  22. ncbi request reprint An integrated study of acute effects of valproic acid in the liver using metabonomics, proteomics, and transcriptomics platforms
    Laura K Schnackenberg
    Division of Systems Toxicology, National Center for Toxicological Research, Food and Drug Administration, Jefferson, Arkansas, 72079, USA
    OMICS 10:1-14. 2006
    ..The combined studies indicated a perturbation in the glycogenolysis pathway following administration of VPA...
  23. doi request reprint Improving proton MR spectroscopy of brain tissue for noninvasive diagnostics
    Pierre Alusta
    Division of Systems Biology, National Center for Toxicological Research, US FDA, Jefferson, Arkansas 72079, USA
    J Magn Reson Imaging 32:818-29. 2010
    ..To examine preprocessing methods affecting the potential use of Magnetic Resonance Spectroscopy (MRS) as a noninvasive modality for detection and characterization of brain lesions and for directing therapy progress...
  24. ncbi request reprint Whole-molecule calculation of log p based on molar volume, hydrogen bonds, and simulated 13C NMR spectra
    Laura K Schnackenberg
    Division of Systems Toxicology, National Center for Toxicological Research, Food and Drug Administration, Jefferson, Arkansas 72079, USA
    J Chem Inf Model 45:360-5. 2005
    ..88. The average r2 for 10 training models of Log P made from 90% of the data was 0.87+/-0.01. The average q2 for 10 leave-10%-out cross-validation test sets was 0.87+/-0.05...
  25. ncbi request reprint The use of carbon thirteen nuclear magnetic resonance spectra to predict dioxin and furan binding affinities to the aryl hydrocarbon receptor
    Lindsay Shade
    Division of Chemistry, National Center for Toxicological Research, U S Food and Drug Administration, Jefferson, Arkansas 72079, USA
    Environ Toxicol Chem 22:501-9. 2003
    ..The SDAR models provide a rapid, simple, and valid way to model the PCDF and PCDD binding activity in relation to the AhR...
  26. pmc The utility of a rodent model in detecting pediatric drug-induced nephrotoxicity
    Parvaneh Espandiari
    Center for Drug Evaluation and Research, Silver Spring, Maryland 20993, USA
    Toxicol Sci 99:637-48. 2007
    ....
  27. ncbi request reprint Monitoring the health to disease continuum with global metabolic profiling and systems biology
    Laura K Schnackenberg
    Division of Systems Toxicology, National Center for Toxicological Research, Food and Drug Administration, Jefferson, AR 72079 9502, USA
    Pharmacogenomics 7:1077-86. 2006
    ..Metabolomics and nutrition will lay the groundwork for the application of personalized medicine in the 21st century...
  28. ncbi request reprint Comparative structural connectivity spectra analysis (CoSCoSA) models of steroids binding to the aromatase enzyme
    Richard D Beger
    Division of Chemistry, National Center for Toxicological Research, Food and Drug Administration, Jefferson, AR 72079, USA
    J Mol Recognit 15:154-62. 2002
    ....
  29. doi request reprint Evaluating effects of penicillin treatment on the metabolome of rats
    Jinchun Sun
    Division of Systems Biology, National Center for Toxicological Research, US FDA, Jefferson, AR 72079, USA
    J Chromatogr B Analyt Technol Biomed Life Sci 932:134-43. 2013
    ..In all, these results clearly show that metabolic profiling is a useful tool to better understand the effects of the antibiotic penicillin has on the gut microbiota and the host. ..
  30. ncbi request reprint In vitro metabolism of hyperforin in rat liver microsomal systems
    Yanyan Cui
    National Center for Toxicological Research, Food and Drug Administration, 3900 NCTR Road, Jefferson, AR 72079, USA
    Drug Metab Dispos 32:28-34. 2004
    ....
  31. doi request reprint Identification of metabolite profiles of the catechol-O-methyl transferase inhibitor tolcapone in rat urine using LC/MS-based metabonomics analysis
    Jinchun Sun
    Division of Systems Toxicology, National Center for Toxicological Research, FDA, Jefferson, AR 72079, USA
    J Chromatogr B Analyt Technol Biomed Life Sci 877:2557-65. 2009
    ....
  32. ncbi request reprint The role of metabolic biomarkers in drug toxicity studies
    Laura K Schnackenberg
    Division of Systems Toxicology, National Center for Toxicological Research, Food and Drug Administration, Jefferson, AR, 72079 9502
    Toxicol Mech Methods 18:301-11. 2008
    ..This review focuses on the advantages of metabolic profiling for drug toxicity studies...
  33. ncbi request reprint Metabolic activation of the tumorigenic pyrrolizidine alkaloid, monocrotaline, leading to DNA adduct formation in vivo
    Yu Ping Wang
    Division of Biochemical Toxicology, National Center for Toxicological Research, 3900 NCTR Road, Jefferson, AR 72079, USA
    Cancer Lett 226:27-35. 2005
    ....
  34. pmc Metabolomics as an extension of proteomic analysis: study of acute kidney injury
    Didier Portilla
    Department of Nephrology, University of Arkansas for Medical Sciences, Little Rock, AR 72205, USA
    Semin Nephrol 27:609-20. 2007
    ..These studies serve to illustrate that metabolomic studies add insight into pathophysiology not provided by proteomic analysis alone...
  35. ncbi request reprint Gene expression profiles in fathead minnow exposed to 2,4-DNT: correlation with toxicity in mammals
    Henri Wintz
    Department of Nutritional Sciences and Toxicology, Morgan Hall and Berkeley Institute of the Environment, University of California, Berkeley, California 94720, USA
    Toxicol Sci 94:71-82. 2006
    ..We present possible modes of action of 2,4-DNT toxicity and suggest that fathead minnow cDNA microarrays can be useful to identify mechanisms of toxicity in fish and as a predictive tool for toxicity in mammals...
  36. pmc Differential gene expression in mouse liver associated with the hepatoprotective effect of clofibrate
    Jeffrey S Moffit
    University of Connecticut, Department of Pharmaceutical Sciences, Storrs, CT 06269, USA
    Toxicol Appl Pharmacol 222:169-79. 2007
    ..HPLC-ESI/MS/MS analysis of liver extracts indicates that enhanced vanin-1 gene expression results in elevated cystamine levels, which could be mechanistically associated with CFB-mediated hepatoprotection...
  37. ncbi request reprint Summary recommendations for standardization and reporting of metabolic analyses
    John C Lindon
    Biological Chemistry, Biomedical Sciences Division, Imperial College London, Sir Alexander Fleming Building, South Kensington, London SW7 2AZ, UK
    Nat Biotechnol 23:833-8. 2005