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  1. Science & Research (NCTR)

Richard Beger Ph.D.

 

Chief, Biomarkers and Alternative Models Branch — Division of Systems Biology

Richard Beger
Richard Beger, Ph.D.

(870) 543-7391
NCTRResearch@fda.hhs.gov  

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About  |  Publications  |  Lab Members


Background

Dr. Beger received his Ph.D. from Purdue University and completed postdoctoral training at Wesleyan University and Johns Hopkins University Medical School. His Ph.D. research focused on normal mode analysis of DNA under a variety of conditions. His postdoctoral appointments concentrated on using homonuclear and heteronuclear nuclear magnetic resonance (NMR) spectroscopy to solve NMR spectroscopy solution structures of zinc fingers, damaged DNA, and protein-protein complexes. During his last postdoctoral appointment he developed an in silico method to use 1H, 13C, and 15N NMR assigned chemical shifts of the protein backbone atoms to form dihedral constraints on the backbone of proteins. This method increased the accuracy of the protein structures and permitted larger proteins to be solved by NMR spectroscopic methods. Dr. Beger is currently the branch chief of the Biomarkers and Alternative Models Branch (BAMB) in the Division of Systems Biology. BAMB consists of a metabolomics team, proteomics team, alternative methods team, and chemical modeling of toxicological endpoints.

Research Interests

Dr. Beger’s current research uses cutting-edge systems biology, proteomics, and metabolomics analysis of biofluid and tissues samples from in vitro, nonclinical, and clinical studies to discover and evaluate translational biomarkers of:

  • drug-induced liver, kidney, heart or neural toxicity
  • drug or chemical addiction
  • disease status.

Dr. Beger is participating in national and international QA/QC metabolomics committees that include the creation of Metabolomics Quality Assurance and Quality Control Consortium (mQACC) and MEtabolomics standaRds Initiative in Toxicology (MERIT) to provide guidance on best practice, quality standards and the reporting of analytical and computational metabolomics methods. He initiated NCTR and FDA research in tissue imaging with the purchase of a MALDI TOF mass spectrometry to image:

  • drugs
  • drug metabolites
  • endogenous metabolites (i.e. neurotransmitters, cholesterol, lipids)
  • chemicals

Tissue imaging can be directly compared to histopathology and other imaging techniques to identify biomarkers and mechanisms in tissue. Dr. Beger is also the primary inventor of spectroscopic data activity relationship (SDAR) as well as three-dimensional SDAR modeling that has been used to model estrogen receptor binding, phospholipidosis, hERG inhibition, and other toxicological endpoints.

Professional Societies/National and International Groups

Metabolomics Society
Member
2004 - Present

Society of Toxicology
Member
2004 - Present

South Central Chapter of the Society of Toxicology
Member
2014 - Present

COnsortium of METabolomics Studies (COMETS)
Member
2016 - Present

MEtabolomics standaRds Initiative in Toxicology (MERIT)
Member
2017 - 2018

Metabolomics Quality Assurance and Quality Control Consortium (mQACC)
Member
2018 - Present

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Select Publications

Aptamer-Based Proteomics Identifies Mortality-Associated Serum Biomarkers in Dialysis-Dependent Acute Kidney Injury Patients.disclaimer icon
Yu L.R., Sun J., Daniels J.R., Cao Z., Schnackenberg L., Choudhury D., Palevsky P.M., Ma J.Z., Beger R.D., and Portilla D.
Kidney International Reports. 2018, doi.org/10.1016/j.ekir.2018.04.012.

Computational Identification of Structural Factors Affecting the Mutagenic Potential of Aromatic Amines: Study Design and Experimental Validation.disclaimer icon
Slavov S.H., Stoyanova-Slavova I., Mattes W., Beger R.D., and Brüschweiler B.J.
Arch Toxicol. 2018, doi.org/10.1007/s00204-018-2216-x.

Immune Response Proteins as Predictive Biomarkers of Doxorubicin-Induced Cardiotoxicity in Breast Cancer Patients.disclaimer icon
Yu L.R., Cao Z., Makhoul I., Daniels J.R., Klimberg S., Wei J.Y., Bai J.B.F., Li J., Lathrop J.T., Beger R.D., and Todorova V.K.
Experimental Biology and Medicine. 2018, 243(3): 248-255.doi.org/10.1177/1535370217746383.

Why Are Most PLD Active Chemicals Also hERG Active?disclaimer icon
Slavov S., Stoyanova-Slavova I., Li S., Shahane S., Huang R., Xia M., and Beger R.D.
Arch Toxicol. 2017, 91(12), 3885-3895. doi: 10.1007/s00204-017-1995-9.

Metabolomics Enables Precision Medicine - "A White Paper, Community Perspective."
Beger R.D., Dunn W., Schmidt M.A., Gross S.S., Kirwan J.A., Cascante M., Brennan L., Wishart D.S., Oresic M., Hankemeier T., Broadhurst D.I., Lane A.N., Suhre K., Kastenmüller G., Thiele I., Sumner S.J., and Kaddurah-Daouk R.
Metabolomics. 2016, 12:149.

Early Metabolomics Changes in Heart and Plasma During Chronic Doxorubicin Treatment in B6C3F1 Mice.
Schnackenberg L.K., Pence L., Vijay V., Moland C.L., Cao Z., Yu L.R., Fuscoe J.C., Beger R.D., and Desai V.G.
J Appl Toxicol. 2016, 36(11):1486-95. doi: 10.1002/jat.3307.

Rigorous 3D-SDAR Modeling Strategy for ToxCast Estrogen Receptor Data Classification, Validation, and Feature Extraction.
Slavov S. and Beger R.D.
Environ Toxicol Chem. 2016.

Translational Biomarkers of Acetaminophen-Induced Acute Liver Injury.
Beger R.D., Bhattacharyya S., Yang X., Gill P.S., Schnackenberg L.K., Sun J., and James L.P.
Arch Toxicol. 2015, 89(9):1497-522.

Potential of Extracellular MicroRNAs as Biomarkers of Acetaminophen Toxicity in Children.
Yang X., Salminen W., Shi Q., Greenhaw J., Gill P., Bhattacharyya S., Beger R., Mendrick D.L., Mattes W.B., and James L.P.
Toxicol Appl Pharmacol. 2015, 284(2):180-7.

Comparison of Bile Acids and Acetaminophen Protein Adducts in Children and Adolescents with Acetaminophen Toxicity.
James L.P., Yan K., Pence L., Simpson P.M., Bhattacharyya S., Gill P., Letzig L., Kearns G.L., and Beger R.D.
PLoS One. 2015, 10(7): e0131010.

Computational Identification of a Phospholipidosis Toxicophore Using 13C and 15N NMR-Distance Based Fingerprints.disclaimer icon
Slavov S., Wilkes J., Buzatu D., Kruhlak N., Willard J., Hanig J., and Beger R.D.
Bioorg. Med. Chem. 22 (2014) 6706–6714.

Targeted Liquid Chromatography-Mass Spectrometry Analysis of Serum Acylcarnitines in Acetaminophen Toxicity in Children.
Bhattacharyya S., Yan K., Pence L., Simpson P.M., Gill P., Letzig L.G., Beger R.D., Sullivan J.E., Kearns G.L., Reed M.D., Marshall J.D., Van Den Anker J.N., and James L.P.
Biomark Med. 2014, 8(2):147-59. doi: 10.2217/bmm.13.150.

A Review of Applications of Metabolomics in Cancer.disclaimer icon
Beger R.D.
Metabolites. 2013, 3(3), 552-574.

Modeling Chemical Interaction Profiles: I. Spectral Data-Activity Relationship and Structure-Activity Relationship Models for Inhibitors and Non-inhibitors of Cytochrome P450 CYP 3A4 and CYP2D6 Isozymes.
McPhail B., Tie Y., Hong H., Pearce B.A., Schnackenberg L.K., Ge W., Valerio Jr L.G., Fuscoe J.C., Tong W., Buzatu D.A., Wilkes J.G., Fowler B.A., Demchuk E., and Beger R.D.
Molecules. 2012, 17(3):3383-406.

Proposed Minimum Reporting Standards for Chemical Analysis Chemical Analysis Working Group (CAWG) Metabolomics Standards Initiative (MSI).
Sumner L.W., Amberg A., Barrett D., Beger R., Beale M.H., Daykin C., Fan T.W.M., Fiehn O., Goodacre R., Griffin J.L., Hardy N., Hiagashi R., Kopka J., Lindon J.C., Lane A.N., Marriott P., Nicholls A.W., Reily M.D., and Viant M.
Metabolomics. 2007, 3(3):211-221.

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Lab Members

Contact information for all lab members:
(870) 543-7391
NCTRResearch@fda.hhs.gov 

Zhijun Cao, Ph.D.
Staff Fellow

Jaclyn Daniels, Ph.D.
ORISE Fellow

Amy Inselman, Ph.D.
Staff Fellow

Elizabeth (Ellen) Jones, Ph.D.
Staff Fellow,

Gwenn Merry, M.S.
Biologist

Noriko Nakamura, Ph.D.
Staff Fellow

Lisa Pence, Ph.D.
Chemist

Tom Schmitt, B.S.
Chemist

Laura Schnackenberg, Ph.D.
Research Chemist

Svetoslav Slavov, Ph.D.
Staff Fellow

Dan Sloper, M.S.
Biologist

Jinchun Sun, Ph.D.
Visiting Scientist

Li-Rong Yu, Ph.D.
Staff Fellow

 

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Contact Information
Richard Beger
(870) 543-7391
Expertise
Expertise
Approach
Domain
Technology & Discipline
Toxicology