University of California San Francisco
Helen Diller Family Comprehensive Cancer Center
John A. Shepherd, PhD

John A. Shepherd, PhD

Associate Adjunct Professor, Department of Radiology and Biomedical Imaging, UCSF

Cancer Center Program Memberships

Breast Oncology

Research Summary

John A. Shepherd, PhD, CCD, is a Professor in the Department of Radiology and the Director of the Breast and Bone Density Imaging Group at the University of California, San Francisco. He is an expert in quantitative breast imaging as well as musculoskeletal imaging using x-ray absorptiometry techniques. Dr. Shepherd received his BS in Engineering Physics from Texas Tech University in Lubbock, Texas, and he obtained his PhD in Engineering Physics from the University of Virginia in Charlottesville, Virginia, followed by a postdoctoral fellowship in Biophysics from Princeton University in Princeton, New Jersey.

Dr. Shepherd’s research interests involve quantitative imaging methods for tissue composition using x-rays. His mammographic methods are used extensively for research around the world and in the San Francisco Mammography Registry Program. Dr. Shepherd’s efforts are focused on the technical imaging aspects of the measurements of the body composition and the translation of these measurements into different fields of study. He has present and future research projects in the following areas: breast cancer risk and detection using breast density and tissue texture measures; dual-energy x-ray diagnostic mammography for characterizing compositional signatures of cancer lesions; total body protein measures, body shape analysis and metabolic diseases; statistics of quality assurance and quality control for quantitative measurements.

Education

Texas Tech University, Lubbock, Texas, B.S., 1988, Engineering Physics
University of Virginia, Charlottesville, Virginia, Ph.D., 1993, Engineering Physics
Princeton University, Princeton, NJ, Postdoctoral Fellow, 1993-1996, Biophysics


Professional Experience

  • 9/93 to 1/96
    Postdoctoral Research Assistant, Biophysics Group, Physics Department, Princeton University, Princeton, NJ
  • 1/96 to 1/98
    Senior Scientist, Research and Development Department, Hologic Inc., Waltham, MA
  • 1/98 to 1/99
    Principal Scientist, Research and Development Department, Hologic Inc., Waltham, MA
  • 1/98 to 1/99
    Science Support Coordinator, Research and Development Department Hologic Inc, Waltham, MA
  • 1/99 to present
    Associate Technical Director, Osteoporosis & Arthritis Research Group, Department of Radiology, UCSF, San Francisco, CA
  • 1/99 to 7/03
    Assistant Adjunct Professor, Department of Radiology, University of California San Francisco
  • 6/01 to present
    Faculty Member, Breast Oncology Program, UCSF Cancer Center
  • 10/01 to present
    Faculty Member, Bioengineering Graduate Group, UCSF and UC Berkeley
  • 7/03 to 7/10
    Assistant Professor in Residence, Department of Radiology, University of California San Francisco
  • 7/10 to present
    Associate Adjunct Professor, Department of Radiology and Biomedical Imaging, University of California San Francisco

Honors & Awards

  • 1985
    Sigma Pi Sigma - Physics Honor Society
  • 1987
    C.C. Schmidt Award for Outstanding Underclassman Physics Student, Dept. of Physics, Texas Tech University
  • 1987
    Kappa Mu Epsilon -- Mathematics Honor Society
  • 1987
    Tau Beta Pi -- Engineering Honor Society
  • 1988
    Outstanding Senior Physics Student, Dept. of Physics, Texas Tech University
  • 2000
    Best Poster Presentation (1 of 7 in Technical Category), 14th International Bone Density Workshop, Warnemunde, Germany
  • 2002
    Building Institutional Research Careers in Women's Health (BIRCWH) Scholar
  • 2002
    Co-President, 15th International Bone Density Workshop
  • 2002, 2004, 2006, 2009, 2011
    Co-chair of the Breast Densitometry Workshops
  • 2007
    ISCD John P. Bilezikian Global Leadership Award

Selected Publications

  1. Bourgeois B, Ng BK, Latimer D, Stannard CR, Romeo L, Li X, Shepherd JA, Heymsfield SB. Clinically applicable optical imaging technology for body size and shape analysis: comparison of systems differing in design. Eur J Clin Nutr. 2017 Sep 06.
    View on PubMed
  2. McCormack SE, Cousminer DL, Chesi A, Mitchell JA, Roy SM, Kalkwarf HJ, Lappe JM, Gilsanz V, Oberfield SE, Shepherd JA, Winer KK, Kelly A, Grant SFA, Zemel BS. Association Between Linear Growth and Bone Accrual in a Diverse Cohort of Children and Adolescents. JAMA Pediatr. 2017 Sep 05; 171(9):e171769.
    View on PubMed
  3. Kerlikowske K, Ma L, Scott CG, Mahmoudzadeh AP, Jensen MR, Sprague BL, Henderson LM, Pankratz VS, Cummings SR, Miglioretti DL, Vachon CM, Shepherd JA. Combining quantitative and qualitative breast density measures to assess breast cancer risk. Breast Cancer Res. 2017 Aug 22; 19(1):97.
    View on PubMed
  4. Maskarinec G, Lim U, Jacobs S, Monroe KR, Ernst T, Buchthal SD, Shepherd JA, Wilkens LR, Le Marchand L, Boushey CJ. Diet Quality in Midadulthood Predicts Visceral Adiposity and Liver Fatness in Older Ages: The Multiethnic Cohort Study. Obesity (Silver Spring). 2017 Aug; 25(8):1442-1450.
    View on PubMed
  5. Hoy JF, Grund B, Roediger M, Schwartz AV, Shepherd J, Avihingsanon A, Badal-Faesen S, de Wit S, Jacoby S, La Rosa A, Pujari S, Schechter M, White D, Engen NW, Ensrud K, Aagaard PD, Carr A. Immediate Initiation of Antiretroviral Therapy for HIV Infection Accelerates Bone Loss Relative to Deferring Therapy: Findings from the START Bone Mineral Density Substudy, a Randomized Trial. J Bone Miner Res. 2017 Sep; 32(9):1945-1955.
    View on PubMed
  6. Yaghjyan L, Tamimi RM, Bertrand KA, Scott CG, Jensen MR, Pankratz VS, Brandt K, Visscher D, Norman A, Couch F, Shepherd J, Fan B, Chen YY, Ma L, Beck AH, Cummings SR, Kerlikowske K, Vachon CM. Interaction of mammographic breast density with menopausal status and postmenopausal hormone use in relation to the risk of aggressive breast cancer subtypes. Breast Cancer Res Treat. 2017 Sep; 165(2):421-431.
    View on PubMed
  7. Shepherd JA, Ng BK, Sommer MJ, Heymsfield SB. Body composition by DXA. Bone. 2017 Nov; 104:101-105.
    View on PubMed
  8. Shepherd JA, Shepherd J. Should postmenopausal women eat more protein? Or do the elite just exercise and eat better? Menopause. 2017 May; 24(5):480-481.
    View on PubMed
  9. Shepherd JA, Ng BK, Fan B, Schwartz AV, Cawthon P, Cummings SR, Kritchevsky S, Nevitt M, Santanasto A, Cootes TF. Modeling the shape and composition of the human body using dual energy X-ray absorptiometry images. PLoS One. 2017; 12(4):e0175857.
    View on PubMed
  10. Gaskins AJ, Pereira A, Quintiliano D, Shepherd JA, Uauy R, Corvalán C, Michels KB. Dairy intake in relation to breast and pubertal development in Chilean girls. Am J Clin Nutr. 2017 May; 105(5):1166-1175.
    View on PubMed
  11. Hinton BJ, Fan B, Ng BK, Shepherd JA. Dual energy X-ray absorptiometry body composition reference values of limbs and trunk from NHANES 1999-2004 with additional visualization methods. PLoS One. 2017; 12(3):e0174180.
    View on PubMed
  12. Looker AC, Sarafrazi Isfahani N, Fan B, Shepherd JA. Trends in osteoporosis and low bone mass in older US adults, 2005-2006 through 2013-2014. Osteoporos Int. 2017 Jun; 28(6):1979-1988.
    View on PubMed
  13. Chesi A, Mitchell JA, Kalkwarf HJ, Bradfield JP, Lappe JM, Cousminer DL, Roy SM, McCormack SE, Gilsanz V, Oberfield SE, Hakonarson H, Shepherd JA, Kelly A, Zemel BS, Grant SF. A Genomewide Association Study Identifies Two Sex-Specific Loci, at SPTB and IZUMO3, Influencing Pediatric Bone Mineral Density at Multiple Skeletal Sites. J Bone Miner Res. 2017 Jun; 32(6):1274-1281.
    View on PubMed
  14. Looker AC, Sarafrazi Isfahani N, Fan B, Shepherd JA. FRAX-based Estimates of 10-year Probability of Hip and Major Osteoporotic Fracture Among Adults Aged 40 and Over: United States, 2013 and 2014. Natl Health Stat Report. 2017 Mar; (103):1-16.
    View on PubMed
  15. Cosman F, Krege JH, Looker AC, Schousboe JT, Fan B, Sarafrazi Isfahani N, Shepherd JA, Krohn KD, Steiger P, Wilson KE, Genant HK. Spine fracture prevalence in a nationally representative sample of US women and men aged =40 years: results from the National Health and Nutrition Examination Survey (NHANES) 2013-2014. Osteoporos Int. 2017 Jun; 28(6):1857-1866.
    View on PubMed
  16. Lewiecki EM, Bilezikian JP, Bukata SV, Camacho P, Clarke BL, McClung MR, Miller PD, Shepherd J. Proceedings of the 2016 Santa Fe Bone Symposium: New Concepts in the Management of Osteoporosis and Metabolic Bone Diseases. J Clin Densitom. 2017 Apr - Jun; 20(2):134-152.
    View on PubMed
  17. Engmann NJ, Scott CG, Jensen MR, Ma L, Brandt KR, Mahmoudzadeh AP, Malkov S, Whaley DH, Hruska CB, Wu FF, Winham SJ, Miglioretti DL, Norman AD, Heine JJ, Shepherd J, Pankratz VS, Vachon CM, Kerlikowske K. Longitudinal Changes in Volumetric Breast Density with Tamoxifen and Aromatase Inhibitors. Cancer Epidemiol Biomarkers Prev. 2017 Jun; 26(6):930-937.
    View on PubMed
  18. Pereira A, Garmendia ML, Uauy R, Neira P, Lopez-Arana S, Malkov S, Shepherd J. Determinants of volumetric breast density in Chilean premenopausal women. Breast Cancer Res Treat. 2017 Apr; 162(2):343-352.
    View on PubMed
  19. Malkov S, Shepherd JA, Scott CG, Tamimi RM, Ma L, Bertrand KA, Couch F, Jensen MR, Mahmoudzadeh AP, Fan B, Norman A, Brandt KR, Pankratz VS, Vachon CM, Kerlikowske K. Erratum to: Mammographic texture and risk of breast cancer by tumor type and estrogen receptor status. Breast Cancer Res. 2017 01 04; 19(1):1.
    View on PubMed
  20. Malkov S, Shepherd JA, Scott CG, Tamimi RM, Ma L, Bertrand KA, Couch F, Jensen MR, Mahmoudzadeh AP, Fan B, Norman A, Brandt KR, Pankratz VS, Vachon CM, Kerlikowske K. Mammographic texture and risk of breast cancer by tumor type and estrogen receptor status. Breast Cancer Res. 2016 12 06; 18(1):122.
    View on PubMed

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