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. Rice MS, Tamimi RM, Bertrand KA, Scott CG, Jensen MR, Norman AD, Visscher DW, Chen YY, Brandt KR, Couch FJ, Shepherd JA, Fan B, Wu FF, Ma L, Collins LC, Cummings SR, Kerlikowske K, Vachon CM. Does mammographic density mediate risk factor associations with breast cancer? An analysis by tumor characteristics. Breast Cancer Res Treat. 2018 Mar 03.
    View on PubMed
  2. Mitchell JA, Chesi A, McCormack SE, Cousminer DL, Kalkwarf HJ, Lappe JM, Gilsanz V, Oberfield SE, Shepherd JA, Kelly A, Grant SFA, Zemel BS. Physical Activity and Bone Accretion: Isotemporal Modeling and Genetic Interactions. Med Sci Sports Exerc. 2018 Feb 20.
    View on PubMed
  3. Binder AM, Corvalan C, Mericq V, Pereira A, Santos JL, Horvath S, Shepherd J, Michels KB. Faster ticking rate of the epigenetic clock is associated with faster pubertal development in girls. Epigenetics. 2018; 13(1):85-94.
    View on PubMed
  4. Hong J, Hatchell KE, Bradfield JP, Andrew B, Alessandra C, Chao-Qiang L, Langefeld CD, Lu L, Lu Y, Lutsey PL, Musani SK, Nalls MA, Robinson-Cohen C, Roizen JD, Saxena R, Tucker KL, Ziegler JT, Arking DE, Bis JC, Boerwinkle E, Bottinger EP, Bowden DW, Gilsanz V, Houston DK, Kalkwarf HJ, Kelly A, Lappe JM, Liu Y, Michos ED, Oberfield SE, Palmer ND, Rotter JI, Sapkota B, Shepherd JA, Wilson JG, Basu S, de Boer IH, Divers J, Freedman BI, Grant SFA, Hakanarson H, Harris TB, Kestenbaum BR, Kritchevsky SB, Loos RJF, Norris JM, Norwood AF, Ordovas JM, Pankow JS, Psaty BM, Sanhgera DK, Wagenknecht LE, Zemel BS, Meigs J, Dupuis J, Florez JC, Wang T, Liu CT, Engelman CD, Billings LK. Trans-ethnic Evaluation Identifies Novel Low Frequency Loci Associated with 25-Hydroxyvitamin D Concentrations. J Clin Endocrinol Metab. 2018 Jan 09.
    View on PubMed
  5. Mitchell JA, Chesi A, Cousminer DL, McCormack SE, Kalkwarf HJ, Lappe JM, Gilsanz V, Oberfield SE, Shepherd JA, Kelly A, Zemel BS, Grant SF. Multidimensional Bone Density Phenotyping Reveals New Insights Into Genetic Regulation of the Pediatric Skeleton. J Bone Miner Res. 2017 Dec 14.
    View on PubMed
  6. Maskarinec G, Lim U, Jacobs S, Monroe KR, Ernst T, Buchthal SD, Shepherd JA, Wilkens LR, Le Marchand L, Boushey CJ. Erratum: Diet Quality Predicts Visceral Adiposity and Liver Fatness: The Multiethnic Cohort Study. Obesity (Silver Spring). 2018 Jan; 26(1):239.
    View on PubMed
  7. Cousminer DL, Mitchell JA, Chesi A, Roy SM, Kalkwarf HJ, Lappe JM, Gilsanz V, Oberfield SE, Shepherd JA, Kelly A, McCormack SE, Voight BF, Zemel BS, Grant SF. Genetically Determined Later Puberty Impacts Lowered Bone Mineral Density in Childhood and Adulthood. J Bone Miner Res. 2018 Mar; 33(3):430-436.
    View on PubMed
  8. Ng BK, Sommer MJ, Shepherd JA. Reversing the Relationship Between Dual-Energy X-ray Absorptiometry and the 4-Component Model With 1 Sign Flip. J Clin Densitom. 2017 Oct - Dec; 20(4):532.
    View on PubMed
  9. 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 Nov; 71(11):1329-1335.
    View on PubMed
  10. 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
  11. 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
  12. 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
  13. 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
  14. 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
  15. Shepherd JA, Ng BK, Sommer MJ, Heymsfield SB. Body composition by DXA. Bone. 2017 Nov; 104:101-105.
    View on PubMed
  16. 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
  17. 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
  18. 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
  19. 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
  20. 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

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