John A Shepherd  PhD
Researcher R5Population Sciences in the Pacific Program (Cancer Epidemiology), University of Hawai‘i Cancer Center
Work Email: email@example.comINTERNET
Dr. Shepherd has a 30-year background in quantitative imaging. Most of his academic research involves developing novel biomarkers for a variety of imaging modalities including dual-energy X-ray Absorptiometry (DXA) scan for bone density and body composition, mammography for breast density and tissue textural measures as risk factors for breast cancer, and 3-D optical whole body scanning for quantifying body shape as a risk factor for metabolic diseases. Using these modalities, he uses advanced statistical methods to extract more information from images. The methods include principal component analysis, shape and appearance modeling, deep learning, and artificial intelligence approaches. While at UCSF he accumulated over 4 million mammograms for the study of breast cancer risk from imaging and was one of the first to show that volumetric breast density measures are a stronger risk predictor than areal density measures. His active research questions include the following: • Can deep learning models for reading mammograms reduce recall rates and unnecessary biopsies for women of the Pacific region? • What is the best way to describe frailty and function using quantitative composition measures? • Can 3-D optical scans of the whole body accurately and precisely quantify body composition and other health risk factors, and improve compliance of nutrition and exercise interventions? He also holds four patents in quantitative imaging. His group has been expert consultants for the NHANES study DXA component for 20 years. He has published over 150 peer-reviewed papers, is a Fulbright Scholar, and a past president of the International Society for Clinical Densitometry.
Recent PublicationsWong, MC., Ng, BK, Kennedy, SF, Hwaung, P, Liu, EY, Kelly, NN, Pagano, IS, Garber, AK, Chow, DC, Heymsfield, SB, Shepherd, JA. (2019). Children and Adolescents’ Anthropometrics Body Composition from 3‐D Optical Surface Scans. Obesity, 27: 1738-1749. doi:10.1002/oby.22637.
- Ng BK, Sommer MJ, Wong MC, Pagano I, Nie Y, Fan B, Kennedy S, Bourgeois B, Kelly N, Liu YE, Hwaung P, Garber AK, Chow D, Vaisse C, Curless B, Heymsfield SB, Shepherd JA. (2019). Detailed 3-dimensional body shape features predict body composition, blood metabolites, and functional strength: the Shape Up! studies. The American Journal of Clinical Nutrition; Dec 1;110(6):1316-1326. doi: 10.1093/ajcn/nqz218. PubMed PMID: 31553429; PubMed Central PMCID: PMC6885475.
- Drukker K, Giger ML, Joe BN, Kerlikowske K, Greenwood H, Drukteinis JS, Niell B, Fan B, Malkov S, Avila J, Kazemi L, Shepherd J. (2019). Combined Benefit of Quantitative Three-Compartment Breast Image Analysis and Mammography Radiomics in the Classification of Breast Masses in a Clinical Data Set. Radiology; Mar;290(3):621-628. doi: 10.1148/radiol.2018180608. Epub 2018 Dec 11. PubMed PMID: 30526359; PubMed Central PMCID: PMC6394732.
- Ng BK, Liu YE, Wang W, Kelly TL, Wilson KE, Schoeller DA, Heymsfield SB, Shepherd JA. (2018). Validation of rapid 4-component body composition assessment with the use of dual-energy X-ray absorptiometry and bioelectrical impedance analysis. The American Journal of Clinical Nutrition; Oct 1;108(4):708-715. doi: 10.1093/ajcn/nqy158. PubMed PMID: 30099474.
- Shepherd JA, Sommer MJ, Fan B, Powers C, Stranix-Chibanda L, Zadzilka A, Basar M, George K, Mukwasi-Kahari C, Siberry G. Advanced Analysis Techniques Improve Infant Bone and Body Composition Measures by Dual-Energy X-Ray Absorptiometry. J Pediatr. 2017 Feb;181:248-253.e3. PMCID: PMC5274603.
- Shepherd JA, Ng BK, Sommer MJ, Heymsfield SB. Body composition by DXA. Bone. 2017 Nov;104:101–105. PMCID: PMC5659281.
- 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. PMCID: PMC5397033.
- Shepherd JA, Fan B, Lu Y, Wu XP, Wacker WK, Ergun DL, Levine MA. A multinational study to develop universal standardization of whole-body bone density and composition using GE Healthcare Lunar and Hologic DXA systems. J Bone Miner Res. 2012 Oct;27(10):2208–2216. PMID: 22623101.
- "DXA Scan Analysist and Quality Control Review for NHANES 2018-2022"
- Shepherd, PI - Funded through NHANES (National Health and Nutrition Examination Survey) 2018 – 2022
- “Shape up! Kids” J.A. Shepherd and Steven Heymsfield, Co- PIs Funded by the NIH/NIDDK 01/20/2017 – 12/31/2021
- “Optical Body Composition and Health Assessment” J.A. Shepherd and Steven Heymsfield, Co- PIs - Funded by the NIH/NIDDK 05/15/2016 – 04/30/2021
- "Deep Learning and Total Body DXA Scans (The TBDXA.I. Project)"
- Shepherd and Steve Cummings, Co-PIs - Funded by Sutter Health/California Medical Center Research Institute 2019 – 2020
- "DXA Body Composition and Bone Mineral Density Review and Analyses for HANDLS"
- Shepherd, Project Investigator - Funded through HANDLS (Healthy Aging in Neighborhoods of Diversity across the Life Span) 2019 – 2020
- "Space-Feasible Body Composition and Body Shape Analysis for Long Duration Missions (Astro3DO)"
- Shepherd and Peter Sadowski, Co-PIs - Funded by TRISH (Translational Research Institute for Space Health) 2019 – 2020
- "IMPAACT 2009 & 2010"
- Shepherd, Project Investigator; Sharon Nachman, PI - Funded through the LOC-IMPAACT Leadership Group 2006 – 2020
Current Graduate StudentsJonathan Bennett, PhD in Nutrition at the University of Hawai‘i at Mānoa (Chair) Thesis: Assessment of Hydration via Five Compartment Body Composition Methods 2019 – Present Dustin Valdez, PhD in Nutrition at the University of Hawai‘i at Mānoa (Chair) Thesis: Evaluating Portable Breast Cancer Screening Technology for Women in the Pacific 2019 – Present Michael Wong, PhD in Nutrition at the University of Hawai‘i at Mānoa (Chair) Thesis: Using 3D Optical Body Shape to Determine Various Health Indices 2018 – Present Lambert Leong, PhD in Molecular Biosciences and Bioengineering at the University of Hawai‘i at Mānoa (Chair) Thesis: Using machine learning and deep learning to reduce the burden of cancer in Hawai‘i and the Pacific 2019 – Present Devon Cataldi, PhD in Kinesiology at the University of Hawai‘i at Mānoa (Chair) Thesis: 4-Component Body Composition Models with Varying Body Fatness and Hydration: The Dakine Study 2019 – Present Past Graduate Students Michael Omori, MS in Information and Computer Sciences at the University of Hawai‘i at Mānoa (Mentor) Thesis: The Development of a Body Composition Imaging System Using 3D Depth Sensors Utilizing Machine Learning for Testing in Microgravity Simulations 2019 – 2020 Current Position: Software Engineer, Oceanit Rosa Consuelo Villegas Valle, PhD in Nutrition at the University of Sonora, Mexico (Chair) Thesis: Tejido Adiposo Visceral (TAV) en Adultos Hispanos y su Relación con Alteraciones Cardiometabólicas 2013 – 2020 Current Position: Assistant Professor, University of Sonora Shane Spencer, MS in Electrical Engineering at the University of Hawai‘i at Mānoa (Chair) Thesis: Applications of Deep Learning Techniques in the Systematic Melanoma Assessment and Risk Triaging (SMART) Pilot Study 2018 – 2020 Current Position: Data Scientist/Software Engineer, DB Engineering, Inc. Caylin Van Hook, PhD in Bioengineering at UC Berkeley/UC San Francisco (Rotation Advisor/Mentor) 2017 – 2017 Current Position: Graduate Student Michaela Piel, MS in Biomedical Imaging at UC San Francisco (Advisor/Mentor) Thesis: Prediction of DXA whole body scan data from 3D optical 2017 – 2017 Current Position: PET/CT TEchnologist, National Institute of Allergy and Infectious Disease (NIAID) Dylan Lowe, PhD in Biological and Biomedical Sciences at UC San Francisco (Advisor/Mentor) Thesis: Energy Intake From Expellant 2016 – 2017 Current Position: Graduate Student; Clinical Consultant, Key Eats Roman Camarda, PhD in Biomedical Sciences, UC San Francisco (Advisor/Mentor) Thesis: Energy Intake From Expellant 2016 – 2017 Current Position: Graduate Student, Goga Lab Cynthia Kahari, PhD in Radiography at the University of Zimbabwe, Harare, Zimbabwe (Research Mentor) 2016 – Present Current Position: PhD Student Lisa Kotowski, MS in Physics at San Francisco State University (Chair) 2014 – 2018 Current Position: Founder, Body Composition Systems, LLC Benjamin Hinton, PhD in Bioengineering at UC Berkeley/UC San Francisco (Rotation Advisor – 2014, Dissertation Mentor – 2015-2018, Chair) 2014 – 2018 Current Position: Senior Algorithm Engineer, Abbott Jesus Avila, PhD in Bioengineering at UC Berkeley/UC San Francisco (Rotation Advisor – 2014, Dissertation Mentor – 2015-2018, Chair) 2014 – 2018 Current Position: Data & Computer Vision Engineer, Genentech Bennett Ng, PhD in Bioengineering at UC Berkeley/UC San Francisco (Rotation Advisor – 2014, Dissertation Mentor – 2014-2018, Chair) 2014 – 2018 Current Position: Research Scientist, Intel Fredrik Strand, PhD in Medical Epidemiology and Biostatistics at the Karolinska Institute, Stockholm Sweden (Mentor) 2013 – 2018 Current Position: Radiologist, Karolinska Hospital Johan Kalvesten, PhD in the Department of Medical and Health Sciences, Linkoping University, Linkoping Sweden (External Opponent/Committee Member) 2015 – 2015 Current Position: Graduate Student Ronald Dendere, PhD in Bioengineering, University of Cape Town, Cape Town, South Africa (External Referee) 2014 – 2014 Current Position: Graduate Student Admire Zanga, MS at the College of Health Sciences, University of Zimbabwe, Harare Zimbabwe (External MS Thesis Advisor) 2013 – 2013 Current Position: Graduate Student Bowen Xie, BS in Bioengineering at UC Berkeley (Advisor/Mentor) 2013 – 2013 Current Position: Surgery Resident at UPMC Paul Keselman, PhD in Bioengineering at UC Berkeley/UC San Francisco (Rotation Advisor/Mentor) 2011 – 2011 Current Position: Senior Scientist, Hoglund Brain Imaging Center – KUMC Paul Johnson, PhD in Bioengineering at UC Berkeley/UC San Francisco (Rotation Advisor/Mentor) 2011 – 2011 Current Position: Senior Display Color & Vision Engineer, Apple Cynthia Mukwasi, MS at the College of Health Sciences, University of Zimbabwe, Harare, Zimbabwe (External MS Thesis Advisor) 2010 – 2015 Current Position: Graduate Student Joseph Wilson, PhD in Bioenginering at UC Berkeley/UC San Francisco (Primary Advisor/Mentor) 2010 – 2015 Current Position: Principal Consultant, American Institutes for Research