Radiomics — Publications

Deep Learning Enables Large-Scale Shape and Appearance Modeling in Total-Body DXA Imaging

Bunnell A, Cataldi D, Glaser Y, Wolfgruber T, Heymsfield SB, Zonderman AB, Kelly TL, Sadowski P, Shepherd J

Lecture notes in computer science, , 262-276 (2025)

Prediction of mammographic breast density based on clinical breast ultrasound images using deep learning: a retrospective analysis

Bunnell A, Valdez D, Wolfgruber T, Quon BK, Hung K, Hernandez BY, Seto TB, Killeen J, Miyoshi M, Sadowski P, Shepherd J

The Lancet Regional Health - Americas, 46, 101096 (2025)

3D Convolutional Deep Learning for Nonlinear Estimation of Body Composition from Whole-Body Morphology

Tian IY, Liu J, Wong MC, Kelly NN, Liu Y, Garber AK, Heymsfield SB, Curless B, Shepherd J

Research Square, , (2024)

Learning a Clinically-Relevant Concept Bottleneck for Lesion Detection in Breast Ultrasound

Bunnell A, Glaser Y, Valdez D, Wolfgruber T, Altamirano A, González CZ, Hernandez BY, Sadowski P, Shepherd J

Lecture notes in computer science, , 650-659 (2024)

Supplementary Figure 2 from Using Digital Pathology to Understand Epithelial Characteristics of Benign Breast Disease among Women Undergoing Diagnostic Image-Guided Breast Biopsy

Mullooly M, Puvanesarajah S, Fan S, Pfeiffer RM, Olsson LT, Hada M, Kirk EL, Vacek PM, Weaver DL, Shepherd J, Mahmoudzadeh AP, Wang J, Malkov S, Johnson JM, Hewitt SM, Herschorn SD, Sherman ME, Troester MA, Gierach GL

Supplementary Figure and Table Legends from Using Digital Pathology to Understand Epithelial Characteristics of Benign Breast Disease among Women Undergoing Diagnostic Image-Guided Breast Biopsy

Mullooly M, Puvanesarajah S, Fan S, Pfeiffer RM, Olsson LT, Hada M, Kirk EL, Vacek PM, Weaver DL, Shepherd J, Mahmoudzadeh AP, Wang J, Malkov S, Johnson JM, Hewitt SM, Herschorn SD, Sherman ME, Troester MA, Gierach GL

Supplementary Table 1 from Using Digital Pathology to Understand Epithelial Characteristics of Benign Breast Disease among Women Undergoing Diagnostic Image-Guided Breast Biopsy

Mullooly M, Puvanesarajah S, Fan S, Pfeiffer RM, Olsson LT, Hada M, Kirk EL, Vacek PM, Weaver DL, Shepherd J, Mahmoudzadeh AP, Wang J, Malkov S, Johnson JM, Hewitt SM, Herschorn SD, Sherman ME, Troester MA, Gierach GL

Supplementary Table 2B from Using Digital Pathology to Understand Epithelial Characteristics of Benign Breast Disease among Women Undergoing Diagnostic Image-Guided Breast Biopsy

Mullooly M, Puvanesarajah S, Fan S, Pfeiffer RM, Olsson LT, Hada M, Kirk EL, Vacek PM, Weaver DL, Shepherd J, Mahmoudzadeh AP, Wang J, Malkov S, Johnson JM, Hewitt SM, Herschorn SD, Sherman ME, Troester MA, Gierach GL

Supplementary Table 4 from Using Digital Pathology to Understand Epithelial Characteristics of Benign Breast Disease among Women Undergoing Diagnostic Image-Guided Breast Biopsy

Mullooly M, Puvanesarajah S, Fan S, Pfeiffer RM, Olsson LT, Hada M, Kirk EL, Vacek PM, Weaver DL, Shepherd J, Mahmoudzadeh AP, Wang J, Malkov S, Johnson JM, Hewitt SM, Herschorn SD, Sherman ME, Troester MA, Gierach GL

Supplementary Table 2A from Using Digital Pathology to Understand Epithelial Characteristics of Benign Breast Disease among Women Undergoing Diagnostic Image-Guided Breast Biopsy

Mullooly M, Puvanesarajah S, Fan S, Pfeiffer RM, Olsson LT, Hada M, Kirk EL, Vacek PM, Weaver DL, Shepherd J, Mahmoudzadeh AP, Wang J, Malkov S, Johnson JM, Hewitt SM, Herschorn SD, Sherman ME, Troester MA, Gierach GL

Supplementary Figure 1 from Using Digital Pathology to Understand Epithelial Characteristics of Benign Breast Disease among Women Undergoing Diagnostic Image-Guided Breast Biopsy

Mullooly M, Puvanesarajah S, Fan S, Pfeiffer RM, Olsson LT, Hada M, Kirk EL, Vacek PM, Weaver DL, Shepherd J, Mahmoudzadeh AP, Wang J, Malkov S, Johnson JM, Hewitt SM, Herschorn SD, Sherman ME, Troester MA, Gierach GL

Supplementary Table 3 from Using Digital Pathology to Understand Epithelial Characteristics of Benign Breast Disease among Women Undergoing Diagnostic Image-Guided Breast Biopsy

Mullooly M, Puvanesarajah S, Fan S, Pfeiffer RM, Olsson LT, Hada M, Kirk EL, Vacek PM, Weaver DL, Shepherd J, Mahmoudzadeh AP, Wang J, Malkov S, Johnson JM, Hewitt SM, Herschorn SD, Sherman ME, Troester MA, Gierach GL

Data from Using Digital Pathology to Understand Epithelial Characteristics of Benign Breast Disease among Women Undergoing Diagnostic Image-Guided Breast Biopsy

Mullooly M, Puvanesarajah S, Fan S, Pfeiffer RM, Olsson LT, Hada M, Kirk EL, Vacek PM, Weaver DL, Shepherd J, Mahmoudzadeh AP, Wang J, Malkov S, Johnson JM, Hewitt SM, Herschorn SD, Sherman ME, Troester MA, Gierach GL

Quantitative Imaging Principles Improves Medical Image Learning

Leong LT, Wong M, Glaser Y, Wolfgruber T, Heymsfield SB, Peter S, Shepherd J

arXiv (Cornell University), , (2022)

Dual-energy three compartment breast imaging (3CB) for novel compositional biomarkers to improve detection of malignant lesions

Leong LT, Malkov S, Drukker K, Niell BL, Sadowski P, Wolfgruber T, Greenwood H, Joe BN, Kerlikowske K, Giger ML, Shepherd J

Research Square, , (2021)

Dual-energy three-compartment breast imaging for compositional biomarkers to improve detection of malignant lesions

Leong LT, Malkov S, Drukker K, Niell BL, Sadowski P, Wolfgruber T, Greenwood H, Joe BN, Kerlikowske K, Giger ML, Shepherd J

Communications Medicine, 1, 29 (2021)

Mammographic Variation Measures, Breast Density, and Breast Cancer Risk

Heine J, Fowler E, Scott CG, Jensen MR, Shepherd J, Hruska CB, Winham SJ, Brandt KR, Wu F, Norman AD, Pankratz VS, Miglioretti DL, Kerlikowske K, Vachon CM

American Journal of Roentgenology, 217, 326-335 (2021)

Deep Learning Predicts Interval and Screening-detected Cancer from Screening Mammograms: A Case-Case-Control Study in 6369 Women

Zhu X, Wolfgruber T, Leong LT, Jensen MR, Scott CG, Winham SJ, Sadowski P, Vachon CM, Kerlikowske K, Shepherd J

Radiology, 301, 550-558 (2021)

Mammary collagen architecture and its association with mammographic density and lesion severity among women undergoing image-guided breast biopsy

Bodelón C, Mullooly M, Pfeiffer RM, Fan S, Abubakar M, Lenz PH, Vacek PM, Weaver DL, Herschorn SD, Johnson JM, Sprague BL, Hewitt SM, Shepherd J, Malkov S, Keely PJ, Eliceiri KW, Sherman ME, Conklin MW, Gierach GL

Breast Cancer Research, 23, 105 (2021)

Abstract NG15: Investigation of relationships between breast cancer risk factors and bilateral mammographic breast density asymmetry among women undergoing diagnostic image-guided breast biopsies

Mullooly M, Fan S, Pfeiffer RM, Sprague BL, Vacek PM, Weaver DL, Shepherd J, Mahmoudzadeh AP, Wang J, Malkov S, Johnson JM, Herschorn SD, Gierach GL

Cancer Research, 80, NG15 (2020)

Three compartment breast machine learning model for improving computer-aided detection

Leong LT, Giger ML, Drukker K, Kerlikowske K, Joe BN, Greenwood H, Malkov S, Niell BL, Shepherd J

Metadata and data files supporting the related article: Application of convolutional neural networks to breast biopsies to delineate tissue correlates of mammographic breast density

Mullooly M, Bejnordi BE, Pfeiffer RM, Fan S, Palakal M, Hada M, Vacek PM, Weaver DL, Shepherd J, Fan B, Mahmoudzadeh AP, Wang J, Malkov S, Johnson JM, Herschorn SD, Sprague BL, Hewitt SM, Brinton LA, Karssemeijer N, Laak JVD, Beck AH, Sherman ME, Gierach GL

Figshare, , (2019)

Using Digital Pathology to Understand Epithelial Characteristics of Benign Breast Disease among Women Undergoing Diagnostic Image-Guided Breast Biopsy

Mullooly M, Puvanesarajah S, Fan S, Pfeiffer RM, Olsson LT, Hada M, Kirk EL, Vacek PM, Weaver DL, Shepherd J, Mahmoudzadeh AP, Wang J, Malkov S, Johnson JM, Hewitt SM, Herschorn SD, Sherman ME, Troester MA, Gierach GL

Cancer Prevention Research, 12, 861-870 (2019)

Derived mammographic masking measures based on simulated lesions predict the risk of interval cancer after controlling for known risk factors: a case‐case analysis

Hinton B, Ma L, Mahmoudzadeh AP, Malkov S, Fan B, Greenwood H, Joe BN, Lee V, Strand F, Kerlikowske K, Shepherd J

Medical Physics, 46, 1309-1316 (2019)

Localized mammographic density is associated with interval cancer and large breast cancer: a nested case-control study

Strand F, Azavedo E, Hellgren R, Humphreys K, Eriksson M, Shepherd J, Hall P, Czene K

Breast Cancer Research, 21, 8 (2019)

Automated volumetric breast density measures: differential change between breasts in women with and without breast cancer

Brandt KR, Scott CG, Miglioretti DL, Jensen MR, Mahmoudzadeh AP, Hruska CB, Ma L, Wu F, Cummings SR, Norman AD, Engmann NJ, Shepherd J, Winham SJ, Kerlikowske K, Vachon CM

Breast Cancer Research, 21, 118 (2019)

Deep learning networks find unique mammographic differences in previous negative mammograms between interval and screen-detected cancers: a case-case study

Hinton B, Ma L, Mahmoudzadeh AP, Malkov S, Fan B, Greenwood H, Joe BN, Lee V, Kerlikowske K, Shepherd J

Cancer Imaging, 19, 41 (2019)

Measurement challenge: protocol for international case–control comparison of mammographic measures that predict breast cancer risk

Dench EK, Bond‐Smith D, Darcey E, Lee G, Aung YK, Chan A, Cuzick J, Ding ZY, Evans CF, Harvey JA, Highnam R, Hsieh M, Kontos D, Li S, Mariapun S, Nickson C, Nguyen TL, Pertuz S, Procopio P, Rajaram N, Repich K, Tan M, Teo S, Trinh NH, Ursin G, Wang C, dos‐Santos‐Silva I, McCormack V, Nielsen M, Shepherd J, Hopper JL, Stone J

BMJ Open, 9, e031041 (2019)

Application of convolutional neural networks to breast biopsies to delineate tissue correlates of mammographic breast density

Mullooly M, Bejnordi BE, Pfeiffer RM, Fan S, Palakal M, Hada M, Vacek PM, Weaver DL, Shepherd J, Fan B, Mahmoudzadeh AP, Wang J, Malkov S, Johnson JM, Herschorn SD, Sprague BL, Hewitt SM, Brinton LA, Karssemeijer N, Laak JVD, Beck AH, Sherman ME, Gierach GL

npj Breast Cancer, 5, 43 (2019)

Abstract 3260: Utilizing digital pathology to understand breast epithelial characteristics of benign breast disease among women undergoing diagnostic image-guided breast biopsy

Mullooly M, Puvanesarajah S, Fan S, Pfeiffer RM, Olsson LT, Hada M, Kirk EL, Vacek PM, Weaver DL, Shepherd J, Mahmoudzadeh AP, Wang J, Hewitt SM, Herschorn SD, Sherman ME, Troester MA, Gierach GL

Cancer Research, 78, 3260 (2018)

Combined Benefit of Quantitative Three-Compartment Breast Image Analysis and Mammography Radiomics in the Classification of Breast Masses in a Clinical Data Set

Drukker K, Giger ML, Joe BN, Kerlikowske K, Greenwood H, Drukteinis JS, Niell BL, Fan B, Malkov S, Avila J, Kazemi L, Shepherd J

Radiology, 290, 621-628 (2018)

Shape and Texture Modeling of Hip Bone Density for Fracture Discrimination.

Shepherd J, Mahmoudzadeh AP, Fan B, Chaplin LA, Cootes T, Cauley JA, Cawthon PM, Cummings S, Liu F, Lindner C, Murphy RA, Visser M, Schwartz AV

Research Explorer (The University of Manchester), , (2017)

Abstract 4235: Application of convolutional neural networks to breast biopsies to uncover tissue correlates of mammographic breast density

Mullooly M, Bejnordi BE, Palakal M, Vacek PM, Weaver DL, Shepherd J, Fan B, Mahmoudzadeh AP, Wang J, Johnson JM, Herschorn SD, Sprague BL, Pfeiffer RM, Brinton LA, Sherman ME, Beck A, Gierach GL

Cancer Research, 77, 4235 (2017)

Deep learning and three-compartment breast imaging in breast cancer diagnosis

Drukker K, Huynh BQ, Giger ML, Malkov S, Avila J, Fan B, Joe BN, Kerlikowske K, Drukteinis JS, Kazemi L, Pereira M, Shepherd J

Proceedings of SPIE, the International Society for Optical Engineering/Proceedings of SPIE, 10134, 101341F (2017)

Modeling the shape and composition of the human body using dual energy X-ray absorptiometry images

Shepherd J, Ng BK, Fan B, Schwartz AV, Cawthon PM, Cummings SR, Kritchevsky SB, Nevitt M, Santanasto AJ, Cootes T

PLoS ONE, 12, e0175857 (2017)

Erratum to: Mammographic texture and risk of breast cancer by tumor type and estrogen receptor status

Malkov S, Shepherd J, Scott CG, Tamimi RM, Ma L, Bertrand KA, Couch FJ, Jensen MR, Mahmoudzadeh AP, Fan B, Norman AD, Brandt KR, Pankratz VS, Vachon CM, Kerlikowske K

Breast Cancer Research, 19, 1 (2017)

Identification, segmentation, and characterization of microcalcifications on mammography

Drukker K, Malkov S, Avila J, Kerlikowske K, Joe BN, Krings G, Creasman JM, Drukteinis JS, Pereira M, Kazemi L, Shepherd J, Giger ML

Proceedings of SPIE, the International Society for Optical Engineering/Proceedings of SPIE, 9785, 97850S (2016)

Do Women with Low Breast Density Have Regionally High Breast Density?

Mahmoudzadeh AP, Malkov S, Hinton B, Sprague BL, Kerlikowske K, Shepherd J

Lecture notes in computer science, , 548-553 (2016)

A Measure of Regional Mammographic Masking Based on the CDMAM Phantom

Hinton B, Malkov S, Avila J, Fan B, Joe BN, Kerlikowske K, Ma L, Mahmoudzadeh AP, Shepherd J

Lecture notes in computer science, , 525-531 (2016)

Calibration Procedure of Three Component Mammographic Breast Imaging

Malkov S, Avila J, Fan B, Joe BN, Kerlikowske K, Giger ML, Drukker K, Drukteinis JS, Kazemi L, Pereira M, Shepherd J

Lecture notes in computer science, , 211-218 (2016)

Novel mammographic image features differentiate between interval and screen-detected breast cancer: a case-case study

Strand F, Humphreys K, Cheddad A, Törnberg S, Azavedo E, Shepherd J, Hall P, Czene K

Breast Cancer Research, 18, 100 (2016)

Relationships between mammographic density, tissue microvessel density, and breast biopsy diagnosis

Felix AS, Lenz PH, Pfeiffer RM, Hewitt SM, Morris J, Patel DA, Geller BM, Vacek PM, Weaver DL, Chicoine RE, Shepherd J, Mahmoudzadeh AP, Wang J, Fan B, Malkov S, Herschorn SD, Johnson JM, Cora R, Brinton LA, Sherman ME, Gierach GL

Breast Cancer Research, 18, 88 (2016)

Mammographic texture and risk of breast cancer by tumor type and estrogen receptor status

Malkov S, Shepherd J, Scott CG, Tamimi RM, Ma L, Bertrand KA, Couch FJ, Jensen MR, Mahmoudzadeh AP, Fan B, Norman AD, Brandt KR, Pankratz VS, Vachon CM, Kerlikowske K

Breast Cancer Research, 18, 122 (2016)

Hip Fractures Risk in Older Men and Women Associated With DXA-Derived Measures of Thigh Subcutaneous Fat Thickness, Cross-Sectional Muscle Area, and Muscle Density

Malkov S, Cawthon PM, Peters K, Cauley JA, Murphy RA, Visser M, Wilson J, Harris T, Satterfield S, Cummings S, Shepherd J, Study FTHA

Journal of Bone and Mineral Research, 30, 1414-1421 (2015)

Clinical Use of Quantitative Computed Tomography–Based Advanced Techniques in the Management of Osteoporosis in Adults: the 2015 ISCD Official Positions—Part III

Engelke K, Lang T, Khosla S, Qin L, Zysset PK, Leslie WD, Shepherd J, Shousboe JT

Journal of Clinical Densitometry, 18, 393-407 (2015)

Clinical Use of Quantitative Computed Tomography (QCT) of the Hip in the Management of Osteoporosis in Adults: the 2015 ISCD Official Positions—Part I

Engelke K, Lang T, Khosla S, Qin L, Zysset PK, Leslie WD, Shepherd J, Schousboe JT

Journal of Clinical Densitometry, 18, 338-358 (2015)

Clinical Use of Quantitative Computed Tomography–Based Finite Element Analysis of the Hip and Spine in the Management of Osteoporosis in Adults: the 2015 ISCD Official Positions—Part II

Zysset PK, Qin L, Lang T, Khosla S, Leslie WD, Shepherd J, Schousboe JT, Engelke K

Journal of Clinical Densitometry, 18, 359-392 (2015)

Statistical appearance modeling of whole-body bone shape and density

Ng BK, Marquino L, Tai V, Sheets C, Mulligan K, Cootes T, Shepherd J

Journal of Orthopaedic Translation, 2, 246-247 (2014)

Roles of biologic breast tissue composition and quantitative image analysis of mammographic images in breast tumor characterization

Drukker K, Giger ML, Duewer F, Malkov S, Flowers CI, Joe BN, Kerlikowske K, Drukteinis JS, Shepherd J

Proceedings of SPIE, the International Society for Optical Engineering/Proceedings of SPIE, 9035, 90351U (2014)

Compositional Three-Component Breast Imaging of Fibroadenoma and Invasive Cancer Lesions: Pilot Study

Malkov S, Duewer F, Kerlikowske K, Drukker K, Giger ML, Shepherd J

Lecture notes in computer science, , 109-114 (2014)

Automated volumetric breast density derived by shape and appearance modeling

Malkov S, Kerlikowske K, Shepherd J

Proceedings of SPIE, the International Society for Optical Engineering/Proceedings of SPIE, 9034, 90342T (2014)

Mammographic quantitative image analysis and biologic image composition for breast lesion characterization and classification

Drukker K, Duewer F, Giger ML, Malkov S, Flowers CI, Joe BN, Kerlikowske K, Drukteinis JS, Li H, Shepherd J

Medical Physics, 41, 031915 (2014)

DXA-based Model for Advanced Analysis of Body Shape Variation

Wilson J, Shepherd J

Journal of Clinical Densitometry, 16, 262 (2013)

Improvements and Performance of Diagnostic Compositional Imaging Using a Novel Dual-Energy X-ray Technique

Duewer F, Flowers CI, Kerlikowske K, Malkov S, Joe BN, Shepherd J

Lecture notes in computer science, , 569-574 (2012)

Toward Semantically Meaningful Feature Spaces for Efficient Indexing in Large Image Databases

Ngu AHH, Shen J, Shepherd J

IGI Global eBooks, , (2011)

Single x‐ray absorptiometry method for the quantitative mammographic measure of fibroglandular tissue volume

Malkov S, Wang J, Kerlikowske K, Cummings SR, Shepherd J

Medical Physics, 36, 5525-5536 (2009)

Magnetic resonance imaging for secondary assessment of breast density in a high-risk cohort

Klifa C, Carballido‐Gamio J, Wilmes LJ, Laprie A, Shepherd J, Gibbs J, Fan B, Noworolski SM, Hylton NM

Magnetic Resonance Imaging, 28, 8-15 (2009)

Dual-Energy and Low-kVp CT in the Abdomen

Yeh BM, Shepherd J, Wang ZJ, Teh HS, Hartman RP, Prevrhal S

American Journal of Roentgenology, 193, 47-54 (2009)

Computer-Assisted Technique to Delineate Osteolytic Lesions Around the Femoral Component in Total Hip Arthroplasty

Prevrhal S, Klifa C, Shepherd J, Ries MD, Genant HK

The Journal of Arthroplasty, 23, 833-838 (2008)

Improvements to Single Energy Absorptiometry Method for Digital Mammography to Quantify Breast Tissue Density

Malkov S, Wang J, Shepherd J

Lecture notes in computer science, , 1-8 (2008)

Comparison of DXA Hip Structural Analysis with Volumetric QCT

Prevrhal S, Shepherd J, Faulkner KG, Gaither KW, Black DM, Lang T

Journal of Clinical Densitometry, 11, 232-236 (2008)

Quantification of breast tissue index from MR data using fuzzy clustering

Klifa C, Carballido‐Gamio J, Wilmes LJ, Laprie A, Lobo C, DeMicco E, Watkins MW, Shepherd J, Gibbs J, Hylton NM

Measurement of Breast Density with Dual X-ray Absorptiometry: Feasibility

Shepherd J, Kerlikowske K, Smith‐Bindman R, Genant HK, Cummings S

Radiology, 223, 554-557 (2002)