About

Babette S. Zemel, PhD, is a Research Professor of Pediatrics at the University of Pennsylvania Perelman School of Medicine, specializing in Gastroenterology, Hepatology, and Nutrition. She is the Director of the Nutrition and Growth Laboratory at the Children's Hospital of Philadelphia and co-Director of the Clinical Grant Proposal Success program at the same institution. Her research focuses on understanding lifelong health by examining childhood antecedents of physical growth and maturation, body composition, population ancestry and genetics, and lifestyle factors including diet and physical activity. Her work has advanced knowledge of bone mineral accretion from early childhood through adulthood and the effects of growth, muscle development, diet, physical activity, and genetics on bone health. Additionally, she conducts research on childhood body composition and health outcomes in both the general population and children with chronic diseases such as Down syndrome, sickle cell disease, kidney disease, cardiac malformations, cancer survivorship, inflammatory bowel disease, and type 2 diabetes.

Research topics

• Biology
• Genetics
• Microbiology
• Biochemistry
• Chemistry
• Demography
• Bioinformatics
• Evolutionary biology
• Endocrinology

Selected publications

• Physical Activity Traits From Wrist Sensors Correlate With Clinical Status in Pediatric Pulmonary Hypertension

  Pulmonary Circulation · 2026-01-01

  articleOpen access

  ABSTRACT Physical activity (PA) estimated by a wearable sensor may reflect clinical status in pediatric pulmonary hypertension (PH). Prior studies used research‐grade hip‐anchored sensors or commercial wrist sensors with proprietary scoring algorithms. Wrist sensors may offer better acceptability in children; however, their ability to detect associations between PA and clinical characteristics is unknown. Youth 8–18 years with PH [Groups 1–4, functional class (FC) I‐II] and healthy controls wore a GENEActiv accelerometer on the non‐dominant wrist for 14 days. Raw acceleration data were processed using the open‐source GGIR R‐package. Participants completed a 6‐min walk distance (6MWD) and quality‐of‐life questionnaire. Muscle mass and strength were assessed by densitometry and handgrip dynamometry. The most recent cardiac testing was extracted from the medical record. Groups were compared by Fisher's exact test, unpaired t ‐test, or Wilcoxon rank sum test. Multivariate regression models assessed for associations between PA and clinical metrics. Thirty PH participants (median 13.9 years, 57% female, 57% Group 1, 50% FC I) and 29 controls were included. Total PA was similar. PH participants demonstrated fewer and shorter bouts of moderate‐to‐vigorous PA ≥ 10 min and more time spent at lower PA intensities. In PH participants, muscle mass was positively associated with PA but 6MWD was negatively associated with PA. PA was not associated with quality of life. Within the PH group, worse PA traits were associated with lower FC and worse clinical testing. Wrist sensors reveal deficits in PA traits including reduced moderate‐to‐vigorous activity bouts and lower intensity gradients in pediatric PH.

  PublisherDOI

• Identifying Barriers and Facilitators to Physical Activity Participation Among Adolescents With CKD: A Qualitative Study Using Semi-Structured Interviews

  Kidney Medicine · 2026-02-27

  articleOpen access

  Rationale & Objective: Physical activity enhances health and wellbeing; however, fewer than 15% of adolescents with chronic kidney disease (CKD) meet physical activity recommendations. Developing interventions to increase physical activity requires identifying CKD-specific barriers and facilitators to physical activity. Digital tools have shown potential to increase physical activity in other chronic disease populations but have not been applied to interventions for children with CKD. This study sought to identify the barriers and facilitators to physical activity experienced by adolescents with CKD and to identify how digital tools can be used to promote physical activity to this population in a relevant and acceptable way. Study Design: A qualitative study using semi-structured interviews. Setting & Participants: Twelve adolescents with CKD stages 2-5 not receiving kidney replacement therapy, and 8 of their caregivers, from a quaternary care pediatric hospital. Analytical Approach: Interviews were audio-recorded, transcribed, and evaluated using thematic analysis. Results: Adolescents' median age was 16 years (IQR range = 13.5-17) with a median CKD duration of 10.5 years (IQR:3.5-13). Social relationships were the primary domain elicited for facilitating physical activity. Fatigue and lack of time related to school obligations were the primary barriers. Adolescent and caregiver participants expressed concerns that physical activity could negatively impact kidney health, which led some adolescents to adjust or limit sports' participation. To promote physical activity, participants thought that wearing a physical activity tracker and earning financial incentives and rewards would be helpful. Limitations: Response bias, most participants lived in suburban neighborhoods, and exclusion of non-English speaking participants. Conclusions: Social engagement was a primary facilitator to physical activity, whereas fatigue and schoolwork were primary barriers. These findings reveal potential specific targets to guide the development of a digital intervention, tailored to adolescents with CKD, to promote physical activity and improve their health-related outcomes.

  PublisherDOI

• The impact of adverse childhood experiences on gut microbiota and markers of inflammation is mediated by obesity and depression

  Brain Behavior and Immunity · 2026-02-05

  articleOpen access
  PublisherOA PDFDOI

• High-resolution peripheral quantitative computed tomography reliability and accuracy of bone density and morphology properties in children

  JBMR Plus · 2025-06-14 · 2 citations

  articleOpen access

  Abstract Volumetric bone density, microarchitecture, and strength measures using HR-pQCT are valuable measures of bone health in pediatrics. Our cross-sectional study evaluated bone measure reproducibility in pediatric participants using repeat HR-pQCT (XtremeCT II, Scanco Medical) scans of non-dominant distal tibia and radius of 30 healthy children and adolescents (7-17 yr, 47% female) by 2 technicians. Additionally, we examined HR-pQCT and micro-CT of 26 cadaveric distal tibia specimens to evaluate agreement between the modalities. All HR-pQCT scans were analyzed using manufacturer-provided software (Image Processing Language, Scanco Medical) and a fully automated, previously validated, in-house algorithm, offering measures of bone microstructure (eg, trabecular plate-rod distribution, transverse trabeculae, trabecular bone strength) currently unavailable in the manufacturer-provided software. Root-mean-squared percent coefficient of variation (RMS-%CV) assessed precision and least significant change. Intraclass correlation coefficients (ICCs) using absolute-agreement, 2-way random-effects models assessed reliability. Pearson’s correlation coefficients and ICC assessed linear relationships and agreements between HR-pQCT and micro-CT, respectively. In children and adolescents, RMS-%CV of HR-pQCT-derived trabecular bone measures at distal tibia and radius ranged from 0.8-4.4 to 0.8-6.0, respectively. Most cortical bone results were in a similar range. Both computational algorithms showed ICC > 0.90. RMS-%CV and least significant change values were lower for tibia than radius. ICCs were lower for cortical than trabecular outcomes. Most cadaveric results showed ICC > 0.83, other than trabecular bone thickness and modulus (ICC = 0.7). Pearson’s r (>0.86) suggested strong correlations for almost all parameters. HR-pQCT and micro-CT results using in-house algorithm did not differ significantly, while manufacturer-provided algorithm results showed lower yet still moderate reliability (ICC > 0.55). Reliability of the second-generation HR-pQCT in pediatric participants is excellent—better in tibia vs radius. Our results support the high reproducibility of XtremeCT II scans and thus the use of this clinical imaging modality in studies of pediatric bone health.

  PublisherOA PDFDOI

• GWAS-informed data integration and non-coding CRISPRi screen illuminate genetic etiology of bone mineral density

  Genome biology · 2025-10-03

  articleOpen access

  BACKGROUND: Over 1100 independent signals have been identified with genome-wide association studies (GWAS) for bone mineral density (BMD), a key risk factor for mortality-increasing fragility fractures; however, the effector gene(s) for most remain unknown. RESULTS: We execute a CRISPRi screen in human fetal osteoblasts (hFOBs) with single-cell RNA-seq read-out for 89 non-coding elements predicted to regulate osteoblast gene expression at BMD GWAS loci. The BMD relevance of hFOBs is supported by heritability enrichment from stratified LD-score regression involving 98 cell types grouped into 15 tissues. Twenty-three genes show perturbation in the screen, with four (ARID5B, CC2D1B, EIF4G2, and NCOA3) exhibiting consistent effects upon siRNA knockdown on three measures of osteoblast maturation and mineralization. Lastly, additional heritability enrichments, genetic correlations, and multi-trait fine-mapping unexpectedly reveal that many BMD GWAS signals are pleiotropic and likely mediate their effects via non-bone tissues. CONCLUSIONS: Our results provide a roadmap for how single-cell CRISPRi screens may be applied to the challenging task of resolving effector gene identities at all BMD GWAS loci. Extending our CRISPRi screening approach to other tissues could play a key role in fully elucidating the etiology of BMD.

  PublisherOA PDFDOI

• Changes in Adolescent Diet Quality During the Middle to High School Transition

  Journal of Nutrition Education and Behavior · 2025-12-05

  articleOpen access
  PublisherOA PDFDOI

• Physical activity traits from wrist sensors correlate with clinical status in pediatric pulmonary hypertension

  medRxiv · 2025-10-28

  preprintOpen access

  Physical activity (PA) estimated by a wearable sensor may reflect clinical status in pediatric pulmonary hypertension (PH). Prior studies used research-grade hip-anchored sensors or commercial wrist sensors with proprietary scoring algorithms. Wrist sensors offer better acceptability in children, however, their ability to detect associations between PA and clinical characteristics is unknown. Youth 8-18 years with PH [Groups 1-4, functional class (FC) I-II] and healthy controls wore a GENEActiv accelerometer on the non-dominant wrist for 14 days. Raw acceleration data were processed using the open-source GGIR R-package. Participants completed a 6-minute walk distance (6MWD) and quality-of-life questionnaire. Muscle mass and strength were assessed by densitometry and handgrip dynamometry. Most recent cardiac testing was extracted from the medical record. Groups were compared by Fisher's exact test, unpaired t-test, or Wilcoxon rank sum test. Multivariate regression models assessed for associations between PA and clinical metrics. Thirty PH participants (median 13.9 years, 57% female, 57% Group 1, 50% FC I) and 29 controls were included. Total PA was similar. PH participants demonstrated fewer and shorter bouts of moderate-to-vigorous PA ≥10 minutes and more time spent at lower PA intensities. In PH participants, muscle mass was positively associated with PA but 6MWD was negatively associated with PA. PA was not associated with quality-of-life. Within the PH group, worse PA traits were associated with lower FC and worse clinical testing. Wrist sensors reveal deficits in PA traits including reduced moderate-to-vigorous activity bouts and lower intensity gradients in pediatric PH.

  PublisherOA PDFDOI

• Changes in Bone Microarchitecture and Inflammatory Cytokines After Cure of Chronic Hepatitis C Infection With Direct-Acting Antiviral Therapy

  Open Forum Infectious Diseases · 2025-08-29 · 1 citations

  articleOpen access

  Abstract Background It remains unclear if cure of hepatitis C virus (HCV) infection with direct-acting antivirals (DAAs) ameliorates HCV-related inflammation and bone deficits. We evaluated changes in cytokines and bone measurements by high-resolution peripheral quantitative computed tomography (HR-pQCT) prior to DAA treatment and 18 months following initiation and compared changes in uninfected controls over 18 months. Methods We conducted a cohort study of 40 participants who initiated DAAs and achieved cure and 48 without HCV as controls. At enrollment and 18 months later, participants had measurements of volumetric bone mineral density, cortical dimensions, and mechanical properties of the radius and tibia by HR-pQCT; visceral fat area and appendicular lean mass by whole-body dual-energy X-ray absorptiometry; and serum tumor necrosis factor alpha (TNF-α), interleukin 6 (IL-6), and interleukin 18 (IL-18). Multivariable linear regression was used to estimate group differences in mean changes in bone measurements and cytokines. Results We observed no significant differences in month 0–18 changes in HR-pQCT measurements between participants with cured HCV and controls in unadjusted models or after adjustment for age, sex, appendicular lean mass index, visceral fat area, and smoking. Participants with cured HCV had decreases in IL-18 (mean change, −0.085 vs +0.086 log pg/mL; P < .001) and TNF-α (mean change, −0.050 vs +0.084 log pg/mL; P < .001), but not IL-6 (mean change, +0.108 vs +0.009 log pg/mL; P = .214) versus controls. Conclusions Participants with cured HCV had no significant changes in bone microarchitecture by HR-pQCT 18 months after DAA initiation compared with controls, but did have decreases in IL-18 and TNF-α versus controls.

  PublisherDOI

• Arterial Stiffness and Central Hemodynamics in South Asian, African American, and White Adolescents and Young Adults—The Charisma Study

  American Journal of Hypertension · 2025-07-18 · 1 citations

  articleOpen access

  BACKGROUND: Compared to individuals of European or African ancestry, individuals of South Asian (SA) ancestry have greater cardiovascular disease (CVD) risk. We aimed to compare arterial stiffness and central hemodynamics, surrogates of CVD, in adolescents and young adults (AYA) of SA, White, and African American (AA) ancestry with overweight or obesity. METHODS: Pulse wave velocity (PWV) and pulse wave analysis (PWA metrics: Pulse Pressure Amplification [PPA]; Augmentation Index adjusted to heart rate of 75 [Aix75]) were performed in a cross-sectional study of 40 (18M/22F) SA, 45 (16M/29F) AA, and 44 (21M/24F) White AYA (age 12-21 years) of comparable age, sex, and BMI. Between-group comparisons of PWV, PPA, and AIx-75 were tested using linear regression models adjusted for covariates (BMI, mean arterial pressure, sex, age), as appropriate. RESULTS: As expected, BMI (kg/m2) did not differ (SA: 27.1, AA: 28.4, White: 27.4). Mean PWV (m/s) did not differ in SA (5.5), AA (5.1), and White (5.5). The typical relationship of BMI with PWV was absent in SA. PPA was lower in SA (1.45, P = 0.001) and AA (1.48, P = 0.014) vs. White (1.56). Aix75 was higher in SA (108, P = 0.004) but not in AA (105, P = 0.12) vs. White (101). CONCLUSIONS: Although their PWV did not differ, SA AYA had lower PPA and higher Aix75 compared to White counterparts. As lower PPA associates with higher likelihood of future CV events, these findings could reflect an early CVD predisposition in SA and underscore the potential value of pulse waveform analysis in studies of emerging adults, a life stage in which interventions may mitigate CVD risk.

  PublisherOA PDFDOI

• Clinical risk factors for body composition deficits in children with inflammatory bowel disease

  Journal of Pediatric Gastroenterology and Nutrition · 2025-05-19

  articleOpen accessSenior author

  OBJECTIVES: Children with inflammatory bowel disease (IBD) often have low body mass index (BMI). BMI does not distinguish between fat and lean mass. Body composition deficits may be associated with worse clinical outcomes. We examined the prevalence of risk factors associated with body composition deficits in youth with pediatric-onset IBD, and factors associated with low lean mass in the presence of a normal BMI Z-score (BMI-Z). METHODS: Newly diagnosed IBD patients ages 5-20 years with whole body dual energy x-ray absorptiometry scans acquired between 2014 and 2019 were included. Appendicular lean soft tissue mass index (AppLSTMI) and fat mass index (FMI) were expressed as age and sex-specific Z-scores. Clinical and demographic data were collected retrospectively. Logistic regression was used to assess associations with body composition outcomes. RESULTS: Five hundred sixteen patients were included, 26% had AppLSTMI Z-score (AppLSTMI-Z) < -2, 4% had BMI-Z < -2, and none had FMI Z-score (FMI-Z) < -2. Increased risk of low AppLSTMI-Z associated with Crohn's diagnosis, Asian ethnicity, disease activity, elevated platelets, and glucocorticoid use. Females had lower FMI-Z. Low AppLSTMI-Z within the context of BMI-Z (n = 112) was associated with Crohn's disease, Asian (odds ratio [OR] = 3.77, p = 0.001) and Black identity (OR = 0.32, p = 0.02), and elevated platelets (OR = 1.76, p = 0.02) compared to those with normal BMI-Z and normal AppLSTMI-Z. CONCLUSIONS: BMI is a poor indicator of body composition in children with IBD as it masks lean mass deficits which are highly prevalent. Future studies regarding the long-term consequences and reversibility of this deficit are warranted.

  PublisherOA PDFDOI

Recent grants

• NIH Grant M01RR000240

  NIH · $6.4M · 2006

• NIH Grant R01HD037748

  NIH · $2.2M · 2005

• Bone Health of Obese Adolescents During Weight Loss

  NIH · $3.2M · 2007–2012

• Genomics of bone and body composition traits in children

  NIH · $3.4M · 2020–2026

• Infant Growth and Microbiome Study 2

  NIH · $3.6M · 2015–2022

Frequent coauthors

• Virginia A. Stallings

  465 shared

• Mary B. Leonard

  Lucile Packard Children's Hospital

  339 shared

• Struan F.A. Grant

  208 shared

• Joan I. Schall

  University of Pennsylvania

  204 shared

• Andrea Kelly

  Children's Hospital of Philadelphia

  202 shared

• Justine Shults

  Children's Hospital of Philadelphia

  154 shared

• Heidi J. Kalkwarf

  132 shared

• John Shepherd

  131 shared

Education

• PhD

  University of Pennsylvania