About

Ron C. Anafi, M.D., Ph.D., is an Associate Professor of Medicine specializing in Sleep Medicine at the Hospital of the University of Pennsylvania. He is a Faculty Scholar at the Penn Institute for Bioinformatics, a Co-Investigator at the Center for Subcellular Genomics, and a member of the Chronobiology and Sleep Institute as well as ITMAT at the University of Pennsylvania. His research focuses on understanding how sleep and molecular rhythms influence physiology in the brain and body, utilizing techniques from machine learning, engineering, and systems biology. His lab investigates the influence of sleep and circadian biology on health and disease, with particular emphasis on how molecular rhythms are disrupted in cancer and neurodegeneration. Anafi's work involves analyzing large human tissue databases to uncover rhythmic signals, aiming to fill gaps in human circadian molecular physiology and understand the impact of these rhythms on illness. His contributions include developing methods to study rhythmic gene expression and metabolism, and exploring how these processes relate to disease progression and prognosis.

Research topics

• Biology
• Computer Science
• Endocrinology
• Internal medicine
• Medicine
• Cell biology
• Oncology
• Cancer research
• Immunology
• Biochemistry
• Neuroscience

Selected publications

• O25 Compared to sun-protected skin, the circadian transcriptome in sun-exposed skin demonstrates dampened, phase-advanced rhythms with fewer cycling genes

  British Journal of Dermatology · 2026-01-01

  article

  Abstract Introduction and aims Daily molecular rhythms modulate skin physiology. However, the effects of chronic sunlight exposure on these rhythms remain unstudied. Methods Twenty women aged 50–65 years who exhibited moderate-to-severe photoageing of the dorsal forearm were recruited. Skin biopsies (3 mm) were taken from upper buttock and dorsal forearm of each individual at noon, 18.00 h, 00.00 h, and 06.00 h, across one 24-h cycle. Skin biopsies were analysed by RNA sequencing. Cosinor analysis was used to identify cycling genes along with their amplitudes and peak expression phases. Nested models identified significant differences between photoprotected and photoexposed samples. Phase set and gene set enrichment analyses identified pathways under circadian control. Results In photoprotected buttock skin 1546 (12%) genes met criteria for cycling. In photoexposed forearm skin the number was reduced to 959 (8%). Overall, 1076 transcripts cycled exclusively in the buttock and 489 exclusively in the forearm. The peak expression times for individual cycling transcripts were clustered in the early morning and mid-afternoon. Focusing on transcripts that cycled in both sites revealed that cycling in the buttock was of overall higher amplitude (P < 2.2e−16). For these transcripts, distributions of peak times were significantly different between forearm and buttock skin (P < 0.001), with peak times advanced in forearm skin. Genes involved in the unfolded protein response, DNA repair, and Myc targets were enriched among those that cycled exclusively in buttock skin. Inflammatory response and epithelial–mesenchymal transition pathway genes were enriched among those that cycled exclusively in forearm skin. Tumour necrosis factor-α signalling pathway genes and Myc targets were also enriched among genes that cycled in both skin sites. Conclusions Altered cycling patterns and a reduced number of cycling genes in photoexposed compared with photoprotected skin, suggest that chronic UV exposure may reprogram circadian output rhythms in anticipation of daily environmental stressors, which may in turn compromise the optimal functioning of other biological processes.

  PublisherDOI

• Single-cell Transcriptomic Variance Analysis Reveals Intercellular Circadian Desynchrony in the Alzheimer’s Affected Human Brain

  bioRxiv (Cold Spring Harbor Laboratory) · 2026-03-25

  articleOpen accessSenior authorCorresponding

  Abstract Bulk tissue rhythms arise from the coordination of thousands of individual cellular oscillations. Bulk rhythm amplitude differences may reflect changes in the amplitude of the underlying cellular oscillators or changes in their temporal coherence. To resolve this fundamental ambiguity, we developed ORPHEUS ( O scillatory R hythm P hase H eterogeneity E stimated U sing S tatistical-moments), an analytical method that quantifies cellular desynchrony by leveraging the unique 12hr rhythmic signature it imparts on intercellular expression variance. After validating ORPHEUS in silico and on data from the mouse suprachiasmatic nucleus (SCN), we applied it to data from the mouse liver and human brain to uncover disease- and pathway-related differences in intercellular synchrony. In both tissues, we found that circadian synchrony is higher in cells and samples with higher MTORC activity. Most critically, we observed a dramatic loss of cellular synchrony in excitatory neurons from subjects with Alzheimer’s Disease (AD) dementia. By decoupling the influence of cellular amplitude and synchrony, ORPHEUS introduces a new, interpretable tool for analyzing circadian coordination in time-course single-cell data.

  PublisherOA PDFDOI

• Sleep and circadian rhythms in cardiovascular resilience: mechanisms, implications, and a Roadmap for research and interventions

  Nature Reviews Cardiology · 2025-09-18 · 5 citations

  reviewOpen access
  PublisherOA PDFDOI

• CYCLOPS 2.0

  2025-05-01

  dissertationOpen access

  Circadian rhythms regulate the timing of thousands of genes across human tissues, aligning physiology with the 24-hour day. However, most transcriptomic datasets lack time-of-day annotations, limiting our ability to study these rhythms and their disruption in disease. We improve CYCLOPS, an unsupervised algorithm for inferring internal circadian time from gene expression data, by introducing CYCLOPS 2.0--a covariate-aware model that adjusts for batch effects and non-circadian confounders simultaneously. Benchmarking confirms its improved accuracy in recovering latent circadian structure under noisy conditions. We apply CYCLOPS 2.0 to breast cancer and GTEx datasets to reconstruct circadian transcriptional order. In breast tumors, especially luminal A, we observe persistent but reprogrammed rhythms, with enhanced cycling in EMT and immune pathways. A novel metric, CYCLOPS magnitude (CMag), quantifies global rhythm strength and correlates with reduced five-year survival. Functional assays confirm that circadian disruption reduces invasiveness, linking molecular rhythms to metastatic behavior. We identify circadian eQTLs (cQTLs)--variants that affect rhythmic parameters of gene expression--in adipose, muscle, and skin. Many cQTLs are not detected by traditional methods and colocalize with GWAS loci and circadian transcription factor motifs. These findings reveal a temporally dynamic layer of gene regulation with clinical and functional relevance.

  PublisherDOI

• Reconstructed Cell-Type Specific Rhythms in Human Brain link Alzheimer’s Pathology, Circadian Stress, and Ribosomal Disruption

  bioRxiv (Cold Spring Harbor Laboratory) · 2025-02-26 · 2 citations

  preprintOpen accessSenior authorCorresponding

  Alzheimer's disease (AD) disrupts behavioral circadian rhythms, but its effects on molecular rhythms in the human brain are poorly understood. Using single-nucleus RNA sequencing from post-mortem cortical samples, we informatically estimated the relative circadian phases of 409 persons with and without AD dementia. We then reconstructed circadian expression profiles across cell types. While core clock rhythms were preserved in AD, many cell-type specific circadian outputs were disrupted. Rhythms in ribosomal biogenesis and oxidative phosphorylation were dampened across cell types. Similar losses in ribosomal gene expression rhythms were observed in APP/PS1 mice, which showed further reductions in ribosomal protein expression and polysome-mediated translation after circadian desynchrony. Exploratory computational modeling reveals that altered translation may contribute to the increased circadian variability seen in AD patients. These findings reveal altered cell-type specific circadian output rhythms in the brains of AD affected patients, and highlight disrupted ribosomal rhythms as a feature of AD.

  PublisherOA PDFDOI

• Waning light, waxing pain: The lunar cycle's association with migraine headache occurrence

  Headache The Journal of Head and Face Pain · 2025-08-28

  articleOpen accessSenior author

  OBJECTIVE: To examine circalunar rhythms in migraine headache occurrence in a prospective cohort of 98 adults with episodic migraine. BACKGROUND: Migraine is a prevalent neurological disorder characterized by paroxysmal attacks. While time-of-day and seasonal rhythmicity in migraine occurrence have been described, little is known about circalunar patterns. Understanding these rhythms may inform headache prediction and guide personalized preventive medication timing. METHODS: We performed a secondary, post-hoc analysis using data from a prospective cohort study (March 2016-October 2017). Participants completed twice-daily electronic diaries, recording various characteristics including headache, and, when applicable, menstrual cycle timing. Participants wore wrist actigraphs for 6 weeks. We tested for a 30-day circalunar rhythm in headache risk at the population-level. We then examined for lunar synchronized rhythms in individuals, adjusting our analysis for participant-specific factors and differences in baseline headache risk. Sleep characteristics and menstrual timing were assessed as potential mediators of the relationship between lunar phase and headache occurrence. RESULTS: Ninety-eight participants were followed for a median length of 43 days (interquartile range [IQR]: 42-45 days) with an average of 24.2% (standard deviation [SD] 13.2) of those days being headache days. Population-level analysis showed a significant relationship between lunar phase and headache risk (trough-to-peak odds ratio: 1.2 [95% confidence interval {CI}: 1.04, 1.49]). Individual-level analysis, adjusted for age, sex/menopausal status, and preventative medication use, showed 1.34 (95% CI: 1.1, 1.72) times higher headache odds at lunar cycle peak versus trough. Risk peaked 1-2 days before new moon. Neither sleep characteristics nor menstrual timing appeared to mediate the lunar phase-headache relationship. CONCLUSIONS: Headache risk varied with the lunar cycle, with 34% higher odds shortly before new moon compared to before full moon. Sleep and menstrual cycle timing did not appear to explain this relationship, suggesting underlying chronobiological mechanisms. Additional studies are needed to confirm these findings and characterize individual variability in rhythmicity.

  PublisherOA PDFDOI

• Tanycyte Bmal1 sex-specifically regulates weight gain and hypothalamic neurogenesis in female mice

  bioRxiv (Cold Spring Harbor Laboratory) · 2025-04-25

  preprintOpen access

  Abstract The hypothalamic radial-glia-like tanycyte population plays important and intertwined roles in feeding and metabolism, reproduction, and seasonality. Although these processes are circadian-regulated and clock genes reportedly show robust cycling along the 3rd ventricle, the role of the clock in tanycytes has not yet been examined. We report here that clock genes cycle with much higher amplitude in ventral tanycytes compared to more dorsal ependymocytes of the 3rd ventricle, and that specific disruption of the tanycyte clock can be achieved by adult Bmal1 deletion using the RaxCreER driver. Adult tanycyte Bmal1 deletion did not affect circadian rhythms of wheel-running and sleep, but did inhibit weight gain on high-fat diet in female mice. Altered tanycyte-derived hypothalamic neurogenesis, which can regulate feeding and weight gain by contributing new neurons to nearby feeding-relevant nuclei, is one mechanism that likely contributes to this phenotype. Fate mapping studies showed that female mice have higher baseline tanycyte-derived neurogenesis than males, with many of the resulting neurons localizing to the feeding-relevant arcuate nucleus. Female but not male mice show reduced tanycyte-derived arcuate neurogenesis after adult tanycyte Bmal1 deletion and an increased percentage of newborn arcuate neurons take on a feeding-suppressing POMC neuropeptidergic fate. Thereby, skewing of feeding and satiety promoting fates link the weight homeostasis and neurogenesis effects. Together, our data establish tanycyte Bmal1 as a sexually dimorphic regulator of weight homeostasis, likely mediated at least in part by a female-specific neurogenesis effect in the feeding circuitry.

  PublisherOA PDFDOI

• Defining and detecting global transcriptional amplitude in circadian gene expression

  bioRxiv (Cold Spring Harbor Laboratory) · 2025-11-16

  preprintOpen accessSenior authorCorresponding

  Abstract Many genes exhibit circadian rhythms in expression. The amplitude of oscillation, both in core clock and circadian output genes, may differ from person to person. Mutations in core clock genes are known to alter global rhythmic properties, and researchers often informally discuss “circadian amplitude.” Yet, it remains unclear whether, in the general population, differences in transcriptional amplitude are largely gene-specific, or if they reflect a global, transcriptome-wide pattern -- whether some individuals have globally higher or lower amplitude across the set of all rhythmic genes. We used Cosinor regression to reanalyze four human skin time-series transcriptomic datasets (paired epidermis/dermis samples, N=11, N=19) and found that, using either absolute or relative amplitude measures, distributions of gene amplitudes tended to cluster by subject. Using a non-parametric, permutation-based statistical test, we found that in many subjects this global amplitude trend was statistically significant ( p ≤ 0.01). Furthermore, we found that when rhythmic genes were divided into two sets based on peak time (genes peaking before-noon and after-noon), the subjects’ global amplitude in one set predicted global amplitude in the other set ( p ≤ 0.05). We also found that in the paired epidermis/dermis datasets, subjects’ global amplitude in epidermis predicted their global amplitude in the dermis ( p ≤ 0.05). After identifying these trends in the skin datasets, we then found that evidence for subject-specific transcriptional rhythm strength replicated across 6 additional human time-course datasets from adipose, muscle, and blood. Perhaps surprisingly, across datasets, we found that neither established metrics of core clock transcriptional organization nor the amplitude of core clock transcription were strongly correlated with subject-specific global amplitude.

  PublisherDOI

• A glial circadian gene expression atlas reveals cell-type and disease-specific reprogramming in response to amyloid pathology or aging

  Nature Neuroscience · 2025-10-23 · 2 citations

  articleOpen access

  While circadian rhythm disruption may promote neurodegenerative disease, the impact of aging and neurodegenerative pathology on circadian gene expression patterns in different brain cell types remains unknown. Here we used a translating ribosome affinity purification to identify the circadian translatomes of astrocytes, microglia and bulk tissue in healthy mouse cortex and in the settings of amyloid-β plaque pathology or aging. We show that glial circadian translatomes are highly cell-type-specific and exhibit profound, context-dependent reprogramming in response to amyloid pathology or aging. Transcripts involved in glial reactivity, immunometabolism and proteostasis, as well as nearly half of all Alzheimer’s disease risk genes, displayed circadian oscillations, many of which were altered by pathology. Microglial oxidative stress and amyloid phagocytosis showed temporal variation in gene expression and function. Thus, circadian rhythms in gene expression are cell-dependent and context dependent, and provide important insights into glial function in health, Alzheimer’s disease and aging. Sheehan et al. have characterized the circadian translatomes of astrocytes and microglia in the mouse cortex in the context of amyloid pathology or aging, revealing cell- and disease-specific reprogramming of neurodegeneration-related pathways.

  PublisherOA PDFDOI

• Comparative circadian transcriptome analysis reveals dampened and phase-advanced rhythms in sun-exposed human skin

  Journal of Investigative Dermatology · 2025-10-02

  preprintOpen accessCorresponding

  Abstract Background Daily molecular rhythms modulate skin physiology. However, the effects of chronic sun exposure on these rhythms remain unstudied. Objectives This study aimed to identify and compare rhythmic genes and pathways in photoprotected and chronically photoexposed human skin in vivo . Methods Twenty healthy White women, aged 51-63, with moderate-severe photoageing of the dorsal forearm were recruited. Skin biopsies (3mm) were taken from photoprotected (upper buttock) and photoexposed (dorsal forearm) skin of each individual at noon, 6PM, midnight, and 6AM, across a 24-hour cycle. Skin biopsies were analysed by RNA sequencing. Cosinor analysis identified cycling genes along with their amplitudes and peak expression phases. Nested models were used to identify genes that were differentially rhythmic between the photoprotected and photoexposed sites. Phase set and gene set analyses identified pathways enriched among rhythmic transcripts or altered between the two sites. Results In the photoprotected buttock skin, 1546 genes (12%) met the criteria for cycling. In photoexposed forearm skin, the number was reduced to 959 (8%). As a group, transcripts that cycled in both sites had overall higher amplitude in photoprotected skin ( p < 2.2e-16). Peak expression times for these transcripts showed a pronounced bimodal distribution and were clustered in the early morning and mid-afternoon. Distributions of peak times were significantly different between photoexposed and photoprotected skin ( p < 0.00025), with peak times advanced in photoexposed skin. We identified 480 genes with significantly different rhythmic properties between the skin sites. Genes involved in DNA repair, MYC targets, E2F and G2M checkpoint pathways were enriched among those that showed higher amplitude oscillations in photoprotected skin. Genes involved in epithelial mesenchymal transition and apical junction pathways showed higher amplitude oscillations in photoexposed skin. Conclusions Temporal rhythms have a marked influence on skin molecular physiology and are altered in photoaged skin. Temporally advanced cycling patterns and a reduced number of rhythmic genes in photoexposed as compared to photoprotected skin suggest that chronic UV exposure may disrupt and/or reprogram circadian output rhythms to further alter skin physiology.

  PublisherDOI

Recent grants

• Integrated Informatic and Experimental Evaluations of Cancer Chronotherapy

  NIH · $3.0M · 2019–2025

• Circadian Organization and Disorder in Alzheimer's Disease

  NIH · $2.0M · 2020–2026

Frequent coauthors

• John B. Hogenesch

  Cincinnati Children's Hospital Medical Center

  57 shared

• Gang Wu

  Cincinnati Children's Hospital Medical Center

  26 shared

• Lauren J. Francey

  Beth Israel Deaconess Medical Center

  26 shared

• David F. Smith

  19 shared

• Brian P. Delisle

  University of Kentucky

  12 shared

• Philip Gehrman

  University of Pennsylvania

  12 shared

• Marc D. Ruben

  Cincinnati Children's Hospital Medical Center

  12 shared

• John Harer

  11 shared

Labs

• Ron C Anafi LabPI

Education

• MD/PhD

  University of Minnesota

Awards & honors

• Faculty Scholar, Penn Institute for Bioinformatics
• Member, Chronobiology and Sleep Institute
• Co-Investigator, Center for Subcellular Genomics