About

Yanxiang Deng, PhD, is an Assistant Professor of Pathology and Laboratory Medicine at the Perelman School of Medicine at the University of Pennsylvania. He is a core member of the Penn Epigenetics Institute and a member of the Penn Institute on Aging, with full membership at the Penn Abramson Cancer Center. His research focuses on spatial omics technologies, including spatially resolved epigenome sequencing, spatial profiling of chromatin accessibility, and multimodal spatial omics modeling. Deng's work involves developing and applying microtechnologies for single-cell and spatial multi-omics, advancing the understanding of tissue complexity and molecular interactions within tissues. He has contributed to the field through numerous publications in high-impact journals, emphasizing the integration of spatial transcriptomics, epigenomics, and proteomics to explore cellular and molecular landscapes in mammalian tissues.

Research topics

• Biology
• Computational biology
• Evolutionary biology
• Internal medicine
• Immunology
• Medicine
• Genetics

Selected publications

• Berberine-taxifolin co-administration attenuates inflammatory response and intestinal barrier injury via nf-κB/NLRP3 suppression in colitis

  Frontiers in Immunology · 2026-01-21 · 1 citations

  articleOpen access

  Inflammatory bowel disease (IBD) is pathologically characterized by dysregulated inflammation and compromised intestinal barrier integrity. While multi-component herbal formulations hold promise for IBD management, the combined potential of specific phytochemical combinations remains underexplored. This study investigates the cooperative therapeutic effects of Berberine and Taxifolin, two anti-inflammatory phytochemicals, in a murine colitis model. Multi-omics network pharmacology initially identified their shared anti-inflammatory and anti-apoptotic targets in IBD pathogenesis. Experimental validation demonstrated that combined treatment with berberine and taxifolin produced stronger protective effects against Dextran Sulfate Sodium (DSS)-induced colitis than either compound alone. Specifically, the combination significantly alleviated body weight loss and colon shortening, reduced macrophage infiltration and the expression of pro-inflammatory cytokines (IL-1β and TNF-α), and preserved intestinal barrier integrity by restoring tight junction proteins (occludin and ZO-1). In addition, the combined treatment attenuated caspase-3-mediated epithelial apoptosis. Molecular docking analysis suggested that berberine and taxifolin may interact with multiple inflammation-related targets, including NF-κB, NLRP3, PPARγ, and STAT3, providing a potential mechanistic basis for the observed effects. These findings establish Berberine-Taxifolin co-administration as a novel multi-target therapeutic strategy that concurrently addresses inflammatory dysregulation, barrier repair, and apoptosis control in IBD, and may provide a phytochemical blueprint for complex inflammatory disorders.

  PublisherDOI

• Author Correction: Resolving tissue complexity by multimodal spatial omics modeling with MISO

  Nature Methods · 2025-01-24 · 3 citations

  erratumOpen access
  PublisherOA PDFDOI

• Author Correction: Resolving tissue complexity by multimodal spatial omics modeling with MISO

  Nature Methods · 2025-03-06 · 3 citations

  erratumOpen access
  PublisherOA PDFDOI

• Synergistic Multi-Target Therapy: berberine-Taxifolin Co-Administration Attenuates Murine Inflammatory Bowel Disease via NF-κB/NLRP3 Suppression and Intestinal Barrier Restoration

  Research Square · 2025-04-15

  preprintOpen access
  PublisherOA PDFDOI

• Resolving tissue complexity by multimodal spatial omics modeling with MISO

  Nature Methods · 2025-01-15 · 52 citations

  articleOpen access
  PublisherOA PDFDOI

• Spatial profiling of chromatin accessibility in formalin-fixed paraffin-embedded tissues

  Nature Communications · 2025-07-01 · 11 citations

  articleOpen accessSenior author

  Formalin-fixed paraffin-embedded (FFPE) samples represent a vast, untapped resource for epigenomic research, yet molecular tools for deep analysis of these specimens remain limited. We introduce spatial FFPE-ATAC-seq, an approach for in situ profiling chromatin accessibility within archived tissues. This approach overcomes formalin-induced crosslinking challenges, allowing high-resolution mapping of chromatin landscapes while preserving tissue architecture. Applying spatial FFPE-ATAC-seq to mouse and human tissues, including brain and thymus, reveals intricate spatial organization and distinct cell types in alignment with tissue morphology. Integration with single-cell RNA sequencing validates the precision of our chromatin profiles in identifying key cell types and regulatory elements. We further apply this method to human melanoma, comprehensively characterizing chromatin accessibility across both tumor and non-tumor regions. This method significantly expands the toolkit for epigenomic research, unlocking the potential of an extensive collection of archived FFPE samples for studying gene regulation and disease mechanisms with spatial context. FFPE tissues are widely used to preserve clinical specimens, but formalin-induced crosslinking limits their use in epigenomic profiling. Here, the authors present spatial FFPE-ATACseq, enabling in situ chromatin accessibility mapping while preserving tissue architecture in archived samples.

  PublisherOA PDFDOI

• Spatial joint profiling of DNA methylome and transcriptome in mammalian tissues

  bioRxiv (Cold Spring Harbor Laboratory) · 2025-07-04

  preprintOpen accessSenior authorCorresponding

  The spatial resolution of omics dynamics is fundamental to understanding tissue biology. Spatial profiling of DNA methylation, which is a canonical epigenetic mark extensively implicated in transcriptional regulation, remains an unmet demand. Here, we introduce a method for whole genome spatial co-profiling of DNA methylation and transcriptome of the same tissue section at near single-cell resolution. Applying this technology to mouse embryogenesis and postnatal brain resulted in rich DNA-RNA bimodal tissue maps. These maps revealed the spatial context of known methylation biology and its interplay with gene expression. The two modalities' concordance and distinction in spatial patterns highlighted a synergistic molecular definition of cell identity in spatial programming of mammalian development and brain function. By integrating spatial maps of mouse embryos at two different developmental stages, we reconstructed the dynamics of both epigenome and transcriptome underlying mammalian embryogenesis, revealing details in sequence, cell type, and region-specific methylation-mediated transcriptional regulation. This method extends the scope of spatial omics to DNA cytosine methylation for a more comprehensive understanding of tissue biology over development and disease.

  PublisherOA PDFDOI

• KnowYourCG: Facilitating base-level sparse methylome interpretation

  Science Advances · 2025-10-24

  articleOpen access

  Decoding DNA methylomes for biological insights is critical in epigenetics research. We present KnowYourCG (KYCG), a data interpretation framework designed for functional DNA methylation analysis. Unlike existing tools that target genes or genomic intervals, KYCG features direct base-level screenings of diverse biological and technical influences, including sequence motifs, transcription factor binding, histone modifications, replication timing, cell-type-specific methylation, and trait associations. Through implementing efficient infrastructure that rapidly screens and investigates thousands of knowledgebases, KYCG addresses the challenges of data sparsity in various methylation datasets, including low-pass or single-cell DNA methylomes, 5-hydroxymethylation (5hmC) profiles, spatial DNA methylation maps, and array-based datasets for epigenome-wide association studies. Applying KYCG to these datasets provides valuable insights into cell differentiation, cancer origins, epigenome-trait associations, and technical issues such as array artifacts, single-cell batch effects, and Nanopore 5hmC detection accuracy. Our tool simplifies large-scale methylation analysis and integrates seamlessly with standard assay technologies.

  PublisherDOI

• Gastric schwannoma with post-surgical gastroparesis: a case report and literature review

  Frontiers in Oncology · 2025-01-13 · 2 citations

  articleOpen access

  Gastric schwannoma is a relatively rare submucosal mesenchymal tumor with low probability of metastasis and arises from Schwann cells of the gastrointestinal nervous plexus. Surgical therapy is the main treatment of gastric schwannoma with symptoms or malignant tendency. Gastroparesis is a potential complication following gastrointestinal surgery, which is a clinical syndrome caused by gastric emptying disorder and characterized by nausea, vomiting, and bloating, resulting in insufficient nutrient intake. Generally, post-surgical etiology is the main potential etiology of gastroparesis, while the most common underlying etiology is diabetes mellitus. So far, reports of gastroparesis arising from resection of gastric schwannoma are rare. We present an 80-year-old woman who was diagnosed with gastrointestinal stromal tumor (GIST) primarily and has undergone laparoscopic wedge-shaped gastrectomy. The pathological and immunohistochemical examination ultimately established the diagnosis of gastric schwannoma. The patient experienced belching, nausea, vomiting, and bloating 1 week after the surgery and confirmed as gastroparesis through gastrointestinal series and gastroscopic examination. A series of treatments were performed, including correcting fluid-electrolyte disorders and vitamin deficiencies, and nutritional support and pharmacological treatments. The patient ultimately recovered well, and the relevant literatures were reviewed to identify and handle similar cases hereafter.

  PublisherOA PDFDOI

• Multiplexed spatial mapping of chromatin features, transcriptome and proteins in tissues

  Nature Methods · 2025-01-27 · 40 citations

  articleOpen accessSenior authorCorresponding
  PublisherOA PDFDOI

Frequent coauthors

• Rong Fan

  90 shared

• Yang Liu

  51 shared

• Graham Su

  Yale University

  47 shared

• Archibald Enninful

  Yale University

  34 shared

• Stephanie Halene

  Yale University

  26 shared

• Zhiliang Bai

  24 shared

• Xiaoyu Qin

  22 shared

• Di Zhang

  Yale University

  19 shared

Education

• PhD, Department of Mechanical, Aerospace and Nuclear Engineering

  Rensselaer Polytechnic Institute

  2018