About

Yi Xing, Ph.D., is a Professor of Pathology and Laboratory Medicine at the University of Pennsylvania and the Director of the Center for Computational and Genomic Medicine at the Children's Hospital of Philadelphia. He also serves as the Executive Director of the Department of Biomedical and Health Informatics at CHOP. Dr. Xing has an extensive publication record in bioinformatics, genomics, and RNA biology. His research merges the fields of computational biology, biomedical data science, RNA genomics, human genetics, precision medicine, and immuno-oncology. His laboratory is broadly interested in the computational biology and genomics of RNA processing and regulation, with applications to human genetics, precision medicine, and cancer immunotherapy. The long-term goal of his research is to elucidate alternative isoform complexity in mammalian transcriptomes and proteomes, and to understand how it is generated and its role in the regulation and function of complex genomes. Dr. Xing develops computational methods and genomic technologies for studying transcriptomic and proteomic complexity in bulk tissues and single cells, and integrates these tools to elucidate RNA regulatory networks in health and disease. His active research topics include transcriptome analysis using sequencing technologies, RNA processing and modifications, RNA regulatory networks, genetic variation in transcriptome regulation, clinical RNA-seq technologies, and multi-omic data integration for precision oncology and immunotherapy.

Research topics

• Anatomy
• Cell biology
• Computational biology
• Biology

Selected publications

• Sintering Evolution, Mechanical Performance and Heavy-Metal Environmental Safety of Coal Gasification Slag-Based Ceramsite

  Applied Sciences · 2026-04-23

  articleOpen access

  Coal gasification slag (CGS) is rich in Si-Al-Ca components and thus has potential for ceramic utilization, but associated heavy metals may pose environmental risks. In this study, CGS from Yili (Xinjiang, China) was used as the major raw material (80 wt%), with clay and waste glass as additives, to prepare ceramsite by firing green pellets (8–12 mm) at 1000–1200 °C. The phase evolution, microstructure, and heavy-metal migration were characterized, and the leaching safety was evaluated. Increasing temperature leads to progressive quartz consumption, enrichment of feldspar-type crystalline phases, and liquid-phase sintering, which together enhance densification. The apparent density and single-particle compressive strength exhibit an “increase-then-decrease” trend with temperature and reach maxima at 1150 °C, where the compressive strength is 15.38 MPa. Heavy-metal behavior is element-specific: As and Zn show stronger volatilization, whereas Mn, Ba, Ni, and Cu are largely retained in the solid phase; Cr shows intermediate, temperature-dependent volatilization. After firing at ≥1150 °C, the leached concentrations of Cr, Mn, Ni, Cu, Zn, As, and Ba under the sulfuric acid–nitric acid test (HJ/T 299-2007) are below the Class III limits of the Chinese Groundwater Quality Standard (GB/T 14848-2017). Considering phase/structure evolution, mechanical performance, and short-term heavy-metal leaching, 1150 °C is identified as the preferred firing temperature in this work.

  PublisherOA PDFDOI

• Targeted long-read RNA sequencing for rare disease diagnosis and variant interpretation

  Science Advances · 2026-04-15

  articleOpen accessSenior author

  Diagnosing rare genetic diseases remains a major challenge despite widespread clinical testing. Long-read RNA sequencing (RNA-seq) offers a powerful approach to capturing the effects of genetic variants on the transcriptome, yet challenges with sequencing coverage, cost, tissue selection, and scalability have limited its clinical adoption. To address this, we developed STRIPE (Sequencing Targeted RNAs Identifies Pathogenic Events), a targeted long-read RNA-seq-based strategy for rare disease diagnosis and variant interpretation. STRIPE enables deep sequencing of full-length transcripts for any customized disease-specific gene panel such that a wide range of clinically informative readouts, including transcript aberrations and sequence variants, can be detected at haplotype-level resolution. Applying STRIPE to 88 individuals spanning two major rare disease groups, we accurately reidentified known pathogenic variants and revealed their transcript consequences, including many unexpected ones. For 8 of 15 splice site region variants, we observed more complex RNA processing defects beyond single exon skipping or cryptic splice site activation. Notably, we find that donor splice site variants frequently activate cryptic intronic polyadenylation sites, leading to premature transcript termination. Leveraging unique strengths of long-read RNA-seq, STRIPE also resolved variants of uncertain significance and uncovered disease-causing variants in five previously undiagnosed individuals. Overall, STRIPE is a powerful, adaptable, and scalable strategy with broad potential to improve clinical variant interpretation and advance genetic diagnosis of rare diseases.

  PublisherDOI

• A Theoretical Model of a Simply Supported Circular Ring Under Impulsive Loads

  Materials · 2026-03-27

  articleOpen access1st authorCorresponding

  Metallic thin-walled circular rings are widely employed as energy-absorption components in impact protection systems. However, the dynamic deformation mechanisms under impact loads remain incompletely understood. In this study, we develop a rigid-perfectly plastic model to analyze a simply supported circular ring subjected to impulsive loads. We present a theoretical survey of the incipient deformation under step loading, establishing the relation between the applied load magnitude and the number and location of the stationary plastic hinges. Our analytical findings reveal that as load magnitude increases, the number of stationary hinges grows, with newly formed hinges progressing closer to the point of loading. We validate these theoretical predictions against finite element analyses, demonstrating the model's accuracy. Additionally, we investigate the complex deformation mechanisms involving both stationary and traveling hinges under rectangular pulse loading. This study provides fundamental insights into the dynamic plastic response of thin-walled structures, offering theoretical guidance for optimizing impact protection systems.

  PublisherOA PDFDOI

• Valorization of silicon cutting waste and high-alumina fly ash for sustainable synthesis of O′-sialon

  RSC Advances · 2026-01-01

  articleOpen accessSenior author

  Si under the present processing conditions. These results demonstrate the feasibility of up-cycling SCW and HAFA into value-added SiAlON-based ceramics, while also highlighting the need for future work on raw-material variability and scale-up.

  PublisherOA PDFDOI

• Nanoconfinement of Pd Ensembles in Ceria’s Bridging Hydroxyl Nests for Enhanced C–H Bond Activation

  Journal of the American Chemical Society · 2026-03-26 · 1 citations

  article

  values are 340 and 402 °C, lowered by 175 and 226 °C, respectively) compared to the single-atom counterpart, alongside exceptional stability and water resistance under practical conditions. This work establishes the engineering of the support's hydroxyl microenvironment as a powerful strategy for designing highly efficient metal ensemble catalysts.

  PublisherDOI

• Ripply1 and Gsc collectively suppress anterior endoderm differentiation from prechordal plate progenitors

  eLife · 2026-03-12

  articleOpen access

  During gastrulation, the mesendoderm is firstly specified by morphogens such as Nodal, and then segregates into endoderm and mesoderm in a Nodal concentration-dependent manner. However, the mechanism underlying the segregation and crosstalk of different sub-groups within the meso- and endoderm lineages remains unclear. Here, taking zebrafish prechordal plate (PP) and anterior endoderm (Endo) as research model, using single-cell multi-omics and live imaging analyses, we show that anterior Endo progenitors originate directly from PP progenitors. A single-cell transcriptomic trajectory analysis of wild-type, ndr1 knockdown and lft1 knockout Nodal explants confirms the diversification of anterior Endo fate from PP progenitors. Gene Ontology (GO) enrichment analysis identifies that the change of chromatin organization potentiates the segregation of anterior endodermal cell fate from PP progenitors. Single-cell ATAC & RNA sequencing further reveals that two transcriptional regulators, gsc and ripply1, exhibit varied activation patterns in PP and anterior Endo cell trajectories at both the chromatin and RNA expression levels. We further demonstrate that Ripply1 functions coordinately with Gsc to repress anterior endodermal cell fate by directly binding to the cis-elements of sox32. Modulating the expression levels of these regulators tilts the cell fate decision between the PP and anterior Endo.

  PublisherDOI

• Progress and Prospects of Rare Metal‐Based Electrochemiluminescence Sensors for Detection of Water Environmental Pollutants

  Rare Metals · 2026-05-01

  articleOpen access1st authorCorresponding

  ABSTRACT Water pollution is becoming increasingly severe, posing a serious hazard to human health and ecological security. Therefore, it is necessary to develop rapid, sensitive, and universal analytical methods to detect residual pollutants in actual water. Electrochemiluminescence (ECL) is a highly promising analytical technology for monitoring pollutants due to its inherent advantages, such as zero background and ultrahigh sensitivity. Rare metals (rare earth metals, precious metals, and refractory rare metals) with unique electronic structures, significant catalytic activity, stable optical properties, and perfect conductivity can significantly enhance the performance of ECL sensors by regulating luminescence efficiency, signal amplification, and specific recognition. Regarding the different functional roles of rare metals in the construction of ECL sensors, their applications are divided into signal amplification materials, ECL nanoemitters, and resonance energy transfer receptors or donors. Focusing on key pollutants (high toxicity, strong bioaccumulation potential, and wide‐ranging impacts) in aqueous environments as analytes, this review classifies rare metal‐based ECL sensors and emphasizes their recent advances. It analyzes the intrinsic pathways through which rare metals enhance ECL efficiency when employed as electrode modification materials, with particular emphasis on the structure–activity relationships between rare metal‐based materials and ECL performance, clarifying the enormous potential of rare metal‐based ECL sensors in breaking through the limitations of existing detection methods. This review also discusses the design methodologies meeting the application requirements of ECL sensors, such as diverse signal amplification strategies and innovative sensing modes in rare metal‐integrated ECL sensors. Finally, it analyzes the current problems of rare metal‐based ECL sensors in water pollutant detection and proposes potential optimization pathways for the future.

  PublisherDOI

• Nitrogen-modulated intercropping boosts yield and quality in Codonopsis pilosula

  BMC Plant Biology · 2026-04-28

  articleOpen access1st authorCorresponding

  Intensive monoculture of Codonopsis pilosula (C. pilosula) reliant on high nitrogen (N) inputs often compromises root quality and long-term sustainability. Here we show that intercropping with faba bean under optimized N application resolves this trade-off by enhancing root yield and the accumulation of active ingredients. To test this, we established a two-factor factorial design with monoculture vs. intercropping across three N rates (0, 60, 120 kg N ha⁻1). Root yield, concentrations of three key active ingredients (lobetyolin, atractylenolide III, and syringin), leaf traits, photosynthetic parameters, and the activities of key carbon and nitrogen metabolic enzyme were measured. Intercropping increased root yield by 3.2%-18.7%, active ingredient concentrations by 5.5%-56.9%, and active ingredients yield by 29.7%-47.1%. Mechanistically, these improvements were associated with key physiological changes: 1) enhanced photosynthetic capacity (larger leaves with higher photosynthetic rate) increasing total carbon assimilation; 2) upregulated C/N metabolism strengthening utilization and storage capacity of photosynthetic assimilates in root. These benefits were achieved despite a decrease in instantaneous water use efficiency, a pattern consistent with a “water-for-carbon” strategy at the leaf level. The intercropping advantage for C. pilosula was maximized at 60 kg N ha−1, while excessive N application (120 kg N ha−1) diminished these benefits and reduced active ingredient concentrations. Our findings demonstrate that faba bean intercropping under moderate N promotes both productivity and medicinal quality of C. pilosula by co-optimizing leaf physiology and C/N metabolism, providing a potential strategy for more sustainable cultivation under the conditions tested.

  PublisherDOI

• Analysis and optimized control of dead-time effects in dual active bridge converters to eliminate voltage hazards under high switching frequency

  Scientific Reports · 2026-04-30

  articleOpen access

  Dual Active Bridge (DAB) converters are more commonly deployed in renewable energy systems, electric vehicles, advanced energy storage, and distributed power grids than conventional DC-DC converters due to the advantages of electrical isolation, high power density, and zero voltage switching (ZVS) capability. Existing studies on DAB mainly focus on conduction loss, reflux power loss, current stress, and high-frequency oscillation based on ideal states, which do not thoroughly consider the dead-time effect. As switching frequencies increase, dead-time causes severe operational hazards such as voltage polarity reversal and voltage sag, potentially damaging power devices. However, existing research addressing dead-time is limited to basic control strategies. To extensively exploit the performance potential of DAB converters, this paper proposes a current stress-optimized Variable Mode Extended-Phase-Shift (VM-EPS) control scheme that explicitly considers dead-time effects. By deriving exact operational characteristics across ten non-ideal modes, the proposed scheme coordinates specific operating modes for light, medium, and heavy load scenarios. By formulating and solving the current stress optimization problem using the Karush-Kuhn-Tucker (KKT) method, optimal phase-shift and dead-time ratios for each mode is designed and eliminates dead-time-induced voltage hazards across the approximate full power range. To summarize, the optimized control achieves approximate full-range ZVS, enabling true soft-switching operation. Experimental validation confirms the effectiveness of the proposed method in eliminating voltage hazards, optimizing current stress, and enhancing the overall performance of DAB converters.

  PublisherDOI

• Biodegradable and non-biodegradable microplastics affect greenhouse gas emissions through chemical diversity and microbial biodiversity

  Journal of Hazardous Materials · 2025-09-30

  article
  PublisherDOI

Recent grants

• ProteoSeq - An Integrative Computational Framework for Proteotranscriptomics

  NIH · $1.1M · 2018–2021

• VARIATION AND REGULATION OF ALTERNATIVE SPLICING IN HUMAN TRANSCRIPTOMES

  NIH · $2.9M · 2010–2023

• NIH Grant R01ES024995

  NIH · $616k · 2017

• Computational tools and resources to study alternative splicing and mRNA isoform variation

  NIH · $569k · 2022–2024

• Targeting alternative splicing for TCR discovery in small cell carcinomas

  NIH · $4.1M · 2018–2024

Frequent coauthors

• Lan Lin

  Children's Hospital of Philadelphia

  71 shared

• Bo Jiang

  Qingdao Municipal Hospital

  65 shared

• Shihao Shen

  51 shared

• Juw Won Park

  University of Louisville

  48 shared

• Chen Hong

  41 shared

• Gang Wang

  41 shared

• Jinkai Wang

  Sun Yat-sen University

  41 shared

• Mingjie Zhou

  Huashan Hospital

  40 shared

Labs

• Xing Lab of Computational and Genomic MedicinePI

Education

• Ph.D., Molecular Biology (Bioinformatics)

  University of California Los Angeles

  2006