Ying Li

Phagocytic activity of perivascular cell promotes CNS injury pathology

The paper identifies perivascular cells as phagocytes that clear CNS debris and shows Axl inhibition reduces pathology and improves recovery after spinal cord injury.

The S1B-Targeting PEDV Neutralizing Antibody C62 Prematurely Activates S-trimer and Mimics Receptor Function

This study determines the structure of PEDV S1B bound by neutralizing and non-neutralizing antibodies, revealing how C62 targets a conserved epitope and influences viral entry and neutralization.

LTBP isoforms differentially encode TGF-β spatial localization and activation

The paper investigates how different LTBP isoforms regulate TGF-β spatial localization and activation through structural and functional analyses.

Integrative AI-Enabled Virtual Cell Modeling Reveals a Clinically Relevant Latent Effector State of Human CD8 T Cells Undetectable by Conventional Analyses

The paper uses AI to model CD8 T-cell responses during ICI therapy, identifying a latent effector state that conventional methods miss.

Conformational dynamics of exopolysaccharides underlie biofilm matrix mechanics in Vibrio cholerae

This study characterizes the physical properties and conformational dynamics of Vibrio cholerae exopolysaccharides to understand their role in biofilm matrix mechanics.

ME1 Programs Latent Effector Capacity and Grounds a Mathematical Model of Reversible T Cell Exhaustion

This paper identifies ME1 as a key regulator of reversible T cell exhaustion and develops a mathematical model to predict ICI responsiveness based on latent effector capacity.

Organoid modeling of tumor-associated macrophages reveals phagocytosis checkpoint blockade-induced conversion to an immunosuppressive SPP1+ phenotype

The paper uses patient-derived organoids to study TAM responses to CD47 checkpoint blockade, revealing a conversion to an immunosuppressive SPP1+ phenotype in clear cell renal cell carcinoma.

Latent Effector Capacity Governs Reversible T Cell Exhaustion: A Mathematical Model for Mechanistically Predictive AI in PD-1 Blockade

This paper develops a mathematical model to explain reversible T cell exhaustion and its response to PD-1 blockade, identifying latent epigenetic states that govern therapeutic outcomes.

Integrated single-cell and spatial multiomic analysis reveals widespread reactivation of developmental programs in diseased human hearts

The paper integrates single-cell and spatial multiomic data to show widespread reactivation of developmental programs in diseased human hearts, with insights into transcriptional factors and localized fetal reactivation.

Alternative splicing expands the functional portfolio of a plant virus to control the viral cycle

This study shows that geminivirus TYLCV uses alternative splicing to generate Rep isoforms with distinct functions in viral replication and gene regulation.

Every Cell Counts: Tomato Root Responses to Nitrogen at Single-Cell Resolution

This study uses single-cell multiomic profiling to map tomato root responses to nitrogen availability, identifying cell types, regulators, and gene networks involved in nitrogen response.

Spatial mapping of RNA turnover kinetics and regulatory landscapes of mRNA stability in the mammalian brain

The paper introduces spatial NT-seq to map RNA turnover and stability in the mouse brain, revealing spatial heterogeneity and kinetics scaling mechanisms in response to ECS.

Preparation and application of YFV-17D-derived Anterograde Trans-neuronal Viral Vectors for Neuroscience Research

The paper describes the preparation and application of anterograde trans-neuronal viral vectors derived from YFV-17D for mapping brain connectivity.

ABCG transporter gene PstABCG2 contributes to multidrug resistance in Puccinia striiformis

This study identifies PstABCG2 as a key ABC transporter mediating multidrug resistance in Puccinia striiformis, revealing its role in fungicide efflux and resistance mechanisms.

To explore the role of NABP2 in the immune microenvironment and metabolic pathway of liver cancer

This study investigates NABP2's role in HCC by analyzing its expression, immune microenvironment, and metabolic pathways, identifying potential therapeutic targets.

Oral supplementation with Nicotinamide Riboside treatment protects RGCs in DBA/2J mouse model

This study shows that oral Nicotinamide Riboside (NR) treatment protects retinal ganglion cells (RGCs) and optic nerve axons in DBA/2J mice, likely through increased retinal NAD+ levels, and also prevents iris depigmentation and delayed IOP elevation.

High-Efficiency Capture and Proteomic Analysis of Plasma-Derived Extracellular Vesicles through Affinity Purification

This paper develops a new method for isolating extracellular vesicles from plasma and identifies potential biomarkers for Parkinson's disease.

Systemic Treatment with Nicotinamide Riboside is Protective in Three Mouse Models of Retinal Degeneration

This study shows that systemic NR treatment protects against retinal degeneration in three mouse models by preserving retinal function and structure and increasing NAD+ levels.

FREQUENT GENE CONVERSION IN HUMAN EMBRYOS INDUCED BY DOUBLE STRAND BREAKS

This study shows that gene conversion and NHEJ are major DNA repair mechanisms in human embryos, with gene conversion potentially useful for gene correction but also causing extensive loss of heterozygosity.

Effect of systemic treatment with N--2-oxopiperidine-3- carboxamide (HIOC) or tauroursodeoxycholic Acid (TUDCA) on retinal ganglion cell death following optic nerve crush

This study investigates the protective effects of HIOC and TUDCA on retinal ganglion cell (RGC) death following optic nerve crush in mice, finding significant RGC survival in treated groups.

Genomic Locus Modulating IOP in the BXD RI Mouse Strains

The paper identifies a genomic locus on chromosome 8 associated with intraocular pressure (IOP) regulation in BXD RI mouse strains, with Cdh11 as the most likely candidate gene.

Genomic Loci Modulating Retinal Ganglion Cell Death Following Elevated IOP in the Mouse

This study identifies a genomic locus on Chromosome 18 associated with retinal ganglion cell loss in a mouse glaucoma model.

Genomic Locus Modulating Corneal Thickness in the Mouse Identifies POU6F2 as a Potential Risk of Developing Glaucoma

The paper identifies a genomic locus modulating corneal thickness in mice and links it to POU6F2, a potential risk factor for glaucoma.

The BXD Mouse Strains are a Model System for Studying Optic Nerve Regeneration

This study shows that genetic background affects optic nerve regeneration, with BXD strains showing significant variation in axonal regrowth.

Prevailing homozygous deletion of interferon and defensin genes in human cancers

The paper identifies widespread homozygous deletions of interferon and defensin genes in human cancers, linked to poor patient survival and altered TNF/IFNγ gene expression.

Using Cell line and Patient samples to improve Drug Response Prediction

The paper compares drug response prediction models using cell lines, patients, and integrated data, finding that integrative models outperform cell line-only models and require fewer patients.

Successful asexual lineages of the Irish potato Famine pathogen are triploid

This study shows that asexual lineages of the potato blight pathogen Phytophthora infestans are mostly triploid, linking ploidy level to reproductive mode and virulence.