Y. Shi

PanCanSurvPlot: A Large-scale Pan-cancer Survival Analysis Web Application

PanCanSurvPlot provides a web tool for large-scale pan-cancer survival analysis with 215 datasets, 45,000 samples, and customizable survival plots.

Genomic heterogeneity and ploidy identify patients with intrinsic resistance to PD-1 blockade in metastatic melanoma

This study identifies genomic heterogeneity and ploidy as markers of intrinsic resistance to PD-1 blockade in metastatic melanoma, with a decision tree model predicting resistance with high confidence.

A high resolution model of the grapevine leaf morphospace predicts synthetic leaves

The paper develops a high-resolution morphospace model of grapevine leaves to predict synthetic leaves and improve classification accuracy.

The Molecular Architecture of the Nuclear Basket

This study uses structural biology to reveal the architecture of the nuclear basket in yeast and mammals, showing how Mlp/Tpr proteins form its structural components.

The ZmHSF20-ZmHSF4-ZmCesA2 module regulates heat stress tolerance in maize

The paper identifies a regulatory module involving ZmHSF20, ZmHSF4, and ZmCesA2 that modulates heat stress tolerance in maize by balancing growth and defense mechanisms.

UXS1 regulates UDP-GlcA levels to support growth of UGDH-high cancer cells

The paper identifies UXS1 as a selectively essential gene in UGDH-high cancer cells, showing it regulates UDP-GlcA levels to prevent toxicity and highlights it as a therapeutic target.

Ultrasound programmable hydrogen-bonded organic frameworks for sono-chemogenetics

This paper introduces ultrasound programmable hydrogen-bonded organic frameworks (HOFs) for targeted drug release and neural circuit modulation in deep brain regions.

Inhibiting Stromal Class I HDACs Curbs Pancreatic Cancer Progression

This study shows that inhibiting stromal Class I HDACs reduces pancreatic cancer progression by targeting desmoplastic and pro-tumorigenic programs in cancer-associated fibroblasts.

ERK3 Is Involved in Regulating Cardiac Fibroblast Function

This study shows ERK3 regulates cardiac fibroblast function by affecting collagen production and motility in response to TGF-β and TAC.

SARS-CoV-2 NSP13 interacts with TEAD to suppress Hippo-YAP signaling

This study identifies SARS-CoV-2 NSP13 as a suppressor of Hippo-YAP signaling by interacting with TEAD and remodeling chromatin to inhibit YAP transcriptional activity.

Fast and accurate disulfide bridge detection

This paper presents a fast and accurate method for detecting disulfide bridges in proteins using mass spectrometry with optimized sample preparation and data analysis.

Correlative single molecule lattice light sheet imaging reveals the dynamic relationship between nucleosomes and the local chromatin environment

The paper uses correlative single molecule lattice light sheet imaging to study nucleosome dynamics and chromatin environment interactions in live cells, revealing differential diffusion and packing with increasing chromatin density.

Biosynthesis- and Metabolomics-guided discovery of antimicrobial cyclopeptides against drug-resistant clinical isolates

This study discovers new Avi(Me)Cys-containing cyclopeptide antibiotics effective against drug-resistant bacteria using genome mining and metabolomics.

The expression of PKM1 and PKM2 in developing, benign, and cancerous prostatic tissues

This study examines PKM1 and PKM2 expression in mouse and human prostatic tissues across development, benign, and cancerous states, revealing distinct patterns in PCa and NEPCa.

A novel MARV glycoprotein-specific antibody with potentials of broad-spectrum neutralization to filovirus

This study identifies a novel human antibody, AF-03, that targets MARV glycoprotein and shows neutralizing activity against MARV and related filoviruses.

In-situ Single-Molecule Investigations of the Impacts of Biochemical Perturbations on Conformational Intermediates of Monomeric α-Synuclein

This study uses in-situ single-molecule techniques to identify a partially folded conformation of α-synuclein and shows its sensitivity to biochemical perturbations and drugs.

Vitamin D promotes DNase1L3 to degrade ecDNA and inhibit the malignant progression of hepatocellular carcinoma

This study shows vitamin D reduces ecDNA in hepatocellular carcinoma by stabilizing DNase1L3 via its transporter GC, leading to tumor suppression.

High-throughput generic single-entity sequencing using droplet microfluidics

This paper introduces GSE-Seq, a high-throughput platform for single-entity sequencing that enables long-read profiling of dsDNA and ssDNA from viruses and bacteria, revealing previously overlooked dark matter and phage-host interactions.

Unveiling Novel Double-Negative Prostate Cancer Subtypes Through Single-Cell RNA Sequencing Analysis

This study identifies two novel double-negative prostate cancer subtypes using scRNA-seq and develops a web tool for visualization.

The actin binding protein profilin 1 is critical for mitochondria function

This study identifies a novel role for profilin 1 in regulating mitochondria function and reveals a potential pathogenic mechanism for ALS-linked PFN1 variants.

Comparative Analysis of Molecular Pathogenic Mechanisms and Antiviral Development Targeting Old and New World Hantaviruses

This study compares molecular mechanisms and antiviral targets of Old and New World hantaviruses using human cell models and identifies potential therapeutic compounds.

ZBTB48 is a pioneer factor regulating B-cell-specific CIITA expression

This study identifies ZBTB48 as a transcription factor that regulates B-cell-specific CIITA expression by binding to its promoter and establishing open chromatin.

WBSCR16 Determines Metabolic Flexibility Via Regulating Mitochondrial 16S rRNA Maturation

This study identifies WBSCR16 as a key regulator of metabolic flexibility by controlling mitochondrial 16S rRNA maturation and switching between glucose and lipid metabolism.

Sustained store-operated calcium entry utilizing activated chromatin state leads to instability in iTregs

This study shows that sustained store-operated calcium entry (SOCE) and chromatin accessibility in iTregs lead to phenotypical instability, unlike tTregs.

Carotenoid assembly regulates quinone diffusion and the Roseiflexus castenholzii reaction center-light harvesting complex architecture

This study investigates how carotenoid assembly affects quinone diffusion and the structure of the reaction center-light harvesting complex in Roseiflexus castenholzii.

Integrated Epigenetic and Transcriptomic Profiling Reveals Dynamic Regulatory Networks Driving Retinoblastoma Pathogenesis

This study uses single-cell multi-omics to map epigenetic and transcriptomic changes in retinoblastoma, identifying key regulators and potential drug targets.

Circulating Microparticles: Optimization and Standardization of Isolation Protocols and Reassessment of Their Characteristics and Functions

This study optimizes MP isolation protocols, identifies 3000g as critical for composition, and reveals functional differences between traditional and new MPs.

Integrin beta4 promotes DNA damage drug resistance in triple-negative breast cancer via TNFAIP2/IQGAP1/Rac1

This study identifies the Integrin β4/TNFAIP2/IQGAP1/RAC1 pathway as a mechanism for DNA damage drug resistance in triple-negative breast cancer.

Simultaneous CRISPR-Cas9-induced double strand breaks are lethal in models of pancreatic cancer

This study shows CRISPR-Cas9-induced DNA double-strand breaks are more cytotoxic to pancreatic cancer cells than radiation-induced breaks, with significant tumor growth inhibition and chromosomal instability.

Comparative Phylogenomics and Phylotranscriptomics Provide Insights into the Genetic Complexity of Nitrogen Fixing Root Nodule Symbiosis

The paper uses phylogenomic and phylotranscriptomic analyses to study the evolution of nitrogen-fixing root nodule symbiosis across the Nitrogen-Fixing Nodulation Clade, finding no convergence at the amino acid level and highlighting the role of NIN as a master regulator.