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.

PA28γ promotes the malignant progression of tumor by elevating mitochondrial function via C1QBP

This study identifies PA28γ's role in promoting oral squamous cell carcinoma progression by enhancing mitochondrial function through interaction with C1QBP.

Structural Dynamics of the Ubiquitin Specific Protease USP30 in Complex with a Cyanopyrrolidine-Containing Covalent Inhibitor

This study investigates the structural dynamics of USP30 inhibition by a covalent inhibitor, revealing its binding mechanism and selectivity advantages over non-covalent inhibitors.

Comprehensive Biosynthetic Analysis of Human Microbiome Reveals Diverse Protective Ribosomal Peptides

This study identifies diverse ribosomally synthesized peptides in the human microbiome and shows some inhibit pathogens and reduce inflammation.

Systematically investigating and identifying bacteriocins in the human gut microbiome

The paper introduces IIBacFinder to identify unmodified class II bacteriocins in the human gut microbiome, showing their widespread distribution and biosynthetic potential.

Dynamic Localization of Leukemia Stem Cells via CXCL12 Regulates Leukemia Progression

This study shows that the CXCL12 gradient, regulated by DPP4 and GPC3, determines leukemia stem cell (LSC) localization and behavior, influencing leukemia progression.

Microsporidian Nosema bombycis secretes serine protease inhibitor to suppress host cell apoptosis via caspase BmICE

This paper identifies NbSPN14, a serine protease inhibitor secreted by Nosema bombycis, which inhibits host cell apoptosis by interacting with BmICE, providing insights into pathogen-host interactions.

Filament structures unveil the dynamic organization of human acetyl-CoA carboxylase

The paper determines cryo-EM structures of human ACC1 in inactive and activated states, revealing structural dynamics and regulatory mechanisms.

CLCC1 Governs Bilayer Equilibration at the Endoplasmic Reticulum to Maintain Cellular and Systemic Lipid Homeostasis

This study identifies CLCC1 as a key regulator of phospholipid trans-bilayer equilibration at the ER, essential for lipid homeostasis and preventing metabolic diseases.

Two-hit mouse model of heart failure with preserved ejection fraction combining diet-induced obesity and renin-mediated hypertension

This paper develops a two-hit mouse model of HFpEF combining diet-induced obesity and renin-mediated hypertension, showing key features of the disease and response to therapy.

Targeting PRMT3 Impairs Methylation and Oligomerization of HSP60 to Boost Anti-Tumor Immunity by Activating cGAS/STING Signaling

This study identifies PRMT3 as a driver of immunotherapy resistance in HCC, showing that targeting it enhances anti-tumor immunity via cGAS/STING activation.

Maladaptation in cereal crop landraces following a soot-producing climate catastrophe

This study assesses how landraces of four cereal crops would maladapt to soot-induced climate changes following a global catastrophe using climate models and genomic data.

Cyclical transcription factor AP2XII-9 is a key activator for asexual division and apicoplast inheritance in Toxoplasma gondii tachyzoite

This study identifies TgAP2XII-9 as a critical S/M-phase transcription factor regulating endodyogeny and apicoplast inheritance in Toxoplasma gondii tachyzoites.

Structural insights into human propionyl-CoA carboxylase (PCC) and 3-methylcrotonyl-CoA carboxylase (MCC)

The paper reports high-resolution cryo-EM structures of human PCC and MCC, revealing substrate binding modes and biotin coordination mechanisms.

CCR7+ Dendritic Cells Define a Type 17 Module in Psoriasis

The paper identifies CCR7+ dendritic cells as the primary source of IL-23 in psoriasis, linking them to type 17 inflammation and relapse.

A posterior approach to correct for focal plane offsets in lattice light sheet structured illumination microscopy

This paper introduces a method to detect and correct axial offset between excitation and detection focal planes in latticeSIM to reduce image artifacts.

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.