Ying Zhang

Homoharringtonine targets XPC to inhibit DNA damage repair and sensitize tumors to platinum-based chemotherapy

This paper identifies homoharringtonine as a DDR inhibitor that targets XPC to impair DNA repair and enhance platinum-based chemotherapy efficacy.

Localized Chromatin Rewiring Shapes Rhythmic Transcription within a Stable 3D Genome in Rice

The paper identifies localized chromatin rewiring in rice's stable 3D genome that coordinates rhythmic transcription across the circadian cycle.

Ref(2)P/p62 protein pleomorphism confers tissue-specific function

One Drosophila Ref(2)P polypeptide takes different structures in midgut and muscle, driving autophagy or mitochondria-associated degradation; deleting disordered region IDR2 switches muscle Ref(2)P to midgut state.

Agentic transcranial functional ultrasound imaging: @fUS

The paper introduces @fUS, an agentic transcranial fUS imaging platform that enables functional brain imaging in mice with high spatial and temporal resolution, supporting longitudinal studies without surgery.

Integrative Structural Modeling of Intrinsically Disordered Regions in a Human HDAC2 Chromatin Remodeling Complex

The paper uses an integrative approach to model the structure of an IDR-driven HDAC2 complex, revealing interactions not captured by AlphaFold alone.

Multicomplex Integrative Structural Modeling of a Human Histone Deacetylase Interactome

The paper builds structural models of HDAC1/2-containing chromatin remodeling complexes using XL-MS and integrative modeling, revealing how the CTD IDR of HDAC1 folds into alpha helices.

Metabolic signatures of cone-dominant and cone-degenerating retinas

This study identifies metabolic changes in cone-dominant and cone-degenerating retinas, revealing key metabolites associated with cone abundance and metabolic vulnerabilities in retinal degeneration.

Early Proteomic and Metabolic Signatures of Liver and Eye in OAT-Deficient Mice

This study identifies early proteomic and metabolic changes in liver and eye tissues of OAT-deficient mice, revealing tissue-specific impacts of OAT deficiency.

The human parasite, Toxoplasma gondii, is paralyzed without two components of the apical polar ring

This study identifies APR9 and KinesinA as essential components of the apical polar ring in Toxoplasma gondii, showing that their combined loss paralyzes the parasite and impairs key life cycle processes.

Nascent protein retention at polysomes reduces kinetic barriers to self-assembly

The paper shows that increasing translation initiation rates accelerates nucleation of aggregating proteins at polysomes, suggesting cotranslational nucleation influences proteome evolution.

A suture-specific oocyst wall protein COWP4 is essential for excystation and infectivity, while COWP6 links wall architecture to host interaction in Cryptosporidium parvum

This paper identifies COWP4 and COWP6 as distinct oocyst wall proteins in Cryptosporidium parvum, showing COWP4 is essential for suture formation and infectivity while COWP6 links wall structure to host interaction.

STING-STAT3-SOX18 Axis Drives EndMT and Epigenetic Reprogramming in SAVI Lung Fibrosis

This study identifies a STING-STAT3-SOX18 axis driving EndMT and epigenetic reprogramming in SAVI lung fibrosis, suggesting STING as a therapeutic target.

Mutations in the ubiA gene are the major mechanism of ethambutol resistance in Mycobacterium avium

This study identifies ubiA gene mutations as the primary mechanism of ethambutol resistance in M. avium by analyzing clinical strains and resistant mutants.

MRN-ATM Pathway Activation in CD4 T-Cell Senescence during Chronic Hepatitis B Virus Infection

This study shows that chronic HBV infection causes CD4 T-cell senescence with DNA damage and telomere erosion, while the MRN-ATM pathway is activated as a compensatory mechanism to maintain T-cell function.

The Spatiotemporal Proteome Landscape of Aging: Structural determinants of age-sensitive proteome remodeling

The paper uses yeast aging to map proteome changes across age, revealing structural determinants of age-sensitive remodeling and providing a resource for aging research.

p300/CBP-Driven Acetylation Stabilizes PARP7 to Reinforce Negative Feedback on IFN-I Signaling

This study identifies p300/CBP-mediated acetylation of PARP7 as a mechanism to suppress IFN-I signaling in tumor cells, with implications for enhancing antitumor immunity.

An ER-Inner Membrane Complex Bridge via VAP-VPS13A-DAT1 Drives Daughter Budding in Toxoplasma gondii

This study identifies a TgVAP-TgVPS13A-TgDAT1 complex that bridges the ER and IMC in Toxoplasma gondii, mediating lipid transport essential for IMC biogenesis and daughter budding.

Identification of a new ORF3a-E fusion subgenomic RNA of SARS-CoV-2 and its biological features in the infection process

The paper identifies a new SARS-CoV-2 subgenomic RNA, ORF3a-E-sgRNA, which enhances viral replication and immune evasion by promoting translation and host protein interactions.

Divergent Minimum Inhibitory Concentrations of Clarithromycin and Azithromycin Against Clinical Isolates of Mycobacterium abscessus Complex

This study compares the in vitro activity of clarithromycin and azithromycin against M. abscessus complex isolates, finding significant resistance differences and discordance in susceptibility profiles.

CTHRC1 is a new therapeutic target and serum diagnostic biomarker for aortic dissection

This paper identifies CTHRC1 as a therapeutic target and serum biomarker for aortic dissection, showing it regulates VSMC phenotype and aortic integrity via the ERK1/2 pathway.

Construction of mirror-image RNA nanostructure for enhanced biostability and drug delivery efficiency

This paper constructs a mirror-image RNA nanostructure to improve biostability and drug delivery efficiency by conjugating siRNA and chemotherapy agents with enhanced endosomal escape.

Selection of Fluorinated Aptamer Targeting RNA Element with Different Chirality

This study selects a 2-fluoro modified mirror-image RNA aptamer targeting a viral frameshift element with opposite chirality, showing improved stability and moderate binding affinity.

Structural basis of nucleosomal H4K20 recognition and methylation by SUV420H1 methyltransferase

This study reveals the structural basis of SUV420H1's recognition and methylation of H4K20 on nucleosomes, showing how H2A.Z enhances its catalytic activity and how mutations affect its function.

DLDTI: A learning-based framework for identification of drug-target interaction using neural networks and network representation

DLDTI predicts drug-target interactions using network representation and neural networks, achieving high AUC performance and validating results with biomedical experiments.

An Array of 60,000 Antibodies for Proteome-Scale Antibody Generation and Target Discovery

The paper develops PETAL, a library of 62,208 mAbs against 15,199 peptides, enabling proteome-scale antibody generation and target discovery across species.

Identification of small regulatory RNAs involved in persister formation

This study identifies seven small regulatory RNAs involved in type II persister formation in uropathogenic E. coli.

Identification of novel genes including rpmF and yjjQ critical for Type II persister formation in Escherichia coli

This study identifies novel genes critical for Type II persister formation in E. coli by analyzing transcriptome changes during persister emergence and abundance and validating their roles through knockout and overexpression experiments.

Identification of Polynucleotide Phosphorylase (PNPase) in Escherichia coli Involved in Persister Formation

This study identifies PNPase as a key regulator of persister formation in E. coli by negatively regulating the crp operon at the post-transcriptional level.

Clofazimine targets essential nucleoid associated protein, mycobacterial integration host factor (mIHF), in Mycobacterium tuberculosis

This study identifies mIHF as the target of clofazimine in Mycobacterium tuberculosis, showing it inhibits DNA binding and gene expression, offering new insights into its mechanism of action.

Identification of a Novel Gene argJ involved in Arginine Biosynthesis Critical for Persister Formation in Staphylococcus aureus

This study identifies argJ, a gene involved in arginine biosynthesis, as critical for persister formation in S. aureus, with implications for developing new treatments for persistent infections.