X. Gao

Transcriptome-wide identification of 5-methylcytosine by deaminase and reader protein-assisted sequencing

This paper introduces DRAM, a method for transcriptome-wide m5C detection using deaminase and reader proteins, showing high overlap with BS-seq data and supporting low-input RNA.

A Combination of Machine Learning and PBPK Modeling Approach for Pharmacokinetics Prediction of Small Molecules in Humans

This paper combines machine learning and PBPK modeling to predict small molecule pharmacokinetics in humans without experimental data, achieving higher accuracy than traditional methods.

Non-mechanical disruption of Bacillus subtilis spores allows sensitive and deep characterization of the minimal proteome for resuming a cellular lifestyle.

This paper introduces a new sample preparation method, SPEED, which improves proteomic analysis of Bacillus subtilis spores by identifying more proteins and enabling differentiation between spore and vegetative cell proteins.

Chromosome-scale pearl millet genomes reveal a CARLACTONOIC ACID METHYL TRANSFERASE as key determinant of strigolactone pattern and Striga susceptibility

The paper identifies a CLAMT1 gene responsible for strigolactone production and Striga susceptibility in pearl millet by comparing genome assemblies of susceptible and resistant lines.

Capsaicin acts as a novel NRF2 agonist to suppress ethanol induced gastric mucosa oxidative damage by directly disrupting the KEAP1-NRF2 interaction

This study shows capsaicin directly binds KEAP1 and allosterically activates NRF2, reducing ethanol-induced gastric oxidative damage and suggesting its potential as a novel NRF2 agonist for oxidative stress-related diseases.

The ICF2 gene Zbtb24 specifically regulates the differentiation of B1 cells via promoting heme synthesis

This study shows that Zbtb24 regulates B1 cell differentiation via heme synthesis, leading to impaired antibody production in T-cell independent responses.

Targeting endothelial FOXO1 protects diabetic β-cells and improves wound healing

This study shows that targeting endothelial FOXO1 reduces IGF2 levels, improves β-cell function, and enhances wound healing in diabetes.

Comparative analysis of methodologies for detecting extrachromosomal circular DNA

This study compares 7 analysis pipelines and 7 experimental methods for detecting extrachromosomal circular DNA, identifying the most effective approaches for short-read and long-read sequencing data.

Preclinical evaluation of RQ3013, a broad-spectrum mRNA vaccine against SARS-CoV-2 variants

This paper evaluates RQ3013, an mRNA vaccine against SARS-CoV-2 variants, showing robust immune responses and protection in animal models.

TSAR, Thermal Shift Analysis in R, identifies endogenous molecules that interact with HIV-1 capsid hexamers

TSAR streamlines thermal shift assay analysis, identifying gallic acid and other metabolites that interact with HIV-1 capsid hexamers and may inhibit HIV-1 replication.

Glioblastoma Margin as a Diffusion Barrier Revealed by Photoactivation of Plasmonic Nanovesicles

This study uses plasmonic nanovesicles to measure diffusion in GBM and finds the tumor margin has the lowest diffusion coefficient, indicating it acts as a diffusion barrier.

Antibodies utilizing VL6-57 light chains target a convergent cryptic epitope on SARS-CoV-2 spike protein driving the genesis of Omicron variants

The paper identifies public antibodies using VL6-57 light chains that target a conserved epitope on SARS-CoV-2 spike protein, showing how Omicron variants evolved to escape these antibodies.

Gut microbial genomes with paired isolates from China signify probiotic and cardiometabolic effects

The paper presents a new microbial reference set with paired isolates from China, showing probiotic and cardiometabolic effects on hosts.

Human FAM111A inhibits vaccinia virus replication by degrading viral DNA-binding protein I3 and is antagonized by poxvirus host range factor SPI-1

This study identifies FAM111A as a restriction factor for vaccinia virus and MVA, showing it degrades viral DNA-binding protein I3 and is counteracted by SPI-1.

Rationally designed multimeric nanovaccines using icosahedral DNA origami for molecularly controlled display of SARS-CoV-2 receptor binding domain

This study designs multimeric nanovaccines using icosahedral DNA origami to display SARS-CoV-2 RBD, showing enhanced B cell activation and immune responses in mice.

Duhuo Jisheng Decoction Regulates Intracellular Zinc Homeostasis by Enhancing Autophagy via PTEN/Akt/mTOR to Improve Knee Cartilage Degeneration

This study investigates how Duhuo Jisheng Decoction protects cartilage by enhancing autophagy through the PTEN/Akt/mTOR pathway and regulating zinc homeostasis.

Wiskott-Aldrich Syndrome Protein Regulates Nucleolar Organization and Function in Innate Immune Response

This study shows that WASP regulates nucleolar structure and function, affecting rRNA transcription and inflammatory cytokine response in macrophages.

SARS-CoV-2 infection of human pluripotent stem cell-derived vascular cells reveals smooth muscle cells as key mediators of vascular pathology during infection

This study infects human pluripotent stem cell-derived vascular cells with SARS-CoV-2 and finds that smooth muscle cells drive vascular inflammation and coagulation.

Patient-derived organoids assist personalized treatment for a patient with multiple metastatic neuroendocrine carcinoma of the cervix

The paper uses patient-derived organoids to model metastatic neuroendocrine carcinoma of the cervix and guide personalized treatment based on drug screening.

METTL16 Controls Kaposi's Sarcoma-Associated Herpesvirus Replication by Regulating S-Adenosylmethionine Cycle

This study shows METTL16 suppresses KSHV lytic replication by regulating the SAM cycle and redox homeostasis.

An isoform-resolution transcriptomic atlas of colorectal cancer from long-read single-cell sequencing

This study builds an isoform-resolution transcriptomic atlas of colorectal cancer using long-read single-cell sequencing and identifies neoepitopes for vaccine development.

Plasma cells are formed in waning germinal centers via an affinity-independent process

The paper tracks Ighg2A10 cells in germinal centers using single-cell RNA-seq and finds that plasma cells form in waning GCs through an affinity-independent process.

MORE IS DIFFERENT: DRUG PROPERTY ANALYSIS ON CELLULAR HIGH-CONTENT IMAGES USING DEEP LEARNING

The paper introduces MID, a deep learning method for high-content image analysis that outperforms existing tools in drug toxicity classification and compound identification.

Pleiotropic Regulatory Locus1 maintains actin microfilament integrity and concomitant cellular homeostasis facilitating root development in Arabidopsis

This study identifies PRL1's role in maintaining actin microfilament integrity and cellular homeostasis, linking actin depolymerization to root developmental defects in Arabidopsis.

PRL1 negatively regulates Rho GTPase-independent and -dependent signaling pathways maintaining actin microfilament dynamic for pavement cell morphogenesis

This study identifies PRL1 as a regulator of actin microfilament dynamics in Arabidopsis pavement cells through both Rho GTPase-dependent and -independent pathways.

CRB3 navigates Rab11 trafficking vesicles to promote γTuRC assembly during ciliogenesis

This study identifies CRB3's role in navigating Rab11 vesicles to promote γTuRC assembly during ciliogenesis and its regulation of Hh and Wnt signaling in tumorigenesis.

cGAS-activating lupus autoantibody for cancer immunotherapy

This study shows a lupus anti-DNA autoantibody activates cGAS and improves survival in glioblastoma models by enhancing CD8+ T cell infiltration.

Multimodal meta-analysis of fecal metagenomes reveals microbial single nucleotide variants as superior biomarkers for early detection of colorectal cancer

This study identifies microbial single nucleotide variants (SNVs) as superior biomarkers for early detection of colorectal cancer, outperforming species-level signatures in multiple validation cohorts.

Epoxyeicosatrienoic acids and sEH inhibition prevent cardiac dysfunction in CVB3-induced myocarditis by positively regulating type I interferon signaling

This study shows that EETs and sEH inhibitors prevent CVB3-induced myocarditis by enhancing type I interferon signaling and improving viral resistance.

Bioengineering of a Lactococcus lactis subsp. lactis strain enhances nisin production and bioactivity.

This study enhances nisin production and antimicrobial activity in Lactococcus lactis subsp. lactis through genetic modifications involving nisA, nisRK, and nisZ genes.