Q. Zhang

LongVerse: verified AI agents for Nanopore and PacBio DNA methylation analysis

LongVerse uses AI agents to generate haplotype-resolved DNA methylation calls from Nanopore and PacBio reads, achieving high agreement with bisulfite sequencing and reducing errors compared to existing methods.

Spatiotemporal transcriptomic profiling reveals the dynamic immunological landscape of alveolar echinococcosis

This study uses spatiotemporal transcriptomics to analyze immune dynamics in E. multilocularis infected mouse liver, identifying key immune cell roles and shifts in immune strategy during infection.

HTLV-1 infected T cells cause bone loss via small extracellular vesicles

This study shows HTLV-1 infected T cells release small extracellular vesicles that promote bone loss by stimulating osteoclasts, independent of RANKL expression.

Epigenetic reader ZMYND11 noncanonical function restricts HNRNPA1-mediated stress granule formation and oncogenic activity

This study identifies a noncanonical function of ZMYND11 as an arginine-methylated HNRNPA1 reader that suppresses stress granule formation and tumor progression.

Ferroptosis mediates the progression of hyperuricemic nephropathy by activating RAGE signaling

This study shows ferroptosis contributes to hyperuricemic nephropathy by activating RAGE signaling, and inhibiting ferroptosis improves renal injury and fibrosis in a mouse model.

Gradual labeling with fluorogenic probes for MINFLUX nanoscopy of densely packed structures

This paper introduces GLF-MINFLUX, a method for nanoscale imaging of densely packed structures, achieving improved localization precision and faster acquisition.

Insulin regulates lymphatic endothelial function via palmitoylation

This study investigates how insulin regulates lymphatic endothelial function through palmitoylation, identifying CD36 as a mediator of this process.

Topoisomerase I is an Evolutionarily Conserved Key Regulator for Satellite DNA Transcription

This study identifies Topoisomerase I as a conserved regulator of satellite DNA transcription across species, showing its role in centromere function and DNA damage response.

Interferon-Inducible Guanylate-Binding Protein 5 Inhibits Replication of Multiple Viruses by Binding to the Oligosaccharyltransferase Complex and Inhibiting Glycoprotein Maturation

This paper identifies GBP5 as an ISG that inhibits viral replication by blocking N-glycosylation of viral proteins, including SARS-CoV-2 spike, through interaction with the OST complex.

Ancient cyanobacterial proto-circadian clock adapted to short day-night cycles ~ 0.95 billion years ago

The paper reconstructs an ancient cyanobacterial circadian clock from ~0.95 billion years ago and shows it adapts to 18-h day-night cycles but lacks endogenous oscillation.

Insulation of ribosomal promoter activity by Fis, H-NS or a divergent promoter within the packed E. coli genome.

The paper shows that Fis and H-NS insulation mechanisms and divergent promoters help regulate ribosomal promoter activity in E. coli, allowing gene duplication without local genomic effects.

Generative Adversarial Networks Accurately Reconstruct Pan-Cancer Histology from Pathologic, Genomic, and Radiographic Latent Features

This paper introduces HistoXGAN, a GAN that reconstructs cancer histology from latent features, showing it retains tumor grade, histologic subtype, and gene expression patterns across 29 cancer types.

Heterogeneous and Novel Transcript Expression in Single Cells of Patient-Derived ccRCC Organoids

This study uses single-cell long-read sequencing to analyze transcriptomes of ccRCC organoids, identifying novel transcripts and highlighting cell-specific alternative splicing events.

Decoupling the molecular versatility of aminoglycosides via drug or target modification enables community-wide antiphage defense

This study uncouples antiphage and antibacterial properties of aminoglycosides through resistance mechanisms, demonstrating community-wide antiphage defense in bacterial co-cultures.

Thymidine Phosphorylase Mediates SARS-CoV-2 Spike Protein Enhanced Thrombosis in K18-hACE2TG Mice

This study identifies thymidine phosphorylase (TYMP) as a mediator of SARS-CoV-2 spike protein-induced thrombosis in mice, showing that TYMP inhibition reduces thrombosis and coagulation.

Ovarian disrupting effects and mechanisms of long- and short-chain per- and polyfluoroalkyl substances in mice

This study investigates the effects of long- and short-chain PFAS on ovarian function in mice, finding that long-chain PFAS disrupt follicle maturation and ovulation via PPARγ activation.

The first discovery of SFTSV in the Centre of Metropolitan Beijing, China

This study identifies SFTSV circulation in central Beijing by surveying ticks and hedgehogs, revealing high seroprevalence and RNA prevalence in urban areas.

A genome-wide arrayed CRISPR screen identifies PLSCR1 as an intrinsic barrier to SARS-CoV-2 entry that recent virus variants have evolved to resist

The paper identifies PLSCR1 as a host factor restricting SARS-CoV-2 entry, which recent variants have evolved to bypass, through a CRISPR screen and integration of genetic studies.

Dysregulation of mitochondrial function by PLK1-mediated PDHA1 phosphorylation promotes Cr(VI)-associated lung cancer progression

This study shows that PLK1-mediated PDHA1 phosphorylation impairs mitochondrial function and promotes Cr(VI)-induced lung cancer progression by disrupting energy metabolism and apoptosis.

BioXNet: a biologically inspired neural network for deciphering anti-cancer drug response in precision medicine

BioXNet predicts anti-cancer drug responses by integrating drug targets and genomic profiles, showing better performance than existing models and revealing differences in response mechanisms between cell lines and humans.

Postharvest partial dehydration of blueberries enhanced blueberry wine aroma via upregulating phenylalanine metabolism and terpene biosynthesis

This study shows that postharvest partial dehydration of blueberries increases phenylalanine-derived and terpene compounds, enhancing blueberry wine aroma through upregulated metabolic pathways.

A Multiscale Spatial Modeling Framework for the Germinal Center Response

This paper develops a multiscale spatial simulation framework to model the germinal center response, recapitulating key molecular, cellular, and morphological events.

Organelle proteomic profiling reveals lysosomal heterogeneity in association with longevity

This study uses proteomic profiling to reveal lysosomal heterogeneity and its role in longevity by identifying protein dynamics and interactions in lysosomes.

Deciphering the Molecular Mechanism of Post-Acute Sequelae of COVID-19 through Comorbidity Network Analysis

This study analyzes longitudinal electronic health records to identify comorbidity patterns influenced by COVID-19 and their biological mechanisms through protein-protein interaction networks.

D-type cyclins regulate DNA mismatch repair in the G1 and S phases of the cell cycle, maintaining genome stability

This study shows D-type cyclins inhibit mismatch repair (MMR) in G1 phase by shielding p21, while their degradation in S phase enables proper MMR function, maintaining genome stability.

Identification of a distinct cluster of GDF15high macrophages exhibiting anti-inflammatory activities

The paper identifies a distinct cluster of GDF15high macrophages with anti-inflammatory properties using single-cell RNA sequencing and functional assays.

RFX6 at locus 6q22 confers metastasis and drug resistance in prostate cancer

This study identifies RFX6 at locus 6q22 as a driver of prostate cancer metastasis and drug resistance through epigenetic and genetic mechanisms.

Coordinated molecular and ecological adaptations underlie a highly successful parasitoid

This study identifies molecular and ecological adaptations in the parasitoid Trichopria drosophilae that enhance its success in parasitizing Drosophila hosts.

Variation of C-terminal domain governs RNA polymerase II genomic locations and alternative splicing in eukaryotic transcription

This study shows how phosphorylation of the CTD regulates condensate formation and alternative splicing across species.

Identification of a Novel Ferroptosis Inducer with Dual Modulatory Effects on GPX4 Activity and Stability

This study identifies MI-2, a novel GPX4 inhibitor that induces ferroptosis by inhibiting GPX4 activity and promoting its degradation, showing synergistic effects with existing cancer drugs.