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.

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.

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.

The tumour suppressor Fat1 is dispensable for normal murine haematopoiesis

This study shows that Fat1 is not required for normal murine haematopoiesis, as knockout mice show no significant differences in blood cell populations or function.

Spatially Dependent Tissue Distribution of Thyroid Hormones by Plasma Thyroid Hormone Binding Proteins

This paper develops a spatial human physiologically based kinetic model of thyroid hormones to show how different binding proteins contribute to tissue-specific hormone distribution.

The phosphoproteome is a first responder in tiered cellular adaptation to chemical stress followed by proteomics and transcriptomics alteration

This study compares transcriptomics, proteomics, and phosphoproteomics responses in HepG2 and AC16 cells to chemical exposure, finding phosphoproteomics changes occur earlier and at lower concentrations than transcriptomics.

Acetyl-CoA carboxylase inhibition increases RPE cell fatty acid oxidation and limits apolipoprotein efflux

This study shows that inhibiting acetyl-CoA carboxylase with Firsocostat increases fatty acid oxidation and reduces lipid deposits in RPE cells, potentially limiting drusen accumulation in AMD.

A force-sensitive adhesion GPCR is indispensable in normal equilibrioception

This study identifies LPHN2/ADGRL2 as a force-sensitive adhesion GPCR essential for normal equilibrioception by regulating mechanoelectrical transduction in utricular hair cells.

Force sensing GPR133 is essential for normal balance and modulates vestibular hair cell membrane excitability via Gi signaling and CNGA3 coupling

This study identifies GPR133 as a force-sensing GPCR essential for balance, showing it modulates vestibular hair cell excitability via Gi signaling and CNGA3 coupling.

Mechanism for controlled assembly of transcriptional condensates by Aire

This paper identifies a multi-layered mechanism by which Aire forms transcriptional condensates on enhancers through coordinated interactions between its CARD, PHD1, and CTT domains.

Proteomic Stratification of Prognosis and Treatment Options for Small Cell Lung Cancer

This study uses proteomic profiling to stratify small cell lung cancer into three subtypes with distinct clinical outcomes and treatment responses, identifying potential therapeutic targets and improving prognosis prediction.

Decoupling of the Onset of Anharmonicity between a Protein and Its Surface Water around 200 K

The paper investigates the onset of anharmonicity in a protein and its surface water around 200 K, finding they are decoupled, with the protein's transition being intrinsic and the water's being a resolution effect.

Staphyloccocus aureus biofilm, in the absence of planktonic bacteria, produces factors that activate counterbalancing inflammatory and immune-suppressive genes in human monocytes

This study shows S. aureus biofilm produces soluble factors that activate inflammatory and immune-suppressive genes in human monocytes, suggesting a role for these factors in modulating immune responses in PJI.