Wei Liu

Deciphering Spatial Cellular Organization through RNA-Anchored Multi-Omics Deconvolution

SMODER deconvolves spatial multi-omics data by prioritizing RNA for cell-type identification and integrating other modalities, improving accuracy and spatial coherence.

Unearthing a fungal giant: Dianjunaceae fam. nov., a novel Paleocene lineage of Xylariales harbouring Dianjunus rex gen. et sp. nov.

The paper describes a new fungal family and species, Dianjunaceae and Dianjunus rex, discovered in Yunnan, China, with large stromata and a Paleocene origin.

AFP-R: An Open Resource Dedicated to Antifreeze Proteins

AFP-R provides a database and predictor for antifreeze proteins, offering curated data and a machine-learning model for AFP identification.

Intracranial Validation of Magnetoencephalography Across Oscillatory Frequency and Depth

This study validates MEG's ability to measure neural activity across frequency and depth using intracranial EEG data from epileptic patients, showing strong agreement for lower frequencies and superficial sources, and sensitivity to deep structures like the hippocampus.

Gene III(R) L-Ergothioneine Ameliorates Exercise-Induced Fatigue by Attenuating Oxidative Stress, Inflammation, and Modulating the AMPK/PGC-1α Signaling Pathway

This study shows that Gene III(R) EGT improves exercise performance and reduces fatigue in mice by lowering oxidative stress, inflammation, and activating the AMPK/PGC-1α pathway.

Complex genetic architecture underlying the plasticity of tobacco leaf width provides insight into across-environment genomic prediction

This study identifies QTLs associated with leaf width and its plasticity in tobacco and develops a GEAI model for cross-environment prediction, improving accuracy by 8.7%.

Homeobox transcription factor MSX2 down-regulates ERα action to facilitate anti-estrogensensitivity in ERα+ breast cancer

The paper identifies MSX2 as a co-repressor of ERα that enhances anti-estrogen sensitivity in ER-positive breast cancer by inhibiting ER-mediated transcription.

Systems Pharmacology Reveals Type I Interferon and Myeloid-Like B Cell Reprogramming as Druggable Axes in Antiphospholipid Syndrome

The paper identifies druggable targets in antiphospholipid syndrome using systems pharmacology, revealing two key modules linked to interferon-I signaling and degranulation pathways.

Heteromorphic tertiary structures of MAT1-1-1 and MAT1-2-1 protein variants simultaneously produced in pairs by Ophiocordyceps sinensis strains

The paper shows that MAT1-1-1 and MAT1-2-1 proteins from O. sinensis strains have divergent tertiary structures, supporting self-sterility and hybrid reproduction.

Mechanical confinement drives monocyte-to-macrophage differentiation

This study shows mechanical confinement drives monocyte-to-macrophage differentiation via a mechanoepigenetic pathway involving KDM6B and H3K27me3 demethylation.

L-Lactate reprograms tumor-associated macrophages to drive pancreatic cancer progression via BCL3 lactylation

This study shows that L-lactate reprograms tumor-associated macrophages via BCL3 lactylation, promoting pancreatic cancer progression by suppressing inflammation and supporting tumor networks.

Gene III Ergothioneine ameliorates alcoholic fatty liver disease: A dual strategy of accelerated ethanol elimination and reducing oxidative stress

This study shows Gene III Ergothioneine reduces alcoholic fatty liver disease by speeding up ethanol elimination and lowering oxidative stress.

Z-RNA-ZBP1 axis drives Tau-mediated neurodegeneration

The paper identifies the Z-RNA-ZBP1 axis as a driver of Tau-mediated neurodegeneration and shows that ZBP1 inhibition can alleviate cognitive deficits in Tau-transgenic mice.

Natural genetic and transcriptomic variation in photosynthesis associated pathways contribute to adaptive traits variation in worldwide Arabidopsis thaliana population

The paper identifies genetic and transcriptomic variations in photosynthesis-related genes across Arabidopsis thaliana populations and links them to adaptive trait variation.

Adipocyte-related genes analysis contributes to the prognosis of atrial fibrillation

The paper identifies adipocyte-related genes associated with atrial fibrillation progression and prognosis using RNA-seq data and immune infiltration analysis.

A spatially-resolved human brain proteome atlas for understanding function and disease

The paper creates a spatially-resolved human brain proteome atlas, revealing protein diversity and functional specialization, and identifies therapeutic targets in epilepsy.

A Population-scale Single-cell Spatial Transcriptomic Atlas of the Human Cortex

This study creates a single-cell spatial transcriptomic atlas of the human cortex, revealing gene expression patterns, aging effects, and disease associations across layers and species.

HIF-1α promotes osteogenic-angiogenic coupling response of BMSCs cell sheets

This study shows HIF-1α enhances osteogenic-angiogenic coupling in BMSCs cell sheets, promoting bone formation and vascular network development in vitro.

Inter-Kingdom Interactions and Environmental Influences on the Oral Microbiome in Severe Early Childhood Caries

This study examines bacterial-fungal dynamics in severe early childhood caries, finding reduced bacterial diversity, increased cariogenic species, and a role for Candida albicans, while showing no link between iron/fluoride and microbial communities.

EasyOmics-A graphical interface for population-scale omics data association, integration and visualization

EasyOmics provides a user-friendly R Shiny interface for population-scale omics data association, integration, and visualization without requiring advanced programming skills.

A Model-Based Clustering via Mixture of Bayesian Hierarchical Models with Covariate Adjustment for Detecting Differentially Expressed Genes from Paired Design

This paper introduces a Bayesian hierarchical mixture model with covariate adjustment to detect differentially expressed genes in paired design whole-genome data, showing improved performance over existing methods.

Spatio-temporal patterns of ovarian development and VgR gene silencing reduced fecundity of parthenogenetic Artemia

This study characterizes ovarian development stages and identifies VgR gene silencing as a factor reducing fecundity in parthenogenetic Artemia.

Spatially resolved gene regulatory and disease vulnerability map of the adult Macaque cortex

The paper integrates single-cell ATAC and transcriptomic data with spatial transcriptomics to map regulatory features and disease vulnerabilities in macaque cortex.

Parallel loss of symbiosis genes in relatives of nitrogen-fixing non-legume Parasponia

The paper shows that non-nodulating relatives of Parasponia lost key symbiosis genes, challenging the hypothesis that nodulation evolved independently multiple times.