X. Huang

π-SPECFormer: A Mass Spectrometry-based Foundation Model for Decoding the Dark Proteome

This paper introduces π-SPECFormer, a foundation model for mass spectrometry-based proteomics that decodes the dark proteome by pre-training on unannotated spectra and outperforms baselines in peptide sequencing and modification detection.

ALS-causing SOD1 mutations H46R and G85R form similar novel amyloid fibril structures and promote ferroptosis in cells

This study shows that two ALS-causing SOD1 mutations form similar amyloid fibrils that promote ferroptosis in neuronal cells.

Coxsackievirus group B3 regulates ASS1-mediated metabolic reprogramming and promotes macrophage inflammatory polarization in viral myocarditis

This study shows CVB3 infection upregulates ASS1 through citrulline consumption, leading to metabolic reprogramming and macrophage inflammatory polarization, contributing to viral myocarditis.

Splenic red pulp macrophages eliminate the liver-resistant Streptococcus pneumoniae during bloodstream infection

The paper identifies that splenic red pulp macrophages, aided by natural antibodies and complement, clear liver-resistant Streptococcus pneumoniae from the bloodstream in mice.

Therapeutic Activity of Resolvin D1 (RvD1) in Murine MASH

This study investigates how RvD1 reduces inflammation, cell death, and fibrosis in MASH by targeting Stat1, ER stress, and MMP pathways.

DELE1 promotes translation-associated homeostasis, growth, and survival in mitochondrial myopathy

The paper identifies DELE1's role in promoting translation-associated homeostasis, growth, and survival in mitochondrial myopathy through the mt-ISR pathway.

A Machine Learning Framework to Identify the Correlates of Disease Severity in Acute Arbovirus Infection

This study uses machine learning to identify key viral and host processes associated with varying severity in bluetongue virus infection in sheep.

Hist2Cell: Deciphering Fine-grained Cellular Architectures from Histology Images

Hist2Cell predicts fine-grained transcriptional cell types from histology images with high accuracy, enabling cellular mapping and cancer prognosis.

SARS-CoV-2 Omicron XBB lineage spike structures, conformations, antigenicity, and receptor recognition

The paper determines cryo-EM structures of SARS-CoV-2 XBB lineage spike proteins, revealing structural changes that enhance immune evasion and receptor binding.

Potent and broadly neutralizing antibodies against sarbecoviruses induced by sequential COVID-19 vaccination

This study identifies potent and broadly neutralizing antibodies against SARS-CoV-2 and related sarbecoviruses from a vaccinated donor, showing their efficacy against multiple variants and providing insights for therapeutic development.

Large-scale multi-omics analyses identified root-microbiome associations underlying plant nitrogen nutrition

The paper identifies root-microbiome associations affecting plant nitrogen nutrition through multi-omics analyses of 1,341 rapeseed samples.

Human Amniotic Epithelial Cells Promote Chx10-/Pax6+ Muller Glia Subpopulation Reprogramming into Photoreceptor-like Cells

This study identifies a specific Muller glia subpopulation that can be reprogrammed into photoreceptor-like cells through transplantation of human amniotic epithelial cells.

Organic macromolecules transport a significant proportion of the calcium precursor for nacre formation.

The paper investigates the transport of calcium precursors in nacre formation, revealing that calcium is transported in lipid bilayer vesicles and binds to proteins.

IOBR2: Multidimensional Decoding Tumor Microenvironment for Immuno-Oncology Research

IOBR2 is a tool for analyzing tumor microenvironment using multi-omics data, offering modules for preprocessing, estimation, interaction analysis, and visualization.

A spatial cell atlas of neuroblastoma reveals developmental, epigenetic and spatial axis of tumor heterogeneity

This paper creates a spatial cell atlas of neuroblastoma, revealing tumor heterogeneity through multi-omics data and identifying spatial compartmentalization and signaling patterns.

Genomic and transcriptomic characteristics of type VI secretion system in Klebsiella pneumoniae

This study analyzes the genomic and transcriptomic features of the Type VI secretion system (T6SS) in Klebsiella pneumoniae, showing its presence in all clinical isolates and its role in interbacterial competition.

Structural insights into specific recognition of PTENα/β-NTE by WDR5 in cancer progression

The paper determines the crystal structure of PTEN-NTE bound to WDR5, revealing a specific binding motif that promotes tumor growth and suggests WDR5 inhibitors as potential cancer therapies.

Lithocholic acid targets TULP3 to activate sirtuins and AMPK to retard ageing

This study identifies LCA's mechanism of action through TULP3-sirtuin-v-ATPase-AMPK pathway to activate AMPK and extend lifespan in model organisms.

MYC-NFATC2 axis maintains cell cycle and mitochondrial function in AML cells

This study identifies NFATC2 as a novel target of KDM4A in AML cells, showing its role in cell cycle progression and mitochondrial function through interactions with MYC and CCND1.

Proximity Labeling Expansion Microscopy (PL-ExM) resolves structure of the interactome

PL-ExM combines proximity labeling and expansion microscopy to visualize 3D interactome structures and assess PL technique performance.

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.

Downregulation of Let-7 miRNA promotes Tc17 differentiation and emphysema via de-repression of RORγt

This study shows that downregulation of let-7 miRNA promotes Tc17 differentiation and emphysema by de-repressing RORγt in mice.

Phosphorylation Promotes DELLA Activity by Enhancing Its Binding to Histone H2A at Target Chromatin in Arabidopsis

This study identifies phosphorylation as a new regulatory mechanism for DELLA activity by enhancing its binding to histone H2A at target chromatin in Arabidopsis.

Cell-autonomous targeting of arabinogalactan by host immune factors inhibits mycobacterial growth

The paper identifies galectin-9 and AG-specific antibodies that inhibit Mtb growth by targeting arabinogalactan, offering a new immunotherapeutic strategy for TB.

Commensal microbiome dysbiosis elicits IL-8 signaling to drive fibrotic skin disease

The paper investigates the role of commensal microbiome dysbiosis in keloid fibrosis, finding elevated IL-8 signaling drives collagen accumulation and fibroblast migration.

Conformational flexibility of HIV-1 envelope glycoproteins modulates transmitted / founder sensitivity to broadly neutralizing antibodies

This paper shows that some HIV-1 transmitted/founder Envs are incompletely closed, making them sensitive to antibodies targeting open conformations, and highlights the importance of Env conformational flexibility for bnAb neutralization.

Probucol mitigates high-fat diet-induced cognitive and social impairments through disruption of redox-inflammation association

This study shows probucol reduces high-fat diet-induced cognitive and social impairments in mice without affecting obesity or metabolic homeostasis, by disrupting redox-inflammation links.

Metagenomic analysis of individual mosquitos reveals the ecology of insect viruses

The paper analyzes the virome of 2,438 individual mosquitoes across China to reveal viral diversity, geographic hotspots, and the impact of host phylogeny on viral composition.

Human TUBA1B short open reading frame product regulates cancer cell growth via importin-β

This study identifies TUBA1B-sORF1, a novel protein from the TUBA1B gene, which promotes cancer cell growth by facilitating nuclear translocation of β-catenin.

Reply to: Contribution of carbon inputs to soil carbon accumulation cannot be neglected

The paper responds to a critique that carbon inputs were neglected in a study on soil carbon storage, arguing that empirical data do not support the critique and that further research is needed.