X. Xiao

Marker-specific pixel attribution for single-cell protein quantification with PixAQ

PixAQ improves single-cell protein quantification in imaging mass cytometry by assigning pixel signals to specific markers using spatial and intensity models.

The Transcription Factor OsNAC5 Mediates Cadmium Stress Response and Accumulation in Rice

This study identifies OsNAC5 as a transcription factor that regulates Cd uptake in rice by activating OsNRAMP1, reducing Cd accumulation in grains.

SwinCell: a transformer-based framework for dense 3D cellular segmentation

SwinCell is a 3D transformer-based framework that improves segmentation of dense cellular images by balancing local feature recognition and contextual understanding.

T cell cholesterol transport is a metabolic checkpoint that links intestinal immune responses to dietary lipid absorption

This study identifies Aster-A as a cholesterol transporter in T cells that regulates immune signaling and metabolic responses by controlling membrane cholesterol levels.

A Community Challenge to Predict Clinical Outcomes After Immune Checkpoint Blockade in Non-Small Cell Lung Cancer

The paper evaluates predictive models for immune checkpoint inhibitor outcomes in NSCLC using clinical trial data from two RCTs, finding that models combining PD-L1, TMB, and immune signatures outperform single biomarkers.

Auditory High Entropy Response (A-HER): A Novel Paradigm for Studying Brain Processing of Uncertain Information

The paper introduces A-HER, a paradigm that maximizes auditory stimulus entropy to study brain processing of uncertain information, showing improved signal-to-noise ratio and repeatability compared to other methods.

Senolytics enhance longevity in Caenorhabditis elegans by altering betaine metabolism

This study identifies betaine metabolism as a key factor in aging in C. elegans and shows that senolytics extend lifespan by increasing betaine levels and enhancing autophagy and antioxidant capacity.

Design of parallel ????-sheet nanofibrils using Monte-Carlo search, coarse-grained simulations, and experimental testing

The paper designs 7-mer peptides that self-assemble into parallel β-sheets using computational screening, simulations, and experimental validation.

Correlative single-cell hard X-ray tomography and X-ray fluorescence imaging

This paper develops a method to combine single-cell X-ray tomography and fluorescence imaging to study cellular structures and chemical element distributions.

Aster-dependent non-vesicular transport facilitates dietary cholesterol uptake

The paper identifies the Aster pathway as critical for dietary cholesterol uptake and shows it can be targeted with a small molecule inhibitor.

Sterile Soil as Prebiotics Mitigate Intergenerational Loss of Gut Microbial Diversity and Anxiety-Like Behavior Induced by Antibiotics in mice

This study shows that sterile soil prebiotics can restore gut microbial diversity and alleviate anxiety-like behavior and intestinal barrier issues caused by antibiotic exposure across generations in mice.

Metal-driven anaerobic oxidation of methane as an important methane sink in methanic cold seep sediments

The paper investigates metal-driven anaerobic methane oxidation in cold seep sediments, finding that Fe-AOM and Mn-AOM contribute ~3% to methane removal.

Cancer associated fibroblasts serve as an ovarian cancer stem cell niche through noncanonical Wnt5a signaling

This study shows that cancer-associated fibroblasts maintain ovarian cancer stem cells via noncanonical Wnt5a signaling, which contributes to chemoresistance and relapse.

Genomic Analysis of Blomia tropicalis Identifies Novel Allergens for Component-Resolved Diagnosis of Mite Allergy

This study identifies a comprehensive allergen profile of Blomia tropicalis and validates novel allergens for component-resolved diagnosis of mite allergy.

Design of 8-mer Peptides that Block Clostridioides difficile Toxin A in Intestinal Cells

The paper designs 8-mer peptides that block Clostridioides difficile toxin A in intestinal cells using a combination of computational and experimental methods.

Unexpected genetic and microbial diversity for arsenic cycling in deep sea cold seep sediments

The paper analyzes metagenomic and metatranscriptomic data from cold seeps to identify As-cycling genes and microbes, revealing unexpected diversity and functional roles in arsenic transformation.

Multi-Omic Analysis of Tyrophagus putrescentiae Reveals Insights into the Allergen Complexity of Storage Mites

This study reveals a comprehensive allergen profile of Tyrophagus putrescentiae using multi-omic approaches, identifying 37 allergen groups and five novel allergens.

Endogenous Plasmids and Reductive Genome Evolution in Host-Associated Bacteria

This study investigates reductive genome evolution in Cardinium endosymbionts, identifying endogenous plasmids and their enzymes as drivers of genome reduction.

Inflammatory bowel disease-associated gut commensals degrade components of the extracellular matrix

This study shows gut commensals degrade extracellular matrix components in vitro and links this activity to IBD progression through proteolytic and enzymatic mechanisms.

Predicting neoadjuvant chemotherapy benefit using deep learning from stromal histology in breast cancer

This study uses deep learning to predict neoadjuvant chemotherapy benefit in breast cancer using stromal histology, introducing the TS-score which outperforms existing predictors.

Circular RNA circGT1C1 drives gastric TIC self-renewal to initiate gastric tumorigenesis and metastasis

The paper was withdrawn due to poor experimental design and irreproducible results.

An expanded deep-branching thermophilic bacterial clade sheds light on the early evolution of bacteria

The paper isolates a novel thermophilic bacterium from a deep-sea hydrothermal vent and identifies it as part of a deep-branching clade that provides insights into early bacterial evolution.

Evolutionary ecology of microbial populations inhabiting deep sea sediments associated with cold seeps

The paper examines intraspecies diversity and evolutionary patterns of microbial populations in deep sea cold seep sediments, finding depth-dependent diversification and purifying selection on key metabolic genes.

PRMT5 as a Novel Druggable Vulnerability for EWSR1-ATF1-driven Clear Cell Sarcoma

This study identifies PRMT5 as a druggable target for EWSR1-ATF1-driven clear cell sarcoma, showing that its inhibition reduces tumor cell growth.

Structure of IgG-Fc hexamer reveals a mutual lock-and-key mode of Fc-Fc interaction

The paper determines the structure of an IgG-Fc hexamer using cryo-EM, revealing a mutual lock-and-key interaction mode between Fc domains.

Multiplexed imaging mass cytometry reveals distincttumor-immune microenvironments linked to immunotherapyresponses in melanoma

This study uses imaging mass cytometry to analyze tumor-immune microenvironments in melanoma patients, identifying distinct microenvironment archetypes linked to responses to anti-PD-1 therapy.

Systems medicine dissection of chromosome 1q amplification reveals oncogenic regulatory circuits and informs targeted therapy in cancer

This study identifies oncogenic regulatory circuits driven by chromosome 1q amplification in cancer and proposes targeted therapy strategies using a systems medicine approach.

DEAD-box RNA helicase 18 disrupts IRF3-binding to the interferon-β promoter

This study identifies DDX18 as a negative regulator of IRF3 binding to the IFN-β promoter, suppressing type I IFN production during viral infection.

Broad ultra-potent neutralization of SARS-CoV-2 variants by monoclonal antibodies specific to the tip of RBD

This paper identifies a monoclonal antibody, 2G1, that neutralizes all SARS-CoV-2 variants with high potency and describes its mechanism of action and therapeutic efficacy in animal models.

Enterotoxigenic Escherichia coli display a distinct growth phase before entry into stationary phase with shifts in tryptophan- fucose- and putrescine metabolism and degradation of neurotransmitter precursors

This paper identifies a transient metabolic and transcriptional phase in ETEC before stationary phase, marked by shifts in amino acid metabolism and neurotransmitter precursor degradation.