Y. Bai

Genomic evolution reshapes cell type diversification in the amniote brain

The paper creates a single-cell atlas of amniote brains to study cell type diversification and identifies species-specific gene expression patterns and novel cell subtypes.

Identifying the gene responsible for NPQ reversal in Phaeodactylum tricornutum

This study identifies ZEP3 as the gene responsible for NPQ reversal in Phaeodactylum tricornutum and shows its impact on photosynthetic efficiency.

Epstein-Barr Virus Orchestrates Spatial Reorganization and Immunomodulation within the Classic Hodgkin Lymphoma Tumor Microenvironment

This study uses spatial multi-omics to compare EBV-positive and EBV-negative cHL, identifying distinct TME features and immunological signatures linked to EBV.

A Spatial Multi-Modal Dissection of Host-Microbiome Interactions within the Colitis Tissue Microenvironment

This study introduces MicroCart, a framework for spatial multi-omics analysis of host-microbiome interactions in colitis, revealing tissue-level immune responses and microbial shifts.

RGS10 deficiency facilitates distant metastasis by inducing epithelial-mesenchymal transition in breast cancer

This study shows RGS10 deficiency promotes breast cancer metastasis via EMT by mechanisms involving lipocalin-2 and miR-539-5p.

LHP1 and INO80 cooperate with ethylene signaling for warm ambient temperature response by activating specific bivalent genes

This study shows that LHP1 and INO80 work with ethylene signaling to activate specific bivalent genes in response to warm temperatures in Arabidopsis.

Degradation of indole-3-acetic acid by plant-associated microbes

This study identifies bacterial isolates capable of degrading indole-3-acetic acid (IAA) from Arabidopsis and rice roots, revealing their functional roles and association with IAA producers.

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.

Screening for metastasis-related genes in mouse melanoma cells through sequential tail vein injection

This study screens for metastasis-related genes in mouse melanoma cells using sequential tail vein injection and identifies differentially expressed genes associated with metastasis.

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.

New insights on the role of SlDMR6-1 in drought avoidance in tomato

This study shows that disabling SlDMR6-1 in tomato increases drought tolerance by reducing transpiration and enhancing water use efficiency, while also improving resistance to Late Blight.

Discovering Novel Prognostic Biomarkers of Hepatocellular Carcinoma using eXplainable Artificial Intelligence

This study uses explainable AI to identify novel genetic biomarkers for HCC prognosis, showing improved accuracy over AFP and highlighting demographic-specific relevance.

Injury induced renal fibrosis promotes cystogenesis and cyst growth in adult mice with autosomal dominant polycystic kidney disease

This study shows that renal fibrosis induced by injury promotes cyst formation and growth in adult ADPKD mice, and targeting EZH2 can reduce fibrosis and cyst growth.

The human LIN28B nucleosome is inherently pre-positioned for efficient binding of multiple OCT4s without H3 K27 acetylation

This study compares two studies on OCT4 and LIN28B nucleosome interactions, finding that nucleosome positioning and H3 K27 acetylation do not significantly affect OCT4 binding.

SARS-CoV-2 N protein-induced Dicer, XPO5, SRSF3, and hnRNPA3 downregulation causes pneumonia

This study shows that SARS-CoV-2 N protein reduces Dicer, XPO5, SRSF3, and hnRNPA3, leading to pneumonia, and that inhibitors can reverse this effect.

Age-related STAT3 signaling regulates severity of respiratory syncytial viral infection in human bronchial epithelial cells

The paper shows that age-related STAT3 signaling impairment in neonatal bronchial epithelial cells increases RSV infection severity, while SARS-CoV-2 is unaffected by age.

Sequential breakdown of the complex Cf-9 leaf mould resistance locus in tomato by Fulvia fulva

This study identifies Avr9B, an effector that allows F. fulva to overcome Cf-9B resistance in tomato, showing sequential breakdown of the Cf-9 locus.

Structural mechanism of synergistic targeting of the CX3CR1 nucleosome by PU.1 and C/EBP

This study reveals how PU.1 and C/EBP synergistically target the CX3CR1 nucleosome by altering DNA positioning and displacing H1 to open chromatin.

Chromosome level assembly of wild spinach provides insights into the divergence of homo- and heteromorphic plant sex-chromosomes.

The paper assembles genomes of wild spinach species and compares them with cultivated spinach to study sex chromosome evolution and divergence.

MAPS: Pathologist-level cell type annotation from tissue images through machine learning

MAPS provides pathologist-level cell type annotation from spatial proteomics data using machine learning, outperforming existing methods in speed and accuracy.

Neo-functionalization and co-option of Pif genes facilitate the evolution of a novel shell microstructure in oysters

This study identifies neo-functionalization and co-option of Pif genes in oysters that contribute to the evolution of a novel shell microstructure called chalky calcite.

The DEAD-box helicase RCF1 plays roles in miRNA biogenesis and RNA splicing in Arabidopsis

This study identifies RCF1 as a key player in miRNA biogenesis and RNA splicing in Arabidopsis by showing its role in pri-miRNA processing and splicing defects in a mutant.

Quorum-sensing gene regulates hormetic effects induced by sulfonamides in Comamonadaceae

The paper shows that sulfonamides induce hormesis in Comamonas testosteroni by activating a quorum-sensing gene that enhances nucleotide synthesis for cell proliferation.

Streamlined regulation of chloroplast development in the liverwort Marchantia polymorpha

The paper investigates chloroplast development regulation in liverwort Marchantia polymorpha, finding that GLK controls chloroplast biogenesis while GATA and SCL have no detectable roles.

Plant selection and ecological microhabitat drive domestications of shrub-associated microbiomes in a revegetated shrub ecosystem

This study examines how plant selection and ecological microhabitats influence the microbiomes of revegetated shrubs, finding that microhabitats, not plant species, primarily drive microbial community composition.

Structural mechanism of LIN28B nucleosome targeting by OCT4 for pluripotency

This study determines the structural mechanism by which OCT4 targets the LIN28B nucleosome through multivalent interactions, DNA unwrapping, and H1 eviction to initiate cell reprogramming.

MYSM1 co-activates ERα action via histone and non-histone deubiquitination to confer antiestrogen resistance in breast cancer

This study identifies MYSM1 as an ER co-activator that promotes antiestrogen resistance in breast cancer through histone and non-histone deubiquitination.

DNA primase large subunit is an essential plant gene for geminiviruses, putatively priming viral ss-DNA replication

This study identifies the DNA primase large subunit (PRiL) as essential for geminiviral DNA replication in plants, showing that mutations in PRiL confer resistance to ToLCNDV.

Mechanistic dissection of alga recognition and uptake in coral-algal endosymbiosis

The paper identifies LePin as a key lectin in coral-algal recognition and uses RNAi and scRNA-seq to uncover gene programs and receptors involved in algal uptake and symbiosome formation.

Analysis and Identification of Necroptosis Landscape on Therapy and Prognosis in Bladder Cancer

This study identifies a necroptosis-related gene signature (NRGscore) to predict prognosis and therapeutic response in bladder cancer patients using TCGA data.