Chen Chen

Distinct processing of visual motion by transcriptomic cell types in the superior colliculus

The paper identifies how three transcriptomic cell types in the superior colliculus process visual motion with distinct feature selectivity, morphology, and connectivity.

DYNAMIC CONFORMATIONS IN THE ACTIVATION OF PINK1 KINASE

This study identifies conformational dynamics and dimer formation in TcPINK1, showing their role in Parkin recruitment and mitophagy.

A multimodal foundation model linking histopathology and DNA methylation

HistoMethyl links histopathology with DNA methylation to predict molecular features from H&E slides alone, improving mutation prediction and survival outcomes across multiple cancer cohorts.

On the state of protein function prediction: a report on the fourth CAFA challenge

This paper reports on the fourth CAFA challenge, showing improvements in Gene Ontology term prediction but highlighting challenges in new evaluation settings.

Repurposing of the assembly chaperone PAC1-PAC2 defines a specialized proteasome landscape in mature mammalian sperm

This study identifies a specialized proteasome structure in mature mammalian sperm using cryo-EM, revealing that PAC1/2 repurposes from a chaperone to a stable regulator, defining a hyperactive 20S variant.

Foxp4+ Mandibular Skeletal Stem Cells Orchestrate Bone/Tooth Development and Regeneration

This study identifies Foxp4+ mandibular skeletal stem cells (mdSSCs) that drive bone/tooth development and regeneration, showing their therapeutic potential in regenerating mandibular structures.

rRNA Expansion Segments Mediate Ribosome Dimerization as a Conserved Stress Response

The paper investigates the cellular response to puromycin-induced translation stress and identifies ribosome dimerization mediated by rRNA expansion segments as a conserved stress response mechanism.

STING agonist-mediated endothelial cell activation drives NK cells and neutrophils-dependent pulmonary inflammation

This study identifies the endothelial cell-NK cell-neutrophil axis as a key driver of STING agonist-induced pulmonary inflammation and toxicity.

Transient centrosome loss in cultured prostate epithelial cells induces chromosomal instability to produce an oncogenic genotype that correlates with poor clinical outcomes

The paper shows that transient centrosome loss in prostate cells causes chromosomal instability, leading to oncogenic changes linked to poor clinical outcomes.

MOH: a novel multilayer multi-omics heterogeneous graph for single-cell clustering

MOH improves single-cell clustering by integrating three omics types into a multilayer heterogeneous graph, achieving better performance than existing methods.

Towards Human Inverse Dynamics from Real Images: A Dataset and Benchmark for Joint Torque Estimation

This paper introduces a dataset and benchmark for estimating joint torques from real human images, achieving state-of-the-art performance on multiple evaluation criteria.

CircSMAD3 represses VSMC phenotype switching and neointima formation via promoting hnRNPA1 ubiquitination degradation

This study identifies circSMAD3 as a regulator that suppresses vascular smooth muscle cell proliferation and neointima formation by promoting hnRNPA1 degradation.

The landscape of tolerated genetic variation in humans and primates

The paper uses primate genetic data to predict human variant pathogenicity with a deep learning classifier trained on 4.3 million common missense variants.

Joint inference of transcription factor activity and context-specific regulatory networks

This paper introduces TIGER, a method that infers transcription factor regulomes and activities from RNA-seq data, showing improved accuracy in yeast and cancer cell lines and potential for single-cell analysis.

METTL8 is required for 3-methylcytosine modification in human mitochondrial tRNAs

This study identifies METTL8 as the enzyme responsible for 3-methylcytosine modification in human mitochondrial tRNAs and shows its role in tRNA folding.

MVP: predicting pathogenicity of missense variants by deep learning

MVP uses deep learning to predict pathogenicity of missense variants, outperforming previous methods in prioritizing pathogenic variants.

An Mtb-Human Protein-Protein Interaction Map Reveals that Bacterial LpqN Antagonizes CBL, a Host Ubiquitin Ligase that Regulates the Balance Between Anti-Viral and Anti-Bacterial Responses

The paper identifies Mtb-human protein-protein interactions, showing LpqN antagonizes CBL, a host ubiquitin ligase that balances anti-viral and anti-bacterial responses in macrophages.

Budding yeast chromatin is dispersed in a crowded nucleoplasm in vivo

This study uses electron cryotomography to show that budding yeast chromatin lacks 30-nm fibers and is in an open configuration, suggesting transcription regulation through local nucleosome interactions.