Hao Chen

Unified cell segmentation for spatial transcriptomics via transcript reassignment

Tracel improves cell segmentation in spatial transcriptomics by assigning transcripts to cells using optimal transport, enhancing cell-type separation and reducing contamination.

Interspecific hybrids reveal a deeply conserved nuclear role of EIF1A-family proteins in zygotic genome activation

The paper uses interspecific hybrid embryos to identify EIF1A-family proteins as conserved nuclear regulators of zygotic genome activation across mammals.

A nanoconfined liquid-in-ice aqueous regime for time-stretched single-molecule dynamics

This paper demonstrates a nanoconfined liquid-in-ice environment that enables real-time single-molecule dynamics measurements in deeply subzero conditions by overcoming water freezing limitations.

Histone modifications analysis reveals enhancers reprogramming during maternal-to-zygotic transition

This study analyzes histone modifications H3K4me1 and H3K27ac during maternal-to-zygotic transition in mouse embryos, revealing dynamic reprogramming and enhancer type changes.

Testicular mRNA-LNP Delivery: A Novel Therapy for Genetic Spermatogenic Disorders

This paper develops a spermatocytes-tropic mRNA-LNP delivery system to treat genetic spermatogenic disorders, showing restoration of spermatogenesis in mouse models.

scChat: A Large Language Model-Powered Co-Pilot for Contextualized Single-Cell RNA Sequencing Analysis

scChat is a large language model co-pilot for scRNA-seq analysis that integrates contextual reasoning to improve hypothesis generation and experimental design.

Depletion of rRNA Methyltranferase METTL5 Enhances Anti-Tumor Immune Response via Neoantigen Generated from Cryptic Translation

This study shows that inhibiting METTL5 increases neoantigen production and enhances anti-tumor immunity through non-canonical translation in murine models.

Early onset memory deficit of WMI rats compared to their nearly isogenic WLIs is reversed by enriched environment in females

This study shows that enriched environment reverses early-onset memory deficits in middle-aged WMI female rats, with associated changes in estradiol and mitochondrial function.

Genetically Programmable Adhesive Protein Hydrogels for Sealing Perforating Corneal Trauma

This paper develops a genetically programmable protein hydrogel for sealing corneal perforations in animal models, showing effective adhesion and biocompatibility.

Heightened Hedonic Impact and Drug Seeking Drive the Dramatic and Heritable Augmentation of Oxycodone Intake in Rats

The paper identifies 'Augmenter' rat strains with increased oxycodone intake during extended access, showing heightened hedonic impact drives heritable, female-biased augmentation of drug consumption.

FGF8 promotes lipid droplet accumulation via the FGFR1/p-p38 axis in chondrocytes

This study shows FGF8 promotes lipid droplet accumulation in chondrocytes through the FGFR1/p-p38 signaling pathway by upregulating perilipin1 expression.

RatXcan: A framework for cross-species integration of genome-wide association and gene expression data

RatXcan extends transcriptome-wide association studies to rats, enabling cross-species integration of GWAS and gene expression data to identify shared genetic mechanisms of complex traits.

The exotic thymidine modification 5-hydroxymethyluridine in dinoflagellate Amphidinium carterae

The paper identifies the enzyme responsible for 5-hydroxymethyluridine (5hmU) production in dinoflagellates and shows its role in silencing transposable elements through epigenetic marking.

The highly abundant mRNA m1A modification: a new layer of gene regulation in dinoflagellates

This study identifies m1A as the prevalent mRNA modification in dinoflagellates, showing its role in post-transcriptional regulation of translation efficiency.

Modeling Protein Structure Using Geometric Vector Field Networks

This paper introduces a novel vector field network for protein structure modeling, achieving improved performance over existing methods in inverse folding tasks.

Automated quantitative trait locus analysis (AutoQTL)

AutoQTL automates QTL analysis and GWAS by applying machine learning to detect both additive and non-additive genetic effects in genetic data.

Genome-Wide Association Study Finds Multiple Loci Associated with Intraocular Pressure in HS Rats

This study performs a GWAS in HS rats to identify genetic loci associated with intraocular pressure, finding three genome-wide significant loci and five candidate genes, including novel ones.

Resetting of H3K4me2 during mammalian parental-to-zygote transition

This study investigates the erasure and re-establishment of H3K4me2 during mouse zygote formation and early embryo development, revealing its role in epigenetic reprogramming and zygotic genome activation.

SVJAM: Joint Analysis of Structural Variants Using Linked Read Sequencing Data

SVJAM improves structural variant calling in linked-read data by jointly analyzing multiple samples, recovering missed variants and correcting incorrect types compared to LongRanger.

Whole genome sequencing of nearly isogeneic WMI and WLI inbred rats identifies genes potentially involved in depression

The paper uses whole genome sequencing to compare nearly isogenic WMI and WLI inbred rats, identifying genetic variants associated with depression and stress-related traits.

Genome wide association study in 3,173 outbred rats identifies multiple loci for body weight, adiposity, and fasting glucose

Computational approaches towards reducing contamination in single-cell RNA-seq data

The paper presents two computational methods to reduce contamination in single-cell RNA-seq data, improving clustering and biological interpretation.

PCIF1 catalyzes m6Am mRNA methylation to regulate gene expression

The paper identifies PCIF1 as the first human m6Am methyltransferase and shows it regulates gene expression by suppressing cap-dependent translation through m6Am methylation.