Hao Zhang

A genetically encoded redox bottleneck constrains human developmental rate

This paper identifies a genetic bottleneck in the G3P shuttle that limits human developmental rate by constraining metabolic flux and the segmentation clock.

A disease dynamics atlas forecasts patient states and maps molecular programs in ALS

The paper develops DynaALS, a disease dynamics atlas for ALS that maps patient states and molecular programs using longitudinal medical records and multi-omics data.

AAB-seq: An antigen-specific and affinity-readable high-throughput BCR sequencing method

AAB-seq identifies antigen-binding antibodies with affinity information from single-cell BCR sequencing in immunized mice.

Time-dependent transcriptomic changes following protoplast isolation in plants

The paper characterizes time-dependent transcriptomic changes in plant protoplasts across species and identifies stress-like cell states in single-cell RNA-seq data.

Core gastric microbiota linked to pathogenesis and preserved across age stratified cohorts

The paper identifies a core gastric microbiota composed of 11 genera that persists across age groups and is linked to gastric disease risk and cancer.

The Vagus Nerve conducts viable translocation of gut flora to the lungs that impacts interstitial lung disease severity in mice

This study shows the vagus nerve translocates gut bacteria to the lungs in mice, affecting lung disease severity and fibrosis.

Mechanical confinement drives monocyte-to-macrophage differentiation

This study shows mechanical confinement drives monocyte-to-macrophage differentiation via a mechanoepigenetic pathway involving KDM6B and H3K27me3 demethylation.

Vacuum and sonication treatment enables efficient transient gene expression in various monocot and eudicot plant seedlings

This paper introduces VAST, a method improving transient gene expression in plant seedlings, showing enhanced efficiency across multiple species.

Functional Locality-Aligned Learning Reveals Structure-Function Causality in Enzyme Kinetics

This paper introduces EnzymePlex, a framework that improves enzyme kinetic parameter prediction by aligning structural and functional representations, achieving better generalization and mechanistic insights.

Vis-OCT Explorer: an open-source software for visible-light optical coherence tomography data processing

Vis-OCT Explorer processes vis-OCT data to improve image quality and measurement repeatability for retinal analysis.

Sampling Function-Related Metastable States of Proteins With DASH

DASH samples function-related metastable states of proteins, revealing new folding states and allosteric sites, verified by experiments and crystal structures.

Superinfection with intact HIV-1 results in conditional replication of defective proviruses and nonsuppressible viremia in people living with HIV-1

The paper investigates superinfection with intact HIV-1 in people living with HIV-1, showing it leads to conditional replication of defective proviruses and nonsuppressible viremia.

RESM: Capturing sequence and structure encoding of RNAs by mapped transfer learning from ESM (evolutionary scale modeling) protein language model

RESM improves RNA sequence-structure-function prediction by transferring knowledge from protein language models, outperforming existing models in multiple tasks.

MFPLI: A Computational Framework for Assessing Biological Authenticity of Protein-Ligand Interactions Using Molecular Fingerprints and Structural Features

MFPLI evaluates protein-ligand binding authenticity using deep learning with physicochemical and structural features, achieving high accuracy in distinguishing native conformations from docking poses.

Elucidation and de novo Reconstitution of Glyceollin Biosynthesis

This study identifies and reconstructs the complete glyceollin biosynthetic pathway in soybean, enabling sustainable production in yeast.

Integrating large-scale meta-GWAS and PigGTEx resources to decipher the genetic basis of complex traits in pig.

The paper performs a multi-breed meta-GWAS in pigs to identify genomic regions associated with complex traits and integrates with PigGTEx to prioritize variant-gene-tissue-trait circuits.

Mitochondrial pyruvate transport regulates presynaptic metabolism and neurotransmission

This study shows that pyruvate supports neuronal viability without glucose and that mitochondrial pyruvate uptake regulates synaptic transmission in hippocampal terminals.

Establishment of a novel non-integrated human pluripotent stem cell-based gastruloid model

This study develops a human pluripotent stem cell-based gastruloid model that mimics early human embryonic development and identifies thalidomide's effect on gastrulation.

NcPath: A novel tool for visualization and enrichment analysis of human non-coding RNA and KEGG signaling pathways

NcPath integrates and visualizes miRNA and lncRNA interactions with KEGG pathways, enabling enrichment analysis of non-coding RNA involvement in biological processes.

Exploration of miRNA-mediated fertility regulation network of cytoplasmic male sterility during flower bud development in soybean

The paper identifies miRNAs and their targets involved in soybean cytoplasmic male sterility by analyzing small RNA and degradome libraries from CMS and restorer lines.

Illuminating microbial metabolic activities in the dark deep ocean with metaproteomics

This study uses metaproteomics to analyze microbial metabolic activity in the deep ocean, revealing key functional groups and metabolic processes involved in carbon cycling.

Sub-voxel light-sheet microscopy for high-resolution, high-throughput volumetric imaging of large biomedical specimens