Zhi Xie

High-quality peptide evidence for annotating non-canonical open reading frames as human proteins

The paper identifies 25% of 7,264 non-canonical open reading frames (ncORFs) as producing translated gene products, supported by over 3,000 peptides from 3.8 billion mass spectra.

AetherCell: A generative engine for virtual cell perturbation and in vivo drug discovery

AetherCell is a generative model that unifies clinical and experimental data to predict drug responses and repurpose existing drugs in human contexts.

Deep Generative Optimization of mRNA Codon Sequences for Enhanced mRNA Translation and Therapeutic Efficacy

RiboDecode generates optimized mRNA codon sequences using deep learning, improving protein expression and therapeutic efficacy in vitro and in vivo.

An expanded reference catalog of translated open reading frames for biomedical research

The paper expands and refines a reference catalog of human non-canonical open reading frames (ncORFs) by incorporating more datasets and introducing a translation signature score framework to prioritize high-quality ncORFs.

Genomic Touchstone: Benchmarking Genomic Language Models in the Context of the Central Dogma

Genomic Touchstone evaluates genomic language models across 36 tasks and 88 datasets, revealing insights on model performance, scaling, and pretraining strategies.

SECE: accurate identification of spatial domain by incorporating global spatial proximity and local expression proximity

SECE improves spatial domain identification by integrating local and global spatial and expression relationships across multiple spatial transcriptomics datasets.

Graph pangenome reveals functional, evolutionary, and phenotypic significance of human nonreference sequences

The paper identifies and analyzes nonreference sequences in human genomes using long-read sequencing and graph-based pangenome methods, revealing their functional, evolutionary, and phenotypic significance.

Temporal landscape and translational regulation of A-to-I editing in mouse retina development

This study characterizes the temporal landscape of A-to-I editing in mouse retina development and shows its dynamic interplay with splicing and translation.

CRISPR-based targeted haplotype-resolved assemblies of a megabase region

This paper demonstrates a CRISPR-based method to construct haplotype-resolved assemblies of targeted genomic regions, achieving comparable accuracy with reduced cost and complexity.

A benchmark of structural variation detection by long reads through a realistic simulated model.

The paper benchmarks structural variation detection using long reads through a simulated model, finding that combining multiple callers improves recall and precision.

Structural variants in Chinese population and their impact on phenotypes, diseases and population adaptation

The paper performs long-read sequencing in 405 Chinese individuals to discover and characterize structural variants, finding novel SVs and their associations with phenotypes and diseases.

Widespread translational control regulates retinal development in mouse

This study identifies widespread translational regulation during mouse retinal development, revealing dynamic translational changes and novel micropeptides involved in retinal function.

On exploring effects of coevolving residues on DNA binding specificity of transcription factors

The paper investigates how coevolving residues in transcription factors influence DNA binding specificity and shows their functional importance in transcriptional regulation.

A spatiotemporal translatome of mouse tissue development

This study quantifies translational regulation in six mouse tissues across development, identifying spatiotemporal patterns of gene expression and new translational components.

riboCIRC: a comprehensive database of translatable circRNAs

riboCIRC provides a database of translatable circRNAs with computational predictions, experimental validations, and cross-species conservation analysis.

MicroPhenoDB associates metagenomic data with pathogenic microbes, microbial core genes, and human disease phenotypes

MicroPhenoDB connects metagenomic data to pathogenic microbes, core genes, and disease phenotypes through curated associations and a score model.

MECAT: an ultra-fast mapping, error correction and de novo assembly tool for single-molecule sequencing reads

MECAT provides an ultra-fast tool for mapping, error correction, and de novo assembly of single-molecule sequencing reads, achieving high-quality assemblies with reduced computational cost.