Shida Zhu

Genos-m: a foundation model for human-associated microbial genomes

Genos-m is a foundation model for human-associated microbial genomes that outperforms existing models in gene-fitness prediction and community structure analysis.

Comparison of double-stranded and single-stranded cfDNA library construction methods for targeted genome and methylation sequencing

This study compares two cfDNA library construction methods for targeted genome and methylation sequencing, finding dsLib better for mutation detection and ssLib better for methylation analysis.

Mendelian randomization analyses support causal relationships between blood metabolites and the gut microbiome

This study uses Mendelian randomization to identify causal relationships between gut microbiome composition and blood metabolites in a Chinese cohort.

Metagenome-genome-wide association studies reveal human genetic impact on the oral microbiome

This study identifies genetic loci associated with the oral microbiome using metagenome-genome-wide association studies in over 1,915 individuals.

Genetic characteristics of human papillomavirus type 16, 18, 52 and 58 in southern China

The paper analyzes the genetic diversity of HPV types 16, 18, 52, and 58 in southern China, identifying sublineages and mutations associated with oncogenic potential.

Clinical and molecular diagnostic study of 320 Chinese children with epilepsy by Genome Sequencing

This study evaluates genome sequencing in 320 Chinese children with epilepsy, finding pathogenic variants in 38.13% and demonstrating its diagnostic and therapeutic value.

Population Bottlenecks and Intra-host Evolution during Human-to-Human Transmission of SARS-CoV-2Population Bottlenecks and Intra-host Evolution during Human-to-Human Transmission of SARS-CoV-2

This study compares SARS-CoV-2 viral populations in COVID-19 patients to show narrow transmission bottlenecks and stochastic dynamics in intra-host and inter-host evolution.

Multiple approaches for massively parallel sequencing of HCoV-19 (SARS-CoV-2) genomes directly from clinical samples

This paper compares amplicon, hybrid capture, and metatranscriptomic sequencing methods for directly sequencing SARS-CoV-2 genomes from clinical samples, finding differences in bias, sensitivity, and accuracy.

Single cell chromatin accessibility of the developmental cephalochordate

This study creates the first single-cell chromatin accessibility atlas of the lancelet, revealing regulatory elements and developmental trajectories.

Genome sequencing combining prenatal ultrasound in the evaluation of fetal CNS structural anomalies

This study evaluates genome sequencing for diagnosing fetal CNS structural anomalies, finding a 38.9% overall diagnostic yield and higher rates in specific malformations.

Whole genome and RNA sequencing of 1,220 cancers reveals hundreds of genes deregulated by rearrangement of cis-regulatory elements

The paper identifies hundreds of genes deregulated by SVs in cancer, showing increased expression linked to SV breakpoints and enhancer elements.

Intratumor Heterogeneity and Evolution of Colorectal Cancer

This study examines intratumor heterogeneity and evolution patterns in colorectal cancer, finding a Darwinian pattern with differences between right-sided and left-sided tumors.

Single cell atlas of trisomy 21 cerebral cortex

This study creates the first single cell atlas of T21 cerebral cortex, identifying dysregulated genes and developing a platform for data exploration.

Single cell atlas of domestic pig brain illuminates the conservation and divergence of cell types at spatial and species levels

This study creates the first single-cell brain atlas of domestic pigs, identifies cell types and their spatial distribution, and compares them with other species to reveal evolutionary and disease-related insights.

PALM-Seq: simultaneous sequencing of cell-free long RNA and small RNA

PALM-Seq simultaneously sequences cell-free long and small RNA, identifying pregnancy-related RNAs and sample-specific signatures in plasma, amniotic fluid, leukocytes, and placentas.

Age-dependent sexual dimorphism in the adult human gut microbiota

This study identifies age-related sex differences in gut microbiota composition and functionality across two population cohorts, showing women have more diverse and stable microbiota than men, with sex differences diminishing in older adults.

Nationwide population genetic screening improves outcomes of newborn screening for hearing loss in China

This study shows that adding genetic screening to newborn hearing tests in China improves detection and reduces loss-to-follow-up, with significant benefits for identifying preventable hearing loss.

Deconvolution of single-cell multi-omics layers reveals regulatory heterogeneity

The paper introduces scCAT-seq, a method to simultaneously assay chromatin accessibility and transcriptome in single cells, and demonstrates its application in human pre-implantation embryos to reveal regulatory heterogeneity.

Single-cell RNA-seq reveals dynamic transcriptome profiling in human early neural differentiation

This study uses single-cell RNA-seq to analyze transcriptome dynamics during human early neural differentiation, identifying novel transcription factors and regulatory elements involved in the process.

Comprehensive analysis of immune evasion in breast cancer by single-cell RNA-seq

This study uses single-cell RNA-seq to analyze the tumor microenvironment of breast cancer, revealing cell type diversity and immune evasion mechanisms.

Recovered and dead outcome patients caused by influenza A (H7N9) virus infection show different pro-inflammatory cytokine dynamics during disease progress and its application in real-time prognosis

This study analyzes cytokine dynamics in H7N9-infected patients with different outcomes, identifying predictors and a real-time prognosis model.

Genomic basis for RNA alterations revealed by whole-genome analyses of 27 cancer types

The paper analyzes RNA alterations across 27 cancer types using whole-genome sequencing data, identifying gene expression associations with DNA variants and structural fusions.