Chi Zhang

Mechanistic Investigation of Reversible Hibernation-Driven Immune Suppression in Thirteen-Lined Ground Squirrels

This study investigates immune suppression during torpor in 13-lined ground squirrels using single-cell RNA sequencing and image analysis, identifying metabolic and lineage-specific programs that conserve energy while preserving immune function.

OsRAD23a negatively regulates salt tolerance and phosphorus uptake in rice

This study shows that OsRAD23a negatively regulates salt tolerance and phosphorus uptake in rice through domain-specific mechanisms involving interactions with OsSPX2 and OsPHR2.

radioGWAS: link radiome to genome to discover driver genes with somatic mutations for heterogeneous tumor image phenotype in pancreatic cancer

This study links radiomic features to genome-wide associations in pancreatic cancer to identify driver genes associated with tumor structural heterogeneity and patient survival.

Identification of RNA-based cell-type markers for the stem cell manufacture system with a statistical scoring function

The paper identifies RNA-based cell-type markers for stem cell manufacture using a statistical scoring function and validates them with deep learning and simulated data.

A role for heritable transcriptomic variation in maize adaptation to temperate environments

This study investigates how heritable transcriptomic variation contributes to maize adaptation to temperate environments through eQTLs, sQTLs, and gene expression patterns.

Deeplearning based MHC epitope prediction for cancer neoantigen discovery

This paper uses XGBoost with tri-peptide similarity to predict MHC epitopes for cancer neoantigen discovery, tested on experimentally validated peptides.

Temporal Gene Coexpression Network Analysis Using A Low-rank plus Sparse Framework

This paper introduces TGCN, a method for analyzing temporal transcriptomic data using a low-rank plus sparse framework, improving covariance estimation and identifying robust gene modules.

The genetic basis of cis-regulatory divergence between the subspecies of cultivated rice (Oryza sativa)

This study characterizes transcriptome and cis-regulatory divergence between rice subspecies Indica and Japonica using transcriptome data from 91 accessions, identifying subspecies-specific eQTL and patterns of genetic diversity.

Using LASSO in gene co-expression network for genome-wide identification of gene interactions responding to salt stress in rice

The paper applies LASSO to a gene co-expression network in rice under salt stress to identify gene interactions linked to salt tolerance.

Phosphate starvation induces replacement of phospholipids with the betaine lipid diacylglycerol-N,N,N-trimethylhomoserine in the human fungal pathogen Candida albicans

This study shows that phosphate starvation in Candida albicans replaces phospholipids with DGTS via CaBTA1, affecting biofilm formation and virulence.