Guoshuai Cai

Large-scale association study identifies lung cancer susceptibility copy number variants and their potential functional role in genetic instability

The paper identifies lung cancer susceptibility copy number variants (CNVs) and shows their potential role in genomic instability through association analyses and functional validation.

YAP/TAZ Signaling in Endothelial Cells Mediates the Pathogenesis of Abdominal Aortic Aneurysm Formation

This study identifies YAP/TAZ signaling in endothelial cells as a key mediator of abdominal aortic aneurysm formation and shows that pharmacological inhibition reduces AAA progression.

Divergent chromatin remodeling in post-sepsis MDSCs underlies MHC class II repression in CCI

The paper profiles chromatin accessibility in post-sepsis MDSCs, showing divergent epigenetic trajectories between rapid recovery and chronic critical illness, with MHC class II repression in CCI.

CN-RNN: a Deep Learning Framework for Copy Number Variation Detection with Exome Sequencing Data

CN-RNN is a deep learning framework for detecting copy number variations from exome sequencing data, showing improved performance over existing methods.

Prolonged Loss of Oxidative Phosphorylation and Mitochondrial Mass Characterize CD66b+ Leukocytes from Patients with Sepsis

This study identifies prolonged reduced oxidative metabolism and mitochondrial mass in CD66b+ leukocytes from sepsis patients, linked to adverse outcomes and gene silencing.

Age- and Sex- Driven Transcriptional and Metabolic Diversity in Myeloid-Derived Suppressor Cells After Mouse Sepsis

This study examines age and sex effects on MDSCs in sepsis using single-cell RNA sequencing, finding differences in expansion, transcriptome, and metabolism.

Pharmacologic Inhibition of Ferroptosis Attenuates Experimental Abdominal Aortic Aneurysm Formation

This study shows that inhibiting ferroptosis with liproxstatin-1 reduces AAA formation by decreasing inflammation and aortic remodeling in mice.

Sepsis Induces Age- and Sex-Specific Chromatin Remodeling in Myeloid-derived Suppressor Cells

This study maps epigenetic changes in MDSCs after sepsis, revealing age- and sex-specific chromatin remodeling linked to immune dysfunction.

Lipoxin A4/FPR2 signaling mitigates ferroptosis of alveolar epithelial cells via NRF2-dependent pathway during lung ischemia-reperfusion injury

This study shows that LxA4/FPR2 signaling reduces ferroptosis in alveolar epithelial cells via NRF2 activation, protecting against lung ischemia-reperfusion injury.

Gasdermin D deficiency attenuates development of ascending aortic dissections in a novel mouse model

This paper develops a novel mouse model of ascending aortic dissection and shows that Gsdmd deficiency reduces dissection severity by modulating cell death and T-cell responses.

HapCNV: A Comprehensive Framework for CNV Detection in Low-input DNA Sequencing Data

HapCNV improves CNV detection in low-input haploid sequencing data by using a pseudo-reference to reduce bias and enhance accuracy, especially for short CNVs.

Spatial pattern and differential expression analysis with spatial transcriptomic data

This paper introduces SPADE, a method for identifying spatially variable genes in spatial transcriptomic data, showing improved performance over existing methods in both within and between-group analyses.

OSCAA: A Two-Dimensional Gaussian Mixture Model for Copy Number Variation Association Analysis

OSCAA improves CNV-disease association analysis by integrating CNV detection and association testing in a single step, enhancing accuracy and power.

A statistical learning method for simultaneous copy number estimation and subclone clustering with single cell sequencing data

This paper introduces FLCNA, a statistical method for simultaneous copy number estimation and subclone clustering in scDNA-seq data, showing improved performance over existing methods in breast cancer samples.

Considering Zeros in Single Cell Sequencing Data Correlation Analysis

This study evaluates methods for estimating correlation coefficients in single-cell sequencing data and finds that filtering zeros and considering drop-out probability improves accuracy.

SEEK to Identify Super Enhancer-Expression Correlated Pairs using Single-cell Multi-omic Data

This study introduces a computational method to identify super enhancer-expression correlated pairs using single-cell multi-omic data and applies it to brain tissues to uncover cell-type markers and functional insights.

BMI-CNV: A Bayesian framework for multiple genotyping platforms detection of copy number variation

BMI-CNV improves CNV detection by integrating WES and microarray data across samples, showing better accuracy and identifying lung cancer risk regions.

Integrating Genomic Correlation Structure Improves Copy Number Variations Detection

This paper introduces LDcnv, a novel algorithm that improves copy number variation detection by integrating genomic correlation structure, showing higher accuracy and precision than existing methods.

SCANNER: A Web Resource for Annotation, Visualization and Sharing of Single Cell RNA-seq Data

SCANNER is a web resource that enables biologists to analyze, visualize, and share scRNA-seq data without coding skills, identifying differences in gene expression related to smoking and cancer-associated cells.

RNA-seq analyses of molecular abundance (RoMA) for detecting differential gene expression

RoMA improves differential gene expression detection in RNA-seq by integrating mRNA abundance and raw counts, showing high accuracy and robustness in simulated and real data.