Xianwen Ren

Visual analysis of spatial transcriptomics data with RedeViz

RedeViz enhances and visualizes spatial transcriptomics data with subcellular resolution, providing HE-stain-like visualization across multiple platforms and scales.

SARS-CoV-2 shedding dynamics in human respiratory tract

This study identifies the dominant modes of SARS-CoV-2 shedding in the human respiratory tract across different infection phases using metagenomic data and a novel algorithm.

Spatial Transcriptomics Prediction from Histology Images at Single-cell Resolution using RedeHist

RedeHist predicts spatial transcriptomics data from histology images at single-cell resolution using deep learning, outperforming existing methods in accuracy and gene imputation.

An immunoediting map of human cancers

The paper constructs an immunoediting map of human cancers by analyzing single-cell data from 11057 tumor samples and 17382 healthy samples, revealing common immune cell state changes across cancer types.

The immune map of human body

The paper constructs a high-resolution immune map using single-cell deconvolution of RNA-seq samples from 30 tissues, revealing immune cell distributions across different sexes and ages.

Rapid and Signal Crowdedness-Robust In-Situ Sequencing through Hybrid Block Coding

The paper introduces SPRINTseq, a spatial transcriptomics method that enables fast, sensitive, and high-resolution data acquisition, revealing cellular and subcellular molecular architecture in Alzheimer's disease.

Cell segmentation and gene imputation for imaging-based spatial transcriptomics

RedeFISH improves imaging-based spatial transcriptomics by simultaneously segmenting cells and imputing gene expression using single-cell RNA sequencing data.

Spatial transcriptomics deconvolution at single-cell resolution by Redeconve

Redeconve deconvolutes spatial transcriptomics data at single-cell resolution, outperforming existing methods in accuracy and speed across multiple datasets.

Human genetic variants associated with COVID-19 severity are enriched in immune and epithelium regulatory networks

Direct Comparative Analysis of 10X Genomics Chromium and Smart-seq2

This study directly compares 10X Genomics Chromium and Smart-seq2 scRNA-seq platforms, finding differences in gene detection, noise, dropout rates, and differential expression, with recommendations for platform selection based on study goals.

Large-scale single-cell analysis reveals critical immune characteristics of COVID-19 patients

This study uses single-cell RNA sequencing to analyze immune responses in COVID-19 patients, identifying key immune cell changes and molecular pathways linked to disease severity.

ROGUE: an entropy-based universal metric for assessing the purity of single cell population

ROGUE quantifies cell cluster purity in scRNA-seq data, identifying subtypes and improving analysis of specific subpopulations across datasets.

Reconstruction of cell spatial organization based on ligand-receptor mediated self-assembly

This paper introduces CSOmap, a computational method to infer spatial organization from scRNA-seq data, successfully reconstructing tumor microenvironments and simulating perturbations to study cellular interactions.

SciBet: a portable and fast single cell type identifier

SciBet is a Bayesian classifier for single-cell RNA sequencing data that predicts cell identity and can be deployed locally via a web client.

SSCC: a computational framework for rapid and accurate clustering of large-scale single cell RNA-seq data

SSCC improves clustering accuracy and speed for single-cell RNA-seq data while reducing memory usage compared to existing methods.