Juan Xie

Circular Data Analysis for Spatial Omics

The paper provides guidance on analyzing circular data in spatial omics, using case studies to illustrate key considerations and methods.

spaCraft: calibrated power analysis and sample-size planning for multi-sample spatial transcriptomics

spaCraft provides calibrated power analysis and sample-size planning for multi-sample spatial transcriptomics by integrating domain recovery and clustering uncertainty.

PRIME-BSPre: A genome-wide protein-RNA binding sites prediction method based on templates

PRIME-BSPre predicts genome-wide protein-RNA binding sites using templates that integrate RNA sequence, secondary, and tertiary structures, showing strong performance on human RBP datasets.

A Gentle Introduction to Spatial Transcriptomic Analysis with 10X Visium Data

This paper introduces foundational steps for analyzing spatial transcriptomic data from 10X Visium, focusing on clustering, spatially variable gene discovery, and cell-cell communication.

spaDesign: A Statistical Framework to Improve the Design of Sequencing-based Spatial Transcriptomics Experiments

spaDesign provides a statistical framework to optimize sequencing depth in spatial transcriptomics experiments by simulating data and estimating required sequencing depth for detecting spatial domains.

LRT: T Cell Trajectory Inference by Integrative Analysis of Single Cell TCR-seq and RNA-seq data

LRT integrates scTCR-seq and scRNA-seq data to infer T cell trajectories by combining clonal relationships with transcriptomic profiles.

Defining transcriptomic niches in human fibrotic lung with multi-sample spatial transcriptomics analysis using the MAPLE algorithm

The paper uses spatial transcriptomics and the MAPLE algorithm to analyze fibrotic lung tissue, identifying spatial biomarkers and fibrotic programs in IPF.

CPPred-sORF: Coding Potential Prediction of sORF based on non-AUG

CPPred-sORF improves coding potential prediction for sORFs by using non-AUG start codons and achieves high sensitivity and specificity.

RMalign: an RNA structural alignment tool based on a size independent scoring function

The paper introduces RMalign, a size-independent RNA 3D structural alignment tool, which improves benchmarking performance over existing methods and updates the PRIME RNA-protein modeling approach.

Deep-RBPPred: Predicting RNA binding proteins in the proteome scale based on deep learning

Deep-RBPPred predicts RNA binding proteins across multiple species using deep learning, achieving high accuracy and speed compared to existing methods.

QUBIC2: A novel biclustering algorithm for large-scale bulk RNA-sequencing and single-cell RNA-sequencing data analysis

QUBIC2 improves biclustering for bulk and single-cell RNA-Seq by addressing sparsity and transcriptional regulation, outperforming existing tools in functional module detection and cell type classification.

GeneQC: A quality control tool for gene expression estimation based on RNA-sequencing reads mapping

GeneQC estimates the reliability of gene expression levels from RNA-Seq data by analyzing mapping uncertainty, improving downstream analysis validity.