Yuxiang Li

DCSMAP: A Hybrid Linear-Pangenome Framework for Accurate and Efficient Read Alignment

DCSMAP improves read alignment accuracy and efficiency by selectively applying pangenome graph alignment to reads with unreliable linear placements.

RegFormer: A Single-Cell Foundation Model Powered by Gene Regulatory Hierarchies

RegFormer improves single-cell RNA sequencing analysis by integrating gene regulatory networks with Mamba-based modeling, outperforming existing models in clustering, integration, and annotation.

DPGT: A spark based high-performance joint variant calling tool for large cohort sequencing

DPGT is a high-performance joint variant calling tool for large cohorts, offering comparable accuracy to existing methods with improved speed and scalability.

Single-Cell Genomics Elucidates Molecular Variations and Regulatory Mechanisms in Circulating Immune Cells

The paper introduces CIMA, a multi-omics atlas of human immune cells, identifying regulatory mechanisms and genetic associations across sex, age, and genetic factors.

FEDRANN: effective long-read overlap detection based on dimensionality reduction and approximate nearest neighbors

FEDRANN improves long-read overlap detection using dimensionality reduction and approximate nearest neighbors, outperforming existing methods on real data.

NanoporeDB: A Structural Resource Of Multimeric Protein Nanopores In Single-Molecule Sensing

NanoporeDB is a structural database of multimeric protein nanopores, providing 3D models and quantitative metrics to support nanopore-based sensing and synthetic biology.

A deep learning and co-conservation framework enable discovery of non-canonical Cas proteins

The paper introduces BioPrinCRISPR, a framework to identify and characterize CRISPR-Cas systems, revealing non-canonical variants and novel domain architectures across bacterial genomes.

Prediction of soil probiotics based on foundation model representation enhancement and stacked aggregation classifier

The paper develops a method to predict soil probiotics using enhanced foundation model representations and a stacked aggregation classifier, achieving high accuracy and AUC on both balanced and imbalanced datasets.

BioLLM: A Standardized Framework for Integrating and Benchmarking Single-Cell Foundation Models

BioLLM integrates and benchmarks single-cell foundation models, revealing scGPTs' robust performance and highlighting limitations of scBERT in gene-level tasks.

Efficient reliability analysis of spatially resolved transcriptomics at varying resolutions using SpaSEG

SpaSEG is a convolutional neural network model for analyzing spatially resolved transcriptomics data, showing superior reliability and efficiency in detecting spatial patterns and intercellular interactions.

UniCell: Towards a Unified Solution for Cell Annotation, Nomenclature Harmonization, Atlas Construction in Single-Cell Transcriptomics

UniCell improves cell type annotation and cross-dataset harmonization by combining Cell Ontology with transcriptomic data, outperforming existing tools in accuracy and rare cell detection.

Quantum algorithm for identifying RNA 3D motifs by processing RNA secondary structure graphs

This paper introduces a quantum algorithm for identifying RNA 3D motifs by processing secondary structure graphs, demonstrating its ability to detect conserved motifs in RNA sequences.

Stereopy: modeling comparative and spatiotemporal cellular heterogeneity via multi-sample spatial transcriptomics

Stereopy provides a framework for analyzing multi-sample spatial transcriptomics data to model comparative and spatiotemporal cellular heterogeneity through three key algorithms.

Tim-3 promotes viral infection by suppressing USP25-TRAF3-IRF7 signaling pathway

This study shows Tim-3 suppresses antiviral immunity by inhibiting the USP25-TRAF3-IRF7 signaling pathway in myeloid cells during VSV encephalitis.

A practical DNA data storage using expanded alphabet introducing 5-methylcytosine

This paper introduces a DNA data storage scheme using 5-methylcytosine to increase information density, achieving high data recovery rates in experimental validation.

ST-GEARS: Advancing 3D Downstream Research through Accurate Spatial Information Recovery

ST-GEARS improves spatial information recovery in 3D spatial transcriptomics by aligning sections and correcting distortions, enhancing accuracy for downstream analysis.

Telomere-to-telomere African wild rice (Oryza longistaminata) reference genome reveals segmental and structural variation

The paper presents a telomere-to-telomere genome assembly for Oryza longistaminata, revealing structural variations and gene duplications that may contribute to its advantageous traits.

Generating single-cell gene expression profiles for high-resolution spatial transcriptomics based on cell boundary images

The paper updates a software tool to generate single-cell spatial gene expression profiles using cell boundary images from Stereo-seq data, showing improved performance on mouse liver and Arabidopsis seed datasets.

SAW: An efficient and accurate data analysis workflow for Stereo-seq spatial transcriptomics

SAW improves the efficiency and accuracy of Stereo-Seq spatial transcriptomics analysis by optimizing key steps and reducing runtime.

spatiAlign: An Unsupervised Contrastive Learning Model for Data Integration of Spatially Resolved Transcriptomics

spatiAlign integrates spatially resolved transcriptomics datasets using contrastive learning, improving batch effect removal and enabling downstream analysis across multiple tissue sections.

Spatially resolved molecular and cellular atlas of the mouse brain

The paper creates a high-resolution spatial transcriptomic atlas of the mouse brain using snRNA-seq and Stereo-seq, identifying new cell clusters, region-specific genes, and transcription factor regulons.

STOmicsDB: a database of Spatial Transcriptomic data

STOmicsDB provides a database for spatial transcriptomics data with tools for dataset visualization, publication search, and data archiving.

VRP Assembler: haplotype-resolved de novo assembly of diploid and polyploid genomes using quantum computing

The paper introduces VRP Assembler, a quantum computing-based method for haplotype-resolved de novo genome assembly, demonstrating its feasibility on synthetic genomes and the human MHC region.

Divide-and-conquer quantum algorithm for hybrid de novo genome assembly of short and long reads

This paper proposes a hybrid quantum algorithm for genome assembly using short and long reads to address repetitive sequences and sequencing errors, showing improved convergence and optimization.

CellBin: a highly accurate single-cell gene expression processing pipeline for high-resolution spatial transcriptomics

CellBin processes high-resolution spatial transcriptomics data to generate accurate single-cell gene expression profiles, improving accuracy and efficiency in mouse brain tissue analysis.

Spatial-ID: a cell typing method for spatially resolved transcriptomics via transfer learning and spatial embedding

Spatial-ID improves cell type annotation in spatial transcriptomics by combining transfer learning and spatial embedding, outperforming existing methods on public datasets.

Spateo: multidimensional spatiotemporal modeling of single-cell spatial transcriptomics

Spateo provides a framework for spatiotemporal modeling of single-cell spatial transcriptomics data to study cell-cell interactions and organ development in 3D space.

Spatiotemporal mapping of gene expression landscapes and developmental trajectories during zebrafish embryogenesis

This study maps gene expression and developmental trajectories in zebrafish embryos using Stereo-seq and scRNA-seq, identifying spatial gene modules and signaling interactions.

High-resolution spatiotemporal transcriptomic maps of developing Drosophila embryos and larvae

This study uses Stereo-seq to generate high-resolution spatiotemporal transcriptomic maps of Drosophila embryos and larvae, revealing new subregions and gene regulatory networks.