Li Song

Common viral infections seed regionally distinct resident memory T cells in the human CNS

The paper identifies regionally distinct CD8+ resident memory T cells in the human CNS shaped by viral infections using single-cell RNA sequencing and T cell receptor analysis.

Lossless compression of protein databases for efficient and accurate metagenomic sequence classification with Centrifuger

The paper introduces a lossless compression algorithm for protein databases, improving memory efficiency and classification accuracy in Centrifuger for metagenomic analysis.

Tumor γδ T-cell abundance is associated with favorable cancer treatment outcomes

This study finds that higher pretreatment γδ T-cell abundance is linked to better outcomes in cancer patients receiving immune checkpoint blockade and improved survival across multiple tumor types.

RAD: A Read-structure Agnostic Demultiplexer for Single-Cell Long-Read Sequencing and Analysis

RAD is a demultiplexer for single-cell long-read sequencing that improves speed and sensitivity over existing methods while supporting complex read structures.

Differential Transcript Usage Reveals Isoform-Level Remodeling of Tumor Biology in Clear Cell Renal Cell Carcinoma

The paper identifies isoform-level changes in ccRCC using DTU analysis, revealing subgroups with distinct survival outcomes and potential biomarkers.

Retroelement Hypomethylation Links Hypoxia Signaling, Immune Phenotypes, and Survival in Clear Cell Renal Cell Carcinoma

This study identifies RE methylation subtypes in ccRCC linked to immune phenotypes and survival, validated across multiple cohorts.

DiffDriver Detects Context-Associated Selection of Cancer Driver Genes

DiffDriver identifies context-specific selection of cancer driver genes by accounting for mutation rate variations and functional sequence information, revealing differential selection in clinical traits and immune subtypes.

Quality control of single-cell ATAC-seq data without peak calling using Chromap

This paper extends Chromap to provide peak-based quality control metrics for single-cell ATAC-seq without peak calling, improving downstream analysis by identifying low-quality cells missed by other methods.

A pan-cancer gamma delta T cell repertoire

This paper analyzes 11,473 tumor samples across 33 cancer types to study gamma delta T cell receptor diversity and its prognostic potential, revealing its significance as a biomarker and therapeutic target.

Centrifuger: lossless compression of microbial genomes for efficient and accurate metagenomic sequence classification

Centrifuger compresses microbial genomes losslessly for faster and more accurate metagenomic classification by reducing memory use and improving taxonomic resolution.

T1K: efficient and accurate KIR and HLA genotyping with next-generation sequencing data

T1K is a computational method for accurately inferring KIR and HLA alleles from next-generation sequencing data, showing enrichment of KIR2DL4 in tumor-specific CD8+ T cells.

Fast alignment and preprocessing of chromatin profiles with Chromap

Chromap provides a fast and accurate method for aligning and preprocessing chromatin profiles, outperforming existing tools in speed while maintaining alignment accuracy.

CLASS: Accurate and Efficient Splice Variant Annotation from RNA-seq Reads

CLASS is a tool for accurate splice variant annotation from RNA-seq reads, outperforming existing methods in accuracy and detection of splicing events.

Lighter: fast and memory-efficient error correction without counting

Lighter corrects sequencing errors efficiently by using Bloom filters instead of k-mer counting, achieving speed and memory efficiency with comparable accuracy.