Aziz M. Al’Khafaji

Scalable single-cell isoform profiling with sequencing-by-expansion

This paper introduces a high-throughput single-cell RNA isoform sequencing method using sequencing-by-expansion (SBX) and the CUDLL algorithm, achieving high accuracy and enabling isoform-level analysis across cell types.

TEscape: Defining the human transposable element transcriptome using multiplatform long-read sequencing

TEscape uses long-read sequencing to comprehensively annotate the human transposable element transcriptome, identifying over 83,000 previously unannotated isoforms.

Structural variant discovery and diagnostic impact in rare diseases from short-read and long-read sequencing

This study evaluates the diagnostic yield of short-read and long-read sequencing in rare diseases, finding limited added value from long-read sequencing despite increased variant discovery.

Discovery of Tcf7 regulators with clonally-resolved CRISPR screens identifies Trim28 as a mediator of CD8 T cell differentiation in tumors

The paper identifies Trim28 as a regulator of CD8 T cell differentiation in tumors using clonally-resolved CRISPR screens and shows its role in maintaining TCF7+ stem-like cells while impairing effector differentiation.

Stitch-seq: Scalable CRISPR gene expression response profiling

Stitch-seq enables high-throughput profiling of CRISPR perturbations and gene/protein expression in millions of cells without cell barcoding or extensive sequencing.

Experimental and Computational Methods for Allelic Imbalance Analysis from Single-Nucleus RNA-seq Data

This paper develops computational tools for allelic imbalance analysis using single-nucleus RNA-seq and demonstrates their application in a Parkinson's disease cohort.

Accurate strand-specific long-read transcript isoform discovery and quantification at bulk, single-cell, and single-nucleus resolution

The paper introduces LRAA, a framework for accurate isoform discovery and quantification in long-read RNA-seq data, outperforming existing methods across multiple benchmarks.

RNA splicing dynamics in CD8 T cells uncovers isoforms that impact T cell-mediated cancer immunotherapy

The paper constructs a single-cell splicing atlas of human CD8 T cells and identifies isoform-specific immune checkpoints that enhance effector function and tumor control.

Pathogenic Viruses, Genome Integrations, and Viral::Human Chimeric Transcripts Detected by VirusIntegrationFinder Across >30k Human Tumor and Normal Samples

The paper develops a tool to detect viral integrations in human genomes and applies it to over 30,000 tumor samples, identifying virus-human chimeric transcripts and insertion hotspots.

Multi-platform evaluation and optimization of single-cell RNA isoform sequencing

The paper evaluates and optimizes single-cell RNA isoform sequencing by analyzing artifacts from three platforms and introducing methods to reduce their impact.

CTAT-LR-fusion: accurate fusion transcript identification from long and short read isoform sequencing at bulk or single cell resolution

CTAT-LR-fusion detects fusion transcripts from long and short read RNA-seq data, improving accuracy in bulk and single cell transcriptomes.

Extraction and quantification of lineage-tracing barcodes with NextClone and CloneDetective

The paper introduces NextClone and CloneDetective for extracting and quantifying lineage-tracing barcodes from scRNA-seq and DNA sequencing data.

High-throughput RNA isoform sequencing using programmable cDNA concatenation

This paper introduces MAS-ISO-seq, a method to boost throughput of long-read RNA sequencing for isoform discovery, showing improved detection of differentially spliced genes and cell clustering in T cells.

Heterogeneous, Population-Level Drug-Tolerant Persisters Exhibit Ion-Channel Remodeling and Ferroptosis Susceptibility

The paper identifies heterogeneous drug-tolerant persisters (DTPs) as population-level states with distinct division and death rates, showing increased ferroptosis susceptibility.

Control of lineage-specific gene expression by functionalized gRNA barcodes

This paper introduces a functionalized lineage tracing tool that enables high diversity lineage tracking and lineage-specific gene expression manipulation.