Brian J. Haas

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.

A long-read RNA sequencing and polysome profiling framework reveals transposable element-driven transcript diversity and translational rewiring in glioblastoma

This study combines long-read RNA sequencing and polysome profiling to show that transposable elements drive transcript diversity and alter translation in glioblastoma stem cells.

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.

Adrenergic signaling coordinates distant and local responses to amputation in axolotl

This paper shows that adrenergic signaling coordinates systemic and local stem cell activation after amputation in axolotls, enhancing regeneration.

Complex HPV-human DNA structures revealed by large-scale DNA analyses in an HPV-cancer derived cell line

The paper uses genomic tools to analyze HPV-human DNA integration structures in a cancer cell line, revealing complex intrachromosomal and extrachromosomal architectures.

TD2: finding protein coding regions in transcripts

TD2 is a new tool for ab initio annotation of protein-coding ORFs in transcripts, showing sensitivity and precision across diverse eukaryotic transcriptomes.

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.

De novo detection of somatic variants in high-quality long-read single-cell RNA sequencing data

LongSom detects somatic variants in LR scRNA-seq data without normal samples, revealing clonal heterogeneity in ovarian cancer.

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.

Targeted in silico characterization of fusion transcripts in tumor and normal tissues via FusionInspector

FusionInspector identifies and characterizes biologically relevant fusion transcripts from RNA-seq data in tumor and normal tissues using clustering and machine learning.

von Willebrand Factor D and EGF Domains is an evolutionarily conserved and required feature of blastemas capable of multi-tissue appendage regeneration

The paper identifies vwde expression as a conserved feature of blastemas involved in appendage regeneration across species and shows its functional requirement in regeneration.

STAR-Fusion: Fast and Accurate Fusion Transcript Detection from RNA-Seq

Filtering STAR's chimeric alignments against gene annotations outscored 15 other fusion callers on 60 cancer cell lines and ran fastest, averaging 2.3 single-core hours per sample.