Angela Norie Brooks

Multi-omic long-read sequencing reveals nucleosome control of transcriptional fidelity at the isoform level

The paper uses long-read sequencing to study how nucleosome positioning affects isoform expression by analyzing chromatin and RNA in yeast.

An Integrated Transcriptomic Landscape of Lung Cancer Identifies Tumor Clusters of Biological Significance

The paper constructs a unified transcriptomic landscape of lung cancer using RNA-seq data from 1,824 tumors, identifying nine molecular clusters with distinct biological and clinical features.

A novel splice site variant in DEGS1 leads to aberrant splicing and loss of DEGS1 enzyme activity, a VUS resolved

The paper identifies a pathogenic splice site variant in DEGS1 causing aberrant splicing and loss of enzyme activity in individuals with HLD18.

SMAdd-seq: Probing chromatin accessibility with small molecule DNA intercalation and nanopore sequencing

The paper introduces SMAdd-seq, a method to profile chromatin accessibility using small molecule intercalation and nanopore sequencing, and demonstrates its application in yeast.

U2AF1 S34F enhances tumorigenic potential of lung cells by exhibiting synergy with KRAS mutation and altering response to environmental stress

This study shows U2AF1S34F enhances lung cell tumorigenicity when combined with KRAS mutations and environmental stress, altering splicing and stress responses.

Detecting haplotype-specific transcript variation in long reads with FLAIR2

The paper develops FLAIR2 to detect haplotype-specific transcript variation using long-read sequencing, revealing ADAR's role in splicing and RNA editing in lung cancer.

Systematic assessment of long-read RNA-seq methods for transcript identification and quantification

Benchmarking six long-read RNA-seq protocol-platform combinations and 14 tools across human, mouse, and manatee shows read length and accuracy drive isoform detection, depth drives quantification.

DeepSea: An efficient deep learning model for single-cell segmentation and tracking of time-lapse microscopy images

DeepSea is a deep learning model for segmenting and tracking single cells in time-lapse microscopy images, showing cell size control in embryonic stem cells during G1 phase.

Fully integrated SNV, fusion, and isoform analysis of cancer drivers with FLAIR3 for improved functional interpretation

FLAIR3 integrates SNV, fusion, and isoform analysis using long-read RNA-seq to better understand cancer drivers by capturing full-length molecules and their variant interactions.

RNA-sequencing as an expression-informed alternative for somatic variant detection and cancer driver identification

This study uses RNA-seq data to detect somatic variants and identify cancer drivers in 1,359 samples, showing RNA-seq can effectively replace WES/WGS for this task.

eVIP2: Expression-based variant impact phenotyping to predict the function of gene variants

The paper introduces eVIP2, a tool to predict the functional impact of gene variants using gene expression data, and validates its predictions with experimental assays.

Transcriptome analysis of alternative splicing-coupled nonsense-mediated mRNA decay in human cells reveals broad regulatory potential

The paper identifies NMD-targeted transcripts in human cells by analyzing RNA-Seq data from NMD-inhibited HeLa cells, revealing broad regulatory potential of alternative splicing coupled with NMD.

Full-length transcript characterization of SF3B1 mutation in chronic lymphocytic leukemia reveals downregulation of retained introns

The paper uses nanopore sequencing to analyze full-length transcripts in CLL samples with and without SF3B1 mutations, revealing altered intron retention and splicing patterns.

Whole genome and RNA sequencing of 1,220 cancers reveals hundreds of genes deregulated by rearrangement of cis-regulatory elements

The paper identifies hundreds of genes deregulated by SVs in cancer, showing increased expression linked to SV breakpoints and enhancer elements.

Nanopore sequencing reveals U2AF1 S34F-associated full-length isoforms

The paper uses long-read sequencing to identify U2AF1 S34F mutation-induced isoform changes in lung cancer, revealing novel transcripts and functional consequences.

Nanopore native RNA sequencing of a human poly(A) transcriptome

The paper uses nanopore sequencing to analyze poly(A) RNA from human cells, identifying long transcripts and modifications not captured by traditional methods.

A Pan-Cancer Transcriptome Analysis Reveals Pervasive Regulation through Tumor-Associated Alternative Promoters

This study identifies alternative promoters as key regulators in the cancer transcriptome using RNA-Seq data from 1,188 cancer samples.

Genomic basis for RNA alterations revealed by whole-genome analyses of 27 cancer types

The paper analyzes RNA alterations across 27 cancer types using whole-genome sequencing data, identifying gene expression associations with DNA variants and structural fusions.

A Next Generation Connectivity Map: L1000 Platform And The First 1,000,000 Profiles

The paper introduces the L1000 platform, a high-throughput gene expression profiling method, and reports 1.3 million perturbational profiles expanding the Connectivity Map for drug mechanism discovery and functional annotation.

Large-Scale Uniform Analysis of Cancer Whole Genomes in Multiple Computing Environments

The paper describes the PCAWG project's large-scale analysis of cancer whole genomes across multiple computing environments, producing validated consensus variants for downstream research.