Susan M. Grimes

This study identifies a unique aneuploidy profile in colorectal cancer brain metastases compared to other cancer types and metastatic sites.

This study identifies the immunosuppressive cellular and genomic features of colorectal cancer brain metastases and their mechanisms of adaptation.

Clonalscope detects cancer subclones using DNA copy number data from single-cell and spatial omic sequencing, identifying spatially segregated subclones and validating them with matched scDNA-seq data.

The paper develops a nanopore sequencing strategy to measure cfDNA methylomes in cancer patients, enabling longitudinal monitoring during treatment.

The paper develops Longcell, a statistical framework for accurate isoform quantification in single cell and spatial long-read sequencing data, revealing intra-cell splicing heterogeneity and validating regulatory targets.

This study develops a single-cell method using nanopore sequencing to identify somatic mutations and gene rearrangements in cancer cells and integrates these with transcriptomes.

The paper develops a single-cell CRISPR base editor method to engineer and assess the transcriptional impact of cancer mutations in cell lines.

The paper integrates scDNA-seq and scRNA-seq data to characterize subclonal architecture and pathway activity in gastric and colorectal cancers.

The paper describes the development of a gastric cancer registry integrating clinical and genomic data to support translational research.

KmerKeys provides a web tool for efficient k-mer-based querying of genome assemblies and variant databases.

The paper develops a single-cell method combining CRISPR edits and long-read sequencing to characterize transcript isoforms and confirm genomic edits at single-cell resolution.

This study identifies a consensus microbiome for colorectal cancer by analyzing 924 tumors across eight RNA-Seq datasets, finding 114 microbial species consistently associated with tumors.

The paper develops a high-coverage sequencing approach to profile microsatellite and chromosomal instability in colorectal cancer, revealing co-occurrence of MSI and CIN features.

Alleloscope analyzes allele-specific copy number and chromatin accessibility in single-cell cancer data, revealing complex copy number events and their role in intratumor heterogeneity.

The paper combines single cell DNA-Seq and RNA-Seq in gastric cancer to reveal subclonal genomic instability and gene expression patterns, showing evidence of tumor evolution.

The paper identifies TP53 genomic deletions as a poor prognosis marker in Stage III colorectal cancer using a new low-coverage whole-genome sequencing protocol.

This paper introduces a targeted sequencing method for low-quality DNA that reduces PCR bias and improves variant detection in clinical samples.