Anuja Sathe

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

The paper identifies progranulin as a mediator of immune suppressive niches in brain metastasis using cross-species spatial transcriptomics and functional analyses.

The paper identifies OLFM4 as a marker of high-risk gastric intestinal metaplasia, showing its restricted localization to epithelial glands and focal expansion with disease severity.

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.

This study uses spatial single-cell analysis to identify 10 cell phenotypes in stage III colorectal cancers and links specific spatial features to recurrence risk.

The paper identifies a 26-gene expression signature in high-risk gastric intestinal metaplasia (GIM) that localizes to intestinal stem-like cells and is associated with increased gastric cancer risk.

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.

The paper introduces niche-differential expression analysis to identify context-dependent cell-cell interactions in spatial transcriptomics data and applies it to colorectal cancer metastases.

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.

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.

scPred is a method for predicting cell types from single-cell RNA sequencing data, achieving high accuracy in classifying cell states and subtypes across multiple tissues and disease contexts.