Closed / Completed Projects

Sep 4, 2022

Last updated:

Analysis of genomic variants in schwannomatosis (COMING SOON)

Development of a pipeline to characterize and prioritize genomic variants in schwannomatosis. Prioritized variants will be used to design additional analyses and the pipeline may be applied to genomic datasets from related rare diseases.

Variant analysis, Variant interpretation, Nextflow pipelines

Nextflow, Bash

CAR-T Cell Parkinsonian Analysis

Use scRNA-Seq to uncover potential causes of parkinsonian symptoms with CAR-T therapy.

scRNA-Seq, Immune Profiling, Data Integration, Linux

R

Cancer to Normal Transformer

Uncovering the relationship between cancers and the normal tissues which they arise from.

Machine Learning, Software development, Data Integration, scRNA-Seq

R, Python

R-loops and Splicing

Analysis of transcriptomic changes and R-loop dynamics with splicing inhibition in Ewing Sarcoma

RNA-Seq, ChIP-Seq, Data Integration

R

Exploratory analysis of CAR-T cell TCR scRNA-Seq

Analysis of T-Cell receptor sequences of CAR-T cells via single-cell RNA-Seq.

Immune Profiling, scRNA-Seq

R

CAR-T Cell Transcriptomics

Transcriptomic analysis of CAR-T cells in relation to their anti-cancer efficacy

RNA-Seq, Data Mining, DE, Pathway Analysis, Immune Profiling

R, Python

BRCA2 and R-loops

Uncovering the relationship between BRCA2 and PAF1 in transcriptional control and regulation of R-loops.

RNA-Seq, ChIP-Seq, Data Integration

R

Rapamycin and Cancer

Analysis of the transcriptomic impact of Rapamycin treatment on colon and gastric cancer.

RNA-Seq, Data Integration

R

lncRNA expression in NAFLD

This project develops a database for exploring lncRNA expression in hepatocytes

Data Mining, RNA-Seq, R-Shiny, Snakemake, Linux

R

RSeq

A best-practices R-loop mapping pipeline

Snakemake, ChIP-Seq, Linux, Software development

Python, R, Bash

R-loops and the Aging Epigenome

Analysis of the role of R-loops in promoting epigenomic aging via enhancer dysregulation.

RNA-Seq, ChIP-Seq, scRNA-Seq, Data Integration, Data Mining, Snakemake, Linux

R, Bash

lncRNA expression in Fibroblasts during Fibrosis

This project develops a database for exploring lncRNA expression in fibroblasts

Data Integration, Data Mining, R-Shiny, Snakemake

R

RMapDB

An atlas of R-loop sites across the genome

API development, REACT.js, Data Integration, Linux, ChIP-Seq

Python, JavaScript, Bash

R-loops across the CCLE (Merck Project)

R-loops are important but poorly understood. This project uses dozens of cancer cell lines to determine what are the genomic, epigenomic, and transcriptomic impacts of R-loops.

RNA-Seq, Data Integration, Data Mining

R