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Closed / Completed Projects

Predict Patient Response to Cancer Immunotherapy with Multi-Omics

Multi-View Learning of Multi-Omics to Predict Patient Response to Cancer Immunotherapy

Machine Learning, Variant analysis, Data Integration


Mutation / CNV co-occurrence in cancer

Co-occurring Mutations and CNV

Variant analysis, Data viz, Genomics


Single cell A-to-I RNA editing

Developing a method for analyzing A-to-I editing in intronic scRNA-Seq sequences. Using this to identify novel cell states.

scRNA-Seq, Linux, Snakemake/NextFlow, Method development

Bash, R, Snakemake or NextFlow

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


Bioinformatics Research Network

This project is attempting to optimize the network, track progress, design a web platform, and ultimate publish the results.

API development, REACT.js, Data Integration, Linux

Python, JavaScript, Bash

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


BRCA1-NRF2 relationship in health and disease

Understanding the interplay of BRCA1 and NRF2 in driving breast cancer metastasis, normal breast development, and Ewing sarcoma differentiation.

RNA-Seq, ChIP-Seq, Data Mining, Data Integration


Predicting Functional Phosphosites with MAVE

Predict Functional Phosphosites Using MAVE Datasets and Machine-Learning

Machine Learning, Method development


Type II Diabetes RNA atlas

Building an expression database for type 2 diabetes

RNA-Seq, Data mining, R-Shiny


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


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


A best-practices R-loop mapping pipeline

Snakemake, ChIP-Seq, Linux, Software development

Python, R, Bash

STAG2 and R-loops in the epigenome

Uncovering the role of STAG2 and R-loops in controlling the epigenome.

RNA-Seq, ChIP-Seq, Data Integration

R, 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


Transcriptomic database for Crohn's Disease

Building an expression database for crohn's disease

RNA-Seq, Data Mining, R-Shiny


Transcriptomic database for IBD

Building an expression database for inflammatory bowl disease

RNA-Seq, Data mining, R-Shiny


lncRNA expression in NAFLD

This project develops a database for exploring lncRNA expression in hepatocytes

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


Cancer to Normal Atlas

An web-based atlas of cancer-normal relationships, based on the "Cancer to Normal Transformer" project.

R-Shiny, Reactive Programming



An atlas of R-loop sites across the genome

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

Python, JavaScript, 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

R-loops and Splicing

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

RNA-Seq, ChIP-Seq, Data Integration


Analysis of genomic variants in schwannomatosis

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


RLDelta involves (1) developing an atlas of differential R-loop dynamics and (b) developing a software package for the differential analysis of R-loop data.

Data Mining, Data Integration, Software development, R-Shiny, Reactive Programming, ChIP-Seq

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


The Loop-ome

This project is attempting to integrate dozens of datasets and build a systems model for R-loop biology

RNA-Seq, ChIP-Seq, Data Integration, Data Mining


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

Lemur Hibernation Genomics

Analysis of gene expression changes during lemur hibernation in collaboration with the Duke Lemur Center alumns.

RNA-Seq, Linux, Comparative genomics

R, Bash

Rapamycin and Cancer

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

RNA-Seq, Data Integration


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