Mutation / CNV co-occurrence in cancer

Co-occurring Mutations and CNV

Variant analysis, Data viz, Genomics

R

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

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

Type II Diabetes RNA atlas

Building an expression database for type 2 diabetes

RNA-Seq, Data mining, R-Shiny

R

Cancer to Normal Atlas

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

R-Shiny, Reactive Programming

R

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

Transcriptomic database for IBD

Building an expression database for inflammatory bowl disease

RNA-Seq, Data mining, R-Shiny

R

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

R

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

R

RLDelta

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

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