Steely, Cody J

Owned by UKY CCS RCD
Aug 02, 2024
1 min read

 

 

Research Group Activities

Dr. Steely’s research is focused on aging and age-related disorders. This work is currently split into two projects. The first is an analysis of somatic mutations in longitudinal whole-genome sequencing data. Samples from these individuals will be sequenced using Illumina sequencing instruments. The second project is focused on analyzing repetitive DNA in whole-genome sequencing and single-cell RNA-sequencing data from Alzheimer’s disease and related dementia samples. All data generated from these projects would be de-identified or come from publicly available resources.

All Projects

Dr. Steely and Bikram Karki (PhD student) will be using HPC resources to work on the following projects:

1. Analysis of somatic mutations in longitudinal, whole-genome sequencing data.

2. Analyzing repetitive DNA in whole-genome sequencing from Alzheimer's disease and related dementia samples.

3. Analyze expression changes in single-cell RNA-sequencing data from Alzheimer's disease and related dementia samples.

 

Computational Methods

Tools for genome and rna alignment, tools for the detection and genotyping of repetitive DNA in sequencing data, tools for the analysis of single-cell RNA seq data, general genomic analysis tools. These tools are all publicly available.

 

List of Software

BWA-mem
Cell Ranger
GangSTR (not currently installed: [https://github.com/gymreklab/GangSTR|https://github.com/gymreklab/GangSTR])
Mobile Element Locator Tool (MELT) (not currently installed: [https://melt.igs.umaryland.edu/downloads.php|https://melt.igs.umaryland.edu/downloads.php])
soloTE (not currently installed: [https://github.com/bvaldebenitom/SoloTE|https://github.com/bvaldebenitom/SoloTE])
plink 2.0 (not currently installed: [https://www.cog-genomics.org/plink/2.0/|https://www.cog-genomics.org/plink/2.0/])
Seurat (not currently installed: [https://satijalab.org/seurat/articles/install_v5.html|https://satijalab.org/seurat/articles/install_v5.html])
TRTools (not currently installed: [https://trtools.readthedocs.io/en/latest/|https://trtools.readthedocs.io/en/latest/])
bcftools
samtools
bedtools

 

UKY Collaborators

Bikram Karki (PhD Student)

Center for Computational Sciences