Skills

Computational Skills

  • Programming Languages
    • Proficient: Python, Java, Javascript, R, HTML/CSS, TypeScript
    • Familiar: C/C++, Go
  • Databases: MySQL, MongoDB
  • Web development: Express.js, Node.js, Angular, Java servlets, Dojo, Bootstrap CSS
  • Testing frameworks: Jasmine, Mocha, Karma, Selenium

Scientific Interests

  • Genetics, genomics, epigenetics
  • Data visualization and presentation

Noteworthy Coursework

  • Introduction to Datamining
  • Numerical Analysis
  • Algorithms and Data Structures
  • Statistics for Bioinformatics
  • Algorithms for Computational Biology

Selected Publications

We present a set of plugins for the genome browser JBrowse that are targeted for epigenomics visualizations. Specifically, we have focused on visualizing DNA base modifications, small non-coding RNAs, stranded read coverage, and sequence motif density. Additionally, we present several plugins for improved user experience such as configurable, high-quality screenshots.
In BMC Bioinf., 2017
PDF Code Project

Previous research has looked at the rate at which spontaneous epialleles arise but it is currently unknown how they are maintained across generations. DNA methylation is stably inherited by offspring and spontaneous epialleles are rare. The epigenotyping procedure that we describe provides an important first step to epigenetic quantitative trait loci mapping in genetically identical individuals.
In Genome Biol, 2017
PDF Code Dataset Project

Recent Publications

(2017). Enhanced JBrowse plugins for epigenomics data visualization. In BMC Bioinf..

PDF Code Project

(2017). Stable inheritance of DNA methylation allows creation of epigenotype maps and the study of epiallele inheritance patterns in the absence of genetic variation. In Genome Biol.

PDF Code Dataset Project

(2017). Arabidopsis protein kinase D6PKL3 is involved in formation of distinct plasma-membrane aperture domains on the pollen surface. In Plant Cell.

(2017). Combining ATAC-seq with nuclei sorting for discovery of cis-regulatory regions in plant genomes. In NAR.

PDF Dataset

(2016). On the origin and evolutionary consequences of gene body DNA methylation. In PNAS.

PDF Dataset

(2016). Base J represses genes at the end of polycistronic gene clusters in Leishmania major by promoting RNAP II termination. In Molecular Microbiology.

PDF

(2016). FASTmC: A Suite of Predictive Models for Nonreference-Based Estimations of DNA Methylation. In G3.

PDF Website

(2016). Histone H3 Variant Regulates RNA Polymerase II Transcription Termination and Dual Strand Transcription of siRNA Loci in Trypanosoma brucei. In PLOS Genet.

PDF

Projects

Web Application for Undergraduate Genetics Education
Epigenomics Visualization
Generational Epigenetic Inheritance

Software

DNA Methylation Inheritance

Documentation for using the scripts, including a sample dataset, are available via GitHub.

Of particular interest is the method using for epigenotyping–using only DNA methylation to determine parent-of-origin in offspring of genetically-identically indivduals.

JBrowse Plugins

These plugins are featured in BMC Bioinformatics.

Epigenomics

User Experience

Undergraduate Genetics Education

This project is in development and not publically available yet.

I built a web application, named Inherit Logic aimed to teach students principles in genetics using problem solving in a virtual lab. This app has been used successfully in several courses at UGA.

Web Development for Collaborative Projects

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