Biography

I am a PhD Candidate in Alexis Battle’s lab at Johns Hopkins University, in the Department of Biomedical Engineering. My undergraduate training was in Biological Engineering at Cornell University.

My research focuses on the application of machine learning methods to study at the dynamic landscape of genetic regulation of gene expression.

Interests

  • Computational Regulatory Genomics
  • Machine Learning
  • Dynamics of Gene Expression

Education

  • PhD in Biomedical Engineering, 2019-2025 (Expected)

    Johns Hopkins University

  • BS in Biological Engineering, 2015-2019

    Cornell University

Publications

Inference after latent variable estimation for single-cell RNA sequencing data

In the analysis of single-cell RNA sequencing data, researchers often characterize the variation between cells by estimating a latent …
Anna Neufeld, Lucy L. Gao, Joshua Popp, Alexis Battle, Daniela Witten
PDF DOI

Human embryoid bodies as a novel system for genomic studies of functionally diverse cell types

Most disease-associated loci, though located in putatively regulatory regions, have not yet been confirmed to affect gene expression. …
Katherine Rhodes, Kenneth A Barr, Joshua M Popp, Benjamin J Strober, Alexis Battle, Yoav Gilad
PDF DOI

Single-Cell Sequencing Reveals Lineage-Specific Dynamic Genetic Regulation of Gene Expression During Human Cardiomyocyte Differentiation

Dynamic and temporally specific gene regulatory changes may underlie unexplained genetic associations with complex disease. During a …
Reem Elorbany*, Joshua M Popp*, Katherine Rhodes, Benjamin J Strober, Kenneth Barr, Guanghao Qi, Yoav Gilad**, Alexis Battle**
PDF DOI

Undergraduate Research

Cornell University

 
 
 
 
 

Computational Genetics

Buckler Lab

Feb 2018 – May 2019 Institute for Genomic Diversity
  • Applied machine learning to large-scale study of genomic sequence information to maximize information available to plant breeders
  • Used variational auto-encoding for feature extraction and efficient peptide sequence representation
  • Created a Docker container platform to conveniently integrate bioinformatics and machine learning programs and minimize system dependencies
 
 
 
 
 

Molecular Bioengineering

Luo Lab

Oct 2016 – May 2019 Department of Biological Engineering
  • Developed a nucleic acid-based biosensor for detection of pathogens in low-tech, point-of-care settings (Honors Thesis)
  • Created protocols for and ran frequent experiments involving microfluidics and molecular biology
  • Designed and fabricated a primitive DNA-based biological robot exhibiting artificial metabolism