I’m a student in the molecular biology doctoral program at CUNY Graduate Center. As a scientists, I am interested in studying molecular evolution of microbial pathogens, and use the vectorborne pathogen Borrelia burgdoferi, the causative agent of Lyme Disease, as a model organism. I do my research at Hunter College under the supervision of Dr. Weigang Qiu in our lab at the Weill Cornell Medicine – Belfer Research Building. Our lab uses computational methods, such as simulations, as well as bionformatics tools and pipelines to study a diverse range of biological problems and phenomena.
In addition to my interests in science and biology, I am also passionate about education and pedagogy. I started my journey as an educator in a small middle school in the Bronx back in 2006. Fast forward to today – I have gotten the opportunity to teach students science at virtually all levels, including puiblic middle school, high school, as well as CUNY community and senior colleges and the Macaulay Honors College. I remain dedicated to empowering my students through thoughtful pedagogy, an open mind, and continued professional development.
Early in my journey towards a Ph.D. a joined the Teaching and Learning Collaborative (TLC) at CUNY Macaulay Honors College and have been working with faculty and students across the network of CUNY senior colleges in developing meaningful experiential learning coursework across disciplines.
Thesis Projects
Bacterial Methylomics
Detection and analysis of global genomic methylation patterns and the identification of novel restriction-modification target motifs
Epigenetic modifications to DNA via Restriction-modificaiton systems have been associated with a range of functions in bacteria, including phage defense, regulation of foreign DNA uptake, gene expression, and virulence. Here I have a developed a set of tools for the downstream analysis of nanopore sequencing data to create methylome profiles and identify enriched methylated DNA motifs within the genomes. My tools are open source and free to download and modify to fit your specific research needs.
Download the tools from my Git repository: https://github.com/bely12/borrelia-methylomics
For a tutorial on using these tools, go here: https://bely12.github.io/
Restriction-modification systems in Borrelia spp.
A phylogenetic analysis of restriction-modification genes across Lyme and Relapsing fever Borrelia groups
The functional role of restriction-modification systems in Borrelia, as well as their potential impact on gene flow and strain structuring within populations all remain unclear. Here is a comprehensive genus-wide phylogenetic analysis on candidate R-M genes to uncover their evolution history and provide insight to their potential impact on population genetics.
Computational modeling of vector-host-pathogen transmission cycles
Simulating the evolution of key virulence genes under immune and adaptive selection
Here I’ve created a framework for simulating vector-host-pathogen transmission cycles using agent based modeling. Fit specifically for Borrelia, the framework can be adapted to a diverse range of vectorborne pathogen and transmission systems.The model combines principals of both ecological and evolutionary modeling to test hypotheses related to the impacts of immune and adaptive selection on gene evolution and population structuring.
Predicting evolutionary trajectories with fitness landscapes
Simulating antigen evolution across fitness landscapes to explore evolutionary constraints and how they may be overcome in rapidly evolving pathogens
Check out the article here
To learn more about the Qiu Lab, our research interests, and publications, visit the lab website:
