Graduating Computational Biology Researchers Take Next Steps
William Casazza
During his time at CMU, William worked in Dr. Schwartz’s lab, revisiting algorithms for building optimal maximum parsimony phylogenetic trees from tissue variation data (e.g. sequencing data, copy number variants and protein sequence data). The model that William reconstructed looks at how certain cells changed from one state to another.
Next year, William is enrolling in a PhD. Program in Bioinformatics at the University of British Columbia and will conduct research with Dr. Sara Mostafavi. He has not yet clearly defined the focus of his project, but he plans to develop statistical models for integrating multiple types of “-omics” data and applying this work to detect gene-by-environment interaction. While not their main focus, Dr. Mostafavi’s lab has researched neurogenomics, the study of how the genome as a whole contributes to the evolution, development, structure and function of the nervous system, which William hopes he can delve into more in the future.
Laura Gunsalus
Laura Gunsalus has studied the epigenetic modifications associated with Alzheimer’s disease in her work with Dr. Andreas Pfenning. She has identified genetic mutations associated with the disease that impact microglia, the brain’s immune response cell. In previous research in the Urban lab at CMU, she observed mouse olfactory behavior. It was only after starting her work with Dr. Pfenning that she discovered her love for computational biology research.
Laura started her time at Carnegie Mellon with limited computer science knowledge, but in her words, “[my computational] coursework has been some of the most rewarding and challenging.” During her time at CMU, she developed an enthusiasm for computer science in its applications in genetics research.
After graduation, Laura will begin working in Cambridge, MA at Syros Pharmaceuticals, a company that identifies possible drug targets by investigating non-coding regulatory DNA regions. Matthew Eaton, PhD., Principal Scientist at Syros, stated, “In the computational biology team at Syros Pharmaceuticals, our mission to bring transformative therapies to patients requires an elegant marriage of computational, statistical, and biological skillsets. To join our team, a candidate must have a strong background in all three. We couldn’t be more excited that Laura Gunsalus is joining our team; the comprehensive education she received in CMU’s computational biology program combined with her hands-on research experience in the lab of Prof. Andreas Pfenning set her apart from the rest of the field of applicants.”
In addition to working for Syros Pharmaceuticals, Laura also plans to continue her education by pursuing a graduate degree in Computational Biology.
Tyler Park
Tyler Park has conducted research with both Dr. Russell Schwartz and Dr. Andreas Pfenning. With Dr. Schwartz, he worked on reconstructing tumor progression from single-cell DNA sequence data, developing methods to estimate evolutionary distances between single cells and evaluating phylogenetic trees built from tumor cell populations. Tyler and Dr. Schwartz plan to use this method to better understand the development and progression of cancers.
Tyler’s work with Dr. Pfenning has centered on the evolution of regulatory elements across multiple species. They focused their study on a set of mouse brain enhancers (i.e., regions of DNA that turn the brain genes “on”), mapping similar regions across different species to identify functional features and extract meaningful information. Over the past year, they have implemented a pipeline for a more accurate mapping procedure and have been using the program to study conservation of the FOS transcription factor binding site in enhancer regions.
After graduation, Tyler will be pursuing his Ph.D. in Quantitative and Computational Biology at Princeton University. He is interested in analyzing genomic variations in both coding and non-coding regions of tumor cells and their effect on cancer progression.