My main research interest are Computational Biology and Bioinformatics.
I am Computer scientist with expertise in (1) software and database development; (2) genomic data analysis and visualization; (3) software for clinical trial management; (4) computational and systems biology; (5) new languages to encode complex biochemical models; (6) languages for computational biology (e.g. SBML, rule-based languages) as well as computer science languages (e.g., Java, Perl, R, C++, SQL, Javascript).
I am a Bioinformatics Engineer in the Biometric Research Program of the Division of Cancer Treatment and Diagnosis (National Cancer Institute, NIH). I work on informatics systems for clinical trial management, and the development of new software tools to visualize genomic sequencing data.
I have a leading role in the development and continual maintenance of software for two nationwide projects led by the National Cancer Institute (NCI). The two projects are the National Cancer Institute Molecular Pro.ling-Based Assignment of Cancer Therapy trial (NCI-MPACT, NCT01827384), and the Patient-Derived Models Tissue Procurement Protocol (NCT02474160). The responsibility of these two precision medicine projects is to unravel the molecular mechanism behind cancer progression and to .find effective therapies based on the mutation pro.file of individual tumors. I provided pivotal bioinformatics contributions and continuous support to these projects which are directly related to clinical trials affecting patient care and deemed critical.
Here at NIH, for three summers, I mentored high school students in the Bnos Yisroel Bridge Program (BYBP). Bnos Yisroel High School is a Jewish, Torah-guided girls' school in Baltimore, MD that sought assistance of Dr. Edelman, a translational cancer researcher at NIH, to create a scienti.c bridge program between the school and the NIH. The students (primarily 11th and 12th grade young women) are very interested in a career in science, but have little exposure in their school curriculum to biomedical science due to both a lack of funds and historical cultural norms. The main goal of the program is to provide them a broad professional exposure to the sciences via a NIH summer internship.
During my previous Post-Doc experience at Virginia Tech, I developed a software tool (called MSMB) that makes the process of writing a complex biological model easier, helping the modelers during the creative process of developing a model, in ways that support their creativity rather than interfering with it. We also introduced a simple but powerful syntax to describe multistate species, a key idea that reduces the number of reactions needed to represent certain molecular systems, and there by reducing the complexity of model creation. The effectiveness of this syntax is going to be presented in a publication about MSMB. In this publication we show how the fact that big models are automatically generated and maintained by the software allows the modelers to focus on testing interesting new biological ideas rather than spending time and effort in keeping the model code valid and updated. During my PhD, I used a stochastic programming language - specifically designed for modeling biological systems - to build and analyze models of the Budding Yeast Cell Cycle, of different sizes and with different levels of abstraction.
So, generally speaking, I am interested in applying computational methods on real biological systems in order to study the mechanisms behind complex interaction networks.