PhD Student: Fatemeh Almodaresi

Fatemeh is a Ph.D. student in Computer Science at Stony Brook University. Having a few years of background and working experience in the field of data mining and data analysis, she has moved to the amazing field of Computational Biology as a pursuit of accomplishing her Ph.D. Most of her focus now is on designing and implementing time and space efficient data structures and algorithms; specifically, those that are scalable to large-scale transcriptomic analysis and complex metagenomic experiments. She has led or been part of implementing a variety of tools developed as reference-based or reference-free indexing schemes that are used for search, alignment, assembly or comparison of the sequencing read datasets; tools such as Rainbowfish, Pufferfish, and Mantis. Along a slight transition to the application side of such existing tools, in a collaboration with the bhk lab, she plans to provide a time and space efficient pipeline to look for the existence of known gene fusions or any new biomarkers effective to help having a better diagnosis of the disease in a cell line and how the abundance of such fusions change with the interference of different drugs.