Alper Kucukural

I have experience in protein structure characterization and prediction, and applications of genetic algorithms in computational biology. My research over the past few years has focused on protein structure analysis using techniques from graph theory. I have also implemented the theories from computer sciences to biology to find solutions in drug design and small molecular docking fields.
RNAs and small RNAs started becoming the most critical area to work on producing new methods to cure many diseases. I have started working on analyzing deep sequencing data to discover key elements of splicing of pre-mRNAs to shed more light on post-transcriptional regulations of RNAs. Moreover, analyzing RNA targets of tdp43 with deep sequencing on Rat and human was another focus of his researches to understand the mechanisms of neuro-degenerative diseases such as Alzheimer and ALS. I recently implemented an algorithm to reduce noise by calling the peaks caused by experimental and alignment biases for RIP and ChipSeq NGS data.
Currently, he designs, implements reusable, robust and production grade bioinformatics analysis pipelines and pipeline generation tools for processing next-generation sequencing data that support researchers in UMass Medical school.