I am a Senior Researcher and Lecturer of computer architecture and bioinformatics at the Department of Computer Science, ETH Zürich. My primary research interest is developing new algorithmic methods and hardware architectures for tackling and accelerating challenging computational problems, adapted to modern heterogeneous computing environments. I am currently working with Onur Mutlu, SAFARI Research Group, on addressing the performance bottlenecks in the realm of bioinformatics and computational genomics.
I earned my PhD in Computer Engineering from Bilkent University, Turkey, where I was awarded the TÜBITAK doctoral fellowship. I am fortunate to work with Can Alkan and Onur Mutlu on my own doctoral research ideas. My PhD thesis, “Accelerating the Understanding of Life's Code Through Better Algorithms and Hardware Design”, received the IEEE Turkey Doctoral Dissertation Award. I also received Yasser Arafat Award and was named as the Best Palestinian PhD Student in Turkey. During my PhD, I joined ZarLab at UCLA to work on metagenomics profiling. I also joined CfAED at TU Dresden to work on hardware accelerators for read mapping. Prior to enrolling at Bilkent, I was a consultant at the High-Performance Computing (HPC) Service Center, PETRONAS, where I led the development of analysis and visualization solutions for offshore oil and gas operations.
PhD in Computer Engineering, 2018
MSc in Electrical and Electronic Engineering, 2013
Universiti Teknologi PETRONAS
BSc in Computer Engineering, 2010
Islamic University of Gaza
The first and the only pre-alignment filter for accelerating sequence alignment calculation (Edlib, Parasail, KSW2) that works efficiently and fast on CPU (C implementation), FPGA (tested on Xilinx Virtex 7 VC709), and GPU (tested on NVIDIA GeForce RTX 2080Ti) architectures.
Microbial community profile visulaization tool for detecting viral and fungal organisms in metagenomic samples. Live demo. MicrobeScope is written in Python and it uses HighCharts.com.
A highly parallel and accurate pre-alignment filter that remarkably reduces the need for computationally-costly dynamic programming algorithms. It is named after a traditional Japanese door that is designed to slide open. Shouji is available in both Verilog and C.
A pre-alignment filter with an extremely low false-positive rate. MAGNET is available in both Matlab and Verilog.
An FPGA-resource-frugal hardware accelerator that functions as a pre-alignment filtering step and quickly filters out most incorrect candidate locations in reference genome. GateKeeper is the first design to accelerate pre-alignment filtering using FPGAs. GateKeeper is designed in Verilog.