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Mohammed Alser

Senior Researcher and Lecturer of Computer Architecture and Bioinformatics

ETH Zürich

Biography

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.

Interests

  • Bioinformatics
  • Computational Genomics
  • Hardware/Software Cooperation
  • Specialized/Heterogeneous Computing Systems
  • Processing-in-Memory

Education

  • PhD in Computer Engineering, 2018

    Bilkent University

  • MSc in Electrical and Electronic Engineering, 2013

    Universiti Teknologi PETRONAS

  • BSc in Computer Engineering, 2010

    Islamic University of Gaza

Latest News:

Recent & Upcoming Talks

A Roadmap for Fast and Efficient Genome Analysis, the University of Tokyo, 20 December 2019

This talk targets medical science students of the University of Tokyo. It describes our ongoing journey in significantly improving the …

A Roadmap for Fast and Efficient Genome Analysis, the University of Tokyo, 19 December 2019

This talk targets computer science students of the University of Tokyo. It describes our ongoing journey in significantly improving the …

Accelerating Genome Analysis Using New Algorithms and Hardware Designs, the University of Tokyo, 18 December 2019

This talk targets computational biology and bioinformatics students of the University of Tokyo. It describes our ongoing journey in …

Selected Publications

SneakySnake: A Fast and Accurate Universal Genome Pre-Alignment Filter for CPUs, GPUs, and FPGAs

Motivation:
We introduce SneakySnake, a highly parallel and highly accurate pre-alignment filter that remarkably reduces the need for …

Techniques for Reducing the Connected-Standby Energy Consumption of Mobile Devices

Motivation:
Modern mobile devices, such as smartphones, tablets, and laptops, are idle most of the time but they remain connected to …

Metalign: Efficient alignment-based metagenomic profiling via containment min hash


Whole-genome shotgun sequencing enables the analysis of microbial communities in unprecedented detail, with major implications in …

Shouji: a fast and efficient pre-alignment filter for sequence alignment

Motivation
The ability to generate massive amounts of sequencing data continues to overwhelm the processing capability of existing …

Accelerating the Understanding of Life's Code Through Better Algorithms and Hardware Design

Our understanding of human genomes today is affected by the ability of modern computing technology to quickly and accurately determine …

Tools:

SneakySnake

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.

MicrobeScope

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.

Shouji

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.

MAGNET

A pre-alignment filter with an extremely low false-positive rate. MAGNET is available in both Matlab and Verilog.

GateKeeper

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.



visitors since Feb 2020