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@CMU-SAFARI @BilkentCompGen
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mealser/README.md

Hi there 👋

I am a Senior Researcher and Lecturer of bioinformatics and computer architecture at SAFARI Research Group, D-ITET, ETH Zürich and a former memeber of D-INFK.

My main research is in bioinformatics, computational genomics, metagenomics, and computer architecture. I am especially excited about building new data structures, algorithms, and architectures that make intelligent computation on population-scale sequencing data a reality. I am also excited about system design, using existing and unconventional (e.g., non-von Neumann) computing paradigms, for bioinformatics and big-data applications. I closely advise and mentor several graduate and undergraduate students (>26 overall) at ETH Zürich, CMU, and Bilkent University. Work with us!

Pinned

  1. CMU-SAFARI/Genome-on-Diet CMU-SAFARI/Genome-on-Diet Public

    Genome-on-Diet is a fast and memory-frugal framework for exemplifying sparsified genomics for read mapping, containment search, and metagenomic profiling. It is much faster & more memory-efficient …

    Roff 11 4

  2. CMU-SAFARI/SneakySnake CMU-SAFARI/SneakySnake Public

    SneakySnake:snake: is the first and the only pre-alignment filtering algorithm that works efficiently and fast on modern CPU, FPGA, and GPU architectures. It greatly (by more than two orders of mag…

    VHDL 46 10

  3. BilkentCompGen/GateKeeper BilkentCompGen/GateKeeper Public

    GateKeeper: Fast Alignment Filter for DNA Short Read Mapping

    VHDL 17 9

  4. CMU-SAFARI/Shouji CMU-SAFARI/Shouji Public

    Shouji is fast and accurate pre-alignment filter for banded sequence alignment calculation. Described in the Bioinformatics journal paper (2019) by Alser et al. at https://academic.oup.com/bioinfor…

    VHDL 16 5

  5. BilkentCompGen/MAGNET BilkentCompGen/MAGNET Public

    MAGNET: Understanding and Improving the Accuracy of Genome Pre-Alignment Filtering

    MATLAB 4 1

  6. smangul1/Microbe-scope smangul1/Microbe-scope Public

    Python 2