Bioinformatics

Overview

We work on cutting-edge computer architecture and genomics research, with the goal of enabling extremely high-performance, energy-efficient, reliable, and secure computing systems and genomic/medical information processing systems of the future.  We are developing new algorithmic methods and hardware architectures for accelerating and improving bioinformatics and computational genomics tools.

We have several group members working on bioinformatics research.  You can find an overview of who is working on these topics, links to their homepages and full publication lists here: https://safari.ethz.ch/group-members/, as well in the publications listed below.


Publications

Mohammed Alser, Jeremy Rotman, Kodi Taraszka, Huwenbo Shi, Pelin Icer Baykal, Harry Taegyun Yang, Victor Xue, Sergey Knyazev, Benjamin D. Singer, Brunilda Balliu, David Koslicki, Pavel Skums, Alex Zelikovsky, Can Alkan, Onur Mutlu, Serghei Mangul, Technology dictates algorithms: Recent developments in read alignment, Genome Biology, August 2021.
[arXiv preprint] [Source Code and Data]


Gagandeep Singh, Mohammed Alser, Damla Senol Cali, Dionysios Diamantopoulos, Juan Gómez-Luna, Henk Corporaal, and Onur Mutlu, FPGA-based Near-Memory Acceleration of Modern Data-Intensive ApplicationsIEEE Micro (IEEE MICRO), 2021.
[Extended arXiv preprint]
[Invited Talk Video by Mohammed Alser: A Roadmap for Fast and Efficient Genome Analysis]
[Invited Talk Video by Mohammed Alser: Accelerating Genome Analysis Using New Algorithms and Hardware Designs]
[Slides (pptx)(pdf)]
[Talk Video (1 hour 2 minutes)]


Mohammed Alser, Jeremie S. Kim, Nour Almadhoun Alserr, Stefan W. Tell, and Onur Mutlu, COVIDHunter: An Accurate, Flexible, and Environment-Aware Open-Source COVID-19 Outbreak Simulation Model
Preprint in arXiv and medRxiv, 6 February 2021.
[medRxiv preprint]
[arXiv preprint]
[COVIDHunter Source Code and Data]
[Switzerland Case Study]


Jeremie S. Kim, Can Firtina, Meryem Banu Cavlak, Damla Senol Cali, Nastaran Hajinazar, Mohammed Alser, Can Alkan, and Onur Mutlu,
AirLift: A Fast and Comprehensive Technique for Remapping Alignments between Reference Genomes
Preprint in arXiv and bioRxiv, 17 February 2021.
[bioRxiv preprint]
[arXiv preprint]
[AirLift Source Code and Data]


Lukas Breitwieser, Ahmad Hesam, Jean de Montigny, Vasileios Vavourakis, Alexandros Iosif, Jack Jennings, Marcus Kaiser, Marco Manca, Alberto Di Meglio, Zaid Al-Ars, Fons Rademakers, Onur Mutlu, and Roman Bauer,
BioDynaMo: A General Platform for Scalable Agent-based Simulation
Preprint in arXiv and bioRxiv, 5 February 2021.
[bioRxiv preprint]
[arXiv preprint]
[BioDynaMo Source Code and Data]


Mohammed Alser, Taha Shahroodi, Juan-Gomez Luna, Can Alkan, and Onur Mutlu,
SneakySnake: A Fast and Accurate Universal Genome Pre-Alignment Filter for CPUs, GPUs, and FPGAs
Bioinformatics, 26 December 2020.
[Source Code]
[Online link at Bioinformatics Journal]


Mohammed Alser, Zulal Bingol, Damla Senol Cali, Jeremie Kim, Saugata Ghose, Can Alkan, and Onur Mutlu, Accelerating Accelerating Genome Analysis: A Primer on an Ongoing Journey, IEEE Micro (IEEE MICRO), Vol. 40, No. 5, pages 65-75, September/October 2020.
Invited Talk Videos:
A Roadmap for Fast and Efficient Genome Analysis (Mohammed Alser)
Accelerating Genome Analysis Using New Algorithms and Hardware Designs
(Mohammed Alser)
AACBB 2019 Keynote Talk (Onur Mutlu) 


Damla Senol Cali, Gurpreet S. Kalsi, Zulal Bingol, Can Firtina, Lavanya Subramanian, Jeremie S. Kim, Rachata Ausavarungnirun, Mohammed Alser, Juan Gomez-Luna, Amirali Boroumand, Anant Nori, Allison Scibisz, Sreenivas Subramoney, Can Alkan, Saugata Ghose, and Onur Mutlu,
GenASM: A High-Performance, Low-Power Approximate String Matching Acceleration Framework for Genome Sequence Analysis
Proceedings of the 53rd International Symposium on Microarchitecture (MICRO), Virtual, October 2020.
[ARM Research Summit Talk Video (21 minutes)]
[ARM Research Summit Short Talk Video (15 minutes)]
[ARM Research Summit Short Talk Video and Q&A (31 minutes)]
[ARM Research Summit Talk Slides (pptx) (pdf)]
[ARM Research Summit Short Talk Slides (pptx) (pdf)]


Can Firtina, Jeremie S. Kim, Mohammed Alser, Damla Senol Cali, A. Ercument Cicek, Can Alkan, and Onur Mutlu, Apollo: A Sequencing-Technology-Independent, Scalable, and Accurate Assembly Polishing Algorithm, Bioinformatics, Volume 36, June 2020, 3669–3679
[Source Code]


Mohammed Alser, Hasan Hassan, Akash Kumar, Onur Mutlu, and Can Alkan, Shouji: A Fast and Efficient Pre-Alignment Filter for Sequence Alignment, Bioinformatics, Volume 35, Nov 2019, 4255–4263
[Source Code]


Damla Senol, Jeremie Kim, Saugata Ghose, Can Alkan, and Onur Mutlu, Nanopore Sequencing Technology and Tools for Genome Assembly: Computational Analysis of the Current State, Bottlenecks and Future Directions, Briefings in Bioinformatics (BIB), 2018.
[Open arxiv.org version]
[Slides (pptx) (pdf)]
[Talk Video at AACBB 2019]


Jeremie S. Kim, Damla Senol Cali, Hongyi Xin, Donghyuk Lee, Saugata Ghose, Mohammed Alser, Hasan Hassan, Oguz Ergin, Can Alkan, and Onur Mutlu, GRIM-Filter: Fast Seed Location Filtering in DNA Read Mapping Using Processing-in-Memory Technologies, BMC Genomics, 2018.
Proceedings of the 16th Asia Pacific Bioinformatics Conference (APBC), Yokohama, Japan, January 2018.
[Slides (pptx) (pdf)]
[Source Code]
[arxiv.org Version (pdf)]
[Talk Video at AACBB 2019]


Mohammed AlserOnur Mutlu, and Can Alkan,
MAGNET: Understanding and Improving the Accuracy of Genome Pre-Alignment Filtering
IPSI Transactions on Internet Research, July 2017.
arXiv.org version, July 2017.
[Source Code]


Mohammed Alser, Hasan Hassan, Hongyi Xin, Oguz Ergin, Onur Mutlu, and Can Alkan
GateKeeper: A New Hardware Architecture for Accelerating Pre-Alignment in DNA Short Read Mapping
Bioinformatics, [published online, May 31], 2017.
[Source Code]
[Online link at Bioinformatics Journal]


Hongyi Xin, Sunny Nahar, Richard Zhu, John Emmons, Gennady Pekhimenko, Carl Kingsford, Can Alkan, and Onur Mutlu,
Optimal Seed Solver: Optimizing Seed Selection in Read Mapping
Bioinformatics, [published online, November 14], 2015.
[Source Code]


Hongyi Xin, John Greth, John Emmons, Gennady Pekhimenko, Carl Kingsford, Can Alkan, and Onur Mutlu,
Shifted Hamming Distance: A Fast and Accurate SIMD-friendly Filter to Accelerate Alignment Verification in Read Mapping
Bioinformatics, [published online, January 10], 2015.
[PDF article] [Source Code]


Donghyuk Lee, Farhad Hormozdiari, Hongyi Xin, Faraz Hach, Onur Mutlu, and Can Alkan,
Fast and Accurate Mapping of Complete Genomics Reads
Methods, [epub October 22], 2014. [PDF article] [Source Code]


Hongyi Xin, Donghyuk Lee, Farhad Hormozdiari, Can Alkan, and Onur Mutlu,
FastHASH: A New GPU-friendly Algorithm for Fast and Comprehensive Next-generation Sequence Mapping
Pacific Symposium on Biocomputing (PSB) Poster Session, Hawaii, January 2012. Poster (pdf) Abstract (pdf) Slides (pdf) Source Code


Can Alkan, Jeffrey M. Kidd, Tomas Marques-Bonet, Gozde Aksay, Francesca Antonacci, Fereydoun Hormozdiari, Jacob O. Kitzman, Carl Baker, Maika Malig, Onur Mutlu, S. Cenk Sahinalp, Richard A. Gibbs, and Evan E. Eichler,
Personalized copy number and segmental duplication maps using next-generation sequencing
Nature Genetics, August 30, [Epub ahead of print], Vol. 41, No. 10, pages 1061-1067, October 2009. Source Code


Presentations

Damla Senol Cali,
GenASM: A High-Performance, Low-Power Approximate String Matching Acceleration Framework for Genome Sequence Analysis
Proceedings of the 53rd International Symposium on Microarchitecture (MICRO), Virtual, October 2020.
[ARM Research Summit Talk Video (21 minutes)]
[ARM Research Summit Short Talk Video (15 minutes)]
[ARM Research Summit Short Talk Video and Q&A (31 minutes)]
[ARM Research Summit Talk Slides (pptx) (pdf)]
[ARM Research Summit Short Talk Slides (pptx) (pdf)]


Mohammed Alser,
A Roadmap for Fast and Efficient Genome Analysis
Invited Talk at the University of Tokyo Shirokanedai Campus, Tokyo, 20 Dec 2019
Slides (pptx) (pdf)
Talk Video


Mohammed Alser,
A Roadmap for Fast and Efficient Genome Analysis
Invited Talk at the University of TokyoTokyo, 19 Dec 2019 
Slides (pptx) (pdf)
Talk Video


Mohammed Alser, Accelerating Genome Analysis Using New Algorithms and Hardware Designs
Talk at Preferred Networks, Tokyo, 16 Dec 2019  [Slides (pptx) (pdf)]
Talk at RIKEN Center for Computational Science, Kobe, 17 Dec 2019  [Slides (pptx) (pdf)]
Talk at the University of Tokyo Kashiwa Campus, Tokyo, 18 Dec 2019  [Slides (pptx) (pdf)] [Talk Video]


Can Firtina, Jeremie S. Kim, Mohammed Alser, Damla Senol Cali, A. Ercument Cicek, Can Alkan, and Onur Mutlu, Apollo: A Sequencing-Technology-Independent, Scalable, and Accurate Assembly Polishing Algorithm
Poster presentation at the Swiss Genomics Forum 2019, Geneva, 27 Sept 2019.
[Poster (pptx) (pdf)]
[Paper, arXiv (pdf)]
[Source code for Apollo]


Mohammed Alser, Can Alkan, Onur Mutlu, SneakySnake: A New Fast and Highly Accurate Pre-Alignment Filter on CPU and FPGA for Accelerating Sequence Alignment
Poster presentation at the Swiss Genomics Forum 2019, Geneva, 27 Sept 2019. 
[Poster (pptx) (pdf)]
[Source code for SneakySnake]


Can Firtina, Jeremie S. Kim, Mohammed Alser, Damla Senol Cali, A. Ercument Cicek, Can Alkan, and Onur Mutlu, Apollo: A Sequencing-Technology-Independent, Scalable, and Accurate Assembly Polishing Algorithm
Poster presentation at the 27th Conference on Intelligent Systems for Molecular Biology (ISMB) and the 18th European Conference on Computational Biology (ECCB), Basel, 21-25 July 2019.
[Poster (pptx) (pdf)]


Damla Senol Cali, Gurpreet S. Kalsi, Lavanya Subramanian, Can Firtina, Anant V. Nori, Jeremie S. Kim, Zulal Bingöl, Rachata Ausavarungnirun, Mohammed Alser, Juan Gomez-Luna, Amirali Boroumand, Allison Scibisz, Sreenivas Subramoney, Can Alkan, Saugata Ghose, and Onur Mutlu,
BitMAC: An In-Memory Accelerator for Bitvector-Based Sequence Alignment of Both Short and Long Genomic Reads
Poster presentation at the 27th Conference on Intelligent Systems for Molecular Biology (ISMB) and the 18th European Conference on Computational Biology (ECCB), Basel, 21-25 July 2019.
[Poster (pptx) (pdf)]


Mohammed Alser, Can Alkan, Onur Mutlu, SneakySnake: A New Fast and Highly Accurate Pre-Alignment Filter on CPU and FPGA for Accelerating Sequence Alignment
Poster presentation at the 27th Conference on Intelligent Systems for Molecular Biology (ISMB) and the 18th European Conference on Computational Biology (ECCB), Basel, 21-25 July 2019.
[Poster (pptx) (pdf)]


Onur Mutlu, Accelerating Genome Analysis: A Primer on an Ongoing Journey
Keynote talk at 2nd Workshop on Accelerator Architecture in Computational Biology and Bioinformatics (AACBB), Washington, DC, USA, February 2019.
[Slides (pptx)(pdf)]
[Talk Video (1 hour 2 minutes)]


Onur Mutlu, Accelerating Genome Analysis: A Primer on an Ongoing Journey
Talk at ETH Zurich Seminar Course on Hardware Architectures for Machine Learning (HAML), Zurich, Switzerland, March 2018.
[Slides (pptx)(pdf)]


Onur Mutlu, Accelerating Genome Analysis: A Primer on an Ongoing Journey
Keynote talk at Workshop on Accelerator Architecture in Computational Biology and Bioinformatics (AACBB), Vienna, Austria, February 2018.
[Slides (pptx) (pdf)]


Mohammed Alser, Hasan Hassan, Hongyi Xin, Oguz Ergin, Onur Mutlu, and Can Alkan, GateKeeper: A New Hardware Architecture for Accelerating Pre-Alignment in DNA Short Read Mapping”
Pacific Symposium on Biocomputing (PSB) Poster Session, Hawaii, January 2018.
[Poster (pdf) (pptx)] [Abstract (pdf)]


Jeremie Kim, Damla Senol Cali, Hongyi Xin, Donghyuk Lee, Saugata Ghose, Mohammed Alser, Hasan Hassan, Oguz Ergin, Can Alkan, and Onur Mutlu,
GRIM-Filter: Fast Seed Location Filtering in DNA Read Mapping Using Processing-in-Memory Technologies
BMC Genomics, 2018.
Proceedings of the 16th Asia Pacific Bioinformatics Conference (APBC), Yokohama, Japan, January 2018.
[Slides (pptx) (pdf)]
[Source Code]
[arxiv.org Version (pdf)]
[Talk Video at AACBB 2019]


Jeremie Kim, Damla Senol, Hongyi Xin, Donghyuk Lee, Mohammed Alser, Hasan Hassan, Oguz Ergin, Can Alkan, and Onur Mutlu, GRIM-Filter: Fast Seed Location Filtering in DNA Read Mapping Using Processing-in-Memory Technologies
Pacific Symposium on Biocomputing (PSB) Poster Session, Hawaii, January 2018.
[Poster (pdf) (pptx)] [Abstract (pdf)]


Damla Senol, Jeremie Kim, Saugata Ghose, Can Alkan, and Onur Mutlu,
Nanopore Sequencing Technology and Tools: Computational Analysis of the Current State, Bottlenecks and Future Directions
Pacific Symposium on Biocomputing (PSB) Poster Session, Hawaii, January 2017.
[Poster (pdf) (pptx)] [Abstract (pdf)]


Jeremie Kim, Damla Senol, Hongyi Xin, Donghyuk Lee, Mohammed Alser, Hasan Hassan, Oguz Ergin, Can Alkan, and Onur Mutlu, Genome Read In-Memory (GRIM) Filter: Fast Location Filtering in DNA Read Mapping Using Emerging Memory Technologies
Pacific Symposium on Biocomputing (PSB) Poster Session, Hawaii, January 2017.
[Poster (pdf) (pptx)] [Abstract (pdf)]


Jeremie Kim, Damla Senol, Hongyi Xin, Donghyuk Lee, Mohammed Alser, Hasan Hassan, Oguz Ergin, Can Alkan, and Onur Mutlu, Genome Read In-Memory (GRIM) Filter: Fast Location Filtering in DNA Read Mapping with Emerging Memory Technologies
20th Annual International Conference on Research in Computational Molecular Biology (RECOMB) Poster Session, Santa Monica, CA, April 2016.
[Poster (pdf) (pptx)]
[Flash Talk Slides (pptx) (pdf)] at 6th RECOMB Satellite Workshop on Massively Parallel Sequencing (RECOMB-SEQ).