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.


Publications

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 Alser, Onur 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

Mohammed Alser, A Roadmap for Fast and Efficient Genome Analysis
Talk at the University of TokyoTokyo, 19 Dec 2019  [Slides (pptx) (pdf)]
Talk at the University of Tokyo Shirokanedai Campus, Tokyo, 20 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)]


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]


Saugata Ghose, Modeling and Mitigating Early Retention Loss and Process Variation in 3D NAND Flash
Talk at the Flash Memory Summit 2019, Santa Clara, CA, 6-8 August 2019.
[Slides (pptx) (pdf)]
[Original Paper]


Saugata Ghose, FLIN: Enabling Fairness and Enhancing Performance in Modern NVMe Solid State Drives
Talk at the Flash Memory Summit 2019, Santa Clara, CA, 6-8 August 2019.
[Slides (pptx) (pdf)]
[Original Paper]
[Source code for MQSim]


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).