Publications

2021

• 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]

2020

• 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, to appear in 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 Genome Analysis: A Primer on an Ongoing Journey"
  IEEE Micro (IEEE MICRO), Vol. 40, No. 5, pages 65-75, September/October 2020.
  [Slides (pptx)(pdf)]
  [Talk Video (1 hour 2 minutes)]
• 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.
  [Slides (pptx) (pdf)]
  [Short Talk Slides (pptx) (pdf)]
  [Lightning Talk Slides (pptx) (pdf)]
  [ARM Research Summit Talk Slides (pptx) (pdf)]
  [ARM Research Summit Short Talk Slides (pptx) (pdf)]
  [Lecture Slides (pptx) (pdf)
  [MICRO 2020 Talk Video (18 minutes)]
  [MICRO 2020 Short Talk Video (6 minutes)]
  [MICRO 2020 Lighting Talk Video (1.5 minutes)]
  [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)]
  [Lecture Video (37 minutes)]
  [GenASM Source Code]
• Jawad Haj-Yahya, Mohammed Alser, Jeremie S. Kim, Lois Orosa, Efraim Rotem, Avi Mendelson, Anupam Chattopadhyay, and Onur Mutlu,
  "FlexWatts: A Power- and Workload-Aware Hybrid Power Delivery Network for Energy-Efficient Microprocessors"
  Proceedings of the 53rd International Symposium on Microarchitecture (MICRO), Virtual, October 2020.
  [Slides (pptx) (pdf)]
  [Lightning Talk Slides (pptx) (pdf)]
  [Short Talk Slides (pptx) (pdf)]
  [Talk Video (15 minutes)]
  [Lightning Talk Video (1.5 minutes)]
  [Short Talk Video and Q&A (15 minutes)]
• Ivan Fernandez, Ricardo Quislant, Christina Giannoula, Mohammed Alser, Juan Gómez-Luna, Eladio Gutiérrez, Oscar Plata, and Onur Mutlu,
  "NATSA: A Near-Data Processing Accelerator for Time Series Analysis"
  Proceedings of the 38th IEEE International Conference on Computer Design (ICCD), Virtual, October 2020.
  [Slides (pptx) (pdf)]
  [Talk Video (10 minutes)]
  
• Jawad Haj-Yahya, Mohammed Alser, Jeremie Kim, A. Giray Yaglikci, Nandita Vijaykumar, Efraim Rotem, and Onur Mutlu,
  "SysScale: Exploiting Multi-domain Dynamic Voltage and Frequency Scaling for Energy Efficient Mobile Processors"
  Proceedings of the 47th International Symposium on Computer Architecture (ISCA), Valencia, Spain, June 2020.
  [Slides (pptx) (pdf)]
  [Lightning Talk Slides (pptx) (pdf)]
  [Talk Video (18 minutes)]
  [Lightning Talk Video (3 minutes)]
• 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, June 2020.
  [Source Code]
  [Online link at Bioinformatics Journal]
• Jawad Haj-Yahya, Yanos Sazeides, Mohammed Alser, Efraim Rotem, and Onur Mutlu,
  "Techniques for Reducing the Connected-Standby Energy Consumption of Mobile Devices"
  Proceedings of the 26th International Symposium on High-Performance Computer Architecture (HPCA), San Diego, CA, USA, February 2020.
  [Slides (pptx) (pdf)]

2019

• Mohammed Alser, Hasan Hassan, Akash Kumar, Onur Mutlu, and Can Alkan,
  "Shouji: A Fast and Efficient Pre-Alignment Filter for Sequence Alignment"
  Bioinformatics, [published online, March 28], 2019.
  [Source Code]
  [Online link at Bioinformatics Journal]
• 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]

2018

• 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)]
• 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)]

2017

• 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]
• 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)]

2016

• 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).