Publications

2022

• F. Meyer, A. Fritz, Z.-L. Deng, D. Koslicki, A. Gurevich, G. Robertson, Mohammed Alser, D. Antipov, F. Beghini, D. Bertrand, J. J. Brito, C.T. Brown, J. Buchmann, A. Buluç, B. Chen, R. Chikhi, P. T. Clausen, A. Cristian, P. W. Dabrowski, A. E. Darling, R. Egan, E. Eskin, E. Georganas, E. Goltsman, M. A. Gray, L. H. Hansen, S. Hofmeyr, P. Huang, L. Irber, H. Jia, T. S. Jørgensen, S. D. Kieser, T. Klemetsen, A. Kola, M. Kolmogorov, A. Korobeynikov, J. Kwan, N. LaPierre, C. Lemaitre, C. Li, A. Limasset, F. Malcher-Miranda, S. Mangul, V. R. Marcelino, C. Marchet, P. Marijon, D. Meleshko, D. R. Mende, A. Milanese, N. Nagarajan, J. Nissen, S. Nurk, L. Oliker, L. Paoli, P. Peterlongo, V. C. Piro, J. S. Porter, S. Rasmussen, E. R. Rees, K. Reinert, B. Renard, E. M. Robertsen, G. L. Rosen, H.-J. Ruscheweyh, V. Sarwal, N. Segata, E. Seiler, L. Shi, F. Sun, S. Sunagawa, S. J. Sørensen, A. Thomas, C. Tong, M. Trajkovski, J. Tremblay, G. Uritskiy, R. Vicedomini, Zi. Wang, Zhe. Wang, Zho. Wang, A. Warren, N. P. Willassen, K. Yelick, R. You, G. Zeller, Z. Zhao, S. Zhu, J. Zhu, R. Garrido-Oter, P. Gastmeier, S. Hacquard, S. Häußler, A. Khaledi, F. Maechler, F. Mesny, S. Radutoiu, P. Schulze-Lefert, N. Smit, T. Strowig, A. Bremges, A. Sczyrba, A. C. McHardy,
  "Critical Assessment of Metagenome Interpretation - the second round of challenges"
  Nature Methods , April 2022.
  Preprint in bioRxiv, 12 July 2021.
• Mohammed Alser, Sharon Waymost, Ram Ayyala, Brendan Lawlor, Richard J Abdill, Neha Rajkumar, Nathan LaPierre, Jaqueline Brito, Andre M Ribeiro-dos-Santos, Can Firtina, Nour Almadhoun, Varuni Sarwal, Eleazar Eskin, Qiyang Hu, Derek Strong, Malak S Abedalthagafi, Onur Mutlu, Serghei Mangul "Packaging, containerization, and virtualization of computational omics methods: Advances, challenges, and opportunities"
  Preprint in arXiv, 30 March 2022.
• Mohammed Alser, Jeremie S. Kim, Nour Almadhoun Alserr, Stefan W. Tell, and Onur Mutlu,
  "COVIDHunter: COVID-19 Pandemic Wave Prediction and Mitigation via Seasonality Aware Modeling"
  Frontiers in Public Health, June 2022.
  [arXiv version with all Supplementary Materials]
  [COVIDHunter Source Code]
  [Switzerland Case Study]
  [Short Talk Video at ISMB/ECCB 2021 (7 minutes)]
• Damla Senol Cali, Konstantinos Kanellopoulos, Joel Lindegger, Zulal Bingol, Gurpreet S. Kalsi, Ziyi Zuo, Can Firtina, Meryem Banu Cavlak, Jeremie Kim, Nika MansouriGhiasi, Gagandeep Singh, Juan Gomez-Luna, Nour Almadhoun Alserr, Mohammed Alser, Sreenivas Subramoney, Can Alkan, Saugata Ghose, and Onur Mutlu,
  "SeGraM: A Universal Hardware Accelerator for Genomic Sequence-to-Graph and Sequence-to-Sequence Mapping"
  Proceedings of the 49th International Symposium on Computer Architecture (ISCA), New York, June 2022.
  [Slides (pptx) (pdf)]
  [arXiv version]
  [Short Talk Slides (pptx) (pdf)]
  [Talk Video (25 minutes)]
  [SAFARI Live Seminar Video (1 hr 26 mins)]
• Safaa Diab, Amir Nassereldine, Mohammed Alser, Juan Gómez Luna, Onur Mutlu, Izzat El Hajj "High-throughput Pairwise Alignment with the Wavefront Algorithm using Processing-in-Memory"
  Preprint in arXiv, 5 April 2022.
• Joël Lindegger, Damla Senol Cali, Mohammed Alser, Juan Gómez-Luna, Onur Mutlu "Algorithmic Improvement and GPU Acceleration of the GenASM Algorithm"
  Preprint in arXiv, 28 March 2022.
• Nika Mansouri Ghiasi, Jisung Park, Harun Mustafa, Jeremie Kim, Ataberk Olgun, Arvid Gollwitzer, Damla Senol Cali, Can Firtina, Haiyu Mao, Nour Almadhoun Alserr, Rachata Ausavarungnirun, Nandita Vijaykumar, Mohammed Alser, and Onur Mutlu,
  "GenStore: A High-Performance and Energy-Efficient In-Storage Computing System for Genome Sequence Analysis"
  Proceedings of the 27th International Conference on Architectural Support for Programming Languages and Operating Systems (ASPLOS), Virtual, February-March 2022.
  [Talk Slides (pptx) (pdf)]
  [Lightning Talk Slides (pptx) (pdf)]
  [Lightning Talk Video (90 seconds)]
  [Talk Video (17 minutes)]

2021

• 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]
• F. Meyer, A. Fritz, Z.-L. Deng, D. Koslicki, A. Gurevich, G. Robertson, Mohammed Alser, D. Antipov, F. Beghini, D. Bertrand, J. J. Brito, C.T. Brown, J. Buchmann, A. Buluç, B. Chen, R. Chikhi, P. T. Clausen, A. Cristian, P. W. Dabrowski, A. E. Darling, R. Egan, E. Eskin, E. Georganas, E. Goltsman, M. A. Gray, L. H. Hansen, S. Hofmeyr, P. Huang, L. Irber, H. Jia, T. S. Jørgensen, S. D. Kieser, T. Klemetsen, A. Kola, M. Kolmogorov, A. Korobeynikov, J. Kwan, N. LaPierre, C. Lemaitre, C. Li, A. Limasset, F. Malcher-Miranda, S. Mangul, V. R. Marcelino, C. Marchet, P. Marijon, D. Meleshko, D. R. Mende, A. Milanese, N. Nagarajan, J. Nissen, S. Nurk, L. Oliker, L. Paoli, P. Peterlongo, V. C. Piro, J. S. Porter, S. Rasmussen, E. R. Rees, K. Reinert, B. Renard, E. M. Robertsen, G. L. Rosen, H.-J. Ruscheweyh, V. Sarwal, N. Segata, E. Seiler, L. Shi, F. Sun, S. Sunagawa, S. J. Sørensen, A. Thomas, C. Tong, M. Trajkovski, J. Tremblay, G. Uritskiy, R. Vicedomini, Zi. Wang, Zhe. Wang, Zho. Wang, A. Warren, N. P. Willassen, K. Yelick, R. You, G. Zeller, Z. Zhao, S. Zhu, J. Zhu, R. Garrido-Oter, P. Gastmeier, S. Hacquard, S. Häußler, A. Khaledi, F. Maechler, F. Mesny, S. Radutoiu, P. Schulze-Lefert, N. Smit, T. Strowig, A. Bremges, A. Sczyrba, A. C. McHardy,
  "Critical Assessment of Metagenome Interpretation - the second round of challenges"
  Preprint in bioRxiv, 12 July 2021.
• 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 Applications"
  IEEE 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)]
• Jawad Haj-Yahya, Jeremie S. Kim, A. Giray Yaglikci, Ivan Puddu, Lois Orosa, Juan Gomez Luna, Mohammed Alser, and Onur Mutlu,
  "IChannels: Exploiting Current Management Mechanisms to Create Covert Channels in Modern Processors"
  Proceedings of the 48th International Symposium on Computer Architecture (ISCA), Virtual, June 2021.
  [Slides (pptx) (pdf)]
  [Short Talk Slides (pptx) (pdf)]
  [Talk Video (21 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]
  [Talk Video (7 minutes)]
  [ISMB/ECCB 2021 Poster (pptx) (pdf)]
  [ISMB/ECCB 2021 Short Talk Slides (pptx) (pdf)]
• Zülal Bingöl, Mohammed Alser, Onur Mutlu, Ozcan Ozturk, and Can Alkan
  "GateKeeper-GPU: Fast and Accurate Pre-Alignment Filtering in Short Read Mapping"
  Preprint in arXiv, 31 March 2021.
  [arXiv preprint]
  [Source Code]
• Nastaran Hajinazar, Geraldo F. Oliveira, Sven Gregorio, Joao Dinis Ferreira, Nika Mansouri Ghiasi, Minesh Patel, Mohammed Alser, Saugata Ghose, Juan Gomez-Luna, and Onur Mutlu,
  "SIMDRAM: An End-to-End Framework for Bit-Serial SIMD Computing in DRAM"
  Proceedings of the 26th International Conference on Architectural Support for Programming Languages and Operating Systems (ASPLOS), Virtual, March-April 2021.
  [2-page Extended Abstract]
  [Short Talk Slides (pptx) (pdf)]
  [Talk Slides (pptx) (pdf)]
  [Short Talk Video (5 mins)]
  [Full Talk Video (27 mins)]
• 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]

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, 2020.
  [Source Code]
  [Online link at Bioinformatics Journal]
  Poster presentation at the Swiss Genomics Forum 2019, Geneva, 27 Sept 2019.
  [Poster (pptx) (pdf)]
  Poster presentation at ISMB/ECCB 2019, Basel, Switzerland July 21 - July 25.
  [Poster (pptx) (pdf)]
• 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"
  Preprint in arXiv , 9 July 2020.
  [arXiv preprint]
  [Source Code and Data]
• Nathan LaPierre, Mohammed Alser, Eleazar Eskin, David Koslicki, Serghei Mangul,
  "Metalign: efficient alignment-based metagenomic profiling via containment min hash"
  Genome Biology, 2020.
  [Source Code]
  [bioRxiv preprint]
  [Online link at Genome Biology 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.
  [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)]
• 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]
  [arXiv preprint]
  [Online link at Bioinformatics Journal]
• Nathan LaPierre, Serghei Mangul, Mohammed Alser, Igor Mandric, Nicholas C Wu, David Koslicki, Eleazar Eskin
  "MiCoP: microbial community profiling method for detecting viral and fungal organisms in metagenomic samples"
  BMC genomics, 2019.
  [Source Code and Data]
  [bioRxiv preprint]
  [Online link at Genome Biology 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).

2015

• Mohammed Alser, Nour Almadhoun, Azita Nouri, Can Alkan, Erman Ayday
  "Can you Really Anonymize the Donors of Genomic Data in Today’s Digital World?"
  The 10th International Workshop on Data Privacy Management (DPM 2015), Vienna, Austria, September 21-22, 2015.
  [Online link at Springer Lecture Notes in Computer Science ]