Publications

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, Onur Mutlu
October 2020 In Proceedings of the 53rd International Symposium on Microarchitecture (MICRO)

GenASM: A High-Performance, Low-Power Approximate String Matching Acceleration Framework for Genome Sequence Analysis

Paper Source Code Talk Video (18 minutes) Talk Slides (PDF) Talk Slides (PPTX) Live Talk and Q/A Video (15 minutes) Short Talk Video (6 minutes) Short Talk Slides (PDF) Short Talk Slides (PPTX) Lightning Talk Video (90 seconds) Lightning Talk Slides (PDF) Lightning Talk Slides (PPTX) Lecture Video (37 minutes) Lecture Slides (PDF) Lecture Slides (PPTX)
Mohammed Alser, Zulal Bingol, Damla Senol Cali, Jeremie S. Kim, Saugata Ghose, Can Alkan, Onur Mutlu
September 2020 IEEE Micro

Accelerating Genome Analysis: A Primer on an Ongoing Journey

Paper
Can Firtina, Jeremie S. Kim, Mohammed Alser, Damla Senol Cali, A. Ercument Cicek, Can Alkan, Onur Mutlu
March 2020 Bioinformatics

Apollo: A Sequencing-Technology-Independent, Scalable, and Accurate Assembly Polishing Algorithm

Paper
Saugata Ghose, Tianshi Li, Nastaran Hajinazar, Damla Senol Cali, Onur Mutlu
July 2019 In Proceedings of the ACM International Conference on Measurement and Modeling of Computer Systems (SIGMETRICS)

Demystifying Workload–DRAM Interactions: An Experimental Study

Paper
Damla Senol Cali, Jeremie S. Kim, Saugata Ghose, Can Alkan, Onur Mutlu
April 2018 Briefings in Bioinformatics

Nanopore Sequencing Technology and Tools for Genome Assembly: Computational Analysis of the Current State, Bottlenecks and Future Directions

Paper arXiv Version AACBB 2019 Talk Video Slides (PDF) Slides (PPTX)
Jeremie S. Kim, Damla Senol Cali, Hongyi Xin, Donghyuk Lee, Saugata Ghose, Mohammed Alser, Hasan Hassan, Oguz Ergin, Can Alkan, Onur Mutlu
January 2018 BMC Genomics

GRIM-Filter: Fast Seed Location Filtering in DNA Read Mapping Using Processing-in-Memory Technologies

Paper