Education

• Ph.D., Computer Engineering, 2021
  • Carnegie Mellon University, Pittsburgh, PA
  • Dissertation: “Accelerating Genome Sequence Analysis via Efficient Hardware/Algorithm Co-Design”.
• M.Sc., Computer Engineering, 2019
  • Carnegie Mellon University, Pittsburgh, PA
• B.Sc., Computer Engineering, 2015
  • Bilkent University, Ankara, Turkey

After Alkan Lab

Damla Senol Cali is a Senior Computational Biologist at 10X Genomics. She received her Ph.D. degree in Computer Engineering from the SAFARI Research Group at Carnegie Mellon University, where she was advised by Prof. Onur Mutlu and Prof. Saugata Ghose. She then worked as a Staff Software Engineer, Hardware Acceleration at Bionano Genomics.

Her research focuses on hardware/software co-design for accelerating bioinformatics applications and genomic data analysis. She is also excited about memory systems and processing-in-memory. During her Ph.D., she also interned at Intel Labs in 2018 and 2020.

Publications

• ApHMM: Accelerating Profile Hidden Markov Models for Fast and Energy-Efficient Genome Analysis. Can Firtina, Kamlesh Pillai, Gurpreet S. Kalsi, Bharathwaj Suresh, Damla Senol Cali, Jeremie Kim, Taha Shahroodi, Meryem Banu Cavlak, Joel Lindegger, Mohammed Alser, Juan Gómez Luna, Sreenivas Subramoney, and Onur Mutlu. arXiv, 2207.09765, 2022.

• FastRemap: A Tool for Quickly Remapping Reads between Genome Assemblies. Jeremie S. Kim, Can Firtina, Meryem Banu Cavlak, Damla Senol Cali, Can Alkan, and Onur Mutlu. Bioinformatics, btac554, 2022.

• SeGraM: A Universal Hardware Accelerator for Genomic Sequence-to-Graph and Sequence-to-Sequence Mapping. Damla Senol Cali, Konstantinos Kanellopoulos, Joël Lindegger, Zülal Bingöl, Gurpreet S. Kalsi, Ziyi Zuo, Can Firtina, Meryem Banu Cavlak, Jeremie Kim, Nika Mansouri Ghiasi, Gagandeep Singh, Juan Gómez-Luna, Nour Almadhoun Alserr, Mohammed Alser, Sreenivas Subramoney, Can Alkan, Saugata Ghose, and Onur Mutlu. Proceedings of the 49th Annual International Symposium on Computer Architecture (ISCA), New York, NY, USA, June 2022.

• GenStore: A High-Performance in-Storage Processing System for Genome Sequence Analysis. 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. Proceedings of the 27th ACM International Conference on Architectural Support for Programming Languages and Operating Systems (ASPLOS), Lausanne, Switzerland, March 2022.

• FPGA-based Near-Memory Acceleration of Modern Data-Intensive Applications. Gagandeep Singh, Mohammed Alser, Damla Senol Cali, Dionysios Diamantopoulos, Juan Gomez-Luna, Henk Corporaal, and Onur Mutlu. IEEE Micro, July 2021.

• BLEND: A Fast, Memory-Efficient, and Accurate Mechanism to Find Fuzzy Seed Matches. Can Firtina, Jisung Park, Mohammed Alser, Jeremie S. Kim, Damla Senol Cali, Taha Shahroodi, Nika Mansouri Ghiasi, Gagandeep Singh, Konstantinos Kanellopoulos, Can Alkan, and Onur Mutlu,. arXiv, 2112.08687, 2021.

• AirLift: A Fast and Comprehensive Technique for Remapping Alignments between Reference Genomes. Jeremie S. Kim, Can Firtina, Meryem Banu Cavlak, Damla Senol Cali, Nastaran Hajinazar, Mohammed Alser, Can Alkan, and Onur Mutlu. bioRxiv, 2021.02.16.431517, 2021.

• GenASM: A High-Performance, Low-Power Approximate String Matching Acceleration Framework for Genome Sequence Analysis. Damla Senol Cali, Gurpreet S. Kalsi, Zülal Bingöl, Can Firtina, Lavanya Subramanian, Jeremie S. Kim, Rachata Ausavarungnirun, Mohammed Alser, Juan Gómez-Luna, Amirali Boroumand, Anant Norion, Allison Scibisz, Sreenivas Subramoney, Can Alkan, Saugata Ghose, and Onur Mutlu. Proceedings of the 53rd International Symposium on Microarchitecture (MICRO), Virtual, October 2020.

• Accelerating Genome Analysis: A Primer on an Ongoing Journey. Mohammed Alser, Zulal Bingol, Damla Senol Cali, Jeremie S. Kim, Saugata Ghose, Can Alkan, and Onur Mutlu. IEEE Micro, September 2020.

• Apollo: A Sequencing-Technology-Independent, Scalable and Accurate Assembly Polishing Algorithm. Can Firtina, Jeremie S. Kim, Mohammed Alser, Damla Senol Cali, A Ercument Cicek, Can Alkan, and Onur Mutlu. Bioinformatics, February 2020.

• Demystifying Workload–DRAM Interactions: An Experimental Study. Saugata Ghose, Tianshi Li, Nastaran Hajinazar, Damla Senol Cali, and Onur Mutlu. ACM SIGMETRICS, June 2019.

• GRIM-Filter: Fast Seed Location Filtering in DNA Read Mapping Using Processing-in-Memory Technologies. Jeremie S. Kim, Damla Senol Cali, Hongyi Xin, Donghyuk Lee, Saugata Ghose, Mohammed Alser, Hasan Hassan, Oguz Ergin, Can Alkan, and Onur Mutlu. BMC Genomics, May 2018.

• Nanopore Sequencing Technology and Tools for Genome Assembly: Computational Analysis of the Current State, Bottlenecks and Future Directions. Damla Senol Cali, Jeremie Kim, Saugata Ghose, Can Alkan, and Onur Mutlu. Briefings in Bioinformatics, April 2018.