Damla Senol Cali

Employment

• BioNano Genomics Inc Staff Software Engineer, Hardware Acceleration
  2021 - Present

Education

• Carnegie Mellon University Ph.D. in Computer Engineering
  2015 - 2021
• Bilkent Üniversitesi B.Sc. in Computer Engineering
  2010 - 2015

Projects & Funding

Projects & funding information is unavailable.

Publications (16)

• AirLift: A Fast and Comprehensive Technique for Remapping Alignments Between Reference Genomes
  IEEE Transactions on Computational Biology and Bioinformatics 2026 DOI: 10.1109/TCBB.2024.3433378
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• ApHMM: Accelerating Profile Hidden Markov Models for Fast and Energy-efficient Genome Analysis
  ACM Transactions on Architecture and Code Optimization 2024 DOI: 10.1145/3632950
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• BLEND: A Fast, Memory-Efficient, and Accurate Mechanism to Find Fuzzy Seed Matches in Genome Analysis
  2022 DOI: 10.1101/2022.11.23.517691
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• FastRemap: a tool for quickly remapping reads between genome assemblies
  Bioinformatics 2022 DOI: 10.1093/bioinformatics/btac554
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• GenStore: a high-performance in-storage processing system for genome sequence analysis
  Proceedings of the 27th ACM International Conference on Architectural Support for Programming Languages and Operating Systems 2022 DOI: 10.1145/3503222.3507702
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• FastRemap: A Tool for Quickly Remapping Reads between Genome Assemblies
  2022 DOI: 10.48550/ARXIV.2201.06255
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• Accelerating Genome Sequence Analysis via Efficient Hardware/Algorithm Co-Design
  2021 DOI: 10.48550/ARXIV.2111.01916
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• FPGA-Based Near-Memory Acceleration of Modern Data-Intensive Applications
  IEEE Micro 2021 DOI: 10.1109/MM.2021.3088396
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• AirLift: A Fast and Comprehensive Technique for Remapping Alignments between Reference Genomes
  2021 DOI: 10.1101/2021.02.16.431517
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• BLEND: A Fast, Memory-Efficient, and Accurate Mechanism to Find Fuzzy Seed Matches
  2021 DOI: 10.48550/ARXIV.2112.08687
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• GenASM: A High-Performance, Low-Power Approximate String Matching Acceleration Framework for Genome Sequence Analysis
  Damla Senol Cali, Gurpreet Singh Kalsi, Zülal Bingöl +13 more
  2020 53rd Annual IEEE/ACM International Symposium on Microarchitecture (MICRO) 2020 DOI: 10.1109/micro50266.2020.00081
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• Accelerating Genome Analysis: A Primer on an Ongoing Journey
  IEEE Micro 2020 DOI: 10.1109/mm.2020.3013728
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• Apollo: a sequencing-technology-independent, scalable and accurate assembly polishing algorithm
  Bioinformatics 2020 DOI: 10.1093/bioinformatics/btaa179
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• Demystifying Complex Workload-DRAM Interactions
  Proceedings of the ACM on Measurement and Analysis of Computing Systems 2019 DOI: 10.1145/3366708
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• Nanopore sequencing technology and tools for genome assembly: computational analysis of the current state, bottlenecks and future directions
  Briefings in Bioinformatics 2019 DOI: 10.1093/bib/bby017
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• GRIM-Filter: Fast seed location filtering in DNA read mapping using processing-in-memory technologies
  BMC Genomics 2018 DOI: 10.1186/s12864-018-4460-0
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