Talks & Service | Can Firtina

Talks and Invited Lectures

Can Firtina, “Rawsamble: Overlapping and Assembling Raw Nanopore Signals using a Hash-based Seeding Mechanism”, Conference Talk, The Biological Data Science Meeting of Cold Spring Harbor Laboratory (CSHL) 2024, Cold Spring Harbor, NY, USA. Nov 14 2024. [Slides (PDF)] [Slides (PPT)]
Can Firtina, “Enabling Fast, Accurate, and Efficient Real-Time Genome Analysis via New Algorithms and Techniques”, PhD Thesis Defense, ETH Zurich, Zurich, Switzerland. Nov 11 2024. [Slides (PDF)] [Slides (PPT)]
Can Firtina, “Enabling Fast, Accurate, and Efficient Real-Time Genomic Sequence Analysis via New Algorithms and Architectures”, Invited Talk, AMD, Virtual. September 13 2024. [Slides (PDF)] [Slides (PPT)]
Can Firtina, “Rawsamble: Overlapping and Assembling Raw Nanopore Signals using a Hash-based Seeding Mechanism”, Conference Talk, 32nd Annual Conference on Intelligent Systems for Molecular Biology (ISMB), Montreal, QC, Canada. July 14 2024. [Slides (PDF)] [Slides (PPT)]
Can Firtina, “Enabling Fast, Accurate, and Efficient Real-Time Genomic Sequence Analysis via New Algorithms and Architectures”, Invited Talk, Huawei Research Center Zurich, Zurich, Switzerland. May 17 2024. [Slides (PDF)] [Slides (PPT)]
Can Firtina, “Real-time Sequence Analysis from Raw Nanopore Electrical Signals with Accurate Hash-based Search Mechanisms”, Invited Talk, The Broad Institute of MIT and Harvard, hosted by Victoria Popic, Ph.D., Cambridge, MA, USA. May 10 2024. [Slides (PDF)] [Slides (PPT)]
Can Firtina, “Real-time Analysis of Genomic Sequences from Nanopore Electrical Signals by Fast and Accurate Hash-based Search”, Invited Talk, The Jackson Laboratory (JAX), hosted by Joshy George, Ph.D., Farmington, CT, USA. May 6 2024. [Slides (PDF)] [Slides (PPT)]
Can Firtina, “Real-time Analysis of Genomic Sequences from Nanopore Electrical Signals by Fast and Accurate Hash-based Search”, Invited Talk, Tufts University - Department of Computer Science, hosted by Prof. Lenore J. Cowen, Medford, MA, USA. May 3 2024. [Slides (PDF)] [Slides (PPT)]
Can Firtina, “Introduction to Real-Time Raw Nanopore Signal Analysis: RawHash and RawHash2”, Invited Lecture, BIO310 - Introduction to Bioinformatics, Sabanci University, Virtual. March 18 2024. [Slides (PDF)] [Slides (PPT)]
Can Firtina, “RawHash and RawHash2: Enabling Fast and Accurate Real-time Analysis of Raw Nanopore Signals for Large Genomes using a Hash-based Seeding Mechanism”, Invited Talk, Leibniz Institute for Immunotherapy (LIT), hosted by Prof. Birte Kehr, Regensburg, Germany. January 17 2024. [Slides (PDF)] [Slides (PPT)]
Can Firtina, “ApHMM: Accelerating Profile Hidden Markov Models for Fast and Energy-Efficient Genome Analysis”, Conference Talk, High Performance, Edge And Cloud computing (HiPEAC) 2024, Munich, Germany. January 17 2024. [Video] [Slides (PDF)] [Slides (PPT)]
Can Firtina, “Enabling Fast, Accurate and Efficient Real-Time Genome Analysis via New Algorithms and Architectures”, Invited Talk, Technical University of Munich (TUM) - School of Computation, Information and Technology (CIT), hosted by Prof. Ulf Schlichtmann, Munich, Germany. January 16 2024. [Slides (PDF)] [Slides (PPT)]
Can Firtina, “Enabling Fast, Accurate and Efficient Real-Time Genome Analysis via New Algorithms and Architectures”, Invited Talk, Huawei Munich Research Center, Munich, Germany. January 15 2024. [Slides (PDF)] [Slides (PPT)]
Can Firtina, “RawHash: enabling fast and accurate real-time analysis of raw nanopore signals for large genomes”, Conference Talk, 31st Annual Conference on Intelligent Systems for Molecular Biology (ISMB) and the 22nd European Conference on Computational Biology (ECCB), Lyon, France. July 25 2023. [Video] [Slides (PDF)] [Slides (PPT)]
Can Firtina, “RawHash: enabling fast and accurate real-time analysis of raw nanopore signals for large genomes”, Workshop Talk, The 5th Workshop on Accelerator Architecture in Computational Biology and Bioinformatics (AACBB), Orlando, Florida, USA. June 18 2023. [Video] [Slides (PDF)] [Slides (PPT)]
Can Firtina, “BLEND: A fast, memory-efficient and accurate mechanism to find fuzzy seed matches in genome analysis”, Conference Talk, 27th Annual International Conference on Research in Computational Molecular Biology (RECOMB), Istanbul, Turkey. April 19 2023. [Video] [Slides (PDF)] [Slides (PPT)]
Can Firtina, “AirLift: A Fast and Comprehensive Technique for Remapping Alignments between Reference Genomes”, Conference Talk, The 21st Asia Pacific Bioinformatics Conference (APBC), Changsha, China. April 16 2023. [Video] [Slides (PDF)] [Slides (PPT)]
Can Firtina, “Enabling Accurate, Fast, and Memory-Efficient Genome Analysis via Efficient and Intelligent Algorithms”, Invited Talk, Department of Electrical Engineering and Computer Sciences, hosted by Giulia Guidi, UC Berkeley, Berkeley, CA, United States. May 27 2022. [Video] [Slides (PDF)] [Slides (PPT)]
Can Firtina, “Enabling Accurate, Fast, and Memory-Efficient Genome Analysis via Efficient and Intelligent Algorithms”, Invited Seminar Talk, BIN590 Graduate Seminar in Bioinformatics, Graduate School of Informatics, Middle East Technical University, Virtual. January 10 2022. [Video] [Slides (PDF)] [Slides (PPT)]
Can Firtina, “Apollo: a sequencing-technology-independent, scalable and accurate assembly polishing algorithm”, Workshop Talk, ExaBiome/PASSION/SAFARI Workshop on Architectures and HPC for Genomics, Virtual. May 26 2021. [Video] [Slides (PDF)] [Slides (PPT)]

Services & Activities

Reviewer/sub-reviewer for RECOMB, RECOMB-Seq, Bioinformatics, BMC Bioinformatics, MICRO, ISCA, HPCA, ASPLOS, PACT, IEEE Micro, FAST, DSN, IEEE Transactions on Computers, ISCAS, ISPASS, USENIX ATC.
Organized BIO-Arch: Workshop on Hardware Acceleration of Bioinformatics Workloads, jointly held with RECOMB 2023.
Organized the Panel on Hardware Acceleration of Bioinformatics Workloads at RECOMB 2023.
Organized the ExaBiome/PASSION/SAFARI Workshop on Architectures and HPC for Genomics workshop with Giulia Guidi. The workshop included 10 presenters from ExaBiome, PASSION, and SAFARI. May 26 2022, Virtual.

Collaborators

Onur Mutlu (ETH Zurich)
Can Alkan (Bilkent University)
Damla Senol Cali (Bionano Genomics)
Jeremie S. Kim (Apple)
Juan Gomez-Luna (NVIDIA)
Mohammad Sadrosadati (ETH Zurich)
Nika Mansouri Ghiasi (ETH Zurich)
Joel Lindegger (ETH Zurich)
Gagandeep Singh (AMD)
Haiyu Mao (ETH Zurich)
Taha Shahroodi (TU Delft)
Andre Kahles (ETH Zurich)
Harun Mustafa (ETH Zurich)
Giulia Guidi (Cornell University)
Sreenivas Subramoney (Intel Labs)
Gurpreet S. Kalsi (Intel Labs)
Kamlesh Pillai (Intel Labs)
Mohammed Alser (ETH Zurich)
Nour Almadhoun Alserr (ETH Zurich)
Jisung Park (POSTECH)
Konstantinos Kanellopoulos (ETH Zurich)
Saugata Ghose (University of Illinois Urbana-Champaign)
Serghei Mangul (USC)
A. Ercument Cicek (Bilkent University)
Oznur Tastan (Sabanci University)
Levent Onural (Bilkent University)
Ziv Bar-Joseph (Carnegie Mellon University)