Can Firtina
Assistant Professor
Designs algorithms, AI/ML methods and specialized hardware systems for fast, energy-efficient real-time genome sequence analysis.
Can Firtina's lab at UMD works on genomics & computational biology, physics, climate & scientific computing and rendering & appearance. 20 papers since 2023, mostly Bioinformatics and Briefings in Bioinformatics. 3 PhD students and 2 master's students. 2 alumni.
At a glance
- papers, 2023–2026
- 5/ year
- at T1 venues
- 0%
- PhD students
- 3
- MS students
- 2
- alumni listed
- 2
Papers by yearfrom the lab homepage, 2023–2026
- 5 papers2026 · T1 0 · collecting
- 2 papers2025 · T1 0
- 8 papers2024 · T1 0
- 5 papers2023 · T1 0
T1 venuesOtherVenues: Bioinformatics, Briefings in Bioinformatics
Research focuspaper titles that use each topic's words
- Genomics & computational biology1 paper
- sequence1 paper
- Physics, climate & scientific computing0 papers
- Rendering & appearance0 papers
- designs algorithms0 papers
Paper list
From the lab homepage.
20265 papers
- Briefings in BioinformaticsDe Bruijn graphs for pangenomics: in-depth performance benchmarking of de Bruijn graph-based tools for read mapping
- Proceedings of the International Symposium on High-Performance Computer Architecture (HPCA ), Sydney, AustraliaGenPairX: A Hardware-Algorithm Co-Designed Accelerator for Paired-End Read Mapping
- TCIn-Storage Heterogeneous Acceleration For Scalable Long-Read Mapping
- BioinformaticsRawsamble: Overlapping Raw Nanopore Signals using a Hash-based Seeding Mechanism
- Proceedings of the International Symposium on High-Performance Computer Architecture (HPCA ), Sydney, AustraliaSAGe: A Lightweight Algorithm-Architecture Co-Design for Mitigating the Data Preparation Bottleneck in Large-Scale Genome Sequence Analysis
20252 papers
- Proceedings of the International Conference on Supercomputing (ICS ), Salt Lake City, Utah, USAMARS: Processing-In-Memory Acceleration of Raw Signal Genome Analysis Inside the Storage Subsystem
- Proceedings of the ACM Conference on Bioinformatics, Computational Biology, and Health Informatics (ACM-BCB ), Philadelphia, PA, USARawBench: A Comprehensive Benchmarking Framework for Raw Nanopore Signal Analysis Techniques
20248 papers
- TCBBAirLift: A Fast and Comprehensive Technique for Remapping Alignments between Reference Genomes
- TACOApHMM: Accelerating Profile Hidden Markov Models for Fast and Energy-efficient Genome Analysis
- Proceedings of the Annual International Symposium on Computer Architecture (ISCA ), Buenos Aires, ArgentinaMegIS: High-Performance, Energy-Efficient, and Low-Cost Metagenomic Analysis with In-Storage Processing
- Nature ProtocolsPackaging and containerization of computational methods
- IEEE AccessRawAlign: Accurate, Fast, and Scalable Raw Nanopore Signal Mapping via Combining Seeding and Alignment
- BioinformaticsRawHash2: Mapping Raw Nanopore Signals Using Hash-Based Seeding and Adaptive Quantization
- Genome BiologyRUBICON: a framework for designing efficient deep learning-based genomic basecallers
- Frontiers in GeneticsTargetCall: Eliminating the Wasted Computation in Basecalling via Pre-Basecalling Filtering
20235 papers
- NARGABBLEND: a fast, memory-efficient and accurate mechanism to find fuzzy seed matches in genome analysis
- Proceedings of the Design Automation Conference (DAC ), San Francisco, CA, USAInvited: Accelerating Genome Analysis via Algorithm-Architecture Co-Design
- Proceedings of the Annual Conference on Intelligent Systems for Molecular Biology and the European Conference on Computational Biology (ISMB/ECCB ), Lyon, FranceRawHash: enabling fast and accurate real-time analysis of raw nanopore signals for large genomes
- Proceedings of the International Symposium on Microarchitecture (MICRO ), Toronto, ON, CanadaSwordfish: A Framework for Evaluating Deep Neural Network-Based Basecalling Using Computation-In-Memory with Non-Ideal Memristors
- Proceedings of the International Symposium on Microarchitecture (MICRO ), Toronto, ON, CanadaUtopia: Fast and Efficient Address Translation via Hybrid Restrictive & Flexible Virtual-to-Physical Address Mappings
Where alumni went2 listed, 0% to industry
Industry 0Academia 1
Also to
- Johns Hopkins University
Apply to UMDFall 2027
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UMD Computer Science PhD
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