Publications
Publications
Our work across top-tier venues in computer architecture, bioinformatics, and systems. See Google Scholar for a complete list.
2026
-
Rawsamble: Overlapping Raw Nanopore Signals using a Hash-based Seeding MechanismBioinformatics, February 2026Social Media Thread [Twitter (X)] [LinkedIn]
-
GenPairX: A Hardware-Algorithm Co-Designed Accelerator for Paired-End Read MappingProceedings of the 32nd International Symposium on High-Performance Computer Architecture (HPCA 2026), Sydney, Australia, January 2026
-
SAGe: A Lightweight Algorithm-Architecture Co-Design for Mitigating the Data Preparation Bottleneck in Large-Scale Genome Sequence AnalysisProceedings of the 32nd International Symposium on High-Performance Computer Architecture (HPCA 2026), Sydney, Australia, January 2026
2025
-
RawBench: A Comprehensive Benchmarking Framework for Raw Nanopore Signal Analysis TechniquesProceedings of the 16th ACM Conference on Bioinformatics, Computational Biology, and Health Informatics (ACM-BCB 2025), Philadelphia, PA, USA, October 2025
-
MARS: Processing-In-Memory Acceleration of Raw Signal Genome Analysis Inside the Storage SubsystemProceedings of the 39th International Conference on Supercomputing (ICS 2025), Salt Lake City, Utah, USA, June 2025
2024
-
RawAlign: Accurate, Fast, and Scalable Raw Nanopore Signal Mapping via Combining Seeding and AlignmentIEEE Access, December 2024
-
TargetCall: Eliminating the Wasted Computation in Basecalling via Pre-Basecalling FilteringFrontiers in Genetics, September 2024
-
AirLift: A Fast and Comprehensive Technique for Remapping Alignments between Reference Genomes
-
RawHash2: Mapping Raw Nanopore Signals Using Hash-Based Seeding and Adaptive QuantizationBioinformatics, July 2024
-
MegIS: High-Performance, Energy-Efficient, and Low-Cost Metagenomic Analysis with In-Storage ProcessingProceedings of the 51st Annual International Symposium on Computer Architecture (ISCA 2024), Buenos Aires, Argentina, July 2024
-
Packaging and containerization of computational methodsNature Protocols, April 2024
-
RUBICON: a framework for designing efficient deep learning-based genomic basecallersGenome Biology, February 2024
-
ApHMM: Accelerating Profile Hidden Markov Models for Fast and Energy-efficient Genome Analysis
2023
-
Swordfish: A Framework for Evaluating Deep Neural Network-Based Basecalling Using Computation-In-Memory with Non-Ideal MemristorsProceedings of the 56th International Symposium on Microarchitecture (MICRO 2023), Toronto, ON, Canada, November 2023
-
Utopia: Fast and Efficient Address Translation via Hybrid Restrictive & Flexible Virtual-to-Physical Address MappingsProceedings of the 56th International Symposium on Microarchitecture (MICRO 2023), Toronto, ON, Canada, November 2023
-
MetaTrinity: Enabling Fast Metagenomic Classification via Seed Counting and Edit Distance ApproximationarXiv, November 2023
-
SequenceLab: A Comprehensive Benchmark of Computational Methods for Comparing Genomic SequencesarXiv, October 2023
-
Invited: Accelerating Genome Analysis via Algorithm-Architecture Co-DesignProceedings of the 60th Design Automation Conference (DAC 2023), San Francisco, CA, USA, July 2023
-
RawHash: enabling fast and accurate real-time analysis of raw nanopore signals for large genomesProceedings of the 31st Annual Conference on Intelligent Systems for Molecular Biology (ISMB 2023) and the 22nd European Conference on Computational Biology (ECCB 2023), Lyon, France, July 2023Preprint (bioRxiv) [online link] [pdf]Social Media Thread [Twitter (X)]
-
BLEND: a fast, memory-efficient and accurate mechanism to find fuzzy seed matches in genome analysisNAR Genomics and Bioinformatics (NARGAB), March 2023Preprint (bioRxiv) [online link] [pdf]Social Media Thread [Twitter (X)] [Twitter (X)]
2022
-
GenPIP: In-Memory Acceleration of Genome Analysis via Tight Integration of Basecalling and Read MappingProceedings of the 55th International Symposium on Microarchitecture (MICRO 2022), Chicago, IL, USA, October 2022
-
FastRemap: a tool for quickly remapping reads between genome assembliesBioinformatics, September 2022
-
From molecules to genomic variations: Accelerating genome analysis via intelligent algorithms and architectures
-
Demeter: A Fast and Energy-Efficient Food Profiler Using Hyperdimensional Computing in MemoryIEEE Access, August 2022
-
SeGraM: A Universal Hardware Accelerator for Genomic Sequence-to-Graph and Sequence-to-Sequence MappingProceedings of the 49th Annual International Symposium on Computer Architecture (ISCA 2022), New York City, NY, USA, June 2022
-
GenStore: A High-Performance in-Storage Processing System for Genome Sequence AnalysisProceedings of the 27th International Conference on Architectural Support for Programming Languages and Operating Systems (ASPLOS 2022), Lusanne, Switzerland, February 2022
2021
-
Modeling Economic Activities and Random Catastrophic Failures of Financial Networks via Gibbs Random FieldsComputational Economics, August 2021
2020
-
GenASM: A High-Performance, Low-Power Approximate String Matching Acceleration Framework for Genome Sequence AnalysisProceedings of the 53rd International Symposium on Microarchitecture (MICRO 2020), Virtual, October 2020
-
Apollo: a sequencing-technology-independent, scalable and accurate assembly polishing algorithmBioinformatics, June 2020
2018
-
Hercules: a profile HMM-based hybrid error correction algorithm for long readsNucleic Acids Research (NAR), November 2018
2017
-
GLANET: genomic loci annotation and enrichment toolBioinformatics, September 2017
2016
-
On genomic repeats and reproducibilityBioinformatics, August 2016
No publications match your search.