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2025
Proceedings of the 30th Asia and South Pacific Design Automation Conference
2025
Fast noisy long read alignment with multi-level parallelism
BMC Bioinformatics
2024
Intelligent Data Analytics for Bioinformatics and Biomedical Systems
2024
2024 ACM/IEEE 51st Annual International Symposium on Computer Architecture (ISCA)
2023
Short-read aligner performance in germline variant identification
Bioinformatics
2023
BiocMAP: a Bioconductor-friendly, GPU-accelerated pipeline for bisulfite-sequencing data
BMC Bioinformatics
2023
HARDWARE ACCELERATION OF DNA READ ALIGNMENT PROGRAMS: CHALLENGES AND OPPORTUNITIES
Fractals
2023
GPMeta: a GPU-accelerated method for ultrarapid pathogen identification from metagenomic sequences
Briefings in Bioinformatics
2022
2022 IEEE International Conference on Bioinformatics and Biomedicine (BIBM)
2022
nGIA: A novel Greedy Incremental Alignment based algorithm for gene sequence clustering
Future Generation Computer Systems
2022
Compressed Sparse FM-Index: Fast Sequence Alignment Using Large K-Steps
IEEE/ACM Transactions on Computational Biology and Bioinformatics
2022
Proceedings of the 27th ACM International Conference on Architectural Support for Programming Languages and Operating Systems
2022
2022 IEEE International Parallel and Distributed Processing Symposium (IPDPS)
2021
A 2.46M Reads/s Seed-Extension Accelerator for Next-Generation Sequencing Using a String-Independent PE Array
IEEE Journal of Solid-State Circuits
2021
Enabling fast and energy-efficient FM-index exact matching using processing-near-memory
The Journal of Supercomputing
2020
A Review on Sequence Alignment Algorithms for Short Reads Based on Next-Generation Sequencing
IEEE Access
2020
Detection of haplotype-dependent allele-specific DNA methylation in WGBS data
Nature Communications
2020
2020 IEEE Custom Integrated Circuits Conference (CICC)
2020
Arioc: High-concurrency short-read alignment on multiple GPUs
PLOS Computational Biology
2020
Accelerating Sequence Alignments Based on FM-Index Using the Intel KNL Processor
IEEE/ACM Transactions on Computational Biology and Bioinformatics
2020
Genome Sequence Alignment - Design Space Exploration for Optimal Performance and Energy Architectures
IEEE Transactions on Computers
2019
Encyclopedia of Bioinformatics and Computational Biology
2019
The Terabase Search Engine: a large-scale relational database of short-read sequences
Bioinformatics
2019
A Parallel-Computing Algorithm for High-Energy Physics Particle Tracking and Decoding Using GPU Architectures
IEEE Access
2018
Parallel synchronous and asynchronous coupled simulated annealing
The Journal of Supercomputing
2018
Arioc: GPU-accelerated alignment of short bisulfite-treated reads
Bioinformatics
2018
2018 IEEE International Parallel and Distributed Processing Symposium Workshops (IPDPSW)
2017
A Survey of Software and Hardware Approaches to Performing Read Alignment in Next Generation Sequencing
IEEE/ACM Transactions on Computational Biology and Bioinformatics
2017
Accelerating metagenomic read classification on CUDA-enabled GPUs
BMC Bioinformatics
2017
Next-generation sequencing: big data meets high performance computing
Drug Discovery Today
2017
Genetically improved BarraCUDA
BioData Mining
2017
Short Read Mapping: An Algorithmic Tour
Proceedings of the IEEE
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