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09/18/2022
GenPIP: In-Memory Acceleration of Genome Analysis via Tight Integration of Basecalling and Read Mapping
Nanopore sequencing is a widely-used high-throughput genome sequencing t...
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08/21/2022
Scrooge: A Fast and Memory-Frugal Genomic Sequence Aligner for CPUs, GPUs, and ASICs
Motivation: Pairwise sequence alignment is a very time-consuming step in...
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07/20/2022
ApHMM: Accelerating Profile Hidden Markov Models for Fast and Energy-Efficient Genome Analysis
Profile hidden Markov models (pHMMs) are widely used in many bioinformat...
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05/12/2022
SeGraM: A Universal Hardware Accelerator for Genomic Sequence-to-Graph and Sequence-to-Sequence Mapping
A critical step of genome sequence analysis is the mapping of sequenced ...
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03/28/2022
Algorithmic Improvement and GPU Acceleration of the GenASM Algorithm
We improve on GenASM, a recent algorithm for genomic sequence alignment,...
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02/21/2022
GenStore: A High-Performance and Energy-Efficient In-Storage Computing System for Genome Sequence Analysis
Read mapping is a fundamental, yet computationally-expensive step in man...
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11/02/2021
Accelerating Genome Sequence Analysis via Efficient Hardware/Algorithm Co-Design
Genome sequence analysis plays a pivotal role in enabling many medical a...
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06/11/2021
FPGA-Based Near-Memory Acceleration of Modern Data-Intensive Applications
Modern data-intensive applications demand high computation capabilities ...
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09/16/2020
GenASM: A High-Performance, Low-Power Approximate String Matching Acceleration Framework for Genome Sequence Analysis
Genome sequence analysis has enabled significant advancements in medical...
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07/30/2020
Accelerating Genome Analysis: A Primer on an Ongoing Journey
Genome analysis fundamentally starts with a process known as read mappin...
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12/18/2019
AirLift: A Fast and Comprehensive Technique for Translating Alignments between Reference Genomes
As genome sequencing tools and techniques improve, researchers are able ...
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02/20/2019
Understanding the Interactions of Workloads and DRAM Types: A Comprehensive Experimental Study
It has become increasingly difficult to understand the complex interacti...
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02/12/2019