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12/09/2022
TargetCall: Eliminating the Wasted Computation in Basecalling via Pre-Basecalling Filtering
Basecalling is an essential step in nanopore sequencing analysis where t...
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11/15/2022
Taming Large-Scale Genomic Analyses via Sparsified Genomics
Searching for similar genomic sequences is an essential and fundamental ...
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11/06/2022
A Framework for Designing Efficient Deep Learning-Based Genomic Basecallers
Nanopore sequencing generates noisy electrical signals that need to be c...
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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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08/02/2022
A Framework for High-throughput Sequence Alignment using Real Processing-in-Memory Systems
Sequence alignment is a fundamentally memory bound computation whose per...
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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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06/14/2022
COVIDHunter: COVID-19 pandemic wave prediction and mitigation via seasonality-aware modeling
Early detection and isolation of COVID-19 patients are essential for suc...
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06/04/2022
Demeter: A Fast and Energy-Efficient Food Profiler using Hyperdimensional Computing in Memory
Food profiling is an essential step in any food monitoring system needed...
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06/02/2022
Exploiting Near-Data Processing to Accelerate Time Series Analysis
Time series analysis is a key technique for extracting and predicting ev...
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05/16/2022
Going From Molecules to Genomic Variations to Scientific Discovery: Intelligent Algorithms and Architectures for Intelligent Genome Analysis
We now need more than ever to make genome analysis more intelligent. We ...
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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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04/05/2022
High-throughput Pairwise Alignment with the Wavefront Algorithm using Processing-in-Memory
We show that the wavefront algorithm can achieve higher pairwise read al...
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03/30/2022
Packaging, containerization, and virtualization of computational omics methods: Advances, challenges, and opportunities
Omics software tools have reshaped the landscape of modern biology and b...
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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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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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06/09/2021
IChannels: Exploiting Current Management Mechanisms to Create Covert Channels in Modern Processors
To operate efficiently across a wide range of workloads with varying pow...
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05/26/2021
SIMDRAM: An End-to-End Framework for Bit-Serial SIMD Computing in DRAM
Processing-using-DRAM has been proposed for a limited set of basic opera...
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04/15/2021
pLUTo: In-DRAM Lookup Tables to Enable Massively Parallel General-Purpose Computation
Data movement between main memory and the processor is a significant con...
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03/27/2021
GateKeeper-GPU: Fast and Accurate Pre-Alignment Filtering in Short Read Mapping
At the last step of short read mapping, the candidate locations of the r...
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02/06/2021
COVIDHunter: An Accurate, Flexible, and Environment-Aware Open-Source COVID-19 Outbreak Simulation Model
Motivation: Early detection and isolation of COVID-19 patients are essen...
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12/22/2020
SIMDRAM: A Framework for Bit-Serial SIMD Processing Using DRAM
Processing-using-DRAM has been proposed for a limited set of basic opera...
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10/05/2020
NATSA: A Near-Data Processing Accelerator for Time Series Analysis
Time series analysis is a key technique for extracting and predicting ev...
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09/18/2020
FlexWatts: A Power- and Workload-Aware Hybrid Power Delivery Network for Energy-Efficient Microprocessors
Modern client processors typically use one of three commonly-used power ...
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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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05/15/2020
SysScale: Exploiting Multi-domain Dynamic Voltage and Frequency Scaling for Energy Efficient Mobile Processors
There are three domains in a modern thermally-constrained mobile system-...
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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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10/20/2019
SneakySnake: A Fast and Accurate Universal Genome Pre-Alignment Filter for CPUs, GPUs, and FPGAs
Motivation: We introduce SneakySnake, a highly parallel and highly accur...
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02/12/2019
Apollo: A Sequencing-Technology-Independent, Scalable, and Accurate Assembly Polishing Algorithm
A large proportion of the basepairs in the long reads that third-generat...
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09/18/2018
Shouji: A Fast and Efficient Pre-Alignment Filter for Sequence Alignment
Motivation: The ability to generate massive amounts of sequencing data c...
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09/18/2018
Shouji: Fast and Efficient Computation of Banded Sequence Alignment
Motivation: The ability to generate massive amounts of sequencing data c...
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09/18/2018
SLIDER: Fast and Efficient Computation of Banded Sequence Alignment
Motivation: The ability to generate massive amounts of sequencing data c...
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04/06/2016