[HTML][HTML] From molecules to genomic variations: Accelerating genome analysis via intelligent algorithms and architectures

M Alser, J Lindegger, C Firtina, N Almadhoun… - Computational and …, 2022 - Elsevier
We now need more than ever to make genome analysis more intelligent. We need to read,
analyze, and interpret our genomes not only quickly, but also accurately and efficiently …

GenStore: A high-performance in-storage processing system for genome sequence analysis

N Mansouri Ghiasi, J Park, H Mustafa, J Kim… - Proceedings of the 27th …, 2022 - dl.acm.org
Read map** is a fundamental step in many genomics applications. It is used to identify
potential matches and differences between fragments (called reads) of a sequenced …

Efficient real-time selective genome sequencing on resource-constrained devices

PJ Shih, H Saadat, S Parameswaran… - …, 2023 - academic.oup.com
Background Third-generation nanopore sequencers offer selective sequencing or “Read
Until” that allows genomic reads to be analyzed in real time and abandoned halfway if not …

SeGraM: A universal hardware accelerator for genomic sequence-to-graph and sequence-to-sequence map**

DS Cali, K Kanellopoulos, J Lindegger… - Proceedings of the 49th …, 2022 - dl.acm.org
A critical step of genome sequence analysis is the map** of sequenced DNA fragments
(ie, reads) collected from an individual to a known linear reference genome sequence (ie …

Accelerated dynamic time war** on GPU for selective nanopore sequencing

H Sadasivan, D Stiffler, A Tirumala, J Israeli… - bioRxiv, 2023 - biorxiv.org
The design and supply of RT-PCR primers for accurate virus testing is a complex process.
The MinION is a revolutionary portable nanopore DNA sequencer that may be used to …

[HTML][HTML] Rapid real-time squiggle classification for read until using rawmap

H Sadasivan, J Wadden, K Goliya… - Archives of clinical …, 2023 - ncbi.nlm.nih.gov
Abstract ReadUntil enables Oxford Nanopore Technology's (ONT) sequencers to selectively
sequence reads of target species in real-time. This enables efficient microbial enrichment for …

GenStore: A High-Performance and Energy-Efficient In-Storage Computing System for Genome Sequence Analysis

NM Ghiasi, J Park, H Mustafa, J Kim, A Olgun… - ar** is a fundamental, yet computationally-expensive step in many genomics
applications. It is used to identify potential matches and differences between fragments …

Accelerated Systems for Portable DNA Sequencing

H Sadasivan - 2023 - deepblue.lib.umich.edu
The MinION is a revolutionary handheld DNA sequencer that is inexpensive, portable, and
can perform real-time sequencing. MinION is increasingly used in Precision Medicine …

Dash-cam: dynamic approximate search content addressable memory for genome classification

Z Jahshan, I Merlin, E Garzón, L Yavits - … of the 56th Annual IEEE/ACM …, 2023 - dl.acm.org
We propose a novel dynamic storage-based approximate search content addressable
memory (DASH-CAM) for computational genomics applications, particularly for identification …

Genpip: In-memory acceleration of genome analysis via tight integration of basecalling and read map**

H Mao, M Alser, M Sadrosadati, C Firtina… - 2022 55th IEEE/ACM …, 2022 - ieeexplore.ieee.org
Nanopore sequencing is a widely-used high-throughput genome sequencing technology
that can sequence long fragments of a genome into raw electrical signals at low cost …