[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 …

GenASM: A high-performance, low-power approximate string matching acceleration framework for genome sequence analysis

DS Cali, GS Kalsi, Z Bingöl, C Firtina… - 2020 53rd Annual …, 2020 - ieeexplore.ieee.org
Genome sequence analysis has enabled significant advancements in medical and scientific
areas such as personalized medicine, outbreak tracing, and the understanding of evolution …

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 mapping is a fundamental step in many genomics applications. It is used to identify
potential matches and differences between fragments (called reads) of a sequenced …

Accelerating genome analysis: A primer on an ongoing journey

M Alser, Z Bingöl, DS Cali, J Kim, S Ghose… - IEEE Micro, 2020 - ieeexplore.ieee.org
Genome analysis fundamentally starts with a process known as read mapping, where
sequenced fragments of an organism's genome are compared against a reference genome …

[HTML][HTML] From GPUs to AI and quantum: three waves of acceleration in bioinformatics

B Schmidt, A Hildebrandt - Drug Discovery Today, 2024 - Elsevier
The enormous growth in the amount of data generated by the life sciences is continuously
shifting the field from model-driven science towards data-driven science. The need for …

WFA-GPU: gap-affine pairwise read-alignment using GPUs

Q Aguado-Puig, M Doblas, C Matzoros… - …, 2023 - academic.oup.com
Motivation Advances in genomics and sequencing technologies demand faster and more
scalable analysis methods that can process longer sequences with higher accuracy …

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… - arXiv preprint arXiv …, 2022 - arxiv.org
Read mapping is a fundamental, yet computationally-expensive step in many genomics
applications. It is used to identify potential matches and differences between fragments …

BIMSA: accelerating long sequence alignment using processing-in-memory

A Alonso-Marín, I Fernandez, Q Aguado-Puig… - …, 2024 - academic.oup.com
Motivation Recent advances in sequencing technologies have stressed the critical role of
sequence analysis algorithms and tools in genomics and healthcare research. In particular …

MRI-based brain tumor segmentation using FPGA-accelerated neural network

S Xiong, G Wu, X Fan, X Feng, Z Huang, W Cao… - BMC …, 2021 - Springer
Background Brain tumor segmentation is a challenging problem in medical image
processing and analysis. It is a very time-consuming and error-prone task. In order to reduce …

Gmx: Instruction set extensions for fast, scalable, and efficient genome sequence alignment

M Doblas, O Lostes-Cazorla, Q Aguado-Puig… - Proceedings of the 56th …, 2023 - dl.acm.org
Sequence alignment remains a fundamental problem in computer science with practical
applications ranging from pattern matching to computational biology. The ever-increasing …