Can Firtina | DeepAI

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∙ 04/30/2023

Accelerating Genome Analysis via Algorithm-Architecture Co-Design

High-throughput sequencing (HTS) technologies have revolutionized the fi...

0 Onur Mutlu, et al. ∙

∙ 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...

0 Meryem Banu Cavlak, et al. ∙

∙ 11/22/2022

Utopia: Efficient Address Translation using Hybrid Virtual-to-Physical Address Mapping

The conventional virtual-to-physical address mapping scheme enables a vi...

0 Konstantinos Kanellopoulos, et al. ∙

∙ 11/06/2022

A Framework for Designing Efficient Deep Learning-Based Genomic Basecallers

Nanopore sequencing generates noisy electrical signals that need to be c...

0 Gagandeep Singh, et al. ∙

∙ 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...

0 Haiyu Mao, et al. ∙

∙ 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...

20 Can Firtina, et al. ∙

∙ 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...

0 Taha Shahroodi, et al. ∙

∙ 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 ...

0 Mohammed Alser, et al. ∙

∙ 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 ...

0 Damla Senol Cali, et al. ∙

∙ 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...

0 Mohammed Alser, et al. ∙

∙ 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...

0 Nika Mansouri-Ghiasi, et al. ∙

∙ 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...

0 Damla Senol Cali, et al. ∙

∙ 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 ...

0 Jeremie S. Kim, et al. ∙

∙ 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...

0 Can Firtina, et al. ∙

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