Onur Mutlu

RawBench: A Comprehensive Benchmarking Framework for Raw Nanopore Signal Analysis Techniques

RawBench benchmarks raw nanopore signal analysis techniques, showing they can achieve competitive quality with reduced resource requirements for real-time and edge deployment.

TargetCall: Eliminating the Wasted Computation in Basecalling via Pre-Basecalling Filtering

TargetCall filters out off-target reads before basecalling to reduce computational waste, improving basecalling performance and efficiency.

BIMSA: Accelerating Long Sequence Alignment Using Processing-In-Memory

BIMSA accelerates long sequence alignment using Processing-In-Memory, achieving significant speedups over existing PIM and CPU implementations.

AirLift: A Fast and Comprehensive Technique for Remapping Alignments between Reference Genomes

AirLift remaps reads from one reference genome to another efficiently and accurately, reducing execution time by up to 27.4x compared to full mapping.

GAPiM: Discovering Genetic Variations on a Real Processing-in-Memory System

The paper implements and evaluates a modified Pair-HMM algorithm on a PiM platform for faster variant calling in genome analysis.

RawHash: Enabling Fast and Accurate Real-Time Analysis of Raw Nanopore Signals for Large Genomes

RawHash enables fast and accurate real-time analysis of nanopore raw signals for large genomes, outperforming existing methods in throughput and accuracy.

BLEND: A Fast, Memory-Efficient, and Accurate Mechanism to Find Fuzzy Seed Matches in Genome Analysis

BLEND improves genomic sequence analysis by efficiently finding fuzzy seed matches, enhancing speed, memory use, and accuracy in read overlapping and mapping.

A Framework for Designing Efficient Deep Learning-Based Genomic Basecallers

This paper introduces RUBICON, a framework for designing efficient deep learning-based genomic basecallers, and demonstrates its effectiveness with RUBICALL, a hardware-optimized mixed-precision basecaller that outperforms existing methods.

BioDynaMo: a general platform for scalable agent-based simulation

BioDynaMo is a scalable agent-based simulation platform that outperforms existing tools by three orders of magnitude, enabling large-scale simulations in neuroscience, oncology, and epidemiology.

LEAP: A Generalization Of The Landau-Vishkin Algorithm With Custom Gap Penalties

The paper introduces LEAP, a generalized algorithm for approximate string matching that outperforms existing methods in speed under various scoring schemes.