Speaker: Prof. Jinho Lee
17 Aprile 2026 | 11:30
DEIB - NECSTLab Meeting Room (Ed. 20)
Online by Zoom
Contatti: Prof. Marco Santambrogio
Sommario
On Friday, April 17th, 2026, we will have a new talk for the series #NECSTFridayTalk.During this talk, we will have, as speaker, Jinho Lee, Assistant Professor at Seoul National University.
As modern sequencing technologies continue to increase throughput faster than compute capabilities scale, genomic sequence alignment has become a major computational bottleneck in bioinformatics pipelines. Although sequence alignment appears highly parallel in principle, practical acceleration is challenging because widely used aligners rely on complex, control-heavy heuristics and exhibit irregular memory access and workload imbalance on GPUs.
This seminar presents a line of work aimed at building ready-to-use GPU-based sequence alignment solutions while preserving the original functionality of widely used aligners such as BWA-MEM and Minimap2. We start by optimizing a simple kernel for efficient GPU parallelization, then extend this effort to support more complex heuristics. Finally, we leverage these kernel-level optimizations to build an end-to-end replacement for widely used alignment solutions.
Across this journey, we show how GPU architectures can be carefully leveraged to accelerate real-world genomic alignment workloads while preserving the algorithmic behaviors that make these aligners effective in practice. We believe this line of work can facilitate broader adoption of accelerators for sequence alignment and contribute to future hardware-software co-design for genomic analysis.
The NECSTLab is a DEIB laboratory, with different research lines on advanced topics in computing systems: from architectural characteristics, to hardware-software codesign methodologies, to security and dependability issues of complex system architectures.
#NECSTLab #Computerscience
Every week, the “NECSTFridayTalk” invites researchers, professionals or entrepreneurs to share their work experiences and projects they are implementing in the “Computing Systems”.