Publications de Stuart Anthony Byma

Parallel and Scalable Precise Clustering

James Richard Larus, Stuart Anthony Byma

This paper describes a new technique for parallelizing protein clustering, an important bioinformatics computation for the analysis of protein sequences. Protein clustering identifies groups of proteins that are similar because they share long sequences of ...

ASSOC COMPUTING MACHINERY2020

Parallel and Scalable Bioinformatics

Stuart Anthony Byma

The field of genomics is likely to become the largest producer of data as a consequence of the large-scale application of next-generation sequencing technology for biological research and personalized medical treatments. The raw sequence data produced by t ...

EPFL2020

IMPACT: Interval-based Multi-pass Proteomic Alignment with Constant Traceback

James Richard Larus, Sahand Kashani, Stuart Anthony Byma

Darwin is a genomics co-processor that achieved a 15000x acceleration on long read assembly through innovative hardware and algorithm co-design. Darwins algorithms and hardware implementation were specifically designed for DNA analysis pipelines. This pape ...

2019

Detailed Heap Profiling

James Richard Larus, Stuart Anthony Byma

Modern software systems heavily use the memory heap. As systems grow more complex and compute with increasing amounts of data, it can be difficult for developers to understand how their programs actually use the bytes that they allocate on the heap and whe ...

ACM2018

Persona: A High-Performance Bioinformatics Framework

James Richard Larus, Edouard Bugnion, Christos Kozyrakis, Stuart Anthony Byma, Sam David Whitlock

Next-generation genome sequencing technology has reached a point at which it is becoming cost-effective to sequence all patients. Biobanks and researchers are faced with an oncoming deluge of genomic data, whose processing requires new and scalable bioinfo ...

2017