17 citations · 17 across the 4 of their papers we have counts for
7 papers · 1 filter
Evaluating the Potential of Disaggregated Memory Systems for HPC applications
Nan Ding, Pieter Maris, Hai Ah Nam +8
Disaggregated memory is a promising approach that addresses the limitations of traditional memory architectures by enabling memory to be decoupled from compute nodes and shared acr…
Extreme-scale many-against-many protein similarity search
Oguz Selvitopi, Saliya Ekanayake, Giulia Guidi +7
Similarity search is one of the most fundamental computations that are regularly performed on ever-increasing protein datasets. Scalability is of paramount importance for uncoverin…
Parallel String Graph Construction and Transitive Reduction for De Novo Genome Assembly
Giulia Guidi, Oguz Selvitopi, Marquita Ellis +3
One of the most computationally intensive tasks in computational biology is de novo genome assembly, the decoding of the sequence of an unknown genome from redundant and erroneous…
diBELLA: Distributed Long Read to Long Read Alignment
Marquita Ellis, Giulia Guidi, Aydın Buluç +2
We present a parallel algorithm and scalable implementation for genome analysis, specifically the problem of finding overlaps and alignments for data from "third generation" long r…
The Parallelism Motifs of Genomic Data Analysis
Katherine Yelick, Aydin Buluc, Muaaz Awan +11
Genomic data sets are growing dramatically as the cost of sequencing continues to decline and small sequencing devices become available. Enormous community databases store and shar…
Extreme Scale De Novo Metagenome Assembly
Evangelos Georganas, Rob Egan, Steven Hofmeyr +6
Metagenome assembly is the process of transforming a set of short, overlapping, and potentially erroneous DNA segments from environmental samples into the accurate representation o…