17 citations · 17 across the 2 of their papers we have counts for
6 papers
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…
LOGAN: High-Performance GPU-Based X-Drop Long-Read Alignment
Alberto Zeni, Giulia Guidi, Marquita Ellis +6
Pairwise sequence alignment is one of the most computationally intensive kernels in genomic data analysis, accounting for more than 90% of the runtime for key bioinformatics applic…
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…
Extreme-Scale De Novo Genome Assembly
Evangelos Georganas, Steven Hofmeyr, Rob Egan +4
De novo whole genome assembly reconstructs genomic sequence from short, overlapping, and potentially erroneous DNA segments and is one of the most important computations in modern…