19 citations · 54 across the 9 of their papers we have counts for
6 papers · 1 filter
10 Years Later: Cloud Computing is Closing the Performance Gap
Giulia Guidi, Marquita Ellis, Aydin Buluc +2
Can cloud computing infrastructures provide HPC-competitive performance for scientific applications broadly? Despite prolific related literature, this question remains open. Answer…
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…
Distributed Many-to-Many Protein Sequence Alignment using Sparse Matrices
Oguz Selvitopi, Saliya Ekanayake, Giulia Guidi +3
Identifying similar protein sequences is a core step in many computational biology pipelines such as detection of homologous protein sequences, generation of similarity protein gra…
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…