10 years later: cloud computing is closing the performance gap
Can cloud computing infrastructures provide HPC-competitive performance for scientific
applications broadly? Despite prolific related literature, this question remains open. Answers are …
applications broadly? Despite prolific related literature, this question remains open. Answers are …
The parallelism motifs of genomic data analysis
…, R Egan, S Ekanayake, M Ellis… - … of the Royal …, 2020 - royalsocietypublishing.org
Genomic datasets are growing dramatically as the cost of sequencing continues to decline
and small sequencing devices become available. Enormous community databases store and …
and small sequencing devices become available. Enormous community databases store and …
Logan: High-performance gpu-based x-drop long-read alignment
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 …
genomic data analysis, accounting for more than 90% of the runtime for key bioinformatics …
diBELLA: Distributed long read to long read alignment
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 read …
the problem of finding overlaps and alignments for data from "third generation" long read …
Distributed-memory k-mer counting on GPUs
A fundamental step in many bioinformatics computations is to count the frequency of fixed-length
sequences, called k-mers, a problem that has received considerable attention as an …
sequences, called k-mers, a problem that has received considerable attention as an …
BELLA: Berkeley efficient long-read to long-read aligner and overlapper
Recent advances in long-read sequencing allow characterization of genome structure and
its variation within and between species at a resolution not previously possible. Detection of …
its variation within and between species at a resolution not previously possible. Detection of …
Parallel string graph construction and transitive reduction for de novo genome assembly
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 …
assembly, the decoding of the sequence of an unknown genome from redundant and …
Performance characterization of de novo genome assembly on leading parallel systems
M Ellis, E Georganas, R Egan, S Hofmeyr… - Euro-Par 2017: Parallel …, 2017 - Springer
De novo genome assembly is one of the most important and challenging computational
problems in modern genomics; further, it shares algorithms and communication patterns …
problems in modern genomics; further, it shares algorithms and communication patterns …
[BOOK][B] Parallelizing irregular applications for distributed memory scalability: Case studies from genomics
MM Ellis - 2020 - search.proquest.com
Generalizable approaches, models, and frameworks for irregular application scalability is an
old yet open area in parallel and distributed computing research. Irregular applications are …
old yet open area in parallel and distributed computing research. Irregular applications are …
Merbench: Pgas benchmarks for high performance genome assembly
E Georganas, M Ellis, R Egan, S Hofmeyr… - Proceedings of the …, 2017 - dl.acm.org
De novo genome assembly is one of the most important and challenging computational
problems in modern genomics; further, it shares algorithms and communication patterns …
problems in modern genomics; further, it shares algorithms and communication patterns …