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04/17/2023
Space Efficient Sequence Alignment for SRAM-Based Computing: X-Drop on the Graphcore IPU
Dedicated accelerator hardware has become essential for processing AI-ba...
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03/03/2023
Extreme-scale many-against-many protein similarity search
Similarity search is one of the most fundamental computations that are r...
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07/10/2022
Distributed-Memory Parallel Contig Generation for De Novo Long-Read Genome Assembly
De novo genome assembly, i.e., rebuilding the sequence of an unknown gen...
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09/16/2021
BuDDI: A Declarative Bloom Language for CALM Programming
Coordination protocols help programmers of distributed systems reason ab...
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11/02/2020
10 Years Later: Cloud Computing is Closing the Performance Gap
Can cloud computing infrastructures provide HPC-competitive performance ...
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10/20/2020
Parallel String Graph Construction and Transitive Reduction for De Novo Genome Assembly
One of the most computationally intensive tasks in computational biology...
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09/30/2020
Distributed Many-to-Many Protein Sequence Alignment using Sparse Matrices
Identifying similar protein sequences is a core step in many computation...
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02/12/2020
LOGAN: High-Performance GPU-Based X-Drop Long-Read Alignment
Pairwise sequence alignment is one of the most computationally intensive...
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01/27/2020
diBELLA: Distributed Long Read to Long Read Alignment
We present a parallel algorithm and scalable implementation for genome a...
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01/20/2020