Listar por autor "Herruzo-Ruiz, José Manuel"
Mostrando ítems 1-5 de 5
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Accelerating Sequence Alignments Based on FM-Index Using the Intel KNL Processor
Herruzo-Ruiz, José Manuel
; González-Navarro, Sonia; Ibáñez, Pablo; Viñals, Victor; Alastruey-Benedé, Jesús; Óscar, Plata[et al.] (IEEE/ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS,, 2020-07-01)
FM-index is a compact data structure suitable for fast matches of short reads to large reference genomes. The matching algorithm using this index exhibits irregular memory access patterns that cause frequent cache misses, ... -
Boosting Backward Search Throughput for FM-Index Using a Compressed Encoding
Herruzo-Ruiz, José Manuel; González-Navarro, Sonia; Ibáñez, Pablo; Viñals, Victor; Alastruey-Benedé, Jesús; Plata-González, Óscar Guillermo[et al.] (2019-04-11)
The rapid development of DNA sequencing technologies has demanded for com- pressed data structures supporting fast pattern matching queries. FM-index is a widely-used compressed data structure that also supports fast ... -
Enabling Fast and Energy-Efficient FM-index Exact Matching using Processing-Near-Memory
Herruzo-Ruiz, José Manuel; Fernández, Iván; González-Navarro, Sonia; Óscar, Plata (Springer, 2021-09)
Memory bandwidth and latency constitutes a major performance bottleneck for many data-intensive applications. While high-locality access patterns take advantage of the deep cache hierarchies available in modern processors, ... -
Genome Sequence Alignment - Design Space Exploration for Optimal Performance and Energy Architectures
Qureshi, Yasir Mahmood; Herruzo-Ruiz, José Manuel; Zapater, Marina; Olcoz, Katzalin; González-Navarro, Sonia; Óscar, Plata; Atienza, David[et al.] (IEEE Transactions on Computers, 2021-12)
Next generation workloads, such as genome sequencing, have an astounding impact in the healthcare sector. Sequence alignment, the first step in genome sequencing, has experienced recent breakthroughs, which resulted in ... -
Genome sequence alignment in processing-In-memory architectures
Herruzo-Ruiz, José Manuel (UMA Editorial, 2021-01-27)
La combinación de la aparición de un cuello de botella en el acceso a los datos y la creciente importancia de las aplicaciones de procesamiento intensivo de datos, muy limitadas por el sistema de memoria, crea un importante ...