Advancing computational toxicology in the big data era by artificial intelligence: data-driven and mechanism-driven modeling for chemical toxicity

HL Ciallella, H Zhu - Chemical research in toxicology, 2019 - ACS Publications
In 2016, the Frank R. Lautenberg Chemical Safety for the 21st Century Act became the first
US legislation to advance chemical safety evaluations by utilizing novel testing approaches …

[HTML][HTML] Computing platforms for big biological data analytics: perspectives and challenges

Z Yin, H Lan, G Tan, M Lu, AV Vasilakos… - Computational and …, 2017 - Elsevier
The last decade has witnessed an explosion in the amount of available biological sequence
data, due to the rapid progress of high-throughput sequencing projects. However, the …

Mars: a MapReduce framework on graphics processors

B He, W Fang, Q Luo, NK Govindaraju… - Proceedings of the 17th …, 2008 - dl.acm.org
We design and implement Mars, a MapReduce framework, on graphics processors (GPUs).
MapReduce is a distributed programming framework originally proposed by Google for the …

A performance study of general-purpose applications on graphics processors using CUDA

S Che, M Boyer, J Meng, D Tarjan, JW Sheaffer… - Journal of parallel and …, 2008 - Elsevier
Graphics processors (GPUs) provide a vast number of simple, data-parallel, deeply
multithreaded cores and high memory bandwidths. GPU architectures are becoming …

CUDASW++ 3.0: accelerating Smith-Waterman protein database search by coupling CPU and GPU SIMD instructions

Y Liu, A Wirawan, B Schmidt - BMC bioinformatics, 2013 - Springer
Background The maximal sensitivity for local alignments makes the Smith-Waterman
algorithm a popular choice for protein sequence database search based on pairwise …

On using lossless compression of debug data in embedded logic analysis

E Anis, N Nicolici - 2007 IEEE International Test Conference, 2007 - ieeexplore.ieee.org
The capacity of on-chip trace buffers employed for embedded logic analysis limits the
observation window of a debug experiment. To increase the debug observation window, we …

Saber: Window-based hybrid stream processing for heterogeneous architectures

A Koliousis, M Weidlich, R Castro Fernandez… - Proceedings of the …, 2016 - dl.acm.org
Modern servers have become heterogeneous, often combining multi-core CPUs with many-
core GPGPUs. Such heterogeneous architectures have the potential to improve the …

CUDASW++: optimizing Smith-Waterman sequence database searches for CUDA-enabled graphics processing units

Y Liu, DL Maskell, B Schmidt - BMC research notes, 2009 - Springer
Abstract Background The Smith-Waterman algorithm is one of the most widely used tools for
searching biological sequence databases due to its high sensitivity. Unfortunately, the Smith …

CUDASW++ 2.0: enhanced Smith-Waterman protein database search on CUDA-enabled GPUs based on SIMT and virtualized SIMD abstractions

Y Liu, B Schmidt, DL Maskell - BMC research notes, 2010 - Springer
Background Due to its high sensitivity, the Smith-Waterman algorithm is widely used for
biological database searches. Unfortunately, the quadratic time complexity of this algorithm …

Accelerating molecular dynamics simulations using Graphics Processing Units with CUDA

W Liu, B Schmidt, G Voss, W Müller-Wittig - Computer physics …, 2008 - Elsevier
Molecular dynamics is an important computational tool to simulate and understand
biochemical processes at the atomic level. However, accurate simulation of processes such …