Translational biomedical informatics in the cloud: present and future

J Chen, F Qian, W Yan, B Shen - BioMed research international, 2013 - Wiley Online Library
Next generation sequencing and other high‐throughput experimental techniques of recent
decades have driven the exponential growth in publicly available molecular and clinical …

Survey of MapReduce frame operation in bioinformatics

Q Zou, XB Li, WR Jiang, ZY Lin, GL Li… - Briefings in …, 2014 - academic.oup.com
Bioinformatics is challenged by the fact that traditional analysis tools have difficulty in
processing large-scale data from high-throughput sequencing. The open source Apache …

Translational bioinformatics for diagnostic and prognostic prediction of prostate cancer in the next‐generation sequencing era

J Chen, D Zhang, W Yan, D Yang… - BioMed research …, 2013 - Wiley Online Library
The discovery of prostate cancer biomarkers has been boosted by the advent of next‐
generation sequencing (NGS) technologies. Nevertheless, many challenges still exist in …

CloudAligner: a fast and full-featured MapReduce based tool for sequence mapping

T Nguyen, W Shi, D Ruden - BMC research notes, 2011 - Springer
Background Research in genetics has developed rapidly recently due to the aid of next
generation sequencing (NGS). However, massively-parallel NGS produces enormous …

[HTML][HTML] Comprehensive comparison of cloud-based NGS data analysis and alignment tools

QB Baker, M Hammad, W Al-Rashdan… - Informatics in Medicine …, 2020 - Elsevier
Abstract Next-Generation Sequencing (NGS) is very helpful for conducting
DeoxyriboNucleic Acid (DNA) Sequencing. DNA sequencing is the process for determining …

Data management challenges in next generation sequencing

S Wandelt, A Rheinländer, M Bux, L Thalheim… - Datenbank …, 2012 - Springer
Since the early days of the Human Genome Project, data management has been recognized
as a key challenge for modern molecular biology research. By the end of the nineties …

Hadoop applications in bioinformatics

X Li, W Jiang, Y Jiang, Q Zou - 2012 7th Open Cirrus Summit, 2012 - ieeexplore.ieee.org
Bioinformatics is in a dilemma that traditional analysis tools work hard on the large-scale
data from the high-throughout sequencing. In recent years, the open source Apache Hadoop …

StreamAligner: a streaming based sequence aligner on Apache Spark

S Rathee, A Kashyap - Journal of Big Data, 2018 - Springer
Abstract Next-Generation Sequencing technologies are generating a huge amount of
genetic data that need to be mapped and analyzed. Single machine sequence alignment …

[HTML][HTML] Biocloud: cloud computing for biological, genomics, and drug design

CH Hsu, CY Lin, M Ouyang, YK Guo - BioMed research …, 2013 - ncbi.nlm.nih.gov
Cloud computing has emerged rapidly as an exciting new paradigm that offers a challenging
model of computing and services. Leveraging cloud computing technology, bioinformatics …

Efficient Distributed Parallel Aligning Reads and Reference Genome with Many Repetitive Subsequences Using Compact de Bruijn Graph

Y Li, C Zhong, D Chen, J Zhang… - 2021 12th International …, 2021 - ieeexplore.ieee.org
A large number of reads generated by the next generation sequencing platform will contain
many repetitive subsequences. Effective localizing and identifying genomic regions …