计算机科学
生物学数据
数据挖掘
时间序列
水准点(测量)
系列(地层学)
相似性(几何)
统计模型
机器学习
人工智能
生物信息学
生物
古生物学
大地测量学
图像(数学)
地理
作者
Dongmei Ai,Lulu Chen,Junfeng Xie,Longwei Cheng,Fang Zhang,Yihui Luan,Yang Li,Shengwei Hou,Fengzhu Sun,Li C. Xia
摘要
Abstract Local associations refer to spatial–temporal correlations that emerge from the biological realm, such as time-dependent gene co-expression or seasonal interactions between microbes. One can reveal the intricate dynamics and inherent interactions of biological systems by examining the biological time series data for these associations. To accomplish this goal, local similarity analysis algorithms and statistical methods that facilitate the local alignment of time series and assess the significance of the resulting alignments have been developed. Although these algorithms were initially devised for gene expression analysis from microarrays, they have been adapted and accelerated for multi-omics next generation sequencing datasets, achieving high scientific impact. In this review, we present an overview of the historical developments and recent advances for local similarity analysis algorithms, their statistical properties, and real applications in analyzing biological time series data. The benchmark data and analysis scripts used in this review are freely available at http://github.com/labxscut/lsareview.
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