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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.<\/jats:p>","DOI":"10.1093\/bib\/bbad390","type":"journal-article","created":{"date-parts":[[2023,11,8]],"date-time":"2023-11-08T01:08:03Z","timestamp":1699405683000},"source":"Crossref","is-referenced-by-count":2,"title":["Identifying local associations in biological time series: algorithms, statistical significance, and applications"],"prefix":"10.1093","volume":"24","author":[{"given":"Dongmei","family":"Ai","sequence":"first","affiliation":[{"name":"School of Mathematics and Physics, University of Science and Technology Beijing , Beijing 100083 , China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Lulu","family":"Chen","sequence":"additional","affiliation":[{"name":"School of Mathematics and Physics, University of Science and Technology Beijing , Beijing 100083 , China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Jiemin","family":"Xie","sequence":"additional","affiliation":[{"name":"Department of Statistics and Financial Mathematics , School of Mathematics, , Guangzhou 510641 , China"},{"name":"South China University of Technology , School of Mathematics, , Guangzhou 510641 , China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Longwei","family":"Cheng","sequence":"additional","affiliation":[{"name":"School of Mathematics and Physics, University of Science and Technology Beijing , Beijing 100083 , China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Fang","family":"Zhang","sequence":"additional","affiliation":[{"name":"Shenwan Hongyuan Securities Co. Ltd. , Shanghai 200031 , China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Yihui","family":"Luan","sequence":"additional","affiliation":[{"name":"School of Mathematics, Shandong University , Jinan 250100 , China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Yang","family":"Li","sequence":"additional","affiliation":[{"name":"Department of Statistics and Financial Mathematics , School of Mathematics, , Guangzhou 510641 , China"},{"name":"South China University of Technology , School of Mathematics, , Guangzhou 510641 , China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Shengwei","family":"Hou","sequence":"additional","affiliation":[{"name":"Department of Ocean Science and Engineering, Southern University of Science and Technology , Shenzhen, 518055 , China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Fengzhu","family":"Sun","sequence":"additional","affiliation":[{"name":"Department of Quantitative and Computational Biology, University of Southern California , California, 90007 , USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-0868-1923","authenticated-orcid":false,"given":"Li Charlie","family":"Xia","sequence":"additional","affiliation":[{"name":"Department of Statistics and Financial Mathematics , School of Mathematics, , Guangzhou 510641 , China"},{"name":"South China University of Technology , School of Mathematics, , Guangzhou 510641 , China"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"286","published-online":{"date-parts":[[2023,11,2]]},"reference":[{"key":"2023110801075074500_ref1","doi-asserted-by":"crossref","first-page":"R50","DOI":"10.1186\/gb-2011-12-5-r50","article-title":"Moving pictures of the human microbiome","volume":"12","author":"Caporaso","year":"2011","journal-title":"Genome Biol"},{"key":"2023110801075074500_ref2","doi-asserted-by":"crossref","first-page":"2573","DOI":"10.1038\/ismej.2015.76","article-title":"Cross-depth analysis of marine bacterial networks suggests downward propagation of temporal changes","volume":"9","author":"Cram","year":"2015","journal-title":"ISME J"},{"key":"2023110801075074500_ref3","doi-asserted-by":"crossref","first-page":"1414","DOI":"10.1038\/ismej.2011.24","article-title":"Marine bacterial, archaeal and protistan association networks reveal ecological linkages","volume":"5","author":"Steele","year":"2011","journal-title":"ISME J"},{"key":"2023110801075074500_ref4","doi-asserted-by":"crossref","first-page":"e00602","DOI":"10.1128\/mBio.00602-12","article-title":"Unexpected diversity during community succession in the apple flower microbiome","volume":"4","author":"Shade","year":"2013","journal-title":"MBio"},{"key":"2023110801075074500_ref5","doi-asserted-by":"crossref","first-page":"65","DOI":"10.1016\/S1097-2765(00)80114-8","article-title":"A genome-wide transcriptional analysis of the mitotic cell cycle","volume":"2","author":"Cho","year":"1998","journal-title":"Mol Cell"},{"key":"2023110801075074500_ref6","doi-asserted-by":"crossref","first-page":"3273","DOI":"10.1091\/mbc.9.12.3273","article-title":"Comprehensive identification of cell cycle-regulated genes of the yeast Saccharomyces cerevisiae by microarray hybridization","volume":"9","author":"Spellman","year":"1998","journal-title":"Mol Biol Cell"},{"key":"2023110801075074500_ref7","doi-asserted-by":"crossref","first-page":"i17","DOI":"10.1093\/bioinformatics\/btv228","article-title":"A hierarchical Bayesian model for flexible module discovery in three-way time-series data","volume":"31","author":"Amar","year":"2015","journal-title":"Bioinformatics"},{"key":"2023110801075074500_ref8","doi-asserted-by":"crossref","first-page":"313","DOI":"10.3389\/fnhum.2013.00313","article-title":"Neural traces of stress: cortisol related sustained enhancement of amygdala-hippocampal functional connectivity","volume":"7","author":"Vaisvaser","year":"2013","journal-title":"Front Hum Neurosci"},{"key":"2023110801075074500_ref9","doi-asserted-by":"crossref","first-page":"16875","DOI":"10.1073\/pnas.252466999","article-title":"Genome-wide coexpression dynamics: theory and application","volume":"99","author":"Li","year":"2002","journal-title":"Proc Natl Acad Sci U S A"},{"key":"2023110801075074500_ref10","doi-asserted-by":"crossref","first-page":"1053","DOI":"10.1006\/jmbi.2000.5219","article-title":"Beyond synexpression relationships: local clustering of time-shifted and inverted gene expression profiles identifies new. 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