{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,4,17]],"date-time":"2026-04-17T02:38:00Z","timestamp":1776393480280,"version":"3.51.2"},"reference-count":22,"publisher":"Oxford University Press (OUP)","issue":"20","content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2006,10,15]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>Motivation: Characterizing the diversity of microbial communities and understanding the environmental factors that influence community diversity are central tenets of microbial ecology. The development and application of cultivation independent molecular tools has allowed for rapid surveying of microbial community composition at unprecedented resolutions and frequencies. There is a growing need to discern robust patterns and relationships within these datasets which provide insight into microbial ecology. Pearson correlation coefficient (PCC) analysis is commonly used for identifying the linear relationship between two species, or species and environmental factors. However, this approach may not be able to capture more complex interactions which occur in situ; thus, alternative analyses were explored.<\/jats:p>\n               <jats:p>Results: In this paper we introduced local similarity analysis (LSA), which is a technique that can identify more complex dependence associations among species as well as associations between species and environmental factors without requiring significant data reduction. To illustrate its capability of identifying relationships that may not otherwise be identified by PCC, we first applied LSA to simulated data. We then applied LSA to a marine microbial observatory dataset and identified unique, significant associations that were not detected by PCC analysis. LSA results, combined with results from PCC analysis were used to construct a theoretical ecological network which allows for easy visualization of the most significant associations. Biological implications of the significant associations detected by LSA were discussed. We also identified additional applications where LSA would be beneficial.<\/jats:p>\n               <jats:p>Availability: The algorithms are implemented in Splus\/R and they are available upon request from the corresponding author.<\/jats:p>\n               <jats:p>Contact: \u00a0fsun@usc.edu<\/jats:p>","DOI":"10.1093\/bioinformatics\/btl417","type":"journal-article","created":{"date-parts":[[2006,8,2]],"date-time":"2006-08-02T18:47:44Z","timestamp":1154544464000},"page":"2532-2538","source":"Crossref","is-referenced-by-count":245,"title":["Local similarity analysis reveals unique associations among marine bacterioplankton species and environmental factors"],"prefix":"10.1093","volume":"22","author":[{"given":"Quansong","family":"Ruan","sequence":"first","affiliation":[{"name":"Department of Mathematics, University of Southern California 1 \u00a0 1 \u00a0 \u00a0 3620 Vermont Avenue, KAP 108, Los Angeles, CA 90089-2532, USA"}]},{"given":"Debojyoti","family":"Dutta","sequence":"additional","affiliation":[{"name":"Molecular and Computational Biology Program, Department of Biological Sciences, University of Southern California 2 \u00a0 2 \u00a0 \u00a0 1050 Childs Way, MCB 201, Los Angeles, CA 90089-2910, USA"}]},{"given":"Michael S.","family":"Schwalbach","sequence":"additional","affiliation":[{"name":"Department of Biological Sciences, University of Southern California 3 \u00a0 3 \u00a0 \u00a0 3616 Trousdale Pkwy, AHF 107, Los Angeles, CA 90089-0371, USA"}]},{"given":"Joshua A.","family":"Steele","sequence":"additional","affiliation":[{"name":"Department of Biological Sciences, University of Southern California 3 \u00a0 3 \u00a0 \u00a0 3616 Trousdale Pkwy, AHF 107, Los Angeles, CA 90089-0371, USA"}]},{"given":"Jed A.","family":"Fuhrman","sequence":"additional","affiliation":[{"name":"Department of Biological Sciences, University of Southern California 3 \u00a0 3 \u00a0 \u00a0 3616 Trousdale Pkwy, AHF 107, Los Angeles, CA 90089-0371, USA"}]},{"given":"Fengzhu","family":"Sun","sequence":"additional","affiliation":[{"name":"Molecular and Computational Biology Program, Department of Biological Sciences, University of Southern California 2 \u00a0 2 \u00a0 \u00a0 1050 Childs Way, MCB 201, Los Angeles, CA 90089-2910, USA"}]}],"member":"286","published-online":{"date-parts":[[2006,7,31]]},"reference":[{"key":"2023012409232391800_b1","first-page":"144.6","article-title":"A molecular technique for identification of bacteria using small subunit ribosomal RNA sequences","volume":"17","author":"Avaniss-Aghajani","year":"1994","journal-title":"Biotechniques"},{"key":"2023012409232391800_b2","doi-asserted-by":"crossref","first-page":"1069","DOI":"10.1093\/bioinformatics\/bti095","article-title":"Clustering of gene expression data using a local shape-based similarity measure","volume":"21","author":"Balasubramaniyan","year":"2005","journal-title":"Bioinformatics"},{"key":"2023012409232391800_b3","doi-asserted-by":"crossref","first-page":"1466","DOI":"10.1111\/j.1462-2920.2005.00835.x","article-title":"Coupling 16S-ITS rDNA clone libraries and ARISA to show marine microbial diversity; development and application to a time series","volume":"7","author":"Brown","year":"2005","journal-title":"Environ. Microbiol."},{"key":"2023012409232391800_b4","doi-asserted-by":"crossref","first-page":"4630","DOI":"10.1128\/AEM.65.10.4630-4636.1999","article-title":"Automated approach for ribosomal intergenic spacer analysis of microbial diversity and its application to freshwater bacterial communities","volume":"65","author":"Fisher","year":"1999","journal-title":"Appl. Environ. Microbiol."},{"key":"2023012409232391800_b5","doi-asserted-by":"crossref","DOI":"10.1073\/pnas.0602399103","article-title":"Annually reoccurring bacterioplankton communities are predictable from ocean conditions","author":"Fuhrman","year":"2006","journal-title":"Proc. Natl Acad. Sci. USA"},{"key":"2023012409232391800_b6","doi-asserted-by":"crossref","first-page":"3425","DOI":"10.1128\/AEM.70.6.3425-3433.2004","article-title":"Richness and density of bacterioplankton species along an estuarine gradient in Moreton Bay, Australia","volume":"70","author":"Hewson","year":"2004","journal-title":"Appl. Environ. Microbiol."},{"key":"2023012409232391800_b7","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. USA"},{"key":"2023012409232391800_b8","doi-asserted-by":"crossref","first-page":"4516","DOI":"10.1128\/aem.63.11.4516-4522.1997","article-title":"Characterization of microbial diversity by determining terminal restriction fragment length polymorphisms of genes encoding 16S rRNA","volume":"63","author":"Liu","year":"1997","journal-title":"Appl. Environ. Microbiol."},{"key":"2023012409232391800_b9","doi-asserted-by":"crossref","first-page":"695","DOI":"10.1128\/aem.59.3.695-700.1993","article-title":"Profiling of complex microbial populations by denaturing gradient gel electrophoresis analysis of polymerase chain reaction-amplified genes coding for 16S rRNA","volume":"59","author":"Muyzer","year":"1993","journal-title":"Appl. Environ. Microbiol."},{"key":"2023012409232391800_b10","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1007\/978-1-4757-0611-6_1","article-title":"The analysis of natural microbial populations by ribosomal RNA sequences","volume":"9","author":"Pace","year":"1986","journal-title":"Adv. Microbial Ecol."},{"key":"2023012409232391800_b11","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, biologically relevant interactions","volume":"314","author":"Qian","year":"2001","journal-title":"J. Mol. Biol."},{"key":"2023012409232391800_b12","doi-asserted-by":"crossref","first-page":"4479","DOI":"10.1128\/AEM.67.10.4479-4487.2001","article-title":"Characterization of bacterial and fungal soil communities by automated ribosomal intergenic spacer analysis fingerprints: biological and methodological variability","volume":"67","author":"Ranjard","year":"2005","journal-title":"Appl. Environ. Microbiol."},{"key":"2023012409232391800_b13","doi-asserted-by":"crossref","first-page":"1508","DOI":"10.1093\/bioinformatics\/btl114","article-title":"A dynamic programming algorithm for binning microbial community profiles","volume":"22","author":"Ruan","year":"2006","journal-title":"Bioinformatics"},{"key":"2023012409232391800_b14","doi-asserted-by":"crossref","first-page":"5814","DOI":"10.1128\/AEM.71.10.5814-5822.2005","article-title":"Use of 16S rRNA gene terminal restriction fragment analysis to assess the impact of solids retention time on the bacterial diversity of activated sludge","volume":"71","author":"Saikaly","year":"2005","journal-title":"Appl. Environ Microbiol."},{"key":"2023012409232391800_b15","doi-asserted-by":"crossref","first-page":"2498","DOI":"10.1101\/gr.1239303","article-title":"Cytoscape: a software environment for integrated models of biomolecular interaction networks","volume":"13","author":"Shannon","year":"2003","journal-title":"Genome Res."},{"key":"2023012409232391800_b16","doi-asserted-by":"crossref","first-page":"85","DOI":"10.3354\/ame031085","article-title":"Covariance of bacterioplankton composition and environmental variables in a temperate delta system","volume":"31","author":"Stepanauskas","year":"2003","journal-title":"Aquat. Microb. Ecol."},{"key":"2023012409232391800_b17","doi-asserted-by":"crossref","first-page":"9440","DOI":"10.1073\/pnas.1530509100","article-title":"Statistical significance for genome-wide experiments","volume":"100","author":"Sorey","year":"2003","journal-title":"Proc. Natl Acad. Sci. USA"},{"key":"2023012409232391800_b18","doi-asserted-by":"crossref","first-page":"13","DOI":"10.3354\/ame028013","article-title":"Bacterial activity and genetic richness along an estuarine gradient (Rhone River plume, France)","volume":"28","author":"Troussellier","year":"2002","journal-title":"Aquat. Microb. Ecol."},{"key":"2023012409232391800_b19","doi-asserted-by":"crossref","first-page":"282","DOI":"10.4319\/lo.2004.49.4.1056","article-title":"Relationship between bacterial community structure, light, and carbon cycling in the eastern subarctic North Pacific","volume":"49","author":"Van Mooy","year":"2004","journal-title":"Limnol. Oceanogr."},{"key":"2023012409232391800_b20","doi-asserted-by":"crossref","DOI":"10.1007\/978-1-4899-6846-3","volume-title":"Introduction to Computational Biology: Maps, Sequences and Genomes","author":"Waterman","year":"1995"},{"key":"2023012409232391800_b21","doi-asserted-by":"crossref","first-page":"214","DOI":"10.1128\/AEM.70.1.214-223.2004","article-title":"Within- and between-lake variablility in the composition of bacterioplankton communities: investigations using multiple spatial scales","volume":"70","author":"Yannarell","year":"2004","journal-title":"Appl. Environ. Microbiol."},{"key":"2023012409232391800_b22","doi-asserted-by":"crossref","first-page":"227","DOI":"10.1128\/AEM.71.1.227-239.2005","article-title":"Geographic and environmental sources of variation in lake bacterial community composition","volume":"71","author":"Yannarell","year":"2005","journal-title":"Appl. Environ. Microbiol."}],"container-title":["Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/22\/20\/2532\/48840773\/bioinformatics_22_20_2532.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/22\/20\/2532\/48840773\/bioinformatics_22_20_2532.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2023,1,24]],"date-time":"2023-01-24T10:08:27Z","timestamp":1674554907000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article\/22\/20\/2532\/218339"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2006,7,31]]},"references-count":22,"journal-issue":{"issue":"20","published-print":{"date-parts":[[2006,10,15]]}},"URL":"https:\/\/doi.org\/10.1093\/bioinformatics\/btl417","relation":{},"ISSN":["1367-4811","1367-4803"],"issn-type":[{"value":"1367-4811","type":"electronic"},{"value":"1367-4803","type":"print"}],"subject":[],"published-other":{"date-parts":[[2006,10,15]]},"published":{"date-parts":[[2006,7,31]]}}}