{"id":"https://openalex.org/W2084729635","doi":"https://doi.org/10.1155/2013/191586","title":"Using Protein Clusters from Whole Proteomes to Construct and Augment a Dendrogram","display_name":"Using Protein Clusters from Whole Proteomes to Construct and Augment a Dendrogram","publication_year":2013,"publication_date":"2013-02-20","ids":{"openalex":"https://openalex.org/W2084729635","doi":"https://doi.org/10.1155/2013/191586","mag":"2084729635","pmid":"https://pubmed.ncbi.nlm.nih.gov/23509450"},"language":"en","primary_location":{"id":"doi:10.1155/2013/191586","is_oa":true,"landing_page_url":"https://doi.org/10.1155/2013/191586","pdf_url":"https://downloads.hindawi.com/archive/2013/191586.pdf","source":{"id":"https://openalex.org/S146125958","display_name":"Advances in Bioinformatics","issn_l":"1687-8027","issn":["1687-8027","1687-8035"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310319869","host_organization_name":"Hindawi Publishing Corporation","host_organization_lineage":["https://openalex.org/P4310319869"],"host_organization_lineage_names":["Hindawi Publishing Corporation"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Advances in Bioinformatics","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","pubmed"],"open_access":{"is_oa":true,"oa_status":"hybrid","oa_url":"https://downloads.hindawi.com/archive/2013/191586.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5055643373","display_name":"Yunyun Zhou","orcid":"https://orcid.org/0000-0002-5604-9546"},"institutions":[{"id":"https://openalex.org/I72951846","display_name":"Washington State University","ror":"https://ror.org/05dk0ce17","country_code":"US","type":"education","lineage":["https://openalex.org/I72951846"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Yunyun Zhou","raw_affiliation_strings":["School of Electrical Engineering and Computer Science, Washington State University, P.O. Box 642752, Pullman, WA 99164-2752, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"School of Electrical Engineering and Computer Science, Washington State University, P.O. Box 642752, Pullman, WA 99164-2752, USA","institution_ids":["https://openalex.org/I72951846"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5085802392","display_name":"Douglas R. Call","orcid":"https://orcid.org/0000-0001-6791-055X"},"institutions":[{"id":"https://openalex.org/I72951846","display_name":"Washington State University","ror":"https://ror.org/05dk0ce17","country_code":"US","type":"education","lineage":["https://openalex.org/I72951846"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Douglas R. Call","raw_affiliation_strings":["Paul G. Allen School for Global Animal Health, Washington State University, P.O. Box 642752, Pullman, WA 99164-2752, USA","School of Electrical Engineering and Computer Science, Washington State University, P.O. Box 642752, Pullman, WA 99164-2752, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Paul G. Allen School for Global Animal Health, Washington State University, P.O. Box 642752, Pullman, WA 99164-2752, USA","institution_ids":["https://openalex.org/I72951846"]},{"raw_affiliation_string":"School of Electrical Engineering and Computer Science, Washington State University, P.O. Box 642752, Pullman, WA 99164-2752, USA","institution_ids":["https://openalex.org/I72951846"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5037467986","display_name":"Shira L. Broschat","orcid":"https://orcid.org/0000-0001-9894-7371"},"institutions":[{"id":"https://openalex.org/I72951846","display_name":"Washington State University","ror":"https://ror.org/05dk0ce17","country_code":"US","type":"education","lineage":["https://openalex.org/I72951846"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Shira L. Broschat","raw_affiliation_strings":["Department of Veterinary Microbiology and Pathology, Washington State University, P.O. Box 642752, Pullman, WA 99164-2752, USA","Paul G. Allen School for Global Animal Health, Washington State University, P.O. Box 642752, Pullman, WA 99164-2752, USA","School of Electrical Engineering and Computer Science, Washington State University, P.O. Box 642752, Pullman, WA 99164-2752, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Veterinary Microbiology and Pathology, Washington State University, P.O. Box 642752, Pullman, WA 99164-2752, USA","institution_ids":["https://openalex.org/I72951846"]},{"raw_affiliation_string":"Paul G. Allen School for Global Animal Health, Washington State University, P.O. Box 642752, Pullman, WA 99164-2752, USA","institution_ids":["https://openalex.org/I72951846"]},{"raw_affiliation_string":"School of Electrical Engineering and Computer Science, Washington State University, P.O. Box 642752, Pullman, WA 99164-2752, USA","institution_ids":["https://openalex.org/I72951846"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":3,"corresponding_author_ids":["https://openalex.org/A5037467986"],"corresponding_institution_ids":["https://openalex.org/I72951846"],"apc_list":null,"apc_paid":null,"fwci":1.1964,"has_fulltext":true,"cited_by_count":10,"citation_normalized_percentile":{"value":0.7866308,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":90,"max":97},"biblio":{"volume":"2013","issue":null,"first_page":"1","last_page":"8"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.9998000264167786,"subfield":{"id":"https://openalex.org/subfields/1312","display_name":"Molecular Biology"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},"topics":[{"id":"https://openalex.org/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.9998000264167786,"subfield":{"id":"https://openalex.org/subfields/1312","display_name":"Molecular Biology"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},{"id":"https://openalex.org/T10519","display_name":"Advanced Proteomics Techniques and Applications","score":0.9941999912261963,"subfield":{"id":"https://openalex.org/subfields/1607","display_name":"Spectroscopy"},"field":{"id":"https://openalex.org/fields/16","display_name":"Chemistry"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}},{"id":"https://openalex.org/T12254","display_name":"Machine Learning in Bioinformatics","score":0.9932000041007996,"subfield":{"id":"https://openalex.org/subfields/1312","display_name":"Molecular Biology"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/dendrogram","display_name":"Dendrogram","score":0.9790778160095215},{"id":"https://openalex.org/keywords/proteome","display_name":"Proteome","score":0.7785277962684631},{"id":"https://openalex.org/keywords/metagenomics","display_name":"Metagenomics","score":0.5355982780456543},{"id":"https://openalex.org/keywords/plasmid","display_name":"Plasmid","score":0.4775570034980774},{"id":"https://openalex.org/keywords/taxon","display_name":"Taxon","score":0.4720260202884674},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.4232121706008911},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.39425790309906006},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.35086655616760254},{"id":"https://openalex.org/keywords/pattern-recognition","display_name":"Pattern recognition (psychology)","score":0.3321593403816223},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.26198962330818176},{"id":"https://openalex.org/keywords/bioinformatics","display_name":"Bioinformatics","score":0.2607213258743286},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.24692276120185852},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.13082265853881836},{"id":"https://openalex.org/keywords/ecology","display_name":"Ecology","score":0.10397151112556458}],"concepts":[{"id":"https://openalex.org/C172312944","wikidata":"https://www.wikidata.org/wiki/Q1957903","display_name":"Dendrogram","level":4,"score":0.9790778160095215},{"id":"https://openalex.org/C104397665","wikidata":"https://www.wikidata.org/wiki/Q860947","display_name":"Proteome","level":2,"score":0.7785277962684631},{"id":"https://openalex.org/C15151743","wikidata":"https://www.wikidata.org/wiki/Q903778","display_name":"Metagenomics","level":3,"score":0.5355982780456543},{"id":"https://openalex.org/C22744801","wikidata":"https://www.wikidata.org/wiki/Q172778","display_name":"Plasmid","level":3,"score":0.4775570034980774},{"id":"https://openalex.org/C71640776","wikidata":"https://www.wikidata.org/wiki/Q16521","display_name":"Taxon","level":2,"score":0.4720260202884674},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.4232121706008911},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.39425790309906006},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.35086655616760254},{"id":"https://openalex.org/C153180895","wikidata":"https://www.wikidata.org/wiki/Q7148389","display_name":"Pattern recognition (psychology)","level":2,"score":0.3321593403816223},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.26198962330818176},{"id":"https://openalex.org/C60644358","wikidata":"https://www.wikidata.org/wiki/Q128570","display_name":"Bioinformatics","level":1,"score":0.2607213258743286},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.24692276120185852},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.13082265853881836},{"id":"https://openalex.org/C18903297","wikidata":"https://www.wikidata.org/wiki/Q7150","display_name":"Ecology","level":1,"score":0.10397151112556458},{"id":"https://openalex.org/C144024400","wikidata":"https://www.wikidata.org/wiki/Q21201","display_name":"Sociology","level":0,"score":0.0},{"id":"https://openalex.org/C149923435","wikidata":"https://www.wikidata.org/wiki/Q37732","display_name":"Demography","level":1,"score":0.0},{"id":"https://openalex.org/C81977670","wikidata":"https://www.wikidata.org/wiki/Q585259","display_name":"Genetic diversity","level":3,"score":0.0},{"id":"https://openalex.org/C2908647359","wikidata":"https://www.wikidata.org/wiki/Q2625603","display_name":"Population","level":2,"score":0.0}],"mesh":[],"locations_count":5,"locations":[{"id":"doi:10.1155/2013/191586","is_oa":true,"landing_page_url":"https://doi.org/10.1155/2013/191586","pdf_url":"https://downloads.hindawi.com/archive/2013/191586.pdf","source":{"id":"https://openalex.org/S146125958","display_name":"Advances in Bioinformatics","issn_l":"1687-8027","issn":["1687-8027","1687-8035"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310319869","host_organization_name":"Hindawi Publishing Corporation","host_organization_lineage":["https://openalex.org/P4310319869"],"host_organization_lineage_names":["Hindawi Publishing Corporation"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Advances in Bioinformatics","raw_type":"journal-article"},{"id":"pmid:23509450","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/23509450","pdf_url":null,"source":{"id":"https://openalex.org/S4306525036","display_name":"PubMed","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1299303238","host_organization_name":"National Institutes of Health","host_organization_lineage":["https://openalex.org/I1299303238"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Advances in bioinformatics","raw_type":null},{"id":"pmh:oai:europepmc.org:2599019","is_oa":true,"landing_page_url":"http://europepmc.org/articles/PMC3590580","pdf_url":null,"source":{"id":"https://openalex.org/S4306400806","display_name":"Europe PMC (PubMed Central)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1303153112","host_organization_name":"European Bioinformatics Institute","host_organization_lineage":["https://openalex.org/I1303153112"],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"","raw_type":"Text"},{"id":"pmh:oai:pubmedcentral.nih.gov:3590580","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/3590580","pdf_url":null,"source":{"id":"https://openalex.org/S2764455111","display_name":"PubMed Central","issn_l":null,"issn":null,"is_oa":true,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1299303238","host_organization_name":"National Institutes of Health","host_organization_lineage":["https://openalex.org/I1299303238"],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Adv Bioinformatics","raw_type":"Text"},{"id":"pmh:oai:research.libraries.wsu.edu:2376/6000","is_oa":true,"landing_page_url":"http://hdl.handle.net/2376/6000","pdf_url":null,"source":{"id":"https://openalex.org/S4377196954","display_name":"Research Exchange (Washington State University)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I72951846","host_organization_name":"Washington State University","host_organization_lineage":["https://openalex.org/I72951846"],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"","raw_type":"Article"}],"best_oa_location":{"id":"doi:10.1155/2013/191586","is_oa":true,"landing_page_url":"https://doi.org/10.1155/2013/191586","pdf_url":"https://downloads.hindawi.com/archive/2013/191586.pdf","source":{"id":"https://openalex.org/S146125958","display_name":"Advances in Bioinformatics","issn_l":"1687-8027","issn":["1687-8027","1687-8035"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310319869","host_organization_name":"Hindawi Publishing Corporation","host_organization_lineage":["https://openalex.org/P4310319869"],"host_organization_lineage_names":["Hindawi Publishing Corporation"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Advances in Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[{"display_name":"Life in Land","score":0.5099999904632568,"id":"https://metadata.un.org/sdg/15"}],"awards":[],"funders":[{"id":"https://openalex.org/F4320309913","display_name":"Washington State University","ror":"https://ror.org/05dk0ce17"},{"id":"https://openalex.org/F4320312408","display_name":"Carl M. Hansen Foundation","ror":null}],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2084729635.pdf","grobid_xml":"https://content.openalex.org/works/W2084729635.grobid-xml"},"referenced_works_count":29,"referenced_works":["https://openalex.org/W1604983895","https://openalex.org/W1858745571","https://openalex.org/W1952802364","https://openalex.org/W1964123789","https://openalex.org/W1967511514","https://openalex.org/W1970668638","https://openalex.org/W1986983672","https://openalex.org/W2004237456","https://openalex.org/W2033656249","https://openalex.org/W2037275405","https://openalex.org/W2040745248","https://openalex.org/W2062399100","https://openalex.org/W2070620318","https://openalex.org/W2087064593","https://openalex.org/W2093172539","https://openalex.org/W2099879074","https://openalex.org/W2104189907","https://openalex.org/W2107031757","https://openalex.org/W2113952909","https://openalex.org/W2114574473","https://openalex.org/W2115590956","https://openalex.org/W2126684840","https://openalex.org/W2132632499","https://openalex.org/W2136232699","https://openalex.org/W2138952930","https://openalex.org/W2140211206","https://openalex.org/W2148788880","https://openalex.org/W2158627511","https://openalex.org/W2158714788"],"related_works":["https://openalex.org/W638577851","https://openalex.org/W2968354375","https://openalex.org/W2359440920","https://openalex.org/W2889550857","https://openalex.org/W3013372948","https://openalex.org/W3135997498","https://openalex.org/W4242417330","https://openalex.org/W4388282505","https://openalex.org/W3198631238","https://openalex.org/W4255657129"],"abstract_inverted_index":{"In":[0],"this":[1,126],"paper":[2],"we":[3],"present":[4],"a":[5,97,104,112,115,132],"new":[6,105,113,127],"ab":[7],"initio":[8],"approach":[9,19],"for":[10,24,48,88,101,118,171],"constructing":[11],"an":[12,18,39],"unrooted":[13],"dendrogram":[14,110,136],"using":[15,59,123,164],"protein":[16,86,116],"clusters,":[17],"that":[20,45],"has":[21],"the":[22,60,92,109,119,135,139,145,178,183,186,198],"potential":[23],"estimating":[25],"relationships":[26],"among":[27],"several":[28],"thousands":[29],"of":[30,154,185],"species":[31,90],"based":[32],"on":[33],"their":[34],"putative":[35],"proteomes.":[36],"We":[37],"employ":[38],"open-source":[40],"software":[41],"program":[42],"called":[43],"pClust":[44,58,81],"was":[46,151],"developed":[47],"use":[49,102],"in":[50,91,144,157],"metagenomic":[51],"studies.":[52],"Sequence":[53],"alignment":[54,69],"is":[55,64,121,129,162],"performed":[56],"by":[57,80],"Smith-Waterman":[61],"algorithm,":[62],"which":[63],"known":[65],"to":[66,84,138,176,181,196],"give":[67],"optimal":[68],"and,":[70],"hence,":[71],"greater":[72],"accuracy":[73],"than":[74],"BLAST-based":[75],"methods.":[76],"Protein":[77],"clusters":[78],"generated":[79],"are":[82],"used":[83,175,195],"create":[85],"profiles":[87,95,143],"each":[89,160],"dendrogram,":[93,179],"these":[94],"forming":[96],"correlation":[98,141,146],"filter":[99,147],"library":[100],"with":[103,111,142],"taxon.":[106],"To":[107],"augment":[108,197],"taxon,":[114],"profile":[117],"taxon":[120,128],"created":[122],"BLASTp,":[124],"and":[125,159,180],"placed":[130],"into":[131],"position":[133],"within":[134],"corresponding":[137],"highest":[140],"library.":[148],"This":[149],"work":[150],"initiated":[152],"because":[153],"our":[155],"interest":[156],"plasmids,":[158],"step":[161],"illustrated":[163],"proteomes":[165],"from":[166],"Gram-negative":[167],"bacterial":[168],"plasmids.":[169],"Proteomes":[170],"527":[172],"plasmids":[173,193],"were":[174,194],"generate":[177],"demonstrate":[182],"utility":[184],"insertion":[187],"algorithm":[188],"twelve":[189],"recently":[190],"sequenced":[191],"pAKD":[192],"dendrogram.":[199]},"counts_by_year":[{"year":2017,"cited_by_count":2},{"year":2016,"cited_by_count":2},{"year":2015,"cited_by_count":3},{"year":2014,"cited_by_count":2},{"year":2013,"cited_by_count":1}],"updated_date":"2026-05-21T06:26:12.895304","created_date":"2025-10-10T00:00:00"}
