{"id":"https://openalex.org/W2138586080","doi":"https://doi.org/10.1186/1471-2105-8-246","title":"Simcluster: clustering enumeration gene expression data on the simplex space","display_name":"Simcluster: clustering enumeration gene expression data on the simplex space","publication_year":2007,"publication_date":"2007-07-11","ids":{"openalex":"https://openalex.org/W2138586080","doi":"https://doi.org/10.1186/1471-2105-8-246","mag":"2138586080","pmid":"https://pubmed.ncbi.nlm.nih.gov/17625017"},"language":"en","primary_location":{"id":"doi:10.1186/1471-2105-8-246","is_oa":true,"landing_page_url":"https://doi.org/10.1186/1471-2105-8-246","pdf_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/1471-2105-8-246","source":{"id":"https://openalex.org/S19032547","display_name":"BMC Bioinformatics","issn_l":"1471-2105","issn":["1471-2105"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320256","host_organization_name":"BioMed Central","host_organization_lineage":["https://openalex.org/P4310320256","https://openalex.org/P4310319965"],"host_organization_lineage_names":["BioMed Central","Springer Nature"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"BMC Bioinformatics","raw_type":"journal-article"},"type":"article","indexed_in":["arxiv","crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/1471-2105-8-246","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":null,"display_name":"Ricardo ZN V\u00eancio","orcid":null},"institutions":[{"id":"https://openalex.org/I3148997608","display_name":"Institute for Systems Biology","ror":"https://ror.org/02tpgw303","country_code":"US","type":"nonprofit","lineage":["https://openalex.org/I3148997608"]},{"id":"https://openalex.org/I4210099575","display_name":"InSysBio (Russia)","ror":"https://ror.org/011fdmv87","country_code":"RU","type":"company","lineage":["https://openalex.org/I4210099575"]}],"countries":["RU","US"],"is_corresponding":false,"raw_author_name":"Ricardo ZN V\u00eancio","raw_affiliation_strings":["Institute for Systems Biology, 1441 North 34th street, Seattle, WA 98103-8904, USA. rvencio@gmail.com","Institute for Systems Biology"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Institute for Systems Biology, 1441 North 34th street, Seattle, WA 98103-8904, USA. rvencio@gmail.com","institution_ids":["https://openalex.org/I3148997608"]},{"raw_affiliation_string":"Institute for Systems Biology","institution_ids":["https://openalex.org/I3148997608","https://openalex.org/I4210099575"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5061018272","display_name":"Leonardo Varuzza","orcid":"https://orcid.org/0000-0002-0827-858X"},"institutions":[{"id":"https://openalex.org/I17974374","display_name":"Universidade de S\u00e3o Paulo","ror":"https://ror.org/036rp1748","country_code":"BR","type":"education","lineage":["https://openalex.org/I17974374"]}],"countries":["BR"],"is_corresponding":false,"raw_author_name":"Leonardo Varuzza","raw_affiliation_strings":["BIOINFO-USP \u2013 N\u00facleo de Pesquisas em Bioinform\u00e1tica, Universidade de S\u00e3o Paulo, S\u00e3o Paulo, Brazil","Universidade de Sao Paulo#TAB#"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"BIOINFO-USP \u2013 N\u00facleo de Pesquisas em Bioinform\u00e1tica, Universidade de S\u00e3o Paulo, S\u00e3o Paulo, Brazil","institution_ids":["https://openalex.org/I17974374"]},{"raw_affiliation_string":"Universidade de Sao Paulo#TAB#","institution_ids":["https://openalex.org/I17974374"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5005785169","display_name":"Carlos Alberto de Bragan\u00e7a Pereira","orcid":"https://orcid.org/0000-0001-6315-7484"},"institutions":[{"id":"https://openalex.org/I17974374","display_name":"Universidade de S\u00e3o Paulo","ror":"https://ror.org/036rp1748","country_code":"BR","type":"education","lineage":["https://openalex.org/I17974374"]}],"countries":["BR"],"is_corresponding":false,"raw_author_name":"Carlos A de B Pereira","raw_affiliation_strings":["BIOINFO-USP \u2013 N\u00facleo de Pesquisas em Bioinform\u00e1tica, Universidade de S\u00e3o Paulo, S\u00e3o Paulo, Brazil","Universidade de Sao Paulo#TAB#"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"BIOINFO-USP \u2013 N\u00facleo de Pesquisas em Bioinform\u00e1tica, Universidade de S\u00e3o Paulo, S\u00e3o Paulo, Brazil","institution_ids":["https://openalex.org/I17974374"]},{"raw_affiliation_string":"Universidade de Sao Paulo#TAB#","institution_ids":["https://openalex.org/I17974374"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5090411219","display_name":"Helena Brentani","orcid":"https://orcid.org/0000-0001-5192-4682"},"institutions":[{"id":"https://openalex.org/I3019035496","display_name":"AC Camargo Hospital","ror":"https://ror.org/03025ga79","country_code":"BR","type":"healthcare","lineage":["https://openalex.org/I3019035496"]}],"countries":["BR"],"is_corresponding":false,"raw_author_name":"Helena Brentani","raw_affiliation_strings":["Hospital do C\u00e2ncer A. C. Camargo, S\u00e3o Paulo, Brazil"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Hospital do C\u00e2ncer A. C. Camargo, S\u00e3o Paulo, Brazil","institution_ids":["https://openalex.org/I3019035496"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5061460061","display_name":"Ilya Shmulevich","orcid":"https://orcid.org/0000-0002-4410-8780"},"institutions":[{"id":"https://openalex.org/I3148997608","display_name":"Institute for Systems Biology","ror":"https://ror.org/02tpgw303","country_code":"US","type":"nonprofit","lineage":["https://openalex.org/I3148997608"]},{"id":"https://openalex.org/I4210099575","display_name":"InSysBio (Russia)","ror":"https://ror.org/011fdmv87","country_code":"RU","type":"company","lineage":["https://openalex.org/I4210099575"]},{"id":"https://openalex.org/I58610484","display_name":"Seattle University","ror":"https://ror.org/02jqc0m91","country_code":"US","type":"education","lineage":["https://openalex.org/I58610484"]}],"countries":["RU","US"],"is_corresponding":false,"raw_author_name":"Ilya Shmulevich","raw_affiliation_strings":["Institute for Systems Biology, 1441 North 34th street, Seattle, WA, 98103-8904, USA","Institute for Systems Biology, Seattle, USA","Institute for Systems Biology"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Institute for Systems Biology, 1441 North 34th street, Seattle, WA, 98103-8904, USA","institution_ids":["https://openalex.org/I3148997608"]},{"raw_affiliation_string":"Institute for Systems Biology, Seattle, USA","institution_ids":["https://openalex.org/I3148997608","https://openalex.org/I58610484"]},{"raw_affiliation_string":"Institute for Systems Biology","institution_ids":["https://openalex.org/I3148997608","https://openalex.org/I4210099575"]}]}],"institutions":[],"countries_distinct_count":3,"institutions_distinct_count":5,"corresponding_author_ids":[],"corresponding_institution_ids":[],"apc_list":{"value":2790,"currency":"USD","value_usd":2790},"apc_paid":{"value":2790,"currency":"USD","value_usd":2790},"fwci":3.352,"has_fulltext":true,"cited_by_count":15,"citation_normalized_percentile":{"value":0.93092428,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":89,"max":96},"biblio":{"volume":"8","issue":"1","first_page":"246","last_page":"246"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T12157","display_name":"Geochemistry and Geologic Mapping","score":0.9495999813079834,"subfield":{"id":"https://openalex.org/subfields/1702","display_name":"Artificial Intelligence"},"field":{"id":"https://openalex.org/fields/17","display_name":"Computer Science"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}},"topics":[{"id":"https://openalex.org/T12157","display_name":"Geochemistry and Geologic Mapping","score":0.9495999813079834,"subfield":{"id":"https://openalex.org/subfields/1702","display_name":"Artificial Intelligence"},"field":{"id":"https://openalex.org/fields/17","display_name":"Computer Science"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}},{"id":"https://openalex.org/T12923","display_name":"Digital Image Processing Techniques","score":0.009600000455975533,"subfield":{"id":"https://openalex.org/subfields/1707","display_name":"Computer Vision and Pattern Recognition"},"field":{"id":"https://openalex.org/fields/17","display_name":"Computer Science"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}},{"id":"https://openalex.org/T12536","display_name":"Topological and Geometric Data Analysis","score":0.005499999970197678,"subfield":{"id":"https://openalex.org/subfields/1703","display_name":"Computational Theory and Mathematics"},"field":{"id":"https://openalex.org/fields/17","display_name":"Computer Science"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/enumeration","display_name":"Enumeration","score":0.8357264399528503},{"id":"https://openalex.org/keywords/cluster-analysis","display_name":"Cluster analysis","score":0.6342491507530212},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.5913192629814148},{"id":"https://openalex.org/keywords/simplex","display_name":"Simplex","score":0.5654058456420898},{"id":"https://openalex.org/keywords/dna-microarray","display_name":"DNA microarray","score":0.524408221244812},{"id":"https://openalex.org/keywords/software","display_name":"Software","score":0.5097491145133972},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.4915672242641449},{"id":"https://openalex.org/keywords/euclidean-space","display_name":"Euclidean space","score":0.45897406339645386},{"id":"https://openalex.org/keywords/expression","display_name":"Expression (computer science)","score":0.4117743670940399},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.35477882623672485},{"id":"https://openalex.org/keywords/theoretical-computer-science","display_name":"Theoretical computer science","score":0.33471089601516724},{"id":"https://openalex.org/keywords/mathematics","display_name":"Mathematics","score":0.2387995719909668},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.21486622095108032},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.17609357833862305},{"id":"https://openalex.org/keywords/gene-expression","display_name":"Gene expression","score":0.1567634642124176},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.14237922430038452},{"id":"https://openalex.org/keywords/combinatorics","display_name":"Combinatorics","score":0.09434887766838074},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.08567392826080322},{"id":"https://openalex.org/keywords/programming-language","display_name":"Programming language","score":0.08034500479698181}],"concepts":[{"id":"https://openalex.org/C156340839","wikidata":"https://www.wikidata.org/wiki/Q2704791","display_name":"Enumeration","level":2,"score":0.8357264399528503},{"id":"https://openalex.org/C73555534","wikidata":"https://www.wikidata.org/wiki/Q622825","display_name":"Cluster analysis","level":2,"score":0.6342491507530212},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.5913192629814148},{"id":"https://openalex.org/C62438384","wikidata":"https://www.wikidata.org/wiki/Q331350","display_name":"Simplex","level":2,"score":0.5654058456420898},{"id":"https://openalex.org/C95371953","wikidata":"https://www.wikidata.org/wiki/Q591745","display_name":"DNA microarray","level":4,"score":0.524408221244812},{"id":"https://openalex.org/C2777904410","wikidata":"https://www.wikidata.org/wiki/Q7397","display_name":"Software","level":2,"score":0.5097491145133972},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.4915672242641449},{"id":"https://openalex.org/C186450821","wikidata":"https://www.wikidata.org/wiki/Q17295","display_name":"Euclidean space","level":2,"score":0.45897406339645386},{"id":"https://openalex.org/C90559484","wikidata":"https://www.wikidata.org/wiki/Q778379","display_name":"Expression (computer science)","level":2,"score":0.4117743670940399},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.35477882623672485},{"id":"https://openalex.org/C80444323","wikidata":"https://www.wikidata.org/wiki/Q2878974","display_name":"Theoretical computer science","level":1,"score":0.33471089601516724},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.2387995719909668},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.21486622095108032},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.17609357833862305},{"id":"https://openalex.org/C150194340","wikidata":"https://www.wikidata.org/wiki/Q26972","display_name":"Gene expression","level":3,"score":0.1567634642124176},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.14237922430038452},{"id":"https://openalex.org/C114614502","wikidata":"https://www.wikidata.org/wiki/Q76592","display_name":"Combinatorics","level":1,"score":0.09434887766838074},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.08567392826080322},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.08034500479698181}],"mesh":[{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D001185","descriptor_name":"Artificial Intelligence","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D001185","descriptor_name":"Artificial Intelligence","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D001185","descriptor_name":"Artificial Intelligence","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D010363","descriptor_name":"Pattern Recognition, Automated","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D010363","descriptor_name":"Pattern Recognition, Automated","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D010363","descriptor_name":"Pattern Recognition, Automated","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011381","descriptor_name":"Programming Languages","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D011381","descriptor_name":"Programming Languages","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D011381","descriptor_name":"Programming Languages","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D014157","descriptor_name":"Transcription Factors","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D014157","descriptor_name":"Transcription Factors","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D014157","descriptor_name":"Transcription Factors","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D016000","descriptor_name":"Cluster Analysis","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D016000","descriptor_name":"Cluster Analysis","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D016000","descriptor_name":"Cluster Analysis","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D020411","descriptor_name":"Oligonucleotide Array Sequence Analysis","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D020411","descriptor_name":"Oligonucleotide Array Sequence Analysis","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D020411","descriptor_name":"Oligonucleotide Array Sequence Analysis","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D020869","descriptor_name":"Gene Expression Profiling","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D020869","descriptor_name":"Gene Expression Profiling","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D020869","descriptor_name":"Gene Expression Profiling","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false}],"locations_count":8,"locations":[{"id":"doi:10.1186/1471-2105-8-246","is_oa":true,"landing_page_url":"https://doi.org/10.1186/1471-2105-8-246","pdf_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/1471-2105-8-246","source":{"id":"https://openalex.org/S19032547","display_name":"BMC Bioinformatics","issn_l":"1471-2105","issn":["1471-2105"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320256","host_organization_name":"BioMed Central","host_organization_lineage":["https://openalex.org/P4310320256","https://openalex.org/P4310319965"],"host_organization_lineage_names":["BioMed Central","Springer Nature"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"BMC Bioinformatics","raw_type":"journal-article"},{"id":"pmid:17625017","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/17625017","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":"BMC bioinformatics","raw_type":null},{"id":"pmh:oai:www.producao.usp.br:BDPI/32736","is_oa":true,"landing_page_url":"http://www.producao.usp.br/handle/BDPI/32736","pdf_url":null,"source":{"id":"https://openalex.org/S4306402433","display_name":"Portuguese National Funding Agency for Science, Research and Technology (RCAAP Project by FCT)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":null,"host_organization_name":null,"host_organization_lineage":[],"host_organization_lineage_names":[],"type":"repository"},"license":"other-oa","license_id":"https://openalex.org/licenses/other-oa","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"reponame:Reposit\u00f3rio Institucional da USP","raw_type":"publishedVersion"},{"id":"pmh:oai:arXiv.org:q-bio/0703007","is_oa":true,"landing_page_url":"http://arxiv.org/abs/q-bio/0703007","pdf_url":"https://arxiv.org/pdf/q-bio/0703007","source":{"id":"https://openalex.org/S4306400194","display_name":"arXiv (Cornell University)","issn_l":"2331-8422","issn":["2331-8422"],"is_oa":true,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I205783295","host_organization_name":"Cornell University","host_organization_lineage":["https://openalex.org/I205783295"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":"text"},{"id":"pmh:002972661","is_oa":true,"landing_page_url":"http://dx.doi.org/10.1186/1471-2105-8-246","pdf_url":null,"source":{"id":"https://openalex.org/S4306402641","display_name":"LA Referencia (Red Federada de Repositorios Institucionales de Publicaciones Cient\u00edficas)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I4383465926","host_organization_name":"LA Referencia","host_organization_lineage":["https://openalex.org/I4383465926"],"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":"reponame:Reposit\u00f3rio Institucional da USP (Biblioteca Digital da Produ\u00e7\u00e3o Intelectual)","raw_type":"info:eu-repo/semantics/publishedVersion"},{"id":"pmh:oai:CiteSeerX.psu:10.1.1.669.7070","is_oa":false,"landing_page_url":"http://citeseerx.ist.psu.edu/viewdoc/summary?doi=10.1.1.669.7070","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"http://precedings.nature.com/documents/202/version/1/files/npre2007202-1.pdf","raw_type":"text"},{"id":"pmh:oai:doaj.org/article:e913f6e902d6409b83449a34d7b37505","is_oa":false,"landing_page_url":"https://doaj.org/article/e913f6e902d6409b83449a34d7b37505","pdf_url":null,"source":{"id":"https://openalex.org/S4306401280","display_name":"DOAJ (DOAJ: Directory of Open Access Journals)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":null,"host_organization_name":null,"host_organization_lineage":[],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"BMC Bioinformatics, Vol 8, Iss 1, p 246 (2007)","raw_type":"article"},{"id":"pmh:oai:pubmedcentral.nih.gov:2147035","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/2147035","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":"BMC Bioinformatics","raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1186/1471-2105-8-246","is_oa":true,"landing_page_url":"https://doi.org/10.1186/1471-2105-8-246","pdf_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/1471-2105-8-246","source":{"id":"https://openalex.org/S19032547","display_name":"BMC Bioinformatics","issn_l":"1471-2105","issn":["1471-2105"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320256","host_organization_name":"BioMed Central","host_organization_lineage":["https://openalex.org/P4310320256","https://openalex.org/P4310319965"],"host_organization_lineage_names":["BioMed Central","Springer Nature"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"BMC Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G124905531","display_name":null,"funder_award_id":"AI057266","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"},{"id":"https://openalex.org/G160394909","display_name":null,"funder_award_id":"U19-AI057266","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"},{"id":"https://openalex.org/G2745195578","display_name":null,"funder_award_id":"U19-AI057266","funder_id":"https://openalex.org/F4320337355","funder_display_name":"National Institute of Allergy and Infectious Diseases"},{"id":"https://openalex.org/G3265217098","display_name":null,"funder_award_id":"U54-AI54253","funder_id":"https://openalex.org/F4320337355","funder_display_name":"National Institute of Allergy and Infectious Diseases"},{"id":"https://openalex.org/G6685758877","display_name":null,"funder_award_id":"AI057266","funder_id":"https://openalex.org/F4320337355","funder_display_name":"National Institute of Allergy and Infectious Diseases"},{"id":"https://openalex.org/G7153736075","display_name":null,"funder_award_id":"P50-GMO-76547","funder_id":"https://openalex.org/F4320332505","funder_display_name":"U.S. Public Health Service"},{"id":"https://openalex.org/G7174733736","display_name":null,"funder_award_id":"P50 GM076547","funder_id":"https://openalex.org/F4320337354","funder_display_name":"National Institute of General Medical Sciences"}],"funders":[{"id":"https://openalex.org/F4320321091","display_name":"Coordena\u00e7\u00e3o de Aperfei\u00e7oamento de Pessoal de N\u00edvel Superior","ror":"https://ror.org/00x0ma614"},{"id":"https://openalex.org/F4320322025","display_name":"Conselho Nacional de Desenvolvimento Cient\u00edfico e Tecnol\u00f3gico","ror":"https://ror.org/03swz6y49"},{"id":"https://openalex.org/F4320332161","display_name":"National Institutes of Health","ror":"https://ror.org/01cwqze88"},{"id":"https://openalex.org/F4320332505","display_name":"U.S. Public Health Service","ror":"https://ror.org/05xf94514"},{"id":"https://openalex.org/F4320337354","display_name":"National Institute of General Medical Sciences","ror":"https://ror.org/04q48ey07"},{"id":"https://openalex.org/F4320337355","display_name":"National Institute of Allergy and Infectious Diseases","ror":"https://ror.org/043z4tv69"}],"has_content":{"grobid_xml":true,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2138586080.pdf","grobid_xml":"https://content.openalex.org/works/W2138586080.grobid-xml"},"referenced_works_count":33,"referenced_works":["https://openalex.org/W176623880","https://openalex.org/W1509684938","https://openalex.org/W1513910506","https://openalex.org/W1549060837","https://openalex.org/W1965061252","https://openalex.org/W1970156673","https://openalex.org/W1992108607","https://openalex.org/W1998251495","https://openalex.org/W2010888033","https://openalex.org/W2035530476","https://openalex.org/W2050163545","https://openalex.org/W2059280444","https://openalex.org/W2061003492","https://openalex.org/W2117059686","https://openalex.org/W2125013165","https://openalex.org/W2128114769","https://openalex.org/W2137348240","https://openalex.org/W2142070680","https://openalex.org/W2145221987","https://openalex.org/W2146516445","https://openalex.org/W2150297520","https://openalex.org/W2153562609","https://openalex.org/W2154231035","https://openalex.org/W2162010421","https://openalex.org/W2166131221","https://openalex.org/W2166325326","https://openalex.org/W2318935314","https://openalex.org/W2341128841","https://openalex.org/W2413421641","https://openalex.org/W4213387068","https://openalex.org/W4232780638","https://openalex.org/W4242673342","https://openalex.org/W4299542564"],"related_works":["https://openalex.org/W2385773526","https://openalex.org/W2377351640","https://openalex.org/W2357922472","https://openalex.org/W2384278689","https://openalex.org/W4312235719","https://openalex.org/W2351833173","https://openalex.org/W4297808600","https://openalex.org/W2372951335","https://openalex.org/W2021962375","https://openalex.org/W2201164805"],"abstract_inverted_index":{"BACKGROUND:":[0],"Transcript":[1],"enumeration":[2,84],"methods":[3,68],"such":[4],"as":[5,117,124],"SAGE,":[6],"MPSS,":[7],"and":[8,123,160],"sequencing-by-synthesis":[9],"EST":[10],"\"digital":[11],"northern\",":[12],"are":[13,50,131],"important":[14],"high-throughput":[15],"techniques":[16,85],"for":[17,71,78,108,146,154],"digital":[18],"gene":[19,171],"expression":[20,172],"measurement.":[21],"As":[22],"other":[23],"counting":[24],"or":[25],"voting":[26],"processes,":[27],"these":[28],"measurements":[29],"constitute":[30],"compositional":[31,147],"data":[32,61,73,80,109,148],"exhibiting":[33],"properties":[34,49,91],"particular":[35],"to":[36,104],"the":[37,41,44,79,111,157],"simplex":[38,112,158],"space":[39],"where":[40],"summation":[42],"of":[43,92,167],"components":[45],"is":[46,62,137,161],"constrained.":[47],"These":[48],"not":[51],"present":[52,98,115],"on":[53,57,110],"regular":[54],"Euclidean":[55],"spaces,":[56],"which":[58,150],"hybridization-based":[59],"microarray":[60,72],"often":[63],"modeled.":[64],"Therefore,":[65],"pattern":[66],"recognition":[67],"commonly":[69],"used":[70],"analysis":[74,107],"may":[75],"be":[76],"non-informative":[77],"generated":[81],"by":[82],"transcript":[83],"since":[86],"they":[87],"ignore":[88],"certain":[89],"fundamental":[90],"this":[93],"space.":[94,113],"RESULTS:":[95],"Here":[96],"we":[97],"a":[99,118,125,142,165],"software":[100],"tool,":[101],"Simcluster,":[102],"designed":[103,138],"perform":[105],"clustering":[106],"We":[114],"Simcluster":[116,136],"stand-alone":[119],"command-line":[120],"C":[121],"package":[122],"user-friendly":[126],"on-line":[127],"tool.":[128],"Both":[129],"versions":[130],"available":[132],"at:":[133],"http://xerad.systemsbiology.net/simcluster.":[134],"CONCLUSION:":[135],"in":[139,164],"accordance":[140],"with":[141,156],"well-established":[143],"mathematical":[144],"framework":[145],"analysis,":[149],"provides":[151],"principled":[152],"procedures":[153],"dealing":[155],"space,":[159],"thus":[162],"applicable":[163],"number":[166],"contexts,":[168],"including":[169],"enumeration-based":[170],"data.":[173]},"counts_by_year":[{"year":2015,"cited_by_count":2},{"year":2014,"cited_by_count":1},{"year":2013,"cited_by_count":1},{"year":2012,"cited_by_count":1}],"updated_date":"2026-07-28T07:46:37.118299","created_date":"2025-10-10T00:00:00"}