{"id":"https://openalex.org/W2495107680","doi":"https://doi.org/10.1142/s021972001650027x","title":"PR2S2Clust: Patched RNA-seq read segments\u2019 structure-oriented clustering","display_name":"PR2S2Clust: Patched RNA-seq read segments\u2019 structure-oriented clustering","publication_year":2016,"publication_date":"2016-07-26","ids":{"openalex":"https://openalex.org/W2495107680","doi":"https://doi.org/10.1142/s021972001650027x","mag":"2495107680","pmid":"https://pubmed.ncbi.nlm.nih.gov/27455882"},"language":"en","primary_location":{"id":"doi:10.1142/s021972001650027x","is_oa":false,"landing_page_url":"https://doi.org/10.1142/s021972001650027x","pdf_url":null,"source":{"id":"https://openalex.org/S155349577","display_name":"Journal of Bioinformatics and Computational Biology","issn_l":"0219-7200","issn":["0219-7200","1757-6334"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310311754","host_organization_name":"Imperial College Press","host_organization_lineage":["https://openalex.org/P4310311754"],"host_organization_lineage_names":["Imperial College Press"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Journal of Bioinformatics and Computational Biology","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","pubmed"],"open_access":{"is_oa":false,"oa_status":"closed","oa_url":null,"any_repository_has_fulltext":false},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5074501326","display_name":"Ashis Kumer Biswas","orcid":"https://orcid.org/0000-0002-7446-4639"},"institutions":[{"id":"https://openalex.org/I189196454","display_name":"The University of Texas at Arlington","ror":"https://ror.org/019kgqr73","country_code":"US","type":"education","lineage":["https://openalex.org/I189196454"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Ashis Kumer Biswas","raw_affiliation_strings":["Department of Computer Science and Engineering, The University of Texas at Arlington, Texas 76019, USA"],"affiliations":[{"raw_affiliation_string":"Department of Computer Science and Engineering, The University of Texas at Arlington, Texas 76019, USA","institution_ids":["https://openalex.org/I189196454"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5015128288","display_name":"Jean Gao","orcid":null},"institutions":[{"id":"https://openalex.org/I189196454","display_name":"The University of Texas at Arlington","ror":"https://ror.org/019kgqr73","country_code":"US","type":"education","lineage":["https://openalex.org/I189196454"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Jean X. Gao","raw_affiliation_strings":["Department of Computer Science and Engineering, The University of Texas at Arlington, Texas 76019, USA"],"affiliations":[{"raw_affiliation_string":"Department of Computer Science and Engineering, The University of Texas at Arlington, Texas 76019, USA","institution_ids":["https://openalex.org/I189196454"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":2,"corresponding_author_ids":["https://openalex.org/A5074501326"],"corresponding_institution_ids":["https://openalex.org/I189196454"],"apc_list":null,"apc_paid":null,"fwci":0.3335,"has_fulltext":false,"cited_by_count":4,"citation_normalized_percentile":{"value":0.67509975,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":95},"biblio":{"volume":"14","issue":"05","first_page":"1650027","last_page":"1650027"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.9993000030517578,"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":0.9993000030517578,"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/T10521","display_name":"RNA and protein synthesis mechanisms","score":0.9991999864578247,"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/T11482","display_name":"RNA modifications and cancer","score":0.9988999962806702,"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/cluster-analysis","display_name":"Cluster analysis","score":0.5313105583190918},{"id":"https://openalex.org/keywords/patched","display_name":"Patched","score":0.5289105176925659},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.4855344295501709},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.41927337646484375},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.41155770421028137},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.3400859236717224},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.25674116611480713},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.15766796469688416},{"id":"https://openalex.org/keywords/hedgehog","display_name":"Hedgehog","score":0.07219952344894409}],"concepts":[{"id":"https://openalex.org/C73555534","wikidata":"https://www.wikidata.org/wiki/Q622825","display_name":"Cluster analysis","level":2,"score":0.5313105583190918},{"id":"https://openalex.org/C2777994357","wikidata":"https://www.wikidata.org/wiki/Q24781250","display_name":"Patched","level":4,"score":0.5289105176925659},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.4855344295501709},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.41927337646484375},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.41155770421028137},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.3400859236717224},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.25674116611480713},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.15766796469688416},{"id":"https://openalex.org/C2778539099","wikidata":"https://www.wikidata.org/wiki/Q6120","display_name":"Hedgehog","level":3,"score":0.07219952344894409}],"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":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D009690","descriptor_name":"Nucleic Acid Conformation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D009690","descriptor_name":"Nucleic Acid Conformation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D009690","descriptor_name":"Nucleic Acid Conformation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016000","descriptor_name":"Cluster Analysis","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016000","descriptor_name":"Cluster Analysis","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016000","descriptor_name":"Cluster Analysis","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D017423","descriptor_name":"Sequence Analysis, RNA","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D017423","descriptor_name":"Sequence Analysis, RNA","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D017423","descriptor_name":"Sequence Analysis, RNA","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D022661","descriptor_name":"RNA, Untranslated","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D022661","descriptor_name":"RNA, Untranslated","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D022661","descriptor_name":"RNA, Untranslated","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D022661","descriptor_name":"RNA, Untranslated","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D022661","descriptor_name":"RNA, Untranslated","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D022661","descriptor_name":"RNA, Untranslated","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D030541","descriptor_name":"Databases, Genetic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D030541","descriptor_name":"Databases, Genetic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D030541","descriptor_name":"Databases, Genetic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false}],"locations_count":2,"locations":[{"id":"doi:10.1142/s021972001650027x","is_oa":false,"landing_page_url":"https://doi.org/10.1142/s021972001650027x","pdf_url":null,"source":{"id":"https://openalex.org/S155349577","display_name":"Journal of Bioinformatics and Computational Biology","issn_l":"0219-7200","issn":["0219-7200","1757-6334"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310311754","host_organization_name":"Imperial College Press","host_organization_lineage":["https://openalex.org/P4310311754"],"host_organization_lineage_names":["Imperial College Press"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Journal of Bioinformatics and Computational Biology","raw_type":"journal-article"},{"id":"pmid:27455882","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/27455882","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":"Journal of bioinformatics and computational biology","raw_type":null}],"best_oa_location":null,"sustainable_development_goals":[],"awards":[],"funders":[],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":32,"referenced_works":["https://openalex.org/W127599202","https://openalex.org/W144423133","https://openalex.org/W1542134689","https://openalex.org/W1543796220","https://openalex.org/W1599547597","https://openalex.org/W1974736226","https://openalex.org/W1976679748","https://openalex.org/W1981509058","https://openalex.org/W1994414793","https://openalex.org/W2004791359","https://openalex.org/W2007144639","https://openalex.org/W2008386840","https://openalex.org/W2054697783","https://openalex.org/W2077770566","https://openalex.org/W2085115334","https://openalex.org/W2088390270","https://openalex.org/W2088938573","https://openalex.org/W2097065948","https://openalex.org/W2109676825","https://openalex.org/W2114094654","https://openalex.org/W2124050695","https://openalex.org/W2125120036","https://openalex.org/W2126997102","https://openalex.org/W2127375279","https://openalex.org/W2139280638","https://openalex.org/W2140302584","https://openalex.org/W2142038007","https://openalex.org/W2149039397","https://openalex.org/W2155858493","https://openalex.org/W2170157200","https://openalex.org/W4235169531","https://openalex.org/W4285719527"],"related_works":["https://openalex.org/W2038576114","https://openalex.org/W2116610035","https://openalex.org/W2135391373","https://openalex.org/W4250169555","https://openalex.org/W2082860237","https://openalex.org/W2610240957","https://openalex.org/W2119695867","https://openalex.org/W2130076355","https://openalex.org/W1990804418","https://openalex.org/W2048922778"],"abstract_inverted_index":{"RNA-seq,":[0],"the":[1,12,43,51,88,93,103,107,135,140,155,178,183,196],"next":[2],"generation":[3],"sequencing":[4],"platform,":[5],"enables":[6],"researchers":[7],"to":[8,36,83,86,101,105],"explore":[9],"deep":[10],"into":[11,109],"transcriptome":[13],"of":[14,31,47,50,92,148,154,182,191],"organisms,":[15],"such":[16],"as":[17,134],"identifying":[18],"functional":[19],"non-coding":[20],"RNAs":[21],"(ncRNAs),":[22],"and":[23,57,151,157,169,180,189],"quantify":[24],"their":[25,37],"expressions":[26],"on":[27],"tissues.":[28],"The":[29,116,186],"functions":[30],"ncRNAs":[32],"are":[33,193],"mostly":[34],"related":[35],"secondary":[38,89],"structures.":[39],"Thus":[40],"by":[41,124],"exploring":[42],"clustering":[44,114,139],"in":[45,60],"terms":[46],"structural":[48,121],"profiles":[49,91,104],"corresponding":[52],"read-segments":[53],"would":[54],"be":[55],"essential":[56],"this":[58,64,67,143],"fuels":[59],"our":[61],"motivation":[62],"behind":[63],"research.":[65],"In":[66,142],"manuscript":[68],"we":[69,132,145],"proposed":[70,184],"PR2S2Clust,":[71],"Patched":[72],"RNA-seq":[73,94,167],"Read":[74],"Segments'":[75],"Structure-oriented":[76],"Clustering,":[77],"which":[78,131],"is":[79],"an":[80],"analysis":[81,172],"platform":[82],"extract":[84],"features":[85],"prepare":[87],"structure":[90],"read":[95],"segments.":[96,141],"It":[97],"provides":[98],"a":[99,170],"strategy":[100],"employ":[102],"annotate":[106],"segments":[108],"ncRNA":[110],"classes":[111],"using":[112],"several":[113],"strategies.":[115],"system":[117],"considers":[118],"seven":[119],"pairwise":[120],"distance":[122],"metrics":[123],"considering":[125],"short-read":[126],"mappings":[127],"onto":[128],"each":[129],"structure,":[130],"term":[133],"\"patched":[136],"structure\"":[137],"while":[138],"regard,":[144],"show":[146],"applications":[147],"both":[149],"classical":[150],"ensemble":[152],"clusterings":[153],"partitional":[156],"hierarchical":[158],"variations.":[159],"Extensive":[160],"real-world":[161],"experiments":[162],"over":[163,173],"three":[164],"publicly":[165],"available":[166,194],"datasets":[168],"comparative":[171],"four":[174],"competitive":[175],"systems":[176],"confirm":[177],"effectiveness":[179],"superiority":[181],"system.":[185],"source":[187],"codes":[188],"dataset":[190],"PR2S2Clust":[192],"at":[195],"http://biomecis.uta.edu/~ashis/res/PR2S2Clust-suppl/":[197],".":[198]},"counts_by_year":[{"year":2025,"cited_by_count":1},{"year":2020,"cited_by_count":1},{"year":2017,"cited_by_count":1},{"year":2016,"cited_by_count":1}],"updated_date":"2025-11-06T03:46:38.306776","created_date":"2025-10-10T00:00:00"}