{"id":"https://openalex.org/W2065505380","doi":"https://doi.org/10.1186/1751-0473-3-8","title":"Analysis by siRNA_profile program displays novel thermodynamic characteristics of highly functional siRNA molecules","display_name":"Analysis by siRNA_profile program displays novel thermodynamic characteristics of highly functional siRNA molecules","publication_year":2008,"publication_date":"2008-05-21","ids":{"openalex":"https://openalex.org/W2065505380","doi":"https://doi.org/10.1186/1751-0473-3-8","mag":"2065505380","pmid":"https://pubmed.ncbi.nlm.nih.gov/18495017"},"language":"en","primary_location":{"id":"doi:10.1186/1751-0473-3-8","is_oa":true,"landing_page_url":"https://doi.org/10.1186/1751-0473-3-8","pdf_url":"https://scfbm.biomedcentral.com/counter/pdf/10.1186/1751-0473-3-8","source":{"id":"https://openalex.org/S45786803","display_name":"Source Code for Biology and Medicine","issn_l":"1751-0473","issn":["1751-0473"],"is_oa":false,"is_in_doaj":false,"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":"Source Code for Biology and Medicine","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","pubmed"],"open_access":{"is_oa":true,"oa_status":"hybrid","oa_url":"https://scfbm.biomedcentral.com/counter/pdf/10.1186/1751-0473-3-8","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5012429565","display_name":"Pirkko Muhonen","orcid":null},"institutions":[{"id":"https://openalex.org/I155660961","display_name":"University of Turku","ror":"https://ror.org/05vghhr25","country_code":"FI","type":"education","lineage":["https://openalex.org/I155660961"]}],"countries":["FI"],"is_corresponding":true,"raw_author_name":"Pirkko Muhonen","raw_affiliation_strings":["Institute of Biomedicine, Department of Anatomy, University of Turku, Kiinamyllynkatu 10, FIN-20520 Turku, Finland. pirkko.muhonen@utu.fi","Institute of Biomedicine, Department of Anatomy, University of Turku, Turku, Finland"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Institute of Biomedicine, Department of Anatomy, University of Turku, Kiinamyllynkatu 10, FIN-20520 Turku, Finland. pirkko.muhonen@utu.fi","institution_ids":["https://openalex.org/I155660961"]},{"raw_affiliation_string":"Institute of Biomedicine, Department of Anatomy, University of Turku, Turku, Finland","institution_ids":["https://openalex.org/I155660961"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5102229019","display_name":"Ranga N. Parthasarathy","orcid":null},"institutions":[{"id":"https://openalex.org/I142740786","display_name":"University of Louisville","ror":"https://ror.org/01ckdn478","country_code":"US","type":"education","lineage":["https://openalex.org/I142740786"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Ranga N Parthasarathy","raw_affiliation_strings":["Veterans Affairs Medical Center, and University of Louisville, Louisville, KY, USA","Veterans Affairs Medical Center, and University of Louisville, Louisville, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Veterans Affairs Medical Center, and University of Louisville, Louisville, KY, USA","institution_ids":["https://openalex.org/I142740786"]},{"raw_affiliation_string":"Veterans Affairs Medical Center, and University of Louisville, Louisville, USA","institution_ids":["https://openalex.org/I142740786"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5110382045","display_name":"Anthony J. Janckila","orcid":null},"institutions":[{"id":"https://openalex.org/I142740786","display_name":"University of Louisville","ror":"https://ror.org/01ckdn478","country_code":"US","type":"education","lineage":["https://openalex.org/I142740786"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Anthony J Janckila","raw_affiliation_strings":["Veterans Affairs Medical Center, and University of Louisville, Louisville, KY, USA","Veterans Affairs Medical Center, and University of Louisville, Louisville, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Veterans Affairs Medical Center, and University of Louisville, Louisville, KY, USA","institution_ids":["https://openalex.org/I142740786"]},{"raw_affiliation_string":"Veterans Affairs Medical Center, and University of Louisville, Louisville, USA","institution_ids":["https://openalex.org/I142740786"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5018532975","display_name":"K\u00e1lman G. B\u00fcki","orcid":null},"institutions":[{"id":"https://openalex.org/I155660961","display_name":"University of Turku","ror":"https://ror.org/05vghhr25","country_code":"FI","type":"education","lineage":["https://openalex.org/I155660961"]}],"countries":["FI"],"is_corresponding":false,"raw_author_name":"Kalman G B\u00fcki","raw_affiliation_strings":["Institute of Biomedicine, Department of Anatomy, University of Turku, Kiinamyllynkatu 10, FIN-20520, Turku, Finland","Institute of Biomedicine, Department of Anatomy, University of Turku, Turku, Finland"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Institute of Biomedicine, Department of Anatomy, University of Turku, Kiinamyllynkatu 10, FIN-20520, Turku, Finland","institution_ids":["https://openalex.org/I155660961"]},{"raw_affiliation_string":"Institute of Biomedicine, Department of Anatomy, University of Turku, Turku, Finland","institution_ids":["https://openalex.org/I155660961"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5018081386","display_name":"H. Kalervo V\u00e4\u00e4n\u00e4nen","orcid":null},"institutions":[{"id":"https://openalex.org/I155660961","display_name":"University of Turku","ror":"https://ror.org/05vghhr25","country_code":"FI","type":"education","lineage":["https://openalex.org/I155660961"]}],"countries":["FI"],"is_corresponding":false,"raw_author_name":"H Kalervo V\u00e4\u00e4n\u00e4nen","raw_affiliation_strings":["Institute of Biomedicine, Department of Anatomy, University of Turku, Kiinamyllynkatu 10, FIN-20520, Turku, Finland","Institute of Biomedicine, Department of Anatomy, University of Turku, Turku, Finland"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Institute of Biomedicine, Department of Anatomy, University of Turku, Kiinamyllynkatu 10, FIN-20520, Turku, Finland","institution_ids":["https://openalex.org/I155660961"]},{"raw_affiliation_string":"Institute of Biomedicine, Department of Anatomy, University of Turku, Turku, Finland","institution_ids":["https://openalex.org/I155660961"]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":5,"corresponding_author_ids":["https://openalex.org/A5012429565"],"corresponding_institution_ids":["https://openalex.org/I155660961"],"apc_list":null,"apc_paid":null,"fwci":0.5616,"has_fulltext":true,"cited_by_count":6,"citation_normalized_percentile":{"value":0.67536123,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":90,"max":94},"biblio":{"volume":"3","issue":"1","first_page":"8","last_page":"8"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10725","display_name":"RNA Interference and Gene Delivery","score":0.9919999837875366,"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/T10725","display_name":"RNA Interference and Gene Delivery","score":0.9919999837875366,"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/T10062","display_name":"MicroRNA in disease regulation","score":0.003100000089034438,"subfield":{"id":"https://openalex.org/subfields/1306","display_name":"Cancer Research"},"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/T10432","display_name":"DNA and Nucleic Acid Chemistry","score":0.0003000000142492354,"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/small-interfering-rna","display_name":"Small interfering RNA","score":0.8027979731559753},{"id":"https://openalex.org/keywords/gene-silencing","display_name":"Gene silencing","score":0.8014816045761108},{"id":"https://openalex.org/keywords/rna-interference","display_name":"RNA interference","score":0.6573998928070068},{"id":"https://openalex.org/keywords/nucleotide","display_name":"Nucleotide","score":0.5689643621444702},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.5591884851455688},{"id":"https://openalex.org/keywords/rna-silencing","display_name":"RNA silencing","score":0.46445369720458984},{"id":"https://openalex.org/keywords/rna","display_name":"RNA","score":0.4556494355201721},{"id":"https://openalex.org/keywords/trans-acting-sirna","display_name":"Trans-acting siRNA","score":0.45046302676200867},{"id":"https://openalex.org/keywords/sense-strand","display_name":"Sense strand","score":0.4486008286476135},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.426107257604599},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.40331897139549255},{"id":"https://openalex.org/keywords/chemistry","display_name":"Chemistry","score":0.3430023193359375},{"id":"https://openalex.org/keywords/cell-biology","display_name":"Cell biology","score":0.3336111307144165},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.24204254150390625}],"concepts":[{"id":"https://openalex.org/C22615655","wikidata":"https://www.wikidata.org/wiki/Q203221","display_name":"Small interfering RNA","level":4,"score":0.8027979731559753},{"id":"https://openalex.org/C119056186","wikidata":"https://www.wikidata.org/wiki/Q1431332","display_name":"Gene silencing","level":3,"score":0.8014816045761108},{"id":"https://openalex.org/C166703698","wikidata":"https://www.wikidata.org/wiki/Q201993","display_name":"RNA interference","level":4,"score":0.6573998928070068},{"id":"https://openalex.org/C512185932","wikidata":"https://www.wikidata.org/wiki/Q28745","display_name":"Nucleotide","level":3,"score":0.5689643621444702},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.5591884851455688},{"id":"https://openalex.org/C2191507","wikidata":"https://www.wikidata.org/wiki/Q7277185","display_name":"RNA silencing","level":5,"score":0.46445369720458984},{"id":"https://openalex.org/C67705224","wikidata":"https://www.wikidata.org/wiki/Q11053","display_name":"RNA","level":3,"score":0.4556494355201721},{"id":"https://openalex.org/C60723119","wikidata":"https://www.wikidata.org/wiki/Q7833577","display_name":"Trans-acting siRNA","level":5,"score":0.45046302676200867},{"id":"https://openalex.org/C95911042","wikidata":"https://www.wikidata.org/wiki/Q6432361","display_name":"Sense strand","level":4,"score":0.4486008286476135},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.426107257604599},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.40331897139549255},{"id":"https://openalex.org/C185592680","wikidata":"https://www.wikidata.org/wiki/Q2329","display_name":"Chemistry","level":0,"score":0.3430023193359375},{"id":"https://openalex.org/C95444343","wikidata":"https://www.wikidata.org/wiki/Q7141","display_name":"Cell biology","level":1,"score":0.3336111307144165},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.24204254150390625}],"mesh":[],"locations_count":3,"locations":[{"id":"doi:10.1186/1751-0473-3-8","is_oa":true,"landing_page_url":"https://doi.org/10.1186/1751-0473-3-8","pdf_url":"https://scfbm.biomedcentral.com/counter/pdf/10.1186/1751-0473-3-8","source":{"id":"https://openalex.org/S45786803","display_name":"Source Code for Biology and Medicine","issn_l":"1751-0473","issn":["1751-0473"],"is_oa":false,"is_in_doaj":false,"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":"Source Code for Biology and Medicine","raw_type":"journal-article"},{"id":"pmid:18495017","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/18495017","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":"Source code for biology and medicine","raw_type":null},{"id":"pmh:oai:pubmedcentral.nih.gov:2424050","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/2424050","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":"Source Code Biol Med","raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1186/1751-0473-3-8","is_oa":true,"landing_page_url":"https://doi.org/10.1186/1751-0473-3-8","pdf_url":"https://scfbm.biomedcentral.com/counter/pdf/10.1186/1751-0473-3-8","source":{"id":"https://openalex.org/S45786803","display_name":"Source Code for Biology and Medicine","issn_l":"1751-0473","issn":["1751-0473"],"is_oa":false,"is_in_doaj":false,"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":"Source Code for Biology and Medicine","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[],"funders":[{"id":"https://openalex.org/F4320323313","display_name":"Turun Yliopisto","ror":"https://ror.org/05vghhr25"}],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2065505380.pdf","grobid_xml":"https://content.openalex.org/works/W2065505380.grobid-xml"},"referenced_works_count":17,"referenced_works":["https://openalex.org/W1514540900","https://openalex.org/W1540299868","https://openalex.org/W1647075334","https://openalex.org/W1984820528","https://openalex.org/W2029827106","https://openalex.org/W2071596792","https://openalex.org/W2082213106","https://openalex.org/W2100600738","https://openalex.org/W2113368761","https://openalex.org/W2116424844","https://openalex.org/W2129205448","https://openalex.org/W2151922790","https://openalex.org/W2152993806","https://openalex.org/W2160923685","https://openalex.org/W2164240862","https://openalex.org/W2166802510","https://openalex.org/W2170781554"],"related_works":["https://openalex.org/W2047147668","https://openalex.org/W1990361557","https://openalex.org/W2161312401","https://openalex.org/W2012188597","https://openalex.org/W2777306702","https://openalex.org/W1992887723","https://openalex.org/W1996864493","https://openalex.org/W2121133384","https://openalex.org/W2763021074","https://openalex.org/W2075257237"],"abstract_inverted_index":{"OBJECTIVE:":[0],"Here":[1],"we":[2],"report":[3],"the":[4,62,92,97,100,106,109,113,125,148,198],"improved":[5],"results":[6],"of":[7,26,65,108,124,137,167,191],"a":[8,134,194,203],"new":[9],"siRNA":[10,29,37,55,78,101,139,156,162],"design":[11,157],"program":[12,127],"and":[13,42,53,112,164,201,216],"analysis":[14],"tool":[15],"called":[16],"siRNA_profile":[17,66,126],"that":[18,49],"reveals":[19],"an":[20],"additional":[21],"criterion":[22,205],"for":[23],"bioinformatic":[24],"search":[25],"highly":[27,76,222],"functional":[28,77],"sequences.":[30],"METHODS:":[31],"We":[32,60],"retrospectively":[33],"analysed":[34],"over":[35],"2400":[36],"sequences":[38,56,140,179],"from":[39,94],"34":[40],"genes":[41],"with":[43,141],"known":[44],"efficacies":[45],"to":[46,96,105,128,206,210],"categorize":[47],"factors":[48],"differentiate":[50],"highly,":[51],"moderately":[52],"non-functional":[54,85],"in":[57,67,103,133,197,208],"more":[58,174],"detail.":[59],"tested":[61],"biological":[63],"relevance":[64],"CHO":[68],"cells":[69],"stably":[70],"expressing":[71],"human":[72],"TRACP.":[73],"RESULTS:":[74],"The":[75,176],"molecules":[79],"exhibited":[80],"lower":[81],"overall":[82],"stabilities":[83],"than":[84],"siRNAs":[86],"after":[87],"taking":[88],"into":[89],"consideration":[90],"all":[91],"nucleotides":[93,117,153],"5'-terminus":[95],"3'-terminus":[98],"along":[99],"molecule,":[102],"addition":[104,209],"5'-section":[107],"antisense":[110],"strand":[111],"region":[114],"between":[115],"9-14":[116],"as":[118],"previously":[119],"has":[120],"been":[121],"acknowledged.":[122],"Comparison":[123],"five":[129],"other":[130,177],"programs":[131,158],"resulted":[132],"wide":[135],"range":[136],"selected":[138,159,170,182],"diverse":[142],"gene":[143],"silencing":[144],"capacities,":[145],"even":[146],"when":[147,220],"target":[149,217],"was":[150],"only":[151,165],"197":[152],"long.":[154],"Six":[155],"24":[160],"different":[161],"sequences,":[163],"6":[166],"them":[168],"were":[169,180],"by":[171,183],"two":[172],"or":[173],"programs.":[175,186],"18":[178],"individually":[181],"these":[184],"six":[185],"CONCLUSION:":[187],"Low":[188],"general":[189],"stability":[190],"dsRNA":[192],"plays":[193],"significant":[195],"role":[196],"RNAi":[199],"pathway":[200],"is":[202],"recommended":[204],"consider,":[207],"5'-instability,":[211],"internal":[212],"instability,":[213],"nucleotide":[214],"preferences":[215],"mRNA":[218],"position,":[219],"designing":[221],"efficient":[223],"siRNAs.":[224]},"counts_by_year":[{"year":2019,"cited_by_count":1},{"year":2016,"cited_by_count":1}],"updated_date":"2026-06-19T15:47:20.252518","created_date":"2025-10-10T00:00:00"}