{"id":"https://openalex.org/W2749289701","doi":"https://doi.org/10.1137/17m1144076","title":"On the Structure of RNA Branching Polytopes","display_name":"On the Structure of RNA Branching Polytopes","publication_year":2018,"publication_date":"2018-01-01","ids":{"openalex":"https://openalex.org/W2749289701","doi":"https://doi.org/10.1137/17m1144076","mag":"2749289701"},"language":"en","primary_location":{"id":"doi:10.1137/17m1144076","is_oa":true,"landing_page_url":"https://doi.org/10.1137/17m1144076","pdf_url":"https://epubs.siam.org/doi/pdf/10.1137/17M1144076","source":{"id":"https://openalex.org/S2996807011","display_name":"SIAM Journal on Applied Algebra and Geometry","issn_l":"2470-6566","issn":["2470-6566"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310320508","host_organization_name":"Society for Industrial and Applied Mathematics","host_organization_lineage":["https://openalex.org/P4310320508"],"host_organization_lineage_names":["Society for Industrial and Applied Mathematics"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"SIAM Journal on Applied Algebra and Geometry","raw_type":"journal-article"},"type":"preprint","indexed_in":["arxiv","crossref","datacite"],"open_access":{"is_oa":true,"oa_status":"bronze","oa_url":"https://epubs.siam.org/doi/pdf/10.1137/17M1144076","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5064808524","display_name":"Fidel Barrera-Cruz","orcid":null},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Fidel Barrera-Cruz","raw_affiliation_strings":[],"raw_orcid":null,"affiliations":[]},{"author_position":"middle","author":{"id":"https://openalex.org/A5075613680","display_name":"Christine Heitsch","orcid":"https://orcid.org/0000-0001-7939-5452"},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Christine Heitsch","raw_affiliation_strings":[],"raw_orcid":null,"affiliations":[]},{"author_position":"last","author":{"id":"https://openalex.org/A5078090638","display_name":"Svetlana Poznanovi\u0107","orcid":"https://orcid.org/0000-0002-8229-8220"},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Svetlana Poznanovi\u0107","raw_affiliation_strings":[],"raw_orcid":"https://orcid.org/0000-0002-8229-8220","affiliations":[]}],"institutions":[],"countries_distinct_count":0,"institutions_distinct_count":0,"corresponding_author_ids":[],"corresponding_institution_ids":[],"apc_list":null,"apc_paid":null,"fwci":0.0,"has_fulltext":false,"cited_by_count":0,"citation_normalized_percentile":{"value":0.00203516,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":null,"biblio":{"volume":"2","issue":"3","first_page":"444","last_page":"461"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10521","display_name":"RNA and protein synthesis mechanisms","score":1.0,"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/T10521","display_name":"RNA and protein synthesis mechanisms","score":1.0,"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/T10604","display_name":"RNA Research and Splicing","score":0.9994999766349792,"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":0.9973999857902527,"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/polytope","display_name":"Polytope","score":0.7960473299026489},{"id":"https://openalex.org/keywords/branching","display_name":"Branching (polymer chemistry)","score":0.7501336336135864},{"id":"https://openalex.org/keywords/parametric-statistics","display_name":"Parametric statistics","score":0.5853080749511719},{"id":"https://openalex.org/keywords/combinatorics","display_name":"Combinatorics","score":0.502821147441864},{"id":"https://openalex.org/keywords/parameter-space","display_name":"Parameter space","score":0.4864165782928467},{"id":"https://openalex.org/keywords/mathematics","display_name":"Mathematics","score":0.45154449343681335},{"id":"https://openalex.org/keywords/space","display_name":"Space (punctuation)","score":0.4398502707481384},{"id":"https://openalex.org/keywords/sequence","display_name":"Sequence (biology)","score":0.4214116036891937},{"id":"https://openalex.org/keywords/physics","display_name":"Physics","score":0.3763936758041382},{"id":"https://openalex.org/keywords/algorithm","display_name":"Algorithm","score":0.3520555794239044},{"id":"https://openalex.org/keywords/statistical-physics","display_name":"Statistical physics","score":0.327297180891037},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.29359811544418335},{"id":"https://openalex.org/keywords/geometry","display_name":"Geometry","score":0.21844017505645752},{"id":"https://openalex.org/keywords/statistics","display_name":"Statistics","score":0.119495689868927},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.1115027368068695},{"id":"https://openalex.org/keywords/chemistry","display_name":"Chemistry","score":0.10476607084274292}],"concepts":[{"id":"https://openalex.org/C145691206","wikidata":"https://www.wikidata.org/wiki/Q747980","display_name":"Polytope","level":2,"score":0.7960473299026489},{"id":"https://openalex.org/C206175624","wikidata":"https://www.wikidata.org/wiki/Q595731","display_name":"Branching (polymer chemistry)","level":2,"score":0.7501336336135864},{"id":"https://openalex.org/C117251300","wikidata":"https://www.wikidata.org/wiki/Q1849855","display_name":"Parametric statistics","level":2,"score":0.5853080749511719},{"id":"https://openalex.org/C114614502","wikidata":"https://www.wikidata.org/wiki/Q76592","display_name":"Combinatorics","level":1,"score":0.502821147441864},{"id":"https://openalex.org/C73586568","wikidata":"https://www.wikidata.org/wiki/Q2600211","display_name":"Parameter space","level":2,"score":0.4864165782928467},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.45154449343681335},{"id":"https://openalex.org/C2778572836","wikidata":"https://www.wikidata.org/wiki/Q380933","display_name":"Space (punctuation)","level":2,"score":0.4398502707481384},{"id":"https://openalex.org/C2778112365","wikidata":"https://www.wikidata.org/wiki/Q3511065","display_name":"Sequence (biology)","level":2,"score":0.4214116036891937},{"id":"https://openalex.org/C121332964","wikidata":"https://www.wikidata.org/wiki/Q413","display_name":"Physics","level":0,"score":0.3763936758041382},{"id":"https://openalex.org/C11413529","wikidata":"https://www.wikidata.org/wiki/Q8366","display_name":"Algorithm","level":1,"score":0.3520555794239044},{"id":"https://openalex.org/C121864883","wikidata":"https://www.wikidata.org/wiki/Q677916","display_name":"Statistical physics","level":1,"score":0.327297180891037},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.29359811544418335},{"id":"https://openalex.org/C2524010","wikidata":"https://www.wikidata.org/wiki/Q8087","display_name":"Geometry","level":1,"score":0.21844017505645752},{"id":"https://openalex.org/C105795698","wikidata":"https://www.wikidata.org/wiki/Q12483","display_name":"Statistics","level":1,"score":0.119495689868927},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.1115027368068695},{"id":"https://openalex.org/C185592680","wikidata":"https://www.wikidata.org/wiki/Q2329","display_name":"Chemistry","level":0,"score":0.10476607084274292},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.0},{"id":"https://openalex.org/C178790620","wikidata":"https://www.wikidata.org/wiki/Q11351","display_name":"Organic chemistry","level":1,"score":0.0},{"id":"https://openalex.org/C111919701","wikidata":"https://www.wikidata.org/wiki/Q9135","display_name":"Operating system","level":1,"score":0.0}],"mesh":[],"locations_count":4,"locations":[{"id":"doi:10.1137/17m1144076","is_oa":true,"landing_page_url":"https://doi.org/10.1137/17m1144076","pdf_url":"https://epubs.siam.org/doi/pdf/10.1137/17M1144076","source":{"id":"https://openalex.org/S2996807011","display_name":"SIAM Journal on Applied Algebra and Geometry","issn_l":"2470-6566","issn":["2470-6566"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310320508","host_organization_name":"Society for Industrial and Applied Mathematics","host_organization_lineage":["https://openalex.org/P4310320508"],"host_organization_lineage_names":["Society for Industrial and Applied Mathematics"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"SIAM Journal on Applied Algebra and Geometry","raw_type":"journal-article"},{"id":"pmh:oai:arXiv.org:1708.05554","is_oa":true,"landing_page_url":"http://arxiv.org/abs/1708.05554","pdf_url":"https://arxiv.org/pdf/1708.05554","source":{"id":"https://openalex.org/S4306400194","display_name":"arXiv (Cornell University)","issn_l":null,"issn":null,"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":"","raw_type":"text"},{"id":"mag:2749289701","is_oa":true,"landing_page_url":"https://arxiv.org/pdf/1708.05554.pdf","pdf_url":null,"source":{"id":"https://openalex.org/S4306400194","display_name":"arXiv (Cornell University)","issn_l":null,"issn":null,"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":"arXiv (Cornell University)","raw_type":null},{"id":"doi:10.48550/arxiv.1708.05554","is_oa":true,"landing_page_url":"https://doi.org/10.48550/arxiv.1708.05554","pdf_url":null,"source":{"id":"https://openalex.org/S4306400194","display_name":"arXiv (Cornell University)","issn_l":null,"issn":null,"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":null,"is_accepted":false,"is_published":null,"raw_source_name":null,"raw_type":"Preprint"}],"best_oa_location":{"id":"doi:10.1137/17m1144076","is_oa":true,"landing_page_url":"https://doi.org/10.1137/17m1144076","pdf_url":"https://epubs.siam.org/doi/pdf/10.1137/17M1144076","source":{"id":"https://openalex.org/S2996807011","display_name":"SIAM Journal on Applied Algebra and Geometry","issn_l":"2470-6566","issn":["2470-6566"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310320508","host_organization_name":"Society for Industrial and Applied Mathematics","host_organization_lineage":["https://openalex.org/P4310320508"],"host_organization_lineage_names":["Society for Industrial and Applied Mathematics"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"SIAM Journal on Applied Algebra and Geometry","raw_type":"journal-article"},"sustainable_development_goals":[{"id":"https://metadata.un.org/sdg/7","display_name":"Affordable and clean energy","score":0.8999999761581421}],"awards":[{"id":"https://openalex.org/G1054332179","display_name":null,"funder_award_id":"DMS-1312817","funder_id":"https://openalex.org/F4320306076","funder_display_name":"National Science Foundation"}],"funders":[{"id":"https://openalex.org/F4320306076","display_name":"National Science Foundation","ror":"https://ror.org/021nxhr62"},{"id":"https://openalex.org/F4320306133","display_name":"Burroughs Wellcome Fund","ror":"https://ror.org/01d35cw23"}],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":19,"referenced_works":["https://openalex.org/W1559047570","https://openalex.org/W1976652160","https://openalex.org/W1990561950","https://openalex.org/W1996897910","https://openalex.org/W2009818318","https://openalex.org/W2018885841","https://openalex.org/W2025763720","https://openalex.org/W2028732503","https://openalex.org/W2054697783","https://openalex.org/W2054931730","https://openalex.org/W2058832897","https://openalex.org/W2080901145","https://openalex.org/W2102470532","https://openalex.org/W2141157874","https://openalex.org/W2142056356","https://openalex.org/W2143754824","https://openalex.org/W2159117141","https://openalex.org/W2266824739","https://openalex.org/W2619328280"],"related_works":["https://openalex.org/W1976652160","https://openalex.org/W2887286941","https://openalex.org/W2925387295","https://openalex.org/W2951586553","https://openalex.org/W2013340478","https://openalex.org/W107409705","https://openalex.org/W1969269683","https://openalex.org/W2753758382","https://openalex.org/W1971442580","https://openalex.org/W2077854862","https://openalex.org/W2417682376","https://openalex.org/W2581816322","https://openalex.org/W2321457778","https://openalex.org/W2791622405","https://openalex.org/W1967278076","https://openalex.org/W2100512869","https://openalex.org/W2055152043","https://openalex.org/W3098906174","https://openalex.org/W1999261470","https://openalex.org/W2526548757"],"abstract_inverted_index":{"The":[0],"prevalent":[1],"method":[2],"for":[3,8,102,142],"RNA":[4],"secondary":[5],"structure":[6],"prediction":[7,54],"a":[9,143],"single":[10],"sequence":[11],"is":[12,34,67],"free":[13],"energy":[14,36],"minimization":[15],"based":[16],"on":[17,55],"the":[18,26,32,35,40,50,53,56,61,64,74,78,87,89,95,110,114,121,125,132],"nearest":[19],"neighbor":[20],"thermodynamic":[21],"model":[22,33],"(NNTM).":[23],"One":[24],"of":[25,31,52,77,86,113,124,147],"least":[27],"well":[28],"developed":[29],"parts":[30,112],"function":[37,66],"assigned":[38],"to":[39,48,72],"multibranch":[41,90],"loops.":[42],"Parametric":[43],"analysis":[44],"can":[45],"be":[46],"performed":[47],"elucidate":[49],"dependence":[51],"branching":[57,79,98],"parameters":[58],"used":[59],"in":[60,138],"NNTM.":[62],"Since":[63],"objective":[65],"linear,":[68],"this":[69,107],"boils":[70],"down":[71],"analyzing":[73],"normal":[75,126],"fans":[76],"polytopes.":[80],"Here":[81],"we":[82,129],"show":[83],"that":[84,131,134],"because":[85],"way":[88],"loops":[91],"are":[92,100,135,140],"scored":[93],"under":[94],"NNTM,":[96],"certain":[97],"patterns":[99],"possible":[101],"all":[103],"sequences.":[104],"We":[105],"do":[106],"by":[108,118],"characterizing":[109],"dominant":[111],"parameter":[115],"space":[116],"obtained":[117,141],"looking":[119],"at":[120],"relevant":[122],"section":[123],"fan;":[127],"therefore,":[128],"conclude":[130],"structures":[133],"normally":[136],"found":[137],"nature":[139],"relatively":[144],"small":[145],"set":[146],"parameters.":[148]},"counts_by_year":[],"updated_date":"2026-07-01T08:55:40.977307","created_date":"2025-10-10T00:00:00"}