{"id":"https://openalex.org/W2927347551","doi":"https://doi.org/10.1093/bioinformatics/btz222","title":"Determining parameters for non-linear models of multi-loop free energy change","display_name":"Determining parameters for non-linear models of multi-loop free energy change","publication_year":2019,"publication_date":"2019-03-27","ids":{"openalex":"https://openalex.org/W2927347551","doi":"https://doi.org/10.1093/bioinformatics/btz222","mag":"2927347551","pmid":"https://pubmed.ncbi.nlm.nih.gov/30923811"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/btz222","is_oa":false,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btz222","pdf_url":null,"source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":false,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"green","oa_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/6821347","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5014798059","display_name":"Max Ward","orcid":"https://orcid.org/0000-0001-9114-7339"},"institutions":[{"id":"https://openalex.org/I177877127","display_name":"University of Western Australia","ror":"https://ror.org/047272k79","country_code":"AU","type":"education","lineage":["https://openalex.org/I177877127"]}],"countries":["AU"],"is_corresponding":true,"raw_author_name":"Max Ward","raw_affiliation_strings":["Computer Science & Software Engineering, The University of Western Australia , Crawley, WA, Australia"],"affiliations":[{"raw_affiliation_string":"Computer Science & Software Engineering, The University of Western Australia , Crawley, WA, Australia","institution_ids":["https://openalex.org/I177877127"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5086422416","display_name":"Hongying Sun","orcid":"https://orcid.org/0000-0003-3144-3544"},"institutions":[{"id":"https://openalex.org/I5388228","display_name":"University of Rochester","ror":"https://ror.org/022kthw22","country_code":"US","type":"education","lineage":["https://openalex.org/I5388228"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Hongying Sun","raw_affiliation_strings":["Center for RNA Biology, University of Rochester , Rochester, NY, USA","Department of Biochemistry & Biophysics, University of Rochester , Rochester, NY, USA"],"affiliations":[{"raw_affiliation_string":"Center for RNA Biology, University of Rochester , Rochester, NY, USA","institution_ids":["https://openalex.org/I5388228"]},{"raw_affiliation_string":"Department of Biochemistry & Biophysics, University of Rochester , Rochester, NY, USA","institution_ids":["https://openalex.org/I5388228"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5005705210","display_name":"Amitava Datta","orcid":"https://orcid.org/0000-0001-6916-7907"},"institutions":[{"id":"https://openalex.org/I177877127","display_name":"University of Western Australia","ror":"https://ror.org/047272k79","country_code":"AU","type":"education","lineage":["https://openalex.org/I177877127"]}],"countries":["AU"],"is_corresponding":false,"raw_author_name":"Amitava Datta","raw_affiliation_strings":["Computer Science & Software Engineering, The University of Western Australia , Crawley, WA, Australia"],"affiliations":[{"raw_affiliation_string":"Computer Science & Software Engineering, The University of Western Australia , Crawley, WA, Australia","institution_ids":["https://openalex.org/I177877127"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5077067779","display_name":"Michael J. Wise","orcid":"https://orcid.org/0000-0001-6559-4303"},"institutions":[{"id":"https://openalex.org/I177877127","display_name":"University of Western Australia","ror":"https://ror.org/047272k79","country_code":"AU","type":"education","lineage":["https://openalex.org/I177877127"]}],"countries":["AU"],"is_corresponding":false,"raw_author_name":"Michael Wise","raw_affiliation_strings":["Computer Science & Software Engineering, The University of Western Australia , Crawley, WA, Australia","The Marshall Centre for Infectious Diseases Research and Training, The University of Western Australia , Crawley, WA, Australia"],"affiliations":[{"raw_affiliation_string":"Computer Science & Software Engineering, The University of Western Australia , Crawley, WA, Australia","institution_ids":["https://openalex.org/I177877127"]},{"raw_affiliation_string":"The Marshall Centre for Infectious Diseases Research and Training, The University of Western Australia , Crawley, WA, Australia","institution_ids":["https://openalex.org/I177877127"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5002272329","display_name":"David H. Mathews","orcid":"https://orcid.org/0000-0002-2907-6557"},"institutions":[{"id":"https://openalex.org/I5388228","display_name":"University of Rochester","ror":"https://ror.org/022kthw22","country_code":"US","type":"education","lineage":["https://openalex.org/I5388228"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"David H Mathews","raw_affiliation_strings":["Department of Biostatistics & Computational Biology, University of Rochester , Rochester, NY, USA"],"affiliations":[{"raw_affiliation_string":"Department of Biostatistics & Computational Biology, University of Rochester , Rochester, NY, USA","institution_ids":["https://openalex.org/I5388228"]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":5,"corresponding_author_ids":["https://openalex.org/A5014798059"],"corresponding_institution_ids":["https://openalex.org/I177877127"],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":null,"fwci":0.2557,"has_fulltext":false,"cited_by_count":10,"citation_normalized_percentile":{"value":0.54771014,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":99},"biblio":{"volume":"35","issue":"21","first_page":"4298","last_page":"4306"},"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/T11482","display_name":"RNA modifications and cancer","score":0.9986000061035156,"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/T10044","display_name":"Protein Structure and Dynamics","score":0.9975000023841858,"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/computer-science","display_name":"Computer science","score":0.7020654678344727},{"id":"https://openalex.org/keywords/linear-model","display_name":"Linear model","score":0.6495349407196045},{"id":"https://openalex.org/keywords/source-code","display_name":"Source code","score":0.5568844079971313},{"id":"https://openalex.org/keywords/algorithm","display_name":"Algorithm","score":0.516288697719574},{"id":"https://openalex.org/keywords/log-linear-model","display_name":"Log-linear model","score":0.4986393451690674},{"id":"https://openalex.org/keywords/loop","display_name":"Loop (graph theory)","score":0.48808515071868896},{"id":"https://openalex.org/keywords/code","display_name":"Code (set theory)","score":0.45978668332099915},{"id":"https://openalex.org/keywords/linear-regression","display_name":"Linear regression","score":0.4489783048629761},{"id":"https://openalex.org/keywords/simple","display_name":"Simple (philosophy)","score":0.43594232201576233},{"id":"https://openalex.org/keywords/energy","display_name":"Energy (signal processing)","score":0.4187888503074646},{"id":"https://openalex.org/keywords/linear-programming","display_name":"Linear programming","score":0.41779008507728577},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.3751834034919739},{"id":"https://openalex.org/keywords/machine-learning","display_name":"Machine learning","score":0.25347915291786194},{"id":"https://openalex.org/keywords/mathematics","display_name":"Mathematics","score":0.19014251232147217},{"id":"https://openalex.org/keywords/statistics","display_name":"Statistics","score":0.07885947823524475}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.7020654678344727},{"id":"https://openalex.org/C163175372","wikidata":"https://www.wikidata.org/wiki/Q3339222","display_name":"Linear model","level":2,"score":0.6495349407196045},{"id":"https://openalex.org/C43126263","wikidata":"https://www.wikidata.org/wiki/Q128751","display_name":"Source code","level":2,"score":0.5568844079971313},{"id":"https://openalex.org/C11413529","wikidata":"https://www.wikidata.org/wiki/Q8366","display_name":"Algorithm","level":1,"score":0.516288697719574},{"id":"https://openalex.org/C70519679","wikidata":"https://www.wikidata.org/wiki/Q6666755","display_name":"Log-linear model","level":3,"score":0.4986393451690674},{"id":"https://openalex.org/C184670325","wikidata":"https://www.wikidata.org/wiki/Q512604","display_name":"Loop (graph theory)","level":2,"score":0.48808515071868896},{"id":"https://openalex.org/C2776760102","wikidata":"https://www.wikidata.org/wiki/Q5139990","display_name":"Code (set theory)","level":3,"score":0.45978668332099915},{"id":"https://openalex.org/C48921125","wikidata":"https://www.wikidata.org/wiki/Q10861030","display_name":"Linear regression","level":2,"score":0.4489783048629761},{"id":"https://openalex.org/C2780586882","wikidata":"https://www.wikidata.org/wiki/Q7520643","display_name":"Simple (philosophy)","level":2,"score":0.43594232201576233},{"id":"https://openalex.org/C186370098","wikidata":"https://www.wikidata.org/wiki/Q442787","display_name":"Energy (signal processing)","level":2,"score":0.4187888503074646},{"id":"https://openalex.org/C41045048","wikidata":"https://www.wikidata.org/wiki/Q202843","display_name":"Linear programming","level":2,"score":0.41779008507728577},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.3751834034919739},{"id":"https://openalex.org/C119857082","wikidata":"https://www.wikidata.org/wiki/Q2539","display_name":"Machine learning","level":1,"score":0.25347915291786194},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.19014251232147217},{"id":"https://openalex.org/C105795698","wikidata":"https://www.wikidata.org/wiki/Q12483","display_name":"Statistics","level":1,"score":0.07885947823524475},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.0},{"id":"https://openalex.org/C114614502","wikidata":"https://www.wikidata.org/wiki/Q76592","display_name":"Combinatorics","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},{"id":"https://openalex.org/C111472728","wikidata":"https://www.wikidata.org/wiki/Q9471","display_name":"Epistemology","level":1,"score":0.0},{"id":"https://openalex.org/C177264268","wikidata":"https://www.wikidata.org/wiki/Q1514741","display_name":"Set (abstract data type)","level":2,"score":0.0},{"id":"https://openalex.org/C138885662","wikidata":"https://www.wikidata.org/wiki/Q5891","display_name":"Philosophy","level":0,"score":0.0}],"mesh":[{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","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":"D012313","descriptor_name":"RNA","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012313","descriptor_name":"RNA","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012313","descriptor_name":"RNA","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D017711","descriptor_name":"Nonlinear Dynamics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D017711","descriptor_name":"Nonlinear Dynamics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D017711","descriptor_name":"Nonlinear Dynamics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true}],"locations_count":4,"locations":[{"id":"doi:10.1093/bioinformatics/btz222","is_oa":false,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btz222","pdf_url":null,"source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":false,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},{"id":"pmid:30923811","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/30923811","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":"Bioinformatics (Oxford, England)","raw_type":null},{"id":"pmh:oai:pure.atira.dk:openaire/41235e77-e685-4892-9c0c-27a55b954214","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/6821347","pdf_url":null,"source":{"id":"https://openalex.org/S4306402523","display_name":"UWA Profiles and Research Repository (University of Western Australia)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I177877127","host_organization_name":"The University of Western Australia","host_organization_lineage":["https://openalex.org/I177877127"],"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":"Ward-Graham, M, Sun, H, Datta, A, Wise, M J & Mathews, D 2019, 'Determining parameters for non-linear models of multi-loop free energy change', Bioinformatics, vol. 35, no. 21, pp. 4298-4306. https://doi.org/10.1093/bioinformatics/btz222","raw_type":"info:eu-repo/semantics/publishedVersion"},{"id":"pmh:oai:pure.atira.dk:publications/41235e77-e685-4892-9c0c-27a55b954214","is_oa":true,"landing_page_url":"https://research-repository.uwa.edu.au/en/publications/41235e77-e685-4892-9c0c-27a55b954214","pdf_url":null,"source":{"id":"https://openalex.org/S4306402523","display_name":"UWA Profiles and Research Repository (University of Western Australia)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I177877127","host_organization_name":"The University of Western Australia","host_organization_lineage":["https://openalex.org/I177877127"],"host_organization_lineage_names":[],"type":"repository"},"license":"other-oa","license_id":"https://openalex.org/licenses/other-oa","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Ward-Graham , M , Sun , H , Datta , A , Wise , M J & Mathews , D 2019 , ' Determining parameters for non-linear models of multi-loop free energy change ' , Bioinformatics , vol. 35 , no. 21 , pp. 4298-4306 . https://doi.org/10.1093/bioinformatics/btz222","raw_type":"article"}],"best_oa_location":{"id":"pmh:oai:pure.atira.dk:openaire/41235e77-e685-4892-9c0c-27a55b954214","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/6821347","pdf_url":null,"source":{"id":"https://openalex.org/S4306402523","display_name":"UWA Profiles and Research Repository (University of Western Australia)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I177877127","host_organization_name":"The University of Western Australia","host_organization_lineage":["https://openalex.org/I177877127"],"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":"Ward-Graham, M, Sun, H, Datta, A, Wise, M J & Mathews, D 2019, 'Determining parameters for non-linear models of multi-loop free energy change', Bioinformatics, vol. 35, no. 21, pp. 4298-4306. https://doi.org/10.1093/bioinformatics/btz222","raw_type":"info:eu-repo/semantics/publishedVersion"},"sustainable_development_goals":[{"display_name":"Affordable and clean energy","id":"https://metadata.un.org/sdg/7","score":0.9100000262260437}],"awards":[{"id":"https://openalex.org/G5804002630","display_name":null,"funder_award_id":"R01GM076485","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"}],"funders":[{"id":"https://openalex.org/F4320332161","display_name":"National Institutes of Health","ror":"https://ror.org/01cwqze88"}],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":71,"referenced_works":["https://openalex.org/W280694366","https://openalex.org/W1533227151","https://openalex.org/W1964180701","https://openalex.org/W1969761972","https://openalex.org/W1973290333","https://openalex.org/W1977937947","https://openalex.org/W1978288629","https://openalex.org/W1980410097","https://openalex.org/W1981576666","https://openalex.org/W1981777358","https://openalex.org/W1988884185","https://openalex.org/W1989454102","https://openalex.org/W1990351127","https://openalex.org/W1995403172","https://openalex.org/W2001165007","https://openalex.org/W2004874474","https://openalex.org/W2004945910","https://openalex.org/W2009818318","https://openalex.org/W2010295655","https://openalex.org/W2017302704","https://openalex.org/W2020546070","https://openalex.org/W2025763720","https://openalex.org/W2042881722","https://openalex.org/W2050110866","https://openalex.org/W2051713039","https://openalex.org/W2057850636","https://openalex.org/W2058815839","https://openalex.org/W2061158331","https://openalex.org/W2070570981","https://openalex.org/W2071883352","https://openalex.org/W2086561953","https://openalex.org/W2086779374","https://openalex.org/W2098553089","https://openalex.org/W2098571862","https://openalex.org/W2099359200","https://openalex.org/W2102017611","https://openalex.org/W2102225325","https://openalex.org/W2105950741","https://openalex.org/W2109638684","https://openalex.org/W2113816707","https://openalex.org/W2117391818","https://openalex.org/W2117819109","https://openalex.org/W2123241418","https://openalex.org/W2126163471","https://openalex.org/W2127518043","https://openalex.org/W2134453550","https://openalex.org/W2136654689","https://openalex.org/W2141157874","https://openalex.org/W2142056356","https://openalex.org/W2146721220","https://openalex.org/W2159117141","https://openalex.org/W2159401492","https://openalex.org/W2162224067","https://openalex.org/W2328479405","https://openalex.org/W2332949416","https://openalex.org/W2414122243","https://openalex.org/W2536860838","https://openalex.org/W2554065905","https://openalex.org/W2570771570","https://openalex.org/W2619328280","https://openalex.org/W2624502278","https://openalex.org/W2759571676","https://openalex.org/W3041019241","https://openalex.org/W4234687846","https://openalex.org/W4239677523","https://openalex.org/W4245270879","https://openalex.org/W4246308822","https://openalex.org/W4251866352","https://openalex.org/W4388317804","https://openalex.org/W6645688431","https://openalex.org/W6683371059"],"related_works":["https://openalex.org/W4242914513","https://openalex.org/W1499586567","https://openalex.org/W2071317420","https://openalex.org/W2093458198","https://openalex.org/W1971020382","https://openalex.org/W2568690444","https://openalex.org/W2247259409","https://openalex.org/W2794544184","https://openalex.org/W2059148462","https://openalex.org/W2181566119"],"abstract_inverted_index":{"Supplementary":[0],"data":[1],"are":[2],"available":[3],"at":[4],"Bioinformatics":[5],"online.":[6]},"counts_by_year":[{"year":2026,"cited_by_count":1},{"year":2025,"cited_by_count":3},{"year":2024,"cited_by_count":2},{"year":2023,"cited_by_count":1},{"year":2022,"cited_by_count":2},{"year":2021,"cited_by_count":1}],"updated_date":"2025-11-06T03:46:38.306776","created_date":"2025-10-10T00:00:00"}