{"id":"https://openalex.org/W2157125786","doi":"https://doi.org/10.1093/bioinformatics/bts160","title":"Rknots: topological analysis of knotted biopolymers with <tt>R</tt>","display_name":"Rknots: topological analysis of knotted biopolymers with <tt>R</tt>","publication_year":2012,"publication_date":"2012-04-05","ids":{"openalex":"https://openalex.org/W2157125786","doi":"https://doi.org/10.1093/bioinformatics/bts160","mag":"2157125786","pmid":"https://pubmed.ncbi.nlm.nih.gov/22492311"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/bts160","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/bts160","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/28/10/1400/16903696/bts160.pdf","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","datacite","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"bronze","oa_url":"https://academic.oup.com/bioinformatics/article-pdf/28/10/1400/16903696/bts160.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5036529265","display_name":"Federico Comoglio","orcid":"https://orcid.org/0000-0002-8970-6610"},"institutions":[{"id":"https://openalex.org/I35440088","display_name":"ETH Zurich","ror":"https://ror.org/05a28rw58","country_code":"CH","type":"education","lineage":["https://openalex.org/I2799323385","https://openalex.org/I35440088"]},{"id":"https://openalex.org/I123338534","display_name":"Universit\u00e0 degli Studi del Piemonte Orientale \u201cAmedeo Avogadro\u201d","ror":"https://ror.org/04387x656","country_code":"IT","type":"education","lineage":["https://openalex.org/I123338534"]},{"id":"https://openalex.org/I4210118307","display_name":"Life Science Zurich","ror":"https://ror.org/02jxpdd90","country_code":"CH","type":"education","lineage":["https://openalex.org/I4210118307"]}],"countries":["CH","IT"],"is_corresponding":true,"raw_author_name":"Federico Comoglio","raw_affiliation_strings":["1 Department of Biosystems Science and Engineering, ETH Zurich, Basel, CH-4058, Switzerland, 2Life Science Zurich PhD Program on Systems Biology and 3Dipartimento di Scienze del Farmaco di Novara, University of Piemonte Orientale \u201cA. Avogadro\u201d, Novara, 28100, Italy"],"affiliations":[{"raw_affiliation_string":"1 Department of Biosystems Science and Engineering, ETH Zurich, Basel, CH-4058, Switzerland, 2Life Science Zurich PhD Program on Systems Biology and 3Dipartimento di Scienze del Farmaco di Novara, University of Piemonte Orientale \u201cA. Avogadro\u201d, Novara, 28100, Italy","institution_ids":["https://openalex.org/I123338534","https://openalex.org/I4210118307","https://openalex.org/I35440088"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5080464564","display_name":"Maurizio Rinaldi","orcid":"https://orcid.org/0000-0003-1346-1634"},"institutions":[{"id":"https://openalex.org/I4210118307","display_name":"Life Science Zurich","ror":"https://ror.org/02jxpdd90","country_code":"CH","type":"education","lineage":["https://openalex.org/I4210118307"]},{"id":"https://openalex.org/I123338534","display_name":"Universit\u00e0 degli Studi del Piemonte Orientale \u201cAmedeo Avogadro\u201d","ror":"https://ror.org/04387x656","country_code":"IT","type":"education","lineage":["https://openalex.org/I123338534"]},{"id":"https://openalex.org/I35440088","display_name":"ETH Zurich","ror":"https://ror.org/05a28rw58","country_code":"CH","type":"education","lineage":["https://openalex.org/I2799323385","https://openalex.org/I35440088"]}],"countries":["CH","IT"],"is_corresponding":false,"raw_author_name":"Maurizio Rinaldi","raw_affiliation_strings":["1 Department of Biosystems Science and Engineering, ETH Zurich, Basel, CH-4058, Switzerland, 2Life Science Zurich PhD Program on Systems Biology and 3Dipartimento di Scienze del Farmaco di Novara, University of Piemonte Orientale \u201cA. Avogadro\u201d, Novara, 28100, Italy"],"affiliations":[{"raw_affiliation_string":"1 Department of Biosystems Science and Engineering, ETH Zurich, Basel, CH-4058, Switzerland, 2Life Science Zurich PhD Program on Systems Biology and 3Dipartimento di Scienze del Farmaco di Novara, University of Piemonte Orientale \u201cA. Avogadro\u201d, Novara, 28100, Italy","institution_ids":["https://openalex.org/I123338534","https://openalex.org/I4210118307","https://openalex.org/I35440088"]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":2,"corresponding_author_ids":["https://openalex.org/A5036529265"],"corresponding_institution_ids":["https://openalex.org/I123338534","https://openalex.org/I35440088","https://openalex.org/I4210118307"],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":null,"fwci":0.4323,"has_fulltext":false,"cited_by_count":5,"citation_normalized_percentile":{"value":0.64912414,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":96},"biblio":{"volume":"28","issue":"10","first_page":"1400","last_page":"1401"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10304","display_name":"Geometric and Algebraic Topology","score":0.9853000044822693,"subfield":{"id":"https://openalex.org/subfields/2608","display_name":"Geometry and Topology"},"field":{"id":"https://openalex.org/fields/26","display_name":"Mathematics"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}},"topics":[{"id":"https://openalex.org/T10304","display_name":"Geometric and Algebraic Topology","score":0.9853000044822693,"subfield":{"id":"https://openalex.org/subfields/2608","display_name":"Geometry and Topology"},"field":{"id":"https://openalex.org/fields/26","display_name":"Mathematics"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}},{"id":"https://openalex.org/T12536","display_name":"Topological and Geometric Data Analysis","score":0.9125000238418579,"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/visualization","display_name":"Visualization","score":0.7309908866882324},{"id":"https://openalex.org/keywords/preprocessor","display_name":"Preprocessor","score":0.6988770365715027},{"id":"https://openalex.org/keywords/simple","display_name":"Simple (philosophy)","score":0.638900637626648},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.5770571231842041},{"id":"https://openalex.org/keywords/syntax","display_name":"Syntax","score":0.5700728297233582},{"id":"https://openalex.org/keywords/topology","display_name":"Topology (electrical circuits)","score":0.5302094221115112},{"id":"https://openalex.org/keywords/topological-data-analysis","display_name":"Topological data analysis","score":0.5110682249069214},{"id":"https://openalex.org/keywords/characterization","display_name":"Characterization (materials science)","score":0.47480738162994385},{"id":"https://openalex.org/keywords/algorithm","display_name":"Algorithm","score":0.23872536420822144},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.23430979251861572},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.2323545217514038},{"id":"https://openalex.org/keywords/mathematics","display_name":"Mathematics","score":0.22728806734085083},{"id":"https://openalex.org/keywords/nanotechnology","display_name":"Nanotechnology","score":0.12896904349327087},{"id":"https://openalex.org/keywords/combinatorics","display_name":"Combinatorics","score":0.10940337181091309},{"id":"https://openalex.org/keywords/materials-science","display_name":"Materials science","score":0.09348174929618835}],"concepts":[{"id":"https://openalex.org/C36464697","wikidata":"https://www.wikidata.org/wiki/Q451553","display_name":"Visualization","level":2,"score":0.7309908866882324},{"id":"https://openalex.org/C34736171","wikidata":"https://www.wikidata.org/wiki/Q918333","display_name":"Preprocessor","level":2,"score":0.6988770365715027},{"id":"https://openalex.org/C2780586882","wikidata":"https://www.wikidata.org/wiki/Q7520643","display_name":"Simple (philosophy)","level":2,"score":0.638900637626648},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.5770571231842041},{"id":"https://openalex.org/C60048249","wikidata":"https://www.wikidata.org/wiki/Q37437","display_name":"Syntax","level":2,"score":0.5700728297233582},{"id":"https://openalex.org/C184720557","wikidata":"https://www.wikidata.org/wiki/Q7825049","display_name":"Topology (electrical circuits)","level":2,"score":0.5302094221115112},{"id":"https://openalex.org/C2776477805","wikidata":"https://www.wikidata.org/wiki/Q4460773","display_name":"Topological data analysis","level":2,"score":0.5110682249069214},{"id":"https://openalex.org/C2780841128","wikidata":"https://www.wikidata.org/wiki/Q5073781","display_name":"Characterization (materials science)","level":2,"score":0.47480738162994385},{"id":"https://openalex.org/C11413529","wikidata":"https://www.wikidata.org/wiki/Q8366","display_name":"Algorithm","level":1,"score":0.23872536420822144},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.23430979251861572},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.2323545217514038},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.22728806734085083},{"id":"https://openalex.org/C171250308","wikidata":"https://www.wikidata.org/wiki/Q11468","display_name":"Nanotechnology","level":1,"score":0.12896904349327087},{"id":"https://openalex.org/C114614502","wikidata":"https://www.wikidata.org/wiki/Q76592","display_name":"Combinatorics","level":1,"score":0.10940337181091309},{"id":"https://openalex.org/C192562407","wikidata":"https://www.wikidata.org/wiki/Q228736","display_name":"Materials science","level":0,"score":0.09348174929618835},{"id":"https://openalex.org/C111472728","wikidata":"https://www.wikidata.org/wiki/Q9471","display_name":"Epistemology","level":1,"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":"D001704","descriptor_name":"Biopolymers","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D001704","descriptor_name":"Biopolymers","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D001704","descriptor_name":"Biopolymers","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true}],"locations_count":4,"locations":[{"id":"doi:10.1093/bioinformatics/bts160","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/bts160","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/28/10/1400/16903696/bts160.pdf","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:22492311","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/22492311","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:www.research-collection.ethz.ch:20.500.11850/48958","is_oa":true,"landing_page_url":"http://hdl.handle.net/20.500.11850/48958","pdf_url":null,"source":{"id":"https://openalex.org/S4306402302","display_name":"Repository for Publications and Research Data (ETH Zurich)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I35440088","host_organization_name":"ETH Zurich","host_organization_lineage":["https://openalex.org/I35440088"],"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":"Bioinformatics, 28 (10)","raw_type":"info:eu-repo/semantics/publishedVersion"},{"id":"doi:10.3929/ethz-b-000048958","is_oa":true,"landing_page_url":"https://doi.org/10.3929/ethz-b-000048958","pdf_url":null,"source":{"id":"https://openalex.org/S7407051236","display_name":"ETH Z\u00fcrich Research Collection","issn_l":null,"issn":[],"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":null,"is_accepted":false,"is_published":null,"raw_source_name":null,"raw_type":"article-journal"}],"best_oa_location":{"id":"doi:10.1093/bioinformatics/bts160","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/bts160","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/28/10/1400/16903696/bts160.pdf","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"},"sustainable_development_goals":[{"score":0.49000000953674316,"id":"https://metadata.un.org/sdg/9","display_name":"Industry, innovation and infrastructure"}],"awards":[],"funders":[],"has_content":{"grobid_xml":true,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2157125786.pdf","grobid_xml":"https://content.openalex.org/works/W2157125786.grobid-xml"},"referenced_works_count":15,"referenced_works":["https://openalex.org/W1974873337","https://openalex.org/W1985768873","https://openalex.org/W1988071203","https://openalex.org/W1997196750","https://openalex.org/W2028916128","https://openalex.org/W2033780266","https://openalex.org/W2050679015","https://openalex.org/W2130479394","https://openalex.org/W2135190106","https://openalex.org/W2136624897","https://openalex.org/W2153258430","https://openalex.org/W2154083418","https://openalex.org/W2154195781","https://openalex.org/W2154319440","https://openalex.org/W2316343226"],"related_works":["https://openalex.org/W3107994849","https://openalex.org/W3036427183","https://openalex.org/W4247143848","https://openalex.org/W2068608913","https://openalex.org/W2735573198","https://openalex.org/W2009883749","https://openalex.org/W29442446","https://openalex.org/W3124914020","https://openalex.org/W2896904446","https://openalex.org/W330727063"],"abstract_inverted_index":{"Rknots":[0,44],"is":[1,21,45],"a":[2,26],"flexible":[3],"R":[4],"package":[5,20],"providing":[6],"tools":[7],"for":[8,29],"the":[9],"detection":[10],"and":[11,24,32,38,40,51,62],"characterization":[12],"of":[13],"topological":[14,36,60],"knots":[15,50],"in":[16],"biological":[17],"polymers.":[18],"The":[19],"well":[22],"documented":[23],"provides":[25],"simple":[27,65],"syntax":[28],"data":[30],"import":[31],"preprocessing,":[33],"structure":[34],"reduction,":[35],"analyses":[37],"2D":[39],"3D":[41],"visualization.":[42],"Remarkably,":[43],"not":[46],"limited":[47],"to":[48,57,63],"protein":[49],"allows":[52],"researchers":[53],"from":[54],"interdisciplinary":[55],"fields":[56],"analyze":[58],"different":[59],"structures":[61],"develop":[64],"yet":[66],"fully":[67],"custom":[68],"pipelines.":[69]},"counts_by_year":[{"year":2019,"cited_by_count":1},{"year":2018,"cited_by_count":1},{"year":2017,"cited_by_count":2},{"year":2014,"cited_by_count":1}],"updated_date":"2025-11-06T03:46:38.306776","created_date":"2016-06-24T00:00:00"}
