{"id":"https://openalex.org/W2972528048","doi":"https://doi.org/10.1093/bioinformatics/btz644","title":"Knot_pull\u2014python package for biopolymer smoothing and knot detection","display_name":"Knot_pull\u2014python package for biopolymer smoothing and knot detection","publication_year":2019,"publication_date":"2019-08-13","ids":{"openalex":"https://openalex.org/W2972528048","doi":"https://doi.org/10.1093/bioinformatics/btz644","mag":"2972528048","pmid":"https://pubmed.ncbi.nlm.nih.gov/31504154"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/btz644","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btz644","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/36/3/953/32369835/btz644.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":"cc-by","license_id":"https://openalex.org/licenses/cc-by","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":"hybrid","oa_url":"https://academic.oup.com/bioinformatics/article-pdf/36/3/953/32369835/btz644.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5023937063","display_name":"Aleksandra I. Jarmolinska","orcid":"https://orcid.org/0000-0002-1259-3611"},"institutions":[{"id":"https://openalex.org/I4210152655","display_name":"Transition Technologies (Poland)","ror":"https://ror.org/03zcr3a74","country_code":"PL","type":"company","lineage":["https://openalex.org/I4210152655"]},{"id":"https://openalex.org/I4654613","display_name":"University of Warsaw","ror":"https://ror.org/039bjqg32","country_code":"PL","type":"education","lineage":["https://openalex.org/I4654613"]}],"countries":["PL"],"is_corresponding":true,"raw_author_name":"Aleksandra I Jarmolinska","raw_affiliation_strings":["Centre of New Technologies , Warsaw 02-097, Poland","Department of Mathematics, Informatics and Mechanics, University of Warsaw , Warsaw 02-097, Poland"],"affiliations":[{"raw_affiliation_string":"Centre of New Technologies , Warsaw 02-097, Poland","institution_ids":["https://openalex.org/I4210152655"]},{"raw_affiliation_string":"Department of Mathematics, Informatics and Mechanics, University of Warsaw , Warsaw 02-097, Poland","institution_ids":["https://openalex.org/I4654613"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5071617273","display_name":"Anna Gambin","orcid":"https://orcid.org/0000-0003-3476-3017"},"institutions":[{"id":"https://openalex.org/I4654613","display_name":"University of Warsaw","ror":"https://ror.org/039bjqg32","country_code":"PL","type":"education","lineage":["https://openalex.org/I4654613"]}],"countries":["PL"],"is_corresponding":false,"raw_author_name":"Anna Gambin","raw_affiliation_strings":["Department of Mathematics, Informatics and Mechanics, University of Warsaw , Warsaw 02-097, Poland"],"affiliations":[{"raw_affiliation_string":"Department of Mathematics, Informatics and Mechanics, University of Warsaw , Warsaw 02-097, Poland","institution_ids":["https://openalex.org/I4654613"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5013867366","display_name":"Joanna I. Su\u0142kowska","orcid":"https://orcid.org/0000-0003-2452-0724"},"institutions":[{"id":"https://openalex.org/I4210152655","display_name":"Transition Technologies (Poland)","ror":"https://ror.org/03zcr3a74","country_code":"PL","type":"company","lineage":["https://openalex.org/I4210152655"]},{"id":"https://openalex.org/I4654613","display_name":"University of Warsaw","ror":"https://ror.org/039bjqg32","country_code":"PL","type":"education","lineage":["https://openalex.org/I4654613"]}],"countries":["PL"],"is_corresponding":true,"raw_author_name":"Joanna I Sulkowska","raw_affiliation_strings":["Centre of New Technologies , Warsaw 02-097, Poland","Faculty of Chemistry, University of Warsaw, Warsaw 02-093 , Poland"],"affiliations":[{"raw_affiliation_string":"Centre of New Technologies , Warsaw 02-097, Poland","institution_ids":["https://openalex.org/I4210152655"]},{"raw_affiliation_string":"Faculty of Chemistry, University of Warsaw, Warsaw 02-093 , Poland","institution_ids":["https://openalex.org/I4654613"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":3,"corresponding_author_ids":["https://openalex.org/A5013867366","https://openalex.org/A5023937063"],"corresponding_institution_ids":["https://openalex.org/I4210152655","https://openalex.org/I4654613"],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":{"value":3618,"currency":"USD","value_usd":3618},"fwci":0.7707,"has_fulltext":false,"cited_by_count":12,"citation_normalized_percentile":{"value":0.71291375,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":90,"max":97},"biblio":{"volume":"36","issue":"3","first_page":"953","last_page":"955"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T13326","display_name":"Biochemical and Structural Characterization","score":0.9940000176429749,"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/T13326","display_name":"Biochemical and Structural Characterization","score":0.9940000176429749,"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/T11041","display_name":"Ubiquitin and proteasome pathways","score":0.9894999861717224,"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/T10617","display_name":"Cellular transport and secretion","score":0.98580002784729,"subfield":{"id":"https://openalex.org/subfields/1307","display_name":"Cell 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/python","display_name":"Python (programming language)","score":0.8458797931671143},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.7009239792823792},{"id":"https://openalex.org/keywords/knot","display_name":"Knot (papermaking)","score":0.6978693604469299},{"id":"https://openalex.org/keywords/mit-license","display_name":"MIT License","score":0.6667341589927673},{"id":"https://openalex.org/keywords/visualization","display_name":"Visualization","score":0.5271719694137573},{"id":"https://openalex.org/keywords/smoothing","display_name":"Smoothing","score":0.4852156937122345},{"id":"https://openalex.org/keywords/computer-graphics","display_name":"Computer graphics (images)","score":0.4803834557533264},{"id":"https://openalex.org/keywords/programming-language","display_name":"Programming language","score":0.46781039237976074},{"id":"https://openalex.org/keywords/trefoil-knot","display_name":"Trefoil knot","score":0.4334949851036072},{"id":"https://openalex.org/keywords/documentation","display_name":"Documentation","score":0.4201074540615082},{"id":"https://openalex.org/keywords/source-code","display_name":"Source code","score":0.41437503695487976},{"id":"https://openalex.org/keywords/theoretical-computer-science","display_name":"Theoretical computer science","score":0.32906484603881836},{"id":"https://openalex.org/keywords/software","display_name":"Software","score":0.30878734588623047},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.2969836890697479},{"id":"https://openalex.org/keywords/computer-vision","display_name":"Computer vision","score":0.18830516934394836},{"id":"https://openalex.org/keywords/knot-theory","display_name":"Knot theory","score":0.1528213620185852},{"id":"https://openalex.org/keywords/engineering","display_name":"Engineering","score":0.08649864792823792}],"concepts":[{"id":"https://openalex.org/C519991488","wikidata":"https://www.wikidata.org/wiki/Q28865","display_name":"Python (programming language)","level":2,"score":0.8458797931671143},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.7009239792823792},{"id":"https://openalex.org/C2779863119","wikidata":"https://www.wikidata.org/wiki/Q6423048","display_name":"Knot (papermaking)","level":2,"score":0.6978693604469299},{"id":"https://openalex.org/C174183944","wikidata":"https://www.wikidata.org/wiki/Q334661","display_name":"MIT License","level":3,"score":0.6667341589927673},{"id":"https://openalex.org/C36464697","wikidata":"https://www.wikidata.org/wiki/Q451553","display_name":"Visualization","level":2,"score":0.5271719694137573},{"id":"https://openalex.org/C3770464","wikidata":"https://www.wikidata.org/wiki/Q775963","display_name":"Smoothing","level":2,"score":0.4852156937122345},{"id":"https://openalex.org/C121684516","wikidata":"https://www.wikidata.org/wiki/Q7600677","display_name":"Computer graphics (images)","level":1,"score":0.4803834557533264},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.46781039237976074},{"id":"https://openalex.org/C19794929","wikidata":"https://www.wikidata.org/wiki/Q168620","display_name":"Trefoil knot","level":4,"score":0.4334949851036072},{"id":"https://openalex.org/C56666940","wikidata":"https://www.wikidata.org/wiki/Q788790","display_name":"Documentation","level":2,"score":0.4201074540615082},{"id":"https://openalex.org/C43126263","wikidata":"https://www.wikidata.org/wiki/Q128751","display_name":"Source code","level":2,"score":0.41437503695487976},{"id":"https://openalex.org/C80444323","wikidata":"https://www.wikidata.org/wiki/Q2878974","display_name":"Theoretical computer science","level":1,"score":0.32906484603881836},{"id":"https://openalex.org/C2777904410","wikidata":"https://www.wikidata.org/wiki/Q7397","display_name":"Software","level":2,"score":0.30878734588623047},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.2969836890697479},{"id":"https://openalex.org/C31972630","wikidata":"https://www.wikidata.org/wiki/Q844240","display_name":"Computer vision","level":1,"score":0.18830516934394836},{"id":"https://openalex.org/C143330242","wikidata":"https://www.wikidata.org/wiki/Q849798","display_name":"Knot theory","level":3,"score":0.1528213620185852},{"id":"https://openalex.org/C127413603","wikidata":"https://www.wikidata.org/wiki/Q11023","display_name":"Engineering","level":0,"score":0.08649864792823792},{"id":"https://openalex.org/C42360764","wikidata":"https://www.wikidata.org/wiki/Q83588","display_name":"Chemical engineering","level":1,"score":0.0}],"mesh":[{"descriptor_ui":"D001704","descriptor_name":"Biopolymers","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D001704","descriptor_name":"Biopolymers","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D001704","descriptor_name":"Biopolymers","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D011506","descriptor_name":"Proteins","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},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true}],"locations_count":3,"locations":[{"id":"doi:10.1093/bioinformatics/btz644","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btz644","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/36/3/953/32369835/btz644.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":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},{"id":"pmid:31504154","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/31504154","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:pubmedcentral.nih.gov:9883683","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/9883683","pdf_url":null,"source":{"id":"https://openalex.org/S2764455111","display_name":"PubMed Central","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":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Bioinformatics","raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1093/bioinformatics/btz644","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btz644","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/36/3/953/32369835/btz644.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":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G4458334638","display_name":null,"funder_award_id":"#2018/29/N/NZ2/02897","funder_id":"https://openalex.org/F4320322511","funder_display_name":"Narodowe Centrum Nauki"},{"id":"https://openalex.org/G8889400128","display_name":null,"funder_award_id":"#2018/29/B/ST6/00681","funder_id":"https://openalex.org/F4320322511","funder_display_name":"Narodowe Centrum Nauki"}],"funders":[{"id":"https://openalex.org/F4320322511","display_name":"Narodowe Centrum Nauki","ror":"https://ror.org/03ha2q922"}],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2972528048.pdf","grobid_xml":"https://content.openalex.org/works/W2972528048.grobid-xml"},"referenced_works_count":17,"referenced_works":["https://openalex.org/W1530495800","https://openalex.org/W1980155855","https://openalex.org/W2027638286","https://openalex.org/W2031814977","https://openalex.org/W2058630951","https://openalex.org/W2078510672","https://openalex.org/W2133301041","https://openalex.org/W2164106566","https://openalex.org/W2167104421","https://openalex.org/W2316343226","https://openalex.org/W2543748880","https://openalex.org/W2620111222","https://openalex.org/W2807115333","https://openalex.org/W2808582129","https://openalex.org/W2899044544","https://openalex.org/W2901992705","https://openalex.org/W3106049385"],"related_works":["https://openalex.org/W2132241624","https://openalex.org/W4311683883","https://openalex.org/W4221030787","https://openalex.org/W4212902261","https://openalex.org/W2790811106","https://openalex.org/W2789551765","https://openalex.org/W3097598351","https://openalex.org/W3170192653","https://openalex.org/W4287775886","https://openalex.org/W4309247532"],"abstract_inverted_index":{"Supplementary":[0],"data":[1],"are":[2],"available":[3],"at":[4],"Bioinformatics":[5],"online.":[6]},"counts_by_year":[{"year":2025,"cited_by_count":1},{"year":2024,"cited_by_count":2},{"year":2022,"cited_by_count":2},{"year":2021,"cited_by_count":3},{"year":2020,"cited_by_count":3},{"year":2019,"cited_by_count":1}],"updated_date":"2026-03-20T23:20:44.827607","created_date":"2025-10-10T00:00:00"}
