{"id":"https://openalex.org/W4402253410","doi":"https://doi.org/10.1093/bioinformatics/btae538","title":"KnotResolver: tracking self-intersecting filaments in microscopy using directed graphs","display_name":"KnotResolver: tracking self-intersecting filaments in microscopy using directed graphs","publication_year":2024,"publication_date":"2024-09-01","ids":{"openalex":"https://openalex.org/W4402253410","doi":"https://doi.org/10.1093/bioinformatics/btae538","pmid":"https://pubmed.ncbi.nlm.nih.gov/39226176"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/btae538","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btae538","pdf_url":null,"source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":true,"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":"gold","oa_url":"https://doi.org/10.1093/bioinformatics/btae538","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5008781951","display_name":"Dhruv Khatri","orcid":"https://orcid.org/0000-0003-2139-9252"},"institutions":[{"id":"https://openalex.org/I181996519","display_name":"Indian Institute of Science Education and Research Pune","ror":"https://ror.org/028qa3n13","country_code":"IN","type":"education","lineage":["https://openalex.org/I181996519"]}],"countries":["IN"],"is_corresponding":true,"raw_author_name":"Dhruv Khatri","raw_affiliation_strings":["Division of Biology, Indian Institute of Science Education and Research Pune (IISER Pune) , Pashan, Pune, Maharashtra 411008, India"],"affiliations":[{"raw_affiliation_string":"Division of Biology, Indian Institute of Science Education and Research Pune (IISER Pune) , Pashan, Pune, Maharashtra 411008, India","institution_ids":["https://openalex.org/I181996519"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5005799447","display_name":"Shivani A. Yadav","orcid":"https://orcid.org/0000-0001-5660-3212"},"institutions":[{"id":"https://openalex.org/I181996519","display_name":"Indian Institute of Science Education and Research Pune","ror":"https://ror.org/028qa3n13","country_code":"IN","type":"education","lineage":["https://openalex.org/I181996519"]}],"countries":["IN"],"is_corresponding":false,"raw_author_name":"Shivani A Yadav","raw_affiliation_strings":["Division of Biology, Indian Institute of Science Education and Research Pune (IISER Pune) , Pashan, Pune, Maharashtra 411008, India"],"affiliations":[{"raw_affiliation_string":"Division of Biology, Indian Institute of Science Education and Research Pune (IISER Pune) , Pashan, Pune, Maharashtra 411008, India","institution_ids":["https://openalex.org/I181996519"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5074207246","display_name":"Chaitanya A. Athale","orcid":"https://orcid.org/0000-0002-9506-2153"},"institutions":[{"id":"https://openalex.org/I181996519","display_name":"Indian Institute of Science Education and Research Pune","ror":"https://ror.org/028qa3n13","country_code":"IN","type":"education","lineage":["https://openalex.org/I181996519"]}],"countries":["IN"],"is_corresponding":false,"raw_author_name":"Chaitanya A Athale","raw_affiliation_strings":["Division of Biology, Indian Institute of Science Education and Research Pune (IISER Pune) , Pashan, Pune, Maharashtra 411008, India"],"affiliations":[{"raw_affiliation_string":"Division of Biology, Indian Institute of Science Education and Research Pune (IISER Pune) , Pashan, Pune, Maharashtra 411008, India","institution_ids":["https://openalex.org/I181996519"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":3,"corresponding_author_ids":["https://openalex.org/A5008781951"],"corresponding_institution_ids":["https://openalex.org/I181996519"],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":{"value":3618,"currency":"USD","value_usd":3618},"fwci":0.3191,"has_fulltext":true,"cited_by_count":1,"citation_normalized_percentile":{"value":0.58347696,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":96,"max":98},"biblio":{"volume":"40","issue":"9","first_page":null,"last_page":null},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10492","display_name":"Microtubule and mitosis dynamics","score":0.9923999905586243,"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"}},"topics":[{"id":"https://openalex.org/T10492","display_name":"Microtubule and mitosis dynamics","score":0.9923999905586243,"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"}},{"id":"https://openalex.org/T12859","display_name":"Cell Image Analysis Techniques","score":0.9873999953269958,"subfield":{"id":"https://openalex.org/subfields/1304","display_name":"Biophysics"},"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/T11304","display_name":"Advanced Neuroimaging Techniques and Applications","score":0.9804999828338623,"subfield":{"id":"https://openalex.org/subfields/2741","display_name":"Radiology, Nuclear Medicine and Imaging"},"field":{"id":"https://openalex.org/fields/27","display_name":"Medicine"},"domain":{"id":"https://openalex.org/domains/4","display_name":"Health Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.6372029781341553},{"id":"https://openalex.org/keywords/robustness","display_name":"Robustness (evolution)","score":0.5355736017227173},{"id":"https://openalex.org/keywords/segmentation","display_name":"Segmentation","score":0.522756814956665},{"id":"https://openalex.org/keywords/pixel","display_name":"Pixel","score":0.5206517577171326},{"id":"https://openalex.org/keywords/curvature","display_name":"Curvature","score":0.49146783351898193},{"id":"https://openalex.org/keywords/computer-vision","display_name":"Computer vision","score":0.43562671542167664},{"id":"https://openalex.org/keywords/microscopy","display_name":"Microscopy","score":0.43269628286361694},{"id":"https://openalex.org/keywords/tracking","display_name":"Tracking (education)","score":0.4219665229320526},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.3946242034435272},{"id":"https://openalex.org/keywords/algorithm","display_name":"Algorithm","score":0.38684308528900146},{"id":"https://openalex.org/keywords/optics","display_name":"Optics","score":0.2991787791252136},{"id":"https://openalex.org/keywords/physics","display_name":"Physics","score":0.23245424032211304},{"id":"https://openalex.org/keywords/geometry","display_name":"Geometry","score":0.19529178738594055},{"id":"https://openalex.org/keywords/mathematics","display_name":"Mathematics","score":0.15906170010566711}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.6372029781341553},{"id":"https://openalex.org/C63479239","wikidata":"https://www.wikidata.org/wiki/Q7353546","display_name":"Robustness (evolution)","level":3,"score":0.5355736017227173},{"id":"https://openalex.org/C89600930","wikidata":"https://www.wikidata.org/wiki/Q1423946","display_name":"Segmentation","level":2,"score":0.522756814956665},{"id":"https://openalex.org/C160633673","wikidata":"https://www.wikidata.org/wiki/Q355198","display_name":"Pixel","level":2,"score":0.5206517577171326},{"id":"https://openalex.org/C195065555","wikidata":"https://www.wikidata.org/wiki/Q214881","display_name":"Curvature","level":2,"score":0.49146783351898193},{"id":"https://openalex.org/C31972630","wikidata":"https://www.wikidata.org/wiki/Q844240","display_name":"Computer vision","level":1,"score":0.43562671542167664},{"id":"https://openalex.org/C147080431","wikidata":"https://www.wikidata.org/wiki/Q1074953","display_name":"Microscopy","level":2,"score":0.43269628286361694},{"id":"https://openalex.org/C2775936607","wikidata":"https://www.wikidata.org/wiki/Q466845","display_name":"Tracking (education)","level":2,"score":0.4219665229320526},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.3946242034435272},{"id":"https://openalex.org/C11413529","wikidata":"https://www.wikidata.org/wiki/Q8366","display_name":"Algorithm","level":1,"score":0.38684308528900146},{"id":"https://openalex.org/C120665830","wikidata":"https://www.wikidata.org/wiki/Q14620","display_name":"Optics","level":1,"score":0.2991787791252136},{"id":"https://openalex.org/C121332964","wikidata":"https://www.wikidata.org/wiki/Q413","display_name":"Physics","level":0,"score":0.23245424032211304},{"id":"https://openalex.org/C2524010","wikidata":"https://www.wikidata.org/wiki/Q8087","display_name":"Geometry","level":1,"score":0.19529178738594055},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.15906170010566711},{"id":"https://openalex.org/C185592680","wikidata":"https://www.wikidata.org/wiki/Q2329","display_name":"Chemistry","level":0,"score":0.0},{"id":"https://openalex.org/C55493867","wikidata":"https://www.wikidata.org/wiki/Q7094","display_name":"Biochemistry","level":1,"score":0.0},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.0},{"id":"https://openalex.org/C15744967","wikidata":"https://www.wikidata.org/wiki/Q9418","display_name":"Psychology","level":0,"score":0.0},{"id":"https://openalex.org/C19417346","wikidata":"https://www.wikidata.org/wiki/Q7922","display_name":"Pedagogy","level":1,"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":"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":"D007091","descriptor_name":"Image Processing, Computer-Assisted","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D007091","descriptor_name":"Image Processing, Computer-Assisted","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D007091","descriptor_name":"Image Processing, Computer-Assisted","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D007091","descriptor_name":"Image Processing, Computer-Assisted","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D007091","descriptor_name":"Image Processing, Computer-Assisted","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D007091","descriptor_name":"Image Processing, Computer-Assisted","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D008853","descriptor_name":"Microscopy","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D008853","descriptor_name":"Microscopy","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D008853","descriptor_name":"Microscopy","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D008853","descriptor_name":"Microscopy","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D008853","descriptor_name":"Microscopy","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D008853","descriptor_name":"Microscopy","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D008870","descriptor_name":"Microtubules","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":true},{"descriptor_ui":"D008870","descriptor_name":"Microtubules","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":true},{"descriptor_ui":"D008870","descriptor_name":"Microtubules","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":true},{"descriptor_ui":"D008870","descriptor_name":"Microtubules","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":true},{"descriptor_ui":"D008870","descriptor_name":"Microtubules","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":true},{"descriptor_ui":"D008870","descriptor_name":"Microtubules","qualifier_ui":"Q000378","qualifier_name":"metabolism","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},{"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/btae538","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btae538","pdf_url":null,"source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":true,"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:39226176","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/39226176","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:11483626","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/11483626","pdf_url":"https://pmc.ncbi.nlm.nih.gov/articles/PMC11483626/pdf/btae538.pdf","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/btae538","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btae538","pdf_url":null,"source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":true,"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/G3628272246","display_name":null,"funder_award_id":"EMR-I","funder_id":"https://openalex.org/F4320320721","funder_display_name":"Council of Scientific and Industrial Research, India"},{"id":"https://openalex.org/G4867707873","display_name":null,"funder_award_id":"2019-EMR-I","funder_id":"https://openalex.org/F4320320721","funder_display_name":"Council of Scientific and Industrial Research, India"},{"id":"https://openalex.org/G8057753460","display_name":null,"funder_award_id":"CEFIPRA","funder_id":"https://openalex.org/F4320320717","funder_display_name":"Department of Biotechnology, Ministry of Science and Technology, India"}],"funders":[{"id":"https://openalex.org/F4320320717","display_name":"Department of Biotechnology, Ministry of Science and Technology, India","ror":"https://ror.org/03tjsyq23"},{"id":"https://openalex.org/F4320320721","display_name":"Council of Scientific and Industrial Research, India","ror":"https://ror.org/021wm7p51"},{"id":"https://openalex.org/F4320321027","display_name":"Indo-French Centre for the Promotion of Advanced Research","ror":"https://ror.org/017aem598"},{"id":"https://openalex.org/F4320327182","display_name":"Indian Institute of Science Education and Research Mohali","ror":"https://ror.org/01vztzd79"}],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":46,"referenced_works":["https://openalex.org/W1548164611","https://openalex.org/W1561442812","https://openalex.org/W1742807430","https://openalex.org/W1973218147","https://openalex.org/W1985125812","https://openalex.org/W1986598071","https://openalex.org/W1987869189","https://openalex.org/W1995510049","https://openalex.org/W2000936608","https://openalex.org/W2005751229","https://openalex.org/W2012454516","https://openalex.org/W2023772919","https://openalex.org/W2026836008","https://openalex.org/W2048733914","https://openalex.org/W2057096287","https://openalex.org/W2061864499","https://openalex.org/W2084404970","https://openalex.org/W2088022890","https://openalex.org/W2093545737","https://openalex.org/W2100614327","https://openalex.org/W2109606373","https://openalex.org/W2111210923","https://openalex.org/W2113579203","https://openalex.org/W2115378800","https://openalex.org/W2116040950","https://openalex.org/W2119916735","https://openalex.org/W2122922916","https://openalex.org/W2128160875","https://openalex.org/W2133059825","https://openalex.org/W2135069767","https://openalex.org/W2147700328","https://openalex.org/W2149374899","https://openalex.org/W2149449254","https://openalex.org/W2224555279","https://openalex.org/W2235929017","https://openalex.org/W2323063542","https://openalex.org/W2803043859","https://openalex.org/W2891602481","https://openalex.org/W2911101326","https://openalex.org/W2950572451","https://openalex.org/W3098200421","https://openalex.org/W3148916402","https://openalex.org/W4285022147","https://openalex.org/W4292343326","https://openalex.org/W4391112822","https://openalex.org/W6662437183"],"related_works":["https://openalex.org/W3135697610","https://openalex.org/W2085033728","https://openalex.org/W4285411112","https://openalex.org/W2171299904","https://openalex.org/W2084086966","https://openalex.org/W55883722","https://openalex.org/W1647606319","https://openalex.org/W2922442631","https://openalex.org/W4390494008","https://openalex.org/W2053596378"],"abstract_inverted_index":{"The":[0],"MATLAB-based":[1],"source":[2],"code":[3],"is":[4,9],"released":[5],"as":[6],"OpenSource":[7],"and":[8],"available":[10],"at":[11],"https://github.com/CyCelsLab/MTKnotResolver.":[12]},"counts_by_year":[{"year":2026,"cited_by_count":1}],"updated_date":"2026-04-10T15:06:20.359241","created_date":"2025-10-10T00:00:00"}
