{"id":"https://openalex.org/W3111754743","doi":"https://doi.org/10.1093/bioinformatics/btaa1019","title":"<i>MorphOT</i> : transport-based interpolation between EM maps with UCSF <i>ChimeraX</i>","display_name":"<i>MorphOT</i> : transport-based interpolation between EM maps with UCSF <i>ChimeraX</i>","publication_year":2020,"publication_date":"2020-11-25","ids":{"openalex":"https://openalex.org/W3111754743","doi":"https://doi.org/10.1093/bioinformatics/btaa1019","mag":"3111754743","pmid":"https://pubmed.ncbi.nlm.nih.gov/33325492"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/btaa1019","is_oa":false,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btaa1019","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.osti.gov/biblio/1811504","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5012815834","display_name":"Arthur Ecoffet","orcid":null},"institutions":[{"id":"https://openalex.org/I141945490","display_name":"University of British Columbia","ror":"https://ror.org/03rmrcq20","country_code":"CA","type":"education","lineage":["https://openalex.org/I141945490"]},{"id":"https://openalex.org/I142476485","display_name":"\u00c9cole Polytechnique","ror":"https://ror.org/05hy3tk52","country_code":"FR","type":"education","lineage":["https://openalex.org/I142476485","https://openalex.org/I4210145102"]}],"countries":["CA","FR"],"is_corresponding":false,"raw_author_name":"Arthur Ecoffet","raw_affiliation_strings":["Department of Applied Mathematics, Ecole Polytechnique , Palaiseau 91120, France","Department of Mathematics, University of British Columbia , Vancouver, BC V6T 1Z4, Canada"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Applied Mathematics, Ecole Polytechnique , Palaiseau 91120, France","institution_ids":["https://openalex.org/I142476485"]},{"raw_affiliation_string":"Department of Mathematics, University of British Columbia , Vancouver, BC V6T 1Z4, Canada","institution_ids":["https://openalex.org/I141945490"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5066230952","display_name":"Fr\u00e9d\u00e9ric Poitevin","orcid":"https://orcid.org/0000-0002-3181-8652"},"institutions":[{"id":"https://openalex.org/I2801935854","display_name":"SLAC National Accelerator Laboratory","ror":"https://ror.org/05gzmn429","country_code":"US","type":"facility","lineage":["https://openalex.org/I1330989302","https://openalex.org/I2801935854","https://openalex.org/I39565521","https://openalex.org/I97018004"]},{"id":"https://openalex.org/I4210136624","display_name":"Linac Coherent Light Source","ror":"https://ror.org/02vkaa689","country_code":"US","type":"facility","lineage":["https://openalex.org/I1330989302","https://openalex.org/I2801935854","https://openalex.org/I39565521","https://openalex.org/I4210136624","https://openalex.org/I97018004"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Fr\u00e9d\u00e9ric Poitevin","raw_affiliation_strings":["Department of LCLS Data Analytics, Linac Coherent Light Source, SLAC National Accelerator Laboratory , Menlo Park, CA 94025, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of LCLS Data Analytics, Linac Coherent Light Source, SLAC National Accelerator Laboratory , Menlo Park, CA 94025, USA","institution_ids":["https://openalex.org/I4210136624","https://openalex.org/I2801935854"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5012430778","display_name":"Khanh Dao Duc","orcid":"https://orcid.org/0000-0002-9685-5171"},"institutions":[{"id":"https://openalex.org/I141945490","display_name":"University of British Columbia","ror":"https://ror.org/03rmrcq20","country_code":"CA","type":"education","lineage":["https://openalex.org/I141945490"]}],"countries":["CA"],"is_corresponding":true,"raw_author_name":"Khanh Dao Duc","raw_affiliation_strings":["Department of Computer Science, University of British Columbia , Vancouver, BC V6T 1Z4, Canada","Department of Mathematics, University of British Columbia , Vancouver, BC V6T 1Z4, Canada","Department of Zoology, University of British Columbia , Vancouver, BC V6T 1Z4, Canada"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Computer Science, University of British Columbia , Vancouver, BC V6T 1Z4, Canada","institution_ids":["https://openalex.org/I141945490"]},{"raw_affiliation_string":"Department of Mathematics, University of British Columbia , Vancouver, BC V6T 1Z4, Canada","institution_ids":["https://openalex.org/I141945490"]},{"raw_affiliation_string":"Department of Zoology, University of British Columbia , Vancouver, BC V6T 1Z4, Canada","institution_ids":["https://openalex.org/I141945490"]}]}],"institutions":[],"countries_distinct_count":3,"institutions_distinct_count":3,"corresponding_author_ids":["https://openalex.org/A5012430778"],"corresponding_institution_ids":["https://openalex.org/I141945490"],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":null,"fwci":0.8636,"has_fulltext":false,"cited_by_count":9,"citation_normalized_percentile":{"value":0.82426405,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":97},"biblio":{"volume":"36","issue":"22-23","first_page":"5528","last_page":"5529"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10857","display_name":"Advanced Electron Microscopy Techniques and Applications","score":0.998199999332428,"subfield":{"id":"https://openalex.org/subfields/1315","display_name":"Structural 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/T10857","display_name":"Advanced Electron Microscopy Techniques and Applications","score":0.998199999332428,"subfield":{"id":"https://openalex.org/subfields/1315","display_name":"Structural 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/T11183","display_name":"Advanced X-ray Imaging Techniques","score":0.00019999999494757503,"subfield":{"id":"https://openalex.org/subfields/3108","display_name":"Radiation"},"field":{"id":"https://openalex.org/fields/31","display_name":"Physics and Astronomy"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}},{"id":"https://openalex.org/T12039","display_name":"Electron and X-Ray Spectroscopy Techniques","score":0.00019999999494757503,"subfield":{"id":"https://openalex.org/subfields/2508","display_name":"Surfaces, Coatings and Films"},"field":{"id":"https://openalex.org/fields/25","display_name":"Materials Science"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/morphing","display_name":"Morphing","score":0.8539438247680664},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.7668310403823853},{"id":"https://openalex.org/keywords/interpolation","display_name":"Interpolation (computer graphics)","score":0.7498056888580322},{"id":"https://openalex.org/keywords/documentation","display_name":"Documentation","score":0.5780683755874634},{"id":"https://openalex.org/keywords/code","display_name":"Code (set theory)","score":0.5435857176780701},{"id":"https://openalex.org/keywords/source-code","display_name":"Source code","score":0.5335493683815002},{"id":"https://openalex.org/keywords/software","display_name":"Software","score":0.5136660933494568},{"id":"https://openalex.org/keywords/metric","display_name":"Metric (unit)","score":0.5114537477493286},{"id":"https://openalex.org/keywords/algorithm","display_name":"Algorithm","score":0.4540945887565613},{"id":"https://openalex.org/keywords/linear-interpolation","display_name":"Linear interpolation","score":0.42846062779426575},{"id":"https://openalex.org/keywords/computer-graphics","display_name":"Computer graphics (images)","score":0.42118024826049805},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.3790683448314667},{"id":"https://openalex.org/keywords/computational-science","display_name":"Computational science","score":0.3595582842826843},{"id":"https://openalex.org/keywords/theoretical-computer-science","display_name":"Theoretical computer science","score":0.3292592465877533},{"id":"https://openalex.org/keywords/image","display_name":"Image (mathematics)","score":0.3116195797920227},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.239169180393219},{"id":"https://openalex.org/keywords/programming-language","display_name":"Programming language","score":0.19677087664604187},{"id":"https://openalex.org/keywords/pattern-recognition","display_name":"Pattern recognition (psychology)","score":0.18862545490264893},{"id":"https://openalex.org/keywords/set","display_name":"Set (abstract data type)","score":0.10575798153877258}],"concepts":[{"id":"https://openalex.org/C50637493","wikidata":"https://www.wikidata.org/wiki/Q1136781","display_name":"Morphing","level":2,"score":0.8539438247680664},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.7668310403823853},{"id":"https://openalex.org/C137800194","wikidata":"https://www.wikidata.org/wiki/Q11713455","display_name":"Interpolation (computer graphics)","level":3,"score":0.7498056888580322},{"id":"https://openalex.org/C56666940","wikidata":"https://www.wikidata.org/wiki/Q788790","display_name":"Documentation","level":2,"score":0.5780683755874634},{"id":"https://openalex.org/C2776760102","wikidata":"https://www.wikidata.org/wiki/Q5139990","display_name":"Code (set theory)","level":3,"score":0.5435857176780701},{"id":"https://openalex.org/C43126263","wikidata":"https://www.wikidata.org/wiki/Q128751","display_name":"Source code","level":2,"score":0.5335493683815002},{"id":"https://openalex.org/C2777904410","wikidata":"https://www.wikidata.org/wiki/Q7397","display_name":"Software","level":2,"score":0.5136660933494568},{"id":"https://openalex.org/C176217482","wikidata":"https://www.wikidata.org/wiki/Q860554","display_name":"Metric (unit)","level":2,"score":0.5114537477493286},{"id":"https://openalex.org/C11413529","wikidata":"https://www.wikidata.org/wiki/Q8366","display_name":"Algorithm","level":1,"score":0.4540945887565613},{"id":"https://openalex.org/C171836373","wikidata":"https://www.wikidata.org/wiki/Q2266329","display_name":"Linear interpolation","level":3,"score":0.42846062779426575},{"id":"https://openalex.org/C121684516","wikidata":"https://www.wikidata.org/wiki/Q7600677","display_name":"Computer graphics (images)","level":1,"score":0.42118024826049805},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.3790683448314667},{"id":"https://openalex.org/C459310","wikidata":"https://www.wikidata.org/wiki/Q117801","display_name":"Computational science","level":1,"score":0.3595582842826843},{"id":"https://openalex.org/C80444323","wikidata":"https://www.wikidata.org/wiki/Q2878974","display_name":"Theoretical computer science","level":1,"score":0.3292592465877533},{"id":"https://openalex.org/C115961682","wikidata":"https://www.wikidata.org/wiki/Q860623","display_name":"Image (mathematics)","level":2,"score":0.3116195797920227},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.239169180393219},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.19677087664604187},{"id":"https://openalex.org/C153180895","wikidata":"https://www.wikidata.org/wiki/Q7148389","display_name":"Pattern recognition (psychology)","level":2,"score":0.18862545490264893},{"id":"https://openalex.org/C177264268","wikidata":"https://www.wikidata.org/wiki/Q1514741","display_name":"Set (abstract data type)","level":2,"score":0.10575798153877258},{"id":"https://openalex.org/C162324750","wikidata":"https://www.wikidata.org/wiki/Q8134","display_name":"Economics","level":0,"score":0.0},{"id":"https://openalex.org/C21547014","wikidata":"https://www.wikidata.org/wiki/Q1423657","display_name":"Operations management","level":1,"score":0.0}],"mesh":[],"locations_count":3,"locations":[{"id":"doi:10.1093/bioinformatics/btaa1019","is_oa":false,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btaa1019","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:33325492","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/33325492","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:osti.gov:1811504","is_oa":true,"landing_page_url":"https://www.osti.gov/biblio/1811504","pdf_url":null,"source":{"id":"https://openalex.org/S4306402487","display_name":"OSTI OAI (U.S. Department of Energy Office of Scientific and Technical Information)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I139351228","host_organization_name":"Office of Scientific and Technical Information","host_organization_lineage":["https://openalex.org/I139351228"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":null}],"best_oa_location":{"id":"pmh:oai:osti.gov:1811504","is_oa":true,"landing_page_url":"https://www.osti.gov/biblio/1811504","pdf_url":null,"source":{"id":"https://openalex.org/S4306402487","display_name":"OSTI OAI (U.S. Department of Energy Office of Scientific and Technical Information)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I139351228","host_organization_name":"Office of Scientific and Technical Information","host_organization_lineage":["https://openalex.org/I139351228"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":null},"sustainable_development_goals":[],"awards":[],"funders":[{"id":"https://openalex.org/F4320334593","display_name":"Natural Sciences and Engineering Research Council of Canada","ror":"https://ror.org/01h531d29"}],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":10,"referenced_works":["https://openalex.org/W1993309788","https://openalex.org/W2009172320","https://openalex.org/W2039013165","https://openalex.org/W2127674094","https://openalex.org/W2344902158","https://openalex.org/W2734356283","https://openalex.org/W2763740855","https://openalex.org/W2945319909","https://openalex.org/W3003257820","https://openalex.org/W3103145119"],"related_works":["https://openalex.org/W3183609115","https://openalex.org/W2985206855","https://openalex.org/W2387056800","https://openalex.org/W2389908107","https://openalex.org/W2108850688","https://openalex.org/W2354295809","https://openalex.org/W2532653122","https://openalex.org/W2359833404","https://openalex.org/W1994390986","https://openalex.org/W2378343395"],"abstract_inverted_index":{"MOTIVATION:":[0],"Cryogenic":[1],"electron":[2],"microscopy":[3],"(cryo-EM)":[4],"offers":[5],"the":[6,28,76,98],"unique":[7],"potential":[8],"to":[9,37,42,59,71],"capture":[10],"conformational":[11],"heterogeneity,":[12,34],"by":[13],"solving":[14],"multiple":[15],"three-dimensional":[16],"classes":[17],"that":[18,68],"co-exist":[19],"within":[20],"a":[21,90],"single":[22],"cryo-EM":[23],"image":[24],"dataset.":[25],"To":[26],"investigate":[27],"extent":[29],"and":[30,48,118],"implications":[31],"of":[32,79,100],"such":[33],"we":[35],"propose":[36],"use":[38,99],"an":[39],"optimal-transport-based":[40],"metric":[41],"interpolate":[43],"barycenters":[44],"between":[45],"EM":[46],"maps":[47],"produce":[49,60],"morphing":[50],"trajectories.":[51],"RESULTS:":[52],"While":[53],"standard":[54],"linear":[55],"interpolation":[56],"mostly":[57],"fails":[58],"realistic":[61],"transitions,":[62],"our":[63],"method":[64,86],"yields":[65],"continuous":[66],"trajectories":[67],"displace":[69],"densities":[70],"morph":[72],"one":[73],"map":[74],"into":[75],"other,":[77],"instead":[78],"blending":[80],"them.":[81],"AVAILABILITY":[82],"AND":[83],"IMPLEMENTATION:":[84],"Our":[85],"is":[87,108],"implemented":[88],"as":[89],"plug-in":[91],"for":[92],"ChimeraX":[93],"called":[94],"MorphOT,":[95],"which":[96],"allows":[97],"both":[101],"CPU":[102],"or":[103],"GPU":[104],"resources.":[105],"The":[106],"code":[107],"publicly":[109],"available":[110,125],"on":[111],"GitHub":[112],"(https://github.com/kdd-ubc/MorphOT.git),":[113],"with":[114],"documentation":[115],"containing":[116],"tutorial":[117],"datasets.":[119],"SUPPLEMENTARY":[120],"INFORMATION:":[121],"Supplementary":[122],"data":[123],"are":[124],"at":[126],"Bioinformatics":[127],"online.":[128]},"counts_by_year":[{"year":2025,"cited_by_count":1},{"year":2024,"cited_by_count":2},{"year":2023,"cited_by_count":3},{"year":2022,"cited_by_count":1},{"year":2021,"cited_by_count":1},{"year":2020,"cited_by_count":1}],"updated_date":"2026-06-22T08:00:12.763002","created_date":"2020-12-21T00:00:00"}
