{"id":"https://openalex.org/W3122068707","doi":"https://doi.org/10.1109/bibm49941.2020.9313185","title":"Efficient Cryo-Electron Tomogram Simulation of Macromolecular Crowding with Application to SARS-CoV-2","display_name":"Efficient Cryo-Electron Tomogram Simulation of Macromolecular Crowding with Application to SARS-CoV-2","publication_year":2020,"publication_date":"2020-12-16","ids":{"openalex":"https://openalex.org/W3122068707","doi":"https://doi.org/10.1109/bibm49941.2020.9313185","mag":"3122068707"},"language":"en","primary_location":{"id":"doi:10.1109/bibm49941.2020.9313185","is_oa":false,"landing_page_url":"https://doi.org/10.1109/bibm49941.2020.9313185","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"2020 IEEE International Conference on Bioinformatics and Biomedicine (BIBM)","raw_type":"proceedings-article"},"type":"article","indexed_in":["crossref"],"open_access":{"is_oa":false,"oa_status":"closed","oa_url":null,"any_repository_has_fulltext":false},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5055794780","display_name":"Sinuo Liu","orcid":"https://orcid.org/0000-0003-2232-6469"},"institutions":[{"id":"https://openalex.org/I92403157","display_name":"University of Science and Technology Beijing","ror":"https://ror.org/02egmk993","country_code":"CN","type":"education","lineage":["https://openalex.org/I92403157"]}],"countries":["CN"],"is_corresponding":true,"raw_author_name":"Sinuo Liu","raw_affiliation_strings":["Beijing Advanced Innovation Center for Materials Genome Engineering, Institute of Artificial Intelligence, University of Science and Technology Beijing, Beijing, China"],"affiliations":[{"raw_affiliation_string":"Beijing Advanced Innovation Center for Materials Genome Engineering, Institute of Artificial Intelligence, University of Science and Technology Beijing, Beijing, China","institution_ids":["https://openalex.org/I92403157"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5036479507","display_name":"Yan Ma","orcid":"https://orcid.org/0000-0002-2947-9233"},"institutions":[{"id":"https://openalex.org/I82880672","display_name":"Beihang University","ror":"https://ror.org/00wk2mp56","country_code":"CN","type":"education","lineage":["https://openalex.org/I82880672"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Yan Ma","raw_affiliation_strings":["School of Computer Science, Beihang University, Beijing, China"],"affiliations":[{"raw_affiliation_string":"School of Computer Science, Beihang University, Beijing, China","institution_ids":["https://openalex.org/I82880672"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5009624071","display_name":"Xiaojuan Ban","orcid":"https://orcid.org/0000-0001-9142-3276"},"institutions":[{"id":"https://openalex.org/I92403157","display_name":"University of Science and Technology Beijing","ror":"https://ror.org/02egmk993","country_code":"CN","type":"education","lineage":["https://openalex.org/I92403157"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Xiaojuan Ban","raw_affiliation_strings":["Beijing Key Laboratory of Knowledge Engineering for Materials Science, University of Science and Technology Beijing, Beijing, China"],"affiliations":[{"raw_affiliation_string":"Beijing Key Laboratory of Knowledge Engineering for Materials Science, University of Science and Technology Beijing, Beijing, China","institution_ids":["https://openalex.org/I92403157"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5086172600","display_name":"Xiangrui Zeng","orcid":"https://orcid.org/0000-0002-8589-4474"},"institutions":[{"id":"https://openalex.org/I74973139","display_name":"Carnegie Mellon University","ror":"https://ror.org/05x2bcf33","country_code":"US","type":"education","lineage":["https://openalex.org/I74973139"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Xiangrui Zeng","raw_affiliation_strings":["Computational Biology Department, Carnegie Mellon University, Pittsburgh, USA"],"affiliations":[{"raw_affiliation_string":"Computational Biology Department, Carnegie Mellon University, Pittsburgh, USA","institution_ids":["https://openalex.org/I74973139"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5112601740","display_name":"Vamsi Nallapareddy","orcid":null},"institutions":[{"id":"https://openalex.org/I4210101034","display_name":"Birla Institute of Technology and Science - Hyderabad Campus","ror":"https://ror.org/014ctt859","country_code":"IN","type":"education","lineage":["https://openalex.org/I4210101034","https://openalex.org/I74796645"]}],"countries":["IN"],"is_corresponding":false,"raw_author_name":"Vamsi Nallapareddy","raw_affiliation_strings":["Department of Computer Science and Information Systems, Birla Institute of Technology and Science, Hyderabad, India"],"affiliations":[{"raw_affiliation_string":"Department of Computer Science and Information Systems, Birla Institute of Technology and Science, Hyderabad, India","institution_ids":["https://openalex.org/I4210101034"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5028784013","display_name":"Ajinkya Chaudhari","orcid":null},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Ajinkya Chaudhari","raw_affiliation_strings":["Computer Engineering Department, Vishwakarma Institute of Technology, Pune, India"],"affiliations":[{"raw_affiliation_string":"Computer Engineering Department, Vishwakarma Institute of Technology, Pune, India","institution_ids":[]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5000807861","display_name":"Min Xu","orcid":"https://orcid.org/0000-0002-0881-5891"},"institutions":[{"id":"https://openalex.org/I74973139","display_name":"Carnegie Mellon University","ror":"https://ror.org/05x2bcf33","country_code":"US","type":"education","lineage":["https://openalex.org/I74973139"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Min Xu","raw_affiliation_strings":["Computational Biology Department, Carnegie Mellon University, Pittsburgh, USA"],"affiliations":[{"raw_affiliation_string":"Computational Biology Department, Carnegie Mellon University, Pittsburgh, USA","institution_ids":["https://openalex.org/I74973139"]}]}],"institutions":[],"countries_distinct_count":3,"institutions_distinct_count":7,"corresponding_author_ids":["https://openalex.org/A5055794780"],"corresponding_institution_ids":["https://openalex.org/I92403157"],"apc_list":null,"apc_paid":null,"fwci":1.3575,"has_fulltext":false,"cited_by_count":10,"citation_normalized_percentile":{"value":0.8575249,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":90,"max":97},"biblio":{"volume":null,"issue":null,"first_page":"80","last_page":"87"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T12859","display_name":"Cell Image Analysis Techniques","score":0.9991000294685364,"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"}},"topics":[{"id":"https://openalex.org/T12859","display_name":"Cell Image Analysis Techniques","score":0.9991000294685364,"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/T10857","display_name":"Advanced Electron Microscopy Techniques and Applications","score":0.9988999962806702,"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/T13114","display_name":"Image Processing Techniques and Applications","score":0.9936000108718872,"subfield":{"id":"https://openalex.org/subfields/2214","display_name":"Media Technology"},"field":{"id":"https://openalex.org/fields/22","display_name":"Engineering"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/benchmark","display_name":"Benchmark (surveying)","score":0.6936742067337036},{"id":"https://openalex.org/keywords/cryo-electron-tomography","display_name":"Cryo-electron tomography","score":0.6799298524856567},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.6643999814987183},{"id":"https://openalex.org/keywords/noise","display_name":"Noise (video)","score":0.4995853900909424},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.48883646726608276},{"id":"https://openalex.org/keywords/artificial-neural-network","display_name":"Artificial neural network","score":0.45626401901245117},{"id":"https://openalex.org/keywords/host","display_name":"Host (biology)","score":0.45320868492126465},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.4477437436580658},{"id":"https://openalex.org/keywords/severe-acute-respiratory-syndrome-coronavirus-2","display_name":"Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2)","score":0.44483867287635803},{"id":"https://openalex.org/keywords/coronavirus-disease-2019","display_name":"Coronavirus disease 2019 (COVID-19)","score":0.42489758133888245},{"id":"https://openalex.org/keywords/domain","display_name":"Domain (mathematical analysis)","score":0.4229351878166199},{"id":"https://openalex.org/keywords/pattern-recognition","display_name":"Pattern recognition (psychology)","score":0.39525866508483887},{"id":"https://openalex.org/keywords/image","display_name":"Image (mathematics)","score":0.3827633261680603},{"id":"https://openalex.org/keywords/machine-learning","display_name":"Machine learning","score":0.35747092962265015},{"id":"https://openalex.org/keywords/tomography","display_name":"Tomography","score":0.17941761016845703},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.14059704542160034},{"id":"https://openalex.org/keywords/physics","display_name":"Physics","score":0.10577595233917236}],"concepts":[{"id":"https://openalex.org/C185798385","wikidata":"https://www.wikidata.org/wiki/Q1161707","display_name":"Benchmark (surveying)","level":2,"score":0.6936742067337036},{"id":"https://openalex.org/C2777993257","wikidata":"https://www.wikidata.org/wiki/Q904576","display_name":"Cryo-electron tomography","level":3,"score":0.6799298524856567},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.6643999814987183},{"id":"https://openalex.org/C99498987","wikidata":"https://www.wikidata.org/wiki/Q2210247","display_name":"Noise (video)","level":3,"score":0.4995853900909424},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.48883646726608276},{"id":"https://openalex.org/C50644808","wikidata":"https://www.wikidata.org/wiki/Q192776","display_name":"Artificial neural network","level":2,"score":0.45626401901245117},{"id":"https://openalex.org/C126831891","wikidata":"https://www.wikidata.org/wiki/Q221673","display_name":"Host (biology)","level":2,"score":0.45320868492126465},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.4477437436580658},{"id":"https://openalex.org/C3007834351","wikidata":"https://www.wikidata.org/wiki/Q82069695","display_name":"Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2)","level":5,"score":0.44483867287635803},{"id":"https://openalex.org/C3008058167","wikidata":"https://www.wikidata.org/wiki/Q84263196","display_name":"Coronavirus disease 2019 (COVID-19)","level":4,"score":0.42489758133888245},{"id":"https://openalex.org/C36503486","wikidata":"https://www.wikidata.org/wiki/Q11235244","display_name":"Domain (mathematical analysis)","level":2,"score":0.4229351878166199},{"id":"https://openalex.org/C153180895","wikidata":"https://www.wikidata.org/wiki/Q7148389","display_name":"Pattern recognition (psychology)","level":2,"score":0.39525866508483887},{"id":"https://openalex.org/C115961682","wikidata":"https://www.wikidata.org/wiki/Q860623","display_name":"Image (mathematics)","level":2,"score":0.3827633261680603},{"id":"https://openalex.org/C119857082","wikidata":"https://www.wikidata.org/wiki/Q2539","display_name":"Machine learning","level":1,"score":0.35747092962265015},{"id":"https://openalex.org/C163716698","wikidata":"https://www.wikidata.org/wiki/Q841267","display_name":"Tomography","level":2,"score":0.17941761016845703},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.14059704542160034},{"id":"https://openalex.org/C121332964","wikidata":"https://www.wikidata.org/wiki/Q413","display_name":"Physics","level":0,"score":0.10577595233917236},{"id":"https://openalex.org/C134306372","wikidata":"https://www.wikidata.org/wiki/Q7754","display_name":"Mathematical analysis","level":1,"score":0.0},{"id":"https://openalex.org/C2779134260","wikidata":"https://www.wikidata.org/wiki/Q12136","display_name":"Disease","level":2,"score":0.0},{"id":"https://openalex.org/C524204448","wikidata":"https://www.wikidata.org/wiki/Q788926","display_name":"Infectious disease (medical specialty)","level":3,"score":0.0},{"id":"https://openalex.org/C18903297","wikidata":"https://www.wikidata.org/wiki/Q7150","display_name":"Ecology","level":1,"score":0.0},{"id":"https://openalex.org/C120665830","wikidata":"https://www.wikidata.org/wiki/Q14620","display_name":"Optics","level":1,"score":0.0},{"id":"https://openalex.org/C205649164","wikidata":"https://www.wikidata.org/wiki/Q1071","display_name":"Geography","level":0,"score":0.0},{"id":"https://openalex.org/C71924100","wikidata":"https://www.wikidata.org/wiki/Q11190","display_name":"Medicine","level":0,"score":0.0},{"id":"https://openalex.org/C142724271","wikidata":"https://www.wikidata.org/wiki/Q7208","display_name":"Pathology","level":1,"score":0.0},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.0},{"id":"https://openalex.org/C13280743","wikidata":"https://www.wikidata.org/wiki/Q131089","display_name":"Geodesy","level":1,"score":0.0}],"mesh":[],"locations_count":1,"locations":[{"id":"doi:10.1109/bibm49941.2020.9313185","is_oa":false,"landing_page_url":"https://doi.org/10.1109/bibm49941.2020.9313185","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"2020 IEEE International Conference on Bioinformatics and Biomedicine (BIBM)","raw_type":"proceedings-article"}],"best_oa_location":null,"sustainable_development_goals":[{"id":"https://metadata.un.org/sdg/3","score":0.7799999713897705,"display_name":"Good health and well-being"}],"awards":[{"id":"https://openalex.org/G2611345958","display_name":null,"funder_award_id":"61873299","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"},{"id":"https://openalex.org/G4412404415","display_name":null,"funder_award_id":"61572075","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"},{"id":"https://openalex.org/G4765083334","display_name":null,"funder_award_id":"618732","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"}],"funders":[{"id":"https://openalex.org/F4320321001","display_name":"National Natural Science Foundation of China","ror":"https://ror.org/01h0zpd94"},{"id":"https://openalex.org/F4320322725","display_name":"China Scholarship Council","ror":"https://ror.org/04atp4p48"}],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":29,"referenced_works":["https://openalex.org/W1798731098","https://openalex.org/W1974978266","https://openalex.org/W2003294049","https://openalex.org/W2028470175","https://openalex.org/W2054520331","https://openalex.org/W2061835758","https://openalex.org/W2069604928","https://openalex.org/W2115251427","https://openalex.org/W2122151115","https://openalex.org/W2123207418","https://openalex.org/W2128796372","https://openalex.org/W2147700328","https://openalex.org/W2279098554","https://openalex.org/W2404809610","https://openalex.org/W2464780468","https://openalex.org/W2523462379","https://openalex.org/W2580555377","https://openalex.org/W2591330651","https://openalex.org/W2618381588","https://openalex.org/W2765543917","https://openalex.org/W2963568497","https://openalex.org/W2988467704","https://openalex.org/W3013800395","https://openalex.org/W3036278922","https://openalex.org/W3058836816","https://openalex.org/W3085208059","https://openalex.org/W3103021984","https://openalex.org/W3122807430","https://openalex.org/W4252486092"],"related_works":["https://openalex.org/W2378211422","https://openalex.org/W2745001401","https://openalex.org/W4321353415","https://openalex.org/W2130974462","https://openalex.org/W972276598","https://openalex.org/W4246352526","https://openalex.org/W2028665553","https://openalex.org/W4230315250","https://openalex.org/W2086519370","https://openalex.org/W2087343574"],"abstract_inverted_index":{"We":[0,131],"propose":[1],"an":[2,94],"efficient":[3],"method":[4],"for":[5,58,74],"simulating":[6],"a":[7,13,23,84],"cryo-Electron":[8],"Tomography":[9],"(cryo-ET)":[10],"image":[11],"of":[12,101,117,128],"target":[14],"macromolecule":[15],"with":[16,33,68,104],"several":[17],"neighbor":[18],"macromolecules":[19],"packed":[20],"to":[21,48,124,138,147,154],"achieve":[22],"realistic":[24],"crowded":[25],"cytoplasm":[26],"content.":[27],"The":[28,79,108],"simulated":[29,98,109,142],"results":[30],"are":[31],"subtomograms":[32],"corresponding":[34],"noise-free":[35],"3D":[36],"density":[37],"maps":[38],"and":[39,46,64,120,153],"pre-specified":[40],"labels":[41,73],"(PDB":[42],"ID,":[43],"center":[44],"locations,":[45],"orientations)":[47],"assist":[49,148],"bioimage":[50],"analysis.":[51],"They":[52],"can":[53],"serve":[54],"as":[55,65],"benchmark":[56],"datasets":[57,67],"testing":[59],"developing":[60],"cryo-ET":[61,110,143,150],"analysis":[62,151],"algorithms":[63],"training":[66],"readily":[69],"available":[70],"ground":[71],"truth":[72],"learning":[75],"neural":[76],"network":[77],"models.":[78],"COVID-19":[80],"pandemic":[81],"has":[82],"sparked":[83],"global":[85],"health":[86],"crisis":[87],"that":[88,140],"severely":[89],"impacting":[90],"lives":[91],"worldwide.":[92],"As":[93],"important":[95],"application,":[96],"we":[97],"the":[99,105,114,118,121,126,149,156],"scene":[100],"SARS-CoV-2":[102],"interacting":[103],"host":[106,122],"cell.":[107],"images":[111],"clearly":[112],"showed":[113],"binding":[115],"domain":[116],"virus":[119],"cell":[123],"facilitate":[125],"research":[127],"SARS-CoV-2'":[129],"infection.":[130],"also":[132],"trained":[133],"two":[134],"different":[135,159],"classification":[136],"models":[137],"demonstrate":[139],"our":[141],"data":[144],"is":[145],"able":[146],"task":[152],"validate":[155],"performance":[157],"between":[158],"methods.":[160]},"counts_by_year":[{"year":2025,"cited_by_count":2},{"year":2024,"cited_by_count":2},{"year":2023,"cited_by_count":1},{"year":2022,"cited_by_count":2},{"year":2021,"cited_by_count":3}],"updated_date":"2026-04-21T08:09:41.155169","created_date":"2025-10-10T00:00:00"}
