{"id":"https://openalex.org/W3004081347","doi":"https://doi.org/10.1021/acs.jcim.9b01099","title":"SPREAD: A Fully Automated Toolkit for Single-Particle Cryogenic Electron Microscopy Data 3D Reconstruction with Image-Network-Aided Orientation Assignment","display_name":"SPREAD: A Fully Automated Toolkit for Single-Particle Cryogenic Electron Microscopy Data 3D Reconstruction with Image-Network-Aided Orientation Assignment","publication_year":2020,"publication_date":"2020-01-28","ids":{"openalex":"https://openalex.org/W3004081347","doi":"https://doi.org/10.1021/acs.jcim.9b01099","mag":"3004081347","pmid":"https://pubmed.ncbi.nlm.nih.gov/31990536"},"language":"en","primary_location":{"id":"doi:10.1021/acs.jcim.9b01099","is_oa":false,"landing_page_url":"https://doi.org/10.1021/acs.jcim.9b01099","pdf_url":null,"source":{"id":"https://openalex.org/S167262187","display_name":"Journal of Chemical Information and Modeling","issn_l":"1549-9596","issn":["1549-9596","1549-960X"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310320006","host_organization_name":"American Chemical Society","host_organization_lineage":["https://openalex.org/P4310320006"],"host_organization_lineage_names":["American Chemical Society"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Journal of Chemical Information and Modeling","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","pubmed"],"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/A5017782155","display_name":"Rui Xie","orcid":"https://orcid.org/0000-0002-7805-4717"},"institutions":[{"id":"https://openalex.org/I183067930","display_name":"Shanghai Jiao Tong University","ror":"https://ror.org/0220qvk04","country_code":"CN","type":"education","lineage":["https://openalex.org/I183067930"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Rui Xie","raw_affiliation_strings":["Institute of Image Processing and Pattern Recognition and Key Laboratory of System Control and Information Processing, Ministry of Education of China, Shanghai Jiao Tong University, Shanghai 200240, China"],"affiliations":[{"raw_affiliation_string":"Institute of Image Processing and Pattern Recognition and Key Laboratory of System Control and Information Processing, Ministry of Education of China, Shanghai Jiao Tong University, Shanghai 200240, China","institution_ids":["https://openalex.org/I183067930"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5075233759","display_name":"Yuxuan Chen","orcid":"https://orcid.org/0000-0002-5701-920X"},"institutions":[{"id":"https://openalex.org/I183067930","display_name":"Shanghai Jiao Tong University","ror":"https://ror.org/0220qvk04","country_code":"CN","type":"education","lineage":["https://openalex.org/I183067930"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Yu-Xuan Chen","raw_affiliation_strings":["Institute of Image Processing and Pattern Recognition and Key Laboratory of System Control and Information Processing, Ministry of Education of China, Shanghai Jiao Tong University, Shanghai 200240, China"],"affiliations":[{"raw_affiliation_string":"Institute of Image Processing and Pattern Recognition and Key Laboratory of System Control and Information Processing, Ministry of Education of China, Shanghai Jiao Tong University, Shanghai 200240, China","institution_ids":["https://openalex.org/I183067930"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5075060388","display_name":"Jiaming Cai","orcid":null},"institutions":[{"id":"https://openalex.org/I183067930","display_name":"Shanghai Jiao Tong University","ror":"https://ror.org/0220qvk04","country_code":"CN","type":"education","lineage":["https://openalex.org/I183067930"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Jia-Ming Cai","raw_affiliation_strings":["Institute of Image Processing and Pattern Recognition and Key Laboratory of System Control and Information Processing, Ministry of Education of China, Shanghai Jiao Tong University, Shanghai 200240, China"],"affiliations":[{"raw_affiliation_string":"Institute of Image Processing and Pattern Recognition and Key Laboratory of System Control and Information Processing, Ministry of Education of China, Shanghai Jiao Tong University, Shanghai 200240, China","institution_ids":["https://openalex.org/I183067930"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5100397381","display_name":"Yang Yang","orcid":"https://orcid.org/0000-0001-5720-773X"},"institutions":[{"id":"https://openalex.org/I183067930","display_name":"Shanghai Jiao Tong University","ror":"https://ror.org/0220qvk04","country_code":"CN","type":"education","lineage":["https://openalex.org/I183067930"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Yang Yang","raw_affiliation_strings":["Department of Computer Science, Shanghai Jiao Tong University, Shanghai 200240, China"],"affiliations":[{"raw_affiliation_string":"Department of Computer Science, Shanghai Jiao Tong University, Shanghai 200240, China","institution_ids":["https://openalex.org/I183067930"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5076024045","display_name":"Hong\u2010Bin Shen","orcid":"https://orcid.org/0000-0002-4029-3325"},"institutions":[{"id":"https://openalex.org/I183067930","display_name":"Shanghai Jiao Tong University","ror":"https://ror.org/0220qvk04","country_code":"CN","type":"education","lineage":["https://openalex.org/I183067930"]}],"countries":["CN"],"is_corresponding":true,"raw_author_name":"Hong-Bin Shen","raw_affiliation_strings":["Department of Computer Science, Shanghai Jiao Tong University, Shanghai 200240, China","Institute of Image Processing and Pattern Recognition and Key Laboratory of System Control and Information Processing, Ministry of Education of China, Shanghai Jiao Tong University, Shanghai 200240, China"],"affiliations":[{"raw_affiliation_string":"Department of Computer Science, Shanghai Jiao Tong University, Shanghai 200240, China","institution_ids":["https://openalex.org/I183067930"]},{"raw_affiliation_string":"Institute of Image Processing and Pattern Recognition and Key Laboratory of System Control and Information Processing, Ministry of Education of China, Shanghai Jiao Tong University, Shanghai 200240, China","institution_ids":["https://openalex.org/I183067930"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":5,"corresponding_author_ids":["https://openalex.org/A5076024045"],"corresponding_institution_ids":["https://openalex.org/I183067930"],"apc_list":null,"apc_paid":null,"fwci":2.3676,"has_fulltext":false,"cited_by_count":18,"citation_normalized_percentile":{"value":0.89545241,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":91,"max":99},"biblio":{"volume":"60","issue":"5","first_page":"2614","last_page":"2625"},"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":1.0,"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":1.0,"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/T12039","display_name":"Electron and X-Ray Spectroscopy Techniques","score":0.9987000226974487,"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"}},{"id":"https://openalex.org/T11482","display_name":"RNA modifications and cancer","score":0.9793000221252441,"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"}}],"keywords":[{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.7359299063682556},{"id":"https://openalex.org/keywords/orientation","display_name":"Orientation (vector space)","score":0.6347272992134094},{"id":"https://openalex.org/keywords/software","display_name":"Software","score":0.6185770630836487},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.5755288600921631},{"id":"https://openalex.org/keywords/cluster-analysis","display_name":"Cluster analysis","score":0.5582413673400879},{"id":"https://openalex.org/keywords/software-suite","display_name":"Software suite","score":0.5274377465248108},{"id":"https://openalex.org/keywords/projection","display_name":"Projection (relational algebra)","score":0.5273443460464478},{"id":"https://openalex.org/keywords/workflow","display_name":"Workflow","score":0.4808681607246399},{"id":"https://openalex.org/keywords/pipeline","display_name":"Pipeline (software)","score":0.46606212854385376},{"id":"https://openalex.org/keywords/ranking","display_name":"Ranking (information retrieval)","score":0.4629244804382324},{"id":"https://openalex.org/keywords/3d-reconstruction","display_name":"3D reconstruction","score":0.4159572422504425},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.41211259365081787},{"id":"https://openalex.org/keywords/image-processing","display_name":"Image processing","score":0.4111129641532898},{"id":"https://openalex.org/keywords/computer-vision","display_name":"Computer vision","score":0.39940690994262695},{"id":"https://openalex.org/keywords/pattern-recognition","display_name":"Pattern recognition (psychology)","score":0.36156022548675537},{"id":"https://openalex.org/keywords/image","display_name":"Image (mathematics)","score":0.3034058213233948},{"id":"https://openalex.org/keywords/algorithm","display_name":"Algorithm","score":0.18931257724761963}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.7359299063682556},{"id":"https://openalex.org/C16345878","wikidata":"https://www.wikidata.org/wiki/Q107472979","display_name":"Orientation (vector space)","level":2,"score":0.6347272992134094},{"id":"https://openalex.org/C2777904410","wikidata":"https://www.wikidata.org/wiki/Q7397","display_name":"Software","level":2,"score":0.6185770630836487},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.5755288600921631},{"id":"https://openalex.org/C73555534","wikidata":"https://www.wikidata.org/wiki/Q622825","display_name":"Cluster analysis","level":2,"score":0.5582413673400879},{"id":"https://openalex.org/C2778736646","wikidata":"https://www.wikidata.org/wiki/Q1143070","display_name":"Software suite","level":3,"score":0.5274377465248108},{"id":"https://openalex.org/C57493831","wikidata":"https://www.wikidata.org/wiki/Q3134666","display_name":"Projection (relational algebra)","level":2,"score":0.5273443460464478},{"id":"https://openalex.org/C177212765","wikidata":"https://www.wikidata.org/wiki/Q627335","display_name":"Workflow","level":2,"score":0.4808681607246399},{"id":"https://openalex.org/C43521106","wikidata":"https://www.wikidata.org/wiki/Q2165493","display_name":"Pipeline (software)","level":2,"score":0.46606212854385376},{"id":"https://openalex.org/C189430467","wikidata":"https://www.wikidata.org/wiki/Q7293293","display_name":"Ranking (information retrieval)","level":2,"score":0.4629244804382324},{"id":"https://openalex.org/C109950114","wikidata":"https://www.wikidata.org/wiki/Q4464732","display_name":"3D reconstruction","level":2,"score":0.4159572422504425},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.41211259365081787},{"id":"https://openalex.org/C9417928","wikidata":"https://www.wikidata.org/wiki/Q1070689","display_name":"Image processing","level":3,"score":0.4111129641532898},{"id":"https://openalex.org/C31972630","wikidata":"https://www.wikidata.org/wiki/Q844240","display_name":"Computer vision","level":1,"score":0.39940690994262695},{"id":"https://openalex.org/C153180895","wikidata":"https://www.wikidata.org/wiki/Q7148389","display_name":"Pattern recognition (psychology)","level":2,"score":0.36156022548675537},{"id":"https://openalex.org/C115961682","wikidata":"https://www.wikidata.org/wiki/Q860623","display_name":"Image (mathematics)","level":2,"score":0.3034058213233948},{"id":"https://openalex.org/C11413529","wikidata":"https://www.wikidata.org/wiki/Q8366","display_name":"Algorithm","level":1,"score":0.18931257724761963},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.0},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.0},{"id":"https://openalex.org/C77088390","wikidata":"https://www.wikidata.org/wiki/Q8513","display_name":"Database","level":1,"score":0.0},{"id":"https://openalex.org/C2524010","wikidata":"https://www.wikidata.org/wiki/Q8087","display_name":"Geometry","level":1,"score":0.0}],"mesh":[{"descriptor_ui":"D000072760","descriptor_name":"Single Molecule Imaging","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000072760","descriptor_name":"Single Molecule Imaging","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000072760","descriptor_name":"Single Molecule Imaging","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"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":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D007091","descriptor_name":"Image Processing, Computer-Assisted","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D007091","descriptor_name":"Image Processing, Computer-Assisted","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D020285","descriptor_name":"Cryoelectron Microscopy","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D020285","descriptor_name":"Cryoelectron Microscopy","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D020285","descriptor_name":"Cryoelectron Microscopy","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D021621","descriptor_name":"Imaging, Three-Dimensional","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D021621","descriptor_name":"Imaging, Three-Dimensional","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D021621","descriptor_name":"Imaging, Three-Dimensional","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true}],"locations_count":2,"locations":[{"id":"doi:10.1021/acs.jcim.9b01099","is_oa":false,"landing_page_url":"https://doi.org/10.1021/acs.jcim.9b01099","pdf_url":null,"source":{"id":"https://openalex.org/S167262187","display_name":"Journal of Chemical Information and Modeling","issn_l":"1549-9596","issn":["1549-9596","1549-960X"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310320006","host_organization_name":"American Chemical Society","host_organization_lineage":["https://openalex.org/P4310320006"],"host_organization_lineage_names":["American Chemical Society"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Journal of Chemical Information and Modeling","raw_type":"journal-article"},{"id":"pmid:31990536","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/31990536","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":"Journal of chemical information and modeling","raw_type":null}],"best_oa_location":null,"sustainable_development_goals":[{"id":"https://metadata.un.org/sdg/9","display_name":"Industry, innovation and infrastructure","score":0.4099999964237213}],"awards":[{"id":"https://openalex.org/G3067877348","display_name":null,"funder_award_id":"61671288","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"},{"id":"https://openalex.org/G3365264765","display_name":null,"funder_award_id":"61972251","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"},{"id":"https://openalex.org/G6154466079","display_name":null,"funder_award_id":"61725302","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"},{"id":"https://openalex.org/G6436593650","display_name":null,"funder_award_id":"17JC1403500","funder_id":"https://openalex.org/F4320321885","funder_display_name":"Science and Technology Commission of Shanghai Municipality"},{"id":"https://openalex.org/G7926175694","display_name":null,"funder_award_id":"2018YFC0910500","funder_id":"https://openalex.org/F4320321540","funder_display_name":"Ministry of Science and Technology of the People's Republic 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/F4320321540","display_name":"Ministry of Science and Technology of the People's Republic of China","ror":"https://ror.org/027s68j25"},{"id":"https://openalex.org/F4320321885","display_name":"Science and Technology Commission of Shanghai Municipality","ror":"https://ror.org/03kt66j61"}],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":29,"referenced_works":["https://openalex.org/W36187607","https://openalex.org/W1630959083","https://openalex.org/W1983751391","https://openalex.org/W2001923477","https://openalex.org/W2016675163","https://openalex.org/W2039688703","https://openalex.org/W2053681566","https://openalex.org/W2070183703","https://openalex.org/W2084306157","https://openalex.org/W2085261163","https://openalex.org/W2089966385","https://openalex.org/W2100455255","https://openalex.org/W2104234755","https://openalex.org/W2123738125","https://openalex.org/W2132629607","https://openalex.org/W2163700272","https://openalex.org/W2167488177","https://openalex.org/W2212589734","https://openalex.org/W2257760214","https://openalex.org/W2278419621","https://openalex.org/W2306803009","https://openalex.org/W2564084673","https://openalex.org/W2587625522","https://openalex.org/W2742721526","https://openalex.org/W2803510301","https://openalex.org/W2887586107","https://openalex.org/W2912476907","https://openalex.org/W2952863642","https://openalex.org/W4232932184"],"related_works":["https://openalex.org/W1981780420","https://openalex.org/W2182707996","https://openalex.org/W45233828","https://openalex.org/W2964988449","https://openalex.org/W2397952901","https://openalex.org/W2029380707","https://openalex.org/W4255934811","https://openalex.org/W2465382974","https://openalex.org/W2010229520","https://openalex.org/W2547528905"],"abstract_inverted_index":{"For":[0,183],"the":[1,42,67,125,133,146,160,180,187,194,213,216,233],"past":[2],"decade,":[3],"cryogenic":[4],"electron":[5],"microscopy":[6],"(cryo-EM)":[7],"has":[8],"become":[9],"an":[10],"important":[11],"technology":[12],"to":[13,131,176],"determine":[14],"three-dimensional":[15],"(3D)":[16],"structures":[17],"of":[18,46,70,145,179,207,210,215],"biomacromolecules.":[19],"Many":[20],"software":[21,48,64,255],"tools":[22,49],"have":[23],"been":[24],"developed":[25,81],"for":[26,90,119,222,258,262],"cryo-EM":[27,38,71,91],"image":[28,61,98,121,162,203],"processing":[29,73],"and":[30,87,106,124,137,153,165,190,219,248],"3D":[31,100,107,154,195],"reconstruction,":[32],"covering":[33,66],"various":[34],"computational":[35],"tasks":[36],"in":[37,149,193,241],"data":[39,72],"analysis.":[40],"Despite":[41],"recent":[43],"progress,":[44],"most":[45],"these":[47,208],"focus":[50],"on":[51,212,232],"a":[52,82,167,201,228,237],"single":[53],"task,":[54],"such":[55],"as":[56],"automatic":[57,84,134,239],"particle":[58,188],"picking":[59],"or":[60],"clustering,":[62],"whereas":[63],"packages":[65],"whole":[68],"pipeline":[69],"are":[74,225,252],"still":[75],"few.":[76],"In":[77,109,156],"this":[78],"study,":[79],"we":[80,111,158,199],"fully":[83,238],"single-particle":[85],"reconstruction":[86],"analysis":[88],"toolkit":[89],"data,":[92],"named":[93,173],"SPREAD,":[94,110,157,198],"which":[95,242],"integrates":[96],"2D":[97,120],"classification,":[99,122],"initial":[101,150],"model":[102,104,135,151],"generation,":[103],"selection,":[105],"refinement.":[108,155],"adopt":[112],"our":[113],"previously":[114],"proposed":[115],"network-based":[116,161],"clustering":[117],"algorithm":[118],"NCEM,":[123],"reference-free":[126],"resolution":[127],"measurement":[128],"method":[129],"SRes":[130],"realize":[132],"ranking":[136],"selection":[138],"procedure.":[139],"Projection":[140],"orientation":[141,170],"assignment":[142,178],"is":[143],"one":[144],"key":[147],"steps":[148],"generation":[152],"use":[159],"similarity":[163],"metric":[164],"introduce":[166],"new":[168],"probabilistic-based":[169],"searching":[171],"method,":[172],"peak":[174],"finding,":[175],"enhance":[177],"projection":[181,191],"orientations.":[182],"dealing":[184],"with":[185],"both":[186,206],"images":[189,192,211],"refinement":[196],"using":[197],"build":[200],"mixture":[202],"network":[204],"containing":[205],"types":[209],"basis":[214],"peak-finding":[217],"results,":[218],"then":[220],"similarities":[221],"node":[223],"pairs":[224],"recomputed":[226],"by":[227],"superposed":[229],"random":[230],"walk":[231],"network.":[234],"SPREAD":[235],"achieves":[236],"workflow":[240],"nearly":[243],"no":[244],"expert":[245],"domain":[246],"knowledge":[247],"interactive":[249],"manual":[250],"operation":[251],"involved.":[253],"Our":[254],"can":[256],"accessed":[257],"free":[259],"at":[260],"http://www.csbio.sjtu.edu.cn/bioinf/SPREAD/":[261],"academic":[263],"use.":[264]},"counts_by_year":[{"year":2025,"cited_by_count":1},{"year":2023,"cited_by_count":3},{"year":2022,"cited_by_count":3},{"year":2021,"cited_by_count":8},{"year":2020,"cited_by_count":3}],"updated_date":"2025-11-06T03:46:38.306776","created_date":"2025-10-10T00:00:00"}