{"id":"https://openalex.org/W4411135761","doi":"https://doi.org/10.1093/bioinformatics/btaf205","title":"Cell Mapping Toolkit: an end-to-end pipeline for mapping subcellular organization","display_name":"Cell Mapping Toolkit: an end-to-end pipeline for mapping subcellular organization","publication_year":2025,"publication_date":"2025-06-01","ids":{"openalex":"https://openalex.org/W4411135761","doi":"https://doi.org/10.1093/bioinformatics/btaf205","pmid":"https://pubmed.ncbi.nlm.nih.gov/40489639"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/btaf205","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btaf205","pdf_url":"https://academic.oup.com/bioinformatics/advance-article-pdf/doi/10.1093/bioinformatics/btaf205/63458038/btaf205.pdf","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://academic.oup.com/bioinformatics/advance-article-pdf/doi/10.1093/bioinformatics/btaf205/63458038/btaf205.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5022990478","display_name":"Joanna Lenkiewicz","orcid":"https://orcid.org/0000-0001-7252-8638"},"institutions":[{"id":"https://openalex.org/I36258959","display_name":"University of California San Diego","ror":"https://ror.org/0168r3w48","country_code":"US","type":"education","lineage":["https://openalex.org/I36258959"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Joanna Lenkiewicz","raw_affiliation_strings":["Department of Medicine, University of California San Diego , La Jolla, CA, 92037,","Department of Medicine, University of California San Diego, La Jolla, CA, 92037, United States"],"affiliations":[{"raw_affiliation_string":"Department of Medicine, University of California San Diego , La Jolla, CA, 92037,","institution_ids":["https://openalex.org/I36258959"]},{"raw_affiliation_string":"Department of Medicine, University of California San Diego, La Jolla, CA, 92037, United States","institution_ids":["https://openalex.org/I36258959"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5008857083","display_name":"Christopher Churas","orcid":"https://orcid.org/0000-0001-9998-705X"},"institutions":[{"id":"https://openalex.org/I36258959","display_name":"University of California San Diego","ror":"https://ror.org/0168r3w48","country_code":"US","type":"education","lineage":["https://openalex.org/I36258959"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Christopher Churas","raw_affiliation_strings":["Department of Medicine, University of California San Diego , La Jolla, CA, 92037,","Department of Medicine, University of California San Diego, La Jolla, CA, 92037, United States"],"affiliations":[{"raw_affiliation_string":"Department of Medicine, University of California San Diego , La Jolla, CA, 92037,","institution_ids":["https://openalex.org/I36258959"]},{"raw_affiliation_string":"Department of Medicine, University of California San Diego, La Jolla, CA, 92037, United States","institution_ids":["https://openalex.org/I36258959"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5077208479","display_name":"Mengzhou Hu","orcid":"https://orcid.org/0000-0002-1571-8029"},"institutions":[{"id":"https://openalex.org/I36258959","display_name":"University of California San Diego","ror":"https://ror.org/0168r3w48","country_code":"US","type":"education","lineage":["https://openalex.org/I36258959"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Mengzhou Hu","raw_affiliation_strings":["Department of Medicine, University of California San Diego , La Jolla, CA, 92037,","Department of Medicine, University of California San Diego, La Jolla, CA, 92037, United States"],"affiliations":[{"raw_affiliation_string":"Department of Medicine, University of California San Diego , La Jolla, CA, 92037,","institution_ids":["https://openalex.org/I36258959"]},{"raw_affiliation_string":"Department of Medicine, University of California San Diego, La Jolla, CA, 92037, United States","institution_ids":["https://openalex.org/I36258959"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5068354417","display_name":"Gege Qian","orcid":"https://orcid.org/0000-0001-5068-0399"},"institutions":[{"id":"https://openalex.org/I36258959","display_name":"University of California San Diego","ror":"https://ror.org/0168r3w48","country_code":"US","type":"education","lineage":["https://openalex.org/I36258959"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Gege Qian","raw_affiliation_strings":["Department of Medicine, University of California San Diego , La Jolla, CA, 92037,","Department of Medicine, University of California San Diego, La Jolla, CA, 92037, United States"],"affiliations":[{"raw_affiliation_string":"Department of Medicine, University of California San Diego , La Jolla, CA, 92037,","institution_ids":["https://openalex.org/I36258959"]},{"raw_affiliation_string":"Department of Medicine, University of California San Diego, La Jolla, CA, 92037, United States","institution_ids":["https://openalex.org/I36258959"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5041216817","display_name":"Mayank Jain","orcid":"https://orcid.org/0000-0003-1176-5167"},"institutions":[{"id":"https://openalex.org/I36258959","display_name":"University of California San Diego","ror":"https://ror.org/0168r3w48","country_code":"US","type":"education","lineage":["https://openalex.org/I36258959"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Mayank Jain","raw_affiliation_strings":["Department of Medicine, University of California San Diego , La Jolla, CA, 92037,","Department of Medicine, University of California San Diego, La Jolla, CA, 92037, United States"],"affiliations":[{"raw_affiliation_string":"Department of Medicine, University of California San Diego , La Jolla, CA, 92037,","institution_ids":["https://openalex.org/I36258959"]},{"raw_affiliation_string":"Department of Medicine, University of California San Diego, La Jolla, CA, 92037, United States","institution_ids":["https://openalex.org/I36258959"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5009037241","display_name":"Maxwell Adam Levinson","orcid":"https://orcid.org/0000-0003-0384-8499"},"institutions":[{"id":"https://openalex.org/I51556381","display_name":"University of Virginia","ror":"https://ror.org/0153tk833","country_code":"US","type":"education","lineage":["https://openalex.org/I51556381"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Maxwell Adam Levinson","raw_affiliation_strings":["Department of Public Health Sciences (Biomedical Informatics), University of Virginia School of Medicine , Charlottesville, VA, 22903,","Department of Public Health Sciences (Biomedical Informatics), University of Virginia School of Medicine, Charlottesville, VA, 22903, United States"],"affiliations":[{"raw_affiliation_string":"Department of Public Health Sciences (Biomedical Informatics), University of Virginia School of Medicine , Charlottesville, VA, 22903,","institution_ids":["https://openalex.org/I51556381"]},{"raw_affiliation_string":"Department of Public Health Sciences (Biomedical Informatics), University of Virginia School of Medicine, Charlottesville, VA, 22903, United States","institution_ids":["https://openalex.org/I51556381"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5046076186","display_name":"Mohammad Sadnan Al Manir","orcid":"https://orcid.org/0000-0003-4647-3877"},"institutions":[{"id":"https://openalex.org/I51556381","display_name":"University of Virginia","ror":"https://ror.org/0153tk833","country_code":"US","type":"education","lineage":["https://openalex.org/I51556381"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Sadnan Al Manir","raw_affiliation_strings":["Department of Public Health Sciences (Biomedical Informatics), University of Virginia School of Medicine , Charlottesville, VA, 22903,","Department of Public Health Sciences (Biomedical Informatics), University of Virginia School of Medicine, Charlottesville, VA, 22903, United States"],"affiliations":[{"raw_affiliation_string":"Department of Public Health Sciences (Biomedical Informatics), University of Virginia School of Medicine , Charlottesville, VA, 22903,","institution_ids":["https://openalex.org/I51556381"]},{"raw_affiliation_string":"Department of Public Health Sciences (Biomedical Informatics), University of Virginia School of Medicine, Charlottesville, VA, 22903, United States","institution_ids":["https://openalex.org/I51556381"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5100632865","display_name":"Yue Qin","orcid":"https://orcid.org/0000-0002-0496-7134"},"institutions":[{"id":"https://openalex.org/I107606265","display_name":"Broad Institute","ror":"https://ror.org/05a0ya142","country_code":"US","type":"nonprofit","lineage":["https://openalex.org/I107606265"]},{"id":"https://openalex.org/I36258959","display_name":"University of California San Diego","ror":"https://ror.org/0168r3w48","country_code":"US","type":"education","lineage":["https://openalex.org/I36258959"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Yue Qin","raw_affiliation_strings":["Department of Medicine, University of California San Diego , La Jolla, CA, 92037,","Eric and Wendy Schmidt Center, Broad Institute of MIT and Harvard , Boston, MA, 02142,","Eric and Wendy Schmidt Center, Broad Institute of MIT and Harvard, Boston, MA, 02142, United States","Department of Medicine, University of California San Diego, La Jolla, CA, 92037, United States"],"affiliations":[{"raw_affiliation_string":"Department of Medicine, University of California San Diego , La Jolla, CA, 92037,","institution_ids":["https://openalex.org/I36258959"]},{"raw_affiliation_string":"Eric and Wendy Schmidt Center, Broad Institute of MIT and Harvard , Boston, MA, 02142,","institution_ids":["https://openalex.org/I107606265"]},{"raw_affiliation_string":"Eric and Wendy Schmidt Center, Broad Institute of MIT and Harvard, Boston, MA, 02142, United States","institution_ids":["https://openalex.org/I107606265"]},{"raw_affiliation_string":"Department of Medicine, University of California San Diego, La Jolla, CA, 92037, United States","institution_ids":["https://openalex.org/I36258959"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5075221471","display_name":"Dylan Fong","orcid":null},"institutions":[{"id":"https://openalex.org/I36258959","display_name":"University of California San Diego","ror":"https://ror.org/0168r3w48","country_code":"US","type":"education","lineage":["https://openalex.org/I36258959"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Dylan Fong","raw_affiliation_strings":["Department of Medicine, University of California San Diego , La Jolla, CA, 92037,","Department of Medicine, University of California San Diego, La Jolla, CA, 92037, United States"],"affiliations":[{"raw_affiliation_string":"Department of Medicine, University of California San Diego , La Jolla, CA, 92037,","institution_ids":["https://openalex.org/I36258959"]},{"raw_affiliation_string":"Department of Medicine, University of California San Diego, La Jolla, CA, 92037, United States","institution_ids":["https://openalex.org/I36258959"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5057223513","display_name":"Keiichiro Ono","orcid":"https://orcid.org/0000-0003-4042-3748"},"institutions":[{"id":"https://openalex.org/I36258959","display_name":"University of California San Diego","ror":"https://ror.org/0168r3w48","country_code":"US","type":"education","lineage":["https://openalex.org/I36258959"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Keiichiro Ono","raw_affiliation_strings":["Department of Medicine, University of California San Diego , La Jolla, CA, 92037,","Department of Medicine, University of California San Diego, La Jolla, CA, 92037, United States"],"affiliations":[{"raw_affiliation_string":"Department of Medicine, University of California San Diego , La Jolla, CA, 92037,","institution_ids":["https://openalex.org/I36258959"]},{"raw_affiliation_string":"Department of Medicine, University of California San Diego, La Jolla, CA, 92037, United States","institution_ids":["https://openalex.org/I36258959"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5100714128","display_name":"Jing Chen","orcid":"https://orcid.org/0000-0002-6227-7393"},"institutions":[{"id":"https://openalex.org/I36258959","display_name":"University of California San Diego","ror":"https://ror.org/0168r3w48","country_code":"US","type":"education","lineage":["https://openalex.org/I36258959"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Jing Chen","raw_affiliation_strings":["Department of Medicine, University of California San Diego , La Jolla, CA, 92037,","Department of Medicine, University of California San Diego, La Jolla, CA, 92037, United States"],"affiliations":[{"raw_affiliation_string":"Department of Medicine, University of California San Diego , La Jolla, CA, 92037,","institution_ids":["https://openalex.org/I36258959"]},{"raw_affiliation_string":"Department of Medicine, University of California San Diego, La Jolla, CA, 92037, United States","institution_ids":["https://openalex.org/I36258959"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5105346036","display_name":"Chengzhan Gao","orcid":null},"institutions":[{"id":"https://openalex.org/I36258959","display_name":"University of California San Diego","ror":"https://ror.org/0168r3w48","country_code":"US","type":"education","lineage":["https://openalex.org/I36258959"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Chengzhan Gao","raw_affiliation_strings":["Department of Medicine, University of California San Diego , La Jolla, CA, 92037,","Department of Medicine, University of California San Diego, La Jolla, CA, 92037, United States"],"affiliations":[{"raw_affiliation_string":"Department of Medicine, University of California San Diego , La Jolla, CA, 92037,","institution_ids":["https://openalex.org/I36258959"]},{"raw_affiliation_string":"Department of Medicine, University of California San Diego, La Jolla, CA, 92037, United States","institution_ids":["https://openalex.org/I36258959"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5086560457","display_name":"Dexter Pratt","orcid":null},"institutions":[{"id":"https://openalex.org/I36258959","display_name":"University of California San Diego","ror":"https://ror.org/0168r3w48","country_code":"US","type":"education","lineage":["https://openalex.org/I36258959"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Dexter Pratt","raw_affiliation_strings":["Department of Medicine, University of California San Diego , La Jolla, CA, 92037,","Department of Medicine, University of California San Diego, La Jolla, CA, 92037, United States"],"affiliations":[{"raw_affiliation_string":"Department of Medicine, University of California San Diego , La Jolla, CA, 92037,","institution_ids":["https://openalex.org/I36258959"]},{"raw_affiliation_string":"Department of Medicine, University of California San Diego, La Jolla, CA, 92037, United States","institution_ids":["https://openalex.org/I36258959"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5014273575","display_name":"Jillian A. Parker","orcid":"https://orcid.org/0000-0003-4535-3486"},"institutions":[{"id":"https://openalex.org/I36258959","display_name":"University of California San Diego","ror":"https://ror.org/0168r3w48","country_code":"US","type":"education","lineage":["https://openalex.org/I36258959"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Jillian A Parker","raw_affiliation_strings":["Department of Medicine, University of California San Diego , La Jolla, CA, 92037,","Department of Medicine, University of California San Diego, La Jolla, CA, 92037, United States"],"affiliations":[{"raw_affiliation_string":"Department of Medicine, University of California San Diego , La Jolla, CA, 92037,","institution_ids":["https://openalex.org/I36258959"]},{"raw_affiliation_string":"Department of Medicine, University of California San Diego, La Jolla, CA, 92037, United States","institution_ids":["https://openalex.org/I36258959"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5037115718","display_name":"Timothy P. Clark","orcid":"https://orcid.org/0000-0002-1562-7661"},"institutions":[{"id":"https://openalex.org/I4210134211","display_name":"University of Virginia Medical Center","ror":"https://ror.org/046kb4y45","country_code":"US","type":"healthcare","lineage":["https://openalex.org/I2799765794","https://openalex.org/I4210134211"]},{"id":"https://openalex.org/I51556381","display_name":"University of Virginia","ror":"https://ror.org/0153tk833","country_code":"US","type":"education","lineage":["https://openalex.org/I51556381"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Timothy Clark","raw_affiliation_strings":["Center for Advanced Medical Analytics, University of Virginia School of Medicine , Charlottesville, VA, 22903,","Department of Public Health Sciences (Biomedical Informatics), University of Virginia School of Medicine , Charlottesville, VA, 22903,","University of Virginia School of Data Science , Charlottesville, VA, 22903,","University of Virginia School of Data Science, Charlottesville, VA, 22903, United States"],"affiliations":[{"raw_affiliation_string":"Center for Advanced Medical Analytics, University of Virginia School of Medicine , Charlottesville, VA, 22903,","institution_ids":["https://openalex.org/I4210134211"]},{"raw_affiliation_string":"Department of Public Health Sciences (Biomedical Informatics), University of Virginia School of Medicine , Charlottesville, VA, 22903,","institution_ids":["https://openalex.org/I51556381"]},{"raw_affiliation_string":"University of Virginia School of Data Science , Charlottesville, VA, 22903,","institution_ids":["https://openalex.org/I51556381"]},{"raw_affiliation_string":"University of Virginia School of Data Science, Charlottesville, VA, 22903, United States","institution_ids":["https://openalex.org/I51556381"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5108140044","display_name":"Trey Ideker","orcid":null},"institutions":[{"id":"https://openalex.org/I36258959","display_name":"University of California San Diego","ror":"https://ror.org/0168r3w48","country_code":"US","type":"education","lineage":["https://openalex.org/I36258959"]},{"id":"https://openalex.org/I4210133661","display_name":"La Jolla Bioengineering Institute","ror":"https://ror.org/03sgbh608","country_code":"US","type":"nonprofit","lineage":["https://openalex.org/I4210133661"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Trey Ideker","raw_affiliation_strings":["Department of Bioengineering, University of California San Diego , La Jolla, CA, 92037,","Department of Computer Science and Engineering, University of California San Diego , La Jolla, CA, 92037,","Department of Medicine, University of California San Diego , La Jolla, CA, 92037,","Department of Bioengineering, University of California San Diego, La Jolla, CA, 92037, United States"],"affiliations":[{"raw_affiliation_string":"Department of Bioengineering, University of California San Diego , La Jolla, CA, 92037,","institution_ids":["https://openalex.org/I4210133661"]},{"raw_affiliation_string":"Department of Computer Science and Engineering, University of California San Diego , La Jolla, CA, 92037,","institution_ids":["https://openalex.org/I36258959"]},{"raw_affiliation_string":"Department of Medicine, University of California San Diego , La Jolla, CA, 92037,","institution_ids":["https://openalex.org/I36258959"]},{"raw_affiliation_string":"Department of Bioengineering, University of California San Diego, La Jolla, CA, 92037, United States","institution_ids":["https://openalex.org/I4210133661"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5037153498","display_name":"Leah V. Schaffer","orcid":"https://orcid.org/0000-0001-6339-9141"},"institutions":[{"id":"https://openalex.org/I36258959","display_name":"University of California San Diego","ror":"https://ror.org/0168r3w48","country_code":"US","type":"education","lineage":["https://openalex.org/I36258959"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Leah V Schaffer","raw_affiliation_strings":["Department of Medicine, University of California San Diego , La Jolla, CA, 92037,","Department of Medicine, University of California San Diego, La Jolla, CA, 92037, United States"],"affiliations":[{"raw_affiliation_string":"Department of Medicine, University of California San Diego , La Jolla, CA, 92037,","institution_ids":["https://openalex.org/I36258959"]},{"raw_affiliation_string":"Department of Medicine, University of California San Diego, La Jolla, CA, 92037, United States","institution_ids":["https://openalex.org/I36258959"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":17,"corresponding_author_ids":["https://openalex.org/A5022990478"],"corresponding_institution_ids":["https://openalex.org/I36258959"],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":{"value":3618,"currency":"USD","value_usd":3618},"fwci":0.0,"has_fulltext":true,"cited_by_count":0,"citation_normalized_percentile":{"value":0.09945804,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":null,"biblio":{"volume":"41","issue":"6","first_page":null,"last_page":null},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T12859","display_name":"Cell Image Analysis Techniques","score":0.9994999766349792,"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":0.9994999766349792,"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/T10887","display_name":"Bioinformatics and Genomic Networks","score":0.9984999895095825,"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/T11289","display_name":"Single-cell and spatial transcriptomics","score":0.9962000250816345,"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/pipeline","display_name":"Pipeline (software)","score":0.7540943026542664},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.6762556433677673},{"id":"https://openalex.org/keywords/end-to-end-principle","display_name":"End-to-end principle","score":0.4841052293777466},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.41988441348075867},{"id":"https://openalex.org/keywords/programming-language","display_name":"Programming language","score":0.21610847115516663},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.18670803308486938},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.17111530900001526}],"concepts":[{"id":"https://openalex.org/C43521106","wikidata":"https://www.wikidata.org/wiki/Q2165493","display_name":"Pipeline (software)","level":2,"score":0.7540943026542664},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.6762556433677673},{"id":"https://openalex.org/C74296488","wikidata":"https://www.wikidata.org/wiki/Q2527392","display_name":"End-to-end principle","level":2,"score":0.4841052293777466},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.41988441348075867},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.21610847115516663},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.18670803308486938},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.17111530900001526}],"mesh":[{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"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},{"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":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true}],"locations_count":3,"locations":[{"id":"doi:10.1093/bioinformatics/btaf205","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btaf205","pdf_url":"https://academic.oup.com/bioinformatics/advance-article-pdf/doi/10.1093/bioinformatics/btaf205/63458038/btaf205.pdf","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:40489639","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/40489639","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:12161986","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/12161986","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/btaf205","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btaf205","pdf_url":"https://academic.oup.com/bioinformatics/advance-article-pdf/doi/10.1093/bioinformatics/btaf205/63458038/btaf205.pdf","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/G2962227492","display_name":null,"funder_award_id":"U24 CA269436","funder_id":"https://openalex.org/F4320337351","funder_display_name":"National Cancer Institute"},{"id":"https://openalex.org/G3713180151","display_name":null,"funder_award_id":"OD032742","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"},{"id":"https://openalex.org/G4403456761","display_name":null,"funder_award_id":"Bridge2AI","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"},{"id":"https://openalex.org/G8517971519","display_name":null,"funder_award_id":"OT2 OD032742","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"}],"funders":[{"id":"https://openalex.org/F4320332161","display_name":"National Institutes of Health","ror":"https://ror.org/01cwqze88"},{"id":"https://openalex.org/F4320337348","display_name":"National Human Genome Research Institute","ror":"https://ror.org/00baak391"},{"id":"https://openalex.org/F4320337351","display_name":"National Cancer Institute","ror":"https://ror.org/040gcmg81"},{"id":"https://openalex.org/F4320338403","display_name":"Common Fund","ror":null}],"has_content":{"grobid_xml":true,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W4411135761.pdf","grobid_xml":"https://content.openalex.org/works/W4411135761.grobid-xml"},"referenced_works_count":44,"referenced_works":["https://openalex.org/W1588972287","https://openalex.org/W1611787727","https://openalex.org/W1871096589","https://openalex.org/W2069860553","https://openalex.org/W2081781433","https://openalex.org/W2103017472","https://openalex.org/W2129716198","https://openalex.org/W2143892509","https://openalex.org/W2145506897","https://openalex.org/W2155142785","https://openalex.org/W2159675211","https://openalex.org/W2561754210","https://openalex.org/W2611725166","https://openalex.org/W2613629789","https://openalex.org/W2757254843","https://openalex.org/W2900569176","https://openalex.org/W2962756421","https://openalex.org/W2991083105","https://openalex.org/W3015964336","https://openalex.org/W3022285953","https://openalex.org/W3043632588","https://openalex.org/W3119506213","https://openalex.org/W3120513454","https://openalex.org/W3154324864","https://openalex.org/W3157357317","https://openalex.org/W3173569745","https://openalex.org/W3183091789","https://openalex.org/W3203161883","https://openalex.org/W3215994910","https://openalex.org/W4205738517","https://openalex.org/W4211185070","https://openalex.org/W4220675433","https://openalex.org/W4221117452","https://openalex.org/W4281716291","https://openalex.org/W4309161067","https://openalex.org/W4323036511","https://openalex.org/W4364355678","https://openalex.org/W4386142019","https://openalex.org/W4391843691","https://openalex.org/W4396917346","https://openalex.org/W4398781551","https://openalex.org/W4404824622","https://openalex.org/W4409283701","https://openalex.org/W6635406461"],"related_works":["https://openalex.org/W4391375266","https://openalex.org/W2899084033","https://openalex.org/W2748952813","https://openalex.org/W2151749779","https://openalex.org/W3179968364","https://openalex.org/W2390279801","https://openalex.org/W4391913857","https://openalex.org/W2358668433","https://openalex.org/W4396701345","https://openalex.org/W2376932109"],"abstract_inverted_index":{"The":[0],"code":[1],"is":[2,6],"freely":[3],"available":[4],"and":[5,14],"hosted":[7],"on":[8],"GitHub":[9],"at":[10,19],"https://github.com/idekerlab/cellmaps_pipeline.":[11],"Comprehensive":[12],"documentation":[13],"practical":[15],"examples":[16],"are":[17],"provided":[18],"https://cellmaps-pipeline.readthedocs.io/.":[20]},"counts_by_year":[],"updated_date":"2026-03-27T14:29:43.386196","created_date":"2025-10-10T00:00:00"}
