{"id":"https://openalex.org/W4396814199","doi":"https://doi.org/10.1093/bib/bbae216","title":"Data-driven selection of analysis decisions in single-cell RNA-seq trajectory inference","display_name":"Data-driven selection of analysis decisions in single-cell RNA-seq trajectory inference","publication_year":2024,"publication_date":"2024-03-27","ids":{"openalex":"https://openalex.org/W4396814199","doi":"https://doi.org/10.1093/bib/bbae216","pmid":"https://pubmed.ncbi.nlm.nih.gov/38725155"},"language":"en","primary_location":{"id":"doi:10.1093/bib/bbae216","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bib/bbae216","pdf_url":"https://academic.oup.com/bib/article-pdf/25/3/bbae216/57465408/bbae216.pdf","source":{"id":"https://openalex.org/S91767247","display_name":"Briefings in Bioinformatics","issn_l":"1467-5463","issn":["1467-5463","1477-4054"],"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-nc","license_id":"https://openalex.org/licenses/cc-by-nc","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Briefings in 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/bib/article-pdf/25/3/bbae216/57465408/bbae216.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5113204364","display_name":"Xiaoru Dong","orcid":null},"institutions":[{"id":"https://openalex.org/I2800717037","display_name":"University of Florida Health","ror":"https://ror.org/04tk2gy88","country_code":"US","type":"education","lineage":["https://openalex.org/I2800717037"]},{"id":"https://openalex.org/I33213144","display_name":"University of Florida","ror":"https://ror.org/02y3ad647","country_code":"US","type":"education","lineage":["https://openalex.org/I33213144"]},{"id":"https://openalex.org/I94062374","display_name":"Florida College","ror":"https://ror.org/010bgev76","country_code":"US","type":"education","lineage":["https://openalex.org/I94062374"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Xiaoru Dong","raw_affiliation_strings":["Department of Biostatistics , College of Public Health and Health Professions, , Gainesville, FL 32610 , United States","University of Florida , College of Public Health and Health Professions, , Gainesville, FL 32610 , United States","Department of Biostatistics, College of Public Health and Health Professions, University of Florida, Gainesville, FL 32610, United States"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Biostatistics , College of Public Health and Health Professions, , Gainesville, FL 32610 , United States","institution_ids":["https://openalex.org/I2800717037"]},{"raw_affiliation_string":"University of Florida , College of Public Health and Health Professions, , Gainesville, FL 32610 , United States","institution_ids":["https://openalex.org/I94062374","https://openalex.org/I33213144"]},{"raw_affiliation_string":"Department of Biostatistics, College of Public Health and Health Professions, University of Florida, Gainesville, FL 32610, United States","institution_ids":["https://openalex.org/I33213144"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5009252068","display_name":"Jack R. Leary","orcid":null},"institutions":[{"id":"https://openalex.org/I2800717037","display_name":"University of Florida Health","ror":"https://ror.org/04tk2gy88","country_code":"US","type":"education","lineage":["https://openalex.org/I2800717037"]},{"id":"https://openalex.org/I33213144","display_name":"University of Florida","ror":"https://ror.org/02y3ad647","country_code":"US","type":"education","lineage":["https://openalex.org/I33213144"]},{"id":"https://openalex.org/I94062374","display_name":"Florida College","ror":"https://ror.org/010bgev76","country_code":"US","type":"education","lineage":["https://openalex.org/I94062374"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Jack R Leary","raw_affiliation_strings":["Department of Biostatistics , College of Public Health and Health Professions, , Gainesville, FL 32610 , United States","University of Florida , College of Public Health and Health Professions, , Gainesville, FL 32610 , United States","Department of Biostatistics, College of Public Health and Health Professions, University of Florida, Gainesville, FL 32610, United States"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Biostatistics , College of Public Health and Health Professions, , Gainesville, FL 32610 , United States","institution_ids":["https://openalex.org/I2800717037"]},{"raw_affiliation_string":"University of Florida , College of Public Health and Health Professions, , Gainesville, FL 32610 , United States","institution_ids":["https://openalex.org/I94062374","https://openalex.org/I33213144"]},{"raw_affiliation_string":"Department of Biostatistics, College of Public Health and Health Professions, University of Florida, Gainesville, FL 32610, United States","institution_ids":["https://openalex.org/I33213144"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5100719384","display_name":"Chuanhao Yang","orcid":"https://orcid.org/0009-0005-3917-167X"},"institutions":[{"id":"https://openalex.org/I2800717037","display_name":"University of Florida Health","ror":"https://ror.org/04tk2gy88","country_code":"US","type":"education","lineage":["https://openalex.org/I2800717037"]},{"id":"https://openalex.org/I33213144","display_name":"University of Florida","ror":"https://ror.org/02y3ad647","country_code":"US","type":"education","lineage":["https://openalex.org/I33213144"]},{"id":"https://openalex.org/I94062374","display_name":"Florida College","ror":"https://ror.org/010bgev76","country_code":"US","type":"education","lineage":["https://openalex.org/I94062374"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Chuanhao Yang","raw_affiliation_strings":["Department of Biostatistics , College of Public Health and Health Professions, , Gainesville, FL 32610 , United States","University of Florida , College of Public Health and Health Professions, , Gainesville, FL 32610 , United States","Department of Biostatistics, College of Public Health and Health Professions, University of Florida, Gainesville, FL 32610, United States"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Biostatistics , College of Public Health and Health Professions, , Gainesville, FL 32610 , United States","institution_ids":["https://openalex.org/I2800717037"]},{"raw_affiliation_string":"University of Florida , College of Public Health and Health Professions, , Gainesville, FL 32610 , United States","institution_ids":["https://openalex.org/I94062374","https://openalex.org/I33213144"]},{"raw_affiliation_string":"Department of Biostatistics, College of Public Health and Health Professions, University of Florida, Gainesville, FL 32610, United States","institution_ids":["https://openalex.org/I33213144"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5103006781","display_name":"Maigan A. Brusko","orcid":"https://orcid.org/0000-0002-4331-2202"},"institutions":[{"id":"https://openalex.org/I33213144","display_name":"University of Florida","ror":"https://ror.org/02y3ad647","country_code":"US","type":"education","lineage":["https://openalex.org/I33213144"]},{"id":"https://openalex.org/I94062374","display_name":"Florida College","ror":"https://ror.org/010bgev76","country_code":"US","type":"education","lineage":["https://openalex.org/I94062374"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Maigan A Brusko","raw_affiliation_strings":["Department of Pathology , Immunology, and Laboratory Medicine, College of Medicine, , Gainesville, FL 32610 , United States","Diabetes Institute, University of Florida , Gainesville, FL 32610 , United States","University of Florida , Immunology, and Laboratory Medicine, College of Medicine, , Gainesville, FL 32610 , United States"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Pathology , Immunology, and Laboratory Medicine, College of Medicine, , Gainesville, FL 32610 , United States","institution_ids":["https://openalex.org/I94062374","https://openalex.org/I33213144"]},{"raw_affiliation_string":"Diabetes Institute, University of Florida , Gainesville, FL 32610 , United States","institution_ids":["https://openalex.org/I33213144"]},{"raw_affiliation_string":"University of Florida , Immunology, and Laboratory Medicine, College of Medicine, , Gainesville, FL 32610 , United States","institution_ids":["https://openalex.org/I94062374","https://openalex.org/I33213144"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5047782710","display_name":"Todd M. Brusko","orcid":"https://orcid.org/0000-0003-2878-9296"},"institutions":[{"id":"https://openalex.org/I33213144","display_name":"University of Florida","ror":"https://ror.org/02y3ad647","country_code":"US","type":"education","lineage":["https://openalex.org/I33213144"]},{"id":"https://openalex.org/I94062374","display_name":"Florida College","ror":"https://ror.org/010bgev76","country_code":"US","type":"education","lineage":["https://openalex.org/I94062374"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Todd M Brusko","raw_affiliation_strings":["Department of Pathology , Immunology, and Laboratory Medicine, College of Medicine, , Gainesville, FL 32610 , United States","Department of Pediatrics , College of Medicine, , Gainesville, FL 32610 , United States","Diabetes Institute, University of Florida , Gainesville, FL 32610 , United States","University of Florida , College of Medicine, , Gainesville, FL 32610 , United States","University of Florida , Immunology, and Laboratory Medicine, College of Medicine, , Gainesville, FL 32610 , United States","Department of Pathology, Immunology, and Laboratory Medicine, College of Medicine, University of Florida, Gainesville, FL 32610, United States"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Pathology , Immunology, and Laboratory Medicine, College of Medicine, , Gainesville, FL 32610 , United States","institution_ids":["https://openalex.org/I94062374","https://openalex.org/I33213144"]},{"raw_affiliation_string":"Department of Pediatrics , College of Medicine, , Gainesville, FL 32610 , United States","institution_ids":["https://openalex.org/I94062374"]},{"raw_affiliation_string":"Diabetes Institute, University of Florida , Gainesville, FL 32610 , United States","institution_ids":["https://openalex.org/I33213144"]},{"raw_affiliation_string":"University of Florida , College of Medicine, , Gainesville, FL 32610 , United States","institution_ids":["https://openalex.org/I94062374","https://openalex.org/I33213144"]},{"raw_affiliation_string":"University of Florida , Immunology, and Laboratory Medicine, College of Medicine, , Gainesville, FL 32610 , United States","institution_ids":["https://openalex.org/I94062374","https://openalex.org/I33213144"]},{"raw_affiliation_string":"Department of Pathology, Immunology, and Laboratory Medicine, College of Medicine, University of Florida, Gainesville, FL 32610, United States","institution_ids":["https://openalex.org/I33213144"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5013112733","display_name":"Rhonda Bacher","orcid":"https://orcid.org/0000-0001-5787-476X"},"institutions":[{"id":"https://openalex.org/I2800717037","display_name":"University of Florida Health","ror":"https://ror.org/04tk2gy88","country_code":"US","type":"education","lineage":["https://openalex.org/I2800717037"]},{"id":"https://openalex.org/I33213144","display_name":"University of Florida","ror":"https://ror.org/02y3ad647","country_code":"US","type":"education","lineage":["https://openalex.org/I33213144"]},{"id":"https://openalex.org/I94062374","display_name":"Florida College","ror":"https://ror.org/010bgev76","country_code":"US","type":"education","lineage":["https://openalex.org/I94062374"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Rhonda Bacher","raw_affiliation_strings":["Department of Biostatistics , College of Public Health and Health Professions, , Gainesville, FL 32610 , United States","Diabetes Institute, University of Florida , Gainesville, FL 32610 , United States","University of Florida , College of Public Health and Health Professions, , Gainesville, FL 32610 , United States","Department of Biostatistics, College of Public Health and Health Professions, University of Florida, Gainesville, FL 32610, United States"],"raw_orcid":"https://orcid.org/0000-0001-5787-476X","affiliations":[{"raw_affiliation_string":"Department of Biostatistics , College of Public Health and Health Professions, , Gainesville, FL 32610 , United States","institution_ids":["https://openalex.org/I2800717037"]},{"raw_affiliation_string":"Diabetes Institute, University of Florida , Gainesville, FL 32610 , United States","institution_ids":["https://openalex.org/I33213144"]},{"raw_affiliation_string":"University of Florida , College of Public Health and Health Professions, , Gainesville, FL 32610 , United States","institution_ids":["https://openalex.org/I94062374","https://openalex.org/I33213144"]},{"raw_affiliation_string":"Department of Biostatistics, College of Public Health and Health Professions, University of Florida, Gainesville, FL 32610, United States","institution_ids":["https://openalex.org/I33213144"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":6,"corresponding_author_ids":["https://openalex.org/A5013112733"],"corresponding_institution_ids":["https://openalex.org/I2800717037","https://openalex.org/I33213144","https://openalex.org/I94062374"],"apc_list":{"value":4011,"currency":"USD","value_usd":4011},"apc_paid":{"value":4011,"currency":"USD","value_usd":4011},"fwci":1.5586,"has_fulltext":true,"cited_by_count":7,"citation_normalized_percentile":{"value":0.82162309,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":94,"max":99},"biblio":{"volume":"25","issue":"3","first_page":null,"last_page":null},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T11289","display_name":"Single-cell and spatial transcriptomics","score":0.9998999834060669,"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"}},"topics":[{"id":"https://openalex.org/T11289","display_name":"Single-cell and spatial transcriptomics","score":0.9998999834060669,"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/T12859","display_name":"Cell Image Analysis Techniques","score":0.9488000273704529,"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/T11307","display_name":"Domain Adaptation and Few-Shot Learning","score":0.946399986743927,"subfield":{"id":"https://openalex.org/subfields/1702","display_name":"Artificial Intelligence"},"field":{"id":"https://openalex.org/fields/17","display_name":"Computer Science"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/trajectory","display_name":"Trajectory","score":0.8534244298934937},{"id":"https://openalex.org/keywords/inference","display_name":"Inference","score":0.7821073532104492},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.7598037123680115},{"id":"https://openalex.org/keywords/profiling","display_name":"Profiling (computer programming)","score":0.5516015291213989},{"id":"https://openalex.org/keywords/benchmarking","display_name":"Benchmarking","score":0.5295069217681885},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.509206235408783},{"id":"https://openalex.org/keywords/dimensionality-reduction","display_name":"Dimensionality reduction","score":0.4530075788497925},{"id":"https://openalex.org/keywords/selection","display_name":"Selection (genetic algorithm)","score":0.4403524398803711},{"id":"https://openalex.org/keywords/expression","display_name":"Expression (computer science)","score":0.4291342794895172},{"id":"https://openalex.org/keywords/machine-learning","display_name":"Machine learning","score":0.40136492252349854},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.37905174493789673}],"concepts":[{"id":"https://openalex.org/C13662910","wikidata":"https://www.wikidata.org/wiki/Q193139","display_name":"Trajectory","level":2,"score":0.8534244298934937},{"id":"https://openalex.org/C2776214188","wikidata":"https://www.wikidata.org/wiki/Q408386","display_name":"Inference","level":2,"score":0.7821073532104492},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.7598037123680115},{"id":"https://openalex.org/C187191949","wikidata":"https://www.wikidata.org/wiki/Q1138496","display_name":"Profiling (computer programming)","level":2,"score":0.5516015291213989},{"id":"https://openalex.org/C86251818","wikidata":"https://www.wikidata.org/wiki/Q816754","display_name":"Benchmarking","level":2,"score":0.5295069217681885},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.509206235408783},{"id":"https://openalex.org/C70518039","wikidata":"https://www.wikidata.org/wiki/Q16000077","display_name":"Dimensionality reduction","level":2,"score":0.4530075788497925},{"id":"https://openalex.org/C81917197","wikidata":"https://www.wikidata.org/wiki/Q628760","display_name":"Selection (genetic algorithm)","level":2,"score":0.4403524398803711},{"id":"https://openalex.org/C90559484","wikidata":"https://www.wikidata.org/wiki/Q778379","display_name":"Expression (computer science)","level":2,"score":0.4291342794895172},{"id":"https://openalex.org/C119857082","wikidata":"https://www.wikidata.org/wiki/Q2539","display_name":"Machine learning","level":1,"score":0.40136492252349854},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.37905174493789673},{"id":"https://openalex.org/C121332964","wikidata":"https://www.wikidata.org/wiki/Q413","display_name":"Physics","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/C144133560","wikidata":"https://www.wikidata.org/wiki/Q4830453","display_name":"Business","level":0,"score":0.0},{"id":"https://openalex.org/C111919701","wikidata":"https://www.wikidata.org/wiki/Q9135","display_name":"Operating system","level":1,"score":0.0},{"id":"https://openalex.org/C1276947","wikidata":"https://www.wikidata.org/wiki/Q333","display_name":"Astronomy","level":1,"score":0.0},{"id":"https://openalex.org/C162853370","wikidata":"https://www.wikidata.org/wiki/Q39809","display_name":"Marketing","level":1,"score":0.0}],"mesh":[{"descriptor_ui":"D000081246","descriptor_name":"RNA-Seq","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D000081246","descriptor_name":"RNA-Seq","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D000081246","descriptor_name":"RNA-Seq","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D000081246","descriptor_name":"RNA-Seq","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D000081246","descriptor_name":"RNA-Seq","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D000081246","descriptor_name":"RNA-Seq","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D000081246","descriptor_name":"RNA-Seq","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D000081246","descriptor_name":"RNA-Seq","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D000081246","descriptor_name":"RNA-Seq","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D000081246","descriptor_name":"RNA-Seq","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D000092386","descriptor_name":"Single-Cell Gene Expression Analysis","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000092386","descriptor_name":"Single-Cell Gene Expression Analysis","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000092386","descriptor_name":"Single-Cell Gene Expression Analysis","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000092386","descriptor_name":"Single-Cell Gene Expression Analysis","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000092386","descriptor_name":"Single-Cell Gene Expression Analysis","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D000092386","descriptor_name":"Single-Cell Gene Expression Analysis","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D000092386","descriptor_name":"Single-Cell Gene Expression Analysis","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D000092386","descriptor_name":"Single-Cell Gene Expression Analysis","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D000092386","descriptor_name":"Single-Cell Gene Expression Analysis","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D000092386","descriptor_name":"Single-Cell Gene Expression Analysis","qualifier_ui":"Q000379","qualifier_name":"methods","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":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000818","descriptor_name":"Animals","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000818","descriptor_name":"Animals","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000818","descriptor_name":"Animals","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000818","descriptor_name":"Animals","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000818","descriptor_name":"Animals","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000818","descriptor_name":"Animals","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":"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":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D017423","descriptor_name":"Sequence Analysis, RNA","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D017423","descriptor_name":"Sequence Analysis, RNA","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D017423","descriptor_name":"Sequence Analysis, RNA","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D017423","descriptor_name":"Sequence Analysis, RNA","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D020869","descriptor_name":"Gene Expression Profiling","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D020869","descriptor_name":"Gene Expression Profiling","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D020869","descriptor_name":"Gene Expression Profiling","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D020869","descriptor_name":"Gene Expression Profiling","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D020869","descriptor_name":"Gene Expression Profiling","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D020869","descriptor_name":"Gene Expression Profiling","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D020869","descriptor_name":"Gene Expression Profiling","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D020869","descriptor_name":"Gene Expression Profiling","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D020869","descriptor_name":"Gene Expression Profiling","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D020869","descriptor_name":"Gene Expression Profiling","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D059010","descriptor_name":"Single-Cell Analysis","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D059010","descriptor_name":"Single-Cell Analysis","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D059010","descriptor_name":"Single-Cell Analysis","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D059010","descriptor_name":"Single-Cell Analysis","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true}],"locations_count":3,"locations":[{"id":"doi:10.1093/bib/bbae216","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bib/bbae216","pdf_url":"https://academic.oup.com/bib/article-pdf/25/3/bbae216/57465408/bbae216.pdf","source":{"id":"https://openalex.org/S91767247","display_name":"Briefings in Bioinformatics","issn_l":"1467-5463","issn":["1467-5463","1477-4054"],"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-nc","license_id":"https://openalex.org/licenses/cc-by-nc","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Briefings in Bioinformatics","raw_type":"journal-article"},{"id":"pmid:38725155","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/38725155","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":"Briefings in bioinformatics","raw_type":null},{"id":"pmh:oai:pubmedcentral.nih.gov:11082074","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/11082074","pdf_url":"https://pmc.ncbi.nlm.nih.gov/articles/PMC11082074/pdf/bbae216.pdf","source":{"id":"https://openalex.org/S2764455111","display_name":"PubMed Central","issn_l":null,"issn":null,"is_oa":true,"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-nc","license_id":"https://openalex.org/licenses/cc-by-nc","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Brief Bioinform","raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1093/bib/bbae216","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bib/bbae216","pdf_url":"https://academic.oup.com/bib/article-pdf/25/3/bbae216/57465408/bbae216.pdf","source":{"id":"https://openalex.org/S91767247","display_name":"Briefings in Bioinformatics","issn_l":"1467-5463","issn":["1467-5463","1477-4054"],"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-nc","license_id":"https://openalex.org/licenses/cc-by-nc","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Briefings in Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[{"id":"https://metadata.un.org/sdg/16","score":0.7400000095367432,"display_name":"Peace, Justice and strong institutions"}],"awards":[{"id":"https://openalex.org/G1815043316","display_name":null,"funder_award_id":"UH3DK122638","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"},{"id":"https://openalex.org/G2538411746","display_name":null,"funder_award_id":"R01DK106191","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"},{"id":"https://openalex.org/G2549099296","display_name":null,"funder_award_id":"R35GM146895","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"},{"id":"https://openalex.org/G8588998619","display_name":null,"funder_award_id":"P01AI042288","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"}],"has_content":{"grobid_xml":false,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W4396814199.pdf"},"referenced_works_count":69,"referenced_works":["https://openalex.org/W1615489511","https://openalex.org/W1984883254","https://openalex.org/W1993608719","https://openalex.org/W2010457001","https://openalex.org/W2026344731","https://openalex.org/W2065058700","https://openalex.org/W2096192437","https://openalex.org/W2128120736","https://openalex.org/W2134857847","https://openalex.org/W2184331293","https://openalex.org/W2187089797","https://openalex.org/W2316095770","https://openalex.org/W2373831850","https://openalex.org/W2516455020","https://openalex.org/W2523620612","https://openalex.org/W2540833380","https://openalex.org/W2598326928","https://openalex.org/W2607948634","https://openalex.org/W2610510965","https://openalex.org/W2747850876","https://openalex.org/W2786672974","https://openalex.org/W2800912249","https://openalex.org/W2884197618","https://openalex.org/W2889291212","https://openalex.org/W2905317377","https://openalex.org/W2916020270","https://openalex.org/W2927507212","https://openalex.org/W2942880491","https://openalex.org/W2947877009","https://openalex.org/W2949067670","https://openalex.org/W2950372712","https://openalex.org/W2951799803","https://openalex.org/W2952100718","https://openalex.org/W2977438002","https://openalex.org/W3045053780","https://openalex.org/W3048538154","https://openalex.org/W3111307227","https://openalex.org/W3145969289","https://openalex.org/W3164852867","https://openalex.org/W3169353165","https://openalex.org/W3174608384","https://openalex.org/W3202846380","https://openalex.org/W3210310966","https://openalex.org/W3215343322","https://openalex.org/W4206099242","https://openalex.org/W4210840193","https://openalex.org/W4212807700","https://openalex.org/W4213324298","https://openalex.org/W4214611015","https://openalex.org/W4220747819","https://openalex.org/W4226175162","https://openalex.org/W4226412678","https://openalex.org/W4233637541","https://openalex.org/W4245699060","https://openalex.org/W4311239350","https://openalex.org/W4318908621","https://openalex.org/W4328105806","https://openalex.org/W4362554774","https://openalex.org/W4377221399","https://openalex.org/W4378212544","https://openalex.org/W4385294687","https://openalex.org/W4385945347","https://openalex.org/W4386156464","https://openalex.org/W4386707745","https://openalex.org/W4392162689","https://openalex.org/W6728888212","https://openalex.org/W6786543096","https://openalex.org/W6796563450","https://openalex.org/W6809048309"],"related_works":["https://openalex.org/W4238897586","https://openalex.org/W435179959","https://openalex.org/W2619091065","https://openalex.org/W2059640416","https://openalex.org/W1490753184","https://openalex.org/W2284465472","https://openalex.org/W2291782699","https://openalex.org/W1993948687","https://openalex.org/W2000169967","https://openalex.org/W2112883198"],"abstract_inverted_index":{"Single-cell":[0],"RNA":[1],"sequencing":[2],"(scRNA-seq)":[3],"experiments":[4],"have":[5,37],"become":[6],"instrumental":[7],"in":[8,28,54,162],"developmental":[9],"and":[10,68,85,112,127,148,167,183],"differentiation":[11],"studies,":[12],"enabling":[13,184],"the":[14,41,64,122,128,151,173],"profiling":[15],"of":[16,40,124,131,150],"cells":[17],"at":[18,191],"a":[19,101,106],"single":[20],"or":[21],"multiple":[22],"time-points":[23],"to":[24,45,58,62,155,176],"uncover":[25],"subtle":[26],"variations":[27],"expression":[29],"profiles":[30],"reflecting":[31],"underlying":[32],"biological":[33,189],"processes.":[34],"Benchmarking":[35],"studies":[36],"compared":[38],"many":[39],"computational":[42],"methods":[43,67,80],"used":[44,76],"reconstruct":[46],"cellular":[47],"dynamics;":[48],"however,":[49],"researchers":[50,171],"still":[51],"encounter":[52],"challenges":[53],"their":[55],"analysis":[56,118,126,141,182],"due":[57],"uncertainty":[59,147],"with":[60,172],"respect":[61],"selecting":[63],"most":[65],"appropriate":[66],"parameters.":[69],"Even":[70],"among":[71],"universal":[72],"data":[73],"processing":[74,132],"steps":[75],"by":[77,117],"trajectory":[78,88,110,114,125,140,156,181],"inference":[79,111,157],"such":[81],"as":[82],"feature":[83],"selection":[84],"dimension":[86],"reduction,":[87],"methods'":[89],"performances":[90],"are":[91],"highly":[92],"dataset-specific.":[93],"To":[94],"address":[95],"these":[96,143],"challenges,":[97],"we":[98],"developed":[99],"Escort,":[100],"novel":[102],"framework":[103],"for":[104,109],"evaluating":[105],"dataset's":[107],"suitability":[108,123],"quantifying":[113],"properties":[115],"influenced":[116],"decisions.":[119],"Escort":[120,137,159],"evaluates":[121],"combined":[129],"effects":[130],"choices":[133],"using":[134],"trajectory-specific":[135],"metrics.":[136],"navigates":[138],"single-cell":[139,192],"through":[142],"data-driven":[144],"assessments,":[145],"reducing":[146],"much":[149],"decision":[152],"burden":[153],"inherent":[154],"analyses.":[158],"is":[160],"implemented":[161],"an":[163],"accessible":[164],"R":[165],"package":[166],"R/Shiny":[168],"application,":[169],"providing":[170],"necessary":[174],"tools":[175],"make":[177],"informed":[178],"decisions":[179],"during":[180],"new":[185],"insights":[186],"into":[187],"dynamic":[188],"processes":[190],"resolution.":[193]},"counts_by_year":[{"year":2026,"cited_by_count":2},{"year":2025,"cited_by_count":3},{"year":2024,"cited_by_count":2}],"updated_date":"2026-03-27T05:58:40.876381","created_date":"2025-10-10T00:00:00"}
