{"id":"https://openalex.org/W2903622309","doi":"https://doi.org/10.1093/bioinformatics/bty1009","title":"DensityPath: an algorithm to visualize and reconstruct cell state-transition path on density landscape for single-cell RNA sequencing data","display_name":"DensityPath: an algorithm to visualize and reconstruct cell state-transition path on density landscape for single-cell RNA sequencing data","publication_year":2018,"publication_date":"2018-12-06","ids":{"openalex":"https://openalex.org/W2903622309","doi":"https://doi.org/10.1093/bioinformatics/bty1009","mag":"2903622309","pmid":"https://pubmed.ncbi.nlm.nih.gov/30535348"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/bty1009","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/bty1009","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/35/15/2593/29012514/bty1009.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":false,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"bronze","oa_url":"https://academic.oup.com/bioinformatics/article-pdf/35/15/2593/29012514/bty1009.pdf","any_repository_has_fulltext":false},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5100637865","display_name":"Ziwei Chen","orcid":"https://orcid.org/0009-0000-8681-3288"},"institutions":[{"id":"https://openalex.org/I19820366","display_name":"Chinese Academy of Sciences","ror":"https://ror.org/034t30j35","country_code":"CN","type":"government","lineage":["https://openalex.org/I19820366"]},{"id":"https://openalex.org/I4210095018","display_name":"National Center for Mathematics and Interdisciplinary Sciences","ror":"https://ror.org/00s97k668","country_code":"CN","type":"facility","lineage":["https://openalex.org/I4210095018"]},{"id":"https://openalex.org/I4210120485","display_name":"Academy of Mathematics and Systems Science","ror":"https://ror.org/02jkmyk67","country_code":"CN","type":"facility","lineage":["https://openalex.org/I19820366","https://openalex.org/I4210120485"]},{"id":"https://openalex.org/I4210165038","display_name":"University of Chinese Academy of Sciences","ror":"https://ror.org/05qbk4x57","country_code":"CN","type":"education","lineage":["https://openalex.org/I19820366","https://openalex.org/I4210165038"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Ziwei Chen","raw_affiliation_strings":["NCMIS, Academy of Mathematics and Systems Science, Chinese Academy of Sciences, Beijing","University of Chinese Academy of Sciences, Beijing"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"NCMIS, Academy of Mathematics and Systems Science, Chinese Academy of Sciences, Beijing","institution_ids":["https://openalex.org/I19820366","https://openalex.org/I4210095018","https://openalex.org/I4210120485"]},{"raw_affiliation_string":"University of Chinese Academy of Sciences, Beijing","institution_ids":["https://openalex.org/I4210165038"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5041848081","display_name":"Shaokun An","orcid":"https://orcid.org/0000-0001-5564-3239"},"institutions":[{"id":"https://openalex.org/I19820366","display_name":"Chinese Academy of Sciences","ror":"https://ror.org/034t30j35","country_code":"CN","type":"government","lineage":["https://openalex.org/I19820366"]},{"id":"https://openalex.org/I4210095018","display_name":"National Center for Mathematics and Interdisciplinary Sciences","ror":"https://ror.org/00s97k668","country_code":"CN","type":"facility","lineage":["https://openalex.org/I4210095018"]},{"id":"https://openalex.org/I4210120485","display_name":"Academy of Mathematics and Systems Science","ror":"https://ror.org/02jkmyk67","country_code":"CN","type":"facility","lineage":["https://openalex.org/I19820366","https://openalex.org/I4210120485"]},{"id":"https://openalex.org/I4210165038","display_name":"University of Chinese Academy of Sciences","ror":"https://ror.org/05qbk4x57","country_code":"CN","type":"education","lineage":["https://openalex.org/I19820366","https://openalex.org/I4210165038"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Shaokun An","raw_affiliation_strings":["NCMIS, Academy of Mathematics and Systems Science, Chinese Academy of Sciences, Beijing","University of Chinese Academy of Sciences, Beijing"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"NCMIS, Academy of Mathematics and Systems Science, Chinese Academy of Sciences, Beijing","institution_ids":["https://openalex.org/I19820366","https://openalex.org/I4210095018","https://openalex.org/I4210120485"]},{"raw_affiliation_string":"University of Chinese Academy of Sciences, Beijing","institution_ids":["https://openalex.org/I4210165038"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5000171463","display_name":"Xiangqi Bai","orcid":"https://orcid.org/0000-0003-4524-8862"},"institutions":[{"id":"https://openalex.org/I19820366","display_name":"Chinese Academy of Sciences","ror":"https://ror.org/034t30j35","country_code":"CN","type":"government","lineage":["https://openalex.org/I19820366"]},{"id":"https://openalex.org/I4210095018","display_name":"National Center for Mathematics and Interdisciplinary Sciences","ror":"https://ror.org/00s97k668","country_code":"CN","type":"facility","lineage":["https://openalex.org/I4210095018"]},{"id":"https://openalex.org/I4210120485","display_name":"Academy of Mathematics and Systems Science","ror":"https://ror.org/02jkmyk67","country_code":"CN","type":"facility","lineage":["https://openalex.org/I19820366","https://openalex.org/I4210120485"]},{"id":"https://openalex.org/I4210165038","display_name":"University of Chinese Academy of Sciences","ror":"https://ror.org/05qbk4x57","country_code":"CN","type":"education","lineage":["https://openalex.org/I19820366","https://openalex.org/I4210165038"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Xiangqi Bai","raw_affiliation_strings":["NCMIS, Academy of Mathematics and Systems Science, Chinese Academy of Sciences, Beijing","University of Chinese Academy of Sciences, Beijing"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"NCMIS, Academy of Mathematics and Systems Science, Chinese Academy of Sciences, Beijing","institution_ids":["https://openalex.org/I19820366","https://openalex.org/I4210095018","https://openalex.org/I4210120485"]},{"raw_affiliation_string":"University of Chinese Academy of Sciences, Beijing","institution_ids":["https://openalex.org/I4210165038"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5062134131","display_name":"Fuzhou Gong","orcid":null},"institutions":[{"id":"https://openalex.org/I19820366","display_name":"Chinese Academy of Sciences","ror":"https://ror.org/034t30j35","country_code":"CN","type":"government","lineage":["https://openalex.org/I19820366"]},{"id":"https://openalex.org/I4210095018","display_name":"National Center for Mathematics and Interdisciplinary Sciences","ror":"https://ror.org/00s97k668","country_code":"CN","type":"facility","lineage":["https://openalex.org/I4210095018"]},{"id":"https://openalex.org/I4210120485","display_name":"Academy of Mathematics and Systems Science","ror":"https://ror.org/02jkmyk67","country_code":"CN","type":"facility","lineage":["https://openalex.org/I19820366","https://openalex.org/I4210120485"]},{"id":"https://openalex.org/I4210165038","display_name":"University of Chinese Academy of Sciences","ror":"https://ror.org/05qbk4x57","country_code":"CN","type":"education","lineage":["https://openalex.org/I19820366","https://openalex.org/I4210165038"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Fuzhou Gong","raw_affiliation_strings":["NCMIS, Academy of Mathematics and Systems Science, Chinese Academy of Sciences, Beijing","University of Chinese Academy of Sciences, Beijing"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"NCMIS, Academy of Mathematics and Systems Science, Chinese Academy of Sciences, Beijing","institution_ids":["https://openalex.org/I19820366","https://openalex.org/I4210095018","https://openalex.org/I4210120485"]},{"raw_affiliation_string":"University of Chinese Academy of Sciences, Beijing","institution_ids":["https://openalex.org/I4210165038"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5100673104","display_name":"Liang Ma","orcid":"https://orcid.org/0000-0002-1428-8426"},"institutions":[{"id":"https://openalex.org/I19820366","display_name":"Chinese Academy of Sciences","ror":"https://ror.org/034t30j35","country_code":"CN","type":"government","lineage":["https://openalex.org/I19820366"]},{"id":"https://openalex.org/I2801577699","display_name":"Beijing Institute of Genomics","ror":"https://ror.org/049gn7z52","country_code":"CN","type":"facility","lineage":["https://openalex.org/I19820366","https://openalex.org/I2801577699"]},{"id":"https://openalex.org/I4210165038","display_name":"University of Chinese Academy of Sciences","ror":"https://ror.org/05qbk4x57","country_code":"CN","type":"education","lineage":["https://openalex.org/I19820366","https://openalex.org/I4210165038"]}],"countries":["CN"],"is_corresponding":true,"raw_author_name":"Liang Ma","raw_affiliation_strings":["Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, China","University of Chinese Academy of Sciences, Beijing"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, China","institution_ids":["https://openalex.org/I19820366","https://openalex.org/I2801577699"]},{"raw_affiliation_string":"University of Chinese Academy of Sciences, Beijing","institution_ids":["https://openalex.org/I4210165038"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5009511375","display_name":"Lin Wan","orcid":"https://orcid.org/0000-0002-3511-0512"},"institutions":[{"id":"https://openalex.org/I19820366","display_name":"Chinese Academy of Sciences","ror":"https://ror.org/034t30j35","country_code":"CN","type":"government","lineage":["https://openalex.org/I19820366"]},{"id":"https://openalex.org/I4210095018","display_name":"National Center for Mathematics and Interdisciplinary Sciences","ror":"https://ror.org/00s97k668","country_code":"CN","type":"facility","lineage":["https://openalex.org/I4210095018"]},{"id":"https://openalex.org/I4210120485","display_name":"Academy of Mathematics and Systems Science","ror":"https://ror.org/02jkmyk67","country_code":"CN","type":"facility","lineage":["https://openalex.org/I19820366","https://openalex.org/I4210120485"]},{"id":"https://openalex.org/I4210165038","display_name":"University of Chinese Academy of Sciences","ror":"https://ror.org/05qbk4x57","country_code":"CN","type":"education","lineage":["https://openalex.org/I19820366","https://openalex.org/I4210165038"]}],"countries":["CN"],"is_corresponding":true,"raw_author_name":"Lin Wan","raw_affiliation_strings":["NCMIS, Academy of Mathematics and Systems Science, Chinese Academy of Sciences, Beijing","University of Chinese Academy of Sciences, Beijing"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"NCMIS, Academy of Mathematics and Systems Science, Chinese Academy of Sciences, Beijing","institution_ids":["https://openalex.org/I19820366","https://openalex.org/I4210095018","https://openalex.org/I4210120485"]},{"raw_affiliation_string":"University of Chinese Academy of Sciences, Beijing","institution_ids":["https://openalex.org/I4210165038"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":5,"corresponding_author_ids":["https://openalex.org/A5009511375","https://openalex.org/A5100673104"],"corresponding_institution_ids":["https://openalex.org/I19820366","https://openalex.org/I2801577699","https://openalex.org/I4210095018","https://openalex.org/I4210120485","https://openalex.org/I4210165038"],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":null,"fwci":1.2372,"has_fulltext":false,"cited_by_count":32,"citation_normalized_percentile":{"value":0.79520391,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":90,"max":99},"biblio":{"volume":"35","issue":"15","first_page":"2593","last_page":"2601"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T11289","display_name":"Single-cell and spatial transcriptomics","score":0.9975000023841858,"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":0.9975000023841858,"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":0.00039999998989515007,"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/T10621","display_name":"Gene Regulatory Network Analysis","score":0.0003000000142492354,"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":0.6311123967170715},{"id":"https://openalex.org/keywords/dimensionality-reduction","display_name":"Dimensionality reduction","score":0.5240773558616638},{"id":"https://openalex.org/keywords/path","display_name":"Path (computing)","score":0.48612284660339355},{"id":"https://openalex.org/keywords/algorithm","display_name":"Algorithm","score":0.47907739877700806},{"id":"https://openalex.org/keywords/visualization","display_name":"Visualization","score":0.4304667115211487},{"id":"https://openalex.org/keywords/shortest-path-problem","display_name":"Shortest path problem","score":0.42181068658828735},{"id":"https://openalex.org/keywords/theoretical-computer-science","display_name":"Theoretical computer science","score":0.4160260558128357},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.317901074886322},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.23376870155334473}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.6311123967170715},{"id":"https://openalex.org/C70518039","wikidata":"https://www.wikidata.org/wiki/Q16000077","display_name":"Dimensionality reduction","level":2,"score":0.5240773558616638},{"id":"https://openalex.org/C2777735758","wikidata":"https://www.wikidata.org/wiki/Q817765","display_name":"Path (computing)","level":2,"score":0.48612284660339355},{"id":"https://openalex.org/C11413529","wikidata":"https://www.wikidata.org/wiki/Q8366","display_name":"Algorithm","level":1,"score":0.47907739877700806},{"id":"https://openalex.org/C36464697","wikidata":"https://www.wikidata.org/wiki/Q451553","display_name":"Visualization","level":2,"score":0.4304667115211487},{"id":"https://openalex.org/C22590252","wikidata":"https://www.wikidata.org/wiki/Q1058754","display_name":"Shortest path problem","level":3,"score":0.42181068658828735},{"id":"https://openalex.org/C80444323","wikidata":"https://www.wikidata.org/wiki/Q2878974","display_name":"Theoretical computer science","level":1,"score":0.4160260558128357},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.317901074886322},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.23376870155334473},{"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/C132525143","wikidata":"https://www.wikidata.org/wiki/Q141488","display_name":"Graph","level":2,"score":0.0}],"mesh":[{"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":"D012313","descriptor_name":"RNA","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D012313","descriptor_name":"RNA","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D012313","descriptor_name":"RNA","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D017423","descriptor_name":"Sequence Analysis, RNA","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D017423","descriptor_name":"Sequence Analysis, RNA","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D017423","descriptor_name":"Sequence Analysis, RNA","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D020869","descriptor_name":"Gene Expression Profiling","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D020869","descriptor_name":"Gene Expression Profiling","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D020869","descriptor_name":"Gene Expression Profiling","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D059010","descriptor_name":"Single-Cell Analysis","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D059010","descriptor_name":"Single-Cell Analysis","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D059010","descriptor_name":"Single-Cell Analysis","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false}],"locations_count":2,"locations":[{"id":"doi:10.1093/bioinformatics/bty1009","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/bty1009","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/35/15/2593/29012514/bty1009.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":false,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},{"id":"pmid:30535348","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/30535348","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}],"best_oa_location":{"id":"doi:10.1093/bioinformatics/bty1009","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/bty1009","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/35/15/2593/29012514/bty1009.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":false,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G2341053655","display_name":null,"funder_award_id":"91630314","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"},{"id":"https://openalex.org/G3044586014","display_name":"\u751f\u7269\uff0f\u533b\u5b66\u65f6\u7a7a\u578b\u6570\u636e\u7684\u5efa\u6a21\u3001\u8ba1\u7b97\u4e0e\u7cfb\u7edf\u7efc\u5408\u7814\u7a76","funder_award_id":"11571349","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"},{"id":"https://openalex.org/G3521868779","display_name":"Mathematical Biosciences Institute","funder_award_id":"1440386","funder_id":"https://openalex.org/F4320306076","funder_display_name":"National Science Foundation"},{"id":"https://openalex.org/G8878881999","display_name":null,"funder_award_id":"81673833","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"}],"funders":[{"id":"https://openalex.org/F4320306076","display_name":"National Science Foundation","ror":"https://ror.org/021nxhr62"},{"id":"https://openalex.org/F4320309374","display_name":"Ohio State University","ror":"https://ror.org/00rs6vg23"},{"id":"https://openalex.org/F4320321001","display_name":"National Natural Science Foundation of China","ror":"https://ror.org/01h0zpd94"},{"id":"https://openalex.org/F4320322847","display_name":"Youth Innovation Promotion Association of the Chinese Academy of Sciences","ror":"https://ror.org/031141b54"},{"id":"https://openalex.org/F8998984417","display_name":"Evelyn F. and William L. McKnight Brain Institute, University of Florida Health","ror":null}],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":45,"referenced_works":["https://openalex.org/W1489950266","https://openalex.org/W1535321247","https://openalex.org/W1554944419","https://openalex.org/W1571975558","https://openalex.org/W1970779075","https://openalex.org/W1984883254","https://openalex.org/W1993287310","https://openalex.org/W1996908140","https://openalex.org/W2001246746","https://openalex.org/W2009288137","https://openalex.org/W2022686119","https://openalex.org/W2028695285","https://openalex.org/W2033403400","https://openalex.org/W2067191022","https://openalex.org/W2094771755","https://openalex.org/W2177432730","https://openalex.org/W2316095770","https://openalex.org/W2344887288","https://openalex.org/W2373831850","https://openalex.org/W2409898194","https://openalex.org/W2509957998","https://openalex.org/W2527487499","https://openalex.org/W2560326406","https://openalex.org/W2567510066","https://openalex.org/W2572662684","https://openalex.org/W2610774430","https://openalex.org/W2735632796","https://openalex.org/W2747877289","https://openalex.org/W2760463524","https://openalex.org/W2769816060","https://openalex.org/W2787894218","https://openalex.org/W2791058611","https://openalex.org/W2793370606","https://openalex.org/W2809365568","https://openalex.org/W2810062864","https://openalex.org/W2913066018","https://openalex.org/W2952650776","https://openalex.org/W2952840385","https://openalex.org/W2963647337","https://openalex.org/W3105265400","https://openalex.org/W3125280081","https://openalex.org/W4252521233","https://openalex.org/W4299828299","https://openalex.org/W6693391185","https://openalex.org/W6714148487"],"related_works":["https://openalex.org/W2068608913","https://openalex.org/W3176621072","https://openalex.org/W3124914020","https://openalex.org/W2141033859","https://openalex.org/W2156434174","https://openalex.org/W2071701083","https://openalex.org/W2383687187","https://openalex.org/W2081517010","https://openalex.org/W2121496884","https://openalex.org/W2387910809"],"abstract_inverted_index":{"MOTIVATION:":[0],"Visualizing":[1],"and":[2,46,64,92,98,173,188],"reconstructing":[3],"cell":[4,52,120,126,138,153,166],"developmental":[5],"trajectories":[6,164],"intrinsically":[7],"embedded":[8,43],"in":[9],"high-dimensional":[10],"expression":[11],"profiles":[12],"of":[13,34,38,49,66,75,95,104,114,136,152,165,209],"single-cell":[14,110],"RNA":[15],"sequencing":[16],"(scRNA-seq)":[17],"snapshot":[18],"data":[19,40,68,223],"are":[20,224],"computationally":[21],"intriguing,":[22],"but":[23],"challenging.":[24],"RESULTS:":[25],"We":[26,156],"propose":[27],"DensityPath,":[28],"an":[29,42,50],"algorithm":[30],"allowing":[31],"(i)":[32,70],"visualization":[33],"the":[35,56,72,96,101,118,124,131,141,150],"intrinsic":[36,73],"structure":[37],"scRNA-seq":[39,67],"on":[41,55,140,191],"2-d":[44],"space":[45],"(ii)":[47,99],"reconstruction":[48],"optimal":[51,125],"state-transition":[53,127],"path":[54,128,148],"density":[57,112,142],"landscape.":[58],"DensityPath":[59,122,159,181,199,214],"powerfully":[60],"handles":[61],"high":[62,183],"dimensionality":[63],"heterogeneity":[65],"by":[69,129],"revealing":[71],"structures":[74,94],"data,":[76],"while":[77,176],"adopting":[78],"a":[79,109,145],"non-linear":[80],"dimension":[81],"reduction":[82],"algorithm,":[83],"termed":[84],"elastic":[85],"embedding,":[86],"which":[87],"can":[88,160],"preserve":[89],"both":[90],"local":[91],"global":[93],"data;":[97],"extracting":[100],"topological":[102],"features":[103],"high-density,":[105],"level-set":[106],"clusters":[107],"from":[108],"multimodal":[111],"landscape":[113],"transcriptional":[115],"heterogeneity,":[116],"as":[117,194,196,205,207],"representative":[119,137],"states.":[121],"reconstructs":[123],"finding":[130],"geodesic":[132],"minimum":[133],"spanning":[134],"tree":[135],"states":[139],"landscape,":[143],"establishing":[144],"least":[146],"action":[147],"with":[149,170],"minimum-transition-energy":[151],"fate":[154],"decisions.":[155],"demonstrate":[157],"that":[158],"ably":[161],"reconstruct":[162],"complex":[163],"development,":[167],"e.g.":[168],"those":[169],"multiple":[171],"bifurcating":[172],"trifurcating":[174],"branches,":[175],"maintaining":[177],"computational":[178],"efficiency.":[179],"Moreover,":[180],"has":[182],"accuracy":[184],"for":[185],"pseudotime":[186],"calculation":[187],"branch":[189],"assignment":[190],"real":[192],"scRNA-seq,":[193],"well":[195,206],"simulated":[197],"datasets.":[198],"is":[200,216],"robust":[201],"to":[202],"parameter":[203],"choices,":[204],"permutations":[208],"data.":[210],"AVAILABILITY":[211],"AND":[212],"IMPLEMENTATION:":[213],"software":[215],"available":[217,225],"at":[218,226],"https://github.com/ucasdp/DensityPath.":[219],"SUPPLEMENTARY":[220],"INFORMATION:":[221],"Supplementary":[222],"Bioinformatics":[227],"online.":[228]},"counts_by_year":[{"year":2026,"cited_by_count":2},{"year":2025,"cited_by_count":4},{"year":2024,"cited_by_count":3},{"year":2023,"cited_by_count":5},{"year":2022,"cited_by_count":3},{"year":2021,"cited_by_count":7},{"year":2020,"cited_by_count":7},{"year":2019,"cited_by_count":1}],"updated_date":"2026-08-06T08:24:18.245995","created_date":"2025-10-10T00:00:00"}
