{"id":"https://openalex.org/W4408746350","doi":"https://doi.org/10.1093/bioinformatics/btaf119","title":"CytoSimplex: visualizing single-cell fates and transitions on a simplex","display_name":"CytoSimplex: visualizing single-cell fates and transitions on a simplex","publication_year":2025,"publication_date":"2025-03-22","ids":{"openalex":"https://openalex.org/W4408746350","doi":"https://doi.org/10.1093/bioinformatics/btaf119","pmid":"https://pubmed.ncbi.nlm.nih.gov/40119904"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/btaf119","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btaf119","pdf_url":"https://academic.oup.com/bioinformatics/advance-article-pdf/doi/10.1093/bioinformatics/btaf119/62523873/btaf119.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/btaf119/62523873/btaf119.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5075561594","display_name":"Jialin Liu","orcid":"https://orcid.org/0000-0002-9984-7695"},"institutions":[{"id":"https://openalex.org/I27837315","display_name":"University of Michigan","ror":"https://ror.org/00jmfr291","country_code":"US","type":"education","lineage":["https://openalex.org/I27837315"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Jialin Liu","raw_affiliation_strings":["Department of Computational Medicine and Bioinformatics, University of Michigan , Ann Arbor, MI, 48109,","Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI United States"],"affiliations":[{"raw_affiliation_string":"Department of Computational Medicine and Bioinformatics, University of Michigan , Ann Arbor, MI, 48109,","institution_ids":["https://openalex.org/I27837315"]},{"raw_affiliation_string":"Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI United States","institution_ids":["https://openalex.org/I27837315"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5100373200","display_name":"Yichen Wang","orcid":"https://orcid.org/0000-0003-4347-5199"},"institutions":[{"id":"https://openalex.org/I27837315","display_name":"University of Michigan","ror":"https://ror.org/00jmfr291","country_code":"US","type":"education","lineage":["https://openalex.org/I27837315"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Yichen Wang","raw_affiliation_strings":["Department of Computational Medicine and Bioinformatics, University of Michigan , Ann Arbor, MI, 48109,","Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI United States"],"affiliations":[{"raw_affiliation_string":"Department of Computational Medicine and Bioinformatics, University of Michigan , Ann Arbor, MI, 48109,","institution_ids":["https://openalex.org/I27837315"]},{"raw_affiliation_string":"Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI United States","institution_ids":["https://openalex.org/I27837315"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5100369816","display_name":"Chen Li","orcid":"https://orcid.org/0000-0002-1790-6664"},"institutions":[{"id":"https://openalex.org/I27837315","display_name":"University of Michigan","ror":"https://ror.org/00jmfr291","country_code":"US","type":"education","lineage":["https://openalex.org/I27837315"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Chen Li","raw_affiliation_strings":["Department of Computational Medicine and Bioinformatics, University of Michigan , Ann Arbor, MI, 48109,","Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI United States"],"affiliations":[{"raw_affiliation_string":"Department of Computational Medicine and Bioinformatics, University of Michigan , Ann Arbor, MI, 48109,","institution_ids":["https://openalex.org/I27837315"]},{"raw_affiliation_string":"Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI United States","institution_ids":["https://openalex.org/I27837315"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5064292648","display_name":"Yichen Gu","orcid":"https://orcid.org/0000-0001-6585-9236"},"institutions":[{"id":"https://openalex.org/I27837315","display_name":"University of Michigan","ror":"https://ror.org/00jmfr291","country_code":"US","type":"education","lineage":["https://openalex.org/I27837315"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Yichen Gu","raw_affiliation_strings":["Department of Electrical and Computer Engineering, University of Michigan , Ann Arbor, MI, 48109,","Department of Electrical and Computer Engineering, University of Michigan, Ann Arbor, MI United States"],"affiliations":[{"raw_affiliation_string":"Department of Electrical and Computer Engineering, University of Michigan , Ann Arbor, MI, 48109,","institution_ids":["https://openalex.org/I27837315"]},{"raw_affiliation_string":"Department of Electrical and Computer Engineering, University of Michigan, Ann Arbor, MI United States","institution_ids":["https://openalex.org/I27837315"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5027078759","display_name":"Noriaki Ono","orcid":"https://orcid.org/0000-0002-3771-8230"},"institutions":[{"id":"https://openalex.org/I919571938","display_name":"The University of Texas Health Science Center at Houston","ror":"https://ror.org/03gds6c39","country_code":"US","type":"education","lineage":["https://openalex.org/I919571938"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Noriaki Ono","raw_affiliation_strings":["University of Texas Health Science Center at Houston School of Dentistry , Houston, TX, 77030,","University of Texas Health Science Center at Houston School of Dentistry, Houston, TX United States"],"affiliations":[{"raw_affiliation_string":"University of Texas Health Science Center at Houston School of Dentistry , Houston, TX, 77030,","institution_ids":["https://openalex.org/I919571938"]},{"raw_affiliation_string":"University of Texas Health Science Center at Houston School of Dentistry, Houston, TX United States","institution_ids":["https://openalex.org/I919571938"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5050036215","display_name":"Joshua Welch","orcid":null},"institutions":[{"id":"https://openalex.org/I27837315","display_name":"University of Michigan","ror":"https://ror.org/00jmfr291","country_code":"US","type":"education","lineage":["https://openalex.org/I27837315"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Joshua Welch","raw_affiliation_strings":["Department of Computational Medicine and Bioinformatics, University of Michigan , Ann Arbor, MI, 48109,","Department of Computer Science and Engineering, University of Michigan , Ann Arbor, MI, 48109,","Department of Computer Science and Engineering, University of Michigan, Ann Arbor, MI United States","Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI United States"],"affiliations":[{"raw_affiliation_string":"Department of Computational Medicine and Bioinformatics, University of Michigan , Ann Arbor, MI, 48109,","institution_ids":["https://openalex.org/I27837315"]},{"raw_affiliation_string":"Department of Computer Science and Engineering, University of Michigan , Ann Arbor, MI, 48109,","institution_ids":["https://openalex.org/I27837315"]},{"raw_affiliation_string":"Department of Computer Science and Engineering, University of Michigan, Ann Arbor, MI United States","institution_ids":["https://openalex.org/I27837315"]},{"raw_affiliation_string":"Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI United States","institution_ids":["https://openalex.org/I27837315"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":6,"corresponding_author_ids":["https://openalex.org/A5075561594"],"corresponding_institution_ids":["https://openalex.org/I27837315"],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":{"value":3618,"currency":"USD","value_usd":3618},"fwci":0.767,"has_fulltext":false,"cited_by_count":1,"citation_normalized_percentile":{"value":0.69276354,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":96,"max":98},"biblio":{"volume":"41","issue":"4","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":0.996399998664856,"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":0.9825000166893005,"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/python","display_name":"Python (programming language)","score":0.7890862822532654},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.7672358751296997},{"id":"https://openalex.org/keywords/visualization","display_name":"Visualization","score":0.6982591152191162},{"id":"https://openalex.org/keywords/dimensionality-reduction","display_name":"Dimensionality reduction","score":0.5097448229789734},{"id":"https://openalex.org/keywords/simplex","display_name":"Simplex","score":0.46757131814956665},{"id":"https://openalex.org/keywords/data-visualization","display_name":"Data visualization","score":0.4443705081939697},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.3449324369430542},{"id":"https://openalex.org/keywords/programming-language","display_name":"Programming language","score":0.22728955745697021},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.15020900964736938},{"id":"https://openalex.org/keywords/mathematics","display_name":"Mathematics","score":0.09877115488052368}],"concepts":[{"id":"https://openalex.org/C519991488","wikidata":"https://www.wikidata.org/wiki/Q28865","display_name":"Python (programming language)","level":2,"score":0.7890862822532654},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.7672358751296997},{"id":"https://openalex.org/C36464697","wikidata":"https://www.wikidata.org/wiki/Q451553","display_name":"Visualization","level":2,"score":0.6982591152191162},{"id":"https://openalex.org/C70518039","wikidata":"https://www.wikidata.org/wiki/Q16000077","display_name":"Dimensionality reduction","level":2,"score":0.5097448229789734},{"id":"https://openalex.org/C62438384","wikidata":"https://www.wikidata.org/wiki/Q331350","display_name":"Simplex","level":2,"score":0.46757131814956665},{"id":"https://openalex.org/C172367668","wikidata":"https://www.wikidata.org/wiki/Q6504956","display_name":"Data visualization","level":3,"score":0.4443705081939697},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.3449324369430542},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.22728955745697021},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.15020900964736938},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.09877115488052368},{"id":"https://openalex.org/C2524010","wikidata":"https://www.wikidata.org/wiki/Q8087","display_name":"Geometry","level":1,"score":0.0}],"mesh":[{"descriptor_ui":"D002454","descriptor_name":"Cell Differentiation","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D002454","descriptor_name":"Cell Differentiation","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D002454","descriptor_name":"Cell Differentiation","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D002454","descriptor_name":"Cell Differentiation","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"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":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":"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":4,"locations":[{"id":"doi:10.1093/bioinformatics/btaf119","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btaf119","pdf_url":"https://academic.oup.com/bioinformatics/advance-article-pdf/doi/10.1093/bioinformatics/btaf119/62523873/btaf119.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:40119904","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/40119904","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:11992338","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/11992338","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":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"Text"},{"id":"pmh:oai:digitalcommons.library.tmc.edu:uthdb_docs-1099","is_oa":false,"landing_page_url":"https://digitalcommons.library.tmc.edu/uthdb_docs/99","pdf_url":null,"source":{"id":"https://openalex.org/S4377196655","display_name":"Digital Commons-TMC (Texas Medical Center)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1337852284","host_organization_name":"Texas Medical Center","host_organization_lineage":["https://openalex.org/I1337852284"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Faculty, Staff and Student Publications","raw_type":"text"}],"best_oa_location":{"id":"doi:10.1093/bioinformatics/btaf119","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btaf119","pdf_url":"https://academic.oup.com/bioinformatics/advance-article-pdf/doi/10.1093/bioinformatics/btaf119/62523873/btaf119.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":[{"display_name":"Partnerships for the goals","score":0.5699999928474426,"id":"https://metadata.un.org/sdg/17"}],"awards":[{"id":"https://openalex.org/G5087455986","display_name":null,"funder_award_id":"R01 DE030630","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"},{"id":"https://openalex.org/G6312648792","display_name":null,"funder_award_id":"R01 HG010883","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/W4408746350.pdf"},"referenced_works_count":27,"referenced_works":["https://openalex.org/W813853026","https://openalex.org/W1971971673","https://openalex.org/W2156155978","https://openalex.org/W2373831850","https://openalex.org/W2407916594","https://openalex.org/W2766437506","https://openalex.org/W2904250115","https://openalex.org/W2916020270","https://openalex.org/W2925075625","https://openalex.org/W2927507212","https://openalex.org/W2948469692","https://openalex.org/W2951799803","https://openalex.org/W3012395571","https://openalex.org/W3047141442","https://openalex.org/W3092493138","https://openalex.org/W3114485724","https://openalex.org/W3160255881","https://openalex.org/W3176035856","https://openalex.org/W3184208286","https://openalex.org/W3197020116","https://openalex.org/W4205496949","https://openalex.org/W4225852114","https://openalex.org/W4281386804","https://openalex.org/W4292110737","https://openalex.org/W4295880122","https://openalex.org/W4305013698","https://openalex.org/W4366984421"],"related_works":["https://openalex.org/W2013728941","https://openalex.org/W4225274103","https://openalex.org/W2154046714","https://openalex.org/W2189613078","https://openalex.org/W2579659702","https://openalex.org/W2923661510","https://openalex.org/W1574055964","https://openalex.org/W1965329638","https://openalex.org/W2542318691","https://openalex.org/W3160708108"],"abstract_inverted_index":{"The":[0,11],"R":[1],"version":[2,13],"of":[3,14],"CytoSimplex":[4,15],"is":[5,16],"available":[6,17],"on":[7,18],"Github":[8,19],"at":[9,20],"https://github.com/welch-lab/CytoSimplex.":[10],"Python":[12],"https://github.com/welch-lab/pyCytoSimplex.":[21]},"counts_by_year":[{"year":2026,"cited_by_count":1}],"updated_date":"2026-04-09T08:11:56.329763","created_date":"2025-10-10T00:00:00"}
