{"id":"https://openalex.org/W2884656343","doi":"https://doi.org/10.1093/bioinformatics/bty664","title":"GPseudoRank: a permutation sampler for single cell orderings","display_name":"GPseudoRank: a permutation sampler for single cell orderings","publication_year":2018,"publication_date":"2018-07-24","ids":{"openalex":"https://openalex.org/W2884656343","doi":"https://doi.org/10.1093/bioinformatics/bty664","mag":"2884656343","pmid":"https://pubmed.ncbi.nlm.nih.gov/30052778"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/bty664","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/bty664","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/35/4/611/27838556/bty664.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":"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","datacite","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"hybrid","oa_url":"https://academic.oup.com/bioinformatics/article-pdf/35/4/611/27838556/bty664.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5005038653","display_name":"Magdalena E Strau\u00df","orcid":"https://orcid.org/0000-0002-6089-8049"},"institutions":[{"id":"https://openalex.org/I241749","display_name":"University of Cambridge","ror":"https://ror.org/013meh722","country_code":"GB","type":"education","lineage":["https://openalex.org/I241749"]},{"id":"https://openalex.org/I4210134973","display_name":"MRC Biostatistics Unit","ror":"https://ror.org/046vje122","country_code":"GB","type":"facility","lineage":["https://openalex.org/I241749","https://openalex.org/I4210087105","https://openalex.org/I4210134973","https://openalex.org/I90344618"]}],"countries":["GB"],"is_corresponding":true,"raw_author_name":"Magdalena E Strau\u00df","raw_affiliation_strings":["MRC Biostatistics Unit, School of Clinical Medicine, University of Cambridge, Cambridge, UK"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"MRC Biostatistics Unit, School of Clinical Medicine, University of Cambridge, Cambridge, UK","institution_ids":["https://openalex.org/I4210134973","https://openalex.org/I241749"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5068447187","display_name":"John E. Reid","orcid":"https://orcid.org/0000-0002-7762-6760"},"institutions":[{"id":"https://openalex.org/I241749","display_name":"University of Cambridge","ror":"https://ror.org/013meh722","country_code":"GB","type":"education","lineage":["https://openalex.org/I241749"]},{"id":"https://openalex.org/I4210128584","display_name":"The Alan Turing Institute","ror":"https://ror.org/035dkdb55","country_code":"GB","type":"facility","lineage":["https://openalex.org/I4210128584"]},{"id":"https://openalex.org/I4210134973","display_name":"MRC Biostatistics Unit","ror":"https://ror.org/046vje122","country_code":"GB","type":"facility","lineage":["https://openalex.org/I241749","https://openalex.org/I4210087105","https://openalex.org/I4210134973","https://openalex.org/I90344618"]}],"countries":["GB"],"is_corresponding":false,"raw_author_name":"John E Reid","raw_affiliation_strings":["Alan Turing Institute, London, UK","MRC Biostatistics Unit, School of Clinical Medicine, University of Cambridge, Cambridge, UK"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Alan Turing Institute, London, UK","institution_ids":["https://openalex.org/I4210128584"]},{"raw_affiliation_string":"MRC Biostatistics Unit, School of Clinical Medicine, University of Cambridge, Cambridge, UK","institution_ids":["https://openalex.org/I4210134973","https://openalex.org/I241749"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5064848972","display_name":"Lorenz Wernisch","orcid":"https://orcid.org/0000-0003-3113-7942"},"institutions":[{"id":"https://openalex.org/I241749","display_name":"University of Cambridge","ror":"https://ror.org/013meh722","country_code":"GB","type":"education","lineage":["https://openalex.org/I241749"]},{"id":"https://openalex.org/I4210134973","display_name":"MRC Biostatistics Unit","ror":"https://ror.org/046vje122","country_code":"GB","type":"facility","lineage":["https://openalex.org/I241749","https://openalex.org/I4210087105","https://openalex.org/I4210134973","https://openalex.org/I90344618"]}],"countries":["GB"],"is_corresponding":false,"raw_author_name":"Lorenz Wernisch","raw_affiliation_strings":["MRC Biostatistics Unit, School of Clinical Medicine, University of Cambridge, Cambridge, UK"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"MRC Biostatistics Unit, School of Clinical Medicine, University of Cambridge, Cambridge, UK","institution_ids":["https://openalex.org/I4210134973","https://openalex.org/I241749"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":3,"corresponding_author_ids":["https://openalex.org/A5005038653"],"corresponding_institution_ids":["https://openalex.org/I241749","https://openalex.org/I4210134973"],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":{"value":3618,"currency":"USD","value_usd":3618},"fwci":1.1729,"has_fulltext":false,"cited_by_count":15,"citation_normalized_percentile":{"value":0.78474885,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":95,"max":98},"biblio":{"volume":"35","issue":"4","first_page":"611","last_page":"618"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T11289","display_name":"Single-cell and spatial transcriptomics","score":0.9746999740600586,"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":0.9746999740600586,"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":0.0032999999821186066,"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":0.0027000000700354576,"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/permutation","display_name":"Permutation (music)","score":0.773323655128479},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.5142002105712891},{"id":"https://openalex.org/keywords/combinatorics","display_name":"Combinatorics","score":0.33441492915153503},{"id":"https://openalex.org/keywords/mathematics","display_name":"Mathematics","score":0.33031192421913147},{"id":"https://openalex.org/keywords/physics","display_name":"Physics","score":0.07820340991020203}],"concepts":[{"id":"https://openalex.org/C21308566","wikidata":"https://www.wikidata.org/wiki/Q7169365","display_name":"Permutation (music)","level":2,"score":0.773323655128479},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.5142002105712891},{"id":"https://openalex.org/C114614502","wikidata":"https://www.wikidata.org/wiki/Q76592","display_name":"Combinatorics","level":1,"score":0.33441492915153503},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.33031192421913147},{"id":"https://openalex.org/C121332964","wikidata":"https://www.wikidata.org/wiki/Q413","display_name":"Physics","level":0,"score":0.07820340991020203},{"id":"https://openalex.org/C24890656","wikidata":"https://www.wikidata.org/wiki/Q82811","display_name":"Acoustics","level":1,"score":0.0}],"mesh":[{"descriptor_ui":"D001499","descriptor_name":"Bayes Theorem","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D001499","descriptor_name":"Bayes Theorem","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D001499","descriptor_name":"Bayes Theorem","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D001499","descriptor_name":"Bayes Theorem","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":"D016000","descriptor_name":"Cluster Analysis","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016000","descriptor_name":"Cluster Analysis","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016000","descriptor_name":"Cluster Analysis","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016000","descriptor_name":"Cluster 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":true},{"descriptor_ui":"D059010","descriptor_name":"Single-Cell Analysis","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D059010","descriptor_name":"Single-Cell Analysis","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D059010","descriptor_name":"Single-Cell Analysis","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true}],"locations_count":5,"locations":[{"id":"doi:10.1093/bioinformatics/bty664","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/bty664","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/35/4/611/27838556/bty664.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":"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:30052778","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/30052778","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:europepmc.org:5368051","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/6230469","pdf_url":null,"source":{"id":"https://openalex.org/S4306400806","display_name":"Europe PMC (PubMed Central)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1303153112","host_organization_name":"European Bioinformatics Institute","host_organization_lineage":["https://openalex.org/I1303153112"],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":"Text"},{"id":"pmh:oai:www.repository.cam.ac.uk:1810/279864","is_oa":true,"landing_page_url":"https://www.repository.cam.ac.uk/handle/1810/279864","pdf_url":null,"source":{"id":"https://openalex.org/S4306401777","display_name":"Apollo (University of Cambridge)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I241749","host_organization_name":"University of Cambridge","host_organization_lineage":["https://openalex.org/I241749"],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":"Article"},{"id":"doi:10.17863/cam.27232","is_oa":true,"landing_page_url":"https://doi.org/10.17863/cam.27232","pdf_url":null,"source":{"id":"https://openalex.org/S7407050737","display_name":"Apollo","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":null,"host_organization_name":null,"host_organization_lineage":[],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":null,"is_accepted":false,"is_published":null,"raw_source_name":null,"raw_type":"JournalArticle"}],"best_oa_location":{"id":"doi:10.1093/bioinformatics/bty664","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/bty664","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/35/4/611/27838556/bty664.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":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G7843624913","display_name":null,"funder_award_id":"MC_UU_00002/1","funder_id":"https://openalex.org/F4320334626","funder_display_name":"Medical Research Council"}],"funders":[{"id":"https://openalex.org/F4320334626","display_name":"Medical Research Council","ror":"https://ror.org/03x94j517"}],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":45,"referenced_works":["https://openalex.org/W621546036","https://openalex.org/W839653734","https://openalex.org/W1503398984","https://openalex.org/W1549853756","https://openalex.org/W1746819321","https://openalex.org/W1874466506","https://openalex.org/W1984883254","https://openalex.org/W1988391018","https://openalex.org/W1993287310","https://openalex.org/W2001141328","https://openalex.org/W2025828346","https://openalex.org/W2053186076","https://openalex.org/W2056760934","https://openalex.org/W2065515536","https://openalex.org/W2067752346","https://openalex.org/W2082572780","https://openalex.org/W2093223772","https://openalex.org/W2103097715","https://openalex.org/W2110768394","https://openalex.org/W2128120736","https://openalex.org/W2130416410","https://openalex.org/W2135937351","https://openalex.org/W2138309709","https://openalex.org/W2140258573","https://openalex.org/W2148534890","https://openalex.org/W2152239989","https://openalex.org/W2319824271","https://openalex.org/W2344887288","https://openalex.org/W2373831850","https://openalex.org/W2407916594","https://openalex.org/W2422879816","https://openalex.org/W2509957998","https://openalex.org/W2747877289","https://openalex.org/W2760415787","https://openalex.org/W2785668899","https://openalex.org/W2950030509","https://openalex.org/W2950173281","https://openalex.org/W2951268343","https://openalex.org/W2951764674","https://openalex.org/W2963977107","https://openalex.org/W4211049957","https://openalex.org/W4251644969","https://openalex.org/W6632854936","https://openalex.org/W6679529799","https://openalex.org/W6748231397"],"related_works":["https://openalex.org/W2899084033","https://openalex.org/W2748952813","https://openalex.org/W4391375266","https://openalex.org/W1979597421","https://openalex.org/W2007980826","https://openalex.org/W2061531152","https://openalex.org/W3002753104","https://openalex.org/W2077600819","https://openalex.org/W2142036596","https://openalex.org/W2072657027"],"abstract_inverted_index":{"MOTIVATION:":[0],"A":[1,18,141],"number":[2,21],"of":[3,10,13,22,28,48,57,60,66,76,82,98,112,143,149],"pseudotime":[4,30,116],"methods":[5,23],"have":[6],"provided":[7],"point":[8],"estimates":[9],"the":[11,26,29,55,58,61,64,74,80,96,136,144,147],"ordering":[12,137],"cells":[14,78,126],"for":[15,38,79,85],"scRNA-seq":[16,92,157],"data.":[17],"still":[19,35],"limited":[20],"also":[24,123],"model":[25],"uncertainty":[27,59,117,134],"estimate.":[31],"However,":[32],"there":[33],"is":[34,164],"a":[36,39,67,119],"need":[37],"method":[40,145,163],"to":[41,51,91,100,109,138,154],"sample":[42,101],"from":[43,102],"complicated":[44],"and":[45,50,104,108,114,132,152],"multi-modal":[46,105],"distributions":[47,107],"orders,":[49],"estimate":[52],"changes":[53],"in":[54,128,135],"amount":[56],"order":[62],"during":[63,118],"course":[65],"biological":[68,120],"development,":[69],"as":[70],"this":[71],"can":[72],"support":[73],"selection":[75],"suitable":[77],"clustering":[81],"genes":[83],"or":[84],"network":[86],"inference.":[87],"RESULTS:":[88],"In":[89],"applications":[90],"data":[93,172],"we":[94],"demonstrate":[95],"potential":[97],"GPseudoRank":[99,122],"complex":[103],"posterior":[106],"identify":[110],"phases":[111],"lower":[113],"higher":[115],"process.":[121],"correctly":[124],"identifies":[125],"precocious":[127],"their":[129],"antiviral":[130],"response":[131],"links":[133],"metastable":[139],"states.":[140],"variant":[142],"extends":[146],"advantages":[148],"Bayesian":[150],"modelling":[151],"MCMC":[153],"large":[155],"droplet-based":[156],"datasets.":[158],"AVAILABILITY":[159],"AND":[160],"IMPLEMENTATION:":[161],"Our":[162],"available":[165,174],"on":[166],"github:":[167],"https://github.com/magStra/GPseudoRank.":[168],"SUPPLEMENTARY":[169],"INFORMATION:":[170],"Supplementary":[171],"are":[173],"at":[175],"Bioinformatics":[176],"online.":[177]},"counts_by_year":[{"year":2025,"cited_by_count":2},{"year":2021,"cited_by_count":6},{"year":2020,"cited_by_count":4},{"year":2019,"cited_by_count":3}],"updated_date":"2026-05-21T06:26:12.895304","created_date":"2025-10-10T00:00:00"}