{"id":"https://openalex.org/W2749500776","doi":"https://doi.org/10.1145/3107411.3107458","title":"Analysis of Single Cells on a Pseudotime Scale along Postnatal Pancreatic Beta Cell Development","display_name":"Analysis of Single Cells on a Pseudotime Scale along Postnatal Pancreatic Beta Cell Development","publication_year":2017,"publication_date":"2017-08-20","ids":{"openalex":"https://openalex.org/W2749500776","doi":"https://doi.org/10.1145/3107411.3107458","mag":"2749500776"},"language":"en","primary_location":{"id":"doi:10.1145/3107411.3107458","is_oa":false,"landing_page_url":"https://doi.org/10.1145/3107411.3107458","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Proceedings of the 8th ACM International Conference on Bioinformatics, Computational Biology,and Health Informatics","raw_type":"proceedings-article"},"type":"article","indexed_in":["crossref"],"open_access":{"is_oa":false,"oa_status":"closed","oa_url":null,"any_repository_has_fulltext":false},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5001352404","display_name":"Francesca Mulas","orcid":null},"institutions":[{"id":"https://openalex.org/I36258959","display_name":"University of California, San Diego","ror":"https://ror.org/0168r3w48","country_code":"US","type":"education","lineage":["https://openalex.org/I36258959"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Francesca Mulas","raw_affiliation_strings":["University of California, San Diego, La Jolla, CA, USA"],"affiliations":[{"raw_affiliation_string":"University of California, San Diego, La Jolla, CA, USA","institution_ids":["https://openalex.org/I36258959"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5086694391","display_name":"Chun Zeng","orcid":"https://orcid.org/0000-0001-9034-7873"},"institutions":[{"id":"https://openalex.org/I36258959","display_name":"University of California, San Diego","ror":"https://ror.org/0168r3w48","country_code":"US","type":"education","lineage":["https://openalex.org/I36258959"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Chun Zeng","raw_affiliation_strings":["University of California, San Diego, La Jolla, CA, USA"],"affiliations":[{"raw_affiliation_string":"University of California, San Diego, La Jolla, CA, USA","institution_ids":["https://openalex.org/I36258959"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5056536617","display_name":"Yinghui Sui","orcid":null},"institutions":[{"id":"https://openalex.org/I36258959","display_name":"University of California, San Diego","ror":"https://ror.org/0168r3w48","country_code":"US","type":"education","lineage":["https://openalex.org/I36258959"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Yinghui Sui","raw_affiliation_strings":["University of California, San Diego, La Jolla, CA, USA"],"affiliations":[{"raw_affiliation_string":"University of California, San Diego, La Jolla, CA, USA","institution_ids":["https://openalex.org/I36258959"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5084656017","display_name":"Tiffany Guan","orcid":null},"institutions":[{"id":"https://openalex.org/I36258959","display_name":"University of California, San Diego","ror":"https://ror.org/0168r3w48","country_code":"US","type":"education","lineage":["https://openalex.org/I36258959"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Tiffany Guan","raw_affiliation_strings":["University of California, San Diego, La Jolla, CA, USA"],"affiliations":[{"raw_affiliation_string":"University of California, San Diego, La Jolla, CA, USA","institution_ids":["https://openalex.org/I36258959"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5048699784","display_name":"Nathanael Miller","orcid":"https://orcid.org/0000-0001-9658-9697"},"institutions":[{"id":"https://openalex.org/I111088046","display_name":"Boston University","ror":"https://ror.org/05qwgg493","country_code":"US","type":"education","lineage":["https://openalex.org/I111088046"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Nathanael Miller","raw_affiliation_strings":["University of California, LA &amp; Boston University, MA, Los Angeles, CA, USA"],"affiliations":[{"raw_affiliation_string":"University of California, LA &amp; Boston University, MA, Los Angeles, CA, USA","institution_ids":["https://openalex.org/I111088046"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5103098097","display_name":"Yuliang Tan","orcid":"https://orcid.org/0000-0003-3152-8994"},"institutions":[{"id":"https://openalex.org/I36258959","display_name":"University of California, San Diego","ror":"https://ror.org/0168r3w48","country_code":"US","type":"education","lineage":["https://openalex.org/I36258959"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Yuliang Tan","raw_affiliation_strings":["University of California, San Diego, La Jolla, CA, USA"],"affiliations":[{"raw_affiliation_string":"University of California, San Diego, La Jolla, CA, USA","institution_ids":["https://openalex.org/I36258959"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5054029303","display_name":"Fenfen Liu","orcid":null},"institutions":[{"id":"https://openalex.org/I36258959","display_name":"University of California, San Diego","ror":"https://ror.org/0168r3w48","country_code":"US","type":"education","lineage":["https://openalex.org/I36258959"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Fenfen Liu","raw_affiliation_strings":["University of California, San Diego, La Jolla, CA, USA"],"affiliations":[{"raw_affiliation_string":"University of California, San Diego, La Jolla, CA, USA","institution_ids":["https://openalex.org/I36258959"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5113689344","display_name":"Wen Jin","orcid":null},"institutions":[{"id":"https://openalex.org/I36258959","display_name":"University of California, San Diego","ror":"https://ror.org/0168r3w48","country_code":"US","type":"education","lineage":["https://openalex.org/I36258959"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Wen Jin","raw_affiliation_strings":["University of California, San Diego, La Jolla, CA, USA"],"affiliations":[{"raw_affiliation_string":"University of California, San Diego, La Jolla, CA, USA","institution_ids":["https://openalex.org/I36258959"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5010667394","display_name":"Andrea C. Carrano","orcid":null},"institutions":[{"id":"https://openalex.org/I36258959","display_name":"University of California, San Diego","ror":"https://ror.org/0168r3w48","country_code":"US","type":"education","lineage":["https://openalex.org/I36258959"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Andrea C. Carrano","raw_affiliation_strings":["University of California, San Diego, La Jolla, CA, USA"],"affiliations":[{"raw_affiliation_string":"University of California, San Diego, La Jolla, CA, USA","institution_ids":["https://openalex.org/I36258959"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5025694971","display_name":"Mark O. Huising","orcid":"https://orcid.org/0000-0002-6594-2205"},"institutions":[{"id":"https://openalex.org/I84218800","display_name":"University of California, Davis","ror":"https://ror.org/05rrcem69","country_code":"US","type":"education","lineage":["https://openalex.org/I84218800"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Mark O. Huising","raw_affiliation_strings":["University of California, Davis, Davis, CA, USA"],"affiliations":[{"raw_affiliation_string":"University of California, Davis, Davis, CA, USA","institution_ids":["https://openalex.org/I84218800"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5065441230","display_name":"Orian Shirihai","orcid":null},"institutions":[{"id":"https://openalex.org/I111088046","display_name":"Boston University","ror":"https://ror.org/05qwgg493","country_code":"US","type":"education","lineage":["https://openalex.org/I111088046"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Orian Shirihai","raw_affiliation_strings":["University of California, LA &amp; Boston University, MA, Los Angeles, CA, USA"],"affiliations":[{"raw_affiliation_string":"University of California, LA &amp; Boston University, MA, Los Angeles, CA, USA","institution_ids":["https://openalex.org/I111088046"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5082310752","display_name":"G Yeo","orcid":null},"institutions":[{"id":"https://openalex.org/I36258959","display_name":"University of California, San Diego","ror":"https://ror.org/0168r3w48","country_code":"US","type":"education","lineage":["https://openalex.org/I36258959"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Gene W. Yeo","raw_affiliation_strings":["University of California, San Diego, La Jolla, CA, USA"],"affiliations":[{"raw_affiliation_string":"University of California, San Diego, La Jolla, CA, USA","institution_ids":["https://openalex.org/I36258959"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5061561620","display_name":"Maike Sander","orcid":"https://orcid.org/0000-0001-5308-7785"},"institutions":[{"id":"https://openalex.org/I36258959","display_name":"University of California, San Diego","ror":"https://ror.org/0168r3w48","country_code":"US","type":"education","lineage":["https://openalex.org/I36258959"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Maike Sander","raw_affiliation_strings":["University of California, San Diego, La Jolla, CA, USA"],"affiliations":[{"raw_affiliation_string":"University of California, San Diego, La Jolla, CA, USA","institution_ids":["https://openalex.org/I36258959"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":13,"corresponding_author_ids":["https://openalex.org/A5001352404"],"corresponding_institution_ids":["https://openalex.org/I36258959"],"apc_list":null,"apc_paid":null,"fwci":0.0,"has_fulltext":false,"cited_by_count":0,"citation_normalized_percentile":{"value":0.0920661,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":null,"biblio":{"volume":null,"issue":null,"first_page":"637","last_page":"637"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T11289","display_name":"Single-cell and spatial transcriptomics","score":0.9947999715805054,"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":0.9947999715805054,"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/T10885","display_name":"Gene expression and cancer classification","score":0.9781000018119812,"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/T10207","display_name":"Advanced biosensing and bioanalysis techniques","score":0.9693999886512756,"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/computational-biology","display_name":"Computational biology","score":0.6104809045791626},{"id":"https://openalex.org/keywords/transcriptome","display_name":"Transcriptome","score":0.5445002913475037},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.5034250617027283},{"id":"https://openalex.org/keywords/principal-component-analysis","display_name":"Principal component analysis","score":0.5026583671569824},{"id":"https://openalex.org/keywords/gene-expression","display_name":"Gene expression","score":0.5008594989776611},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.46659305691719055},{"id":"https://openalex.org/keywords/gene-regulatory-network","display_name":"Gene regulatory network","score":0.4631113111972809},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.4431096911430359},{"id":"https://openalex.org/keywords/microarray-analysis-techniques","display_name":"Microarray analysis techniques","score":0.4428706169128418},{"id":"https://openalex.org/keywords/beta","display_name":"BETA (programming language)","score":0.42616114020347595},{"id":"https://openalex.org/keywords/bioinformatics","display_name":"Bioinformatics","score":0.37751781940460205},{"id":"https://openalex.org/keywords/algorithm","display_name":"Algorithm","score":0.3751355707645416},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.2889786660671234},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.24146774411201477}],"concepts":[{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.6104809045791626},{"id":"https://openalex.org/C162317418","wikidata":"https://www.wikidata.org/wiki/Q252857","display_name":"Transcriptome","level":4,"score":0.5445002913475037},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.5034250617027283},{"id":"https://openalex.org/C27438332","wikidata":"https://www.wikidata.org/wiki/Q2873","display_name":"Principal component analysis","level":2,"score":0.5026583671569824},{"id":"https://openalex.org/C150194340","wikidata":"https://www.wikidata.org/wiki/Q26972","display_name":"Gene expression","level":3,"score":0.5008594989776611},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.46659305691719055},{"id":"https://openalex.org/C67339327","wikidata":"https://www.wikidata.org/wiki/Q1502576","display_name":"Gene regulatory network","level":4,"score":0.4631113111972809},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.4431096911430359},{"id":"https://openalex.org/C8415881","wikidata":"https://www.wikidata.org/wiki/Q6839217","display_name":"Microarray analysis techniques","level":4,"score":0.4428706169128418},{"id":"https://openalex.org/C2776174256","wikidata":"https://www.wikidata.org/wiki/Q830842","display_name":"BETA (programming language)","level":2,"score":0.42616114020347595},{"id":"https://openalex.org/C60644358","wikidata":"https://www.wikidata.org/wiki/Q128570","display_name":"Bioinformatics","level":1,"score":0.37751781940460205},{"id":"https://openalex.org/C11413529","wikidata":"https://www.wikidata.org/wiki/Q8366","display_name":"Algorithm","level":1,"score":0.3751355707645416},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.2889786660671234},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.24146774411201477},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.0}],"mesh":[],"locations_count":1,"locations":[{"id":"doi:10.1145/3107411.3107458","is_oa":false,"landing_page_url":"https://doi.org/10.1145/3107411.3107458","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Proceedings of the 8th ACM International Conference on Bioinformatics, Computational Biology,and Health Informatics","raw_type":"proceedings-article"}],"best_oa_location":null,"sustainable_development_goals":[{"score":0.5199999809265137,"display_name":"Life in Land","id":"https://metadata.un.org/sdg/15"}],"awards":[],"funders":[],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":2,"referenced_works":["https://openalex.org/W184776721","https://openalex.org/W2147370995"],"related_works":["https://openalex.org/W2399513595","https://openalex.org/W1975632186","https://openalex.org/W3027745756","https://openalex.org/W3205213561","https://openalex.org/W2531880140","https://openalex.org/W4388386498","https://openalex.org/W2126145365","https://openalex.org/W2036609560","https://openalex.org/W346861917","https://openalex.org/W1982897783"],"abstract_inverted_index":{"Single-cell":[0],"RNA-seq":[1,102],"generates":[2],"gene":[3,145,246,253],"expression":[4,247,254],"profiles":[5],"of":[6,14,35,44,50,58,62,87,156,220,236,281,290],"individual":[7,36],"cells":[8,37,121,188],"and":[9,17,115,143,163,197,217,273],"has":[10,264],"furthered":[11],"our":[12,180,190,207],"understanding":[13],"the":[15,33,41,84,136,150,234,257,269,279],"developmental":[16,85,258],"cellular":[18],"hierarchy":[19],"within":[20],"complex":[21],"tissues.":[22],"One":[23],"computational":[24],"challenge":[25],"in":[26,185,214,218,233,245],"analyzing":[27],"single-cell":[28,51,101],"data":[29,103,138,191,204,255],"sets":[30,104,146],"is":[31],"reconstructing":[32],"progression":[34,63],"with":[38,202],"respect":[39],"to":[40,82,99,135,171,277],"gradual":[42],"transition":[43],"their":[45,168],"transcriptomes.":[46],"While":[47],"a":[48,96,123,154,228,265,287],"number":[49],"ordering":[52,77,187],"tools":[53],"have":[54],"been":[55],"proposed,":[56],"many":[57],"these":[59,231],"require":[60],"knowledge":[61],"markers":[64],"or":[65],"time":[66,111,259],"delineators.":[67],"Here,":[68],"we":[69,94,118],"adapted":[70],"an":[71],"algorithm":[72],"previously":[73,194],"developed":[74],"for":[75,167,189,199,230],"temporally":[76],"bulk":[78,252],"microarray":[79],"samples":[80],"[1]":[81],"reconstruct":[83],"trajectory":[86,125,280],"pancreatic":[88],"beta-cells":[89,107],"postnatally.":[90],"To":[91],"accomplish":[92],"this,":[93],"applied":[95],"multi-step":[97],"pipeline":[98,241],"analyze":[100],"from":[105],"isolated":[106],"at":[108],"five":[109],"different":[110],"points":[112],"between":[113],"birth":[114],"post-weaning.":[116],"Specifically,":[117],"i)":[119],"ordered":[120],"along":[122,149,286],"linear":[124],"(the":[126],"Pseudotime":[127],"Scale)":[128],"by":[129],"applying":[130],"one-dimensional":[131],"principal":[132],"component":[133],"analysis":[134,208],"normalized":[137],"matrix;":[139],"ii)":[140],"identified":[141,242],"annotated":[142],"de-novo":[144],"significantly":[147],"regulated":[148],"trajectory;":[151],"iii)":[152],"built":[153],"network":[155,169],"top-regulated":[157],"genes":[158,166],"using":[159],"protein":[160],"interaction":[161],"repositories;":[162],"iv)":[164],"scored":[165],"connectivity":[170],"transcription":[172],"factors":[173],"[2].":[174],"A":[175],"systematic":[176],"comparison":[177],"showed":[178],"that":[179],"approach":[181],"was":[182],"more":[183],"accurate":[184],"correctly":[186],"set":[192],"than":[193],"reported":[195],"methods":[196],"allowed":[198],"direct":[200],"comparisons":[201],"external":[203],"sets.":[205],"Importantly,":[206],"revealed":[209],"never":[210],"before":[211],"seen":[212],"changes":[213,232,244],"beta-cell":[215,238],"metabolism":[216],"levels":[219],"mitochondrial":[221],"reactive":[222],"oxygen":[223],"species.":[224],"We":[225],"demonstrated":[226],"experimentally":[227],"role":[229],"regulation":[235],"postnatal":[237],"proliferation.":[239],"Our":[240],"maturation-related":[243],"not":[248],"captured":[249],"when":[250],"evaluating":[251],"across":[256],"course.":[260],"The":[261],"proposed":[262],"methodology":[263],"broad":[266],"applicability":[267],"beyond":[268],"context":[270],"here":[271],"described":[272],"could":[274],"be":[275],"used":[276],"examine":[278],"other":[282],"single":[283],"cell":[284,291],"types":[285],"continuous":[288],"course":[289],"state":[292],"changes.":[293]},"counts_by_year":[],"updated_date":"2025-11-06T03:46:38.306776","created_date":"2025-10-10T00:00:00"}
