{"id":"https://openalex.org/W2918679453","doi":"https://doi.org/10.1093/bioinformatics/btz074","title":"DIFFpop: a stochastic computational approach to simulate differentiation hierarchies with single cell barcoding","display_name":"DIFFpop: a stochastic computational approach to simulate differentiation hierarchies with single cell barcoding","publication_year":2019,"publication_date":"2019-02-25","ids":{"openalex":"https://openalex.org/W2918679453","doi":"https://doi.org/10.1093/bioinformatics/btz074","mag":"2918679453","pmid":"https://pubmed.ncbi.nlm.nih.gov/30816920","pmcid":"https://www.ncbi.nlm.nih.gov/pmc/articles/6761956"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/btz074","doi":"https://doi.org/10.1093/bioinformatics/btz074","is_oa":false,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btz074","pdf_url":null,"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,"listed_in":["abdc-a","anvur-class-a","anvur-scientific","ccf-a","cwts-core","doaj","dongbi-b","doyens","jufo-3","ki-jl-2","medline","norway-2","oarl","poland-200","russia-white-list-1","vabb-shw"],"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"},"volume":null,"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"green","oa_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/6761956","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5049266550","display_name":"Jeremy Ferlic","orcid":"https://orcid.org/0000-0001-9062-5503","observed_orcids":["https://orcid.org/0000-0001-9062-5503"]},"institutions":[{"id":"https://openalex.org/I136199984","display_name":"Harvard University","ror":"https://ror.org/03vek6s52","country_code":"US","type":"education","lineage":["https://openalex.org/I136199984"]},{"id":"https://openalex.org/I4210117453","display_name":"Dana-Farber Cancer Institute","ror":"https://ror.org/02jzgtq86","country_code":"US","type":"facility","lineage":["https://openalex.org/I4210117453"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Jeremy Ferlic","raw_affiliation_strings":["Department of Biostatistics, Harvard T. H. Chan School of Public Health , Boston, MA, USA","Department of Data Science, Dana-Farber Cancer Institute , Boston, MA, USA"],"raw_orcid":"https://orcid.org/0000-0001-9062-5503","affiliations":[{"raw_affiliation_string":"Department of Biostatistics, Harvard T. H. Chan School of Public Health , Boston, MA, USA","institution_ids":["https://openalex.org/I136199984"]},{"raw_affiliation_string":"Department of Data Science, Dana-Farber Cancer Institute , Boston, MA, USA","institution_ids":["https://openalex.org/I4210117453"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5040409553","display_name":"Jiantao Shi","orcid":"https://orcid.org/0000-0002-0039-8800","observed_orcids":["https://orcid.org/0000-0002-0039-8800"]},"institutions":[{"id":"https://openalex.org/I136199984","display_name":"Harvard University","ror":"https://ror.org/03vek6s52","country_code":"US","type":"education","lineage":["https://openalex.org/I136199984"]},{"id":"https://openalex.org/I4210117453","display_name":"Dana-Farber Cancer Institute","ror":"https://ror.org/02jzgtq86","country_code":"US","type":"facility","lineage":["https://openalex.org/I4210117453"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Jiantao Shi","raw_affiliation_strings":["Department of Biostatistics, Harvard T. H. Chan School of Public Health , Boston, MA, USA","Department of Data Science, Dana-Farber Cancer Institute , Boston, MA, USA","Department of Stem Cell and Regenerative Biology, Harvard University , Cambridge, MA, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Biostatistics, Harvard T. H. Chan School of Public Health , Boston, MA, USA","institution_ids":["https://openalex.org/I136199984"]},{"raw_affiliation_string":"Department of Data Science, Dana-Farber Cancer Institute , Boston, MA, USA","institution_ids":["https://openalex.org/I4210117453"]},{"raw_affiliation_string":"Department of Stem Cell and Regenerative Biology, Harvard University , Cambridge, MA, USA","institution_ids":["https://openalex.org/I136199984"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5051162687","display_name":"Thomas O. McDonald","orcid":"https://orcid.org/0000-0002-5272-0187","observed_orcids":["https://orcid.org/0000-0002-5272-0187"]},"institutions":[{"id":"https://openalex.org/I136199984","display_name":"Harvard University","ror":"https://ror.org/03vek6s52","country_code":"US","type":"education","lineage":["https://openalex.org/I136199984"]},{"id":"https://openalex.org/I4210117453","display_name":"Dana-Farber Cancer Institute","ror":"https://ror.org/02jzgtq86","country_code":"US","type":"facility","lineage":["https://openalex.org/I4210117453"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Thomas O McDonald","raw_affiliation_strings":["Center for Cancer Evolution, Dana-Farber Cancer Institute , Boston, MA, USA","Department of Biostatistics, Harvard T. H. Chan School of Public Health , Boston, MA, USA","Department of Data Science, Dana-Farber Cancer Institute , Boston, MA, USA","Department of Stem Cell and Regenerative Biology, Harvard University , Cambridge, MA, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Center for Cancer Evolution, Dana-Farber Cancer Institute , Boston, MA, USA","institution_ids":["https://openalex.org/I4210117453"]},{"raw_affiliation_string":"Department of Biostatistics, Harvard T. H. Chan School of Public Health , Boston, MA, USA","institution_ids":["https://openalex.org/I136199984"]},{"raw_affiliation_string":"Department of Data Science, Dana-Farber Cancer Institute , Boston, MA, USA","institution_ids":["https://openalex.org/I4210117453"]},{"raw_affiliation_string":"Department of Stem Cell and Regenerative Biology, Harvard University , Cambridge, MA, USA","institution_ids":["https://openalex.org/I136199984"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5091861581","display_name":"Franziska Michor A","orcid":"https://orcid.org/0000-0003-4869-8842","observed_orcids":["https://orcid.org/0000-0003-4869-8842","https://orcid.org/0009-0003-8552-7767"]},"institutions":[{"id":"https://openalex.org/I107606265","display_name":"Broad Institute","ror":"https://ror.org/05a0ya142","country_code":"US","type":"nonprofit","lineage":["https://openalex.org/I107606265"]},{"id":"https://openalex.org/I136199984","display_name":"Harvard University","ror":"https://ror.org/03vek6s52","country_code":"US","type":"education","lineage":["https://openalex.org/I136199984"]},{"id":"https://openalex.org/I4210117453","display_name":"Dana-Farber Cancer Institute","ror":"https://ror.org/02jzgtq86","country_code":"US","type":"facility","lineage":["https://openalex.org/I4210117453"]},{"id":"https://openalex.org/I63966007","display_name":"Massachusetts Institute of Technology","ror":"https://ror.org/042nb2s44","country_code":"US","type":"education","lineage":["https://openalex.org/I63966007"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Franziska Michor","raw_affiliation_strings":["Center for Cancer Evolution, Dana-Farber Cancer Institute , Boston, MA, USA","Department of Biostatistics, Harvard T. H. Chan School of Public Health , Boston, MA, USA","Department of Data Science, Dana-Farber Cancer Institute , Boston, MA, USA","Department of Stem Cell and Regenerative Biology, Harvard University , Cambridge, MA, USA","The Broad Institute of Harvard and MIT , Cambridge, MA, USA","The Ludwig Center at Harvard , Boston, MA, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Center for Cancer Evolution, Dana-Farber Cancer Institute , Boston, MA, USA","institution_ids":["https://openalex.org/I4210117453"]},{"raw_affiliation_string":"Department of Biostatistics, Harvard T. H. Chan School of Public Health , Boston, MA, USA","institution_ids":["https://openalex.org/I136199984"]},{"raw_affiliation_string":"Department of Data Science, Dana-Farber Cancer Institute , Boston, MA, USA","institution_ids":["https://openalex.org/I4210117453"]},{"raw_affiliation_string":"Department of Stem Cell and Regenerative Biology, Harvard University , Cambridge, MA, USA","institution_ids":["https://openalex.org/I136199984"]},{"raw_affiliation_string":"The Broad Institute of Harvard and MIT , Cambridge, MA, USA","institution_ids":["https://openalex.org/I107606265","https://openalex.org/I63966007"]},{"raw_affiliation_string":"The Ludwig Center at Harvard , Boston, MA, USA","institution_ids":["https://openalex.org/I136199984"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":4,"corresponding_author_ids":["https://openalex.org/A5091861581"],"corresponding_institution_ids":["https://openalex.org/I107606265","https://openalex.org/I136199984","https://openalex.org/I4210117453","https://openalex.org/I63966007"],"apc_list":{"value":3989,"currency":"USD","value_usd":3989},"apc_paid":null,"fwci":0.1654,"has_fulltext":false,"cited_by_count":3,"citation_normalized_percentile":{"value":0.42801254,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":88,"max":93},"biblio":{"volume":"35","issue":"19","first_page":"3849","last_page":"3851"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T11289","display_name":"Single-cell and spatial transcriptomics","score":0.9452999830245972,"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":0.9452999830245972,"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/T11764","display_name":"Evolution and Genetic Dynamics","score":0.02800000086426735,"subfield":{"id":"https://openalex.org/subfields/1311","display_name":"Genetics"},"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/T11287","display_name":"Cancer Genomics and Diagnostics","score":0.006099999882280827,"subfield":{"id":"https://openalex.org/subfields/1306","display_name":"Cancer Research"},"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/single-cell-barcoding","display_name":"single-cell barcoding","score":0.8240000009536743},{"id":"https://openalex.org/keywords/clonal-evolution","display_name":"clonal evolution","score":0.9100000262260437},{"id":"https://openalex.org/keywords/driver-mutations","display_name":"driver mutations","score":0.9950000047683716},{"id":"https://openalex.org/keywords/infinite-allele-model","display_name":"infinite allele model","score":0.9350000023841858},{"id":"https://openalex.org/keywords/lineage-tracing","display_name":"lineage tracing","score":0.49900001287460327},{"id":"https://openalex.org/keywords/r-package","display_name":"R package","score":0.7170000076293945}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.7345497012138367},{"id":"https://openalex.org/C2777904410","wikidata":"https://www.wikidata.org/wiki/Q7397","display_name":"Software","level":2,"score":0.6882750988006592},{"id":"https://openalex.org/C2984074130","wikidata":"https://www.wikidata.org/wiki/Q73539779","display_name":"R package","level":2,"score":0.5815151929855347},{"id":"https://openalex.org/C3020440742","wikidata":"https://www.wikidata.org/wiki/Q1176855","display_name":"Software package","level":3,"score":0.5734987854957581},{"id":"https://openalex.org/C2908647359","wikidata":"https://www.wikidata.org/wiki/Q2625603","display_name":"Population","level":2,"score":0.5030960440635681},{"id":"https://openalex.org/C98045186","wikidata":"https://www.wikidata.org/wiki/Q205663","display_name":"Process (computing)","level":2,"score":0.49175742268562317},{"id":"https://openalex.org/C80444323","wikidata":"https://www.wikidata.org/wiki/Q2878974","display_name":"Theoretical computer science","level":1,"score":0.41237300634384155},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.3789709508419037},{"id":"https://openalex.org/C11413529","wikidata":"https://www.wikidata.org/wiki/Q8366","display_name":"Algorithm","level":1,"score":0.3386704623699188},{"id":"https://openalex.org/C459310","wikidata":"https://www.wikidata.org/wiki/Q117801","display_name":"Computational science","level":1,"score":0.16354626417160034},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.11112058162689209},{"id":"https://openalex.org/C149923435","wikidata":"https://www.wikidata.org/wiki/Q37732","display_name":"Demography","level":1,"score":0.0},{"id":"https://openalex.org/C144024400","wikidata":"https://www.wikidata.org/wiki/Q21201","display_name":"Sociology","level":0,"score":0.0}],"mesh":[{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D002454","descriptor_name":"Cell Differentiation","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":"D013269","descriptor_name":"Stochastic Processes","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","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":"D060965","descriptor_name":"Clonal Evolution","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false}],"locations_count":3,"locations":[{"id":"doi:10.1093/bioinformatics/btz074","doi":"https://doi.org/10.1093/bioinformatics/btz074","is_oa":false,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btz074","pdf_url":null,"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,"listed_in":["abdc-a","anvur-class-a","anvur-scientific","ccf-a","cwts-core","doaj","dongbi-b","doyens","jufo-3","ki-jl-2","medline","norway-2","oarl","poland-200","russia-white-list-1","vabb-shw"],"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":"pmh:oai:pubmedcentral.nih.gov:6761956","doi":null,"is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/6761956","pdf_url":null,"source":{"id":"https://openalex.org/S2764455111","display_name":"PubMed Central","issn_l":null,"issn":null,"is_oa":true,"is_in_doaj":false,"is_core":false,"listed_in":[],"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","raw_type":"Text"},{"id":"pmid:30816920","doi":null,"is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/30816920","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,"listed_in":[],"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":"Journal Article"}],"best_oa_location":{"id":"pmh:oai:pubmedcentral.nih.gov:6761956","doi":null,"is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/6761956","pdf_url":null,"source":{"id":"https://openalex.org/S2764455111","display_name":"PubMed Central","issn_l":null,"issn":null,"is_oa":true,"is_in_doaj":false,"is_core":false,"listed_in":[],"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","raw_type":"Text"},"sustainable_development_goals":[],"study_designs":[],"awards":[{"id":"https://openalex.org/G1559214842","display_name":"Statistical and Quantitative Training in Big Data Health Science","funder_award_id":"T32LM012411","funder_id":"https://openalex.org/F4320337372","funder_display_name":"U.S. National Library of Medicine"},{"id":"https://openalex.org/G2947589114","display_name":"Evolution and Treatment Response of Brain, Breast, and Hematologic Malignancies","funder_award_id":"U54CA193461","funder_id":"https://openalex.org/F4320337351","funder_display_name":"National Cancer Institute"}],"funders":[{"id":"https://openalex.org/F4320332161","display_name":"National Institutes of Health","ror":"https://ror.org/01cwqze88"},{"id":"https://openalex.org/F4320337351","display_name":"National Cancer Institute","ror":"https://ror.org/040gcmg81"},{"id":"https://openalex.org/F4320337372","display_name":"U.S. National Library of Medicine","ror":"https://ror.org/0060t0j89"}],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":14,"referenced_works":["https://openalex.org/W1523572153","https://openalex.org/W1985823023","https://openalex.org/W1987191607","https://openalex.org/W2031855875","https://openalex.org/W2084924279","https://openalex.org/W2124661665","https://openalex.org/W2142043313","https://openalex.org/W2149858388","https://openalex.org/W2154699417","https://openalex.org/W2155418451","https://openalex.org/W2156106394","https://openalex.org/W2469412979","https://openalex.org/W2556090403","https://openalex.org/W4235035462"],"related_works":["https://openalex.org/W2596774623","https://openalex.org/W3138371475","https://openalex.org/W261778542","https://openalex.org/W1525021111","https://openalex.org/W2113892406","https://openalex.org/W2104690544","https://openalex.org/W7097295990","https://openalex.org/W2949067670","https://openalex.org/W3026224769","https://openalex.org/W4226092339"],"abstract_inverted_index":{"SUMMARY:":[0],"DIFFpop":[1,84],"is":[2,85],"an":[3,88],"R":[4],"package":[5],"designed":[6],"to":[7,23,28,72],"simulate":[8,24],"cellular":[9],"differentiation":[10],"hierarchies":[11],"using":[12],"either":[13],"exponentially-expanding":[14],"or":[15,66],"fixed":[16],"population":[17],"sizes.":[18],"The":[19,53],"software":[20,54],"includes":[21],"functionalities":[22],"clonal":[25],"evolution":[26],"due":[27],"the":[29,35,56],"emergence":[30],"of":[31,46,64,76],"driver":[32],"mutations":[33],"under":[34],"infinite-allele":[36],"assumption":[37],"as":[38,40,87],"well":[39],"options":[41],"for":[42],"simulation":[43],"and":[44,50,61,79],"analysis":[45],"single":[47],"cell":[48,77],"barcoding":[49],"labeling":[51],"data.":[52],"uses":[55],"Gillespie":[57],"Stochastic":[58],"Simulation":[59],"Algorithm":[60],"a":[62,73],"modification":[63],"expanding":[65],"fixed-size":[67],"stochastic":[68],"process":[69],"models":[70],"expanded":[71],"large":[74],"number":[75],"types":[78],"scenarios.":[80],"AVAILABILITY":[81],"AND":[82],"IMPLEMENTATION:":[83],"available":[86,101],"R-package":[89],"along":[90],"with":[91],"vignettes":[92],"on":[93],"Github":[94],"(https://github.com/ferlicjl/diffpop).":[95],"SUPPLEMENTARY":[96],"INFORMATION:":[97],"Supplementary":[98],"data":[99],"are":[100],"at":[102],"Bioinformatics":[103],"online.":[104]},"counts_by_year":[{"year":2023,"cited_by_count":1},{"year":2021,"cited_by_count":1},{"year":2020,"cited_by_count":1}],"updated_date":"2026-10-31T12:09:11.096373","created_date":"2019-03-11T00:00:00"}