{"id":"https://openalex.org/W2145677203","doi":"https://doi.org/10.1093/bioinformatics/btg087","title":"ALES: cell lineage analysis and mapping of developmental events","display_name":"ALES: cell lineage analysis and mapping of developmental events","publication_year":2003,"publication_date":"2003-04-30","ids":{"openalex":"https://openalex.org/W2145677203","doi":"https://doi.org/10.1093/bioinformatics/btg087","mag":"2145677203"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/btg087","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btg087","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/19/7/851/48904305/bioinformatics_19_7_851.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"],"open_access":{"is_oa":true,"oa_status":"bronze","oa_url":"https://academic.oup.com/bioinformatics/article-pdf/19/7/851/48904305/bioinformatics_19_7_851.pdf","any_repository_has_fulltext":false},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5058329623","display_name":"V Braun","orcid":"https://orcid.org/0009-0004-7860-3714"},"institutions":[{"id":"https://openalex.org/I4210151100","display_name":"DKFZ-ZMBH Alliance","ror":"https://ror.org/05x8b4491","country_code":"DE","type":"facility","lineage":["https://openalex.org/I1305996414","https://openalex.org/I17937529","https://openalex.org/I223822909","https://openalex.org/I4210151100"]},{"id":"https://openalex.org/I17937529","display_name":"German Cancer Research Center","ror":"https://ror.org/04cdgtt98","country_code":"DE","type":"facility","lineage":["https://openalex.org/I1305996414","https://openalex.org/I17937529"]}],"countries":["DE"],"is_corresponding":true,"raw_author_name":"V. Braun","raw_affiliation_strings":["Division of Medical and Biological Informatics, Deutsches Krebsforschungszentrum, Im Neuenheimer Feld 280, D-69120, Heidelberg, Germany,","German cancer Research Center (DKFZ);"],"affiliations":[{"raw_affiliation_string":"Division of Medical and Biological Informatics, Deutsches Krebsforschungszentrum, Im Neuenheimer Feld 280, D-69120, Heidelberg, Germany,","institution_ids":["https://openalex.org/I4210151100","https://openalex.org/I17937529"]},{"raw_affiliation_string":"German cancer Research Center (DKFZ);","institution_ids":["https://openalex.org/I17937529"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5076747646","display_name":"Ricardo B. R. Azevedo","orcid":"https://orcid.org/0000-0001-5402-7071"},"institutions":[{"id":"https://openalex.org/I47508984","display_name":"Imperial College London","ror":"https://ror.org/041kmwe10","country_code":"GB","type":"education","lineage":["https://openalex.org/I47508984"]},{"id":"https://openalex.org/I44461941","display_name":"University of Houston","ror":"https://ror.org/048sx0r50","country_code":"US","type":"education","lineage":["https://openalex.org/I44461941"]}],"countries":["GB","US"],"is_corresponding":false,"raw_author_name":"R. B. R. Azevedo","raw_affiliation_strings":["Department of Biology and Biochemistry, University of Houston, Houston, TX 77204, USA","Department of Biology, Imperial College, Silwood Park, Ascot, Berks SL5 5PY, UK and","University of Houston","Imperial College London"],"affiliations":[{"raw_affiliation_string":"Department of Biology and Biochemistry, University of Houston, Houston, TX 77204, USA","institution_ids":["https://openalex.org/I44461941"]},{"raw_affiliation_string":"Department of Biology, Imperial College, Silwood Park, Ascot, Berks SL5 5PY, UK and","institution_ids":["https://openalex.org/I47508984"]},{"raw_affiliation_string":"University of Houston","institution_ids":["https://openalex.org/I44461941"]},{"raw_affiliation_string":"Imperial College London","institution_ids":["https://openalex.org/I47508984"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5040886993","display_name":"Markus Gumbel","orcid":"https://orcid.org/0000-0001-7657-9678"},"institutions":[{"id":"https://openalex.org/I4210151100","display_name":"DKFZ-ZMBH Alliance","ror":"https://ror.org/05x8b4491","country_code":"DE","type":"facility","lineage":["https://openalex.org/I1305996414","https://openalex.org/I17937529","https://openalex.org/I223822909","https://openalex.org/I4210151100"]},{"id":"https://openalex.org/I17937529","display_name":"German Cancer Research Center","ror":"https://ror.org/04cdgtt98","country_code":"DE","type":"facility","lineage":["https://openalex.org/I1305996414","https://openalex.org/I17937529"]}],"countries":["DE"],"is_corresponding":false,"raw_author_name":"M. Gumbel","raw_affiliation_strings":["Division of Medical and Biological Informatics, Deutsches Krebsforschungszentrum, Im Neuenheimer Feld 280, D-69120, Heidelberg, Germany,","German cancer Research Center (DKFZ);"],"affiliations":[{"raw_affiliation_string":"Division of Medical and Biological Informatics, Deutsches Krebsforschungszentrum, Im Neuenheimer Feld 280, D-69120, Heidelberg, Germany,","institution_ids":["https://openalex.org/I4210151100","https://openalex.org/I17937529"]},{"raw_affiliation_string":"German cancer Research Center (DKFZ);","institution_ids":["https://openalex.org/I17937529"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5113686222","display_name":"P.-M. Agapow","orcid":null},"institutions":[{"id":"https://openalex.org/I47508984","display_name":"Imperial College London","ror":"https://ror.org/041kmwe10","country_code":"GB","type":"education","lineage":["https://openalex.org/I47508984"]}],"countries":["GB"],"is_corresponding":false,"raw_author_name":"P.-M. Agapow","raw_affiliation_strings":["Department of Biology, Imperial College, Silwood Park, Ascot, Berks SL5 5PY, UK and","Imperial College London,#TAB#"],"affiliations":[{"raw_affiliation_string":"Department of Biology, Imperial College, Silwood Park, Ascot, Berks SL5 5PY, UK and","institution_ids":["https://openalex.org/I47508984"]},{"raw_affiliation_string":"Imperial College London,#TAB#","institution_ids":["https://openalex.org/I47508984"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5113992080","display_name":"Armand M. Leroi","orcid":null},"institutions":[{"id":"https://openalex.org/I47508984","display_name":"Imperial College London","ror":"https://ror.org/041kmwe10","country_code":"GB","type":"education","lineage":["https://openalex.org/I47508984"]}],"countries":["GB"],"is_corresponding":false,"raw_author_name":"A. M. Leroi","raw_affiliation_strings":["Department of Biology, Imperial College, Silwood Park, Ascot, Berks SL5 5PY, UK and","Imperial College London,#TAB#"],"affiliations":[{"raw_affiliation_string":"Department of Biology, Imperial College, Silwood Park, Ascot, Berks SL5 5PY, UK and","institution_ids":["https://openalex.org/I47508984"]},{"raw_affiliation_string":"Imperial College London,#TAB#","institution_ids":["https://openalex.org/I47508984"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5110249460","display_name":"H.-P. Meinzer","orcid":null},"institutions":[{"id":"https://openalex.org/I17937529","display_name":"German Cancer Research Center","ror":"https://ror.org/04cdgtt98","country_code":"DE","type":"facility","lineage":["https://openalex.org/I1305996414","https://openalex.org/I17937529"]},{"id":"https://openalex.org/I4210151100","display_name":"DKFZ-ZMBH Alliance","ror":"https://ror.org/05x8b4491","country_code":"DE","type":"facility","lineage":["https://openalex.org/I1305996414","https://openalex.org/I17937529","https://openalex.org/I223822909","https://openalex.org/I4210151100"]}],"countries":["DE"],"is_corresponding":false,"raw_author_name":"H.-P. Meinzer","raw_affiliation_strings":["Division of Medical and Biological Informatics, Deutsches Krebsforschungszentrum, Im Neuenheimer Feld 280, D-69120, Heidelberg, Germany,","Imaging and Radiooncology"],"affiliations":[{"raw_affiliation_string":"Division of Medical and Biological Informatics, Deutsches Krebsforschungszentrum, Im Neuenheimer Feld 280, D-69120, Heidelberg, Germany,","institution_ids":["https://openalex.org/I4210151100","https://openalex.org/I17937529"]},{"raw_affiliation_string":"Imaging and Radiooncology","institution_ids":[]}]}],"institutions":[],"countries_distinct_count":3,"institutions_distinct_count":6,"corresponding_author_ids":["https://openalex.org/A5058329623"],"corresponding_institution_ids":["https://openalex.org/I17937529","https://openalex.org/I4210151100"],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":null,"fwci":0.7298,"has_fulltext":true,"cited_by_count":28,"citation_normalized_percentile":{"value":0.65821389,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":96},"biblio":{"volume":"19","issue":"7","first_page":"851","last_page":"858"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10676","display_name":"Genetics, Aging, and Longevity in Model Organisms","score":0.9983000159263611,"subfield":{"id":"https://openalex.org/subfields/1302","display_name":"Aging"},"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/T10676","display_name":"Genetics, Aging, and Longevity in Model Organisms","score":0.9983000159263611,"subfield":{"id":"https://openalex.org/subfields/1302","display_name":"Aging"},"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":0.9979000091552734,"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/T10887","display_name":"Bioinformatics and Genomic Networks","score":0.9966999888420105,"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/lineage","display_name":"Lineage (genetic)","score":0.8735333681106567},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.703102707862854},{"id":"https://openalex.org/keywords/java","display_name":"Java","score":0.5719771981239319},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.4318956136703491},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.42391911149024963},{"id":"https://openalex.org/keywords/range","display_name":"Range (aeronautics)","score":0.4221023619174957},{"id":"https://openalex.org/keywords/evolutionary-biology","display_name":"Evolutionary biology","score":0.4129788279533386},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.37285393476486206},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.24586451053619385},{"id":"https://openalex.org/keywords/programming-language","display_name":"Programming language","score":0.1217494010925293}],"concepts":[{"id":"https://openalex.org/C2776817793","wikidata":"https://www.wikidata.org/wiki/Q6553369","display_name":"Lineage (genetic)","level":3,"score":0.8735333681106567},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.703102707862854},{"id":"https://openalex.org/C548217200","wikidata":"https://www.wikidata.org/wiki/Q251","display_name":"Java","level":2,"score":0.5719771981239319},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.4318956136703491},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.42391911149024963},{"id":"https://openalex.org/C204323151","wikidata":"https://www.wikidata.org/wiki/Q905424","display_name":"Range (aeronautics)","level":2,"score":0.4221023619174957},{"id":"https://openalex.org/C78458016","wikidata":"https://www.wikidata.org/wiki/Q840400","display_name":"Evolutionary biology","level":1,"score":0.4129788279533386},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.37285393476486206},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.24586451053619385},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.1217494010925293},{"id":"https://openalex.org/C159985019","wikidata":"https://www.wikidata.org/wiki/Q181790","display_name":"Composite material","level":1,"score":0.0},{"id":"https://openalex.org/C192562407","wikidata":"https://www.wikidata.org/wiki/Q228736","display_name":"Materials science","level":0,"score":0.0}],"mesh":[],"locations_count":1,"locations":[{"id":"doi:10.1093/bioinformatics/btg087","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btg087","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/19/7/851/48904305/bioinformatics_19_7_851.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"}],"best_oa_location":{"id":"doi:10.1093/bioinformatics/btg087","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btg087","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/19/7/851/48904305/bioinformatics_19_7_851.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":[],"funders":[{"id":"https://openalex.org/F4320332167","display_name":"Directorate for Biological Sciences","ror":"https://ror.org/001xhss06"},{"id":"https://openalex.org/F4320334631","display_name":"Natural Environment Research Council","ror":"https://ror.org/02b5d8509"}],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2145677203.pdf","grobid_xml":"https://content.openalex.org/works/W2145677203.grobid-xml"},"referenced_works_count":40,"referenced_works":["https://openalex.org/W1009009446","https://openalex.org/W1486498922","https://openalex.org/W1493346936","https://openalex.org/W1507651926","https://openalex.org/W1596141725","https://openalex.org/W1638203394","https://openalex.org/W1702768734","https://openalex.org/W1922647928","https://openalex.org/W1961420666","https://openalex.org/W1964289914","https://openalex.org/W1965652261","https://openalex.org/W1966131183","https://openalex.org/W1969042688","https://openalex.org/W1969996060","https://openalex.org/W1986006829","https://openalex.org/W1989952069","https://openalex.org/W2000324184","https://openalex.org/W2002089154","https://openalex.org/W2004436791","https://openalex.org/W2006242478","https://openalex.org/W2011389479","https://openalex.org/W2035993805","https://openalex.org/W2041837169","https://openalex.org/W2050276219","https://openalex.org/W2057924146","https://openalex.org/W2080882038","https://openalex.org/W2090360081","https://openalex.org/W2093082135","https://openalex.org/W2110974835","https://openalex.org/W2130727968","https://openalex.org/W2178606245","https://openalex.org/W2225309729","https://openalex.org/W2313677986","https://openalex.org/W2417162181","https://openalex.org/W2485343961","https://openalex.org/W4230960895","https://openalex.org/W4231648965","https://openalex.org/W4232336112","https://openalex.org/W4302339081","https://openalex.org/W6602406204"],"related_works":["https://openalex.org/W2160430275","https://openalex.org/W1554470851","https://openalex.org/W2920061786","https://openalex.org/W2654359665","https://openalex.org/W2625912121","https://openalex.org/W4389300316","https://openalex.org/W2621246910","https://openalex.org/W4379055781","https://openalex.org/W2000015384","https://openalex.org/W2136345656"],"abstract_inverted_index":{"Abstract":[0],"Motivation:":[1],"Animals":[2],"build":[3],"their":[4],"bodies":[5],"by":[6],"altering":[7],"the":[8,22,28,40,56,97,106],"fates":[9,29],"of":[10,24,30,102,108,120,129,160],"cells.":[11,32,89],"The":[12,127,171],"way":[13],"in":[14,21,59,162],"which":[15],"they":[16],"do":[17],"so":[18],"is":[19,186],"reflected":[20],"topology":[23],"cell":[25,60,70,81,103],"lineages":[26,34,82,104,148,154],"and":[27,54,100,111,191],"terminal":[31],"Cell":[33],"should,":[35],"therefore,":[36],"contain":[37],"information":[38,57],"about":[39,167],"molecular":[41,110],"events":[42,113,132],"that":[43,122],"determined":[44],"them.":[45],"Here":[46],"we":[47],"introduce":[48],"new":[49],"tools":[50,63],"for":[51,188],"visualizing,":[52],"manipulating,":[53],"extracting":[55],"contained":[58],"lineages.":[61],"Our":[62],"enable":[64],"us":[65],"to":[66,137,157,164],"analyze":[67],"very":[68],"large":[69],"lineages,":[71],"where":[72],"previously":[73],"analyses":[74],"have":[75],"only":[76],"been":[77],"carried":[78],"out":[79],"on":[80,175],"no":[83],"larger":[84],"than":[85],"a":[86,118,158,180],"few":[87],"dozen":[88],"Results:":[90],"Ales":[91,116,185],"(A":[92],"Lineage":[93],"Evaluation":[94],"System)":[95],"allows":[96],"display,":[98],"evaluation":[99],"comparison":[101],"with":[105,179],"aim":[107],"identifying":[109],"cellular":[112,143],"underlying":[114],"development.":[115],"introduces":[117],"series":[119],"algorithms":[121],"locate":[123],"putative":[124],"developmental":[125],"events.":[126],"distribution":[128],"these":[130],"predicted":[131],"can":[133,149,173,192],"then":[134],"be":[135,150,193,204],"compared":[136],"gene":[138],"expression":[139],"patterns":[140],"or":[141,152],"other":[142],"characteristics.":[144],"In":[145],"addition,":[146],"artificial":[147],"generated,":[151],"existing":[153],"modified,":[155],"according":[156],"range":[159],"models,":[161],"order":[163],"test":[165],"hypotheses":[166],"lineage":[168],"evolution.":[169],"Availability:":[170],"program":[172],"run":[174],"any":[176],"operating":[177],"system":[178],"compliant":[181],"Java":[182],"2":[183],"environment.":[184],"free":[187],"academic":[189],"use":[190],"downloaded":[194],"from":[195],"http://mbi.dkfz-heidelberg.de/mbi/research/cellsim/ales.":[196],"Contact:":[197],"CellO@dkfz-heidelberg.de":[198],"*":[199],"To":[200],"whom":[201],"correspondence":[202],"should":[203],"addressed.":[205]},"counts_by_year":[{"year":2020,"cited_by_count":1},{"year":2014,"cited_by_count":1},{"year":2012,"cited_by_count":2}],"updated_date":"2025-11-06T03:46:38.306776","created_date":"2016-06-24T00:00:00"}
