{"id":"https://openalex.org/W4393763573","doi":"https://doi.org/10.5281/zenodo.6401895","title":"Deterministic evolution and stringent selection during pre-neoplasia","display_name":"Deterministic evolution and stringent selection during pre-neoplasia","publication_year":2023,"publication_date":"2023-04-05","ids":{"openalex":"https://openalex.org/W4393763573","doi":"https://doi.org/10.5281/zenodo.6401895"},"language":"en","primary_location":{"id":"doi:10.5281/zenodo.6401895","is_oa":true,"landing_page_url":"https://doi.org/10.5281/zenodo.6401895","pdf_url":null,"source":{"id":"https://openalex.org/S4306400562","display_name":"Zenodo (CERN European Organization for Nuclear Research)","issn_l":null,"issn":null,"is_oa":true,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I67311998","host_organization_name":"European Organization for Nuclear Research","host_organization_lineage":["https://openalex.org/I67311998"],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":null,"is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":"Dataset"},"type":"dataset","indexed_in":["datacite"],"open_access":{"is_oa":true,"oa_status":"green","oa_url":"https://doi.org/10.5281/zenodo.6401895","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5042031442","display_name":"Kasper Karlsson","orcid":"https://orcid.org/0000-0003-0162-1354"},"institutions":[{"id":"https://openalex.org/I97018004","display_name":"Stanford University","ror":"https://ror.org/00f54p054","country_code":"US","type":"education","lineage":["https://openalex.org/I97018004"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Karlsson, Kasper","raw_affiliation_strings":["Stanford University, CA, USA"],"raw_orcid":"https://orcid.org/0000-0003-0162-1354","affiliations":[{"raw_affiliation_string":"Stanford University, CA, USA","institution_ids":["https://openalex.org/I97018004"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5074626747","display_name":"Moritz J. Przybilla","orcid":"https://orcid.org/0000-0001-5645-9492"},"institutions":[{"id":"https://openalex.org/I97018004","display_name":"Stanford University","ror":"https://ror.org/00f54p054","country_code":"US","type":"education","lineage":["https://openalex.org/I97018004"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Przybilla, Moritz J.","raw_affiliation_strings":["Stanford University, CA, USA"],"raw_orcid":"https://orcid.org/0000-0001-5645-9492","affiliations":[{"raw_affiliation_string":"Stanford University, CA, USA","institution_ids":["https://openalex.org/I97018004"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5013151095","display_name":"Eran Kotler","orcid":"https://orcid.org/0000-0002-1463-7462"},"institutions":[{"id":"https://openalex.org/I97018004","display_name":"Stanford University","ror":"https://ror.org/00f54p054","country_code":"US","type":"education","lineage":["https://openalex.org/I97018004"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Kotler, Eran","raw_affiliation_strings":["Stanford University, CA, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Stanford University, CA, USA","institution_ids":["https://openalex.org/I97018004"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5050509301","display_name":"Aziz Khan","orcid":"https://orcid.org/0000-0002-6459-6224"},"institutions":[{"id":"https://openalex.org/I97018004","display_name":"Stanford University","ror":"https://ror.org/00f54p054","country_code":"US","type":"education","lineage":["https://openalex.org/I97018004"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Khan, Aziz","raw_affiliation_strings":["Stanford University, CA, USA"],"raw_orcid":"https://orcid.org/0000-0002-6459-6224","affiliations":[{"raw_affiliation_string":"Stanford University, CA, USA","institution_ids":["https://openalex.org/I97018004"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5100736944","display_name":"Hang Xu","orcid":"https://orcid.org/0000-0002-5847-655X"},"institutions":[{"id":"https://openalex.org/I97018004","display_name":"Stanford University","ror":"https://ror.org/00f54p054","country_code":"US","type":"education","lineage":["https://openalex.org/I97018004"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Xu, Hang","raw_affiliation_strings":["Stanford University, CA, USA"],"raw_orcid":"https://orcid.org/0000-0002-5847-655X","affiliations":[{"raw_affiliation_string":"Stanford University, CA, USA","institution_ids":["https://openalex.org/I97018004"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5035624512","display_name":"Kremena Karagyozova","orcid":"https://orcid.org/0000-0001-5484-5680"},"institutions":[{"id":"https://openalex.org/I97018004","display_name":"Stanford University","ror":"https://ror.org/00f54p054","country_code":"US","type":"education","lineage":["https://openalex.org/I97018004"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Karagyozova, Kremena","raw_affiliation_strings":["Stanford University, CA, USA"],"raw_orcid":"https://orcid.org/0000-0001-5484-5680","affiliations":[{"raw_affiliation_string":"Stanford University, CA, USA","institution_ids":["https://openalex.org/I97018004"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5084890610","display_name":"Alexandra Sockell","orcid":"https://orcid.org/0000-0002-8725-9415"},"institutions":[{"id":"https://openalex.org/I97018004","display_name":"Stanford University","ror":"https://ror.org/00f54p054","country_code":"US","type":"education","lineage":["https://openalex.org/I97018004"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Sockell, Alexandra","raw_affiliation_strings":["Stanford University, CA, USA"],"raw_orcid":"https://orcid.org/0000-0002-8725-9415","affiliations":[{"raw_affiliation_string":"Stanford University, CA, USA","institution_ids":["https://openalex.org/I97018004"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5015401462","display_name":"Wing Hung Wong","orcid":"https://orcid.org/0000-0001-7466-2339"},"institutions":[{"id":"https://openalex.org/I97018004","display_name":"Stanford University","ror":"https://ror.org/00f54p054","country_code":"US","type":"education","lineage":["https://openalex.org/I97018004"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Wong, Wing H.","raw_affiliation_strings":["Stanford University, CA, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Stanford University, CA, USA","institution_ids":["https://openalex.org/I97018004"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5091371230","display_name":"Katherine Liu","orcid":"https://orcid.org/0000-0002-9616-9403"},"institutions":[{"id":"https://openalex.org/I97018004","display_name":"Stanford University","ror":"https://ror.org/00f54p054","country_code":"US","type":"education","lineage":["https://openalex.org/I97018004"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Liu, Katherine","raw_affiliation_strings":["Stanford University, CA, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Stanford University, CA, USA","institution_ids":["https://openalex.org/I97018004"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5030948779","display_name":"Amanda T. Mah","orcid":"https://orcid.org/0000-0001-9137-4937"},"institutions":[{"id":"https://openalex.org/I97018004","display_name":"Stanford University","ror":"https://ror.org/00f54p054","country_code":"US","type":"education","lineage":["https://openalex.org/I97018004"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Mah, Amanda","raw_affiliation_strings":["Stanford University, CA, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Stanford University, CA, USA","institution_ids":["https://openalex.org/I97018004"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5109231448","display_name":"Yuan\u2010Hung Lo","orcid":"https://orcid.org/0000-0002-9704-3124"},"institutions":[{"id":"https://openalex.org/I97018004","display_name":"Stanford University","ror":"https://ror.org/00f54p054","country_code":"US","type":"education","lineage":["https://openalex.org/I97018004"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Lo, Yuan-Hung","raw_affiliation_strings":["Stanford University, CA, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Stanford University, CA, USA","institution_ids":["https://openalex.org/I97018004"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5050387311","display_name":"Bingxin Lu","orcid":"https://orcid.org/0000-0002-0606-5150"},"institutions":[{"id":"https://openalex.org/I45129253","display_name":"University College London","ror":"https://ror.org/02jx3x895","country_code":"GB","type":"education","lineage":["https://openalex.org/I124357947","https://openalex.org/I45129253"]}],"countries":["GB"],"is_corresponding":false,"raw_author_name":"Lu, Bingxin","raw_affiliation_strings":["University College London, London, UK"],"raw_orcid":"https://orcid.org/0000-0002-0606-5150","affiliations":[{"raw_affiliation_string":"University College London, London, UK","institution_ids":["https://openalex.org/I45129253"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5087801978","display_name":"Kathleen E. Houlahan","orcid":"https://orcid.org/0000-0002-2273-2099"},"institutions":[{"id":"https://openalex.org/I97018004","display_name":"Stanford University","ror":"https://ror.org/00f54p054","country_code":"US","type":"education","lineage":["https://openalex.org/I97018004"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Houlahan, Kathleen E.","raw_affiliation_strings":["Stanford University, CA, USA"],"raw_orcid":"https://orcid.org/0000-0002-2273-2099","affiliations":[{"raw_affiliation_string":"Stanford University, CA, USA","institution_ids":["https://openalex.org/I97018004"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5025947508","display_name":"Zhicheng Ma","orcid":"https://orcid.org/0000-0001-8499-0045"},"institutions":[{"id":"https://openalex.org/I97018004","display_name":"Stanford University","ror":"https://ror.org/00f54p054","country_code":"US","type":"education","lineage":["https://openalex.org/I97018004"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Ma, Zhicheng","raw_affiliation_strings":["Stanford University, CA, USA"],"raw_orcid":"https://orcid.org/0000-0001-8499-0045","affiliations":[{"raw_affiliation_string":"Stanford University, CA, USA","institution_ids":["https://openalex.org/I97018004"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5081896361","display_name":"Carlos J. Suarez","orcid":"https://orcid.org/0000-0002-4531-9723"},"institutions":[{"id":"https://openalex.org/I97018004","display_name":"Stanford University","ror":"https://ror.org/00f54p054","country_code":"US","type":"education","lineage":["https://openalex.org/I97018004"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Suarez, Carlos J.","raw_affiliation_strings":["Stanford University, CA, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Stanford University, CA, USA","institution_ids":["https://openalex.org/I97018004"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5031424617","display_name":"C. Barnes","orcid":"https://orcid.org/0000-0002-9459-1395"},"institutions":[{"id":"https://openalex.org/I45129253","display_name":"University College London","ror":"https://ror.org/02jx3x895","country_code":"GB","type":"education","lineage":["https://openalex.org/I124357947","https://openalex.org/I45129253"]}],"countries":["GB"],"is_corresponding":false,"raw_author_name":"Barnes, Chris P.","raw_affiliation_strings":["University College London, London, UK"],"raw_orcid":"https://orcid.org/0000-0002-9459-1395","affiliations":[{"raw_affiliation_string":"University College London, London, UK","institution_ids":["https://openalex.org/I45129253"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5056685479","display_name":"Calvin J. Kuo","orcid":"https://orcid.org/0000-0002-7427-5985"},"institutions":[{"id":"https://openalex.org/I97018004","display_name":"Stanford University","ror":"https://ror.org/00f54p054","country_code":"US","type":"education","lineage":["https://openalex.org/I97018004"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Kuo, Calvin J.","raw_affiliation_strings":["Stanford University, CA, USA"],"raw_orcid":"https://orcid.org/0000-0002-7427-5985","affiliations":[{"raw_affiliation_string":"Stanford University, CA, USA","institution_ids":["https://openalex.org/I97018004"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5036849769","display_name":"Christina Curtis","orcid":"https://orcid.org/0000-0003-0166-3802"},"institutions":[{"id":"https://openalex.org/I97018004","display_name":"Stanford University","ror":"https://ror.org/00f54p054","country_code":"US","type":"education","lineage":["https://openalex.org/I97018004"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Curtis, Christina","raw_affiliation_strings":["Stanford University, CA, USA"],"raw_orcid":"https://orcid.org/0000-0003-0166-3802","affiliations":[{"raw_affiliation_string":"Stanford University, CA, USA","institution_ids":["https://openalex.org/I97018004"]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":2,"corresponding_author_ids":[],"corresponding_institution_ids":[],"apc_list":null,"apc_paid":null,"fwci":null,"has_fulltext":false,"cited_by_count":0,"citation_normalized_percentile":null,"cited_by_percentile_year":null,"biblio":{"volume":null,"issue":null,"first_page":null,"last_page":null},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T13656","display_name":"Science, Research, and Medicine","score":0.125,"subfield":{"id":"https://openalex.org/subfields/2743","display_name":"Reproductive Medicine"},"field":{"id":"https://openalex.org/fields/27","display_name":"Medicine"},"domain":{"id":"https://openalex.org/domains/4","display_name":"Health Sciences"}},"topics":[{"id":"https://openalex.org/T13656","display_name":"Science, Research, and Medicine","score":0.125,"subfield":{"id":"https://openalex.org/subfields/2743","display_name":"Reproductive Medicine"},"field":{"id":"https://openalex.org/fields/27","display_name":"Medicine"},"domain":{"id":"https://openalex.org/domains/4","display_name":"Health Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/selection","display_name":"Selection (genetic algorithm)","score":0.7038300037384033},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.40622809529304504},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.3800661861896515},{"id":"https://openalex.org/keywords/evolutionary-biology","display_name":"Evolutionary biology","score":0.3682878911495209},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.2175423502922058}],"concepts":[{"id":"https://openalex.org/C81917197","wikidata":"https://www.wikidata.org/wiki/Q628760","display_name":"Selection (genetic algorithm)","level":2,"score":0.7038300037384033},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.40622809529304504},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.3800661861896515},{"id":"https://openalex.org/C78458016","wikidata":"https://www.wikidata.org/wiki/Q840400","display_name":"Evolutionary biology","level":1,"score":0.3682878911495209},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.2175423502922058}],"mesh":[],"locations_count":1,"locations":[{"id":"doi:10.5281/zenodo.6401895","is_oa":true,"landing_page_url":"https://doi.org/10.5281/zenodo.6401895","pdf_url":null,"source":{"id":"https://openalex.org/S4306400562","display_name":"Zenodo (CERN European Organization for Nuclear Research)","issn_l":null,"issn":null,"is_oa":true,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I67311998","host_organization_name":"European Organization for Nuclear Research","host_organization_lineage":["https://openalex.org/I67311998"],"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":"Dataset"}],"best_oa_location":{"id":"doi:10.5281/zenodo.6401895","is_oa":true,"landing_page_url":"https://doi.org/10.5281/zenodo.6401895","pdf_url":null,"source":{"id":"https://openalex.org/S4306400562","display_name":"Zenodo (CERN European Organization for Nuclear Research)","issn_l":null,"issn":null,"is_oa":true,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I67311998","host_organization_name":"European Organization for Nuclear Research","host_organization_lineage":["https://openalex.org/I67311998"],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":null,"is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":"Dataset"},"sustainable_development_goals":[],"awards":[],"funders":[],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":0,"referenced_works":[],"related_works":["https://openalex.org/W2748952813","https://openalex.org/W2082860237","https://openalex.org/W2119695867","https://openalex.org/W2130076355","https://openalex.org/W1990804418","https://openalex.org/W1993764875","https://openalex.org/W2046158694","https://openalex.org/W2788277189","https://openalex.org/W2013243191","https://openalex.org/W2061542922"],"abstract_inverted_index":{"The":[0],"earliest":[1,148],"events":[2],"during":[3],"human":[4,35],"tumor":[5],"initiation,":[6],"while":[7],"poorly":[8],"characterized,":[9],"may":[10],"hold":[11],"clues":[12],"to":[13,158],"malignancy":[14],"detection":[15,165],"and":[16,45,70,131,152,156,166],"prevention.":[17],"Here":[18],"we":[19],"model":[20],"occult":[21],"pre-neoplasia":[22],"by":[23],"bi-allelically":[24],"inactivating":[25],"<em>TP53</em>,":[26],"a":[27,132],"common":[28],"early":[29],"event":[30],"in":[31,34,53,74,138,146],"gastric":[32,36,75,88],"cancer,":[33],"organoids.":[37,141],"Causal":[38],"relationships":[39],"between":[40],"this":[41],"initiating":[42],"genetic":[43],"lesion":[44],"resulting":[46],"phenotypes":[47],"were":[48],"established":[49],"using":[50],"experimental":[51,124],"evolution":[52,125],"multiple":[54],"clonally":[55],"derived":[56],"cultures":[57],"over":[58],"two":[59],"years.":[60],"<em>TP53</em>":[61,86],"loss":[62],"elicited":[63],"progressive":[64],"aneuploidy,":[65],"including":[66],"copy":[67],"number":[68],"alterations":[69],"structural":[71],"variants":[72],"prevalent":[73],"cancers,":[76],"with":[77,101,112,161],"evident":[78],"preferred":[79],"orders.":[80],"Longitudinal":[81],"single":[82],"cell":[83],"sequencing":[84],"of":[85,135,150,168],"deficient":[87],"organoids":[89],"similarly":[90],"indicates":[91],"progression":[92],"towards":[93],"malignant":[94,159],"transcriptional":[95,114],"programs.":[96],"Moreover,":[97],"high-throughput":[98],"lineage":[99],"tracing":[100],"expressed":[102],"cellular":[103],"barcodes":[104],"demonstrates":[105],"reproducible":[106],"dynamics":[107],"whereby":[108],"initially":[109],"rare":[110],"subclones":[111],"shared":[113],"programs":[115],"repeatedly":[116],"attain":[117],"clonal":[118,129],"dominance.":[119],"This":[120],"powerful":[121],"platform":[122],"for":[123,163],"exposes":[126],"stringent":[127],"selection,":[128],"interference,":[130],"striking":[133],"degree":[134],"phenotypic":[136],"convergence":[137],"pre-malignant":[139],"epithelial":[140],"These":[142],"data":[143],"imply":[144],"predictability":[145],"the":[147],"stages":[149],"tumorigenesis":[151],"reveal":[153],"evolutionary":[154],"constraints":[155],"barriers":[157],"transformation":[160],"implications":[162],"earlier":[164],"interception":[167],"aggressive,":[169],"genome":[170],"instable":[171],"tumors.":[172]},"counts_by_year":[],"updated_date":"2026-07-01T06:00:48.157686","created_date":"2025-10-10T00:00:00"}
