{"id":"https://openalex.org/W2765219164","doi":"https://doi.org/10.1093/bioinformatics/btx812","title":"TCGA-assembler 2: software pipeline for retrieval and processing of TCGA/CPTAC data","display_name":"TCGA-assembler 2: software pipeline for retrieval and processing of TCGA/CPTAC data","publication_year":2017,"publication_date":"2017-12-19","ids":{"openalex":"https://openalex.org/W2765219164","doi":"https://doi.org/10.1093/bioinformatics/btx812","mag":"2765219164","pmid":"https://pubmed.ncbi.nlm.nih.gov/29272348"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/btx812","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btx812","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/34/9/1615/25120883/btx812.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","pubmed"],"open_access":{"is_oa":true,"oa_status":"bronze","oa_url":"https://academic.oup.com/bioinformatics/article-pdf/34/9/1615/25120883/btx812.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5006470567","display_name":"Lin Wei","orcid":"https://orcid.org/0000-0001-7146-891X"},"institutions":[{"id":"https://openalex.org/I1339509835","display_name":"NorthShore University HealthSystem","ror":"https://ror.org/04tpp9d61","country_code":"US","type":"healthcare","lineage":["https://openalex.org/I1339509835"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Lin Wei","raw_affiliation_strings":["Program of Computational Genomics & Medicine, NorthShore University HealthSystem, Evanston, IL, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Program of Computational Genomics & Medicine, NorthShore University HealthSystem, Evanston, IL, USA","institution_ids":["https://openalex.org/I1339509835"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5057878360","display_name":"Zhilin Jin","orcid":"https://orcid.org/0000-0003-0963-6155"},"institutions":[{"id":"https://openalex.org/I145311948","display_name":"Johns Hopkins University","ror":"https://ror.org/00za53h95","country_code":"US","type":"education","lineage":["https://openalex.org/I145311948"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Zhilin Jin","raw_affiliation_strings":["Department of Applied Mathematics & Statistics, Johns Hopkins University, Baltimore, MD, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Applied Mathematics & Statistics, Johns Hopkins University, Baltimore, MD, USA","institution_ids":["https://openalex.org/I145311948"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5032772839","display_name":"Shengjie Yang","orcid":"https://orcid.org/0000-0001-6398-317X"},"institutions":[{"id":"https://openalex.org/I1339509835","display_name":"NorthShore University HealthSystem","ror":"https://ror.org/04tpp9d61","country_code":"US","type":"healthcare","lineage":["https://openalex.org/I1339509835"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Shengjie Yang","raw_affiliation_strings":["Program of Computational Genomics & Medicine, NorthShore University HealthSystem, Evanston, IL, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Program of Computational Genomics & Medicine, NorthShore University HealthSystem, Evanston, IL, USA","institution_ids":["https://openalex.org/I1339509835"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5056825063","display_name":"Yanxun Xu","orcid":"https://orcid.org/0000-0001-5554-8637"},"institutions":[{"id":"https://openalex.org/I145311948","display_name":"Johns Hopkins University","ror":"https://ror.org/00za53h95","country_code":"US","type":"education","lineage":["https://openalex.org/I145311948"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Yanxun Xu","raw_affiliation_strings":["Department of Applied Mathematics & Statistics, Johns Hopkins University, Baltimore, MD, USA"],"raw_orcid":"https://orcid.org/0000-0001-5554-8637","affiliations":[{"raw_affiliation_string":"Department of Applied Mathematics & Statistics, Johns Hopkins University, Baltimore, MD, USA","institution_ids":["https://openalex.org/I145311948"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5110108746","display_name":"Yitan Zhu","orcid":null},"institutions":[{"id":"https://openalex.org/I1339509835","display_name":"NorthShore University HealthSystem","ror":"https://ror.org/04tpp9d61","country_code":"US","type":"healthcare","lineage":["https://openalex.org/I1339509835"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Yitan Zhu","raw_affiliation_strings":["Program of Computational Genomics & Medicine, NorthShore University HealthSystem, Evanston, IL, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Program of Computational Genomics & Medicine, NorthShore University HealthSystem, Evanston, IL, USA","institution_ids":["https://openalex.org/I1339509835"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5080090747","display_name":"Yuan Ji","orcid":"https://orcid.org/0000-0003-4712-5567"},"institutions":[{"id":"https://openalex.org/I1339509835","display_name":"NorthShore University HealthSystem","ror":"https://ror.org/04tpp9d61","country_code":"US","type":"healthcare","lineage":["https://openalex.org/I1339509835"]},{"id":"https://openalex.org/I169222155","display_name":"Chicago Department of Public Health","ror":"https://ror.org/045v7ay82","country_code":"US","type":"government","lineage":["https://openalex.org/I169222155"]},{"id":"https://openalex.org/I40347166","display_name":"University of Chicago","ror":"https://ror.org/024mw5h28","country_code":"US","type":"education","lineage":["https://openalex.org/I40347166"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Yuan Ji","raw_affiliation_strings":["Department of Public Health Sciences, University of Chicago, Chicago, IL, USA","Program of Computational Genomics & Medicine, NorthShore University HealthSystem, Evanston, IL, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Public Health Sciences, University of Chicago, Chicago, IL, USA","institution_ids":["https://openalex.org/I169222155","https://openalex.org/I40347166"]},{"raw_affiliation_string":"Program of Computational Genomics & Medicine, NorthShore University HealthSystem, Evanston, IL, USA","institution_ids":["https://openalex.org/I1339509835"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":6,"corresponding_author_ids":["https://openalex.org/A5080090747","https://openalex.org/A5110108746"],"corresponding_institution_ids":["https://openalex.org/I1339509835","https://openalex.org/I169222155","https://openalex.org/I40347166"],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":null,"fwci":17.0245,"has_fulltext":true,"cited_by_count":234,"citation_normalized_percentile":{"value":0.99477354,"is_in_top_1_percent":true,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":99,"max":100},"biblio":{"volume":"34","issue":"9","first_page":"1615","last_page":"1617"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T11297","display_name":"Ferroptosis and cancer prognosis","score":0.8798999786376953,"subfield":{"id":"https://openalex.org/subfields/2740","display_name":"Pulmonary and Respiratory 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/T11297","display_name":"Ferroptosis and cancer prognosis","score":0.8798999786376953,"subfield":{"id":"https://openalex.org/subfields/2740","display_name":"Pulmonary and Respiratory Medicine"},"field":{"id":"https://openalex.org/fields/27","display_name":"Medicine"},"domain":{"id":"https://openalex.org/domains/4","display_name":"Health Sciences"}},{"id":"https://openalex.org/T11289","display_name":"Single-cell and spatial transcriptomics","score":0.05079999938607216,"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/T11287","display_name":"Cancer Genomics and Diagnostics","score":0.013000000268220901,"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/upload","display_name":"Upload","score":0.691778838634491},{"id":"https://openalex.org/keywords/pipeline","display_name":"Pipeline (software)","score":0.5817270874977112},{"id":"https://openalex.org/keywords/software","display_name":"Software","score":0.5674504637718201},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.5565382242202759},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.4998457431793213},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.3625047206878662},{"id":"https://openalex.org/keywords/world-wide-web","display_name":"World Wide Web","score":0.1795683205127716},{"id":"https://openalex.org/keywords/operating-system","display_name":"Operating system","score":0.141845703125}],"concepts":[{"id":"https://openalex.org/C71901391","wikidata":"https://www.wikidata.org/wiki/Q7126699","display_name":"Upload","level":2,"score":0.691778838634491},{"id":"https://openalex.org/C43521106","wikidata":"https://www.wikidata.org/wiki/Q2165493","display_name":"Pipeline (software)","level":2,"score":0.5817270874977112},{"id":"https://openalex.org/C2777904410","wikidata":"https://www.wikidata.org/wiki/Q7397","display_name":"Software","level":2,"score":0.5674504637718201},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.5565382242202759},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.4998457431793213},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.3625047206878662},{"id":"https://openalex.org/C136764020","wikidata":"https://www.wikidata.org/wiki/Q466","display_name":"World Wide Web","level":1,"score":0.1795683205127716},{"id":"https://openalex.org/C111919701","wikidata":"https://www.wikidata.org/wiki/Q9135","display_name":"Operating system","level":1,"score":0.141845703125}],"mesh":[{"descriptor_ui":"D009369","descriptor_name":"Neoplasms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D009369","descriptor_name":"Neoplasms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D009369","descriptor_name":"Neoplasms","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":"D016247","descriptor_name":"Information Storage and Retrieval","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016247","descriptor_name":"Information Storage and Retrieval","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016247","descriptor_name":"Information Storage and Retrieval","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016678","descriptor_name":"Genome","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016678","descriptor_name":"Genome","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016678","descriptor_name":"Genome","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D023281","descriptor_name":"Genomics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D023281","descriptor_name":"Genomics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D023281","descriptor_name":"Genomics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D040901","descriptor_name":"Proteomics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D040901","descriptor_name":"Proteomics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D040901","descriptor_name":"Proteomics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false}],"locations_count":3,"locations":[{"id":"doi:10.1093/bioinformatics/btx812","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btx812","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/34/9/1615/25120883/btx812.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"},{"id":"pmid:29272348","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/29272348","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:pubmedcentral.nih.gov:5925773","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/5925773","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,"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"}],"best_oa_location":{"id":"doi:10.1093/bioinformatics/btx812","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btx812","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/34/9/1615/25120883/btx812.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":[{"score":0.4000000059604645,"display_name":"Partnerships for the goals","id":"https://metadata.un.org/sdg/17"}],"awards":[{"id":"https://openalex.org/G4432308873","display_name":null,"funder_award_id":"2R01 CA132897","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"}],"funders":[{"id":"https://openalex.org/F4320332161","display_name":"National Institutes of Health","ror":"https://ror.org/01cwqze88"}],"has_content":{"grobid_xml":true,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2765219164.pdf","grobid_xml":"https://content.openalex.org/works/W2765219164.grobid-xml"},"referenced_works_count":9,"referenced_works":["https://openalex.org/W2044702943","https://openalex.org/W2095463689","https://openalex.org/W2096283457","https://openalex.org/W2105435586","https://openalex.org/W2120016245","https://openalex.org/W2230320310","https://openalex.org/W2329659234","https://openalex.org/W2464880876","https://openalex.org/W2560367415"],"related_works":["https://openalex.org/W4391375266","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/W1971568933"],"abstract_inverted_index":{"Motivation:":[0],"The":[1],"Cancer":[2],"Genome":[3],"Atlas":[4],"(TCGA)":[5],"program":[6],"has":[7],"produced":[8],"huge":[9],"amounts":[10],"of":[11,32,60,71,130,166],"cancer":[12],"genomics":[13],"data":[14,39,45,61,70,101,118,161,199],"providing":[15],"unprecedented":[16],"opportunities":[17],"for":[18,28,90],"research.":[19,164],"In":[20,36,66],"2014,":[21],"we":[22],"developed":[23],"TCGA-Assembler,":[24],"a":[25,57],"software":[26,137],"pipeline":[27],"retrieval":[29,64],"and":[30,63,99,105,116,121,136,156,159,173,183,187],"processing":[31],"public":[33],"TCGA":[34,38,44,72,158,182],"data.":[35,185],"2016,":[37],"were":[40,87],"transferred":[41],"from":[42,102,119,151],"the":[43,48,78,128],"portal":[46],"to":[47,97,113,132,154,170,176],"Genomic":[49],"Data":[50],"Commons":[51],"(GDCs),":[52],"which":[53,86],"is":[54,95],"supported":[55],"by":[56,77],"different":[58],"set":[59],"storage":[62],"mechanisms.":[65],"addition,":[67],"new":[68,174],"proteomics":[69],"samples":[73],"have":[74,145],"been":[75],"generated":[76],"Clinical":[79],"Proteomic":[80],"Tumor":[81],"Analysis":[82],"Consortium":[83],"(CPTAC)":[84],"program,":[85],"not":[88],"available":[89,201],"downloading":[91],"through":[92],"TCGA-Assembler.":[93],"It":[94],"desirable":[96],"acquire":[98],"integrate":[100,117],"both":[103],"GDC":[104,120],"CPTAC.":[106,122],"Results:":[107],"We":[108,123],"develop":[109],"TCGA-assembler":[110],"2":[111],"(TA2)":[112],"automatically":[114],"download":[115],"make":[124],"substantial":[125],"improvement":[126],"on":[127,181],"functionality":[129],"TA2":[131,139,167],"enhance":[133],"user":[134],"experience":[135],"performance.":[138],"together":[140],"with":[141],"its":[142],"previous":[143],"version":[144],"helped":[146],"more":[147],"than":[148],"2000":[149],"researchers":[150],"64":[152],"countries":[153],"access":[155],"utilize":[157],"CPTAC":[160,184],"in":[162],"their":[163],"Availability":[165,186],"will":[168],"continue":[169],"allow":[171],"existing":[172],"users":[175],"conduct":[177],"reproducible":[178],"research":[179],"based":[180],"implementation:":[188],"http://www.compgenome.org/TCGA-Assembler/":[189],"or":[190,194],"https://github.com/compgenome365/TCGA-Assembler-2.":[191],"Contact:":[192],"zhuyitan@gmail.com":[193],"koaeraser@gmail.com.":[195],"Supplementary":[196,198],"information:":[197],"are":[200],"at":[202],"Bioinformatics":[203],"online.":[204]},"counts_by_year":[{"year":2026,"cited_by_count":3},{"year":2025,"cited_by_count":7},{"year":2024,"cited_by_count":39},{"year":2023,"cited_by_count":33},{"year":2022,"cited_by_count":29},{"year":2021,"cited_by_count":40},{"year":2020,"cited_by_count":40},{"year":2019,"cited_by_count":32},{"year":2018,"cited_by_count":11}],"updated_date":"2026-05-21T06:26:12.895304","created_date":"2025-10-10T00:00:00"}
