{"id":"https://openalex.org/W4403394724","doi":"https://doi.org/10.1093/bioinformatics/btae608","title":"Xenomake: a pipeline for processing and sorting xenograft reads from spatial transcriptomic experiments","display_name":"Xenomake: a pipeline for processing and sorting xenograft reads from spatial transcriptomic experiments","publication_year":2024,"publication_date":"2024-10-10","ids":{"openalex":"https://openalex.org/W4403394724","doi":"https://doi.org/10.1093/bioinformatics/btae608","pmid":"https://pubmed.ncbi.nlm.nih.gov/39400332"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/btae608","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btae608","pdf_url":"https://academic.oup.com/bioinformatics/advance-article-pdf/doi/10.1093/bioinformatics/btae608/59748027/btae608.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":true,"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":"cc-by","license_id":"https://openalex.org/licenses/cc-by","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":"gold","oa_url":"https://academic.oup.com/bioinformatics/advance-article-pdf/doi/10.1093/bioinformatics/btae608/59748027/btae608.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5009742044","display_name":"Benjamin S Strope","orcid":null},"institutions":[{"id":"https://openalex.org/I181547552","display_name":"Baylor College of Medicine","ror":"https://ror.org/02pttbw34","country_code":"US","type":"education","lineage":["https://openalex.org/I181547552","https://openalex.org/I2801539370"]},{"id":"https://openalex.org/I4210150362","display_name":"Children's Cancer Center","ror":"https://ror.org/04rxd8128","country_code":"US","type":"nonprofit","lineage":["https://openalex.org/I4210150362"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Benjamin S Strope","raw_affiliation_strings":["Dan L Duncan Cancer Center, Baylor College of Medicine , Houston, TX, 77030,","Lester and Sue Smith Breast Center, Baylor College of Medicine , Houston, TX, 77030,","Dan L Duncan Cancer Center, Baylor College of Medicine, Houston, TX United States","Lester and Sue Smith Breast Center, Baylor College of Medicine, Houston, TX United States"],"affiliations":[{"raw_affiliation_string":"Dan L Duncan Cancer Center, Baylor College of Medicine , Houston, TX, 77030,","institution_ids":["https://openalex.org/I4210150362","https://openalex.org/I181547552"]},{"raw_affiliation_string":"Lester and Sue Smith Breast Center, Baylor College of Medicine , Houston, TX, 77030,","institution_ids":["https://openalex.org/I181547552"]},{"raw_affiliation_string":"Dan L Duncan Cancer Center, Baylor College of Medicine, Houston, TX United States","institution_ids":["https://openalex.org/I4210150362","https://openalex.org/I181547552"]},{"raw_affiliation_string":"Lester and Sue Smith Breast Center, Baylor College of Medicine, Houston, TX United States","institution_ids":["https://openalex.org/I181547552"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5068140710","display_name":"Katherine E. Pendleton","orcid":"https://orcid.org/0000-0001-9761-7303"},"institutions":[{"id":"https://openalex.org/I181547552","display_name":"Baylor College of Medicine","ror":"https://ror.org/02pttbw34","country_code":"US","type":"education","lineage":["https://openalex.org/I181547552","https://openalex.org/I2801539370"]},{"id":"https://openalex.org/I4210150362","display_name":"Children's Cancer Center","ror":"https://ror.org/04rxd8128","country_code":"US","type":"nonprofit","lineage":["https://openalex.org/I4210150362"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Katherine E Pendleton","raw_affiliation_strings":["Dan L Duncan Cancer Center, Baylor College of Medicine , Houston, TX, 77030,","Department of Molecular and Human Genetics, Baylor College of Medicine , Houston, TX, 77030,","Lester and Sue Smith Breast Center, Baylor College of Medicine , Houston, TX, 77030,","Lester and Sue Smith Breast Center, Baylor College of Medicine, Houston, TX United States","Dan L Duncan Cancer Center, Baylor College of Medicine, Houston, TX United States"],"affiliations":[{"raw_affiliation_string":"Dan L Duncan Cancer Center, Baylor College of Medicine , Houston, TX, 77030,","institution_ids":["https://openalex.org/I4210150362","https://openalex.org/I181547552"]},{"raw_affiliation_string":"Department of Molecular and Human Genetics, Baylor College of Medicine , Houston, TX, 77030,","institution_ids":["https://openalex.org/I181547552"]},{"raw_affiliation_string":"Lester and Sue Smith Breast Center, Baylor College of Medicine , Houston, TX, 77030,","institution_ids":["https://openalex.org/I181547552"]},{"raw_affiliation_string":"Lester and Sue Smith Breast Center, Baylor College of Medicine, Houston, TX United States","institution_ids":["https://openalex.org/I181547552"]},{"raw_affiliation_string":"Dan L Duncan Cancer Center, Baylor College of Medicine, Houston, TX United States","institution_ids":["https://openalex.org/I4210150362","https://openalex.org/I181547552"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5112829673","display_name":"William Bowie","orcid":null},"institutions":[{"id":"https://openalex.org/I181547552","display_name":"Baylor College of Medicine","ror":"https://ror.org/02pttbw34","country_code":"US","type":"education","lineage":["https://openalex.org/I181547552","https://openalex.org/I2801539370"]},{"id":"https://openalex.org/I4210150362","display_name":"Children's Cancer Center","ror":"https://ror.org/04rxd8128","country_code":"US","type":"nonprofit","lineage":["https://openalex.org/I4210150362"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"William Z Bowie","raw_affiliation_strings":["Dan L Duncan Cancer Center, Baylor College of Medicine , Houston, TX, 77030,","Lester and Sue Smith Breast Center, Baylor College of Medicine , Houston, TX, 77030,","Dan L Duncan Cancer Center, Baylor College of Medicine, Houston, TX United States","Lester and Sue Smith Breast Center, Baylor College of Medicine, Houston, TX United States"],"affiliations":[{"raw_affiliation_string":"Dan L Duncan Cancer Center, Baylor College of Medicine , Houston, TX, 77030,","institution_ids":["https://openalex.org/I4210150362","https://openalex.org/I181547552"]},{"raw_affiliation_string":"Lester and Sue Smith Breast Center, Baylor College of Medicine , Houston, TX, 77030,","institution_ids":["https://openalex.org/I181547552"]},{"raw_affiliation_string":"Dan L Duncan Cancer Center, Baylor College of Medicine, Houston, TX United States","institution_ids":["https://openalex.org/I4210150362","https://openalex.org/I181547552"]},{"raw_affiliation_string":"Lester and Sue Smith Breast Center, Baylor College of Medicine, Houston, TX United States","institution_ids":["https://openalex.org/I181547552"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5060919268","display_name":"Gloria V. Echeverria","orcid":"https://orcid.org/0000-0002-3772-9298"},"institutions":[{"id":"https://openalex.org/I181547552","display_name":"Baylor College of Medicine","ror":"https://ror.org/02pttbw34","country_code":"US","type":"education","lineage":["https://openalex.org/I181547552","https://openalex.org/I2801539370"]},{"id":"https://openalex.org/I4210150362","display_name":"Children's Cancer Center","ror":"https://ror.org/04rxd8128","country_code":"US","type":"nonprofit","lineage":["https://openalex.org/I4210150362"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Gloria V Echeverria","raw_affiliation_strings":["Dan L Duncan Cancer Center, Baylor College of Medicine , Houston, TX, 77030,","Department of Molecular and Cellular Biology, Baylor College of Medicine , Houston, TX, 77030,","Lester and Sue Smith Breast Center, Baylor College of Medicine , Houston, TX, 77030,","Dan L Duncan Cancer Center, Baylor College of Medicine, Houston, TX United States","Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX United States","Lester and Sue Smith Breast Center, Baylor College of Medicine, Houston, TX United States"],"affiliations":[{"raw_affiliation_string":"Dan L Duncan Cancer Center, Baylor College of Medicine , Houston, TX, 77030,","institution_ids":["https://openalex.org/I4210150362","https://openalex.org/I181547552"]},{"raw_affiliation_string":"Department of Molecular and Cellular Biology, Baylor College of Medicine , Houston, TX, 77030,","institution_ids":["https://openalex.org/I181547552"]},{"raw_affiliation_string":"Lester and Sue Smith Breast Center, Baylor College of Medicine , Houston, TX, 77030,","institution_ids":["https://openalex.org/I181547552"]},{"raw_affiliation_string":"Dan L Duncan Cancer Center, Baylor College of Medicine, Houston, TX United States","institution_ids":["https://openalex.org/I4210150362","https://openalex.org/I181547552"]},{"raw_affiliation_string":"Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX United States","institution_ids":["https://openalex.org/I181547552"]},{"raw_affiliation_string":"Lester and Sue Smith Breast Center, Baylor College of Medicine, Houston, TX United States","institution_ids":["https://openalex.org/I181547552"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5100616624","display_name":"Qian Zhu","orcid":"https://orcid.org/0000-0001-7062-8221"},"institutions":[{"id":"https://openalex.org/I181547552","display_name":"Baylor College of Medicine","ror":"https://ror.org/02pttbw34","country_code":"US","type":"education","lineage":["https://openalex.org/I181547552","https://openalex.org/I2801539370"]},{"id":"https://openalex.org/I4210150362","display_name":"Children's Cancer Center","ror":"https://ror.org/04rxd8128","country_code":"US","type":"nonprofit","lineage":["https://openalex.org/I4210150362"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Qian Zhu","raw_affiliation_strings":["Dan L Duncan Cancer Center, Baylor College of Medicine , Houston, TX, 77030,","Department of Molecular and Human Genetics, Baylor College of Medicine , Houston, TX, 77030,","Lester and Sue Smith Breast Center, Baylor College of Medicine , Houston, TX, 77030,","Lester and Sue Smith Breast Center, Baylor College of Medicine, Houston, TX United States","Dan L Duncan Cancer Center, Baylor College of Medicine, Houston, TX United States"],"affiliations":[{"raw_affiliation_string":"Dan L Duncan Cancer Center, Baylor College of Medicine , Houston, TX, 77030,","institution_ids":["https://openalex.org/I4210150362","https://openalex.org/I181547552"]},{"raw_affiliation_string":"Department of Molecular and Human Genetics, Baylor College of Medicine , Houston, TX, 77030,","institution_ids":["https://openalex.org/I181547552"]},{"raw_affiliation_string":"Lester and Sue Smith Breast Center, Baylor College of Medicine , Houston, TX, 77030,","institution_ids":["https://openalex.org/I181547552"]},{"raw_affiliation_string":"Lester and Sue Smith Breast Center, Baylor College of Medicine, Houston, TX United States","institution_ids":["https://openalex.org/I181547552"]},{"raw_affiliation_string":"Dan L Duncan Cancer Center, Baylor College of Medicine, Houston, TX United States","institution_ids":["https://openalex.org/I4210150362","https://openalex.org/I181547552"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":5,"corresponding_author_ids":["https://openalex.org/A5009742044"],"corresponding_institution_ids":["https://openalex.org/I181547552","https://openalex.org/I4210150362"],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":{"value":3618,"currency":"USD","value_usd":3618},"fwci":0.7084,"has_fulltext":true,"cited_by_count":3,"citation_normalized_percentile":{"value":0.70865338,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":90,"max":96},"biblio":{"volume":"40","issue":"11","first_page":null,"last_page":null},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T11289","display_name":"Single-cell and spatial transcriptomics","score":0.9995999932289124,"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":0.9995999932289124,"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/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.9898999929428101,"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/T11970","display_name":"Molecular Biology Techniques and Applications","score":0.9897000193595886,"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/pipeline","display_name":"Pipeline (software)","score":0.8735647201538086},{"id":"https://openalex.org/keywords/sorting","display_name":"Sorting","score":0.7347807288169861},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.7320888042449951},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.5618489980697632},{"id":"https://openalex.org/keywords/transcriptome","display_name":"Transcriptome","score":0.536470353603363},{"id":"https://openalex.org/keywords/relevance","display_name":"Relevance (law)","score":0.5281457901000977},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.3553308844566345},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.20479008555412292},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.19225099682807922},{"id":"https://openalex.org/keywords/gene-expression","display_name":"Gene expression","score":0.10845348238945007},{"id":"https://openalex.org/keywords/algorithm","display_name":"Algorithm","score":0.07718268036842346},{"id":"https://openalex.org/keywords/programming-language","display_name":"Programming language","score":0.0642341673374176},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.06059589982032776}],"concepts":[{"id":"https://openalex.org/C43521106","wikidata":"https://www.wikidata.org/wiki/Q2165493","display_name":"Pipeline (software)","level":2,"score":0.8735647201538086},{"id":"https://openalex.org/C111696304","wikidata":"https://www.wikidata.org/wiki/Q2303697","display_name":"Sorting","level":2,"score":0.7347807288169861},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.7320888042449951},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.5618489980697632},{"id":"https://openalex.org/C162317418","wikidata":"https://www.wikidata.org/wiki/Q252857","display_name":"Transcriptome","level":4,"score":0.536470353603363},{"id":"https://openalex.org/C158154518","wikidata":"https://www.wikidata.org/wiki/Q7310970","display_name":"Relevance (law)","level":2,"score":0.5281457901000977},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.3553308844566345},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.20479008555412292},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.19225099682807922},{"id":"https://openalex.org/C150194340","wikidata":"https://www.wikidata.org/wiki/Q26972","display_name":"Gene expression","level":3,"score":0.10845348238945007},{"id":"https://openalex.org/C11413529","wikidata":"https://www.wikidata.org/wiki/Q8366","display_name":"Algorithm","level":1,"score":0.07718268036842346},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.0642341673374176},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.06059589982032776},{"id":"https://openalex.org/C17744445","wikidata":"https://www.wikidata.org/wiki/Q36442","display_name":"Political science","level":0,"score":0.0},{"id":"https://openalex.org/C199539241","wikidata":"https://www.wikidata.org/wiki/Q7748","display_name":"Law","level":1,"score":0.0}],"mesh":[{"descriptor_ui":"D000818","descriptor_name":"Animals","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000818","descriptor_name":"Animals","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000818","descriptor_name":"Animals","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000818","descriptor_name":"Animals","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000818","descriptor_name":"Animals","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D009369","descriptor_name":"Neoplasms","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D009369","descriptor_name":"Neoplasms","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D009369","descriptor_name":"Neoplasms","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D009369","descriptor_name":"Neoplasms","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D009369","descriptor_name":"Neoplasms","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D009369","descriptor_name":"Neoplasms","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D009369","descriptor_name":"Neoplasms","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D009369","descriptor_name":"Neoplasms","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D009369","descriptor_name":"Neoplasms","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D009369","descriptor_name":"Neoplasms","qualifier_ui":"Q000378","qualifier_name":"metabolism","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":"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":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D020869","descriptor_name":"Gene Expression Profiling","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D020869","descriptor_name":"Gene Expression Profiling","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D020869","descriptor_name":"Gene Expression Profiling","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D020869","descriptor_name":"Gene Expression Profiling","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D020869","descriptor_name":"Gene Expression Profiling","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D051379","descriptor_name":"Mice","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D051379","descriptor_name":"Mice","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D051379","descriptor_name":"Mice","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D051379","descriptor_name":"Mice","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D051379","descriptor_name":"Mice","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D059467","descriptor_name":"Transcriptome","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D059467","descriptor_name":"Transcriptome","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D059467","descriptor_name":"Transcriptome","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D059467","descriptor_name":"Transcriptome","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D059467","descriptor_name":"Transcriptome","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true}],"locations_count":4,"locations":[{"id":"doi:10.1093/bioinformatics/btae608","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btae608","pdf_url":"https://academic.oup.com/bioinformatics/advance-article-pdf/doi/10.1093/bioinformatics/btae608/59748027/btae608.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":true,"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":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},{"id":"pmid:39400332","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/39400332","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:11583937","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/11583937","pdf_url":"https://pmc.ncbi.nlm.nih.gov/articles/PMC11583937/pdf/btae608.pdf","source":{"id":"https://openalex.org/S2764455111","display_name":"PubMed Central","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":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Bioinformatics","raw_type":"Text"},{"id":"pmh:oai:digitalcommons.library.tmc.edu:baylor_docs-3317","is_oa":false,"landing_page_url":"https://digitalcommons.library.tmc.edu/baylor_docs/2343","pdf_url":null,"source":{"id":"https://openalex.org/S4377196655","display_name":"Digital Commons-TMC (Texas Medical Center)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1337852284","host_organization_name":"Texas Medical Center","host_organization_lineage":["https://openalex.org/I1337852284"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Faculty and Staff Publications","raw_type":"text"}],"best_oa_location":{"id":"doi:10.1093/bioinformatics/btae608","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btae608","pdf_url":"https://academic.oup.com/bioinformatics/advance-article-pdf/doi/10.1093/bioinformatics/btae608/59748027/btae608.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":true,"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":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G1629133690","display_name":null,"funder_award_id":"RR200009","funder_id":"https://openalex.org/F4320308129","funder_display_name":"Cancer Prevention and Research Institute of Texas"},{"id":"https://openalex.org/G2036696608","display_name":null,"funder_award_id":"Moonshot","funder_id":"https://openalex.org/F4320332521","funder_display_name":"University of Texas MD Anderson Cancer Center"},{"id":"https://openalex.org/G2428140889","display_name":null,"funder_award_id":"CPRIT","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"},{"id":"https://openalex.org/G2532755588","display_name":null,"funder_award_id":"OD023469","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"},{"id":"https://openalex.org/G2891067765","display_name":null,"funder_award_id":"S10OD023469","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"},{"id":"https://openalex.org/G4159563929","display_name":null,"funder_award_id":"P30CA12512","funder_id":"https://openalex.org/F4320337351","funder_display_name":"National Cancer Institute"},{"id":"https://openalex.org/G4408295732","display_name":null,"funder_award_id":"P30CA12512","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"},{"id":"https://openalex.org/G4539825073","display_name":null,"funder_award_id":"CA1251","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"},{"id":"https://openalex.org/G5060956145","display_name":null,"funder_award_id":"CA125123","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"},{"id":"https://openalex.org/G5465708471","display_name":null,"funder_award_id":"CA125123","funder_id":"https://openalex.org/F4320337351","funder_display_name":"National Cancer Institute"},{"id":"https://openalex.org/G5789768335","display_name":null,"funder_award_id":"R200009","funder_id":"https://openalex.org/F4320308129","funder_display_name":"Cancer Prevention and Research Institute of Texas"},{"id":"https://openalex.org/G6839110211","display_name":null,"funder_award_id":"1S10OD023469","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"},{"id":"https://openalex.org/G7557813972","display_name":null,"funder_award_id":"CA125123","funder_id":"https://openalex.org/F4320310591","funder_display_name":"Dan L. Duncan Cancer Center, Baylor College of Medicine"},{"id":"https://openalex.org/G7837447426","display_name":null,"funder_award_id":"CA125123","funder_id":"https://openalex.org/F4320308129","funder_display_name":"Cancer Prevention and Research Institute of Texas"},{"id":"https://openalex.org/G8022820296","display_name":null,"funder_award_id":"1S10OD0","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"},{"id":"https://openalex.org/G8359624776","display_name":null,"funder_award_id":"P30CA125123","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"},{"id":"https://openalex.org/G8449249302","display_name":null,"funder_award_id":"P30CA125123","funder_id":"https://openalex.org/F4320310591","funder_display_name":"Dan L. Duncan Cancer Center, Baylor College of Medicine"},{"id":"https://openalex.org/G8481070465","display_name":null,"funder_award_id":"P30CA125123","funder_id":"https://openalex.org/F4320337351","funder_display_name":"National Cancer Institute"}],"funders":[{"id":"https://openalex.org/F4320308129","display_name":"Cancer Prevention and Research Institute of Texas","ror":"https://ror.org/0003xa228"},{"id":"https://openalex.org/F4320310591","display_name":"Dan L. Duncan Cancer Center, Baylor College of Medicine","ror":"https://ror.org/02pttbw34"},{"id":"https://openalex.org/F4320332161","display_name":"National Institutes of Health","ror":"https://ror.org/01cwqze88"},{"id":"https://openalex.org/F4320332521","display_name":"University of Texas MD Anderson Cancer Center","ror":"https://ror.org/04twxam07"},{"id":"https://openalex.org/F4320337351","display_name":"National Cancer Institute","ror":"https://ror.org/040gcmg81"},{"id":"https://openalex.org/F4320338247","display_name":"Moonshot Research and Development Program","ror":null},{"id":"https://openalex.org/F4320338404","display_name":"Cancer Moonshot","ror":null}],"has_content":{"grobid_xml":true,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W4403394724.pdf","grobid_xml":"https://content.openalex.org/works/W4403394724.grobid-xml"},"referenced_works_count":28,"referenced_works":["https://openalex.org/W2110417468","https://openalex.org/W2116688916","https://openalex.org/W2118952409","https://openalex.org/W2121964616","https://openalex.org/W2169456326","https://openalex.org/W2471536144","https://openalex.org/W2564066883","https://openalex.org/W2800392236","https://openalex.org/W2899235059","https://openalex.org/W2901738572","https://openalex.org/W2915848182","https://openalex.org/W2936989468","https://openalex.org/W2952109315","https://openalex.org/W2955247249","https://openalex.org/W3007935255","https://openalex.org/W3100967665","https://openalex.org/W3112563877","https://openalex.org/W3122109253","https://openalex.org/W3134482219","https://openalex.org/W3148116804","https://openalex.org/W3164692211","https://openalex.org/W4210644165","https://openalex.org/W4229033508","https://openalex.org/W4285819568","https://openalex.org/W4365148379","https://openalex.org/W4367625847","https://openalex.org/W4386034444","https://openalex.org/W4394823981"],"related_works":["https://openalex.org/W2399513595","https://openalex.org/W4388386498","https://openalex.org/W2028462563","https://openalex.org/W2982720988","https://openalex.org/W2739612537","https://openalex.org/W3150324899","https://openalex.org/W4392059188","https://openalex.org/W4388725868","https://openalex.org/W2104762330","https://openalex.org/W4379374180"],"abstract_inverted_index":{"Xenomake":[0],"is":[1,6],"an":[2],"open-source":[3],"program":[4],"that":[5],"available":[7],"on":[8],"Github":[9],"(https://github.com/qianzhulab/Xenomake).":[10],"Complete":[11],"documentation":[12],"can":[13],"be":[14],"found":[15],"at":[16],"the":[17],"link.":[18]},"counts_by_year":[{"year":2025,"cited_by_count":2},{"year":2024,"cited_by_count":1}],"updated_date":"2026-03-25T14:56:36.534964","created_date":"2025-10-10T00:00:00"}
