{"id":"https://openalex.org/W7221124496","doi":"https://doi.org/10.64898/2026.10.03.756406","title":"\u2018broadSeq\u2019, a benchmarking tool to contrast differential gene expression methods and identify when genomic neighbourhood matters","display_name":"\u2018broadSeq\u2019, a benchmarking tool to contrast differential gene expression methods and identify when genomic neighbourhood matters","publication_year":2026,"publication_date":"2026-10-09","ids":{"openalex":"https://openalex.org/W7221124496","doi":"https://doi.org/10.64898/2026.10.03.756406"},"language":"en","primary_location":{"id":"doi:10.64898/2026.10.03.756406","doi":"https://doi.org/10.64898/2026.10.03.756406","is_oa":true,"landing_page_url":"https://doi.org/10.64898/2026.10.03.756406","pdf_url":"https://www.biorxiv.org/content/biorxiv/early/2026/10/09/2026.10.03.756406.full.pdf","source":{"id":"https://openalex.org/S4306402567","display_name":"bioRxiv (Cold Spring Harbor Laboratory)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"listed_in":[],"host_organization":"https://openalex.org/I2750212522","host_organization_name":"Cold Spring Harbor Laboratory","host_organization_lineage":["https://openalex.org/I2750212522"],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by-nd","license_id":"https://openalex.org/licenses/cc-by-nd","version":"acceptedVersion","is_accepted":true,"is_published":false,"raw_source_name":"bioRxiv","raw_type":"posted-content"},"volume":null,"type":"preprint","is_traditional":true,"indexed_in":["crossref"],"open_access":{"is_oa":true,"oa_status":"green","oa_url":"https://www.biorxiv.org/content/biorxiv/early/2026/10/09/2026.10.03.756406.full.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5020176343","display_name":"Rishi Das Roy","orcid":"https://orcid.org/0000-0002-3276-7279","observed_orcids":["https://orcid.org/0000-0002-3276-7279"]},"institutions":[{"id":"https://openalex.org/I133731052","display_name":"University of Helsinki","ror":"https://ror.org/040af2s02","country_code":"FI","type":"education","lineage":["https://openalex.org/I133731052"]},{"id":"https://openalex.org/I4391768107","display_name":"HiLIFE \u2013 El\u00e4m\u00e4ntieteiden Instituutti","ror":"https://ror.org/018bh0m68","country_code":"FI","type":"facility","lineage":["https://openalex.org/I133731052","https://openalex.org/I4391768107"]}],"countries":["FI"],"is_corresponding":true,"raw_author_name":"Rishi Das Roy","raw_affiliation_strings":["Institute of Biotechnology, Helsinki Institute of Life Science, University of Helsinki, Helsinki, Finland"],"raw_orcid":"https://orcid.org/0000-0002-3276-7279","affiliations":[{"raw_affiliation_string":"Institute of Biotechnology, Helsinki Institute of Life Science, University of Helsinki, Helsinki, Finland","institution_ids":["https://openalex.org/I133731052","https://openalex.org/I4391768107"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5003720548","display_name":"Outi K. Hallikas","orcid":"https://orcid.org/0000-0001-9791-2628","observed_orcids":["https://orcid.org/0000-0001-9791-2628"]},"institutions":[{"id":"https://openalex.org/I133731052","display_name":"University of Helsinki","ror":"https://ror.org/040af2s02","country_code":"FI","type":"education","lineage":["https://openalex.org/I133731052"]},{"id":"https://openalex.org/I4391768107","display_name":"HiLIFE \u2013 El\u00e4m\u00e4ntieteiden Instituutti","ror":"https://ror.org/018bh0m68","country_code":"FI","type":"facility","lineage":["https://openalex.org/I133731052","https://openalex.org/I4391768107"]}],"countries":["FI"],"is_corresponding":false,"raw_author_name":"Outi K. Hallikas","raw_affiliation_strings":["Institute of Biotechnology, Helsinki Institute of Life Science, University of Helsinki, Helsinki, Finland"],"raw_orcid":"https://orcid.org/0000-0001-9791-2628","affiliations":[{"raw_affiliation_string":"Institute of Biotechnology, Helsinki Institute of Life Science, University of Helsinki, Helsinki, Finland","institution_ids":["https://openalex.org/I133731052","https://openalex.org/I4391768107"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5028639293","display_name":"Satu Kuure","orcid":"https://orcid.org/0000-0002-9076-0622","observed_orcids":["https://orcid.org/0000-0002-9076-0622"]},"institutions":[{"id":"https://openalex.org/I133731052","display_name":"University of Helsinki","ror":"https://ror.org/040af2s02","country_code":"FI","type":"education","lineage":["https://openalex.org/I133731052"]},{"id":"https://openalex.org/I4391768107","display_name":"HiLIFE \u2013 El\u00e4m\u00e4ntieteiden Instituutti","ror":"https://ror.org/018bh0m68","country_code":"FI","type":"facility","lineage":["https://openalex.org/I133731052","https://openalex.org/I4391768107"]}],"countries":["FI"],"is_corresponding":false,"raw_author_name":"Satu H. Kuure","raw_affiliation_strings":["GM Unit, Helsinki Institute of Life Science, University of Helsinki, Helsinki, Finland","STEMM, Research Programs Unit, Faculty of Medicine, University of Helsinki, Helsinki, Finland"],"raw_orcid":"https://orcid.org/0000-0002-9076-0622","affiliations":[{"raw_affiliation_string":"GM Unit, Helsinki Institute of Life Science, University of Helsinki, Helsinki, Finland","institution_ids":["https://openalex.org/I133731052","https://openalex.org/I4391768107"]},{"raw_affiliation_string":"STEMM, Research Programs Unit, Faculty of Medicine, University of Helsinki, Helsinki, Finland","institution_ids":["https://openalex.org/I133731052"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5020804258","display_name":"Jukka Jernvall","orcid":"https://orcid.org/0000-0001-6575-8486","observed_orcids":["https://orcid.org/0000-0001-6575-8486"]},"institutions":[{"id":"https://openalex.org/I133731052","display_name":"University of Helsinki","ror":"https://ror.org/040af2s02","country_code":"FI","type":"education","lineage":["https://openalex.org/I133731052"]},{"id":"https://openalex.org/I4391768107","display_name":"HiLIFE \u2013 El\u00e4m\u00e4ntieteiden Instituutti","ror":"https://ror.org/018bh0m68","country_code":"FI","type":"facility","lineage":["https://openalex.org/I133731052","https://openalex.org/I4391768107"]}],"countries":["FI"],"is_corresponding":false,"raw_author_name":"Jukka Jernvall","raw_affiliation_strings":["Department of Geosciences and Geography, University of Helsinki, Helsinki, Finland","Institute of Biotechnology, Helsinki Institute of Life Science, University of Helsinki, Helsinki, Finland"],"raw_orcid":"https://orcid.org/0000-0001-6575-8486","affiliations":[{"raw_affiliation_string":"Department of Geosciences and Geography, University of Helsinki, Helsinki, Finland","institution_ids":["https://openalex.org/I133731052"]},{"raw_affiliation_string":"Institute of Biotechnology, Helsinki Institute of Life Science, University of Helsinki, Helsinki, Finland","institution_ids":["https://openalex.org/I133731052","https://openalex.org/I4391768107"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":2,"corresponding_author_ids":["https://openalex.org/A5020176343"],"corresponding_institution_ids":["https://openalex.org/I133731052","https://openalex.org/I4391768107"],"apc_list":null,"apc_paid":null,"fwci":null,"has_fulltext":true,"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/T10885","display_name":"Gene expression and cancer classification","score":0.9901999831199646,"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/T10885","display_name":"Gene expression and cancer classification","score":0.9901999831199646,"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":0.004399999976158142,"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":0.0035000001080334187,"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/differential-gene-expression","display_name":"differential gene expression","score":0.9089999794960022},{"id":"https://openalex.org/keywords/benchmarking","display_name":"benchmarking","score":0.531000018119812},{"id":"https://openalex.org/keywords/highly-expressed-genes","display_name":"highly expressed genes","score":0.7599999904632568},{"id":"https://openalex.org/keywords/developmental-gene-regulation","display_name":"developmental gene regulation","score":0.6570000052452087},{"id":"https://openalex.org/keywords/mouse-embryonic-development","display_name":"mouse embryo development","score":0.7839999794960022},{"id":"https://openalex.org/keywords/human-tumors","display_name":"human cancer","score":0.6549999713897705},{"id":"https://openalex.org/keywords/bioconductor-package","display_name":"Bioconductor package","score":0.6449999809265137},{"id":"https://openalex.org/keywords/deseq2","display_name":"DESeq2","score":0.6859999895095825},{"id":"https://openalex.org/keywords/limma","display_name":"limma","score":0.9279999732971191},{"id":"https://openalex.org/keywords/edger","display_name":"edgeR","score":0.7910000085830688}],"concepts":[{"id":"https://openalex.org/C86251818","wikidata":"https://www.wikidata.org/wiki/Q816754","display_name":"Benchmarking","level":2,"score":0.7397000193595886},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.676800012588501},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.6294000148773193},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.6017000079154968},{"id":"https://openalex.org/C2779694297","wikidata":"https://www.wikidata.org/wiki/Q2888953","display_name":"Bioconductor","level":3,"score":0.4733000099658966},{"id":"https://openalex.org/C18431079","wikidata":"https://www.wikidata.org/wiki/Q1502169","display_name":"Gene expression profiling","level":4,"score":0.45019999146461487},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.4399000108242035},{"id":"https://openalex.org/C2987395477","wikidata":"https://www.wikidata.org/wiki/Q135085","display_name":"Gene ontology","level":4,"score":0.4343999922275543},{"id":"https://openalex.org/C150194340","wikidata":"https://www.wikidata.org/wiki/Q26972","display_name":"Gene expression","level":3,"score":0.41179999709129333},{"id":"https://openalex.org/C141231307","wikidata":"https://www.wikidata.org/wiki/Q7020","display_name":"Genome","level":3,"score":0.40720000863075256},{"id":"https://openalex.org/C189206191","wikidata":"https://www.wikidata.org/wiki/Q222046","display_name":"Genomics","level":4,"score":0.4027000069618225},{"id":"https://openalex.org/C185798385","wikidata":"https://www.wikidata.org/wiki/Q1161707","display_name":"Benchmark (surveying)","level":2,"score":0.4007999897003174},{"id":"https://openalex.org/C2908923196","wikidata":"https://www.wikidata.org/wiki/Q5205742","display_name":"Gene Annotation","level":4,"score":0.3937999904155731},{"id":"https://openalex.org/C161677786","wikidata":"https://www.wikidata.org/wiki/Q2478475","display_name":"Neighbourhood (mathematics)","level":2,"score":0.3522999882698059},{"id":"https://openalex.org/C105565629","wikidata":"https://www.wikidata.org/wiki/Q1248292","display_name":"Gene prediction","level":4,"score":0.35109999775886536},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.34119999408721924},{"id":"https://openalex.org/C197077220","wikidata":"https://www.wikidata.org/wiki/Q720988","display_name":"Human genome","level":4,"score":0.3328999876976013},{"id":"https://openalex.org/C2776502983","wikidata":"https://www.wikidata.org/wiki/Q690182","display_name":"Contrast (vision)","level":2,"score":0.32420000433921814},{"id":"https://openalex.org/C165864922","wikidata":"https://www.wikidata.org/wiki/Q411391","display_name":"Regulation of gene expression","level":3,"score":0.3240000009536743},{"id":"https://openalex.org/C90559484","wikidata":"https://www.wikidata.org/wiki/Q778379","display_name":"Expression (computer science)","level":2,"score":0.32190001010894775},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.3199000060558319},{"id":"https://openalex.org/C60644358","wikidata":"https://www.wikidata.org/wiki/Q128570","display_name":"Bioinformatics","level":1,"score":0.3167000114917755},{"id":"https://openalex.org/C93226319","wikidata":"https://www.wikidata.org/wiki/Q193137","display_name":"Differential (mechanical device)","level":2,"score":0.2944999933242798},{"id":"https://openalex.org/C2776321320","wikidata":"https://www.wikidata.org/wiki/Q857525","display_name":"Annotation","level":2,"score":0.28679999709129333},{"id":"https://openalex.org/C177264268","wikidata":"https://www.wikidata.org/wiki/Q1514741","display_name":"Set (abstract data type)","level":2,"score":0.2782000005245209},{"id":"https://openalex.org/C127716648","wikidata":"https://www.wikidata.org/wiki/Q104053","display_name":"Phenotype","level":3,"score":0.2556999921798706},{"id":"https://openalex.org/C95371953","wikidata":"https://www.wikidata.org/wiki/Q591745","display_name":"DNA microarray","level":4,"score":0.2540999948978424}],"mesh":[],"locations_count":1,"locations":[{"id":"doi:10.64898/2026.10.03.756406","doi":"https://doi.org/10.64898/2026.10.03.756406","is_oa":true,"landing_page_url":"https://doi.org/10.64898/2026.10.03.756406","pdf_url":"https://www.biorxiv.org/content/biorxiv/early/2026/10/09/2026.10.03.756406.full.pdf","source":{"id":"https://openalex.org/S4306402567","display_name":"bioRxiv (Cold Spring Harbor Laboratory)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"listed_in":[],"host_organization":"https://openalex.org/I2750212522","host_organization_name":"Cold Spring Harbor Laboratory","host_organization_lineage":["https://openalex.org/I2750212522"],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by-nd","license_id":"https://openalex.org/licenses/cc-by-nd","version":"acceptedVersion","is_accepted":true,"is_published":false,"raw_source_name":"bioRxiv","raw_type":"posted-content"}],"best_oa_location":{"id":"doi:10.64898/2026.10.03.756406","doi":"https://doi.org/10.64898/2026.10.03.756406","is_oa":true,"landing_page_url":"https://doi.org/10.64898/2026.10.03.756406","pdf_url":"https://www.biorxiv.org/content/biorxiv/early/2026/10/09/2026.10.03.756406.full.pdf","source":{"id":"https://openalex.org/S4306402567","display_name":"bioRxiv (Cold Spring Harbor Laboratory)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"listed_in":[],"host_organization":"https://openalex.org/I2750212522","host_organization_name":"Cold Spring Harbor Laboratory","host_organization_lineage":["https://openalex.org/I2750212522"],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by-nd","license_id":"https://openalex.org/licenses/cc-by-nd","version":"acceptedVersion","is_accepted":true,"is_published":false,"raw_source_name":"bioRxiv","raw_type":"posted-content"},"sustainable_development_goals":[],"study_designs":[],"awards":[],"funders":[{"id":"https://openalex.org/F4320322725","display_name":"China Scholarship Council","ror":"https://ror.org/04atp4p48"},{"id":"https://openalex.org/F4320333873","display_name":"Helsinki Institute of Life Science, Helsingin Yliopisto","ror":"https://ror.org/018bh0m68"}],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W7221124496.pdf","grobid_xml":"https://content.openalex.org/works/W7221124496.grobid-xml"},"referenced_works_count":0,"referenced_works":[],"related_works":["https://openalex.org/W3197067492","https://openalex.org/W2793274076","https://openalex.org/W2114405789","https://openalex.org/W4308863994","https://openalex.org/W2163915946","https://openalex.org/W2899618079","https://openalex.org/W2730135604","https://openalex.org/W2119034410","https://openalex.org/W4405178313","https://openalex.org/W2611100408"],"abstract_inverted_index":{"Abstract":[0],"Several":[1],"tools":[2,227],"are":[3,123,177],"available":[4],"to":[5,18,48,80,155,185,209,234],"detect":[6],"differential":[7,217],"gene":[8,22,37,164],"expression.":[9],"The":[10,120],"predominant":[11],"approach":[12],"of":[13,142,152,206,219],"different":[14,100,111],"statistical":[15],"methods":[16,84,137,240],"is":[17],"consider":[19],"changes":[20],"in":[21,40,53,59,214],"expression":[23,38,218],"independent":[24],"from":[25,110,124],"their":[26,242],"genomic":[27,42],"context.":[28],"Previously,":[29],"DELocal":[30,45,147,176,207],"was":[31,46],"introduced":[32],"that":[33,103,135,170],"takes":[34],"into":[35],"consideration":[36],"dynamics":[39],"the":[41,125,156,160,171,186,190,203,212,226,238],"neighbourhood.":[43],"Whereas":[44],"shown":[47],"identify":[49],"developmentally":[50],"regulated":[51],"genes":[52,153,162,174,187,197],"developing":[54,107],"mouse":[55,108],"tooth,":[56],"its":[57],"performance":[58],"other":[60,70,157,191],"biological":[61],"conditions":[62],"remains":[63],"undetermined.":[64],"To":[65],"benchmark":[66],"DElocal":[67],"together":[68],"with":[69],"methods,":[71],"we":[72,95,224],"develop":[73],"another":[74],"tool":[75],"\u2018broadSeq\u2019.":[76],"It":[77],"provides":[78],"easy":[79],"use":[81],"interface":[82],"for":[83,211,241],"like":[85],"DELocal,":[86],"deseq2,":[87],"limma,":[88],"edger,":[89],"EBSeq":[90],"and":[91,115,131,165,180,236,244],"many":[92],"more.":[93],"Here":[94],"report":[96],"benchmarking":[97],"results":[98],"on":[99],"data":[101,243],"sets":[102,151],"comprise":[104],"wild":[105],"type":[106],"organs":[109],"embryonic":[112],"time":[113],"points,":[114],"also":[116,181],"human":[117],"cancer":[118],"data.":[119],"examined":[121],"datasets":[122],"heart,":[126],"kidney,":[127],"liver,":[128],"brain,":[129],"forebrain,":[130],"hindbrain.":[132],"We":[133],"found":[134],"most":[136],"produce":[138],"relatively":[139,199],"comparable":[140],"lists":[141],"differentially":[143],"expressed":[144,183,196,221],"genes.":[145,222],"Nevertheless,":[146],"identifies":[148],"partially":[149],"distinct":[150],"compared":[154,184],"methods.":[158,192],"Evaluating":[159],"identified":[161,188],"using":[163],"disease":[166],"ontology":[167],"terms":[168],"show":[169,198],"uniquely":[172],"detected":[173],"by":[175,189],"biologically":[178],"relevant":[179],"highly":[182,195,220],"Because":[193],"consistently":[194],"subtle":[200],"fold":[201],"changes,":[202],"neighbourhood":[204],"concept":[205],"appears":[208],"correct":[210],"difficulty":[213],"detecting":[215],"these":[216],"Finally,":[223],"provide":[225],"as":[228],"combined":[229],"bioconductor":[230],"packages,":[231],"allowing":[232],"researchers":[233],"explore":[235],"decide":[237],"best":[239],"questions.":[245]},"counts_by_year":[],"updated_date":"2026-11-08T12:12:28.789561","created_date":"2026-10-10T00:00:00"}
