{"id":"https://openalex.org/W7201848571","doi":"https://doi.org/10.1186/s12859-026-06632-8","title":"PathwayBench: a multi-criterion benchmark of pseudobulk pathway activity scoring methods reveals rank-window truncation as a two-sided mechanism of biological signal loss in single-cell RNA-seq","display_name":"PathwayBench: a multi-criterion benchmark of pseudobulk pathway activity scoring methods reveals rank-window truncation as a two-sided mechanism of biological signal loss in single-cell RNA-seq","publication_year":2026,"publication_date":"2026-09-08","ids":{"openalex":"https://openalex.org/W7201848571","doi":"https://doi.org/10.1186/s12859-026-06632-8","pmid":"https://pubmed.ncbi.nlm.nih.gov/42466400","pmcid":"https://www.ncbi.nlm.nih.gov/pmc/articles/13370622"},"language":"en","primary_location":{"id":"doi:10.1186/s12859-026-06632-8","doi":"https://doi.org/10.1186/s12859-026-06632-8","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s12859-026-06632-8","pdf_url":null,"source":{"id":"https://openalex.org/S19032547","display_name":"BMC Bioinformatics","issn_l":"1471-2105","issn":["1471-2105"],"is_oa":true,"is_in_doaj":true,"is_core":true,"listed_in":["anvur-class-a","anvur-scientific","ccf-c","cwts-core","doaj","dongbi-c","doyens","jufo-1","ki-jl-1","medline","norway-2","oarl","poland-100","russia-white-list-1","vabb-shw"],"host_organization":"https://openalex.org/P4310320256","host_organization_name":"BioMed Central","host_organization_lineage":["https://openalex.org/P4310320256","https://openalex.org/P4310319965"],"host_organization_lineage_names":["BioMed Central","Springer Nature"],"type":"journal"},"license":"cc-by-nc-nd","license_id":"https://openalex.org/licenses/cc-by-nc-nd","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"BMC Bioinformatics","raw_type":"journal-article"},"parent_works":[],"lineage":["https://openalex.org/W7201848571"],"child_works_count":0,"type":"article","is_traditional":true,"indexed_in":["crossref","datacite","pubmed"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://doi.org/10.1186/s12859-026-06632-8","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5027472939","display_name":"Fadhl Alakwaa","orcid":"https://orcid.org/0000-0001-5349-7960","observed_orcids":["https://orcid.org/0000-0001-5349-7960"]},"institutions":[{"id":"https://openalex.org/I27837315","display_name":"University of Michigan","ror":"https://ror.org/00jmfr291","country_code":"US","type":"education","lineage":["https://openalex.org/I27837315"]},{"id":"https://openalex.org/I4210114445","display_name":"Michigan Medicine","ror":"https://ror.org/01zcpa714","country_code":"US","type":"healthcare","lineage":["https://openalex.org/I4210114445"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Fadhl M. Alakwaa","raw_affiliation_strings":["Division of Nephrology, Department of Internal Medicine, University of Michigan, Ann Arbor, MI, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Division of Nephrology, Department of Internal Medicine, University of Michigan, Ann Arbor, MI, USA","institution_ids":["https://openalex.org/I27837315","https://openalex.org/I4210114445"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5139582286","display_name":"Ahmed Elbaz","orcid":null,"observed_orcids":[]},"institutions":[{"id":"https://openalex.org/I80693520","display_name":"American University in Cairo","ror":"https://ror.org/0176yqn58","country_code":"EG","type":"education","lineage":["https://openalex.org/I80693520"]}],"countries":["EG"],"is_corresponding":false,"raw_author_name":"Ahmed Elbaz","raw_affiliation_strings":["American University in Cairo, Cairo, Egypt"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"American University in Cairo, Cairo, Egypt","institution_ids":["https://openalex.org/I80693520"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5133465600","display_name":"Sara Al Azzam","orcid":null,"observed_orcids":[]},"institutions":[{"id":"https://openalex.org/I156983542","display_name":"Jordan University of Science and Technology","ror":"https://ror.org/03y8mtb59","country_code":"JO","type":"education","lineage":["https://openalex.org/I156983542"]}],"countries":["JO"],"is_corresponding":false,"raw_author_name":"Sara Al Azzam","raw_affiliation_strings":["Jordan University of Science and Technology, Irbid, Jordan"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Jordan University of Science and Technology, Irbid, Jordan","institution_ids":["https://openalex.org/I156983542"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5133438002","display_name":"Tasnim Alshebani","orcid":null,"observed_orcids":[]},"institutions":[{"id":"https://openalex.org/I185443292","display_name":"Wayne State University","ror":"https://ror.org/01070mq45","country_code":"US","type":"education","lineage":["https://openalex.org/I185443292"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Tasnim Alshebani","raw_affiliation_strings":["Wayne State University, Detroit, MI, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Wayne State University, Detroit, MI, USA","institution_ids":["https://openalex.org/I185443292"]}]}],"institutions":[],"countries_distinct_count":3,"institutions_distinct_count":5,"corresponding_author_ids":["https://openalex.org/A5027472939"],"corresponding_institution_ids":["https://openalex.org/I27837315","https://openalex.org/I4210114445"],"apc_list":{"value":2990,"currency":"USD","value_usd":2990},"apc_paid":{"value":2990,"currency":"USD","value_usd":2990},"fwci":0.0,"has_fulltext":false,"cited_by_count":0,"citation_normalized_percentile":{"value":0.0,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"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/T10887","display_name":"Bioinformatics and Genomic Networks","score":0.5220000147819519,"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/T10887","display_name":"Bioinformatics and Genomic Networks","score":0.5220000147819519,"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/T11289","display_name":"Single-cell and spatial transcriptomics","score":0.47360000014305115,"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/T10885","display_name":"Gene expression and cancer classification","score":0.0006000000284984708,"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/single-cell-rna-sequencing","display_name":"single-cell RNA sequencing","score":0.9259999990463257},{"id":"https://openalex.org/keywords/pseudobulk-analysis","display_name":"pseudobulk analysis","score":0.8320000171661377},{"id":"https://openalex.org/keywords/case-control-comparison","display_name":"case-control comparison","score":0.5479999780654907},{"id":"https://openalex.org/keywords/benchmarking","display_name":"benchmarking","score":0.593999981880188},{"id":"https://openalex.org/keywords/aucell","display_name":"AUCell","score":0.9079999923706055},{"id":"https://openalex.org/keywords/ssgsea","display_name":"single-sample gene set enrichment analysis","score":0.9750000238418579},{"id":"https://openalex.org/keywords/gene-set-variation-analysis","display_name":"gene set variation analysis","score":0.9919999837875366},{"id":"https://openalex.org/keywords/z-score","display_name":"Z-score","score":0.7120000123977661},{"id":"https://openalex.org/keywords/extracellular-matrix-remodeling","display_name":"extracellular matrix remodeling","score":0.6069999933242798},{"id":"https://openalex.org/keywords/chronic-kidney-disease","display_name":"chronic kidney disease","score":0.9980000257492065},{"id":"https://openalex.org/keywords/outlier-robustness","display_name":"outlier robustness","score":0.49300000071525574}],"concepts":[{"id":"https://openalex.org/C185798385","wikidata":"https://www.wikidata.org/wiki/Q1161707","display_name":"Benchmark (surveying)","level":2,"score":0.766700029373169},{"id":"https://openalex.org/C63479239","wikidata":"https://www.wikidata.org/wiki/Q7353546","display_name":"Robustness (evolution)","level":3,"score":0.7289000153541565},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.4772999882698059},{"id":"https://openalex.org/C89611455","wikidata":"https://www.wikidata.org/wiki/Q6804646","display_name":"Mechanism (biology)","level":2,"score":0.4767000079154968},{"id":"https://openalex.org/C106195933","wikidata":"https://www.wikidata.org/wiki/Q7847935","display_name":"Truncation (statistics)","level":2,"score":0.39800000190734863},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.3522999882698059},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.3488999903202057},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.34119999408721924},{"id":"https://openalex.org/C73000952","wikidata":"https://www.wikidata.org/wiki/Q17007827","display_name":"Discretization","level":2,"score":0.3384999930858612},{"id":"https://openalex.org/C186060115","wikidata":"https://www.wikidata.org/wiki/Q30336093","display_name":"Biological system","level":1,"score":0.3334999978542328},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.32420000433921814},{"id":"https://openalex.org/C11413529","wikidata":"https://www.wikidata.org/wiki/Q8366","display_name":"Algorithm","level":1,"score":0.319599986076355},{"id":"https://openalex.org/C9893847","wikidata":"https://www.wikidata.org/wiki/Q1425625","display_name":"Reproducibility","level":2,"score":0.296999990940094},{"id":"https://openalex.org/C201797286","wikidata":"https://www.wikidata.org/wiki/Q4914986","display_name":"Biological data","level":2,"score":0.2815999984741211},{"id":"https://openalex.org/C179518139","wikidata":"https://www.wikidata.org/wiki/Q5140297","display_name":"Coding (social sciences)","level":2,"score":0.28060001134872437},{"id":"https://openalex.org/C2779843651","wikidata":"https://www.wikidata.org/wiki/Q7390335","display_name":"SIGNAL (programming language)","level":2,"score":0.26930001378059387},{"id":"https://openalex.org/C164226766","wikidata":"https://www.wikidata.org/wiki/Q7293202","display_name":"Rank (graph theory)","level":2,"score":0.2687999904155731},{"id":"https://openalex.org/C60644358","wikidata":"https://www.wikidata.org/wiki/Q128570","display_name":"Bioinformatics","level":1,"score":0.26460000872612},{"id":"https://openalex.org/C106487976","wikidata":"https://www.wikidata.org/wiki/Q685816","display_name":"Matrix (chemical analysis)","level":2,"score":0.2619999945163727},{"id":"https://openalex.org/C152662350","wikidata":"https://www.wikidata.org/wiki/Q815297","display_name":"Systems biology","level":2,"score":0.2605000138282776},{"id":"https://openalex.org/C169822122","wikidata":"https://www.wikidata.org/wiki/Q230187","display_name":"Crosstalk","level":2,"score":0.25999999046325684},{"id":"https://openalex.org/C153180895","wikidata":"https://www.wikidata.org/wiki/Q7148389","display_name":"Pattern recognition (psychology)","level":2,"score":0.25369998812675476}],"mesh":[],"locations_count":5,"locations":[{"id":"doi:10.1186/s12859-026-06632-8","doi":"https://doi.org/10.1186/s12859-026-06632-8","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s12859-026-06632-8","pdf_url":null,"source":{"id":"https://openalex.org/S19032547","display_name":"BMC Bioinformatics","issn_l":"1471-2105","issn":["1471-2105"],"is_oa":true,"is_in_doaj":true,"is_core":true,"listed_in":["anvur-class-a","anvur-scientific","ccf-c","cwts-core","doaj","dongbi-c","doyens","jufo-1","ki-jl-1","medline","norway-2","oarl","poland-100","russia-white-list-1","vabb-shw"],"host_organization":"https://openalex.org/P4310320256","host_organization_name":"BioMed Central","host_organization_lineage":["https://openalex.org/P4310320256","https://openalex.org/P4310319965"],"host_organization_lineage_names":["BioMed Central","Springer Nature"],"type":"journal"},"license":"cc-by-nc-nd","license_id":"https://openalex.org/licenses/cc-by-nc-nd","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"BMC Bioinformatics","raw_type":"journal-article"},{"id":"doi:10.21203/rs.3.rs-10271634/v1","doi":"https://doi.org/10.21203/rs.3.rs-10271634/v1","is_oa":true,"landing_page_url":"https://doi.org/10.21203/rs.3.rs-10271634/v1","pdf_url":"https://www.researchsquare.com/article/rs-10271634/latest.pdf","source":{"id":"https://openalex.org/S4306525896","display_name":"Research Square","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"listed_in":[],"host_organization":null,"host_organization_name":null,"host_organization_lineage":[],"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":"Research Square","raw_type":"posted-content"},{"id":"pmid:42466400","doi":null,"is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/42466400","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,"listed_in":[],"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":"Research square","raw_type":"Journal Article"},{"id":"pmh:oai:pubmedcentral.nih.gov:13370622","doi":null,"is_oa":true,"landing_page_url":"https://pmc.ncbi.nlm.nih.gov/articles/PMC13370622/","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,"listed_in":[],"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":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Res Sq","raw_type":"Text"},{"id":"doi:10.5281/zenodo.21838565","doi":"https://doi.org/10.5281/zenodo.21838565","is_oa":true,"landing_page_url":"https://doi.org/10.5281/zenodo.21838565","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,"listed_in":[],"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":null,"license_id":null,"version":null,"is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":"Software"}],"best_oa_location":{"id":"doi:10.1186/s12859-026-06632-8","doi":"https://doi.org/10.1186/s12859-026-06632-8","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s12859-026-06632-8","pdf_url":null,"source":{"id":"https://openalex.org/S19032547","display_name":"BMC Bioinformatics","issn_l":"1471-2105","issn":["1471-2105"],"is_oa":true,"is_in_doaj":true,"is_core":true,"listed_in":["anvur-class-a","anvur-scientific","ccf-c","cwts-core","doaj","dongbi-c","doyens","jufo-1","ki-jl-1","medline","norway-2","oarl","poland-100","russia-white-list-1","vabb-shw"],"host_organization":"https://openalex.org/P4310320256","host_organization_name":"BioMed Central","host_organization_lineage":["https://openalex.org/P4310320256","https://openalex.org/P4310319965"],"host_organization_lineage_names":["BioMed Central","Springer Nature"],"type":"journal"},"license":"cc-by-nc-nd","license_id":"https://openalex.org/licenses/cc-by-nc-nd","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"BMC Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[{"display_name":"Good health and well-being","id":"https://metadata.un.org/sdg/3","score":0.4043000042438507}],"study_designs":[],"awards":[{"id":"https://openalex.org/G1023528727","display_name":"Harvard Chronic Kidney Disease Research Biopsy Center","funder_award_id":"UH3DK114915","funder_id":"https://openalex.org/F4320337357","funder_display_name":"National Institute of Diabetes and Digestive and Kidney Diseases"},{"id":"https://openalex.org/G5160156487","display_name":"Multidimensional cellular interrogation of the kidney in AKI and CKD","funder_award_id":"UH3DK114937","funder_id":"https://openalex.org/F4320337357","funder_display_name":"National Institute of Diabetes and Digestive and Kidney Diseases"},{"id":"https://openalex.org/G5780173849","display_name":"Phenotyping REnal Cases In Sepsis and surgery for Early Acute Kidney Injury (PReCISE AKI)","funder_award_id":"UH3DK114861","funder_id":"https://openalex.org/F4320337357","funder_display_name":"National Institute of Diabetes and Digestive and Kidney Diseases"},{"id":"https://openalex.org/G7004197887","display_name":"Kidney Precision Medicine Program (KPMP): Columbia AKI Recruitment Site","funder_award_id":"UH3DK114926","funder_id":"https://openalex.org/F4320337357","funder_display_name":"National Institute of Diabetes and Digestive and Kidney Diseases"},{"id":"https://openalex.org/G9000856193","display_name":"Spatial Elucidation of Human Acute Kidney Injury and Chronic Kidney Disease using Imaging Mass Cytometry","funder_award_id":"U01DK133768","funder_id":"https://openalex.org/F4320337357","funder_display_name":"National Institute of Diabetes and Digestive and Kidney Diseases"},{"id":"https://openalex.org/G9000859861","display_name":"PREcision Medicine through IntErrogation of Rna in the kidnEy (PREMIERE)","funder_award_id":"U01DK114907","funder_id":"https://openalex.org/F4320337357","funder_display_name":"National Institute of Diabetes and Digestive and Kidney Diseases"},{"id":"https://openalex.org/G9000869596","display_name":"Minnesota Precision Medicine CKD & Resilient Diabetes Recruiting Site: Engagement, Enrollment & Ethics","funder_award_id":"U01DK133097","funder_id":"https://openalex.org/F4320337357","funder_display_name":"National Institute of Diabetes and Digestive and Kidney Diseases"},{"id":"https://openalex.org/G9000878163","display_name":"Integrated spatial interrogation of cellular and molecular signatures of human kidney disease","funder_award_id":"U01DK114923","funder_id":"https://openalex.org/F4320337357","funder_display_name":"National Institute of Diabetes and Digestive and Kidney Diseases"},{"id":"https://openalex.org/G9000878898","display_name":"Single cell multiomic and spatial atlas of acute and chronic kidney injury","funder_award_id":"U01DK114933","funder_id":"https://openalex.org/F4320337357","funder_display_name":"National Institute of Diabetes and Digestive and Kidney Diseases"},{"id":"https://openalex.org/G9000888682","display_name":"Mount Sinai Health System Kidney Precision Medicine Project","funder_award_id":"U01DK133093","funder_id":"https://openalex.org/F4320337357","funder_display_name":"National Institute of Diabetes and Digestive and Kidney Diseases"},{"id":"https://openalex.org/G9000889908","display_name":"University of Illinois at Chicago KPMP CKD Recruitment Site","funder_award_id":"U01DK133081","funder_id":"https://openalex.org/F4320337357","funder_display_name":"National Institute of Diabetes and Digestive and Kidney Diseases"},{"id":"https://openalex.org/G9000890966","display_name":"AKI Matched Phenotype Linked Evaluation with Tissue (AMPLE-Tissue)","funder_award_id":"U01DK114866","funder_id":"https://openalex.org/F4320337357","funder_display_name":"National Institute of Diabetes and Digestive and Kidney Diseases"},{"id":"https://openalex.org/G9000895139","display_name":"Central Hub for Kidney Precision Medicine","funder_award_id":"U24DK114886","funder_id":"https://openalex.org/F4320337357","funder_display_name":"National Institute of Diabetes and Digestive and Kidney Diseases"},{"id":"https://openalex.org/G9000900554","display_name":"Multimodal Imaging Mass Spectrometry and Spatial Omics for the Human Kidney","funder_award_id":"U01DK133766","funder_id":"https://openalex.org/F4320337357","funder_display_name":"National Institute of Diabetes and Digestive and Kidney Diseases"},{"id":"https://openalex.org/G9000904238","display_name":"Boston Chronic Kidney Disease Research Biopsy Center","funder_award_id":"U01DK133092","funder_id":"https://openalex.org/F4320337357","funder_display_name":"National Institute of Diabetes and Digestive and Kidney Diseases"},{"id":"https://openalex.org/G9000905979","display_name":"Cleveland Precision Medicine Chronic Kidney Disease Cohort","funder_award_id":"U01DK114908","funder_id":"https://openalex.org/F4320337357","funder_display_name":"National Institute of Diabetes and Digestive and Kidney Diseases"},{"id":"https://openalex.org/G9000906433","display_name":"Kidney Precision Medicine Project - Patient Engagement","funder_award_id":"U01DK133091","funder_id":"https://openalex.org/F4320337357","funder_display_name":"National Institute of Diabetes and Digestive and Kidney Diseases"},{"id":"https://openalex.org/G9000909158","display_name":"KPMP Kidney Mapping and Atlas Project (KMAP)","funder_award_id":"U01DK133090","funder_id":"https://openalex.org/F4320337357","funder_display_name":"National Institute of Diabetes and Digestive and Kidney Diseases"},{"id":"https://openalex.org/G9000912333","display_name":"Geographic and Environmental Health Equity in Kidney Precision Medicine","funder_award_id":"U01DK133095","funder_id":"https://openalex.org/F4320337357","funder_display_name":"National Institute of Diabetes and Digestive and Kidney Diseases"},{"id":"https://openalex.org/G9000912358","display_name":"Spatial Multi-Omics to Profile Metabolic Pathways for Kidney Disease","funder_award_id":"U01DK114920","funder_id":"https://openalex.org/F4320337357","funder_display_name":"National Institute of Diabetes and Digestive and Kidney Diseases"},{"id":"https://openalex.org/G9000916121","display_name":"Spatial Mapping of Proteomic and Transcriptional Signatures in Kidney Disease","funder_award_id":"U01DK133113","funder_id":"https://openalex.org/F4320337357","funder_display_name":"National Institute of Diabetes and Digestive and Kidney Diseases"}],"funders":[{"id":"https://openalex.org/F4320332161","display_name":"National Institutes of Health","ror":"https://ror.org/01cwqze88"},{"id":"https://openalex.org/F4320332682","display_name":"Medical School, University of Michigan","ror":"https://ror.org/00jmfr291"},{"id":"https://openalex.org/F4320337357","display_name":"National Institute of Diabetes and Digestive and Kidney Diseases","ror":"https://ror.org/00adh9b73"}],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W7201848571.pdf","grobid_xml":"https://content.openalex.org/works/W7201848571.grobid-xml"},"referenced_works_count":36,"referenced_works":["https://openalex.org/W1992045522","https://openalex.org/W2114104545","https://openalex.org/W2123879591","https://openalex.org/W2130410032","https://openalex.org/W2131495509","https://openalex.org/W2146512944","https://openalex.org/W2159707944","https://openalex.org/W2179438025","https://openalex.org/W2273101790","https://openalex.org/W2616922646","https://openalex.org/W2621172390","https://openalex.org/W2792647356","https://openalex.org/W2800392236","https://openalex.org/W2884197618","https://openalex.org/W2927507212","https://openalex.org/W2942678593","https://openalex.org/W3007199577","https://openalex.org/W3024643080","https://openalex.org/W3034168389","https://openalex.org/W3041062936","https://openalex.org/W3093169545","https://openalex.org/W3108941787","https://openalex.org/W3131249490","https://openalex.org/W3158574224","https://openalex.org/W3174072032","https://openalex.org/W3202649987","https://openalex.org/W4200349851","https://openalex.org/W4214876469","https://openalex.org/W4223992851","https://openalex.org/W4225598893","https://openalex.org/W4283257569","https://openalex.org/W4312192950","https://openalex.org/W4378212544","https://openalex.org/W4384816663","https://openalex.org/W4388539829","https://openalex.org/W4404793799"],"related_works":["https://openalex.org/W4402755359","https://openalex.org/W4399345992","https://openalex.org/W3093169545","https://openalex.org/W2947877009","https://openalex.org/W3032847236","https://openalex.org/W7140171445","https://openalex.org/W3015184839","https://openalex.org/W7202077259","https://openalex.org/W4393095987","https://openalex.org/W3007199577"],"abstract_inverted_index":{"Pathway":[0],"activity":[1],"scoring":[2,74],"is":[3,16,20,170,232,283,347,357,378],"a":[4,67,126,178,307,313,331,351,359,381],"widely":[5,71],"used":[6,72],"step":[7],"in":[8,27,181,246],"single-cell":[9,36,40,230],"RNA-seq":[10],"(scRNA-seq)":[11],"analysis,":[12],"yet":[13],"where":[14,250],"it":[15],"applied,":[17],"method":[18,271,366,399],"choice":[19],"rarely":[21],"guided":[22],"by":[23,129],"systematic,":[24],"multi-criterion":[25],"evidence":[26,299],"the":[28,53,57,147,168,173,213,219,228,277,292,297,302],"pseudobulk":[29,55,236],"case-control":[30,85],"regime":[31],"that":[32,161,211,227,268],"now":[33],"dominates":[34],"applied":[35],"disease":[37],"studies.":[38],"Prior":[39],"pathway-scoring":[41],"benchmarks":[42],"have":[43],"focused":[44],"on":[45,207,326],"perturbation":[46],"ground":[47],"truth":[48],"at":[49,222],"cell-level":[50],"resolution,":[51],"leaving":[52],"donor-level":[54],"setting\u2014and":[56],"question":[58],"of":[59,183,218],"why":[60],"methods":[61,75,133,197,253,321,325],"disagree\u2014largely":[62],"unaddressed.":[63],"We":[64,121,329],"present":[65],"PathwayBench,":[66],"benchmark":[68,384],"comparing":[69],"five":[70,88,102,274],"pathway":[73,143,187],"(ssGSEA,":[76,339],"GSVA,":[77],"z-score,":[78],"AUCell,":[79],"UCell)":[80,135],"across":[81,172,259],"eight":[82],"pseudobulked":[83],"scRNA-seq":[84,327],"datasets":[86],"spanning":[87],"tissues":[89],"(brain,":[90],"heart,":[91],"kidney,":[92],"lung,":[93],"blood)":[94],"and":[95,112,151,194,287,300,322,341,363,392,401],"682":[96],"donors.":[97],"Methods":[98],"are":[99],"evaluated":[100],"against":[101],"criteria":[103,275],"covering":[104],"biological":[105,137],"relevance":[106],"(direction":[107],"accuracy,":[108],"AUROC,":[109],"effect":[110,169],"size)":[111],"four":[113],"robustness":[114],"axes":[115],"(aggregation,":[116],"outlier,":[117],"normalization,":[118],"sample-size":[119],"stability).":[120],"identify":[122],"rank-window":[123],"truncation":[124,311],"as":[125,265,296,306,380],"two-sided":[127],"mechanism":[128],"which":[130],"top-window":[131,251,323,342],"rank":[132,196,214,252,344],"(AUCell,":[134,345],"lose":[136],"signal:":[138],"they":[139,152],"go":[140],"blind":[141],"when":[142,156,186],"genes":[144,159,188],"fall":[145,189],"outside":[146],"fixed":[148],"top-rank":[149],"window,":[150,193],"attenuate":[153],"or":[154,256,372],"invert":[155,198],"non-pathway":[157],"competitor":[158,202],"invade":[160],"window.":[162],"A":[163,204],"49-condition":[164],"simulation":[165],"sweep":[166],"shows":[167,210],"broad":[171],"parameter":[174],"grid:":[175],"AUCell":[176],"returns":[177],"null":[179],"score":[180],"33":[182],"49":[184],"conditions":[185],"below":[190],"its":[191],"default":[192,229],"both":[195],"sign":[199],"under":[200,276],"heavy":[201],"burden.":[203],"window-parameter":[205],"experiment":[206],"real":[208],"data":[209],"widening":[212],"window":[215,231],"recovers":[216],"most":[217],"lost":[220],"signal":[221],"an":[223,388],"intermediate":[224],"setting,":[225],"confirming":[226],"mis-set":[233],"for":[234,316,369],"dense":[235],"profiles.":[237],"Real-data":[238],"illustration":[239],"comes":[240],"from":[241],"extracellular":[242],"matrix":[243],"(ECM)":[244],"remodeling":[245],"chronic":[247],"kidney":[248],"disease,":[249],"produce":[254],"near-zero":[255],"wrong-direction":[257],"effects":[258],"three":[260],"normalizations.":[261],"Discretizing":[262],"per-criterion":[263],"performance":[264],"Good/Intermediate/Poor":[266],"indicates":[267],"no":[269],"single":[270],"satisfies":[272],"all":[273],"primary":[278,298],"thresholds.":[279],"Because":[280],"this":[281],"classification":[282],"sensitive":[284],"to":[285,396],"threshold":[286],"weighting":[288],"choices,":[289],"we":[290],"report":[291],"underlying":[293],"continuous":[294],"scores":[295],"use":[301],"discrete":[303],"scoreboard":[304],"only":[305],"summary":[308],"aid.":[309],"Rank-window":[310],"provides":[312],"mechanistic":[314],"explanation":[315],"systematic":[317],"divergence":[318],"between":[319],"whole-distribution":[320],"truncated-rank":[324],"data.":[328],"adopt":[330],"three-family":[332],"taxonomy\u2014cross-sample":[333],"standardized":[334],"magnitude":[335],"(z-score),":[336],"rank-enrichment":[337],"hybrids":[338],"GSVA),":[340],"truncated":[343],"UCell)\u2014which":[346],"more":[348],"accurate":[349],"than":[350],"two-way":[352],"magnitude-versus-rank":[353],"split,":[354],"since":[355],"ssGSEA":[356],"itself":[358],"rank-based":[360],"enrichment":[361],"statistic":[362],"should":[364],"guide":[365],"selection,":[367],"particularly":[368],"fibrotic,":[370],"inflammatory,":[371],"otherwise":[373],"broadly":[374],"remodeled":[375],"transcriptomes.":[376],"PathwayBench":[377],"delivered":[379],"versioned,":[382],"extensible":[383],"with":[385],"per-dataset":[386],"scores,":[387],"interactive":[389],"advisor":[390],"application,":[391],"complete":[393],"reproducibility":[394],"infrastructure":[395],"support":[397],"evidence-based":[398],"selection":[400],"community":[402],"extension.":[403]},"counts_by_year":[],"updated_date":"2026-11-14T11:04:58.165337","created_date":"2026-08-08T00:00:00"}