{"id":"https://openalex.org/W7214230950","doi":"https://doi.org/10.64898/2026.09.23.753907","title":"NicheScribe: consistent and generalizable annotation of stromal cells in the murine bone marrow niche","display_name":"NicheScribe: consistent and generalizable annotation of stromal cells in the murine bone marrow niche","publication_year":2026,"publication_date":"2026-09-24","ids":{"openalex":"https://openalex.org/W7214230950","doi":"https://doi.org/10.64898/2026.09.23.753907","pmid":"https://pubmed.ncbi.nlm.nih.gov/42818377","pmcid":"https://www.ncbi.nlm.nih.gov/pmc/articles/13622281"},"language":"en","primary_location":{"id":"doi:10.64898/2026.09.23.753907","doi":"https://doi.org/10.64898/2026.09.23.753907","is_oa":true,"landing_page_url":"https://doi.org/10.64898/2026.09.23.753907","pdf_url":"https://www.biorxiv.org/content/biorxiv/early/2026/09/24/2026.09.23.753907.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-nc-nd","license_id":"https://openalex.org/licenses/cc-by-nc-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","pubmed"],"open_access":{"is_oa":true,"oa_status":"green","oa_url":"https://www.biorxiv.org/content/biorxiv/early/2026/09/24/2026.09.23.753907.full.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5088801050","display_name":"James W. Swann","orcid":"https://orcid.org/0000-0001-7988-9997","observed_orcids":["https://orcid.org/0000-0001-7988-9997"]},"institutions":[{"id":"https://openalex.org/I78577930","display_name":"Columbia University","ror":"https://ror.org/00hj8s172","country_code":"US","type":"education","lineage":["https://openalex.org/I78577930"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"James W. Swann","raw_affiliation_strings":["Columbia Stem Cell Initiative, Department of Genetics & Development, Columbia University, New York, NY 10032, USA"],"raw_orcid":"https://orcid.org/0000-0001-7988-9997","affiliations":[{"raw_affiliation_string":"Columbia Stem Cell Initiative, Department of Genetics & Development, Columbia University, New York, NY 10032, USA","institution_ids":["https://openalex.org/I78577930"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5031897693","display_name":"Jun Hou Fung","orcid":"https://orcid.org/0000-0002-3734-6721","observed_orcids":["https://orcid.org/0000-0002-3734-6721"]},"institutions":[{"id":"https://openalex.org/I78577930","display_name":"Columbia University","ror":"https://ror.org/00hj8s172","country_code":"US","type":"education","lineage":["https://openalex.org/I78577930"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Jun Hou Fung","raw_affiliation_strings":["Program for Mathematical Genomics, Department of Biomedical Informatics and Department of Systems Biology, Columbia University, New York, 10032, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Program for Mathematical Genomics, Department of Biomedical Informatics and Department of Systems Biology, Columbia University, New York, 10032, USA","institution_ids":["https://openalex.org/I78577930"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5152756936","display_name":"Ruiyuan Zhang","orcid":null,"observed_orcids":[]},"institutions":[{"id":"https://openalex.org/I78577930","display_name":"Columbia University","ror":"https://ror.org/00hj8s172","country_code":"US","type":"education","lineage":["https://openalex.org/I78577930"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Ruiyuan Zhang","raw_affiliation_strings":["Columbia Stem Cell Initiative, Department of Genetics & Development, Columbia University, New York, NY 10032, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Columbia Stem Cell Initiative, Department of Genetics & Development, Columbia University, New York, NY 10032, USA","institution_ids":["https://openalex.org/I78577930"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5056128255","display_name":"Ra\u00fal Rabad\u00e1n","orcid":"https://orcid.org/0000-0001-7946-9255","observed_orcids":["https://orcid.org/0000-0001-7946-9255"]},"institutions":[{"id":"https://openalex.org/I78577930","display_name":"Columbia University","ror":"https://ror.org/00hj8s172","country_code":"US","type":"education","lineage":["https://openalex.org/I78577930"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Raul Rabadan","raw_affiliation_strings":["Program for Mathematical Genomics, Department of Biomedical Informatics and Department of Systems Biology, Columbia University, New York, 10032, USA"],"raw_orcid":"https://orcid.org/0000-0001-7946-9255","affiliations":[{"raw_affiliation_string":"Program for Mathematical Genomics, Department of Biomedical Informatics and Department of Systems Biology, Columbia University, New York, 10032, USA","institution_ids":["https://openalex.org/I78577930"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5016128169","display_name":"Emmanuelle A. Passegue","orcid":"https://orcid.org/0000-0002-3516-297X","observed_orcids":["https://orcid.org/0000-0002-3516-297X"]},"institutions":[{"id":"https://openalex.org/I78577930","display_name":"Columbia University","ror":"https://ror.org/00hj8s172","country_code":"US","type":"education","lineage":["https://openalex.org/I78577930"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Emmanuelle Passegu\u00e9","raw_affiliation_strings":["Columbia Stem Cell Initiative, Department of Genetics & Development, Columbia University, New York, NY 10032, USA"],"raw_orcid":"https://orcid.org/0000-0002-3516-297X","affiliations":[{"raw_affiliation_string":"Columbia Stem Cell Initiative, Department of Genetics & Development, Columbia University, New York, NY 10032, USA","institution_ids":["https://openalex.org/I78577930"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":1,"corresponding_author_ids":["https://openalex.org/A5016128169"],"corresponding_institution_ids":["https://openalex.org/I78577930"],"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/T11289","display_name":"Single-cell and spatial transcriptomics","score":0.9775000214576721,"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":0.9775000214576721,"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/T10345","display_name":"Hematopoietic Stem Cell Transplantation","score":0.0203000009059906,"subfield":{"id":"https://openalex.org/subfields/2720","display_name":"Hematology"},"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/T10176","display_name":"Mesenchymal stem cell research","score":0.0003000000142492354,"subfield":{"id":"https://openalex.org/subfields/1307","display_name":"Cell 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/bone-marrow-microenvironment","display_name":"bone marrow microenvironment","score":0.8830000162124634},{"id":"https://openalex.org/keywords/stromal-cells","display_name":"stromal cells","score":0.9340000152587891},{"id":"https://openalex.org/keywords/hematopoietic-stem-and-progenitor-cells","display_name":"hematopoietic stem and progenitor cells","score":0.9670000076293945},{"id":"https://openalex.org/keywords/cell-type-identification","display_name":"cell type annotation","score":0.9340000152587891},{"id":"https://openalex.org/keywords/classifiers","display_name":"machine learning classifiers","score":0.3479999899864197},{"id":"https://openalex.org/keywords/inflammation","display_name":"inflammation","score":0.6159999966621399},{"id":"https://openalex.org/keywords/cancer","display_name":"cancer","score":0.9539999961853027},{"id":"https://openalex.org/keywords/aging","display_name":"aging","score":0.777999997138977}],"concepts":[{"id":"https://openalex.org/C16930146","wikidata":"https://www.wikidata.org/wiki/Q4381253","display_name":"Stromal cell","level":2,"score":0.8148000240325928},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.7117999792098999},{"id":"https://openalex.org/C2780007613","wikidata":"https://www.wikidata.org/wiki/Q546523","display_name":"Bone marrow","level":2,"score":0.6205000281333923},{"id":"https://openalex.org/C153991713","wikidata":"https://www.wikidata.org/wiki/Q17142856","display_name":"Niche","level":2,"score":0.5572999715805054},{"id":"https://openalex.org/C109159458","wikidata":"https://www.wikidata.org/wiki/Q919283","display_name":"Haematopoiesis","level":3,"score":0.5382999777793884},{"id":"https://openalex.org/C201750760","wikidata":"https://www.wikidata.org/wiki/Q1896218","display_name":"Progenitor cell","level":3,"score":0.4884999990463257},{"id":"https://openalex.org/C28328180","wikidata":"https://www.wikidata.org/wiki/Q48196","display_name":"Stem cell","level":2,"score":0.4496000111103058},{"id":"https://openalex.org/C198826908","wikidata":"https://www.wikidata.org/wiki/Q1922379","display_name":"Mesenchymal stem cell","level":2,"score":0.4442000091075897},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.43290001153945923},{"id":"https://openalex.org/C189014844","wikidata":"https://www.wikidata.org/wiki/Q189118","display_name":"Cell type","level":3,"score":0.4214000105857849},{"id":"https://openalex.org/C95444343","wikidata":"https://www.wikidata.org/wiki/Q7141","display_name":"Cell biology","level":1,"score":0.374099999666214},{"id":"https://openalex.org/C2776321320","wikidata":"https://www.wikidata.org/wiki/Q857525","display_name":"Annotation","level":2,"score":0.37299999594688416},{"id":"https://openalex.org/C2908647359","wikidata":"https://www.wikidata.org/wiki/Q2625603","display_name":"Population","level":2,"score":0.34540000557899475},{"id":"https://openalex.org/C1491633281","wikidata":"https://www.wikidata.org/wiki/Q7868","display_name":"Cell","level":2,"score":0.335999995470047},{"id":"https://openalex.org/C81885089","wikidata":"https://www.wikidata.org/wiki/Q189082","display_name":"Cell culture","level":2,"score":0.32089999318122864},{"id":"https://openalex.org/C15729860","wikidata":"https://www.wikidata.org/wiki/Q2329919","display_name":"Progenitor","level":4,"score":0.29269999265670776},{"id":"https://openalex.org/C67705224","wikidata":"https://www.wikidata.org/wiki/Q11053","display_name":"RNA","level":3,"score":0.2892000079154968},{"id":"https://openalex.org/C162317418","wikidata":"https://www.wikidata.org/wiki/Q252857","display_name":"Transcriptome","level":4,"score":0.27219998836517334},{"id":"https://openalex.org/C203014093","wikidata":"https://www.wikidata.org/wiki/Q101929","display_name":"Immunology","level":1,"score":0.2705000042915344},{"id":"https://openalex.org/C60644358","wikidata":"https://www.wikidata.org/wiki/Q128570","display_name":"Bioinformatics","level":1,"score":0.2526000142097473}],"mesh":[],"locations_count":3,"locations":[{"id":"doi:10.64898/2026.09.23.753907","doi":"https://doi.org/10.64898/2026.09.23.753907","is_oa":true,"landing_page_url":"https://doi.org/10.64898/2026.09.23.753907","pdf_url":"https://www.biorxiv.org/content/biorxiv/early/2026/09/24/2026.09.23.753907.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-nc-nd","license_id":"https://openalex.org/licenses/cc-by-nc-nd","version":"acceptedVersion","is_accepted":true,"is_published":false,"raw_source_name":"bioRxiv","raw_type":"posted-content"},{"id":"pmid:42818377","doi":null,"is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/42818377","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":"bioRxiv : the preprint server for biology","raw_type":"Journal Article"},{"id":"pmh:oai:pubmedcentral.nih.gov:13622281","doi":null,"is_oa":true,"landing_page_url":"https://pmc.ncbi.nlm.nih.gov/articles/PMC13622281/","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-nc-nd","license_id":"https://openalex.org/licenses/cc-by-nc-nd","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"bioRxiv","raw_type":"Text"}],"best_oa_location":{"id":"doi:10.64898/2026.09.23.753907","doi":"https://doi.org/10.64898/2026.09.23.753907","is_oa":true,"landing_page_url":"https://doi.org/10.64898/2026.09.23.753907","pdf_url":"https://www.biorxiv.org/content/biorxiv/early/2026/09/24/2026.09.23.753907.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-nc-nd","license_id":"https://openalex.org/licenses/cc-by-nc-nd","version":"acceptedVersion","is_accepted":true,"is_published":false,"raw_source_name":"bioRxiv","raw_type":"posted-content"},"sustainable_development_goals":[{"id":"https://metadata.un.org/sdg/3","display_name":"Good health and well-being","score":0.428600013256073}],"study_designs":[],"awards":[{"id":"https://openalex.org/G1205896015","display_name":"Emergency Myelopoiesis Pathways in the Control of Blood Production","funder_award_id":"R35HL135763","funder_id":"https://openalex.org/F4320337338","funder_display_name":"National Heart, Lung, and Blood Institute"},{"id":"https://openalex.org/G144283012","display_name":null,"funder_award_id":"P30-CA013696","funder_id":"https://openalex.org/F4320333627","funder_display_name":"Irving Medical Center, Columbia University"},{"id":"https://openalex.org/G2959128849","display_name":null,"funder_award_id":"P30CA013696","funder_id":"https://openalex.org/F4320306271","funder_display_name":"Damon Runyon Cancer Research Foundation"},{"id":"https://openalex.org/G4549015468","display_name":null,"funder_award_id":"DRG-2493-23","funder_id":"https://openalex.org/F4320306271","funder_display_name":"Damon Runyon Cancer Research Foundation"},{"id":"https://openalex.org/G6671084440","display_name":null,"funder_award_id":"R35HL135763","funder_id":"https://openalex.org/F4320306271","funder_display_name":"Damon Runyon Cancer Research Foundation"},{"id":"https://openalex.org/G9000899809","display_name":"Towards a quantitative understanding of tumor evolution","funder_award_id":"R35CA253126","funder_id":"https://openalex.org/F4320337351","funder_display_name":"National Cancer Institute"},{"id":"https://openalex.org/G9000916142","display_name":"Cancer Center Support Grant","funder_award_id":"P30CA013696","funder_id":"https://openalex.org/F4320337351","funder_display_name":"National Cancer Institute"}],"funders":[{"id":"https://openalex.org/F4320306271","display_name":"Damon Runyon Cancer Research Foundation","ror":"https://ror.org/01gd7b947"},{"id":"https://openalex.org/F4320332161","display_name":"National Institutes of Health","ror":"https://ror.org/01cwqze88"},{"id":"https://openalex.org/F4320333627","display_name":"Irving Medical Center, Columbia University","ror":"https://ror.org/01esghr10"},{"id":"https://openalex.org/F4320337338","display_name":"National Heart, Lung, and Blood Institute","ror":"https://ror.org/012pb6c26"},{"id":"https://openalex.org/F4320337351","display_name":"National Cancer Institute","ror":"https://ror.org/040gcmg81"}],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W7214230950.pdf","grobid_xml":"https://content.openalex.org/works/W7214230950.grobid-xml"},"referenced_works_count":1,"referenced_works":["https://openalex.org/W7143344215"],"related_works":["https://openalex.org/W4323294384","https://openalex.org/W4310108914","https://openalex.org/W4245850249","https://openalex.org/W4318624607","https://openalex.org/W4391771285","https://openalex.org/W4405049037","https://openalex.org/W2907449174","https://openalex.org/W2946949132","https://openalex.org/W4396659238","https://openalex.org/W3213210508"],"abstract_inverted_index":{"Hematopoietic":[0],"stem":[1],"and":[2,18,46,90,117,122,139,145,183,196],"progenitor":[3],"cells":[4,12,112,151,172,202],"(HSPC)":[5],"depend":[6],"on":[7],"interactions":[8],"with":[9],"nearby":[10],"stromal":[11,71,82,111,150,171,189,201],"to":[13,21,76,92,181,207],"support":[14],"their":[15],"homeostatic":[16],"functions":[17],"mount":[19],"responses":[20,206],"perturbations.":[22,209],"The":[23],"murine":[24,69,136,174],"bone":[25,115,175],"marrow":[26,176],"(BM)":[27],"niche":[28,138],"can":[29,51],"be":[30,52],"profiled":[31],"using":[32,65],"single-cell":[33,182],"RNA":[34],"sequencing":[35],"(scRNA-seq),":[36],"but":[37],"there":[38],"is":[39,87,179],"considerable":[40],"inconsistency":[41],"in":[42,134,173,193],"cell":[43,100,131,190],"type":[44,132],"identification,":[45],"uncertainty":[47],"over":[48],"how":[49],"populations":[50,67],"isolated":[53],"prospectively":[54],"by":[55],"flow":[56],"cytometry.":[57],"Here,":[58],"we":[59,74],"produced":[60],"new":[61,127,140],"scRNA-seq":[62],"reference":[63],"datasets":[64,94],"purified":[66],"of":[68,96,108,170],"BM":[70,137],"cells,":[72],"which":[73,178],"used":[75,98],"create":[77],"a":[78,164],"bespoke":[79],"classifier":[80],"for":[81,99,129,142,167],"cells.":[83],"Our":[84,124],"NicheScribe":[85],"approach":[86,166],"consistent,":[88],"accurate,":[89],"generalizable":[91],"query":[93],"irrespective":[95],"methods":[97],"isolation.":[101],"Moreover,":[102],"consistent":[103,130,168],"annotation":[104,133,169],"permits":[105],"comparative":[106],"analyses":[107],"the":[109,135],"same":[110],"across":[113],"different":[114,194,208],"types":[116],"perturbations":[118],"like":[119],"inflammation,":[120],"neoplasia,":[121],"aging.":[123],"work":[125],"provides":[126],"tools":[128],"insights":[141],"combined":[143],"molecular":[144],"functional":[146],"analyses.":[147],"HIGHLIGHTS:":[148],"mesenchymal":[149,200],"adopt":[152],"diverse":[153,204],"transcriptional":[154,205],"programs":[155],"upon":[156],"stimulation.":[157],"eTOC":[158],"BLURB:":[159],"Swann":[160],"et":[161],"al.":[162],"develop":[163],"computational":[165],"niche,":[177],"applicable":[180],"spatial":[184],"transcriptomics.":[185],"They":[186],"find":[187],"that":[188,197],"frequencies":[191],"vary":[192],"bones,":[195],"leptin":[198],"receptor-expressing":[199],"exhibit":[203]},"counts_by_year":[],"updated_date":"2026-11-04T10:54:05.112534","created_date":"2026-09-25T00:00:00"}