{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,10,10]],"date-time":"2026-10-10T01:50:23Z","timestamp":1791597023845,"version":"4.3.4"},"reference-count":101,"publisher":"Elsevier BV","issue":"9","license":[{"start":{"date-parts":[[2026,9,1]],"date-time":"2026-09-01T00:00:00Z","timestamp":1788220800000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/www.elsevier.com\/tdm\/userlicense\/1.0\/"},{"start":{"date-parts":[[2026,9,1]],"date-time":"2026-09-01T00:00:00Z","timestamp":1788220800000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/www.elsevier.com\/legal\/tdmrep-license"},{"start":{"date-parts":[[2026,8,4]],"date-time":"2026-08-04T00:00:00Z","timestamp":1785801600000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/100000001","name":"National Science Foundation","doi-asserted-by":"publisher","award":["2035827"],"award-info":[{"award-number":["2035827"]}],"id":[{"id":"10.13039\/100000001","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000057","name":"National Institute of General Medical Sciences","doi-asserted-by":"publisher","award":["GM150581"],"award-info":[{"award-number":["GM150581"]}],"id":[{"id":"10.13039\/100000057","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000181","name":"Air Force Office of Scientific Research","doi-asserted-by":"publisher","award":["FA9550-22-1-0215"],"award-info":[{"award-number":["FA9550-22-1-0215"]}],"id":[{"id":"10.13039\/100000181","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000185","name":"Defense Advanced Research Projects Agency","doi-asserted-by":"publisher","award":["HR00112490472"],"award-info":[{"award-number":["HR00112490472"]}],"id":[{"id":"10.13039\/100000185","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":["cell.com","elsevier.com","sciencedirect.com"],"crossmark-restriction":true},"short-container-title":["iScience"],"published-print":{"date-parts":[[2026,9]]},"DOI":"10.1016\/j.isci.2026.117266","type":"journal-article","created":{"date-parts":[[2026,8,25]],"date-time":"2026-08-25T19:06:34Z","timestamp":1787684794000},"page":"117266","update-policy":"https:\/\/doi.org\/10.1016\/elsevier_cm_policy","source":"Crossref","is-referenced-by-count":0,"title":["Transcriptional landscape of direct reprogramming toward the hematopoietic lineage"],"prefix":"10.1016","volume":"29","author":[{"ORCID":"https:\/\/orcid.org\/0009-0000-0317-3052","authenticated-orcid":false,"given":"Jillian","family":"Cwycyshyn","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-2413-8314","authenticated-orcid":false,"given":"Cooper","family":"Stansbury","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Sarah","family":"Golts","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Hyunsu","family":"Lee","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-8763-3200","authenticated-orcid":false,"given":"Joshua","family":"Pickard","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Walter","family":"Meixner","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Indika","family":"Rajapakse","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-1756-0325","authenticated-orcid":false,"given":"Lindsey A.","family":"Muir","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"78","reference":[{"key":"10.1016\/j.isci.2026.117266_bib1","doi-asserted-by":"crossref","first-page":"1274","DOI":"10.1038\/s41587-024-02360-7","article-title":"Long-Term Engrafting Multilineage Hematopoietic Cells Differentiated from Human Induced Pluripotent Stem Cells","volume":"43","author":"Ng","year":"2025","journal-title":"Nat. Biotechnol."},{"key":"10.1016\/j.isci.2026.117266_bib2","doi-asserted-by":"crossref","first-page":"1581","DOI":"10.1038\/s41409-022-01764-w","article-title":"Disease Progression, Treatments, Hospitalization, and Clinical Outcomes in Acute GVHD: A Multicenter Chart Review","volume":"57","author":"Holtan","year":"2022","journal-title":"Bone Marrow Transplant."},{"key":"10.1016\/j.isci.2026.117266_bib3","doi-asserted-by":"crossref","first-page":"58","DOI":"10.1038\/nbt.3070","article-title":"A Comparison of Non-Integrating Reprogramming Methods","volume":"33","author":"Schlaeger","year":"2015","journal-title":"Nat. Biotechnol."},{"key":"10.1016\/j.isci.2026.117266_bib4","doi-asserted-by":"crossref","DOI":"10.1242\/dmm.042317","article-title":"Addressing variability in iPSC-derived models of human disease: guidelines to promote reproducibility","volume":"13","author":"Volpato","year":"2020","journal-title":"Dis. Model. Mech."},{"key":"10.1016\/j.isci.2026.117266_bib5","doi-asserted-by":"crossref","first-page":"410","DOI":"10.1038\/s41580-021-00335-z","article-title":"Direct Cell Reprogramming: Approaches, Mechanisms and Progress","volume":"22","author":"Wang","year":"2021","journal-title":"Nat. Rev. Mol. Cell Biol."},{"key":"10.1016\/j.isci.2026.117266_bib6","doi-asserted-by":"crossref","first-page":"97","DOI":"10.1089\/scd.2021.0255","article-title":"Distinctive Clinical and Pathologic Features of Immature Teratomas Arising from Induced Pluripotent Stem Cell-Derived Beta Cell Injection in a Diabetes Patient","volume":"31","author":"Han","year":"2022","journal-title":"Stem Cells Dev."},{"key":"10.1016\/j.isci.2026.117266_bib7","doi-asserted-by":"crossref","DOI":"10.1016\/j.stemcr.2025.102543","article-title":"Elimination of Tumorigenic Pluripotent Stem Cells from Their Differentiated Cell Therapy Products: An Important Step toward Ensuring Safe Cell Therapy","volume":"20","author":"Movahed","year":"2025","journal-title":"Stem Cell Rep."},{"key":"10.1016\/j.isci.2026.117266_bib8","doi-asserted-by":"crossref","first-page":"521","DOI":"10.1038\/nature09591","article-title":"Direct Conversion of Human Fibroblasts to Multilineage Blood Progenitors","volume":"468","author":"Szabo","year":"2010","journal-title":"Nature"},{"key":"10.1016\/j.isci.2026.117266_bib9","doi-asserted-by":"crossref","first-page":"202","DOI":"10.1016\/j.tcb.2015.10.002","article-title":"Making a Hematopoietic Stem Cell","volume":"26","author":"Daniel","year":"2016","journal-title":"Trends Cell Biol."},{"key":"10.1016\/j.isci.2026.117266_bib10","doi-asserted-by":"crossref","first-page":"2821","DOI":"10.1016\/j.celrep.2018.11.032","article-title":"Cooperative Transcription Factor Induction Mediates Hemogenic Reprogramming","volume":"25","author":"Gomes","year":"2018","journal-title":"Cell Rep."},{"key":"10.1016\/j.isci.2026.117266_bib11","doi-asserted-by":"crossref","DOI":"10.3791\/60112","article-title":"Hemogenic Reprogramming of Human Fibroblasts by Enforced Expression of Transcription Factors","author":"Silv\u00e9rio-Alves","year":"2019","journal-title":"JoVE J."},{"key":"10.1016\/j.isci.2026.117266_bib12","doi-asserted-by":"crossref","first-page":"3266","DOI":"10.1002\/1873-3468.13621","article-title":"Induction of Human Hemogenesis in Adult Fibroblasts by Defined Factors and Hematopoietic Coculture","volume":"593","author":"Daniel","year":"2019","journal-title":"FEBS Lett."},{"key":"10.1016\/j.isci.2026.117266_bib13","doi-asserted-by":"crossref","first-page":"752","DOI":"10.1016\/j.tcb.2020.07.006","article-title":"Hematopoietic Reprogramming Entangles with Hematopoiesis","volume":"30","author":"Wei","year":"2020","journal-title":"Trends Cell Biol."},{"key":"10.1016\/j.isci.2026.117266_bib14","article-title":"Computational Tools for Analyzing Single-Cell Data in Pluripotent Cell Differentiation Studies","volume":"1","author":"Ding","year":"2021","journal-title":"Cell Rep. Methods"},{"key":"10.1016\/j.isci.2026.117266_bib15","doi-asserted-by":"crossref","first-page":"3","DOI":"10.1007\/s12015-019-09935-x","article-title":"Advances in Pluripotent Stem Cells: History, Mechanisms, Technologies, and Applications","volume":"16","author":"Liu","year":"2020","journal-title":"Stem Cell Rev. Rep."},{"key":"10.1016\/j.isci.2026.117266_bib16","doi-asserted-by":"crossref","first-page":"1663","DOI":"10.1016\/j.cell.2015.11.013","article-title":"Transcriptional Heterogeneity and Lineage Commitment in Myeloid Progenitors","volume":"163","author":"Paul","year":"2015","journal-title":"Cell"},{"key":"10.1016\/j.isci.2026.117266_bib17","doi-asserted-by":"crossref","DOI":"10.1126\/science.aaw3381","article-title":"Lineage Tracing on Transcriptional Landscapes Links State to Fate during Differentiation","volume":"367","author":"Weinreb","year":"2020","journal-title":"Science"},{"key":"10.1016\/j.isci.2026.117266_bib18","doi-asserted-by":"crossref","first-page":"1415","DOI":"10.1182\/blood-2018-08-835355","article-title":"New Insights into Hematopoietic Differentiation Landscapes from Single-Cell RNA Sequencing","volume":"133","author":"Watcham","year":"2019","journal-title":"Blood"},{"key":"10.1016\/j.isci.2026.117266_bib19","doi-asserted-by":"crossref","first-page":"2395","DOI":"10.1038\/s41467-019-10291-0","article-title":"A Comprehensive Single Cell Transcriptional Landscape of Human Hematopoietic Progenitors","volume":"10","author":"Pellin","year":"2019","journal-title":"Nat. Commun."},{"key":"10.1016\/j.isci.2026.117266_bib20","doi-asserted-by":"crossref","first-page":"472","DOI":"10.1016\/j.stem.2020.11.015","article-title":"Integrative Single-Cell RNA-Seq and ATAC-Seq Analysis of Human Developmental Hematopoiesis","volume":"28","author":"Ranzoni","year":"2021","journal-title":"Cell Stem Cell"},{"key":"10.1016\/j.isci.2026.117266_bib21","doi-asserted-by":"crossref","first-page":"389","DOI":"10.1038\/s41586-024-07066-z","article-title":"Deciphering Cell States and Genealogies of Human Haematopoiesis","volume":"627","author":"Weng","year":"2024","journal-title":"Nature"},{"key":"10.1016\/j.isci.2026.117266_bib22","doi-asserted-by":"crossref","first-page":"635","DOI":"10.1016\/j.stem.2022.03.001","article-title":"Capybara: A Computational Tool to Measure Cell Identity and Fate Transitions","volume":"29","author":"Kong","year":"2022","journal-title":"Cell Stem Cell"},{"key":"10.1016\/j.isci.2026.117266_bib23","doi-asserted-by":"crossref","first-page":"616","DOI":"10.1038\/s41586-023-06139-9","article-title":"Transfer learning enables predictions in network biology","volume":"618","author":"Theodoris","year":"2023","journal-title":"Nature"},{"key":"10.1016\/j.isci.2026.117266_bib24","doi-asserted-by":"crossref","first-page":"690","DOI":"10.1038\/s41586-024-08172-8","article-title":"An Integrated Transcriptomic Cell Atlas of Human Neural Organoids","volume":"635","author":"He","year":"2024","journal-title":"Nature"},{"key":"10.1016\/j.isci.2026.117266_bib25","doi-asserted-by":"crossref","first-page":"1085","DOI":"10.1038\/s41586-024-08411-y","article-title":"A Cell Atlas Foundation Model for Scalable Search of Similar Human Cells","volume":"638","author":"Heimberg","year":"2025","journal-title":"Nature"},{"key":"10.1016\/j.isci.2026.117266_bib26","doi-asserted-by":"crossref","first-page":"11832","DOI":"10.1073\/pnas.1712350114","article-title":"Algorithm for Cellular Reprogramming","volume":"114","author":"Ronquist","year":"2017","journal-title":"Proc. Natl. Acad. Sci. USA"},{"key":"10.1016\/j.isci.2026.117266_bib27","doi-asserted-by":"crossref","first-page":"550","DOI":"10.1038\/s41576-023-00586-w","article-title":"Best Practices for Single-Cell Analysis across Modalities","volume":"24","author":"Heumos","year":"2023","journal-title":"Nat. Rev. Genet."},{"key":"10.1016\/j.isci.2026.117266_bib28","article-title":"The Tabula Sapiens: A Multiple-Organ, Single-Cell Transcriptomic Atlas of Humans","volume":"376","author":"Tabula Sapiens Consortium\u2217","year":"2022","journal-title":"Science"},{"key":"10.1016\/j.isci.2026.117266_bib29","doi-asserted-by":"crossref","first-page":"193","DOI":"10.1038\/s41576-025-00899-y","article-title":"Redefining cellular reprogramming with advanced genomic technologies","volume":"27","author":"Morris","year":"2026","journal-title":"Nat. Rev. Genet."},{"key":"10.1016\/j.isci.2026.117266_bib30","doi-asserted-by":"crossref","first-page":"1053","DOI":"10.1038\/s41592-018-0229-2","article-title":"Deep Generative Modeling for Single-Cell Transcriptomics","volume":"15","author":"Lopez","year":"2018","journal-title":"Nat. Methods"},{"key":"10.1016\/j.isci.2026.117266_bib31","first-page":"2579","article-title":"Visualizing Data Using T-SNE","volume":"9","author":"van der Maaten","year":"2008","journal-title":"J. Mach. Learn. Res."},{"key":"10.1016\/j.isci.2026.117266_bib32","doi-asserted-by":"crossref","DOI":"10.1093\/database\/baz046","article-title":"PanglaoDB: A Web Server for Exploration of Mouse and Human Single-Cell RNA Sequencing Data","volume":"2019","author":"Franz\u00e9n","year":"2019","journal-title":"Database"},{"key":"10.1016\/j.isci.2026.117266_bib33","doi-asserted-by":"crossref","first-page":"310","DOI":"10.1007\/s12185-016-2035-x","article-title":"Regulation of hematopoietic development by ZBTB transcription factors","volume":"104","author":"Maeda","year":"2016","journal-title":"Int. J. Hematol."},{"key":"10.1016\/j.isci.2026.117266_bib34","doi-asserted-by":"crossref","first-page":"296","DOI":"10.1038\/s41586-020-2424-4","article-title":"Structural cells are key regulators of organ-specific immune responses","volume":"583","author":"Krausgruber","year":"2020","journal-title":"Nature"},{"key":"10.1016\/j.isci.2026.117266_bib35","doi-asserted-by":"crossref","first-page":"494","DOI":"10.1038\/s41586-018-0414-6","article-title":"RNA Velocity of Single Cells","volume":"560","author":"La Manno","year":"2018","journal-title":"Nature"},{"key":"10.1016\/j.isci.2026.117266_bib36","doi-asserted-by":"crossref","first-page":"1408","DOI":"10.1038\/s41587-020-0591-3","article-title":"Generalizing RNA Velocity to Transient Cell States through Dynamical Modeling","volume":"38","author":"Bergen","year":"2020","journal-title":"Nat. Biotechnol."},{"key":"10.1016\/j.isci.2026.117266_bib37","doi-asserted-by":"crossref","first-page":"845","DOI":"10.1038\/nmeth.3971","article-title":"Diffusion Pseudotime Robustly Reconstructs Lineage Branching","volume":"13","author":"Haghverdi","year":"2016","journal-title":"Nat. Methods"},{"key":"10.1016\/j.isci.2026.117266_bib38","doi-asserted-by":"crossref","DOI":"10.15252\/msb.20209620","article-title":"Probabilistic Harmonization and Annotation of Single-cell Transcriptomics Data with Deep Generative Models","volume":"17","author":"Xu","year":"2021","journal-title":"Mol. Syst. Biol."},{"key":"10.1016\/j.isci.2026.117266_bib39","doi-asserted-by":"crossref","first-page":"451","DOI":"10.1038\/s41587-019-0068-4","article-title":"Characterization of Cell Fate Probabilities in Single-Cell Data with Palantir","volume":"37","author":"Setty","year":"2019","journal-title":"Nat. Biotechnol."},{"key":"10.1016\/j.isci.2026.117266_bib40","article-title":"UMAP: Uniform Manifold Approximation and Projection for Dimension Reduction","author":"McInnes","year":"2018","journal-title":"arXiv"},{"key":"10.1016\/j.isci.2026.117266_bib41","doi-asserted-by":"crossref","first-page":"1145","DOI":"10.1038\/nbt.3711","article-title":"Revealing the vectors of cellular identity with single-cell genomics","volume":"34","author":"Wagner","year":"2016","journal-title":"Nat. Biotechnol."},{"key":"10.1016\/j.isci.2026.117266_bib42","doi-asserted-by":"crossref","first-page":"535","DOI":"10.1016\/j.cell.2016.03.014","article-title":"On the dependency of cellular protein levels on mRNA abundance","volume":"165","author":"Liu","year":"2016","journal-title":"Cell"},{"key":"10.1016\/j.isci.2026.117266_bib43","doi-asserted-by":"crossref","first-page":"432","DOI":"10.1038\/nature22370","article-title":"Haematopoietic Stem and Progenitor Cells from Human Pluripotent Stem Cells","volume":"545","author":"Sugimura","year":"2017","journal-title":"Nature"},{"key":"10.1016\/j.isci.2026.117266_bib44","doi-asserted-by":"crossref","first-page":"143","DOI":"10.1038\/s41570-020-0162-7","article-title":"Single-cell analysis targeting the proteome","volume":"4","author":"Labib","year":"2020","journal-title":"Nat. Rev. Chem"},{"key":"10.1016\/j.isci.2026.117266_bib45","doi-asserted-by":"crossref","first-page":"437","DOI":"10.1038\/nrm.2017.27","article-title":"Alternative splicing as a regulator of development and tissue identity","volume":"18","author":"Baralle","year":"2017","journal-title":"Nat. Rev. Mol. Cell Biol."},{"key":"10.1016\/j.isci.2026.117266_bib46","doi-asserted-by":"crossref","first-page":"1177","DOI":"10.1038\/nmeth.2714","article-title":"Assessment of transcript reconstruction methods for RNA-seq","volume":"10","author":"Steijger","year":"2013","journal-title":"Nat. Methods"},{"key":"10.1016\/j.isci.2026.117266_bib47","doi-asserted-by":"crossref","first-page":"25","DOI":"10.1038\/75556","article-title":"Gene ontology: tool for the unification of biology","volume":"25","author":"Ashburner","year":"2000","journal-title":"Nat. Genet."},{"key":"10.1016\/j.isci.2026.117266_bib48","doi-asserted-by":"crossref","DOI":"10.1093\/genetics\/iyad031","article-title":"The gene ontology knowledgebase in 2023","volume":"224","author":"Gene Ontology Consortium","year":"2023","journal-title":"Genetics"},{"key":"10.1016\/j.isci.2026.117266_bib49","doi-asserted-by":"crossref","first-page":"D870","DOI":"10.1093\/nar\/gkac947","article-title":"CellMarker 2.0: an updated database of manually curated cell markers in human\/mouse and web tools based on scRNA-seq data","volume":"51","author":"Hu","year":"2023","journal-title":"Nucleic Acids Res."},{"key":"10.1016\/j.isci.2026.117266_bib50","doi-asserted-by":"crossref","first-page":"697","DOI":"10.1038\/s41576-022-00514-4","article-title":"Alternative Splicing as a Source of Phenotypic Diversity","volume":"23","author":"Wright","year":"2022","journal-title":"Nat. Rev. Genet."},{"key":"10.1016\/j.isci.2026.117266_bib51","doi-asserted-by":"crossref","first-page":"1096","DOI":"10.1038\/s41431-025-01905-x","article-title":"The role of untranslated region variants in Mendelian disease: a review","volume":"33","author":"Wieder","year":"2025","journal-title":"Eur. J. Hum. Genet."},{"key":"10.1016\/j.isci.2026.117266_bib52","doi-asserted-by":"crossref","first-page":"4645","DOI":"10.1038\/s41467-023-40391-x","article-title":"GATA2 Mitotic Bookmarking Is Required for Definitive Haematopoiesis","volume":"14","author":"Silv\u00e9rio-Alves","year":"2023","journal-title":"Nat. Commun."},{"key":"10.1016\/j.isci.2026.117266_bib53","doi-asserted-by":"crossref","first-page":"1191","DOI":"10.1634\/stemcells.2004-0033","article-title":"Enforced Activation of STAT5A Facilitates the Generation of Embryonic Stem\u2013Derived Hematopoietic Stem Cells That Contribute to Hematopoiesis In Vivo","volume":"22","author":"Schuringa","year":"2004","journal-title":"Stem Cell."},{"key":"10.1016\/j.isci.2026.117266_bib54","doi-asserted-by":"crossref","first-page":"623","DOI":"10.1084\/jem.20041024","article-title":"Constitutive Activation of STAT5A Promotes Human Hematopoietic Stem Cell Self-Renewal and Erythroid Differentiation","volume":"200","author":"Schuringa","year":"2004","journal-title":"J. Exp. Med."},{"key":"10.1016\/j.isci.2026.117266_bib55","doi-asserted-by":"crossref","first-page":"2347","DOI":"10.1182\/blood.2021010980","article-title":"A STAT5B\u2013CD9 axis determines self-renewal in hematopoietic and leukemic stem cells","volume":"138","author":"Kollmann","year":"2021","journal-title":"Blood"},{"key":"10.1016\/j.isci.2026.117266_bib56","doi-asserted-by":"crossref","first-page":"519","DOI":"10.1016\/j.exphem.2016.03.010","article-title":"The NF-\u03ba B family: Key players during embryonic development and HSC emergence. English","volume":"44","author":"Esp\u00edn-Palaz\u00f3n","year":"2016","journal-title":"Exp. Hematol."},{"key":"10.1016\/j.isci.2026.117266_bib57","doi-asserted-by":"crossref","first-page":"1070","DOI":"10.1016\/j.cell.2014.10.031","article-title":"Proinflammatory signaling regulates hematopoietic stem cell emergence","volume":"159","author":"Esp\u00edn-Palaz\u00f3n","year":"2014","journal-title":"Cell"},{"key":"10.1016\/j.isci.2026.117266_bib58","doi-asserted-by":"crossref","first-page":"1098","DOI":"10.1182\/blood-2014-09-601542","article-title":"Inflammatory signaling regulates hematopoietic stem and progenitor cell emergence in vertebrates","volume":"125","author":"He","year":"2015","journal-title":"Blood"},{"key":"10.1016\/j.isci.2026.117266_bib59","doi-asserted-by":"crossref","first-page":"11","DOI":"10.1038\/sj.leu.2403171","article-title":"NF-\u03baB\/Rel-mediated Regulation of Apoptosis in Hematologic Malignancies and Normal Hematopoietic Progenitors","volume":"18","author":"Turco","year":"2004","journal-title":"Leukemia"},{"key":"10.1016\/j.isci.2026.117266_bib60","doi-asserted-by":"crossref","first-page":"695","DOI":"10.1177\/1947601911421925","article-title":"The C-Rel Transcription Factor in Development and Disease","volume":"2","author":"Gilmore","year":"2011","journal-title":"Genes Cancer"},{"key":"10.1016\/j.isci.2026.117266_bib61","doi-asserted-by":"crossref","first-page":"15","DOI":"10.1080\/1547691X.2016.1250849","article-title":"Impact of C-rel Inhibition of Cord Blood-Derived B-T-and NK Cells","volume":"14","author":"Fallahi","year":"2017","journal-title":"J. Immunotoxicol."},{"key":"10.1016\/j.isci.2026.117266_bib62","doi-asserted-by":"crossref","first-page":"535","DOI":"10.1038\/leu.2014.231","article-title":"NF-\u03baB\/STAT5\/miR-155 network targets PU. 1 in FLT3-ITD-driven acute myeloid leukemia","volume":"29","author":"Gerloff","year":"2015","journal-title":"Leukemia"},{"key":"10.1016\/j.isci.2026.117266_bib63","doi-asserted-by":"crossref","first-page":"534","DOI":"10.1038\/s41586-022-04571-x","article-title":"Mapping Human Haematopoietic Stem Cells from Haemogenic Endothelium to Birth","volume":"604","author":"Calvanese","year":"2022","journal-title":"Nature"},{"key":"10.1016\/j.isci.2026.117266_bib64","doi-asserted-by":"crossref","first-page":"205","DOI":"10.1016\/j.stem.2013.05.024","article-title":"Induction of a Hemogenic Program in Mouse Fibroblasts","volume":"13","author":"Pereira","year":"2013","journal-title":"Cell Stem Cell"},{"key":"10.1016\/j.isci.2026.117266_bib65","doi-asserted-by":"crossref","first-page":"1871","DOI":"10.1016\/j.celrep.2014.11.002","article-title":"Direct Reprogramming of Murine Fibroblasts to Hematopoietic Progenitor Cells","volume":"9","author":"Batta","year":"2014","journal-title":"Cell Rep."},{"key":"10.1016\/j.isci.2026.117266_bib66","doi-asserted-by":"crossref","first-page":"24","DOI":"10.1111\/nyas.12989","article-title":"Converting Cell Fates: Generating Hematopoietic Stem Cells de Novo via Transcription Factor Reprogramming","volume":"1370","author":"Daniel","year":"2016","journal-title":"Ann. N. Y. Acad. Sci."},{"key":"10.1016\/j.isci.2026.117266_bib67","doi-asserted-by":"crossref","first-page":"357","DOI":"10.1016\/j.celrep.2013.09.016","article-title":"Global Splicing Pattern Reversion during Somatic Cell Reprogramming","volume":"5","author":"Ohta","year":"2013","journal-title":"Cell Rep."},{"key":"10.1016\/j.isci.2026.117266_bib68","doi-asserted-by":"crossref","first-page":"100","DOI":"10.1186\/s12864-019-5438-2","article-title":"Conserved Regulation of RNA Processing in Somatic Cell Reprogramming","volume":"20","author":"Kanitz","year":"2019","journal-title":"BMC Genom."},{"key":"10.1016\/j.isci.2026.117266_bib69","doi-asserted-by":"crossref","first-page":"171","DOI":"10.1186\/s13059-021-02372-5","article-title":"Dynamics of Alternative Splicing during Somatic Cell Reprogramming Reveals Functions for RNA-binding Proteins CPSF3, hnRNP UL1, and TIA1","volume":"22","author":"Vivori","year":"2021","journal-title":"Genome Biol."},{"key":"10.1016\/j.isci.2026.117266_bib70","doi-asserted-by":"crossref","first-page":"8","DOI":"10.1016\/j.ceb.2017.12.002","article-title":"RNA Splicing and Its Connection with Other Regulatory Layers in Somatic Cell Reprogramming","volume":"52","author":"Zavolan","year":"2018","journal-title":"Curr. Opin. Cell Biol."},{"key":"10.1016\/j.isci.2026.117266_bib71","doi-asserted-by":"crossref","first-page":"241","DOI":"10.1038\/nature12270","article-title":"MBNL Proteins Repress ES-cell-specific Alternative Splicing and Reprogramming","volume":"498","author":"Han","year":"2013","journal-title":"Nature"},{"key":"10.1016\/j.isci.2026.117266_bib72","doi-asserted-by":"crossref","first-page":"2597","DOI":"10.1016\/j.celrep.2016.05.049","article-title":"RNAi Reveals Phase-Specific Global Regulators of Human Somatic Cell Reprogramming","volume":"15","author":"Toh","year":"2016","journal-title":"Cell Rep."},{"key":"10.1016\/j.isci.2026.117266_bib73","doi-asserted-by":"crossref","first-page":"572","DOI":"10.1016\/j.devcel.2016.01.024","article-title":"Dynamic Gene Regulatory Networks Drive Hematopoietic Specification and Differentiation","volume":"36","author":"Goode","year":"2016","journal-title":"Dev. Cell"},{"key":"10.1016\/j.isci.2026.117266_bib74","doi-asserted-by":"crossref","first-page":"446","DOI":"10.1016\/j.devcel.2020.01.006","article-title":"YAP Regulates Hematopoietic Stem Cell Formation in Response to the Biomechanical Forces of Blood Flow","volume":"52","author":"Lundin","year":"2020","journal-title":"Dev. Cell"},{"key":"10.1016\/j.isci.2026.117266_bib75","doi-asserted-by":"crossref","first-page":"154","DOI":"10.3390\/metabo11030154","article-title":"YAP and TAZ Mediators at the Crossroad between Metabolic and Cellular Reprogramming","volume":"11","author":"Di Benedetto","year":"2021","journal-title":"Metabolites"},{"key":"10.1016\/j.isci.2026.117266_bib76","series-title":"The Strategy of the Genes","author":"Waddington","year":"2014"},{"key":"10.1016\/j.isci.2026.117266_bib77","doi-asserted-by":"crossref","first-page":"826","DOI":"10.1038\/nrg1471","article-title":"Biological Robustness","volume":"5","author":"Kitano","year":"2004","journal-title":"Nat. Rev. Genet."},{"key":"10.1016\/j.isci.2026.117266_bib78","doi-asserted-by":"crossref","first-page":"R458","DOI":"10.1016\/j.cub.2012.03.045","article-title":"Bistability, Bifurcations, and Waddington\u2019s Epigenetic Landscape","volume":"22","author":"Ferrell","year":"2012","journal-title":"Curr. Biol."},{"key":"10.1016\/j.isci.2026.117266_bib79","doi-asserted-by":"crossref","first-page":"32","DOI":"10.1016\/j.coisb.2018.02.009","article-title":"Exploring Intermediate Cell States through the Lens of Single Cells","volume":"9","author":"MacLean","year":"2018","journal-title":"Curr. Opin. Syst. Biol."},{"key":"10.1016\/j.isci.2026.117266_bib80","doi-asserted-by":"crossref","first-page":"1831","DOI":"10.1038\/s12276-023-01076-z","article-title":"A single-cell atlas of in vitro multiculture systems uncovers the in vivo lineage trajectory and cell state in the human lung. en","volume":"55","author":"Lee","year":"2023","journal-title":"Exp. Mol. Med."},{"key":"10.1016\/j.isci.2026.117266_bib81","article-title":"Single-cell transcriptomic analysis of chondrocytes in cartilage and pathogenesis of osteoarthritis","volume":"12","author":"Huang","year":"2025","journal-title":"Genes Dis."},{"key":"10.1016\/j.isci.2026.117266_bib82","doi-asserted-by":"crossref","first-page":"4520","DOI":"10.1016\/j.cell.2024.07.035","article-title":"Toward a Foundation Model of Causal Cell and Tissue Biology with a Perturbation Cell and Tissue Atlas","volume":"187","author":"Rood","year":"2024","journal-title":"Cell"},{"key":"10.1016\/j.isci.2026.117266_bib83","doi-asserted-by":"crossref","first-page":"1430","DOI":"10.1038\/s41592-024-02353-z","article-title":"Transformers in Single-Cell Omics: A Review and New Perspectives","volume":"21","author":"Sza\u0142ata","year":"2024","journal-title":"Nat. Methods"},{"key":"10.1016\/j.isci.2026.117266_bib84","doi-asserted-by":"crossref","first-page":"261","DOI":"10.1038\/s41592-019-0686-2","article-title":"SciPy 1.0: Fundamental Algorithms for Scientific Computing in Python","volume":"17","author":"Virtanen","year":"2020","journal-title":"Nat. Methods"},{"key":"10.1016\/j.isci.2026.117266_bib85","doi-asserted-by":"crossref","first-page":"33","DOI":"10.12688\/f1000research.29032.2","article-title":"Sustainable data analysis with Snakemake","volume":"10","author":"M\u00f6lder","year":"2021","journal-title":"F1000Res."},{"key":"10.1016\/j.isci.2026.117266_bib86","doi-asserted-by":"crossref","first-page":"15","DOI":"10.1186\/s13059-017-1382-0","article-title":"SCANPY: Large-Scale Single-Cell Gene Expression Data Analysis","volume":"19","author":"Wolf","year":"2018","journal-title":"Genome Biol."},{"key":"10.1016\/j.isci.2026.117266_bib87","article-title":"scverse\/rapids_singlecell: v0.10.6","author":"Dicks","year":"2024","journal-title":"Zenodo"},{"key":"10.1016\/j.isci.2026.117266_bib88","doi-asserted-by":"crossref","first-page":"163","DOI":"10.1038\/s41587-021-01206-w","article-title":"A Python Library for Probabilistic Analysis of Single-Cell Omics Data","volume":"40","author":"Gayoso","year":"2022","journal-title":"Nat. Biotechnol."},{"key":"10.1016\/j.isci.2026.117266_bib89","doi-asserted-by":"crossref","first-page":"1289","DOI":"10.1038\/s41592-019-0619-0","article-title":"Fast, Sensitive and Accurate Integration of Single-Cell Data with Harmony","volume":"16","author":"Korsunsky","year":"2019","journal-title":"Nat. Methods"},{"key":"10.1016\/j.isci.2026.117266_bib90","doi-asserted-by":"crossref","first-page":"40","DOI":"10.1186\/s13059-018-1417-1","article-title":"SUPPA2: Fast, Accurate, and Uncertainty-Aware Differential Splicing Analysis across Multiple Conditions","volume":"19","author":"Trincado","year":"2018","journal-title":"Genome Biol."},{"key":"10.1016\/j.isci.2026.117266_bib91","series-title":"Proceedings of Workshop on Machine Learning Systems (LearningSys) in The Thirty-first Annual Conference on Neural Information Processing Systems","article-title":"CuPy: A NumPy-Compatible Library for NVIDIA GPU Calculations","author":"Okuta","year":"2017"},{"key":"10.1016\/j.isci.2026.117266_bib92","article-title":"YosefLab\/scib-metrics: scib-metrics 0.5.8 (v0.5.8)","author":"Gayoso","year":"2026","journal-title":"Zenodo"},{"key":"10.1016\/j.isci.2026.117266_bib93","doi-asserted-by":"crossref","DOI":"10.1371\/journal.pone.0098679","article-title":"ForceAtlas2, a Continuous Graph Layout Algorithm for Handy Network Visualization Designed for the Gephi Software","volume":"9","author":"Jacomy","year":"2014","journal-title":"PLoS One"},{"key":"10.1016\/j.isci.2026.117266_bib94","doi-asserted-by":"crossref","DOI":"10.1093\/bioinformatics\/btae102","article-title":"Flexiplex: A Versatile Demultiplexer and Search Tool for Omics Data","volume":"40","author":"Cheng","year":"2024","journal-title":"Bioinformatics"},{"key":"10.1016\/j.isci.2026.117266_bib95","doi-asserted-by":"crossref","first-page":"3094","DOI":"10.1093\/bioinformatics\/bty191","article-title":"Minimap2: Pairwise Alignment for Nucleotide Sequences","volume":"34","author":"Li","year":"2018","journal-title":"Bioinformatics"},{"key":"10.1016\/j.isci.2026.117266_bib96","doi-asserted-by":"crossref","first-page":"309","DOI":"10.1038\/nature20123","article-title":"Single-Cell RNA-seq Supports a Developmental Hierarchy in Human Oligodendroglioma","volume":"539","author":"Tirosh","year":"2016","journal-title":"Nature"},{"key":"10.1016\/j.isci.2026.117266_bib97","doi-asserted-by":"crossref","first-page":"289","DOI":"10.1111\/j.2517-6161.1995.tb02031.x","article-title":"Controlling the False Discovery Rate: A Practical and Powerful Approach to Multiple Testing","volume":"57","author":"Benjamini","year":"1995","journal-title":"Journal of the Royal Statistical Society Series B: Statistical Methodology"},{"key":"10.1016\/j.isci.2026.117266_bib98","doi-asserted-by":"crossref","first-page":"41","DOI":"10.1038\/s41592-021-01336-8","article-title":"Benchmarking Atlas-Level Data Integration in Single-Cell Genomics","volume":"19","author":"Luecken","year":"2022","journal-title":"Nat. Methods"},{"key":"10.1016\/j.isci.2026.117266_bib99","doi-asserted-by":"crossref","first-page":"59","DOI":"10.1186\/s13059-019-1663-x","article-title":"PAGA: Graph Abstraction Reconciles Clustering with Trajectory Inference through a Topology Preserving Map of Single Cells","volume":"20","author":"Wolf","year":"2019","journal-title":"Genome Biol."},{"key":"10.1016\/j.isci.2026.117266_bib100","doi-asserted-by":"crossref","first-page":"6790","DOI":"10.1038\/s41467-021-27159-x","article-title":"Discrete Regulatory Modules Instruct Hematopoietic Lineage Commitment and Differentiation","volume":"12","author":"Georgolopoulos","year":"2021","journal-title":"Nat. Commun."},{"key":"10.1016\/j.isci.2026.117266_bib101","doi-asserted-by":"crossref","first-page":"lqab028","DOI":"10.1093\/nargab\/lqab028","article-title":"The Long and the Short of It: Unlocking Nanopore Long-Read RNA Sequencing Data with Short-Read Differential Expression Analysis Tools","volume":"3","author":"Dong","year":"2021","journal-title":"NAR Genom. Bioinform."}],"container-title":["iScience"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/api.elsevier.com\/content\/article\/PII:S2589004226026441?httpAccept=text\/xml","content-type":"text\/xml","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/api.elsevier.com\/content\/article\/PII:S2589004226026441?httpAccept=text\/plain","content-type":"text\/plain","content-version":"vor","intended-application":"text-mining"}],"deposited":{"date-parts":[[2026,10,10]],"date-time":"2026-10-10T01:12:57Z","timestamp":1791594777000},"score":1,"resource":{"primary":{"URL":"https:\/\/linkinghub.elsevier.com\/retrieve\/pii\/S2589004226026441"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2026,9]]},"references-count":101,"journal-issue":{"issue":"9","published-print":{"date-parts":[[2026,9]]}},"alternative-id":["S2589004226026441"],"URL":"https:\/\/doi.org\/10.1016\/j.isci.2026.117266","relation":{},"ISSN":["2589-0042"],"issn-type":[{"value":"2589-0042","type":"print"}],"subject":[],"published":{"date-parts":[[2026,9]]},"assertion":[{"value":"Elsevier","name":"publisher","label":"This article is maintained by"},{"value":"Transcriptional landscape of direct reprogramming toward the hematopoietic lineage","name":"articletitle","label":"Article Title"},{"value":"iScience","name":"journaltitle","label":"Journal Title"},{"value":"https:\/\/doi.org\/10.1016\/j.isci.2026.117266","name":"articlelink","label":"CrossRef DOI link to publisher maintained version"},{"value":"article","name":"content_type","label":"Content Type"},{"value":"\u00a9 2026 The Author(s). Published by Elsevier Inc.","name":"copyright","label":"Copyright"}],"article-number":"117266"}}