{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,6,5]],"date-time":"2026-06-05T04:18:25Z","timestamp":1780633105046,"version":"3.54.1"},"reference-count":169,"publisher":"American Society of Hematology","issue":"23","content-domain":{"domain":["ashpublications.org"],"crossmark-restriction":true},"short-container-title":[],"published-print":{"date-parts":[[2026,6,4]]},"abstract":"<jats:sec>\n                    <jats:title>Abstract<\/jats:title>\n                    <jats:p>For over 60 years, blood researchers have been counting clones with every tool at their disposal. Inspired by phage and fly geneticists, Till and McCulloch irradiated mice to induce chromosomal aberrations. Using this labeling strategy, they demonstrated that different types of blood cells shared the same mutation in every spleen colony, thereby proving the existence of hematopoietic stem cells. Since their breakthrough, technological advances have enabled researchers to quantify hematopoiesis at single-cell resolution in increasingly complex samples across both mice and humans. With these modern sophisticated lineage-tracing methods, our foundational understanding of the blood system is being reshaped. For instance, we now interpret hematopoietic architecture as arising from stem and progenitor cells of diverse developmental origins, each with distinct fate biases encoded by unique regulatory states. Interacting with this regulatory layer, genetic mutations and epimutations arise, expanding clonally and becoming pervasive with age. Together, clonal heterogeneity and age-driven clonal selection may underlie the perplexing diversity of therapy responses in cancer and beyond. As these paradigm-shifting insights gain traction, clonal tracing is being adopted across dozens of biological and clinical studies. Here, we review the modern toolbox of clonal tracking technologies, with a focus on next-generation sequencing-based approaches, and provide a practical guide for matching specific research questions with optimal experimental strategies.<\/jats:p>\n                  <\/jats:sec>","DOI":"10.1182\/blood.2024028195","type":"journal-article","created":{"date-parts":[[2025,9,22]],"date-time":"2025-09-22T21:52:43Z","timestamp":1758577963000},"page":"2728-2739","update-policy":"https:\/\/doi.org\/10.1182\/blood.2019cm0000","source":"Crossref","is-referenced-by-count":3,"title":["Clonal tracing of blood stem cells across mouse and human lifespans"],"prefix":"10.1182","volume":"147","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-4017-8714","authenticated-orcid":false,"given":"Alejo E.","family":"Rodriguez-Fraticelli","sequence":"first","affiliation":[{"name":"Institute for Research in Biomedicine (IRB Barcelona), Barcelona Institute of Science and Technology, Barcelona, Spain"},{"name":"Catalan Institution for Research and Advanced Studies, Barcelona, Catalonia, Spain"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"234","reference":[{"issue":"5","key":"2026060411215327700_bib1","doi-asserted-by":"crossref","first-page":"193","DOI":"10.1016\/j.it.2009.03.001","article-title":"A new paradigm for hematopoietic cell lineages: revision of the classical concept of the myeloid-lymphoid dichotomy","volume":"30","author":"Kawamoto","year":"2009","journal-title":"Trends Immunol"},{"key":"2026060411215327700_bib2","author":"Garc\u00eda-Marqu\u00e9s","year":"2025"},{"issue":"6616","key":"2026060411215327700_bib3","doi-asserted-by":"crossref","first-page":"eabm5874","DOI":"10.1126\/science.abm5874","article-title":"Cellular barcoding to decipher clonal dynamics in disease","volume":"378","author":"Sankaran","year":"2022","journal-title":"Science"},{"key":"2026060411215327700_bib4","doi-asserted-by":"crossref","first-page":"14","DOI":"10.1016\/j.ceb.2016.07.002","article-title":"Clonal analysis of stem cells in differentiation and disease","volume":"43","author":"Colom","year":"2016","journal-title":"Curr Opin Cell Biol"},{"issue":"1","key":"2026060411215327700_bib5","doi-asserted-by":"crossref","first-page":"7","DOI":"10.1016\/j.devcel.2020.10.021","article-title":"Next-generation lineage tracing and fate mapping to interrogate development","volume":"56","author":"VanHorn","year":"2021","journal-title":"Dev Cell"},{"issue":"1","key":"2026060411215327700_bib6","doi-asserted-by":"crossref","first-page":"18","DOI":"10.1097\/MOH.0000000000000624","article-title":"Systems analysis of hematopoiesis using single-cell lineage tracing","volume":"28","author":"Rodriguez-Fraticelli","year":"2021","journal-title":"Curr Opin Hematol"},{"key":"2026060411215327700_bib7","doi-asserted-by":"crossref","first-page":"26","DOI":"10.1016\/j.exphem.2020.07.007","article-title":"Single-cell lineage tracing approaches in hematology research: technical considerations","volume":"89","author":"Carrelha","year":"2020","journal-title":"Exp Hematol"},{"issue":"2","key":"2026060411215327700_bib8","doi-asserted-by":"crossref","first-page":"218","DOI":"10.1016\/j.stem.2007.05.015","article-title":"Long-term propagation of distinct hematopoietic differentiation programs in vivo","volume":"1","author":"Dykstra","year":"2007","journal-title":"Cell Stem Cell"},{"issue":"4","key":"2026060411215327700_bib9","doi-asserted-by":"crossref","first-page":"1302","DOI":"10.1182\/blood.V100.4.1302.h81602001302_1302_1309","article-title":"Deterministic regulation of hematopoietic stem cell self-renewal and differentiation","volume":"100","author":"M\u00fcller-Sieburg","year":"2002","journal-title":"Blood"},{"issue":"6","key":"2026060411215327700_bib10","doi-asserted-by":"crossref","first-page":"2311","DOI":"10.1182\/blood-2005-07-2970","article-title":"The hematopoietic stem compartment consists of a limited number of discrete stem cell subsets","volume":"107","author":"Sieburg","year":"2006","journal-title":"Blood"},{"issue":"22","key":"2026060411215327700_bib11","doi-asserted-by":"crossref","first-page":"8736","DOI":"10.1073\/pnas.87.22.8736","article-title":"Quantitative assay for totipotent reconstituting hematopoietic stem cells by a competitive repopulation strategy","volume":"87","author":"Szilvassy","year":"1990","journal-title":"Proc Natl Acad Sci U S A"},{"issue":"9","key":"2026060411215327700_bib12","doi-asserted-by":"crossref","first-page":"3584","DOI":"10.1073\/pnas.87.9.3584","article-title":"Functional characterization of individual human hematopoietic stem cells cultured at limiting dilution on supportive marrow stromal layers","volume":"87","author":"Sutherland","year":"1990","journal-title":"Proc Natl Acad Sci U S A"},{"issue":"25","key":"2026060411215327700_bib13","doi-asserted-by":"crossref","first-page":"13648","DOI":"10.1073\/pnas.94.25.13648","article-title":"Expansion in vitro of adult murine hematopoietic stem cells with transplantable lympho-myeloid reconstituting ability","volume":"94","author":"Miller","year":"1997","journal-title":"Proc Natl Acad Sci U S A"},{"issue":"2","key":"2026060411215327700_bib14","doi-asserted-by":"crossref","first-page":"393","DOI":"10.1182\/blood.V64.2.393.393","article-title":"Analysis of differentiation of mouse hemopoietic stem cells in culture by sequential replating of paired progenitors","volume":"64","author":"Suda","year":"1984","journal-title":"Blood"},{"issue":"3","key":"2026060411215327700_bib15","doi-asserted-by":"crossref","first-page":"295","DOI":"10.1084\/jem.20030929","article-title":"Asymmetric division and lineage commitment at the level of hematopoietic stem cells: inference from differentiation in daughter cell and granddaughter cell pairs","volume":"199","author":"Takano","year":"2004","journal-title":"J Exp Med"},{"issue":"21","key":"2026060411215327700_bib16","doi-asserted-by":"crossref","first-page":"8185","DOI":"10.1073\/pnas.0602548103","article-title":"High-resolution video monitoring of hematopoietic stem cells cultured in single-cell arrays identifies new features of self-renewal","volume":"103","author":"Dykstra","year":"2006","journal-title":"Proc Natl Acad Sci U S A"},{"issue":"3","key":"2026060411215327700_bib17","doi-asserted-by":"crossref","first-page":"560","DOI":"10.1182\/blood-2007-10-117820","article-title":"Steel factor coordinately regulates the molecular signature and biologic function of hematopoietic stem cells","volume":"112","author":"Kent","year":"2008","journal-title":"Blood"},{"issue":"4","key":"2026060411215327700_bib18","doi-asserted-by":"crossref","first-page":"659","DOI":"10.1016\/S1074-7613(01)00220-5","article-title":"Upregulation of Flt3 expression within the bone marrow Lin(-)Sca1(+)c-kit(+) stem cell compartment is accompanied by loss of self-renewal capacity","volume":"15","author":"Adolfsson","year":"2001","journal-title":"Immunity"},{"issue":"4","key":"2026060411215327700_bib19","doi-asserted-by":"crossref","first-page":"428","DOI":"10.1016\/j.stem.2007.07.005","article-title":"Elucidation of the phenotypic, functional, and molecular topography of a myeloerythroid progenitor cell hierarchy","volume":"1","author":"Pronk","year":"2007","journal-title":"Cell Stem Cell"},{"issue":"6","key":"2026060411215327700_bib20","doi-asserted-by":"crossref","first-page":"1535","DOI":"10.1016\/j.cell.2018.03.074","article-title":"Integrated single-cell analysis maps the continuous regulatory landscape of human hematopoietic differentiation","volume":"173","author":"Buenrostro","year":"2018","journal-title":"Cell"},{"issue":"4","key":"2026060411215327700_bib21","doi-asserted-by":"crossref","first-page":"271","DOI":"10.1038\/ncb3493","article-title":"Human haematopoietic stem cell lineage commitment is a continuous process","volume":"19","author":"Velten","year":"2017","journal-title":"Nat Cell Biol"},{"issue":"21","key":"2026060411215327700_bib22","doi-asserted-by":"crossref","first-page":"e1","DOI":"10.1182\/blood-2017-12-821413","article-title":"A single-cell hematopoietic landscape resolves 8 lineage trajectories and defects in Kit mutant mice","volume":"131","author":"Dahlin","year":"2018","journal-title":"Blood"},{"issue":"7687","key":"2026060411215327700_bib23","doi-asserted-by":"crossref","first-page":"212","DOI":"10.1038\/nature25168","article-title":"Clonal analysis of lineage fate in native haematopoiesis","volume":"553","author":"Rodriguez-Fraticelli","year":"2018","journal-title":"Nature"},{"issue":"7","key":"2026060411215327700_bib24","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"},{"issue":"7","key":"2026060411215327700_bib25","doi-asserted-by":"crossref","first-page":"836","DOI":"10.1038\/s41556-018-0121-4","article-title":"Single-cell characterization of haematopoietic progenitors and their trajectories in homeostasis and perturbed haematopoiesis","volume":"20","author":"Giladi","year":"2018","journal-title":"Nat Cell Biol"},{"issue":"6","key":"2026060411215327700_bib26","doi-asserted-by":"crossref","first-page":"712","DOI":"10.1016\/j.stem.2015.04.004","article-title":"Combined single-cell functional and gene expression analysis resolves heterogeneity within stem cell populations","volume":"16","author":"Wilson","year":"2015","journal-title":"Cell Stem Cell"},{"issue":"4","key":"2026060411215327700_bib27","doi-asserted-by":"crossref","first-page":"363","DOI":"10.1038\/ncb2709","article-title":"Characterization of transcriptional networks in blood stem and progenitor cells using high-throughput single-cell gene expression analysis","volume":"15","author":"Moignard","year":"2013","journal-title":"Nat Cell Biol"},{"issue":"5937","key":"2026060411215327700_bib28","doi-asserted-by":"crossref","first-page":"217","DOI":"10.1126\/science.1171461","article-title":"Hematopoietic cytokines can instruct lineage choice","volume":"325","author":"Rieger","year":"2009","journal-title":"Science"},{"issue":"7","key":"2026060411215327700_bib29","doi-asserted-by":"crossref","first-page":"581","DOI":"10.1038\/nmeth.1614","article-title":"High-throughput analysis of single hematopoietic stem cell proliferation in microfluidic cell culture arrays","volume":"8","author":"Lecault","year":"2011","journal-title":"Nat Methods"},{"issue":"7231","key":"2026060411215327700_bib30","doi-asserted-by":"crossref","first-page":"896","DOI":"10.1038\/nature07760","article-title":"Continuous single-cell imaging of blood generation from haemogenic endothelium","volume":"457","author":"Eilken","year":"2009","journal-title":"Nature"},{"issue":"7611","key":"2026060411215327700_bib31","doi-asserted-by":"crossref","first-page":"299","DOI":"10.1038\/nature18320","article-title":"Early myeloid lineage choice is not initiated by random PU.1 to GATA1 protein ratios","volume":"535","author":"Hoppe","year":"2016","journal-title":"Nature"},{"issue":"13","key":"2026060411215327700_bib32","doi-asserted-by":"crossref","first-page":"1482","DOI":"10.1182\/blood.2022016880","article-title":"Combining single-cell tracking and omics improves blood stem cell fate regulator identification","volume":"140","author":"Wehling","year":"2022","journal-title":"Blood"},{"issue":"13","key":"2026060411215327700_bib33","doi-asserted-by":"crossref","first-page":"2011","DOI":"10.1182\/blood.2020009778","article-title":"Asymmetric organelle inheritance predicts human blood stem cell fate","volume":"139","author":"Loeffler","year":"2022","journal-title":"Blood"},{"issue":"7774","key":"2026060411215327700_bib34","doi-asserted-by":"crossref","first-page":"426","DOI":"10.1038\/s41586-019-1531-6","article-title":"Asymmetric lysosome inheritance predicts activation of haematopoietic stem cells","volume":"573","author":"Loeffler","year":"2019","journal-title":"Nature"},{"issue":"13","key":"2026060411215327700_bib35","doi-asserted-by":"crossref","first-page":"1406","DOI":"10.1182\/blood-2018-09-835397","article-title":"Understanding cell fate control by continuous single-cell quantification","volume":"133","author":"Loeffler","year":"2019","journal-title":"Blood"},{"issue":"12","key":"2026060411215327700_bib36","doi-asserted-by":"crossref","first-page":"1691","DOI":"10.1182\/blood-2016-05-714329","article-title":"CSF-1-induced Src signaling can instruct monocytic lineage choice","volume":"129","author":"Endele","year":"2017","journal-title":"Blood"},{"issue":"8","key":"2026060411215327700_bib37","doi-asserted-by":"crossref","first-page":"816","DOI":"10.1182\/blood-2018-02-832998","article-title":"Inflammatory signals directly instruct PU.1 in HSCs via TNF","volume":"133","author":"Etzrodt","year":"2019","journal-title":"Blood"},{"issue":"7444","key":"2026060411215327700_bib38","doi-asserted-by":"crossref","first-page":"229","DOI":"10.1038\/nature12013","article-title":"Diverse and heritable lineage imprinting of early haematopoietic progenitors","volume":"496","author":"Naik","year":"2013","journal-title":"Nature"},{"issue":"5","key":"2026060411215327700_bib39","doi-asserted-by":"crossref","first-page":"944","DOI":"10.1016\/j.cell.2017.02.010","article-title":"Epigenetic memory underlies cell-autonomous heterogeneous behavior of hematopoietic stem cells","volume":"168","author":"Yu","year":"2017","journal-title":"Cell"},{"issue":"6479","key":"2026060411215327700_bib40","doi-asserted-by":"crossref","first-page":"eaaw3381","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"},{"issue":"6","key":"2026060411215327700_bib41","doi-asserted-by":"crossref","first-page":"1338","DOI":"10.1016\/j.immuni.2021.03.012","article-title":"Clonal multi-omics reveals Bcor as a negative regulator of emergency dendritic cell development","volume":"54","author":"Tian","year":"2021","journal-title":"Immunity"},{"issue":"1","key":"2026060411215327700_bib42","doi-asserted-by":"crossref","first-page":"13","DOI":"10.1016\/j.stemcr.2022.12.003","article-title":"Single-cell multi-omics and lineage tracing to dissect cell fate decision-making","volume":"18","author":"Haghverdi","year":"2023","journal-title":"Stem Cell Rep"},{"issue":"6","key":"2026060411215327700_bib43","doi-asserted-by":"crossref","first-page":"946","DOI":"10.1038\/s41587-023-01931-4","article-title":"Single-cell lineage capture across genomic modalities with CellTag-multi reveals fate-specific gene regulatory changes","volume":"42","author":"Jindal","year":"2024","journal-title":"Nat Biotechnol"},{"issue":"7817","key":"2026060411215327700_bib44","doi-asserted-by":"crossref","first-page":"585","DOI":"10.1038\/s41586-020-2503-6","article-title":"Single-cell lineage tracing unveils a role for TCF15 in haematopoiesis","volume":"583","author":"Rodriguez-Fraticelli","year":"2020","journal-title":"Nature"},{"issue":"4","key":"2026060411215327700_bib45","doi-asserted-by":"crossref","first-page":"eadk2132","DOI":"10.1126\/sciadv.adk2132","article-title":"Quantitative association between gene expression and blood cell production of individual hematopoietic stem cells in mice","volume":"10","author":"Jiang","year":"2024","journal-title":"Sci Adv"},{"issue":"1","key":"2026060411215327700_bib46","doi-asserted-by":"crossref","first-page":"156","DOI":"10.1073\/pnas.84.1.156","article-title":"Lineage analysis in the vertebrate nervous system by retrovirus-mediated gene transfer","volume":"84","author":"Price","year":"1987","journal-title":"Proc Natl Acad Sci U S A"},{"issue":"2","key":"2026060411215327700_bib47","doi-asserted-by":"crossref","first-page":"545","DOI":"10.1182\/blood-2003-05-1558","article-title":"Lentivector-mediated clonal tracking reveals intrinsic heterogeneity in the human hematopoietic stem cell compartment and culture-induced stem cell impairment","volume":"103","author":"Mazurier","year":"2004","journal-title":"Blood"},{"issue":"8","key":"2026060411215327700_bib48","doi-asserted-by":"crossref","first-page":"598","DOI":"10.1016\/j.exphem.2014.05.003","article-title":"Cellular barcoding: a technical appraisal","volume":"42","author":"Naik","year":"2014","journal-title":"Exp Hematol"},{"issue":"10","key":"2026060411215327700_bib49","doi-asserted-by":"crossref","first-page":"928","DOI":"10.1038\/nbt.1977","article-title":"Tracking single hematopoietic stem cells in vivo using high-throughput sequencing in conjunction with viral genetic barcoding","volume":"29","author":"Lu","year":"2011","journal-title":"Nat Biotechnol"},{"issue":"4","key":"2026060411215327700_bib50","doi-asserted-by":"crossref","first-page":"1436","DOI":"10.1038\/s41596-019-0290-z","article-title":"Clonal tracking using embedded viral barcoding and high-throughput sequencing","volume":"15","author":"Bramlett","year":"2020","journal-title":"Nat Protoc"},{"issue":"4","key":"2026060411215327700_bib51","doi-asserted-by":"crossref","first-page":"617","DOI":"10.1016\/j.celrep.2014.01.016","article-title":"Determining lineage pathways from cellular barcoding experiments","volume":"6","author":"Peri\u00e9","year":"2014","journal-title":"Cell Rep"},{"issue":"4","key":"2026060411215327700_bib52","doi-asserted-by":"crossref","first-page":"564","DOI":"10.1016\/j.stem.2025.01.012","article-title":"Pre-existing stem cell heterogeneity dictates clonal responses to the acquisition of leukemic driver mutations","volume":"32","author":"Singh","year":"2025","journal-title":"Cell Stem Cell"},{"issue":"3","key":"2026060411215327700_bib53","doi-asserted-by":"crossref","first-page":"750","DOI":"10.1038\/s41596-019-0247-2","article-title":"CellTagging: combinatorial indexing to simultaneously map lineage and identity at single-cell resolution","volume":"15","author":"Kong","year":"2020","journal-title":"Nat Protoc"},{"issue":"7891","key":"2026060411215327700_bib54","doi-asserted-by":"crossref","first-page":"125","DOI":"10.1038\/s41586-021-04206-7","article-title":"Non-genetic determinants of malignant clonal fitness at single-cell resolution","volume":"601","author":"Fennell","year":"2022","journal-title":"Nature"},{"issue":"7893","key":"2026060411215327700_bib55","doi-asserted-by":"crossref","first-page":"397","DOI":"10.1038\/s41586-021-04230-7","article-title":"Individual human cortical progenitors can produce excitatory and inhibitory neurons","volume":"601","author":"Delgado","year":"2022","journal-title":"Nature"},{"issue":"3","key":"2026060411215327700_bib56","doi-asserted-by":"crossref","first-page":"285","DOI":"10.1038\/s41593-022-01011-x","article-title":"Clonal relations in the mouse brain revealed by single-cell and spatial transcriptomics","volume":"25","author":"Ratz","year":"2022","journal-title":"Nat Neurosci"},{"issue":"7873","key":"2026060411215327700_bib57","doi-asserted-by":"crossref","first-page":"576","DOI":"10.1038\/s41586-021-03796-6","article-title":"Cycling cancer persister cells arise from lineages with distinct programs","volume":"596","author":"Oren","year":"2021","journal-title":"Nature"},{"issue":"4","key":"2026060411215327700_bib58","doi-asserted-by":"crossref","first-page":"473","DOI":"10.1016\/j.stem.2023.02.007","article-title":"Mapping of clonal lineages across developmental stages in human neural differentiation","volume":"30","author":"You","year":"2023","journal-title":"Cell Stem Cell"},{"issue":"2","key":"2026060411215327700_bib59","doi-asserted-by":"crossref","first-page":"128","DOI":"10.1038\/s43588-024-00595-7","article-title":"Extracting, filtering and simulating cellular barcodes using CellBarcode tools","volume":"4","author":"Sun","year":"2024","journal-title":"Nat Comput Sci"},{"key":"2026060411215327700_bib60","doi-asserted-by":"crossref","first-page":"65","DOI":"10.1007\/978-1-0716-4310-5_4","article-title":"Single-cell lineage tracing and clonal state-fate analysis","volume":"2886","author":"Rodriguez Fraticelli","year":"2025","journal-title":"Methods Mol Biol"},{"issue":"12","key":"2026060411215327700_bib61","doi-asserted-by":"crossref","first-page":"950","DOI":"10.1016\/j.cels.2022.11.005","article-title":"The sound of silence: transgene silencing in mammalian cell engineering","volume":"13","author":"Cabrera","year":"2022","journal-title":"Cell Syst"},{"issue":"6","key":"2026060411215327700_bib62","doi-asserted-by":"crossref","first-page":"983","DOI":"10.1038\/s41592-024-02260-3","article-title":"Multiplex profiling of developmental cis-regulatory elements with quantitative single-cell expression reporters","volume":"21","author":"Lalanne","year":"2024","journal-title":"Nat Methods"},{"key":"2026060411215327700_bib63","doi-asserted-by":"crossref","first-page":"102","DOI":"10.1016\/j.coviro.2016.08.016","article-title":"Lentiviral vector interactions with the host cell","volume":"21","author":"Borsotti","year":"2016","journal-title":"Curr Opin Virol"},{"key":"2026060411215327700_bib64","doi-asserted-by":"crossref","first-page":"103802","DOI":"10.1016\/j.cellimm.2018.04.012","article-title":"Modulation of immune responses in lentiviral vector-mediated gene transfer","volume":"342","author":"Annoni","year":"2019","journal-title":"Cell Immunol"},{"issue":"4","key":"2026060411215327700_bib65","doi-asserted-by":"crossref","first-page":"774","DOI":"10.1038\/mt.2014.3","article-title":"Uncovering and dissecting the genotoxicity of self-inactivating lentiviral vectors in vivo","volume":"22","author":"Cesana","year":"2014","journal-title":"Mol Ther"},{"issue":"1","key":"2026060411215327700_bib66","doi-asserted-by":"crossref","first-page":"217","DOI":"10.1084\/jem.20171341","article-title":"Geographic clonal tracking in macaques provides insights into HSPC migration and differentiation","volume":"215","author":"Wu","year":"2018","journal-title":"J Exp Med"},{"key":"2026060411215327700_bib67","doi-asserted-by":"publisher","DOI":"10.1101\/2024.03.28.587126","article-title":"Amulti-tracklandscape of haematopoiesis informed by cellular barcoding and agent-based modelling","author":"Lin","year":"30  2024","journal-title":"bioRxiv"},{"key":"2026060411215327700_bib68","doi-asserted-by":"publisher","DOI":"10.1101\/2025.07.28.667115","article-title":"The hidden predictors of human haematopoietic clonal fate","author":"Tomei","year":"1  2025","journal-title":"bioRxiv"},{"key":"2026060411215327700_bib69","doi-asserted-by":"crossref","first-page":"e66922","DOI":"10.7554\/eLife.66922","article-title":"Erythropoietin directly remodels the clonal composition of murine hematopoietic multipotent progenitor cells","volume":"11","author":"Eisele","year":"2022","journal-title":"Elife"},{"issue":"6742","key":"2026060411215327700_bib70","doi-asserted-by":"crossref","first-page":"60","DOI":"10.1126\/science.adq9248","article-title":"Ectoderm barcoding reveals neural and cochlear compartmentalization","volume":"388","author":"de Haan","year":"2025","journal-title":"Science"},{"issue":"8073","key":"2026060411215327700_bib71","doi-asserted-by":"crossref","first-page":"1097","DOI":"10.1038\/s41586-025-09070-3","article-title":"In vivo haemopoietic stem cell gene therapy enabled by postnatal trafficking","volume":"643","author":"Milani","year":"2025","journal-title":"Nature"},{"issue":"1","key":"2026060411215327700_bib72","doi-asserted-by":"crossref","first-page":"7","DOI":"10.1016\/S1534-5807(03)00399-X","article-title":"Talking about a revolution: the impact of site-specific recombinases on genetic analyses in mice","volume":"6","author":"Branda","year":"2004","journal-title":"Dev Cell"},{"key":"2026060411215327700_bib73","unstructured":"MouseCre\n          . Mouse CRE and CreERT2 zoo. Accessed 14 August 2025. https:\/\/mousecre.phenomin.fr."},{"issue":"6","key":"2026060411215327700_bib74","doi-asserted-by":"crossref","first-page":"791","DOI":"10.1016\/j.stem.2014.11.002","article-title":"Estrogen signaling selectively induces apoptosis of hematopoietic progenitors and myeloid neoplasms without harming steady-state hematopoiesis","volume":"15","author":"S\u00e1nchez-Aguilera","year":"2014","journal-title":"Cell Stem Cell"},{"issue":"7540","key":"2026060411215327700_bib75","doi-asserted-by":"crossref","first-page":"542","DOI":"10.1038\/nature14242","article-title":"Fundamental properties of unperturbed haematopoiesis from stem cells in vivo","volume":"518","author":"Busch","year":"2015","journal-title":"Nature"},{"key":"2026060411215327700_bib76","doi-asserted-by":"crossref","first-page":"e41258","DOI":"10.7554\/eLife.41258","article-title":"Murine HSCs contribute actively to native hematopoiesis but with reduced differentiation capacity upon aging","volume":"7","author":"S\u00e4wen","year":"2018","journal-title":"Elife"},{"issue":"1","key":"2026060411215327700_bib77","doi-asserted-by":"crossref","first-page":"17","DOI":"10.1038\/ncb3444","article-title":"Clonal fate mapping quantifies the number of haematopoietic stem cells that arise during development","volume":"19","author":"Henninger","year":"2017","journal-title":"Nat Cell Biol"},{"issue":"14","key":"2026060411215327700_bib78","doi-asserted-by":"crossref","first-page":"3882","DOI":"10.1016\/j.cell.2025.04.026","article-title":"LoxCode in vivo barcoding reveals epiblast clonal fate bias to fetal organs","volume":"188","author":"Weber","year":"2025","journal-title":"Cell"},{"issue":"6","key":"2026060411215327700_bib79","doi-asserted-by":"crossref","first-page":"1820","DOI":"10.1038\/s41596-019-0163-5","article-title":"Using Cre-recombinase-driven Polylox barcoding for in vivo fate mapping in mice","volume":"14","author":"Pei","year":"2019","journal-title":"Nat Protoc"},{"issue":"7668","key":"2026060411215327700_bib80","doi-asserted-by":"crossref","first-page":"456","DOI":"10.1038\/nature23653","article-title":"Polylox barcoding reveals haematopoietic stem cell fates realized in vivo","volume":"548","author":"Pei","year":"2017","journal-title":"Nature"},{"issue":"3","key":"2026060411215327700_bib81","doi-asserted-by":"crossref","first-page":"383","DOI":"10.1016\/j.stem.2020.07.018","article-title":"Resolving fates and single-cell transcriptomes of hematopoietic stem cell clones by PolyloxExpress barcoding","volume":"27","author":"Pei","year":"2020","journal-title":"Cell Stem Cell"},{"issue":"1","key":"2026060411215327700_bib82","doi-asserted-by":"crossref","first-page":"41","DOI":"10.1038\/s41467-022-35744-x","article-title":"In vivo clonal tracking reveals evidence of haemangioblast and haematomesoblast contribution to yolk sac haematopoiesis","volume":"14","author":"Biben","year":"2023","journal-title":"Nat Commun"},{"issue":"3","key":"2026060411215327700_bib83","doi-asserted-by":"crossref","first-page":"405","DOI":"10.1016\/j.immuni.2022.01.016","article-title":"Clonal lineage tracing reveals shared origin of conventional and plasmacytoid dendritic cells","volume":"55","author":"Feng","year":"2022","journal-title":"Immunity"},{"issue":"7522","key":"2026060411215327700_bib84","doi-asserted-by":"crossref","first-page":"322","DOI":"10.1038\/nature13824","article-title":"Clonal dynamics of native haematopoiesis","volume":"514","author":"Sun","year":"2014","journal-title":"Nature"},{"issue":"4","key":"2026060411215327700_bib85","doi-asserted-by":"crossref","first-page":"e2317929121","DOI":"10.1073\/pnas.2317929121","article-title":"Clonal barcoding of endogenous adult hematopoietic stem cells reveals a spectrum of lineage contributions","volume":"121","author":"Feng","year":"2024","journal-title":"Proc Natl Acad Sci U S A"},{"issue":"7915","key":"2026060411215327700_bib86","doi-asserted-by":"crossref","first-page":"747","DOI":"10.1038\/s41586-022-04804-z","article-title":"Lifelong multilineage contribution by embryonic-born blood progenitors","volume":"606","author":"Patel","year":"2022","journal-title":"Nature"},{"issue":"6405","key":"2026060411215327700_bib87","doi-asserted-by":"crossref","first-page":"eaat9804","DOI":"10.1126\/science.aat9804","article-title":"Developmental barcoding of whole mouse via homing CRISPR","volume":"361","author":"Kalhor","year":"2018","journal-title":"Science"},{"issue":"6","key":"2026060411215327700_bib88","doi-asserted-by":"crossref","first-page":"1058","DOI":"10.1016\/j.neuron.2020.09.023","article-title":"Emergence of neuronal diversity during vertebrate brain development","volume":"108","author":"Raj","year":"2020","journal-title":"Neuron"},{"issue":"5","key":"2026060411215327700_bib89","doi-asserted-by":"crossref","first-page":"442","DOI":"10.1038\/nbt.4103","article-title":"Simultaneous single-cell profiling of lineages and cell types in the vertebrate brain","volume":"36","author":"Raj","year":"2018","journal-title":"Nat Biotechnol"},{"issue":"6298","key":"2026060411215327700_bib90","doi-asserted-by":"crossref","first-page":"aaf7907","DOI":"10.1126\/science.aaf7907","article-title":"Whole-organism lineage tracing by combinatorial and cumulative genome editing","volume":"353","author":"McKenna","year":"2016","journal-title":"Science"},{"key":"2026060411215327700_bib91","doi-asserted-by":"publisher","DOI":"10.1101\/2025.02.23.639689","article-title":"Hematopoietic stem cells undergo bidirectional fate transitions","author":"Fukushima","year":"26  2025","journal-title":"bioRxiv"},{"issue":"8","key":"2026060411215327700_bib92","doi-asserted-by":"crossref","first-page":"2319","DOI":"10.1038\/s41596-025-01141-z","article-title":"DARLIN mouse for in vivo lineage tracing at high efficiency and clonal diversity","volume":"20","author":"Li","year":"2025","journal-title":"Nat Protoc"},{"issue":"23","key":"2026060411215327700_bib93","doi-asserted-by":"crossref","first-page":"5183","DOI":"10.1016\/j.cell.2023.09.019","article-title":"A mouse model with high clonal barcode diversity for joint lineage, transcriptomic, and epigenomic profiling in single cells","volume":"186","author":"Li","year":"2023","journal-title":"Cell"},{"key":"2026060411215327700_bib94","doi-asserted-by":"crossref","first-page":"281","DOI":"10.1007\/978-1-0716-4310-5_14","article-title":"CARLIN: a mouse line for simultaneous readout of lineage histories and gene expression","volume":"2886","author":"Bowling","year":"2025","journal-title":"Methods Mol Biol"},{"issue":"7","key":"2026060411215327700_bib95","doi-asserted-by":"crossref","first-page":"1693","DOI":"10.1016\/j.cell.2020.06.018","article-title":"An engineered CRISPR-Cas9 mouse line for simultaneous readout of lineage histories and gene expression profiles in single cells","volume":"181","author":"Bowling","year":"2020","journal-title":"Cell"},{"issue":"8","key":"2026060411215327700_bib96","doi-asserted-by":"crossref","first-page":"1244","DOI":"10.1038\/s41592-023-01947-3","article-title":"Comprehensive spatiotemporal mapping of single-cell lineages in developing mouse brain by CRISPR-based barcoding","volume":"20","author":"Xie","year":"2023","journal-title":"Nat Methods"},{"issue":"1","key":"2026060411215327700_bib97","doi-asserted-by":"crossref","first-page":"2184","DOI":"10.1038\/s41467-023-37167-8","article-title":"DRAG in situ barcoding reveals an increased number of HSPCs contributing to myelopoiesis with age","volume":"14","author":"Urbanus","year":"2023","journal-title":"Nat Commun"},{"issue":"1","key":"2026060411215327700_bib98","doi-asserted-by":"crossref","first-page":"107","DOI":"10.1016\/j.stem.2016.04.016","article-title":"In vivo tracking of human hematopoiesis reveals patterns of clonal dynamics during early and steady-state reconstitution phases","volume":"19","author":"Biasco","year":"2016","journal-title":"Cell Stem Cell"},{"issue":"8041","key":"2026060411215327700_bib99","doi-asserted-by":"crossref","first-page":"162","DOI":"10.1038\/s41586-024-08250-x","article-title":"Long-term lineage commitment in haematopoietic stem cell gene therapy","volume":"636","author":"Calabria","year":"2024","journal-title":"Nature"},{"issue":"19","key":"2026060411215327700_bib100","doi-asserted-by":"crossref","first-page":"1937","DOI":"10.1182\/blood.2023022666","article-title":"Circulating hematopoietic stem\/progenitor cell subsets contribute to human hematopoietic homeostasis","volume":"143","author":"Quaranta","year":"2024","journal-title":"Blood"},{"issue":"1","key":"2026060411215327700_bib101","doi-asserted-by":"crossref","first-page":"3068","DOI":"10.1038\/s41467-023-38448-y","article-title":"Hematopoietic reconstitution dynamics of mobilized- and bone marrow-derived human hematopoietic stem cells after gene therapy","volume":"14","author":"Scala","year":"2023","journal-title":"Nat Commun"},{"issue":"7906","key":"2026060411215327700_bib102","doi-asserted-by":"crossref","first-page":"517","DOI":"10.1038\/s41586-022-04618-z","article-title":"Somatic mutation rates scale with lifespan across mammals","volume":"604","author":"Cagan","year":"2022","journal-title":"Nature"},{"issue":"7913","key":"2026060411215327700_bib103","doi-asserted-by":"crossref","first-page":"343","DOI":"10.1038\/s41586-022-04786-y","article-title":"Clonal dynamics of haematopoiesis across the human lifespan","volume":"606","author":"Mitchell","year":"2022","journal-title":"Nature"},{"issue":"9","key":"2026060411215327700_bib104","doi-asserted-by":"crossref","first-page":"2308","DOI":"10.1016\/j.celrep.2018.11.014","article-title":"Somatic mutations reveal lineage relationships and age-related mutagenesis in human hematopoiesis","volume":"25","author":"Osorio","year":"2018","journal-title":"Cell Rep"},{"issue":"3","key":"2026060411215327700_bib105","doi-asserted-by":"crossref","first-page":"514","DOI":"10.1016\/j.stem.2021.02.001","article-title":"Reconstructing the lineage histories and differentiation trajectories of individual cancer cells in myeloproliferative neoplasms","volume":"28","author":"Van Egeren","year":"2021","journal-title":"Cell Stem Cell"},{"issue":"3","key":"2026060411215327700_bib106","doi-asserted-by":"crossref","first-page":"100054","DOI":"10.1016\/j.crmeth.2021.100054","article-title":"Retrospective cell lineage reconstruction in humans by using short tandem repeats","volume":"1","author":"Tao","year":"2021","journal-title":"Cell Rep Methods"},{"issue":"10","key":"2026060411215327700_bib107","doi-asserted-by":"crossref","first-page":"1161","DOI":"10.1038\/ng.2398","article-title":"A direct characterization of human mutation based on microsatellites","volume":"44","author":"Sun","year":"2012","journal-title":"Nat Genet"},{"issue":"4","key":"2026060411215327700_bib108","doi-asserted-by":"crossref","first-page":"602","DOI":"10.1101\/gr.255851.119","article-title":"RETrace: simultaneous retrospective lineage tracing and methylation profiling of single cells","volume":"30","author":"Wei","year":"2020","journal-title":"Genome Res"},{"issue":"6","key":"2026060411215327700_bib109","doi-asserted-by":"crossref","first-page":"2291","DOI":"10.1109\/TCBB.2020.2992813","article-title":"Comparing phylogenetic approaches to reconstructing cell lineage from microsatellites with missing data","volume":"18","author":"Lyne","year":"2021","journal-title":"IEEE\/ACM Trans Comput Biol Bioinform"},{"issue":"11","key":"2026060411215327700_bib110","doi-asserted-by":"crossref","first-page":"1588","DOI":"10.1101\/gr.202903.115","article-title":"A generic, cost-effective, and scalable cell lineage analysis platform","volume":"26","author":"Biezuner","year":"2016","journal-title":"Genome Res"},{"issue":"4","key":"2026060411215327700_bib111","doi-asserted-by":"crossref","first-page":"363","DOI":"10.1038\/ng0497-363","article-title":"A high observed substitution rate in the human mitochondrial DNA control region","volume":"15","author":"Parsons","year":"1997","journal-title":"Nat Genet"},{"issue":"8","key":"2026060411215327700_bib112","doi-asserted-by":"crossref","first-page":"1665","DOI":"10.1038\/s41588-024-01838-z","article-title":"Mitochondrial DNA mosaicism in normal human somatic cells","volume":"56","author":"An","year":"2024","journal-title":"Nat Genet"},{"issue":"5","key":"2026060411215327700_bib113","doi-asserted-by":"crossref","first-page":"720","DOI":"10.1038\/s41587-021-01109-w","article-title":"Fluctuating methylation clocks for cell lineage tracing at high temporal resolution in human tissues","volume":"40","author":"Gabbutt","year":"2022","journal-title":"Nat Biotechnol"},{"issue":"8","key":"2026060411215327700_bib114","doi-asserted-by":"crossref","first-page":"828","DOI":"10.1038\/s41588-020-0661-y","article-title":"Imprecise DNMT1 activity coupled with neighbor-guided correction enables robust yet flexible epigenetic inheritance","volume":"52","author":"Wang","year":"2020","journal-title":"Nat Genet"},{"issue":"11","key":"2026060411215327700_bib115","doi-asserted-by":"crossref","first-page":"1207","DOI":"10.1038\/ng.2442","article-title":"Epigenetic polymorphism and the stochastic formation of differentially methylated regions in normal and cancerous tissues","volume":"44","author":"Landan","year":"2012","journal-title":"Nat Genet"},{"issue":"7724","key":"2026060411215327700_bib116","doi-asserted-by":"crossref","first-page":"473","DOI":"10.1038\/s41586-018-0497-0","article-title":"Population dynamics of normal human blood inferred from somatic mutations","volume":"561","author":"Lee-Six","year":"2018","journal-title":"Nature"},{"issue":"6","key":"2026060411215327700_bib117","doi-asserted-by":"crossref","first-page":"1866","DOI":"10.1038\/s41596-024-00962-8","article-title":"Reconstructing phylogenetic trees from genome-wide somatic mutations in clonal samples","volume":"19","author":"Coorens","year":"2024","journal-title":"Nat Protoc"},{"issue":"36","key":"2026060411215327700_bib118","doi-asserted-by":"crossref","first-page":"14508","DOI":"10.1073\/pnas.1208715109","article-title":"Detection of ultra-rare mutations by next-generation sequencing","volume":"109","author":"Schmitt","year":"2012","journal-title":"Proc Natl Acad Sci U S A"},{"issue":"7859","key":"2026060411215327700_bib119","doi-asserted-by":"crossref","first-page":"405","DOI":"10.1038\/s41586-021-03477-4","article-title":"Somatic mutation landscapes at single-molecule resolution","volume":"593","author":"Abascal","year":"2021","journal-title":"Nature"},{"issue":"6485","key":"2026060411215327700_bib120","doi-asserted-by":"crossref","first-page":"1449","DOI":"10.1126\/science.aay9333","article-title":"The evolutionary dynamics and fitness landscape of clonal hematopoiesis","volume":"367","author":"Watson","year":"2020","journal-title":"Science"},{"issue":"6","key":"2026060411215327700_bib121","doi-asserted-by":"crossref","first-page":"1147","DOI":"10.1038\/s41588-024-01755-1","article-title":"Analysis of somatic mutations in whole blood from 200,618 individuals identifies pervasive positive selection and novel drivers of clonal hematopoiesis","volume":"56","author":"Bernstein","year":"2024","journal-title":"Nat Genet"},{"issue":"7913","key":"2026060411215327700_bib122","doi-asserted-by":"crossref","first-page":"335","DOI":"10.1038\/s41586-022-04785-z","article-title":"The longitudinal dynamics and natural history of clonal haematopoiesis","volume":"606","author":"Fabre","year":"2022","journal-title":"Nature"},{"issue":"4","key":"2026060411215327700_bib123","doi-asserted-by":"crossref","first-page":"269","DOI":"10.1182\/blood.2019001807","article-title":"Concordance for clonal hematopoiesis is limited in elderly twins","volume":"135","author":"Fabre","year":"2020","journal-title":"Blood"},{"issue":"8040","key":"2026060411215327700_bib124","doi-asserted-by":"crossref","first-page":"926","DOI":"10.1038\/s41586-024-08128-y","article-title":"Clonal dynamics after allogeneic haematopoietic cell transplantation","volume":"635","author":"Spencer Chapman","year":"2024","journal-title":"Nature"},{"issue":"12","key":"2026060411215327700_bib125","doi-asserted-by":"crossref","first-page":"3175","DOI":"10.1038\/s41591-023-02636-6","article-title":"Clonal selection of hematopoietic stem cells after gene therapy for sickle cell disease","volume":"29","author":"Spencer Chapman","year":"2023","journal-title":"Nat Med"},{"issue":"8063","key":"2026060411215327700_bib126","doi-asserted-by":"crossref","first-page":"681","DOI":"10.1038\/s41586-025-08625-8","article-title":"Clonal dynamics and somatic evolution of haematopoiesis in mouse","volume":"641","author":"Kapadia","year":"2025","journal-title":"Nature"},{"issue":"11","key":"2026060411215327700_bib127","doi-asserted-by":"crossref","first-page":"1921","DOI":"10.1038\/s41591-021-01521-4","article-title":"Distinction of lymphoid and myeloid clonal hematopoiesis","volume":"27","author":"Niroula","year":"2021","journal-title":"Nat Med"},{"issue":"2","key":"2026060411215327700_bib128","doi-asserted-by":"crossref","first-page":"100744","DOI":"10.1016\/j.xgen.2024.100744","article-title":"Single-cell DNA sequencing reveals pervasive positive selection throughout preleukemic evolution","volume":"5","author":"Poon","year":"2025","journal-title":"Cell Genom"},{"issue":"1","key":"2026060411215327700_bib129","doi-asserted-by":"crossref","first-page":"e20220679","DOI":"10.1084\/jem.20220679","article-title":"Clonal lineage tracing reveals mechanisms skewing CD8+ T cell fate decisions in chronic infection","volume":"220","author":"Kasmani","year":"2023","journal-title":"J Exp Med"},{"issue":"4","key":"2026060411215327700_bib130","doi-asserted-by":"crossref","first-page":"776","DOI":"10.1016\/j.ccell.2023.03.009","article-title":"Lineage tracing reveals clonal progenitors and long-term persistence of tumor-specific T cells during immune checkpoint blockade","volume":"41","author":"Pai","year":"2023","journal-title":"Cancer Cell"},{"issue":"6675","key":"2026060411215327700_bib131","doi-asserted-by":"crossref","first-page":"eadf8486","DOI":"10.1126\/science.adf8486","article-title":"Spatial transcriptomics of B cell and T cell receptors reveals lymphocyte clonal dynamics","volume":"382","author":"Engblom","year":"2023","journal-title":"Science"},{"issue":"5","key":"2026060411215327700_bib132","doi-asserted-by":"crossref","first-page":"706","DOI":"10.1016\/j.stem.2023.04.001","article-title":"Clonally resolved single-cell multi-omics identifies routes of cellular differentiation in acute myeloid leukemia","volume":"30","author":"Beneyto-Calabuig","year":"2023","journal-title":"Cell Stem Cell"},{"issue":"12","key":"2026060411215327700_bib133","doi-asserted-by":"crossref","first-page":"2790","DOI":"10.1038\/s41588-024-01999-x","article-title":"Single-cell multiomics analysis reveals dynamic clonal evolution and targetable phenotypes in acute myeloid leukemia with complex karyotype","volume":"56","author":"Lepp\u00e4","year":"2024","journal-title":"Nat Genet"},{"issue":"1","key":"2026060411215327700_bib134","doi-asserted-by":"crossref","first-page":"1366","DOI":"10.1038\/s41467-021-21650-1","article-title":"Identification of leukemic and pre-leukemic stem cells by clonal tracking from single-cell transcriptomics","volume":"12","author":"Velten","year":"2021","journal-title":"Nat Commun"},{"key":"2026060411215327700_bib135","doi-asserted-by":"publisher","DOI":"10.1101\/2025.03.19.644196","article-title":"Measuring longitudinal genome-wide clonal evolution of pediatric acute lymphoblastic leukemia at single-cell resolution","author":"Pang","year":"19  2025","journal-title":"bioRxiv"},{"issue":"6","key":"2026060411215327700_bib136","doi-asserted-by":"crossref","first-page":"832","DOI":"10.1038\/s41587-022-01551-4","article-title":"Functional analysis of structural variants in single cells using Strand-seq","volume":"41","author":"Jeong","year":"2023","journal-title":"Nat Biotechnol"},{"issue":"3","key":"2026060411215327700_bib137","doi-asserted-by":"crossref","first-page":"343","DOI":"10.1038\/s41587-019-0366-x","article-title":"Single-cell analysis of structural variations and complex rearrangements with tri-channel processing","volume":"38","author":"Sanders","year":"2020","journal-title":"Nat Biotechnol"},{"issue":"6","key":"2026060411215327700_bib138","doi-asserted-by":"crossref","first-page":"1134","DOI":"10.1038\/s41588-024-01754-2","article-title":"Cell-type-specific consequences of mosaic structural variants in hematopoietic stem and progenitor cells","volume":"56","author":"Grimes","year":"2024","journal-title":"Nat Genet"},{"issue":"5","key":"2026060411215327700_bib139","doi-asserted-by":"crossref","first-page":"200061","DOI":"10.1098\/rsob.200061","article-title":"The rise and rise of mitochondrial DNA mutations","volume":"10","author":"Lawless","year":"2020","journal-title":"Open Biol"},{"issue":"5","key":"2026060411215327700_bib140","doi-asserted-by":"crossref","first-page":"1416","DOI":"10.1038\/s41596-022-00795-3","article-title":"Mitochondrial single-cell ATAC-seq for high-throughput multi-omic detection of mitochondrial genotypes and chromatin accessibility","volume":"18","author":"Lareau","year":"2023","journal-title":"Nat Protoc"},{"issue":"7","key":"2026060411215327700_bib141","doi-asserted-by":"crossref","first-page":"1355","DOI":"10.1038\/s41588-024-01794-8","article-title":"Mitochondrial genetics through the lens of single-cell multi-omics","volume":"56","author":"Nitsch","year":"2024","journal-title":"Nat Genet"},{"issue":"7","key":"2026060411215327700_bib142","doi-asserted-by":"crossref","first-page":"1198","DOI":"10.1038\/s41588-023-01433-8","article-title":"Single-cell multi-omics of mitochondrial DNA disorders reveals dynamics of purifying selection across human immune cells","volume":"55","author":"Lareau","year":"2023","journal-title":"Nat Genet"},{"key":"2026060411215327700_bib143","doi-asserted-by":"publisher","DOI":"10.21203\/rs.3.rs-3083262\/v1","article-title":"Mitochondrial mutation, drift and selection during human development and ageing","author":"Campbell","year":"26  2023","journal-title":"Res Sq"},{"issue":"8003","key":"2026060411215327700_bib144","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":"2026060411215327700_bib145","doi-asserted-by":"publisher","DOI":"10.1101\/2024.08.23.609473","article-title":"Robustness and reliability of single-cell regulatory multi-omics with deep mitochondrial mutation profiling","author":"Weng","year":"24  2024","journal-title":"bioRxiv"},{"key":"2026060411215327700_bib146","doi-asserted-by":"publisher","DOI":"10.1101\/2024.07.28.605517","article-title":"Artifacts in single-cell mitochondrial DNA mutation analyses misinform phylogenetic inference","author":"Lareau","year":"29  2024","journal-title":"bioRxiv"},{"issue":"7","key":"2026060411215327700_bib147","doi-asserted-by":"crossref","first-page":"1030","DOI":"10.1038\/s41587-022-01210-8","article-title":"Mitochondrial variant enrichment from high-throughput single-cell RNA sequencing resolves clonal populations","volume":"40","author":"Miller","year":"2022","journal-title":"Nat Biotechnol"},{"issue":"10","key":"2026060411215327700_bib148","doi-asserted-by":"crossref","first-page":"1246","DOI":"10.1038\/s41587-021-00927-2","article-title":"Scalable, multimodal profiling of chromatin accessibility, gene expression and protein levels in single cells","volume":"39","author":"Mimitou","year":"2021","journal-title":"Nat Biotechnol"},{"issue":"6","key":"2026060411215327700_bib149","doi-asserted-by":"crossref","first-page":"1325","DOI":"10.1016\/j.cell.2019.01.022","article-title":"Lineage tracing in humans enabled by mitochondrial mutations and single-cell genomics","volume":"176","author":"Ludwig","year":"2019","journal-title":"Cell"},{"issue":"4","key":"2026060411215327700_bib150","doi-asserted-by":"crossref","first-page":"451","DOI":"10.1038\/s41587-020-0645-6","article-title":"Massively parallel single-cell mitochondrial DNA genotyping and chromatin profiling","volume":"39","author":"Lareau","year":"2021","journal-title":"Nat Biotechnol"},{"issue":"4","key":"2026060411215327700_bib151","doi-asserted-by":"crossref","first-page":"1241","DOI":"10.1053\/j.gastro.2010.12.036","article-title":"Use of methylation patterns to determine expansion of stem cell clones in human colon tissue","volume":"140","author":"Graham","year":"2011","journal-title":"Gastroenterology"},{"key":"2026060411215327700_bib152","doi-asserted-by":"crossref","first-page":"8","DOI":"10.1186\/1471-230X-4-8","article-title":"Tracing ancestry with methylation patterns: most crypts appear distantly related in normal adult human colon","volume":"4","author":"Kim","year":"2004","journal-title":"BMC Gastroenterol"},{"issue":"12","key":"2026060411215327700_bib153","doi-asserted-by":"crossref","first-page":"4828","DOI":"10.1073\/pnas.0810276106","article-title":"Inferring clonal expansion and cancer stem cell dynamics from DNA methylation patterns in colorectal cancers","volume":"106","author":"Siegmund","year":"2009","journal-title":"Proc Natl Acad Sci U S A"},{"issue":"19","key":"2026060411215327700_bib154","doi-asserted-by":"crossref","first-page":"10839","DOI":"10.1073\/pnas.191225998","article-title":"Investigating stem cells in human colon by using methylation patterns","volume":"98","author":"Yatabe","year":"2001","journal-title":"Proc Natl Acad Sci U S A"},{"key":"2026060411215327700_bib155","doi-asserted-by":"crossref","first-page":"2","DOI":"10.1186\/1741-7007-4-2","article-title":"Human hair genealogies and stem cell latency","volume":"4","author":"Kim","year":"2006","journal-title":"BMC Biol"},{"issue":"10","key":"2026060411215327700_bib156","doi-asserted-by":"crossref","first-page":"1469","DOI":"10.1038\/s41588-021-00927-7","article-title":"Epigenetic encoding, heritability and plasticity of glioma transcriptional cell states","volume":"53","author":"Chaligne","year":"2021","journal-title":"Nat Genet"},{"issue":"7757","key":"2026060411215327700_bib157","doi-asserted-by":"crossref","first-page":"576","DOI":"10.1038\/s41586-019-1198-z","article-title":"Epigenetic evolution and lineage histories of chronic lymphocytic leukaemia","volume":"569","author":"Gaiti","year":"2019","journal-title":"Nature"},{"issue":"8071","key":"2026060411215327700_bib158","doi-asserted-by":"crossref","first-page":"478","DOI":"10.1038\/s41586-025-09041-8","article-title":"Clonal tracing with somatic epimutations reveals dynamics of blood ageing","volume":"643","author":"Scherer","year":"2025","journal-title":"Nature"},{"issue":"3","key":"2026060411215327700_bib159","doi-asserted-by":"crossref","first-page":"488","DOI":"10.1038\/s41592-024-02567-1","article-title":"High-resolution, noninvasive single-cell lineage tracing in mice and humans based on DNA methylation epimutations","volume":"22","author":"Chen","year":"2025","journal-title":"Nat Methods"},{"issue":"1","key":"2026060411215327700_bib160","doi-asserted-by":"crossref","first-page":"229","DOI":"10.1186\/s13059-022-02796-7","article-title":"scTAM-seq enables targeted high-confidence analysis of DNA methylation in single cells","volume":"23","author":"Bianchi","year":"2022","journal-title":"Genome Biol"},{"key":"2026060411215327700_bib161","doi-asserted-by":"crossref","DOI":"10.1038\/s41592-025-02805-0","article-title":"Functional phenotyping of genomic variants using joint multiomic single-cell DNA-RNA sequencing","author":"Lindenhofer","year":"2025;22(10):2032-2041","journal-title":"Nat Methods"},{"issue":"2","key":"2026060411215327700_bib162","doi-asserted-by":"crossref","first-page":"149","DOI":"10.1016\/j.cels.2024.01.004","article-title":"Clonally heritable gene expression imparts a layer of diversity within cell types","volume":"15","author":"Mold","year":"2024","journal-title":"Cell Syst"},{"issue":"1","key":"2026060411215327700_bib163","doi-asserted-by":"crossref","first-page":"2744","DOI":"10.1038\/s41467-024-47158-y","article-title":"Gene-expression memory-based prediction of cell lineages from scRNA-seq datasets","volume":"15","author":"Eisele","year":"2024","journal-title":"Nat Commun"},{"issue":"D1","key":"2026060411215327700_bib164","doi-asserted-by":"crossref","first-page":"D1173","DOI":"10.1093\/nar\/gkae913","article-title":"scLTdb: a comprehensive single-cell lineage tracing database","volume":"53","author":"Jiang","year":"2025","journal-title":"Nucleic Acids Res"},{"key":"2026060411215327700_bib165","doi-asserted-by":"crossref","first-page":"104136","DOI":"10.1016\/j.exphem.2023.12.001","article-title":"Ex vivo hematopoietic stem cell expansion technologies: recent progress, applications, and open questions","volume":"130","author":"Meaker","year":"2024","journal-title":"Exp Hematol"},{"issue":"7950","key":"2026060411215327700_bib166","doi-asserted-by":"crossref","first-page":"127","DOI":"10.1038\/s41586-023-05739-9","article-title":"Chemically defined cytokine-free expansion of human haematopoietic stem cells","volume":"615","author":"Sakurai","year":"2023","journal-title":"Nature"},{"issue":"2","key":"2026060411215327700_bib167","doi-asserted-by":"crossref","first-page":"628","DOI":"10.1038\/s41596-019-0263-2","article-title":"Long-term ex vivo expansion of mouse hematopoietic stem cells","volume":"15","author":"Wilkinson","year":"2020","journal-title":"Nat Protoc"},{"issue":"7","key":"2026060411215327700_bib168","doi-asserted-by":"crossref","first-page":"1066","DOI":"10.1038\/s41587-022-01209-1","article-title":"CoSpar identifies early cell fate biases from single-cell transcriptomic and lineage information","volume":"40","author":"Wang","year":"2022","journal-title":"Nat Biotechnol"},{"key":"2026060411215327700_bib169","doi-asserted-by":"publisher","DOI":"10.1101\/2024.11.15.623687","article-title":"Unbiased profiling of multipotency landscapes reveals spatial modulators of clonal fate biases","author":"Erickson","year":"17  2024","journal-title":"bioRxiv"}],"container-title":["Blood"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/ashpublications.org\/blood\/article-pdf\/147\/23\/2728\/2524514\/blood_bld-2024-028195-c-main.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/ashpublications.org\/blood\/article-pdf\/147\/23\/2728\/2524514\/blood_bld-2024-028195-c-main.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2026,6,4]],"date-time":"2026-06-04T15:22:16Z","timestamp":1780586536000},"score":1,"resource":{"primary":{"URL":"https:\/\/ashpublications.org\/blood\/article\/147\/23\/2728\/547406\/Clonal-tracing-of-blood-stem-cells-across-mouse"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2026,6,4]]},"references-count":169,"journal-issue":{"issue":"23","published-print":{"date-parts":[[2026,6,4]]}},"URL":"https:\/\/doi.org\/10.1182\/blood.2024028195","relation":{},"ISSN":["0006-4971","1528-0020"],"issn-type":[{"value":"0006-4971","type":"print"},{"value":"1528-0020","type":"electronic"}],"subject":[],"published-other":{"date-parts":[[2026,6,4]]},"published":{"date-parts":[[2026,6,4]]}}}