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A Rainbow Reporter Tracks Single Cells and Reveals Heterogeneous Cellular Dynamics among Pluripotent Stem Cells and Their Differentiated Derivatives

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Single-cell transcriptome analyses reveal critical roles of RNA splicing during leukemia progression

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FLOW-MAP: a graph-based, force-directed layout algorithm for trajectory mapping in single-cell time course datasets

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Neural stem cell relay from B1 to B2 cells in the adult mouse ventricular-subventricular zone

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Negative Regulation of the Differentiation of Flk2− CD34− LSK Hematopoietic Stem Cells by EKLF/KLF1

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Sox2 modulation increases naïve pluripotency plasticity

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Comparative Transcriptomic Analysis of the Hematopoietic System between Human and Mouse by Single Cell RNA Sequencing

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Hand of FATe: lipid metabolism in hematopoietic stem cells

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GRNUlar: A Deep Learning Framework for Recovering Single-Cell Gene Regulatory Networks

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CellexalVR: A virtual reality platform to visualise and analyse single-cell dataPreprint

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Inhibition of longevity regulator PAPP‐A modulates tissue homeostasis via restraint of mesenchymal stromal cells

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Peripheral Ischemia Imprints Epigenetic Changes in Hematopoietic Stem Cells to Propagate Inflammation and Atherosclerosis

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Single-cell transcriptomic atlas of goat ovarian aging

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Selective induction of human renal interstitial progenitor-like cell lineages from iPSCs reveals development of mesangial and EPO-producing cells

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CD301b+ monocyte-derived dendritic cells mediate resistance to radiotherapy

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Single-cell molecular connectomics of intracortically-projecting neuronsPreprint

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Function of hematopoiesis and bone marrow niche in inflammation and non-hematopoietic diseases

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netAE: semi-supervised dimensionality reduction of single-cell RNA sequencing to facilitate cell labeling

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Time-course single-cell RNA sequencing reveals transcriptional dynamics and heterogeneity of limbal stem cells derived from human pluripotent stem cells

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PCGF1-PRC1 links chromatin repression with DNA replication during hematopoietic cell lineage commitment

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Regulation of lymphoid-myeloid lineage bias through regnase-1/3-mediated control of Nfkbiz

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GraphDDP: a graph-embedding approach to detect differentiation pathways in single-cell-data using prior class knowledge

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Modelling acute myeloid leukaemia in a continuum of differentiation states

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Single-cell fate decisions of bipotential hematopoietic progenitors

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Wnt-5A/B Signaling in Hematopoiesis throughout Life

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Divergent erythroid megakaryocyte fates in Blvrb-deficient mice establish non-overlapping cytoprotective functions during stress hematopoiesis

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JMJD6 promotes self-renewal and regenerative capacity of hematopoietic stem cells

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Recent advances in T-cell lymphoid neoplasms

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CIDER: an interpretable meta-clustering framework for single-cell RNA-seq data integration and evaluation

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CSF1R as a Therapeutic Target in Bone Diseases: Obvious but Not so Simple

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Identification of chondrocyte subpopulations in osteoarthritis using single-cell sequencing analysis

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Metabolic Functions of Biliverdin IXβ Reductase in Redox-Regulated Hematopoietic Cell Fate

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Integration of single‐cell transcriptome and proteome technologies: Toward spatial resolution levels

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Deep Learning in Gene Regulatory Network Inference: A Survey

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Modeling continuous levels of resistance to multidrug therapy in cancer

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CITED2 coordinates key hematopoietic regulatory pathways to maintain the HSC pool in both steady-state hematopoiesis and transplantation

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Claudin18.2-positive gastric cancer-specific changes in neoadjuvant chemotherapy-driven immunosuppressive tumor microenvironment

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Downregulation of MALAT1 is a hallmark of tissue and peripheral proliferative T cells in COVID-19

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GCLink: a graph contrastive link prediction framework for gene regulatory network inference

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Normalizing single-cell RNA sequencing data with internal spike-in-like genes

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Improving Single-Cell RNA-seq Clustering by Integrating Pathways

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Distinguishing three subtypes of hematopoietic cells based on gene expression profiles using a support vector machine

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New genetic tools for the in vivo study of hematopoietic stem cell function

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Gata2-L359V impairs primitive and definitive hematopoiesis and blocks cell differentiation in murine chronic myelogenous leukemia model

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SETD5 modulates homeostasis of hematopoietic stem cells by mediating RNA Polymerase II pausing in cooperation with HCF-1

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One Cell At a Time (OCAT): a unified framework to integrate and analyze single-cell RNA-seq data

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Resolving the hematopoietic stem cell state by linking functional and molecular assays

Jassinskaja, M., Gońka, M., & Kent, D. G. (2023) · Blood · doi:10.1182/blood.2022017864 · Cited by 15

Differential expression of endothelial protein C receptor (EPCR) in hematopoietic stem and multipotent progenitor cells in young and old mice

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Selenoprotein-mediated redox regulation shapes the cell fate of HSCs and mature lineages

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High fat diet feeding impairs neutrophil phagocytosis, bacterial killing, and neutrophil-induced hematopoietic regeneration

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Inferring gene regulatory networks by hypergraph generative model

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Frontline Science: Cxxc5 expression alters cell cycle and myeloid differentiation of mouse hematopoietic stem and progenitor cells

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The OCIAD protein family: comparative developmental biology and stem cell application

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An analytical framework for interpretable and generalizable single-cell data analysis

Zhou, J., & Troyanskaya, O. G. (2021) · Nature Methods · doi:10.1038/s41592-021-01286-1 · Cited by 14

The role of specialized cell cycles during erythroid lineage development: insights from single-cell RNA sequencing

Socolovsky, M. (2022) · International Journal of Hematology · doi:10.1007/s12185-022-03406-9 · Cited by 14

In vivo generation of bone marrow from embryonic stem cells in interspecies chimeras

Wen, B., Wang, G., Li, E., Kolesnichenko, O. A., Tu, Z., Divanovic, S., Kalin, T. V., & Kalinichenko, V. V. (2022) · eLife · doi:10.7554/elife.74018 · Cited by 14

Hematopoietic and Chronic Myeloid Leukemia Stem Cells: Multi-Stability versus Lineage Restriction

Brown, G. (2022) · International Journal of Molecular Sciences · doi:10.3390/ijms232113570 · Cited by 14

Retina-derived signals control pace of neurogenesis in visual brain areas but not circuit assembly

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DANCE: a deep learning library and benchmark platform for single-cell analysis

Ding, J., Liu, R., Wen, H., Tang, W., Li, Z., Venegas, J., Su, R., Molho, D., Jin, W., Wang, Y., et al. (2024) · Genome biology · doi:10.1186/s13059-024-03211-z · Cited by 18

The changing face of hematopoiesis: a spectrum of options is available to stem cells

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scOrange—a tool for hands-on training of concepts from single-cell data analytics

Stražar, M., Žagar, L., Kokošar, J., Tanko, V., Erjavec, A., Poličar, P. G., Starič, A., Demšar, J., Shaulsky, G., Menon, V., et al. (2019) · Bioinformatics · doi:10.1093/bioinformatics/btz348 · Cited by 14

Extrahepatic deficiency of transferrin receptor 2 is associated with increased erythropoiesis independent of iron overload

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“Hierarchy” and “Holacracy”; A Paradigm of the Hematopoietic System

Yokota, T. (2019) · Cells · doi:10.3390/cells8101138 · Cited by 14

Dimension reduction and denoising of single-cell RNA sequencing data in the presence of observed confounding variablesPreprint

Huang, M. C., Zhang, Z., & Zhang, N. R. (2020) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2020.08.03.234765 · Cited by 14

The impacts of active and self-supervised learning on efficient annotation of single-cell expression data

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Quo Vadis? Immunodynamics of Myeloid Cells after Myocardial Infarction

Moggio, A., Schunkert, H., Kessler, T., & Sager, H. B. (2022) · International Journal of Molecular Sciences · doi:10.3390/ijms232415814 · Cited by 15

Asymmetric cell division of hematopoietic stem cells: recent advances, emerging concepts, and future perspectives

Nunes, J. J., & Loeffler, D. (2024) · Frontiers in Hematology · doi:10.3389/frhem.2024.1373554 · Cited by 14

Maintenance of hematopoietic stem cells by tyrosine-unphosphorylated STAT5 and JAK inhibition

Williams, M., Wang, X., Bastos, H. P., Grondys-Kotarba, G., Johnson, C., Mende, N., Calderbank, E. F., Wantoch, M., Park, H. J., Wu, Q., et al. (2024) · Blood Advances · doi:10.1182/bloodadvances.2024014046 · Cited by 17

Pirfenidone antagonizes TGF-β1-mediated gabapentin resistance via reversal of desmoplasia and the ‘cold’ microenvironment in pancreatic cancer

Zhang, J., Zhang, J., Lin, R., Hou, P. K., Zheng, L., Jiang, C., Zhang, D., Huang, H., & Teng, T. (2024) · Cancer Letters · doi:10.1016/j.canlet.2024.217287 · Cited by 13

Neuroblastoma plasticity during metastatic progression stems from the dynamics of an early sympathetic transcriptomic trajectory

Villalard, B., Boltjes, A., Reynaud, F., Imbaud, O., Thoinet, K., Timmerman, I., Croze, S., Théoulle, E., Atzeni, G., Lachuer, J., et al. (2024) · Nature Communications · doi:10.1038/s41467-024-53776-3 · Cited by 13

Suppression of the Prostaglandin I2–Type 1 Interferon Axis Induces Extramedullary Hematopoiesis to Promote Cardiac Repair After Myocardial Infarction

Lv, H., Wang, C., Liu, Z., Quan, M., Li, K., Gou, F., Shi, X., Liu, Q., Yu, Y., Zhu, P., et al. (2025) · Circulation · doi:10.1161/circulationaha.124.069420 · Cited by 14

Single‐Cell Sequencing in Normal and Malignant Hematopoiesis

Wilson, N. K., & Göttgens, B. (2018) · HemaSphere · doi:10.1097/hs9.0000000000000034 · Cited by 13

Bloody Zebrafish: Novel Methods in Normal and Malignant Hematopoiesis

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The role of nicotinic receptors in SARS-CoV-2 receptor ACE2 expression in intestinal epithelia

ten Hove, A. S., Brinkman, D. J., Yim, A. Y. F. L., Verseijden, C., Hakvoort, T. B. M., Admiraal, I., Welting, O., van Hamersveld, P. H. P., Sinniger, V., Bonaz, B. L., et al. (2020) · Bioelectronic Medicine · doi:10.1186/s42234-020-00057-1 · Cited by 13

DrivAER: Identification of driving transcriptional programs in single-cell RNA sequencing data

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Integration of single cell data by disentangled representation learning

Guo, T., Chen, Y., Shi, M., Li, X., & Zhang, M. Q. (2021) · Nucleic Acids Research · doi:10.1093/nar/gkab978 · Cited by 13

S100A6 as a Constituent and Potential Marker of Adult and Cancer Stem Cells

Leśniak, W., & Filipek, A. (2022) · Stem Cell Reviews and Reports · doi:10.1007/s12015-022-10403-2 · Cited by 13

Gene Regulatory Network Inference Using Convolutional Neural Networks from scRNA-seq Data

Mao, G., Pang, Z., Zuo, K., & Liu, J. (2023) · Journal of Computational Biology · doi:10.1089/cmb.2022.0355 · Cited by 13

Integrative analysis of single-cell RNA-seq and ATAC-seq reveals heterogeneity of induced pluripotent stem cell-derived hepatic organoids

Kim, J.-H., Mun, S. J., Kim, J., Son, M. J., & Kim, S. (2023) · iScience · doi:10.1016/j.isci.2023.107675 · Cited by 13

Gastrulation-stage gene expression in Nipbl +/− mouse embryos foreshadows the development of syndromic birth defects

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