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Comprehensive network modeling from single cell RNA sequencing of human and mouse reveals well conserved transcription regulation of hematopoiesis

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WDR82-binding long noncoding RNA lncEry controls mouse erythroid differentiation and maturation

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A Single-Cell Immune Atlas of Triple Negative Breast Cancer Reveals Novel Immune Cell SubsetsPreprint

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SIS-seq, a molecular ‘time machine’, connects single cell fate with gene programs

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Developmental gene expression patterns driving species-specific cortical features

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AttentionGRN: a functional and directed graph transformer for gene regulatory network reconstruction from scRNA-seq data

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Optimal transport reveals dynamic gene regulatory networks via gene velocity estimation

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A single-cell framework identifies functionally and molecularly distinct multipotent progenitors in adult human hematopoiesis

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PRODUCTION OF A PRELIMINARY QUALITY CONTROL PIPELINE FOR SINGLE NUCLEI RNA-SEQ AND ITS APPLICATION IN THE ANALYSIS OF CELL TYPE DIVERSITY OF POST-MORTEM HUMAN BRAIN NEOCORTEX

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Temporary serine protease inhibition and the role of SPINK2 in human bone marrow

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DeepIMAGER: Deeply Analyzing Gene Regulatory Networks from scRNA-seq Data

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In-vivo differentiation of adult hematopoietic stem cells from a single-cell point of view

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Advanced technologies for single-cell in situ protein profiling

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Predicting residual stress of aluminum nitride thin-film by incorporating manifold learning and tree-based ensemble classifier

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Assessing the reliability of spike-in normalization for analyses of single-cell RNA sequencing dataPreprint

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FASTGenomics: An analytical ecosystem for single-cell RNA sequencing dataPreprint

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Heme induces innate immune memory

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Cells and Molecules Underpinning Cannabis-Related Variations in Cortical Thickness during Adolescence

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Niche-derived Semaphorin 4A safeguards functional identity of myeloid-biased hematopoietic stem cells

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An erythroid-biased FOShi hematopoietic multipotent progenitor subpopulation contributes to adaptation to chronic hypoxia

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Sequential emergence and contraction of epithelial subtypes in the prenatal human choroid plexus revealed by a stem cell model

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Treg activation during allograft tolerance induction requires mitochondrion-induced TGF-β1 in type 1 conventional dendritic cells

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Single Cell Transcriptomics to Understand HSC Heterogeneity and Its Evolution upon Aging

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Molecular Dissection of Somatic Skeletal Disease in Neurofibromatosis Type 1

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Characterization of leukemia progression in the Cbfb-MYH11 knockin mice by single cell RNA sequencing

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RING1 missense variants reveal sensitivity of DNA damage repair to H2A monoubiquitination dosage during neurogenesis

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Defining the Emerging Blood System During Development at Single-Cell Resolution

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Induced cell-autonomous neutropenia systemically perturbs hematopoiesis in Cebpa enhancer-null mice

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Gene Selection and Classification of scRNA‐seq Data Combining Information Gain Ratio and Genetic Algorithm with Dynamic Crossover

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Illuminating stem cell transcription factor dynamics: long-term single-cell imaging of fluorescent protein fusions

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AP-2γ Is Required for Maintenance of Multipotent Mammary Stem Cells

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Hematopoiesis in aging: Current concepts and challenges

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Diffusive topology preserving manifold distances for single-cell data analysis

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p53-inducible lncRNA LOC644656 causes genotoxic stress-induced stem cell maldifferentiation and cancer chemoresistance

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Towards a New Understanding of Decision-Making by Hematopoietic Stem Cells

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Proteasome inhibitor bortezomib stabilizes and activates p53 in hematopoietic stem/progenitors and double-negative T cells in vivo

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Dynamic transcriptional atlas of male germ cells during porcine puberty

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High-throughput single-cell fate potential assay of murine hematopoietic progenitors in vitro

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GPseudoClust: deconvolution of shared pseudo-profiles at single-cell resolution

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Hematopoietic Stem Cells in Health and Disease—Insights from Single-Cell Multi-omic Approaches

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Introduction and Classification of Leukemias

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Novel Molecular Hallmarks of Group 3 Medulloblastoma by Single-Cell Transcriptomics

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Single-cell analysis at the protein level delineates intracellular signaling dynamic during hematopoiesis

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An integrative view of the regulatory and transcriptional landscapes in mouse hematopoiesisPreprint

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Single cell transcriptomics and developmental trajectories of murine cranial neural crest cell fate determination and cell cycle progressionPreprint

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A germline point mutation in the MYC-FBW7 phosphodegron initiates hematopoietic malignanciesPreprint

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Approaches for Benchmarking Single-Cell Gene Regulatory Network Methods

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Axial nephron fate switching demonstrates a plastic system tunable on demand

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Human Hearts Intrinsically Increase Cardiomyocyte Mitosis After Myocardial Infarction

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Chronic jetlag accelerates pancreatic neoplasia in conditional Kras -mutant mice

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Zebrafish functional xenograft vasculature platform identifies PF-502 as a durable vasculature normalization drug

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Modification of Seurat v4 for the Development of a Phase Assignment Tool Able to Distinguish between G2 and Mitotic Cells

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scBoolSeq: Linking scRNA-seq statistics and Boolean dynamics

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Baf155 controls hematopoietic differentiation and regeneration through chromatin priming

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Single-Cell RNA Sequencing and Combinatorial Approaches for Understanding Heart Biology and Disease

Wang, L., & Jin, B. (2024) · Biology · doi:10.3390/biology13100783 · Cited by 7

Manipulating cell fate while confronting reproducibility concerns

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Comprehensive analysis of single-cell RNA sequencing data from healthy human marrow hematopoietic cells

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MAT2: manifold alignment of single-cell transcriptomes with cell triplets

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ACUTE AND SUSTAINED ALTERATIONS TO THE BONE MARROW IMMUNE MICROENVIRONMENT FOLLOWING POLYMICROBIAL INFECTION

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Stemness‐related genes revealed by single‐cell profiling of naïve and stimulated human CD34 + cells from CB and mPB

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Trajectory Algorithms to Infer Stem Cell Fate Decisions

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Protein arginine methyltransferase 1 in the generation of immune megakaryocytes: A perspective review

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Overlapping Definitive Progenitor Waves Divide and Conquer to Build a Layered Hematopoietic SystemPreprint

Freyer, L., Iturri, L., Biton, A., & Perdiguero, E. G. (2020) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2020.12.24.424302 · Cited by 7

Small molecule BLVRB redox inhibitor promotes megakaryocytopoiesis and stress thrombopoiesis in vivo

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DMGAT: predicting ncRNA-drug resistance associations based on diffusion map and heterogeneous graph attention network

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FedscGen: privacy-preserving federated batch effect correction of single-cell RNA sequencing data

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GRDGNN: A directed graph neural network framework for multi-relational inference of gene regulatory networks

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Olfactomedin-4 + neutrophils exacerbate intestinal epithelial damage in Clostridioides difficile infection

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Species-specific chromatin architecture and neurogenesis mediated by a human enhancer

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Dissecting the cellular architecture of breast cancer brain metastases reveals prognostically distinct immune landscapes

Jassowicz, L., Feng, F., Warta, R., Heinicke, F., Wöllner, A., Briesch, H., Sor, F., Soller, J., Lotsch, C., Wong, J. K. L., et al. (2026) · Cancer Cell · doi:10.1016/j.ccell.2026.03.016 · Cited by 6

Fbxw11 impairs the repopulation capacity of hematopoietic stem/progenitor cells

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Single‐cell transcriptome analysis of the germ cells and somatic cells during mitotic quiescence stage in goats

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Single-cell transcriptomic analysis of immune cell dynamics in the healthy human endometrium

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SPOCK2 controls the proliferation and function of immature pancreatic β-cells through MMP2

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Modeling GATA2 deficiency in mice: the R396Q mutation disrupts normal hematopoiesis

Hall, T., Mehmood, R., da Bandeira, D. S., Cotton, A., Klein, J. D., Pruett‐Miller, S. M., Izraeli, S., Clements, W. K., & Crispino, J. D. (2025) · Leukemia · doi:10.1038/s41375-024-02508-z · Cited by 6

KEGNI: knowledge graph enhanced framework for gene regulatory network inference

Li, P., Li, L., Nan, J., Chen, J., Sun, J., & Cao, Y. (2025) · Genome biology · doi:10.1186/s13059-025-03780-7 · Cited by 7

A kinetics-based model of haematopoiesis reveals extrinsic regulation of skewed lineage output from stem cells

Rodriguez-Correa, E., Grünschläger, F., Nizharadze, T., Anstee, N., Al-Sabah, J., Kumpošt, V., Sedlmeier, A., Li, C., Ball, M., Fotopoulou, F., et al. (2026) · Nature Cell Biology · doi:10.1038/s41556-026-01958-0 · Cited by 6

Current Trends on Hemopoietic Stem Cells

Okeke, C., Silas, U., Okeke, C., & Chikwendu, C. (2020) · Current Stem Cell Research & Therapy · doi:10.2174/1574888x15999200729162021 · Cited by 6

Deconvolution of the hematopoietic stem cell microenvironment reveals a high degree of specialization and conservation

Ye, J., Calvo, I. A., Cenzano, I., Vilas‐Zornoza, A., Martinez‐de‐Morentin, X., Lasaga, M., Alignani, D., Paiva, B., Viñado, A. C., Martín‐Úriz, P. S., et al. (2022) · iScience · doi:10.1016/j.isci.2022.104225 · Cited by 6

The Social Norm of Hematopoietic Stem Cells and Dysregulation in Leukemia

Brown, G. (2022) · International Journal of Molecular Sciences · doi:10.3390/ijms23095063 · Cited by 6

SCIBER: a simple method for removing batch effects from single-cell RNA-sequencing data

Gan, D., & Li, J. (2022) · Bioinformatics · doi:10.1093/bioinformatics/btac819 · Cited by 6

The contributions of DNA accessibility and transcription factor occupancy to enhancer activity during cellular differentiation

Long, T., Bhattacharyya, T., Repele, A., Naylor, M., Nooti, S. K., Krueger, S., & Manu (2023) · G3 Genes Genomes Genetics · doi:10.1093/g3journal/jkad269 · Cited by 8

Single-cell sequencing analysis within biologically relevant dimensions

Kousnetsov, R., Bourque, J., Surnov, A., Fallahee, I., & Hawiger, D. (2024) · Cell Systems · doi:10.1016/j.cels.2023.12.005 · Cited by 6

Phosphatidylinositol-3 kinase signaling controls survival and stemness of hematopoietic stem and progenitor cells

Blokzijl-Franke, S., Ponsioen, B., Schulte‐Merker, S., Herbomel, P., Kissa, K., Choorapoikayil, S., & den Hertog, J. (2021) · Oncogene · doi:10.1038/s41388-021-01733-5 · Cited by 7

Recent Developments and Applications of Single-Cell RNA Sequencing Technology in Cell Classification

Khan, S. U., & Khan, M. U. (2021) · Journal of Biomedical Research & Environmental Sciences · doi:10.37871/jbres1383 · Cited by 6

Oncogenesis induced by combined Phf6 and Idh2 mutations through increased oncometabolites and impaired DNA repair

Chen, T., Yao, C., Chen, Y., Yuan, C., Lin, C., Hsu, Y.-C., Chuang, P., Kao, C., Li, Y.-H., Hou, H., et al. (2022) · Oncogene · doi:10.1038/s41388-022-02193-1 · Cited by 7

Estimating heterogeneous gene regulatory networks from zero-inflated single-cell expression data

Wu, Q., & Luo, X. (2022) · The Annals of Applied Statistics · doi:10.1214/21-aoas1582 · Cited by 6

Identification of three distinct cell populations for urate excretion in human kidneys

Sakaguchi, Y. M., Wiriyasermkul, P., Matsubayashi, M., Miyasaka, M., Sakaguchi, N., Sahara, Y., Takasato, M., Kinugawa, K., Sugie, K., Eriguchi, M., et al. (2024) · The Journal of Physiological Sciences · doi:10.1186/s12576-023-00894-0 · Cited by 6

Immunophenotypic Identification of Early Myeloerythroid Development

Pronk, C. J., & Bryder, D. (2017) · Methods in molecular biology · doi:10.1007/978-1-4939-7346-0_13 · Cited by 6

Aging in a Relativistic Biological Space-Time

Maestrini, D., Abler, D., Adhikarla, V., Armenian, S. H., Branciamore, S., Carlesso, N., Kuo, Y., Marcucci, G., Sahoo, P., & Rockne, R. C. (2018) · Frontiers in Cell and Developmental Biology · doi:10.3389/fcell.2018.00055 · Cited by 7

Time-Resolved scRNA-Seq Tracks the Adaptation of a Sensitive MCL Cell Line to Ibrutinib Treatment

Fuhr, V., Vafadarnejad, E., Dietrich, O., Arampatzi, P., Riedel, A., Saliba, A., Rosenwald, A., & Rauert‐Wunderlich, H. (2021) · International Journal of Molecular Sciences · doi:10.3390/ijms22052276 · Cited by 6

Molecular Characteristics and Differentiation Control Mechanisms of Bergmann Glia‐Like Progenitors in the Postnatal Mouse Cerebellum

Suyama, K., Adachi, T., Mizuno, M., Ji, K., Isogai, E., Hasegawa, I., Nishitani, K., Sone, M., Miyashita, S., Owa, T., et al. (2026) · Glia · doi:10.1002/glia.70160 · Cited by 5

SFINN: inferring gene regulatory network from single-cell and spatial transcriptomic data with shared factor neighborhood and integrated neural network

Wang, Y., Zhou, F., & Guan, J. (2024) · Bioinformatics · doi:10.1093/bioinformatics/btae433 · Cited by 5

Deconvolution from bulk gene expression by leveraging sample-wise and gene-wise similarities and single-cell RNA-seq data

Wang, C., Lin, Y., Li, S., & Guan, J. (2024) · BMC Genomics · doi:10.1186/s12864-024-10728-x · Cited by 5

Divergent PTEN–p53 interaction upon DNA damage in a human thyroid organoid model with germline PTEN mutations

Venegas, J. A., Onur, O. E., Kang, S. C., Hitomi, M., & Eng, C. (2025) · Endocrine Related Cancer · doi:10.1530/erc-24-0216 · Cited by 5

Data-driven inference of Boolean networks from transcriptomes to predict cellular differentiation and reprogramming

Chevalier, S., Becker, J., Gui, Y., Noël, V., Su, C., Jung, S., Calzone, L., Zinovyev, A. Y., del Sol, A., Pang, J., et al. (2025) · npj Systems Biology and Applications · doi:10.1038/s41540-025-00569-z · Cited by 8

Premature senescence impairs hematopoietic stem cell function during sickle cell disease in mice and humans

Barve, A., Dabas, P., Cornwell, A., Sriram, P., Kopyov, O. V., Zhai, M., Kooienga, E., Kelley, Z., Johnson, J., Myers, J., et al. (2026) · Science Translational Medicine · doi:10.1126/scitranslmed.adv0628 · Cited by 6

Lineage Decision-Making within Normal Haematopoietic and Leukemic Stem Cells

Brown, G., Sánchez, L., & Sánchez-Garcı́a, I. (2020) · International Journal of Molecular Sciences · doi:10.3390/ijms21062247 · Cited by 5

Advancing haematopoietic stem and progenitor cell biology through single‐cell profiling

Hamey, F., Nestorowa, S., Wilson, N. K., & Göttgens, B. (2016) · FEBS Letters · doi:10.1002/1873-3468.12231 · Cited by 5

Additional file 2 of Comprehensive analysis of single-cell RNA sequencing data from healthy human marrow hematopoietic cells

Zhao, X., Gao, S., Kajigaya, S., Liu, Q., Wu, Z., Feng, X., Zhang, F., & Young, N. S. (2020) · Figshare · doi:10.6084/m9.figshare.13212449

Early Molecular Steps in Human Bone Marrow Stem Cell Differentiation Trajectories

Komic, H., Yu, W., Simoes, C. P., Schmachtel, T., Nilsson, M. S., Prósper, F., Paiva, B., Thorén, F. B., & Rieger, M. A. (2023) · Blood · doi:10.1182/blood-2023-185490 · Cited by 1

Mapping the transcriptional landscape of haematopoietic stem and progenitor cells

Shaw, S. (2019) · Apollo (University of Cambridge) · doi:10.17863/cam.42813

Charting the single-cell transcriptional landscape of haematopoiesis

Hamey, F. (2018) · Apollo (University of Cambridge) · doi:10.17863/cam.35245