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SLAM Family Receptors Distinguish Hematopoietic Stem and Progenitor Cells and Reveal Endothelial Niches for Stem Cells

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Massively parallel single-cell RNA-seq for marker-free decomposition of tissues into cell types

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BdLT-Seq as a barcode decay-based method to unravel lineage-linked transcriptome plasticity

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Depicting pseudotime-lagged causality across single-cell trajectories for accurate gene-regulatory inference

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NG-SEM: an effective non-Gaussian structural equation modeling framework for gene regulatory network inference from single-cell RNA-seq data

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A Data-Distribution and Successive Spline Points based discretization approach for evolving gene regulatory networks from scRNA-Seq time-series data using Cartesian Genetic Programming

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CVGAE: A Self-Supervised Generative Method for Gene Regulatory Network Inference Using Single-Cell RNA Sequencing Data

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Clustering-independent estimation of cell abundances in bulk tissues using single-cell RNA-seq data

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Transcriptional dynamics of the murine heart during perinatal development at single-cell resolution

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Demystifying blood stem cell fates

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Lightening the way of hematopoiesis: Infrared laser-mediated lineage tracing with high spatial-temporal resolution

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Isolation of Murine Myeloid Progenitor Populations by CD34/CD150 Surface Markers

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In Silico Localization of Perilymph Proteins Enriched in Meńier̀e Disease Using Mammalian Cochlear Single-cell Transcriptomics

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Maf1 controls retinal neuron number by both RNA Pol III- and Pol II-dependent mechanisms

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Differential Network Analysis Reveals Regulatory Patterns in Neural Stem Cell Fate Decision

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Gene expression at a single-molecule level: implications for myelodysplastic syndromes and acute myeloid leukemia

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Successful allogeneic hematopoietic stem cell transplantation in a patient with type I CD36 deficiency: a case study and literature review

Okuyama, S., Sumi, M., Ishikawa, R., Shishido, T., Koyama, D., Ueki, T., Takahashi, D., Kobayashi, H., Kobayashi, H., & Tsuno, N. H. (2023) · International Journal of Hematology · doi:10.1007/s12185-023-03637-4 · Cited by 5

Genetic pathways regulating hematopoietic lineage speciation: Factorial latent variable model analysis of single cell transcriptome

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A deep single cell mass cytometry approach to capture canonical and noncanonical cell cycle states

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G-CSF–induced hematopoietic stem cell mobilization from the embryonic hematopoietic niche does not require neutrophils and macrophages

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COFFEE: consensus single cell-type specific inference for gene regulatory networks

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AutoGRN: An Automated Graph Neural Network Framework for Gene Regulatory Network Inference

Gao, J., Wu, S., Xiao, S., & Wu, Z. (2025) · IEEE Journal of Biomedical and Health Informatics · doi:10.1109/jbhi.2025.3609408 · Cited by 5

uPAR expression in M-MDSCs under high LDHA activity in pancreatic ductal adenocarcinoma

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Benchmarking RNA velocity methods across 17 independent studies

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Density-based detection of cell transition states to construct disparate and bifurcating trajectories

Lan, T., Hutvágner, G., Zhang, X., Liu, T., Wong, L., & Li, J. (2022) · Nucleic Acids Research · doi:10.1093/nar/gkac785 · Cited by 4

Late fetal hematopoietic failure results from ZBTB11 deficiency despite abundant HSC specification

Cao, H., Naik, S. H., Amann‐Zalcenstein, D., Hickey, P. F., Salim, A., Cao, B., Nilsson, S. K., Keightley, M.-C., & Lieschke, G. J. (2023) · Blood Advances · doi:10.1182/bloodadvances.2022009580 · Cited by 4

scGAMNN: Graph Antoencoder-Based Single-Cell RNA Sequencing Data Integration Algorithm Using Mutual Nearest Neighbors

Zhang, B., Wu, H., Wang, Y., Xuan, C., & Gao, J. (2023) · IEEE Journal of Biomedical and Health Informatics · doi:10.1109/jbhi.2023.3311340 · Cited by 4

TDP2 is a regulator of estrogen-responsive oncogene expression

Manguso, N., Kim, M., Joshi, N., Mahmud, M. R. A., Aldaco, J., Suzuki, R., Cortés‐Ledesma, F., Cui, X., Yamada, S., Takeda, S., et al. (2024) · NAR Cancer · doi:10.1093/narcan/zcae016 · Cited by 4

Single-cell Quantitation of mRNA and Surface Protein Expression in Simian Immunodeficiency Virus-infected CD4+ T Cells Isolated from Rhesus macaques

Tokarev, A., Creegan, M., Eller, M. A., Roederer, M., & Bolton, D. L. (2018) · Journal of Visualized Experiments · doi:10.3791/57776 · Cited by 4

Prostacyclin is an Endosteal Bone Marrow Niche Component and its Clinical Analog Iloprost Protects Hematopoietic Stem Cell Potential During Stress

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The chromatin repressors EZH2 and Suv4‐20h coregulate cell fate specification during hippocampal development

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B-lineage acute lymphoblastic leukemia causes cellautonomous defects in long-term hematopoietic stem cell function

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Extensive exploration of T cell heterogeneity in cancers by single cell sequencing

Wang, X., & Li, Y. (2019) · Chinese Journal of Cancer Research · doi:10.21147/j.issn.1000-9604.2019.02.15 · Cited by 4

Quasi-universality in single-cell sequencing dataPreprint

Aparicio, L., Bordyuh, M., Blumberg, A. J., & Rabadán, R. (2018) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/426239 · Cited by 5

RISC: robust integration of single-cell RNA-seq datasets with different extents of cell cluster overlapPreprint

Liu, Y., Wang, T., & Zheng, D. (2018) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/483297 · Cited by 4

A survey of the methodological process of modeling, inference, and evaluation of gene regulatory networks using scRNA-Seq data

da Silva, J. E. H., Bernardino, H. S., de Oliveira, I. L., & Camata, J. J. (2025) · Biosystems · doi:10.1016/j.biosystems.2025.105464 · Cited by 4

SPSID: A Single-Parameter Shrinkage Inverse-Diffusion for Denoising Gene-Regulatory Networks

Chen, H., Han, G., Ding, W., & Grazian, C. (2026) · IEEE Journal of Biomedical and Health Informatics · doi:10.1109/jbhi.2026.3674779 · Cited by 4

The molecular and cellular choreography of early mammalian lung development

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IDH2 mutation accelerates TPO‐induced myelofibrosis with enhanced S100a8/a9 and NFκB signaling in vivo

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Redistribution of PU.1 partner transcription factor RUNX1 binding secures cell survival during leukemogenesis

Bender, A., Boydere, F., Jayavelu, A. K., Tibello, A., König, T., Aleth, H., zu Hörste, G. M., Vogl, T. J., & Rosenbauer, F. (2024) · The EMBO Journal · doi:10.1038/s44318-024-00295-y · Cited by 3

Inhibition of DEK restores hematopoietic stem cell function in Fanconi anemia

Chen, Z., Wu, F., Li, Y., Li, L., Lei, Y., Gao, S., Chen, T., Xie, Y., Xiao, J., Zeng, H., et al. (2024) · The Journal of Experimental Medicine · doi:10.1084/jem.20241248 · Cited by 3

A semi-supervised non-negative matrix factorization model for scRNA-seq data analysis

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Integrated analysis of single-cell RNA-seq and ATAC-seq in lens epithelial cells: Unveiling the role of ATF6 as a key transcription factor

Lu, H., Liu, X., Zhou, Q., Li, R., Zuo, H., Hu, K., Tian, M., Wang, H., Li, J., Li, N., et al. (2025) · Genes & Diseases · doi:10.1016/j.gendis.2025.101610 · Cited by 3

Transcriptional landscape of canine hematopoiesis and cross-species comparisons revealed by single-cell RNA sequencing

Ammons, D. T., Contursi, C., Olsen, M., Yoshimoto, J. A., Owens, E., Harris, M., Gillen, A. E., Dow, S., Avery, A. C., & Harris, R. A. (2026) · Scientific Reports · doi:10.1038/s41598-026-69222-x · Cited by 3

DuCGRN: A dual context-aware model for Gene Regulatory Network prediction from ScRNA-seq data

Dong, D., & Li, W. (2025) · Knowledge-Based Systems · doi:10.1016/j.knosys.2025.113724 · Cited by 4

Construction of a prostate adenocarcinoma molecular classification: integrating spatial transcriptomics with retrospective cohort validation

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Quantitative phase imaging with temporal kinetics predicts hematopoietic stem cell diversity

Yogo, T., Iwamoto, Y., Becker, H., Kimura, T., Ishida, R., Sugiyama-Finnis, A., Yokomizo, T., Suda, T., Ota, S., & Yamazaki, S. (2025) · Nature Communications · doi:10.1038/s41467-025-61846-3 · Cited by 3

CBFβ-SMMHC–driven leukemogenesis requires enhanced RUNX1-DNA binding affinity in mice

Zhen, T., Cao, Y., Dou, T., Chen, Y., Lopez, G., Menezes, A. C., Wu, X., Hammer, J. A., Cheng, J., Garrett, L. J., et al. (2025) · Journal of Clinical Investigation · doi:10.1172/jci192923 · Cited by 3

Lessons to cancer from studies of leukemia and hematopoiesis

Brown, G. (2022) · Frontiers in Cell and Developmental Biology · doi:10.3389/fcell.2022.993915 · Cited by 3

SRGS: sparse partial least squares-based recursive gene selection for gene regulatory network inference

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Alloantigen Infusion Activates the Transcriptome of Type 2 Conventional Dendritic Cells

Schroth, S. L., Jones, R., & Thorp, E. B. (2023) · ImmunoHorizons · doi:10.4049/immunohorizons.2300067 · Cited by 3

GRNRI: Gene Regulatory Network Inference using Unsupervised Graph Neural Network

Abdulhameed, F., Abbas, H. M., & Salama, C. R. (2024) · International Journal of Computing and Digital Systems · doi:10.12785/ijcds/150110 · Cited by 3

Single-cell Profiling of Reprogrammed Human Neural Stem Cells Unveils High Similarity to Neural Progenitors in the Developing Central Nervous System

Spathopoulou, A., Podlesnic, M., Gaetano, L. D., Kirsch, E. M., Tisch, M., Finotello, F., Aigner, L., Günther, K., & Edenhofer, F. (2024) · Stem Cell Reviews and Reports · doi:10.1007/s12015-024-10698-3 · Cited by 3

Single-cell analysis of peripheral blood and pleural effusion reveals functional diversity of γδ T cells in tuberculosis infection

Feng, Y., Chen, Y., Zhang, W., Shen, X., Yan, J., Lin, Y., Zhang, L., Niu, Y., Zhang, J., Tang, P., et al. (2025) · Frontiers in Immunology · doi:10.3389/fimmu.2025.1605827 · Cited by 3

LineGRN: A Line Graph Neural Network for Gene Regulatory Network Inference

Wang, Z., Xu, G., Yu, W., & Ou-Yang, L. (2025) · IEEE Journal of Biomedical and Health Informatics · doi:10.1109/jbhi.2025.3591840 · Cited by 7

Hematopoietic Stem Cells: Nature and Niche Nurture

Brown, G. (2021) · Bioengineering · doi:10.3390/bioengineering8050067 · Cited by 4

MKG: a mutual information based method to infer single cell gene regulatory network

Zeng, Y., Yan, X., Liang, Z., Zheng, R., & Li, M. (2021) · IEEE International Conference on Bioinformatics and Biomedicine (BIBM) · doi:10.1109/bibm52615.2021.9669880 · Cited by 3

Hematopoietic stem cells depend on HIM and HER

Kent, D. G. (2022) · Experimental Hematology · doi:10.1016/j.exphem.2022.10.004 · Cited by 3

Complete miRNA-15/16 loss in mice promotes hematopoietic progenitor expansion and a myeloid-biased hyperproliferative state

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Are Leukaemic Stem Cells Restricted to a Single Cell Lineage?

Brown, G., Sánchez, L., & Sánchez-Garcı́a, I. (2019) · International Journal of Molecular Sciences · doi:10.3390/ijms21010045 · Cited by 3

Characterization of eight new Hydractinia i-cell markers reveals underlying heterogeneity in the adult pluripotent stem cell populationPreprint

Waletich, J., de Jong, D., & Schnitzler, C. E. (2024) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2024.07.07.602406 · Cited by 3

Cell Lineage Affiliation During Hematopoiesis

Brown, G. (2025) · International Journal of Molecular Sciences · doi:10.3390/ijms26073346 · Cited by 2

DualNetM: an adaptive dual network framework for inferring functional-oriented markers

Dai, B., Li, H., Wang, P., Hu, P., Xing, J., Hu, Y., Xi, Q., & Zuo, Y. (2025) · BMC Biology · doi:10.1186/s12915-025-02367-9 · Cited by 2

Mapping Hematopoietic Fate after Transplantation

Hurwitz, S. N. (2025) · Stem Cell Reviews and Reports · doi:10.1007/s12015-025-10946-0 · Cited by 2

Leveraging mutual information in Variational Autoencoders for improved dimensionality reduction of single-cell RNA sequencing data: The scInfoMaxVAE approach

Duy, P. N., Thao, N. P., Le, T. M., & Trinh, L. V. (2025) · Computational Biology and Chemistry · doi:10.1016/j.compbiolchem.2025.108637 · Cited by 2

TransGRN: A Transfer Learning-Based Framework for Inferring Gene Regulatory Networks Across Cell Lines

Xu, G., Wang, Z., Zhou, J., Yu, W., & Ou-Yang, L. (2025) · IEEE Journal of Biomedical and Health Informatics · doi:10.1109/jbhi.2025.3628564 · Cited by 3

Impaired Complex I dysregulates neural/glial precursors and corpus callosum development revealing postnatal defects in Leigh syndrome mice

Biswas, S. R., Tomsick, P. L., Kelly, C., Lester, B. A., Milner, J. P., Henry, S. N., Soto, Y., Brindley, S., DeFoor, N., Morton, P. D., et al. (2025) · EMBO Molecular Medicine · doi:10.1038/s44321-025-00367-4 · Cited by 2

AutoGERN: single-cell RNA-seq gene regulatory network inference via explicit link modeling and adaptive architectures

Wang, J., Chen, Y., Zou, Q., & Luo, X. (2026) · Bioinformatics · doi:10.1093/bioinformatics/btag143 · Cited by 2

A machine learning-based megakaryocyte identification system uncovers resident organs, markers, and functional diversity

Xia, M., Ma, Y., Cai, Y., Zhao, J., Zhong, Y., Guo, S., Li, M., Su, P., Shen, B., He, H., et al. (2026) · Developmental Cell · doi:10.1016/j.devcel.2026.04.005 · Cited by 2

A CD4-lineage erythro–myeloid progenitor within the adult bone marrow defines an alternative pathway for macrophage generation

Tikoo, S., Rohit, J., Martinez, B., Song, R., Wielscher, M., Márquez-Burgoa, C., Hladik, A., Rizzetto, S., Shaw, L. E., Ghannadan, M., et al. (2026) · Nature Immunology · doi:10.1038/s41590-026-02686-1 · Cited by 2

Identification of Neuronal Cells in Sciatic Nerves of Adult Rats

Liu, Y., Zhou, S., Zhao, L., & Gu, X. (2022) · Frontiers in Cellular Neuroscience · doi:10.3389/fncel.2022.816814 · Cited by 2

An unsupervised deep learning framework for gene regulatory network inference from single-cell expression data

Mao, G., & Liu, J. (2023) · IEEE International Conference on Bioinformatics and Biomedicine (BIBM) · doi:10.1109/bibm58861.2023.10385528 · Cited by 2

Short cell cycle duration is a phenotype of human epidermal stem cells

Xiao, T., Eze, U. C., Charruyer, A., Weisenberger, T., Khalifa, A., Abegaze, B., Schwab, G. K., Elsabagh, R. H., Parenteau, T. R., Kochanowski, K., et al. (2024) · Stem Cell Research & Therapy · doi:10.1186/s13287-024-03670-y · Cited by 2

Mapping the two distinct proliferative bursts early in T‐cell development

Oh, S., Parikh, D., Xiao, J., Liu, X., Gu, K., & Chong, M. M. W. (2023) · Immunology and Cell Biology · doi:10.1111/imcb.12670 · Cited by 2

Competing dynamic gene regulatory networks involved in fibroblast reprogramming to hematopoietic progenitor cells

Shafiq, S., Hamashima, K., Guest, L. A., Al-Anbaki, A., Amaral, F. M. R., Wiseman, D. H., Kouskoff, V., Lacaud, G., Loh, Y., & Batta, K. (2025) · Stem Cell Reports · doi:10.1016/j.stemcr.2025.102473 · Cited by 2

Delineating Mpl-dependent and -independent phenotypes of Jak2 V617F–positive MPNs in vivo

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Substrate stiffness dictates unique paths towards proliferative arrest in WI-38 cells

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JAM-C/Jam-C Expression Is Primarily Expressed in Mouse Hematopoietic Stem Cells

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Conceptualizing the interplay of knowledge accumulation and integration capabilities in service innovation-based competitive strategy : a project-oriented firm context

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Single-Cell Analysis of Hematopoietic Stem Cells

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Aging in a relativistic biological space-timePreprint

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Emergence of the erythroid lineage from multipotent hematopoiesisPreprint

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Tipping-point analysis uncovers critical transition signals from gene expression profilesPreprint

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