Resetting transcription factor control circuitry toward ground-state pluripotency in human

Regulation and function of the mammalian tricarboxylic acid cycle

Arnold, P. K., & Finley, L. W. S. (2023) · Journal of Biological Chemistry · doi:10.1016/j.jbc.2022.102838 · Cited by 535 · see citing works

Metabolic signatures of cancer cells and stem cells

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Analytic Models of Oxygen and Nutrient Diffusion, Metabolism Dynamics, and Architecture Optimization in Three-Dimensional Tissue Constructs with Applications and Insights in Cerebral Organoids

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Reprogramming roadmap reveals route to human induced trophoblast stem cells

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Naïve human pluripotent stem cells respond to Wnt, Nodal and LIF signalling to produce expandable naïve extra-embryonic endoderm

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Mitochondrial plasticity in cell fate regulation

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Genome-Scale CRISPR Screens Identify Human Pluripotency-Specific Genes

Ihry, R. J., Salick, M. R., Ho, D. J., Sondey, M., Kommineni, S., Paula, S., Raymond, J., Henry, B., Frias, E., Wang, Q., et al. (2019) · Cell Reports · doi:10.1016/j.celrep.2019.03.043 · Cited by 71 · see citing works

Early human development and stem cell-based human embryo models

Shahbazi, M. N., & Pasque, V. (2024) · Cell stem cell · doi:10.1016/j.stem.2024.09.002 · Cited by 81 · see citing works

Metabolism in pluripotency: Both driver and passenger?

Dahan, P., Lu, V., Nguyen, R., Kennedy, S. A. L., & Teitell, M. A. (2018) · Journal of Biological Chemistry · doi:10.1074/jbc.tm117.000832 · Cited by 74 · see citing works

The transcription factor ERG regulates a low shear stress-induced anti-thrombotic pathway in the microvasculature

Peghaire, C. R., Dufton, N., Lang, M., Salles‐Crawley, I. I., Ahnström, J., Kalna, V., Raimondi, C., Pericleous, C., Inuabasi, L., Kiseleva, R. Y., et al. (2019) · Nature Communications · doi:10.1038/s41467-019-12897-w · Cited by 45 · see citing works

Induction and application of human naive pluripotency

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Deep learning the cis-regulatory code of chromatin dynamics during cellular reprogrammingPreprint

Nair, S., Ameen, M., Sundaram, L., Pampari, A., Schreiber, J. M., Balsubramani, A., Wang, Y. X., Burns, D., Blau, H. M., Karakikes, I., et al. (2023) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2023.10.04.560808 · Cited by 38 · see citing works

Chromatin and Epigenetic Rearrangements in Embryonic Stem Cell Fate Transitions

Sun, L., Fu, X., Ma, G., & Hutchins, A. P. (2021) · Frontiers in Cell and Developmental Biology · doi:10.3389/fcell.2021.637309 · Cited by 38 · see citing works

Roles of Diffusion Dynamics in Stem Cell Signaling and Three-Dimensional Tissue Development

McMurtrey, R. J. (2017) · Stem Cells and Development · doi:10.1089/scd.2017.0066 · Cited by 37 · see citing works

Wnt signaling in stem cells during development and cell lineage specification

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Psat1-generated α-ketoglutarate and glutamine promote muscle stem cell activation and regenerationPreprint

Ciuffoli, V., Feng, X., Jiang, K., Acevedo-Luna, N., Ko, K. D., Wang, A. H. J., Riparini, G., Khateb, M., Glancy, B. C., Dell’Orso, S., et al. (2024) · Genes & Development · doi:10.1101/gad.351428.123 · Cited by 37 · see citing works

Elevated retrotransposon activity and genomic instability in primed pluripotent stem cells

Fu, H., Zhang, W., Li, N., Yang, J., Ye, X., Tian, C., Lu, X., & Liu, L. (2021) · Genome biology · doi:10.1186/s13059-021-02417-9 · Cited by 27 · see citing works

Deep learning-based models for preimplantation mouse and human embryos based on single-cell RNA sequencing

Proks, M., Salehin, N., & Brickman, J. M. (2024) · Nature Methods · doi:10.1038/s41592-024-02511-3 · Cited by 27 · see citing works

RAS Regulates the Transition from Naive to Primed Pluripotent Stem Cells

Altshuler, A., Verbuk, M., Bhattacharya, S., Abramovich, I., Haklai, R., Hanna, J. H., Kloog, Y., Gottlieb, E., & Shalom‐Feuerstein, R. (2018) · Stem Cell Reports · doi:10.1016/j.stemcr.2018.01.004 · Cited by 24 · see citing works

Recent Advances in Understanding the Reversal of Gene Silencing During X Chromosome Reactivation

Talón, I., Janiszewski, A., Chappell, J., Vanheer, L., & Pasque, V. (2019) · Frontiers in Cell and Developmental Biology · doi:10.3389/fcell.2019.00169 · Cited by 23 · see citing works

Signal regulators of human naïve pluripotency

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Pluripotent Stem Cell-Derived Hepatocyte-like Cells: Induction Methods and Applications

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Recent insights into the regulation of X-chromosome inactivation

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Dietary phytochemical approaches to stem cell regulation

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Mitochondrial regulation in human pluripotent stem cells during reprogramming and β cell differentiation

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Naïve-like conversion enhances the difference in innate in vitro differentiation capacity between rabbit ES cells and iPS cells

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Bioengineering hemophilia A–specific microvascular grafts for delivery of full-length factor VIII into the bloodstream

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ID proteins promote the survival and primed-to-naive transition of human embryonic stem cells through TCF3-mediated transcription

Jiang, H., Du, M., Li, Y., Zhou, T., Lei, J., Liang, H., Zhong, Z., Al‐Lamki, R. S., Jiang, M., & Yang, J. H. (2022) · Cell Death and Disease · doi:10.1038/s41419-022-04958-8 · Cited by 15 · see citing works

Primate stem cells: bridge the translation from basic research to clinic application

Li, T., Ai, Z., & Ji, W. (2018) · Science China Life Sciences · doi:10.1007/s11427-018-9334-2 · Cited by 14 · see citing works

The selection arena in early human blastocysts resolves the pluripotent inner cell massPreprint

Singh, M., Widmann, T. J., Bansal, V., Cortés, J. L., Schumann, G. G., Wunderlich, S., Martin, U., Garcia-Perez, J. L., Hurst, L. D., & Izsvák, Z. (2018) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/318329 · Cited by 13 · see citing works

X-chromosome activity in naive human pluripotent stem cells—are we there yet?

Khan, S. A., Audergon, P. N. C. B., & Payer, B. (2017) · Stem Cell Investigation · doi:10.21037/sci.2017.06.03 · Cited by 11 · see citing works

A lncRNA-miRNA-mRNA network for human primed, naive and extended pluripotent stem cells

Ma, Z., Li, Y., Zhang, Y., Chen, J., Tan, T., & Fan, Y. (2020) · PLoS ONE · doi:10.1371/journal.pone.0234628 · Cited by 11 · see citing works

Suppression of ERK signalling promotes pluripotent epiblast in the human blastocystPreprint

Simon, C. S., McCarthy, A., Woods, L. M., Staneva, D. P., Huang, Q., Linneberg-Agerholm, M., Faulkner, A., Papathanasiou, A., Elder, K. T., Snell, P., et al. (2024) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2024.02.01.578414 · Cited by 11 · see citing works

Single-cell 3D genome structure reveals distinct human pluripotent states

Li, N., Jin, K., Liu, B., Yang, M., Shi, P., Heng, D., Wang, J., & Liu, L. (2024) · Genome biology · doi:10.1186/s13059-024-03268-w · Cited by 10 · see citing works

Folate Carrier Deficiency Drives Differential Methylation and Enhanced Cellular Potency in the Neural Plate Border

Jimenez, N. A., & Strobl‐Mazzulla, P. H. (2022) · Frontiers in Cell and Developmental Biology · doi:10.3389/fcell.2022.834625 · Cited by 9 · see citing works

Reversal of X chromosome inactivation: lessons from pluripotent reprogramming of mouse and human somatic cells

Cantone, I. (2017) · Journal of Translational Genetics and Genomics · doi:10.20517/jtgg.2017.19 · Cited by 9 · see citing works

Non-transmissible MV Vector with Segmented RNA Genome Establishes Different Types of iPSCs from Hematopoietic Cells

Hiramoto, T., Tahara, M., Liao, J., Soda, Y., Miura, Y., Kurita, R., Hamana, H., Inoue, K., Kohara, H., Miyamoto, S., et al. (2019) · Molecular Therapy · doi:10.1016/j.ymthe.2019.09.007 · Cited by 8 · see citing works

The nuclear matrix stabilizes primed-specific genes in human pluripotent stem cells

Ma, G., Fu, X., Zhou, L. B., Babarinde, I. A., Shi, L., Yang, W., Chen, J., Xiao, Z., Qiao, Y., Ma, L., et al. (2025) · Nature Cell Biology · doi:10.1038/s41556-024-01595-5 · Cited by 9 · see citing works

Transcriptional and epigenetic control of cell fate decisions in early embryos

Alberio, R. (2017) · Reproduction Fertility and Development · doi:10.1071/rd17403 · Cited by 7 · see citing works

Human trophoblast stem cell-state acquisition from pluripotent stem cells and somatic cells

Naama, M., & Buganim, Y. (2023) · Current Opinion in Genetics & Development · doi:10.1016/j.gde.2023.102084 · Cited by 7 · see citing works

The quest for pluripotency: a comparative analysis across mammalian species

Devika, A. S., Wruck, W., Adjaye, J., & Sudheer, S. (2019) · Reproduction · doi:10.1530/rep-18-0083 · Cited by 7 · see citing works

Protocol for Human Blastoids Modeling Blastocyst Development and Implantation

Kagawa, H., Javali, A., Khoei, H. H., et al. (2022) · Journal of Visualized Experiments · doi:10.3791/63388 · Cited by 6 · see citing works

Transcription factor-based transdifferentiation of human embryonic to trophoblast stem cells

Balestrini, P. A., Abdelbaki, A., McCarthy, A., Devito, L., Senner, C. E., Chen, A. E., Munusamy, P., Blakeley, P., Elder, K. T., Snell, P., et al. (2024) · Development · doi:10.1101/2021.08.18.456785 · Cited by 12 · see citing works

Human-animal interspecies chimerism via blastocyst complementation: advances, challenges and perspectives: a narrative review

Li, Y., & Huang, K. (2021) · Stem Cell Investigation · doi:10.21037/sci-2020-074 · Cited by 5 · see citing works

Organoids containing neural-like cells derived from chicken iPSCs respond to poly:IC through the RLR family

Katayama, M., Onuma, M., Kato, N., Nakajima, N., & Fukuda, T. (2023) · PLoS ONE · doi:10.1371/journal.pone.0285356 · Cited by 5 · see citing works

Cellular remodeling and JAK inhibition promote zygotic gene expression in the Ciona germline

Ohta, N., & Christiaen, L. (2024) · EMBO Reports · doi:10.1038/s44319-024-00139-0 · Cited by 4 · see citing works

Moving toward totipotency: the molecular and cellular features of totipotent and naive pluripotent stem cells

Hua, L., Peng, Y., Yan, L., Yuan, P., & Qiao, J. (2025) · Human Reproduction Update · doi:10.1093/humupd/dmaf006 · Cited by 4 · see citing works

TASOR expression in naive embryonic stem cells safeguards their developmental potential

Pinzón-Arteaga, C. A., O’Hara, R. A., Mazzagatti, A., Ballard, E. B., Hu, Y., Pan, A., Schmitz, D. A., Wei, Y., Sakurai, M., Ly, P., et al. (2024) · Cell Reports · doi:10.1016/j.celrep.2024.114887 · Cited by 4 · see citing works

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 · see citing works

Protocol for Human Blastoids Modeling Blastocyst Development and Implantation

Kagawa, H., Javali, A., Khoei, H. H., et al. (2022) · Journal of Visualized Experiments · doi:10.3791/63388-v · Cited by 3 · see citing works

A Deep Learning Approach to Assessing Cell Identity in Stem Cell–Based Embryo Models

Salehin, N., Proks, M., & Brickman, J. M. (2025) · Methods in molecular biology · doi:10.1007/7651_2025_654 · Cited by 2 · see citing works

Reduced MEK inhibition preserves genomic stability in naïve human ES cells

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Pramef12 enhances reprogramming into naïve iPS cells

Haraguchi, D., & Nakamura, T. (2022) · Biochemistry and Biophysics Reports · doi:10.1016/j.bbrep.2022.101267 · Cited by 2 · see citing works

Deep Learning Based Models for Preimplantation Mouse and Human DevelopmentPreprint

Proks, M., Salehin, N., & Brickman, J. M. (2024) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2024.02.16.580649 · Cited by 2 · see citing works

Induction of Pluripotent Stem Cells from Muscle Cells of Large Yellow Croaker (Larimichthys Crocea) Via Electrotransfection

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Adaptation of induced pluripotent stem cell technology for avian species

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Acetylation of lysine 49 on Ctnnb1 drives naïve pluripotency in murine stem cells by modulating Nanog function

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Metabolic plasticity complements the unique nature and demands of distinct pluripotency states

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Transcriptomic analysis of feeder-free culture system for maintaining naïve-state pluripotency in human pluripotent stem cells

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Multiplexed single-cell transcriptome analysis reveals molecular characteristics of monkey pluripotent stem cell lines

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Standing on the shoulders of giants: The changing landscape of pluripotent stem cells in research

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Differentiation and Expansion of Human Extra-Embryonic Endoderm Cell Lines from Naïve Pluripotent Stem Cells

Linneberg-Agerholm, M., & Brickman, J. M. (2021) · Methods in molecular biology · doi:10.1007/978-1-0716-1908-7_8 · Cited by 1 · see citing works

Modeling anthracycline-induced cardiotoxicity with patient-specific iPSCs

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Cellular remodeling and JAK inhibition promote zygotic gene expression in the Ciona germlinePreprint

Ohta, N., & Christiaen, L. (2021) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2021.07.12.452040 · Cited by 1 · see citing works

The Derivation and Characterisation of Bovine Embryonic Stem Cells

Waldron, N. (2022) · doi:10.26686/wgtn.19589863 · Cited by 1 · see citing works

Temporal Dynamics of Tet1 and Oct4 Gene Activation Resolve Distinct Stages of Global DNA Demethylation and Transcriptomic Changes in the Final Phases of Induced PluripotencyPreprint

Bartoccetti, M., Luo, X., van der Veer, B., Khoueiry, R., Janiszewski, A., Xu, J., Verfaillie, C. M., Pasque, V., Thienpont, B., & Koh, K. P. (2019) · SSRN Electronic Journal · doi:10.2139/ssrn.3376662

Mecanismos moleculares envolvidos na transição entre o estado primed e naïve de células-tronco embrionárias

Corveloni, A. C. (2020) · doi:10.11606/d.17.2020.tde-03112020-115800

Genome-Scale CRISPR Screening Identifies Novel Human Pluripotent Gene NetworksPreprint

Ihry, R. J., Salick, M. R., Ho, D. J., Sondey, M., Kommineni, S., Paula, S., Raymond, J., Frias, E., Worringer, K. A., Russ, C., et al. (2018) · SSRN Electronic Journal · doi:10.2139/ssrn.3189387 · Cited by 1 · see citing works

Rostral Hypothalamic Differentiation With Minimal Exogenous Signals in Human Naive Induced Pluripotent Stem CellsPreprint

Ozaki, H., Suga, H., Sakakibara, M., et al. (2022) · Research Square · doi:10.21203/rs.3.rs-1202298/v1

Faculty Opinions recommendation of Comparative Principles of DNA Methylation Reprogramming during Human and Mouse In Vitro Primordial Germ Cell Specification.

Western, P. S. (2016) · Faculty Opinions – Post-Publication Peer Review of the Biomedical Literature · doi:10.3410/f.726835249.793525224

Bevacizumab treatment of patients with breast cancer is associated with differential expression and up-regulation of the leukemia inhibitory factor receptor (LIFR).Preprint

Mamoor, S. (2020) · doi:10.31219/osf.io/zb6dm

Avaliação de modelos in vitro para o estudo da inativação do cromossomo X em humanos

Orsi, A. E. R. (2023) · doi:10.11606/d.41.2023.tde-23102023-180216

Metabolic Quadrivalency in RSeT Human Embryonic Stem CellsPreprint

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Additional file 6 of Elevated retrotransposon activity and genomic instability in primed pluripotent stem cells

Fu, H., Zhang, W., Li, N., Yang, J., Ye, X., Tian, C., Lu, X., & Liu, L. (2021) · Figshare · doi:10.6084/m9.figshare.14944930

Additional file 4 of Elevated retrotransposon activity and genomic instability in primed pluripotent stem cells

Fu, H., Zhang, W., Li, N., Yang, J., Ye, X., Tian, C., Lu, X., & Liu, L. (2021) · Figshare · doi:10.6084/m9.figshare.14944924

Additional file 7 of Elevated retrotransposon activity and genomic instability in primed pluripotent stem cells

Fu, H., Zhang, W., Li, N., Yang, J., Ye, X., Tian, C., Lu, X., & Liu, L. (2021) · Figshare · doi:10.6084/m9.figshare.14944933

Additional file 5 of Elevated retrotransposon activity and genomic instability in primed pluripotent stem cells

Fu, H., Zhang, W., Li, N., Yang, J., Ye, X., Tian, C., Lu, X., & Liu, L. (2021) · Figshare · doi:10.6084/m9.figshare.14944927

Additional file 2 of Elevated retrotransposon activity and genomic instability in primed pluripotent stem cells

Fu, H., Zhang, W., Li, N., Yang, J., Ye, X., Tian, C., Lu, X., & Liu, L. (2021) · Figshare · doi:10.6084/m9.figshare.14944915

Additional file 3 of Elevated retrotransposon activity and genomic instability in primed pluripotent stem cells

Fu, H., Zhang, W., Li, N., Yang, J., Ye, X., Tian, C., Lu, X., & Liu, L. (2021) · Figshare · doi:10.6084/m9.figshare.14944921

Protocol for deriving human preimplantation epiblast stem cells and 8-cell embryo-like cells

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Milestones of Trophectoderm and Naïve-to-Primed Pluripotency Transition in Human Embryos Reveals Stage-Match of Human BlastoidsPreprint

Chevolleau, S., Moinard, E., Bruneau, A., Girard, O., Lammers, J., van Genderen, E., Karvas, R. M., Besseau, S., Garraud, C., Loubersac, S., et al. (2025) · SSRN Electronic Journal · doi:10.2139/ssrn.5266550

Structural characterization of stem cell factors Oct4, Sox2, Nanog and Esrrb disordered domains, and a method to identify their phospho-dependent binding partnersPreprint

Bouguechtouli, C., Ghouil, R., Alik, A., et al. (2023) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2023.03.05.531149 · Cited by 3 · see citing works

Cancer Stem Cells in Glioblastoma Multiforme

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Association of High Expression Levels of SOX2, NANOG, and OCT4 in Gastric Cancer Tumor Tissues with Progression and Poor Prognosis

Basati, G., Mohammadpour, H., & Razavi, À. E. (2019) · Journal of Gastrointestinal Cancer · doi:10.1007/s12029-018-00200-x · Cited by 74 · see citing works

NANOG overexpression and its correlation with stem cell and differentiation markers in meningiomas of different WHO grades

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The HPV16 E7 oncoprotein increases the expression of Oct3/4 and stemness-related genes and augments cell self-renewal

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