Multi-omic Profiling Reveals Dynamics of the Phased Progression of Pluripotency

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H3K18 lactylation marks tissue-specific active enhancers

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Derivation of Intermediate Pluripotent Stem Cells Amenable to Primordial Germ Cell Specification

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Decoding the function of bivalent chromatin in development and cancerPreprint

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PhosR Enables Processing and Functional Analysis of Phosphoproteomic Data

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Formative pluripotent stem cells show features of epiblast cells poised for gastrulation

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Temporal dissection of an enhancer cluster reveals distinct temporal and functional contributions of individual elements

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Personalized phosphoproteomics identifies functional signaling

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Phosphoproteomics reveals rewiring of the insulin signaling network and multi-nodal defects in insulin resistance

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Abscission Couples Cell Division to Embryonic Stem Cell Fate

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PRC2.1- and PRC2.2-specific accessory proteins drive recruitment of different forms of canonical PRC1

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Enhancer cooperativity can compensate for loss of activity over large genomic distances

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Global phosphoproteomics reveals DYRK1A regulates CDK1 activity in glioblastoma cells

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Enhancer-associated H3K4 methylation safeguards in vitro germline competence

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Multi-omics profiling visualizes dynamics of cardiac development and functions

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Fine-tuning of gene expression through the Mettl3-Mettl14-Dnmt1 axis controls ESC differentiation

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Integrated molecular-phenotypic profiling reveals metabolic control of morphological variation in a stem-cell-based embryo model

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noisyR : enhancing biological signal in sequencing datasets by characterizing random technical noise

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Esrrb guides naive pluripotent cells through the formative transcriptional programme

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Chromatin and Epigenetic Rearrangements in Embryonic Stem Cell Fate Transitions

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Stable maternal proteins underlie distinct transcriptome, translatome, and proteome reprogramming during mouse oocyte-to-embryo transition

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The Key Role of MicroRNAs in Self-Renewal and Differentiation of Embryonic Stem Cells

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Computational Stem Cell Biology: Open Questions and Guiding Principles

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RNA polymerase II pausing in development: orchestrating transcription

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Phosphoproteomics of Acute Cell Stressors Targeting Exercise Signaling Networks Reveal Drug Interactions Regulating Protein Secretion

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INO80 promotes H2A.Z occupancy to regulate cell fate transition in pluripotent stem cells

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Loss of MLL3/4 decouples enhancer H3K4 monomethylation, H3K27 acetylation, and gene activation during embryonic stem cell differentiation

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A proteome signature for acute incisional pain in dorsal root ganglia of mice

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Stirred suspension bioreactors maintain naïve pluripotency of human pluripotent stem cells

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Cardiopoietic stem cell therapy restores infarction-altered cardiac proteome

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Dissection of two routes to naïve pluripotency using different kinase inhibitors

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Trafficking regulator of GLUT4-1 (TRARG1) is a GSK3 substrate

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Molecular versatility during pluripotency progression

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Signaling Heterogeneity is Defined by Pathway Architecture and Intercellular Variability in Protein Expression

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RNA Pol II pausing facilitates phased pluripotency transitions by buffering transcriptionPreprint

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FoxO transcription factors actuate the formative pluripotency specific gene expression programme

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Optogenetic manipulation identifies the roles of ERK and AKT dynamics in controlling mouse embryonic stem cell exit from pluripotency

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Impact of eIF2α phosphorylation on the translational landscape of mouse embryonic stem cells

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MicroRNA-dependent inhibition of PFN2 orchestrates ERK activation and pluripotent state transitions by regulating endocytosis

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bulkAnalyseR: an accessible, interactive pipeline for analysing and sharing bulk multi-modal sequencing data

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Three-dimensional geometry controls division symmetry in stem cell colonies

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Progression of the pluripotent epiblast depends upon the NMD factor UPF2

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A high-content endogenous GLUT4 trafficking assay reveals new aspects of adipocyte biology

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The application of cell surface markers to demarcate distinct human pluripotent states

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Phosphorylation of the HP1β hinge region sequesters KAP1 in heterochromatin and promotes the exit from naïve pluripotency

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Transcriptional network dynamics during the progression of pluripotency revealed by integrative statistical learning

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Temporal ordering of omics and multiomic events inferred from time-series data

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Metabolic characterization of a paused-like pluripotent state

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A defined glycosylation regulatory network modulates total glycome dynamics during pluripotency state transition

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Unraveling the Spatiotemporal Human Pluripotency in Embryonic Development

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High temporal resolution proteome and phosphoproteome profiling of stem cell-derived hepatocyte development

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Nanog regulates Pou3f1 expression at the exit from pluripotency during gastrulation

Barral, A., Rollan, I., Sánchez-Iranzo, H., Jawaid, W., Badía-Careaga, C., Menchero, S., Gómez, M., Torroja, C., Sánchez-Cabo, F., Göttgens, B., et al. (2019) · Biology Open · doi:10.1242/bio.046367 · Cited by 14

Comprehensive chromatin proteomics resolves functional phases of pluripotency and identifies changes in regulatory components

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A transient transcriptional activation governs unpolarized-to-polarized morphogenesis during embryo implantation

Lyu, X., Cui, Y., Kong, Y., Yang, M., Shen, H., Liao, S., Li, S., An, C., Wang, H., Zhang, Z., et al. (2024) · Molecular Cell · doi:10.1016/j.molcel.2024.06.005 · Cited by 12

Pluripotency factor Tex10 finetunes Wnt signaling for spermatogenesis and primordial germ cell development

Yuan, F., Yang, J., Ma, F., Hu, Z., Malik, V., Zang, R., Li, D., Shi, X., Huang, X., Zhou, H., et al. (2025) · Nature Communications · doi:10.1038/s41467-025-57165-2 · Cited by 14

Regulation of NANOG and SOX2 expression by activin A and a canonical WNT agonist in bovine embryonic stem cells and blastocysts

Xiao, Y., Sosa, F., Ross, P. J., Diffenderfer, K. E., & Hansen, P. J. (2021) · Biology Open · doi:10.1242/bio.058669 · Cited by 13

Computational systems approach towards phosphoproteomics and their downstream regulation

Xiao, D., Chen, C., & Yang, P. (2022) · PROTEOMICS · doi:10.1002/pmic.202200068 · Cited by 12

Epithelial cadherin regulates transition between the naïve and primed pluripotent states in mouse embryonic stem cells

Sharaireh, A. M., FitzPatrick, L. M., Ward, C. M., McKay, T. R., & Unwin, R. D. (2020) · Stem Cells · doi:10.1002/stem.3249 · Cited by 11

Comparative Phosphoproteomics of Classical Bordetellae Elucidates the Potential Role of Serine, Threonine and Tyrosine Phosphorylation in Bordetella Biology and Virulence

Luu, L. D. W., Zhong, L., Kaur, S., Raftery, M. J., & Lan, R. (2021) · Frontiers in Cellular and Infection Microbiology · doi:10.3389/fcimb.2021.660280 · Cited by 11

An extensive and dynamic trans-omic network illustrating prominent regulatory mechanisms in response to insulin in the liver

Matsuzaki, F., Uda, S., Yamauchi, Y., Matsumoto, M., Soga, T., Maehara, K., Ohkawa, Y., Nakayama, K. I., Kuroda, S., & Kubota, H. (2021) · Cell Reports · doi:10.1016/j.celrep.2021.109569 · Cited by 11

Poised PABP–RNA hubs implement signal-dependent mRNA decay in development

Modic, M., Kuret, K., Steinhauser, S., Faraway, R., van Genderen, E., Mozos, I. R. D. L., Novljan, J., Vičič, Ž., Lee, F. C. Y., ten Berge, D., et al. (2024) · Nature Structural & Molecular Biology · doi:10.1038/s41594-024-01363-x · Cited by 11

Transcriptional and epigenetic control of germline competence and specification.

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Combinatorial metabolism drives the naive to primed pluripotent chromatin landscape

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Aurora B controls microtubule stability to regulate abscission dynamics in stem cells

Kodba, S., Öztop, A., van Berkum, E., Katrukha, E. A., Iwanski, M. K., Nijenhuis, W., Kapitein, L. C., & Chaigne, A. (2025) · Cell Reports · doi:10.1016/j.celrep.2025.115238 · Cited by 11

KMT2C/KMT2D-dependent H3K4me1 mediates changes in DNA replication timing and origin activity during a cell fate transition

Gökbuget, D., Goehring, L. J., Boileau, R. M., Lenshoek, K., Huang, T. T., & Blelloch, R. H. (2025) · Cell Reports · doi:10.1016/j.celrep.2025.115272 · Cited by 9

A systems view of cellular heterogeneity: Unlocking the “wheel of fate”

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A Review of Complex Systems Approaches to Cancer Networks

Uthamacumaran, A. (2020) · Complex Systems · doi:10.25088/complexsystems.29.4.779 · Cited by 10

Functional analysis of the stable phosphoproteome reveals cancer vulnerabilities

Xiao, D., Kim, H. J., Pang, C. N. I., & Yang, P. (2022) · Bioinformatics · doi:10.1093/bioinformatics/btac015 · Cited by 8

Modeling the early development of a primate embryo

Tam, P. (2019) · Science · doi:10.1126/science.aaz6976 · Cited by 9

Epigenetics as “conductor” in “orchestra” of pluripotent states

Baral, I., Varghese, P. C., & Dutta, D. (2022) · Cell and Tissue Research · doi:10.1007/s00441-022-03667-0 · Cited by 9

The transcription factor OCT6 promotes the dissolution of the naïve pluripotent state by repressing Nanog and activating a formative state gene regulatory network

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Enhancer-associated H3K4 methylation safeguards in vitro germline competence

Bleckwehl, T., Crispatzu, G., Schaaf, K., Respuela, P., Bartusel, M., Benson, L. J., Clark, S. J., Dorighi, K. M., Barral, A., Laugsch, M., et al. (2020) · Kölner Universitäts PublikationsServer (Universität zu Köln) · doi:10.17863/cam.76317 · Cited by 8

Time-resolved phosphoproteome and proteome analysis reveals kinase signaling on master transcription factors during myogenesis

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Organelle biogenesis: ribosomes as organizer and performer

Wang, Q., Wang, Y., Li, S., Zhou, A., & Qin, Y. (2022) · 中国科学通报：英文版 · doi:10.1016/j.scib.2022.07.023 · Cited by 8

Integrative analysis reveals histone demethylase LSD1 promotes RNA polymerase II pausing

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Quantitative Proteomics and Phosphoproteomics Analysis of Patient-Derived Ovarian Cancer Stem Cells

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