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

Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2

Love, M. I., Huber, W., & Anders, S. (2014) · Genome Biology · doi:10.1186/s13059-014-0550-8 · Cited by 95,106 · see citing works

STAR: ultrafast universal RNA-seq aligner

Dobin, A., Davis, C. A., Schlesinger, F., Drenkow, J., Zaleski, C., Jha, S., Batut, P., Chaisson, M., & Gingeras, T. R. (2013) · Bioinformatics · doi:10.1093/bioinformatics/bts635 · Cited by 51,709 · see citing works

<tt>edgeR</tt> : a Bioconductor package for differential expression analysis of digital gene expression data

Robinson, M. D., McCarthy, D. J., & Smyth, G. K. (2010) · Bioinformatics · doi:10.1093/bioinformatics/btp616 · Cited by 41,364 · see citing works

limma powers differential expression analyses for RNA-sequencing and microarray studies

Ritchie, M. E., Phipson, B., Wu, D., Hu, Y., Law, C. W., Shi, W., & Smyth, G. K. (2015) · Nucleic Acids Research · doi:10.1093/nar/gkv007 · Cited by 40,458 · see citing works

Ultrafast and memory-efficient alignment of short DNA sequences to the human genome.

Langmead, B., Trapnell, C., Pop, M., & Salzberg, S. L. (2009) · Genome Biology · doi:10.1186/gb-2009-10-3-r25 · Cited by 21,849 · see citing works

HTSeq—a Python framework to work with high-throughput sequencing data

Anders, S., Pyl, P. T., & Huber, W. (2015) · Bioinformatics · doi:10.1093/bioinformatics/btu638 · Cited by 21,464 · see citing works

MaxQuant enables high peptide identification rates, individualized p.p.b.-range mass accuracies and proteome-wide protein quantification

Cox, J., & Mann, M. (2008) · Nature Biotechnology · doi:10.1038/nbt.1511 · Cited by 14,855 · see citing works

In silico prediction of protein-protein interactions in human macrophages

Souiai, O., Guerfali, F. Z., Miled, S. B., Brun, C., & Benkahla, A. (2014) · BMC Research Notes · doi:10.1186/1756-0500-7-157 · Cited by 10,785 · see citing works

Significance analysis of microarrays applied to the ionizing radiation response

Tusher, V. G., Tibshirani, R., & Chu, G. (2001) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.091062498 · Cited by 10,568 · see citing works

Adjusting batch effects in microarray expression data using empirical Bayes methods

Johnson, W. E., Li, C., & Rabinovic, A. (2007) · Biostatistics · doi:10.1093/biostatistics/kxj037 · Cited by 8,658 · see citing works

Global quantification of mammalian gene expression control

Schwanhäusser, B., Busse, D., Li, N., Dittmar, G., Schuchhardt, J., Wolf, J., Chen, W., & Selbach, M. (2011) · Nature · doi:10.1038/nature10098 · Cited by 6,566 · see citing works

The MaxQuant computational platform for mass spectrometry-based shotgun proteomics

Tyanova, S., Temu, T., & Cox, J. (2016) · Nature Protocols · doi:10.1038/nprot.2016.136 · Cited by 4,691 · see citing works

Gene Ontology Consortium: going forward

The Gene Ontology Consortium (2015) · Nucleic Acids Research · doi:10.1093/nar/gku1179 · Cited by 3,492 · see citing works

The ground state of embryonic stem cell self-renewal

Ying, Q.-L., Wray, J., Nichols, J., Batlle-Morera, L., Doble, B., Woodgett, J., Cohen, P., & Smith, A. (2008) · Nature · doi:10.1038/nature06968 · Cited by 3,442 · see citing works

Mass-spectrometric exploration of proteome structure and function

Aebersold, R., & Mann, M. (2016) · Nature · doi:10.1038/nature19949 · Cited by 2,334 · see citing works

BioMart and Bioconductor: a powerful link between biological databases and microarray data analysis

Durinck, S., Moreau, Y., Kasprzyk, A., Davis, S. R., Moor, B. D., Brāzma, A., & Huber, W. K. (2005) · Computer applications in the biosciences · doi:10.1093/bioinformatics/bti525 · Cited by 2,327 · see citing works

BEDTools: The Swiss‐Army Tool for Genome Feature Analysis

Quinlan, A. R. (2014) · Current Protocols in Bioinformatics · doi:10.1002/0471250953.bi1112s47 · Cited by 2,286 · see citing works

New cell lines from mouse epiblast share defining features with human embryonic stem cells

Tesar, P. J., Chenoweth, J. G., Brook, F. A., Davies, T. J., Evans, E. P., Mack, D. L., Gardner, R. L., & McKay, R. D. G. (2007) · Nature · doi:10.1038/nature05972 · Cited by 2,153 · see citing works

The Fibroblast Growth Factor signaling pathway

Ornitz, D. M., & Itoh, N. (2015) · WIREs Developmental Biology · doi:10.1002/wdev.176 · Cited by 2,050 · see citing works

Derivation of pluripotent epiblast stem cells from mammalian embryos

Brons, I. G. M., Smithers, L. E., Trotter, M. W. B., Rugg‐Gunn, P. J., Sun, B., Lopes, S. M. C. D. S., Howlett, S., Clarkson, A., Ährlund‐Richter, L., Pedersen, R. A., et al. (2007) · Nature · doi:10.1038/nature05950 · Cited by 2,007 · see citing works

Naive and Primed Pluripotent States

Nichols, J., & Smith, A. G. (2009) · Cell stem cell · doi:10.1016/j.stem.2009.05.015 · Cited by 1,835 · see citing works

The Ras-ERK and PI3K-mTOR pathways: cross-talk and compensation

Mendoza, M. C., Er, E. E., & Blenis, J. (2011) · Trends in Biochemical Sciences · doi:10.1016/j.tibs.2011.03.006 · Cited by 1,817 · see citing works

Single-cell RNA-Seq profiling of human preimplantation embryos and embryonic stem cells

Yan, L., Yang, M., Guo, H., Yang, L., Wu, J., Li, R., Liu, P., Lian, Y., Zheng, X., Yan, J., et al. (2013) · Nature Structural &amp; Molecular Biology · doi:10.1038/nsmb.2660 · Cited by 1,740 · see citing works

Minimal, encapsulated proteomic-sample processing applied to copy-number estimation in eukaryotic cells

Kulak, N. A., Pichler, G., Paron, I., Nagaraj, N., & Mann, M. (2014) · Nature Methods · doi:10.1038/nmeth.2834 · Cited by 1,719 · see citing works

PhosphoSitePlus: a comprehensive resource for investigating the structure and function of experimentally determined post-translational modifications in man and mouse

Hornbeck, P. V., Kornhauser, J. M., Tkachev, S., Zhang, B., Skrzypek, E., Murray, B. W., Latham, V. M., & Sullivan, M. (2011) · Nucleic Acids Research · doi:10.1093/nar/gkr1122 · Cited by 1,636 · see citing works

Reconstitution of the mouse germ cell specification pathway in culture by pluripotent stem cells.

Hayashi, K., Ohta, H., Kurimoto, K., Aramaki, S., & Saitou, M. (2011) · Cell · doi:10.1016/j.cell.2011.06.052 · Cited by 1,324 · see citing works

Global signatures of protein and mRNA expression levels

de Sousa Abreu, R., Penalva, L. O., Marcotte, E. M., & Vogel, C. (2009) · Molecular BioSystems · doi:10.1039/b908315d · Cited by 1,248 · see citing works

Proliferation, survival and metabolism: the role of PI3K/AKT/mTOR signalling in pluripotency and cell fate determination

Yu, J., & Cui, W. (2016) · Development · doi:10.1242/dev.137075 · Cited by 1,137 · see citing works

Single-Cell RNA-Seq Reveals Lineage and X Chromosome Dynamics in Human Preimplantation Embryos

Petropoulos, S., Edsgärd, D., Reinius, B., Deng, Q., Panula, S. P., Codeluppi, S., Plaza Reyes, A., Linnarsson, S., Sandberg, R., & Lanner, F. (2016) · Cell · doi:10.1016/j.cell.2016.03.023 · Cited by 1,063 · see citing works

Derivation of novel human ground state naive pluripotent stem cells

Gafni, O., Weinberger, L., Mansour, A. A., Manor, Y. S., Chomsky, E., Ben‐Yosef, D., Kalma, Y., Viukov, S. V., Maza, I., Zviran, A., et al. (2013) · Nature · doi:10.1038/nature12745 · Cited by 1,047 · see citing works

Resetting Transcription Factor Control Circuitry toward Ground-State Pluripotency in Human

Takashima, Y., Guo, G., Loos, R., Nichols, J., Ficz, G., Krueger, F., Oxley, D., Santos, F., Clarke, J., Mansfield, W., et al. (2014) · Cell · doi:10.1016/j.cell.2014.08.029 · Cited by 980 · see citing works

Ultradeep Human Phosphoproteome Reveals a Distinct Regulatory Nature of Tyr and Ser/Thr-Based Signaling

Sharma, K., D’Souza, R. C. J., Tyanova, S., Schaab, C., Wiśniewski, J. R., Cox, J., & Mann, M. (2014) · Cell Reports · doi:10.1016/j.celrep.2014.07.036 · Cited by 971 · see citing works

A unique regulatory phase of DNA methylation in the early mammalian embryo

Smith, Z. D., Chan, M. M., Mikkelsen, T. S., Gu, H., Gnirke, A., Regev, A., & Meissner, A. (2012) · Nature · doi:10.1038/nature10960 · Cited by 964 · see citing works

Systematic Identification of Culture Conditions for Induction and Maintenance of Naive Human Pluripotency

Theunissen, T. W., Powell, B. E., Wang, H., Mitalipova, M., Faddah, D. A., Reddy, J., Fan, Z. P., Maetzel, D., Ganz, K., Shi, L., et al. (2014) · Cell stem cell · doi:10.1016/j.stem.2014.07.002 · Cited by 888 · see citing works

The Transcriptional and Epigenomic Foundations of Ground State Pluripotency

Marks, H., Kalkan, T., Menafra, R., Denissov, S., Jones, K. A., Hofemeister, H., Nichols, J., Kranz, A., Stewart, A., Smith, A. G., et al. (2012) · Cell · doi:10.1016/j.cell.2012.03.026 · Cited by 881 · see citing works

A parallel circuit of LIF signalling pathways maintains pluripotency of mouse ES cells

Niwa, H., Ogawa, K., Shimosato, D., & Adachi, K. (2009) · Nature · doi:10.1038/nature08113 · Cited by 872 · see citing works

The ProteomeXchange consortium in 2017: supporting the cultural change in proteomics public data deposition

Deutsch, E. W., Csordás, A., Sun, Z., Jarnuczak, A. F., Pérez‐Riverol, Y., Ternent, T., Campbell, D. S., Llinares, M. B., Okuda, S., Kawano, S., et al. (2016) · Nucleic Acids Research · doi:10.1093/nar/gkw936 · Cited by 864 · see citing works

A Molecular Roadmap of Reprogramming Somatic Cells into iPS Cells

Polo, J. M., Anderssen, E., Walsh, R. M., Schwarz, B. A., Nefzger, C. M., Lim, S. M., Borkent, M., Apostolou, E., Alaei, S., Cloutier, J., et al. (2012) · Cell · doi:10.1016/j.cell.2012.11.039 · Cited by 861 · see citing works

Ensembl 2012

Flicek, P., Amode, M. R., Barrell, D. G., Beal, K. M., Brent, S., Carvalho‐Silva, D., Clapham, P., Coates, G. M. P., Fairley, S., Fitzgerald, S. F., et al. (2011) · Nucleic Acids Research · doi:10.1093/nar/gkr991 · Cited by 818 · see citing works

FGF stimulation of the Erk1/2 signalling cascade triggers transition of pluripotent embryonic stem cells from self-renewal to lineage commitment

Kunath, T., Saba-El-Leil, M. K., Almosailleakh, M., Wray, J. P., Meloche, S., & Smith, A. G. (2007) · Development · doi:10.1242/dev.02880 · Cited by 785 · see citing works

Next-generation proteomics: towards an integrative view of proteome dynamics

Altelaar, M. A. F., Muñoz, J., & Heck, A. J. R. (2012) · Nature Reviews Genetics · doi:10.1038/nrg3356 · Cited by 776 · see citing works

Improved visualization of protein consensus sequences by iceLogo

Colaert, N., Helsens, K., Martens, L., Vandekerckhove, J. S., & Gevaert, K. (2009) · Nature Methods · doi:10.1038/nmeth1109-786 · Cited by 746 · see citing works

Dynamic stem cell states: Naive to primed pluripotency in rodents and humans

Weinberger, L., Ayyash, M., Novershtern, N., & Hanna, J. H. (2016) · Nature Reviews Molecular Cell Biology · doi:10.1038/nrm.2015.28 · Cited by 622 · see citing works

Critical function of Prdm14 for the establishment of the germ cell lineage in mice

Yamaji, M., Seki, Y., Kurimoto, K., Yabuta, Y., Yuasa, M., Shigeta, M., Yamanaka, K., Ohinata, Y., & Saitou, M. (2008) · Nature Genetics · doi:10.1038/ng.186 · Cited by 592 · see citing works

Negative feedback regulation of the ERK1/2 MAPK pathway

Lake, D., Corrêa, S. A. L., & Müller, J. (2016) · Cellular and Molecular Life Sciences · doi:10.1007/s00018-016-2297-8 · Cited by 565 · see citing works

Cooperative Binding of Transcription Factors Orchestrates Reprogramming

Chronis, C., Fiziev, P., Papp, B., Butz, S., Bonora, G., Sabri, S., Ernst, J., & Plath, K. (2017) · Cell · doi:10.1016/j.cell.2016.12.016 · Cited by 555 · see citing works

Combination of FASP and StageTip-based fractionation allows in-depth analysis of the hippocampal membrane proteome

Wiśniewski, J. R., Zougman, A., & Mann, M. (2009) · Journal of Proteome Research · doi:10.1021/pr900748n · Cited by 545 · see citing works

Direct interaction between DNMT1 and G9a coordinates DNA and histone methylation during replicationPreprint

Estève, P., Chin, H. G., Smallwood, A., Feehery, G. R., Gangisetty, O., Karpf, A. R., Carey, M., & Pradhan, S. (2006) · Genes & Development · doi:10.1101/gad.1463706 · Cited by 539 · see citing works

Dual‐specificity MAP kinase phosphatases (MKPs): Shaping the outcome of MAP kinase signalling

Caunt, C. J., & Keyse, S. M. (2013) · The FEBS Journal · doi:10.1111/j.1742-4658.2012.08716.x · Cited by 535 · see citing works

Methylation of Histone H3 at Lys-9 Is an Early Mark on the X Chromosome during X Inactivation

Heard, É., Rougeulle, C., Arnaud, D., Avner, P. R., Allis, C. D., & Spector, D. L. (2001) · Cell · doi:10.1016/s0092-8674(01)00598-0 · Cited by 513 · see citing works

Reorganization of enhancer patterns in transition from naive to primed pluripotency

Buecker, C., Srinivasan, R., Wu, Z., Calo, E., Acampora, D., Faial, T., Simeone, A., Tan, M., Swigut, T., & Wysocka, J. (2014) · Cell Stem Cell · doi:10.1016/j.stem.2014.04.003 · Cited by 507 · see citing works

Genenames.org: the HGNC resources in 2015

Gray, K. A., Yates, B., Seal, R. L., Wright, M. W., & Bruford, E. A. (2014) · Nucleic Acids Research · doi:10.1093/nar/gku1071 · Cited by 493 · see citing works

Derivation of naïve human embryonic stem cells

Ware, C. B., Nelson, A. M., Mecham, B. H., Hesson, J., Zhou, W., Jonlin, E. C., Jiménez‐Caliani, A. J., Deng, X., Cavanaugh, C., Cook, S. M., et al. (2014) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1319738111 · Cited by 470 · see citing works

Defining the three cell lineages of the human blastocyst by single-cell RNA-seq

Blakeley, P., Fogarty, N. M. E., del Valle, I., Wamaitha, S. E., Hu, T. X., Elder, K. T., Snell, P., Christie, L., Robson, P., & Niakan, K. K. (2015) · Development · doi:10.1242/dev.123547 · Cited by 466 · see citing works

High-throughput phosphoproteomics reveals in vivo insulin signaling dynamics

Humphrey, S. J., Azimifar, S. B., & Mann, M. (2015) · Nature Biotechnology · doi:10.1038/nbt.3327 · Cited by 460 · see citing works

System-wide temporal characterization of the proteome and phosphoproteome of human embryonic stem cell differentiation

Rigbolt, K. T. G., Prokhorova, T. A., Akimov, V., Henningsen, J., Johansen, P. T., Kratchmarova, I., Kassem, M., Mann, M., Olsen, J. V., & Blagoev, B. (2011) · Science Signaling · doi:10.1126/scisignal.2001570 · Cited by 451 · see citing works

Formative pluripotency: the executive phase in a developmental continuum

Smith, A. G. (2017) · Development · doi:10.1242/dev.142679 · Cited by 449 · see citing works

The ability of inner-cell-mass cells to self-renew as embryonic stem cells is acquired following epiblast specification

Boroviak, T., Loos, R., Bertone, P., Smith, A. G., & Nichols, J. (2014) · Nature Cell Biology · doi:10.1038/ncb2965 · Cited by 440 · see citing works

G9a/GLP complexes independently mediate H3K9 and DNA methylation to silence transcription

Tachibana, M., Matsumura, Y., Fukuda, M., Kimura, H., & Shinkai, Y. (2008) · The EMBO Journal · doi:10.1038/emboj.2008.192 · Cited by 431 · see citing works

Lineage-Specific Profiling Delineates the Emergence and Progression of Naive Pluripotency in Mammalian Embryogenesis

Boroviak, T., Loos, R., Lombard, P., Okahara, J., Behr, R., Sasaki, E., Nichols, J., Smith, A. G., & Bertone, P. (2015) · Developmental Cell · doi:10.1016/j.devcel.2015.10.011 · Cited by 421 · see citing works

The role of FGF/Erk signaling in pluripotent cells

Lanner, F., & Rossant, J. (2010) · Development · doi:10.1242/dev.050146 · Cited by 404 · see citing works

Regulatory Principles of Pluripotency: From the Ground State Up

Hackett, J. A., & Surani, M. A. (2014) · Cell stem cell · doi:10.1016/j.stem.2014.09.015 · Cited by 404 · see citing works

Induction of a Human Pluripotent State with Distinct Regulatory Circuitry that Resembles Preimplantation Epiblast

Chan, Y.-S., Göke, J., Ng, J.-H., Lu, X., Gonzales, K. A. U., Tan, C.-P., Tng, W. J., Hong, Z.-Z., Lim, Y. S., & Ng, H. (2013) · Cell stem cell · doi:10.1016/j.stem.2013.11.015 · Cited by 392 · see citing works

Hallmarks of pluripotency

Angeles, A. D. L., Ferrari, F., Xi, R., Fujiwara, Y., Benvenisty, N., Deng, H., Hochedlinger, K., Jaenisch, R., Lee, S., Leitch, H. G., et al. (2015) · Nature · doi:10.1038/nature15515 · Cited by 390 · see citing works

High-throughput and high-sensitivity phosphoproteomics with the EasyPhos platform

Humphrey, S. J., Karayel, Ö., James, D. E., & Mann, M. (2018) · Nature Protocols · doi:10.1038/s41596-018-0014-9 · Cited by 359 · see citing works

Phosphorylation Is a Central Mechanism for Circadian Control of Metabolism and Physiology

Robles, M. S., Humphrey, S. J., & Mann, M. (2016) · Cell Metabolism · doi:10.1016/j.cmet.2016.10.004 · Cited by 355 · see citing works

Exit from Pluripotency Is Gated by Intracellular Redistribution of the bHLH Transcription Factor Tfe3

Betschinger, J., Nichols, J., Dietmann, S., Corrin, P. D., Paddison, P. J., & Smith, A. G. (2013) · Cell · doi:10.1016/j.cell.2013.03.012 · Cited by 335 · see citing works

Phosphorylation Dynamics during Early Differentiation of Human Embryonic Stem Cells

Hoof, D. V., Muñoz, J., Braam, S. R., Pinkse, M. W. H., Linding, R., Heck, A. J. R., Mummery, C. L., & Krijgsveld, J. (2009) · Cell stem cell · doi:10.1016/j.stem.2009.05.021 · Cited by 323 · see citing works

Illuminating the dark phosphoproteome

Needham, E. J., Parker, B. L., Burykin, T., James, D. E., & Humphrey, S. J. (2019) · Science Signaling · doi:10.1126/scisignal.aau8645 · Cited by 322 · see citing works

The Transcriptional and Functional Properties of Mouse Epiblast Stem Cells Resemble the Anterior Primitive Streak

Kojima, Y., Kaufman‐Francis, K., Studdert, J. B., Steiner, K. A., Power, M., Loebel, D. A. F., Jones, V. J., Hor, A. C. C., de Alencastro, G., Logan, G. J., et al. (2013) · Cell stem cell · doi:10.1016/j.stem.2013.09.014 · Cited by 303 · see citing works

AnimalTFDB: a comprehensive animal transcription factor database

Zhang, H., Chen, H., Liu, W., Liu, H., Gong, J., Wang, H., & Guo, A.-Y. (2011) · Nucleic Acids Research · doi:10.1093/nar/gkr965 · Cited by 301 · see citing works

PRDM14 Ensures Naive Pluripotency through Dual Regulation of Signaling and Epigenetic Pathways in Mouse Embryonic Stem Cells

Yamaji, M., Ueda, J., Hayashi, K., Ohta, H., Yabuta, Y., Kurimoto, K., Nakato, R., Yamada, Y., Shirahige, K., & Saitou, M. (2013) · Cell stem cell · doi:10.1016/j.stem.2012.12.012 · Cited by 294 · see citing works

Modular Stop and Go Extraction Tips with Stacked Disks for Parallel and Multidimensional Peptide Fractionation in Proteomics

Ishihama, Y., Rappsilber, J., & Mann, M. (2006) · Journal of Proteome Research · doi:10.1021/pr050385q · Cited by 285 · see citing works

Naive Human Pluripotent Cells Feature a Methylation Landscape Devoid of Blastocyst or Germline Memory

Pastor, W. A., Chen, D., Liu, W., Kim, R., Sahakyan, A., Lukianchikov, A., Plath, K., Jacobsen, S. E., & Clark, A. T. (2016) · Cell stem cell · doi:10.1016/j.stem.2016.01.019 · Cited by 284 · see citing works

Inhibition of mTOR induces a paused pluripotent state

Bulut-Karslioglu, A., Biechele, S., Jin, H., Macrae, T. A., Hejna, M., Gertsenstein, M., Song, J. S., & Ramalho-Santos, M. (2016) · Nature · doi:10.1038/nature20578 · Cited by 283 · see citing works

Tracking the embryonic stem cell transition from ground state pluripotency

Kalkan, T., Olova, N. N., Roode, M., Mulas, C., Lee, H. J., Nett, I. R. E., Marks, H., Walker, R. V., Stunnenberg, H. G., Lilley, K. S., et al. (2017) · Development · doi:10.1242/dev.142711 · Cited by 281 · see citing works

Prolonged Mek1/2 suppression impairs the developmental potential of embryonic stem cells

Choi, J., Huebner, A. J., Clement, K., Walsh, R. M., Savol, A. J., Lin, K., Gu, H., Stefano, B. D., Brumbaugh, J., Kim, S. Y., et al. (2017) · Nature · doi:10.1038/nature23274 · Cited by 272 · see citing works

Phosphoproteomics in the Age of Rapid and Deep Proteome Profiling

Riley, N. M., & Coon, J. J. (2016) · Analytical Chemistry · doi:10.1021/acs.analchem.5b04123 · Cited by 265 · see citing works

New Insights into Early Human Development: Lessons for Stem Cell Derivation and Differentiation

Rossant, J., & Tam, P. (2017) · Cell stem cell · doi:10.1016/j.stem.2016.12.004 · Cited by 251 · see citing works

Pluripotent state transitions coordinate morphogenesis in mouse and human embryos

Shahbazi, M. N., Scialdone, A., Skorupska, N., Weberling, A., Recher, G., Zhu, M., Jędrusik, A., Devito, L., Noli, L., Macaulay, I. C., et al. (2017) · Nature · doi:10.1038/nature24675 · Cited by 249 · see citing works

Integrative Analyses of Human Reprogramming Reveal Dynamic Nature of Induced Pluripotency

Cacchiarelli, D., Trapnell, C., Ziller, M. J., Soumillon, M., Cesana, M., Karnik, R., Donaghey, J., Smith, Z. D., Ratanasirintrawoot, S., Zhang, X., et al. (2015) · Cell · doi:10.1016/j.cell.2015.06.016 · Cited by 228 · see citing works

A draft map of the mouse pluripotent stem cell spatial proteome

Christoforou, A., Mulvey, C. M., Breckels, L. M., Geladaki, A., Hurrell, T., Hayward, P. C., Naake, T., Gatto, L., Viner, R., Arias, A. M., et al. (2016) · Nature Communications · doi:10.1038/ncomms9992 · Cited by 221 · see citing works

Histone-Fold Domain Protein NF-Y Promotes Chromatin Accessibility for Cell Type-Specific Master Transcription Factors

Oldfield, A., Yang, P., Conway, A. E., Cinghu, S., Freudenberg, J., Yellaboina, S., & Jothi, R. (2014) · Molecular Cell · doi:10.1016/j.molcel.2014.07.005 · Cited by 216 · see citing works

Epiblast Stem Cell Subpopulations Represent Mouse Embryos of Distinct Pregastrulation Stages

Han, D., Tàpia, N., Joo, J. Y., Greber, B., Araúzo-Bravo, M. J., Bernemann, C., Ko, K., Wu, G., Stehling, M., Tae, J., et al. (2010) · Cell · doi:10.1016/j.cell.2010.10.015 · Cited by 203 · see citing works

Human embryonic stem cell phosphoproteome revealed by electron transfer dissociation tandem mass spectrometry

Swaney, D. L., Wenger, C. D., Thomson, J. A., & Coon, J. J. (2009) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0811964106 · Cited by 192 · see citing works

Phosphoproteomic Analysis of Human Embryonic Stem Cells

Brill, L. M., Xiong, W., Lee, K., Ficarro, S. B., Crain, A., Xu, Y., Terskikh, A. V., Snyder, E. Y., & Ding, S. (2009) · Cell stem cell · doi:10.1016/j.stem.2009.06.002 · Cited by 189 · see citing works

In Vivo Differentiation Potential of Epiblast Stem Cells Revealed by Chimeric Embryo Formation

Huang, Y., Osorno, R., Tsakiridis, A., & Wilson, V. A. (2012) · Cell Reports · doi:10.1016/j.celrep.2012.10.022 · Cited by 184 · see citing works

Quantitative Dynamics of Chromatin Remodeling during Germ Cell Specification from Mouse Embryonic Stem Cells.

Kurimoto, K., Yabuta, Y., Hayashi, K., Ohta, H., Kiyonari, H., Mitani, T., Moritoki, Y., Kohri, K., Kimura, H., Yamamoto, T., et al. (2015) · Cell Stem Cell · doi:10.1016/j.stem.2015.03.002 · Cited by 182 · see citing works

Comprehensive Cell Surface Protein Profiling Identifies Specific Markers of Human Naive and Primed Pluripotent States

Collier, A. J., Panula, S., Schell, J. P., Chovanec, P., Reyes, Á. P., Sophie Petropoulos, A., Corcoran, A. E., Walker, R. V., Douagi, I., Lanner, F., et al. (2017) · Cell stem cell · doi:10.1016/j.stem.2017.02.014 · Cited by 178 · see citing works

The Impact II, a Very High-Resolution Quadrupole Time-of-Flight Instrument (QTOF) for Deep Shotgun Proteomics *

Beck, S., Michalski, A., Raether, O., Lubeck, M., Kaspar, S., Goedecke, N., Baessmann, C., Hornburg, D., Meier, F., Paron, I., et al. (2015) · Molecular & Cellular Proteomics · doi:10.1074/mcp.m114.047407 · Cited by 176 · see citing works

Dynamic Pluripotent Stem Cell States and Their Applications

Wu, J., & Belmonte, J. C. I. (2015) · Cell stem cell · doi:10.1016/j.stem.2015.10.009 · Cited by 163 · see citing works

Epigenomic Comparison Reveals Activation of “Seed” Enhancers during Transition from Naive to Primed Pluripotency

Factor, D. C., Corradin, O., Zentner, G. E., Saiakhova, A., Song, L., Chenoweth, J. G., McKay, R. D. G., Crawford, G. E., Scacheri, P. C., & Tesar, P. J. (2014) · Cell stem cell · doi:10.1016/j.stem.2014.05.005 · Cited by 159 · see citing works

The pluripotent state in mouse and human

Davidson, K. C., Mason, E. A., & Pera, M. F. (2015) · Development · doi:10.1242/dev.116061 · Cited by 155 · see citing works

The Naive State of Human Pluripotent Stem Cells: A Synthesis of Stem Cell and Preimplantation Embryo Transcriptome Analyses

Huang, K. Y., Maruyama, T., & Fan, G. (2014) · Cell stem cell · doi:10.1016/j.stem.2014.09.014 · Cited by 149 · see citing works

Global Landscape and Regulatory Principles of DNA Methylation Reprogramming for Germ Cell Specification by Mouse Pluripotent Stem Cells.

Shirane, K., Kurimoto, K., Yabuta, Y., Yamaji, M., Satoh, J., Ito, S., Watanabe, A., Hayashi, K., Saitou, M., & Sasaki, H. (2016) · Developmental Cell · doi:10.1016/j.devcel.2016.08.008 · Cited by 120 · see citing works

GRHL2-Dependent Enhancer Switching Maintains a Pluripotent Stem Cell Transcriptional Subnetwork after Exit from Naive Pluripotency

Chen, A. F., Liu, A. J., Krishnakumar, R., Freimer, J. W., DeVeale, B., & Blelloch, R. H. (2018) · Cell stem cell · doi:10.1016/j.stem.2018.06.005 · Cited by 95 · see citing works

Large‐scale identification of proteins expressed in mouse embryonic stem cells

Nagano, K., Taoka, M., Yamauchi, Y., Itagaki, C., Shinkawa, T., Nunomura, K., Okamura, N., Takahashi, N., Izumi, T., & Isobe, T. (2005) · PROTEOMICS · doi:10.1002/pmic.200400990 · Cited by 89 · see citing works

LIN28 phosphorylation by MAPK/ERK couples signalling to the post-transcriptional control of pluripotency

Tsanov, K. M., Pearson, D. S., Wu, Z., Han, A., Triboulet, R., Seligson, M. T., Powers, J. T., Osborne, J. K., Kane, S., Gygi, S. P., et al. (2016) · Nature Cell Biology · doi:10.1038/ncb3453 · Cited by 78 · see citing works

Prospective Isolation of Rare Poised iPSC Intermediates Reveals Principles of Cellular Reprogramming

Schwarz, B. A., Çetinbas, M., Clement, K., Walsh, R. M., Cheloufi, S., Gu, H., Langkabel, J., Kamiya, A., Schorle, H., Meissner, A., et al. (2018) · Cell Stem Cell · doi:10.1016/j.stem.2018.06.013 · Cited by 69 · see citing works

Cripto is essential to capture mouse epiblast stem cell and human embryonic stem cell pluripotency

Fiorenzano, A., Pascale, E., D’Aniello, C., Acampora, D., Bassalert, C., Russo, F., Andolfi, G., Biffoni, M., Francescangeli, F., Zeuner, A., et al. (2016) · Nature Communications · doi:10.1038/ncomms12589 · Cited by 64 · see citing works

Global Phosphoproteome Profiling Reveals Unanticipated Networks Responsive to Cisplatin Treatment of Embryonic Stem Cells

Pines, A., Kelstrup, C. D., Vrouwe, M. G., Puigvert, J. C., Typas, D., Mišovic, B., de Groot, A., von Stechow, L., van de Water, B., Danen, E. H. J., et al. (2011) · Molecular and Cellular Biology · doi:10.1128/mcb.05258-11 · Cited by 61 · see citing works

Pluripotency and Nuclear Reprogramming

Déjosez, M., & Zwaka, T. P. (2012) · Annual Review of Biochemistry · doi:10.1146/annurev-biochem-052709-104948 · Cited by 44 · see citing works

Knowledge-Based Analysis for Detecting Key Signaling Events from Time-Series Phosphoproteomics Data

Yang, P., Zheng, X., Jayaswal, V., Hu, G., Yang, J. Y. H., & Jothi, R. (2015) · PLoS Computational Biology · doi:10.1371/journal.pcbi.1004403 · Cited by 39 · see citing works

Positive-unlabeled ensemble learning for kinase substrate prediction from dynamic phosphoproteomics data

Yang, P., Humphrey, S. J., James, D. E., Yang, J. Y. H., & Jothi, R. (2015) · Bioinformatics · doi:10.1093/bioinformatics/btv550 · Cited by 38 · see citing works

Negative feedback via RSK modulates Erk‐dependent progression from naïve pluripotency

Nett, I. R. E., Mulas, C., Gatto, L., Lilley, K. S., & Smith, A. G. (2018) · EMBO Reports · doi:10.15252/embr.201745642 · Cited by 34 · see citing works

KinasePA: Phosphoproteomics data annotation using hypothesis driven kinase perturbation analysis

Yang, P., Patrick, E., Humphrey, S. J., Ghazanfar, S., James, D. E., Jothi, R., & Yang, J. Y. H. (2016) · PROTEOMICS · doi:10.1002/pmic.201600068 · Cited by 33 · see citing works

Stable Methylation at Promoters Distinguishes Epiblast Stem Cells from Embryonic Stem Cells and the In Vivo Epiblasts

Veillard, A.-C., Marks, H., Bernardo, A. S., Jouneau, L., Laloë, D., Boulanger, L., Kaan, A., Brochard, V., Tosolini, M., Pedersen, R. A., et al. (2014) · Stem Cells and Development · doi:10.1089/scd.2013.0639 · Cited by 33 · see citing works

Large Scale Phosphoproteome Profiles Comprehensive Features of Mouse Embryonic Stem Cells

Li, Q., Xing, X., Chen, T., Li, R.-X., Dai, J., Sheng, Q., Xin, S., Zhu, L., Jin, Y., Pei, G., et al. (2010) · Molecular & Cellular Proteomics · doi:10.1074/mcp.m110.001750 · Cited by 32 · see citing works

Direction pathway analysis of large-scale proteomics data reveals novel features of the insulin action pathway

Yang, P., Patrick, E., Tan, S., Fazakerley, D. J., Burchfield, J. G., Gribben, C., Prior, M. J., James, D. E., & Yang, J. Y. H. (2013) · Bioinformatics · doi:10.1093/bioinformatics/btt616 · Cited by 30 · see citing works

Ensemble deep learning in bioinformatics

Cao, Y., Geddes, T. A., Yang, J. Y. H., & Yang, P. (2020) · Nature Machine Intelligence · doi:10.1038/s42256-020-0217-y · Cited by 357 · see citing works

H3K18 lactylation marks tissue-specific active enhancers

Galle, E., Wong, C.-W., Ghosh, A., Desgeorges, T., Melrose, K., Hinte, L. C., Castellano‐Castillo, D., Engl, M., de Sousa, J. A., Ruiz‐Ojeda, F. J., et al. (2022) · Genome biology · doi:10.1186/s13059-022-02775-y · Cited by 242 · see citing works

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

Yu, L., Wei, Y., Sun, H., Mahdi, A. K., Pinzon-Arteaga, C., Sakurai, M., Schmitz, D. A., Zheng, C.-B., Ballard, E. D., Li, J., et al. (2020) · Cell Stem Cell · doi:10.1016/j.stem.2020.11.003 · Cited by 166 · see citing works

Applications of transformer-based language models in bioinformatics: a survey

Zhang, S., Fan, R., Liu, Y., Chen, S., Liu, Q., & Zeng, W. (2023) · Bioinformatics Advances · doi:10.1093/bioadv/vbad001 · Cited by 176 · see citing works

Decoding the function of bivalent chromatin in development and cancerPreprint

Kumar, D., Cinghu, S., Oldfield, A., Yang, P., & Jothi, R. (2021) · Genome Research · doi:10.1101/gr.275736.121 · Cited by 139 · see citing works

PhosR Enables Processing and Functional Analysis of Phosphoproteomic Data

Kim, H. J., Kim, T.-Y., Hoffman, N. J., Xiao, D., James, D. E., Humphrey, S. J., & Yang, P. (2020) · Cell Reports · doi:10.1016/j.celrep.2021.108771 · Cited by 120 · see citing works

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

Wang, X., Xiang, Y., Yu, Y., Wang, R., Zhang, Y., Xu, Q., Sun, H., Zhao, Z., Jiang, X., Wang, X., et al. (2021) · Cell Research · doi:10.1038/s41422-021-00477-x · Cited by 101 · see citing works

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

Thomas, H. F., Kotova, E., Jayaram, S., Pilz, A., Romeike, M., Lackner, A., Penz, T., Bock, C., Leeb, M., Halbritter, F., et al. (2021) · Molecular Cell · doi:10.1016/j.molcel.2020.12.047 · Cited by 98 · see citing works

Personalized phosphoproteomics identifies functional signaling

Needham, E. J., Hingst, J. R., Parker, B. L., Morrison, K. R., Yang, G., Onslev, J., Kristensen, J. M., Højlund, K., Ling, N. X. Y., Oakhill, J. S., et al. (2021) · Nature Biotechnology · doi:10.1038/s41587-021-01099-9 · Cited by 98 · see citing works

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

Fazakerley, D. J., van Gerwen, J., Cooke, K. C., Duan, X., Needham, E. J., Díaz‐Vegas, A., Madsen, S., Norris, D. M., Shun-Shion, A. S., Krycer, J. R., et al. (2023) · Nature Communications · doi:10.1038/s41467-023-36549-2 · Cited by 80 · see citing works

Abscission Couples Cell Division to Embryonic Stem Cell Fate

Chaigne, A., Labouesse, C., White, I. J., Agnew, M., Hannezo, É., Chalut, K. J., & Paluch, E. K. (2020) · Developmental Cell · doi:10.1016/j.devcel.2020.09.001 · Cited by 67 · see citing works

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

Glancy, E., Wang, C., Tuck, E., Healy, E., Amato, S., Neikes, H. K., Mariani, A., Mucha, M., Vermeulen, M., Pasini, D., et al. (2023) · Molecular Cell · doi:10.1016/j.molcel.2023.03.018 · Cited by 71 · see citing works

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

Antonović, M., Feng, S., Haslhofer, F., Huber, M., Gallardo, M. G., Loubiere, V., Vanina, D., Pitasi, M., Stark, A., & Buecker, C. (2024) · Molecular Cell · doi:10.1016/j.molcel.2024.11.008 · Cited by 50 · see citing works

Global phosphoproteomics reveals DYRK1A regulates CDK1 activity in glioblastoma cells

Recasens, A., Humphrey, S. J., Ellis, M., Hoque, M., Abbassi, R. H., Chen, B., Longworth, M., Needham, E. J., James, D. E., Johns, T. G., et al. (2021) · Cell Death Discovery · doi:10.1038/s41420-021-00456-6 · Cited by 52 · see citing works

Enhancer-associated H3K4 methylation safeguards in vitro germline competence

Bleckwehl, T., Crispatzu, G., Schaaf, K., Respuela, P., Bartusel, M., Benson, L., Clark, S. J., Dorighi, K. M., Barral, A., Laugsch, M., et al. (2021) · Nature Communications · doi:10.1038/s41467-021-26065-6 · Cited by 39 · see citing works

Multi-omics profiling visualizes dynamics of cardiac development and functions

Gu, Y., Zhou, Y., Ju, S., Liu, X., Zhang, Z., Guo, J., Gao, J., Zang, J., Sun, H., Chen, Q., et al. (2022) · Cell Reports · doi:10.1016/j.celrep.2022.111891 · Cited by 49 · see citing works

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

Quarto, G., Li Greci, A., Bizet, M., Penning, A., Primac, I., Murisier, F., Garcia-Martinez, L., Borges, R. L., Gao, Q., Cingaram, P. K. R., et al. (2025) · Cell · doi:10.1016/j.cell.2024.12.009 · Cited by 50 · see citing works

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

Luque, A. V., Savill, R. G., López-Anguita, N., Bolondi, A., Garai, S., Gassaloglu, S. I., Rouatbi, R., Schmeißer, K., Poddar, A., Bauer, L., et al. (2025) · Cell stem cell · doi:10.1016/j.stem.2025.03.012 · Cited by 48 · see citing works

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

Moutsopoulos, I., Maischak, L., Lauzikaite, E., Urbina, S. A. V., Williams, E. C., Drost, H., & Mohorianu, I. I. (2021) · Nucleic Acids Research · doi:10.1093/nar/gkab433 · Cited by 45 · see citing works

Esrrb guides naive pluripotent cells through the formative transcriptional programme

Carbognin, E., Carlini, V., Panariello, F., Chieregato, M., Guerzoni, E., Benvegnù, D., Perrera, V., Malucelli, C., Cesana, M., Grimaldi, A., et al. (2023) · Nature Cell Biology · doi:10.1038/s41556-023-01131-x · Cited by 37 · 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

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

Zhang, H., Ji, S., Zhang, K., Chen, Y., Ming, J., Kong, F., Wang, L., Wang, S., Zou, Z., Xiong, Z., et al. (2023) · Genome biology · doi:10.1186/s13059-023-02997-8 · Cited by 38 · see citing works

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

Divisato, G., Passaro, F., Russo, T., & Parisi, S. (2020) · International Journal of Molecular Sciences · doi:10.3390/ijms21176285 · Cited by 37 · see citing works

Computational Stem Cell Biology: Open Questions and Guiding Principles

Cahan, P., Cacchiarelli, D., Dunn, S.-J., Hemberg, M., Lopes, S. M. C. D. S., Morris, S. A., Rackham, O. J. L., del Sol, A., & Wells, C. A. (2021) · Cell stem cell · doi:10.1016/j.stem.2020.12.012 · Cited by 36 · see citing works

RNA polymerase II pausing in development: orchestrating transcription

Abuhashem, A., Garg, V., & Hadjantonakis, A. (2022) · Open Biology · doi:10.1098/rsob.210220 · Cited by 36 · see citing works

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

Needham, E. J., Humphrey, S. J., Cooke, K. C., Fazakerley, D. J., Duan, X., Parker, B. L., & James, D. E. (2019) · Cell Reports · doi:10.1016/j.celrep.2019.10.001 · Cited by 33 · see citing works

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

Yu, H., Wang, J., Lackford, B. L., Bennett, B. D., Li, J., & Hu, G. (2021) · Nucleic Acids Research · doi:10.1093/nar/gkab476 · Cited by 34 · see citing works

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

Boileau, R. M., Chen, K. X., & Blelloch, R. H. (2023) · Genome biology · doi:10.1186/s13059-023-02883-3 · Cited by 33 · see citing works

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

Pogatzki-Zahn, E. M., Gómez‐Varela, D., Erdmann, G., Kaschube, K., Segelcke, D., & Schmidt, M. (2021) · Pain · doi:10.1097/j.pain.0000000000002207 · Cited by 30 · see citing works

Cardiopoietic stem cell therapy restores infarction-altered cardiac proteome

Arrell, D. K., Rosenow, C. S., Yamada, S., Behfar, A., & Terzic, A. (2020) · npj Regenerative Medicine · doi:10.1038/s41536-020-0091-6 · Cited by 30 · see citing works

Stirred suspension bioreactors maintain naïve pluripotency of human pluripotent stem cells

Rohani, L., Borys, B. S., Razian, G., Naghsh, P., Liu, S., Johnson, A. A., Machiraju, P., Holland, H., Lewis, I. A., Groves, R. A., et al. (2020) · Communications Biology · doi:10.1038/s42003-020-01218-3 · Cited by 31 · see citing works

Dissection of two routes to naïve pluripotency using different kinase inhibitors

Martínez‐Val, A., Lynch, C. J., Calvo, I., Ximénez‐Embún, P., Garcı́a, F., Zarzuela, E., Serrano, M., & Muñoz, J. (2021) · Nature Communications · doi:10.1038/s41467-021-22181-5 · Cited by 26 · see citing works

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

Duan, X., Norris, D. M., Humphrey, S. J., Yang, P., Cooke, K. C., Bultitude, W. P., Parker, B. L., Conway, O. J., Burchfield, J. G., Krycer, J. R., et al. (2022) · Biochemical Journal · doi:10.1042/bcj20220153 · Cited by 22 · see citing works

Molecular versatility during pluripotency progression

Furlan, G., Huyghe, A., Combémorel, N., & Lavial, F. (2023) · Nature Communications · doi:10.1038/s41467-022-35775-4 · Cited by 18 · see citing works

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

Norris, D. M., Yang, P., Shin, S., Kearney, A. L., Kim, H. J., Geddes, T. A., Senior, A. M., Fazakerley, D. J., Nguyen, L. K., James, D. E., et al. (2021) · iScience · doi:10.1016/j.isci.2021.102118 · Cited by 19 · see citing works

RNA Pol II pausing facilitates phased pluripotency transitions by buffering transcriptionPreprint

Abuhashem, A., Chivu, A. G., Zhao, Y., Rice, E. J., Siepel, A. C., Danko, C. G., & Hadjantonakis, A. (2022) · Genes & Development · doi:10.1101/gad.349565.122 · Cited by 22 · see citing works

FoxO transcription factors actuate the formative pluripotency specific gene expression programme

Santini, L., Kowald, S., Cerron-Alvan, L. M., Huth, M., Fabing, A. P., Sestini, G., Rivron, N. C., & Leeb, M. (2024) · Nature Communications · doi:10.1038/s41467-024-51794-9 · Cited by 21 · see citing works

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

Arekatla, G., Trenzinger, C., Reimann, A., Loeffler, D., Kull, T., & Schroeder, T. (2023) · Developmental Cell · doi:10.1016/j.devcel.2023.04.013 · Cited by 21 · see citing works

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

Amiri, M., Kiniry, S. J., Possemato, A., Mahmood, N., Basiri, T., Dufour, C., Tabatabaei, N., Deng, Q., Bellucci, M. A., Harwalkar, K., et al. (2023) · Cell Reports · doi:10.1016/j.celrep.2023.113615 · Cited by 13 · see citing works

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

Sangokoya, C., & Blelloch, R. H. (2020) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.2002750117 · Cited by 20 · see citing works

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

Moutsopoulos, I., Williams, E. C., & Mohorianu, I. I. (2022) · Briefings in Bioinformatics · doi:10.1093/bib/bbac591 · Cited by 19 · see citing works

Three-dimensional geometry controls division symmetry in stem cell colonies

Chaigne, A., Smith, M. B., Cavestany, R. L., Hannezo, É., Chalut, K. J., & Paluch, E. K. (2021) · Journal of Cell Science · doi:10.1242/jcs.255018 · Cited by 17 · see citing works

Progression of the pluripotent epiblast depends upon the NMD factor UPF2

Chousal, J. N., Sohni, A., Vitting‐Seerup, K., Cho, K., Kim, M., Tan, K., Porse, B. T., Wilkinson, M., & Cook‐Andersen, H. (2022) · Development · doi:10.1242/dev.200764 · Cited by 18 · see citing works

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

Díaz‐Vegas, A., Norris, D. M., Jall-Rogg, S., Cooke, K. C., Conway, O. J., Shun-Shion, A. S., Duan, X., Potter, M., van Gerwen, J., Baird, H. J. M., et al. (2022) · Life Science Alliance · doi:10.26508/lsa.202201585 · Cited by 17 · see citing works

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

Goodwin, J., Laslett, A. L., & Rugg‐Gunn, P. J. (2019) · Experimental Cell Research · doi:10.1016/j.yexcr.2019.111749 · Cited by 18 · see citing works

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

Qin, W., Ugur, E., Mulholland, C. B., Bultmann, S., Solovei, I. V., Modic, M., Smets, M., Wierer, M., Forné, I., Imhof, A., et al. (2021) · Nucleic Acids Research · doi:10.1093/nar/gkab548 · Cited by 18 · see citing works

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

Kim, H. J., Osteil, P., Humphrey, S. J., Cinghu, S., Oldfield, A., Patrick, E., Wilkie, E. E., Peng, G., Suo, S., Jothi, R., et al. (2019) · Nucleic Acids Research · doi:10.1093/nar/gkz1179 · Cited by 17 · see citing works

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

Kaur, S., Peters, T. J., Yang, P., Luu, L. D. W., Vuong, J., Krycer, J. R., & O’Donoghue, S. I. (2020) · npj Systems Biology and Applications · doi:10.1038/s41540-020-0141-0 · Cited by 15 · see citing works

Metabolic characterization of a paused-like pluripotent state

Sousa, M. I., Correia, B., Rodrigues, A. S., & Ramalho‐Santos, J. (2020) · Biochimica et Biophysica Acta (BBA) - General Subjects · doi:10.1016/j.bbagen.2020.129612 · Cited by 16 · see citing works

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

Pecori, F., Yokota, I., Hanamatsu, H., Miura, T., Ogura, C., Ota, H., Furukawa, J., Oki, S., Yamamoto, K., Yoshie, O., et al. (2021) · Scientific Reports · doi:10.1038/s41598-020-79666-4 · Cited by 17 · see citing works

Unraveling the Spatiotemporal Human Pluripotency in Embryonic Development

Ávila‐González, D., Portillo, W., Garcı́a-López, G., Molina‐Hernández, A., Diaz-Martinez, N. E., & Díaz, N. F. (2021) · Frontiers in Cell and Developmental Biology · doi:10.3389/fcell.2021.676998 · Cited by 15 · see citing works

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

Krumm, J., Sekine, K., Samaras, P., Brazovskaja, A., Breunig, M., Yasui, R., Kleger, A., Taniguchi, H., Wilhelm, M., Treutlein, B., et al. (2022) · Cell Reports · doi:10.1016/j.celrep.2022.110604 · Cited by 15 · see citing works

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 · see citing works

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

Ugur, E., de la Porte, A., Qin, W., Bultmann, S., Ivanova, A., Drukker, M., Mann, M., Wierer, M., & Leonhardt, H. (2023) · Nucleic Acids Research · doi:10.1093/nar/gkad058 · Cited by 13 · see citing works

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 13 · see citing works

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

Yuan, F., Yang, J.-H., Ma, F., Hu, Z., Malik, V., Zang, R., Li, D., Shi, X., Huang, X., Zhou, H.-W., et al. (2025) · Nature Communications · doi:10.1038/s41467-025-57165-2 · Cited by 12 · see citing works

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 · see citing works

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 · see citing works

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 · see citing works

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 · see citing works

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 · see citing works

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 · see citing works

Transcriptional and epigenetic control of germline competence and specification.

Bleckwehl, T., & Rada-Iglesias, Á. (2019) · Current Opinion in Cell Biology · doi:10.1016/j.ceb.2019.05.006 · Cited by 10 · see citing works

Combinatorial metabolism drives the naive to primed pluripotent chromatin landscape

Ehnes, D. D., Hussein, A. M., Ware, C. B., Mathieu, J., & Ruohola‐Baker, H. (2020) · Experimental Cell Research · doi:10.1016/j.yexcr.2020.111913 · Cited by 10 · see citing works

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 10 · see citing works

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 · see citing works

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

Movasat, H., Giacopino, E., Shahdoost, A., Nokoorani, Y. D., Abrbekouh, A. H., Tahamtani, Y., & Shakiba, N. (2025) · Cell Systems · doi:10.1016/j.cels.2025.101300 · Cited by 14 · see citing works

A Review of Complex Systems Approaches to Cancer Networks

Uthamacumaran, A. (2020) · Complex Systems · doi:10.25088/complexsystems.29.4.779 · Cited by 9 · see citing works

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 9 · see citing works

Modeling the early development of a primate embryo

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

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 · see citing works

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

Waisman, A., Sevlever, F., Saulnier, D., Francia, M. G., Blanco, R., Amín, G., Lombardi, A., Biani, C., Palma, M. B., Scarafía, A., et al. (2024) · Scientific Reports · doi:10.1038/s41598-024-59247-5 · Cited by 8 · see citing works

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 · see citing works

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

Xiao, D., Caldow, M. K., Kim, H. J., Blazev, R., Koopman, R., Manandi, D., Parker, B. L., & Yang, P. (2022) · iScience · doi:10.1016/j.isci.2022.104489 · Cited by 8 · see citing works

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 · see citing works

Integrative analysis reveals histone demethylase LSD1 promotes RNA polymerase II pausing

Kim, H. J., Li, P., Kim, T.-Y., Oldfield, A., Zheng, X., & Yang, P. (2022) · iScience · doi:10.1016/j.isci.2022.105049 · Cited by 7 · see citing works

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

Franciosa, G., Nieddu, V., Battistini, C., Caffarini, M., Lupia, M., Colombo, N., Fusco, N., Olsen, J. V., & Cavallaro, U. (2025) · Molecular & Cellular Proteomics · doi:10.1016/j.mcpro.2025.100965 · Cited by 7 · see citing works

The ETS transcription factor ERF controls the exit from the naïve pluripotent state in a MAPK-dependent manner

Vega-Sendino, M., Olbrich, T., Tillo, D., Tran, A. D., Domingo, C. N., Franco, M., FitzGerald, P. C., Kruhlak, M. J., & Ruiz, S. (2021) · Science Advances · doi:10.1126/sciadv.abg8306 · Cited by 7 · see citing works

Culture of Neurospheres Derived from the Neurogenic Niches in Adult Prairie Voles

Ávila‐González, D., Young, L. J., Camacho, F., Paredes, R. G., Díaz, N. F., & Portillo, W. (2020) · Journal of Visualized Experiments · doi:10.3791/61402 · Cited by 7 · see citing works

SRRM2 splicing factor modulates cell fate in early development

Carvalho, S., Zea-Redondo, L., Tang, T. C. C., Stachel-Braum, P., Miller, D. C., Caldas, P., Kukalev, A., Diecke, S., Grosswendt, S., Grosso, A. R., et al. (2024) · Biology Open · doi:10.1242/bio.060415 · Cited by 6 · see citing works

Postmitotic transcription and 3D regulation show locus-specific and differentiation-specific sensitivity to cohesin depletion

Lee, U., Laguillo-Diego, A., Magliulo, D., Wong, W., Kasliwal, K., Ni, Z., Cheng, L., Li, J., Pelham‐Webb, B., Pertsinidis, A., et al. (2026) · Nature Genetics · doi:10.1038/s41588-026-02556-4 · Cited by 9 · see citing works

SnapKin: a snapshot deep learning ensemble for kinase-substrate prediction from phosphoproteomics data

Xiao, D., Lin, M., Liu, C., Geddes, T. A., Burchfield, J. G., Parker, B. L., Humphrey, S. J., & Yang, P. (2023) · NAR Genomics and Bioinformatics · doi:10.1093/nargab/lqad099 · Cited by 5 · see citing works

Proteomic analysis of B cells in peripheral lymphatic system reveals the dynamics during the systemic lupus erythematosus progression

Sun, L., Yin, Y., Cao, Y., Chen, C., Guo, Y., Cai, Z., Wu, J., & Li, Q. (2024) · Biophysics Reports · doi:10.52601/bpr.2024.240045 · Cited by 5 · see citing works

AMPK activation by glycogen expenditure primes the exit of naïve pluripotency

Kim, S.-M., Kwon, E., Oh, J., Kim, H. S., Park, S., Jang, G., Tae, J., Kim, K.-T., & Cha, H. (2025) · EMBO Reports · doi:10.1038/s44319-025-00384-x · Cited by 6 · see citing works

Bivalent chromatin protects reversibly repressed genes from irreversible silencingPreprint

Kumar, D., & Jothi, R. (2020) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2020.12.02.406751 · Cited by 6 · see citing works

MLL3/MLL4 enzymatic activity shapes DNA replication timingPreprint

Gökbuget, D., Boileau, R. M., Lenshoek, K., & Blelloch, R. H. (2023) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2023.12.07.569680 · Cited by 5 · see citing works

Non-catalytic role for MLL2 in controlling chromatin organisation and mobility during priming of pluripotent cells for differentiationPreprint

Steindel, M., Davis, O., Neumann, K., Agsu, G. G., Mao, L., Kranz, A., Pirvan, L., Adhya, D., Morf, J., Zhang, Z., et al. (2025) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2025.02.21.639010 · Cited by 5 · see citing works

RNA Degradation in Pluripotent Stem Cells: Mechanisms, Crosstalk, and Fate Regulation

Jeong, S., Oh, M., Han, J., & Kim, S.-K. (2025) · Cells · doi:10.3390/cells14201634 · Cited by 4 · see citing works

The dynamical organization of the core pluripotency transcription factors responds to differentiation cues in early S-phase

Oses, C., Francia, M. G., Verneri, P., Echegaray, C. V., Guberman, A., & Levi, V. (2023) · Frontiers in Cell and Developmental Biology · doi:10.3389/fcell.2023.1125015 · 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

The human amniotic epithelium confers a bias to differentiate toward the neuroectoderm lineage in human embryonic stem cells

Ávila‐González, D., Portillo, W., Barragán-Álvarez, C. P., Hernández‐Montes, G., Flores-Garza, E., Molina‐Hernández, A., Diaz-Martinez, N. E., & Díaz, N. F. (2022) · eLife · doi:10.7554/elife.68035 · Cited by 4 · see citing works

Human amnion-derived mesenchymal stem cells attenuate acute lung injury in two different acute lung injury mice models

Wu, Y., Sun, H., Qin, L., Zhang, X., Zhou, H., Wang, Y., Wang, L., Li, M., Liu, J., & Zhang, J. (2023) · Frontiers in Pharmacology · doi:10.3389/fphar.2023.1149659 · Cited by 4 · see citing works

Multi-omics reveals an ecdysone-activated Eip75B-FABP signaling axis coordinating nutrient metabolism for development in Hermetia illucens

Dong, M., Zhang, Z., Li, Z., Yan, T., Henawy, A. R., Meng, Y., Li, Y. H., Li, M., Huang, F., Cai, M., et al. (2025) · Journal of Advanced Research · doi:10.1016/j.jare.2025.12.018 · Cited by 4 · see citing works

The FIRE biosensor illuminates iron regulatory protein activity and cellular iron homeostasis

Sangokoya, C. (2025) · Cell Reports Methods · doi:10.1016/j.crmeth.2024.100960 · Cited by 3 · see citing works

Small molecule- and cell contact-inducible systems for controlling expression and differentiation in mouse embryonic stem cells

Soliman, S. S., Shah, D. H., El‐Samad, H., & Weinberg, Z. Y. (2025) · Development · doi:10.1242/dev.204505 · Cited by 3 · see citing works

Ubiquitin Dynamics in Stem Cell Biology: Current Challenges and Perspectives

de Dieuleveult, M., & Miotto, B. (2020) · BioEssays · doi:10.1002/bies.201900129 · Cited by 2 · see citing works

Homocysteine impedes neurite outgrowth recovery after intracerebral haemorrhage by downregulating pCAMK2A

Guo, G., Yang, J., Guo, W., Deng, H., Yu, H., Bai, S., Li, G., Tang, Y., Ping, Z., Xu, Y., et al. (2023) · Stroke and Vascular Neurology · doi:10.1136/svn-2022-002165 · Cited by 3 · see citing works

Parallel Genome-Wide CRISPR Screens to Identify State-Dependent Self-Renewal Regulators of Mouse Embryonic Stem Cells

Wang, J., Zhang, C., Huang, Y., Ruan, Y., Yan, H., Wang, J., Wang, F., Yu, M., Xu, Y., Liu, L., et al. (2023) · Stem Cells and Development · doi:10.1089/scd.2023.0053 · Cited by 3 · see citing works

AKT1 induces Nanog promoter in a SUMOylation-dependent manner in different pluripotent contexts

Francia, M. G., Verneri, P., Oses, C., Echegaray, C. V., García, M. R., Toro, A. R., Levi, V., & Guberman, A. (2023) · BMC Research Notes · doi:10.1186/s13104-023-06598-3 · Cited by 3 · see citing works

ZFP982 confers mouse embryonic stem cell characteristics by regulating expression of Nanog, Zfp42, and Dppa3

Dehghanian, F., Bovio, P. P., Gather, F., Probst, S., Nilchi, A. N., & Vogel, T. (2024) · Biochimica et Biophysica Acta (BBA) - Molecular Cell Research · doi:10.1016/j.bbamcr.2024.119686 · Cited by 3 · see citing works

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 · see citing works

Crosstalk between Signaling Pathways and Energy Metabolism in Pluripotency

Kim, K.-T., Kim, S.-M., & Cha, H. (2024) · International Journal of Stem Cells · doi:10.15283/ijsc23173 · Cited by 8 · see citing works

The exploration of pluripotency space: Charting cell state transitions in peri-implantation development

Pera, M. F., & Rossant, J. (2021) · Cell stem cell · doi:10.1016/j.stem.2021.10.001 · Cited by 86 · see citing works

Epigenetic Regulation of Transition Among Different Pluripotent States: Concise Review

Geng, T., Zhang, D.-H., & Jiang, W. (2019) · Stem Cells · doi:10.1002/stem.3064 · Cited by 26 · see citing works

Pluripotency genes of mammals: a network at work

Cancedda, R., & Mastrogiacomo, M. (2025) · Frontiers in Bioengineering and Biotechnology · doi:10.3389/fbioe.2025.1578499 · Cited by 5 · see citing works