A single-embryo, single-cell time-resolved model for mouse gastrulation
Open accessAbstract
Mouse embryonic development is a canonical model system for studying mammalian cell fate acquisition. Recently, single-cell atlases comprehensively charted embryonic transcriptional landscapes, yet inference of the coordinated dynamics of cells over such atlases remains challenging. Here, we introduce a temporal model for mouse gastrulation, consisting of data from 153 individually sampled embryos spanning 36 h of molecular diversification. Using algorithms and precise timing, we infer differentiation flows and lineage specification dynamics over the embryonic transcriptional manifold. Rapid transcriptional bifurcations characterize the commitment of early specialized node and blood cells. However, for most lineages, we observe combinatorial multi-furcation dynamics rather than hierarchical transcriptional transitions. In the mesoderm, dozens of transcription factors combinatorially regulate multifurcations, as we exemplify using time-matched chimeric embryos of Foxc1/Foxc2 mutants. Our study rejects the notion of differentiation being governed by a series of binary choices, providing an alternative quantitative model for cell fate acquisition.
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Cell fate choice involves a more distributed form of control relying on combinatorial activities of dozens of TFs rather than an organization strictly dominated by a few master TFs.
“recent insights into the understanding of cell fate choice, which have suggested a more distributed form of control relying on combinatorial activities of dozens of TFs rather than an organization strictly dominated by a few master TFs (Chubb et al, 2021; Mittnenzweig et al, 2021).”
From An extended transcription factor regulatory network controls hepatocyte identity (2023) · cites this paper as Mittnenzweig et al, 2021
The Results section, “Evidence for combinatorial regulation of mesodermal multifurcation,” supports combinatorial involvement of many TFs in mouse mesodermal fate transitions and analyzes 63 variably expressed TFs. It also allows that master-regulator cascades can drive differentiation of specialized cell types. The claim extends the mesoderm finding to cell fate choice generally and treats dozens of TFs as active regulators, which the analysis does not establish. (LLM, conf=0.83)
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Cites
Network Flows: Theory, Algorithms, and Applications.
Smith, D. K., Ahuja, R. K., Magnanti, T. L., & Orlin, J. B. (1994) · Journal of the Operational Research Society · doi:10.2307/2583863 · Cited by 8,121 · see citing works
The single-cell transcriptional landscape of mammalian organogenesis
Cao, J., Spielmann, M., Qiu, X., Huang, X., Ibrahim, D. M., Hill, A. J., Zhang, F., Mundlos, S., Christiansen, L., Steemers, F. J., et al. (2019) · Nature · doi:10.1038/s41586-019-0969-x · Cited by 4,490 · see citing works
La Manno, G., Soldatov, R., Zeisel, A., Braun, E., Hochgerner, H., Petukhov, V., Lidschreiber, K., Kastriti, M. E., Lönnerberg, P., Furlan, A., et al. (2018) · Nature · doi:10.1038/s41586-018-0414-6 · Cited by 4,118 · see citing works
Ben‐Porath, I., Thomson, M., Carey, V. J., Ge, R., Bell, G. W., Regev, A., & Weinberg, R. A. (2008) · Nature Genetics · doi:10.1038/ng.127 · Cited by 2,523 · 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
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
Massively parallel single-cell RNA-seq for marker-free decomposition of tissues into cell types
Jaitin, D. A., Kenigsberg, E., Keren-Shaul, H., Elefant, N., Paul, F., Zaretsky, I., Mildner, A., Cohen, N., Jung, S., Tanay, A., et al. (2014) · Science · doi:10.1126/science.1247651 · Cited by 1,795 · see citing works
Self-citationMapping the Mouse Cell Atlas by Microwell-Seq
Han, X., Wang, R., Zhou, Y., Fei, L., Sun, H., Lai, S., Saadatpour, A., Zhou, Z., Chen, H., Ye, F., et al. (2018) · Cell · doi:10.1016/j.cell.2018.02.001 · Cited by 1,597 · see citing works
CCTop: An intuitive, flexible and reliable CRISPR/Cas9 target prediction tool
Stemmer, M., Thumberger, T., del Sol Keyer, M., Wittbrodt, J., & Mateo, J. L. (2015) · PLoS ONE · doi:10.1371/journal.pone.0124633 · Cited by 1,088 · see citing works
Development of erythroid and myeloid progenitors in the yolk sac and embryo proper of the mouse
Palis, J., Robertson, S. M., Kennedy, M., Wall, C., & Keller, G. M. (1999) · Development · doi:10.1242/dev.126.22.5073 · Cited by 1,050 · see citing works
A single-cell molecular map of mouse gastrulation and early organogenesis
Pijuan-Sala, B., Griffiths, J. A., Guibentif, C., Hiscock, T. W., Jawaid, W., Calero-Nieto, F. J., Mulas, C., Ibarra-Soria, X., Tyser, R. C. V., Ho, D. L. L., et al. (2019) · Nature · doi:10.1038/s41586-019-0933-9 · Cited by 1,033 · see citing works
McMahon, J. A., Takada, S., Zimmerman, L. B., Fan, C., Harland, R. M., & McMahon, A. P. (1998) · Genes & Development · doi:10.1101/gad.12.10.1438 · Cited by 844 · see citing works
Schiebinger, G., Shu, J., Tabaka, M., Cleary, B., Subramanian, V., Solomon, A., Gould, J., Liu, S., Lin, S., Berube, P., et al. (2019) · Cell · doi:10.1016/j.cell.2019.01.006 · Cited by 829 · see citing works
Making a commitment: cell lineage allocation and axis patterning in the early mouse embryo
Arnold, S. J., & Robertson, E. J. (2009) · Nature Reviews Molecular Cell Biology · doi:10.1038/nrm2618 · Cited by 816 · see citing works
Scaling single-cell genomics from phenomenology to mechanism
Tanay, A., & Regev, A. (2017) · Nature · doi:10.1038/nature21350 · Cited by 792 · see citing works
Self-citationHaemangioblast commitment is initiated in the primitive streak of the mouse embryo
Huber, T. L., Kouskoff, V., Fehling, H. J., Palis, J., & Keller, G. M. (2004) · Nature · doi:10.1038/nature03122 · Cited by 697 · see citing works
The House Mouse: Atlas of Embryonic Development
Theiler, K., & Westphal, H. (1972) · Medical Entomology and Zoology · Cited by 680 · see citing works
Blastocyst lineage formation, early embryonic asymmetries and axis patterning in the mouse
Rossant, J., & Tam, P. (2009) · Development · doi:10.1242/dev.017178 · Cited by 629 · see citing works
Simultaneous single-cell profiling of lineages and cell types in the vertebrate brain
Raj, B., Wagner, D. E., McKenna, A., Pandey, S., Klein, A. M., Shendure, J., Gagnon, J. A., & Schier, A. F. (2018) · Nature Biotechnology · doi:10.1038/nbt.4103 · Cited by 622 · see citing works
Correction of a genetic disease in mouse via use of CRISPR-Cas9
Wu, Y., Liang, D., Wang, Y., Bai, M., Tang, W., Bao, S., Yan, Z., Li, D., & Li, J. (2013) · Cell stem cell · doi:10.1016/j.stem.2013.10.016 · Cited by 614 · see citing works
Mouse gastrulation: the formation of a mammalian body plan
Tam, P., & Behringer, R. R. (1997) · Mechanisms of Development · doi:10.1016/s0925-4773(97)00123-8 · Cited by 612 · see citing works
Staging of gastrulating mouse embryos by morphological landmarks in the dissecting microscope
Downs, K. M., & Davies, T. J. (1993) · Development · doi:10.1242/dev.118.4.1255 · Cited by 582 · see citing works
Nodal Flow and the Generation of Left-Right Asymmetry
Hirokawa, N., Tanaka, Y., Okada, Y., & Takeda, S. (2006) · Cell · doi:10.1016/j.cell.2006.03.002 · Cited by 576 · see citing works
Simultaneous lineage tracing and cell-type identification using CRISPR–Cas9-induced genetic scars
Spanjaard, B., Hu, B., Mitic, N., Olivares-Chauvet, P., Janjuha, S., Ninov, N., & Junker, J. P. (2018) · Nature Biotechnology · doi:10.1038/nbt.4124 · Cited by 531 · see citing works
Multi-omics profiling of mouse gastrulation at single-cell resolution
Argelaguet, R., Clark, S. J., Mohammed, H., Stapel, L. C., Krueger, C., Kapourani, C.-A., Imaz-Rosshandler, I., Lohoff, T., Xiang, Y., Hanna, C. W., et al. (2019) · Nature · doi:10.1038/s41586-019-1825-8 · Cited by 450 · see citing works
Perea-Gomez, A., Vella, F., Shawlot, W., Oulad-Abdelghani, M., Chazaud, C., Meno, C., Pfister, V., Chen, L., Robertson, E., Hamada, H., et al. (2002) · Developmental Cell · doi:10.1016/s1534-5807(02)00321-0 · Cited by 410 · see citing works
MetaCell: analysis of single-cell RNA-seq data using K-nn graph partitions
Baran, Y., Bercovich, A., Sebé-Pedrós, A., Lubling, Y., Giladi, A., Chomsky, E., Meir, Z., Hoichman, M., Lifshitz, A., & Tanay, A. (2019) · Genome biology · doi:10.1186/s13059-019-1812-2 · Cited by 407 · see citing works
Self-citationChen, J., Knowles, H. J., Hebert, J. L., & Hackett, B. P. (1998) · Journal of Clinical Investigation · doi:10.1172/jci4786 · Cited by 405 · see citing works
Kwon, G. S., Viotti, M., & Hadjantonakis, A.-K. (2008) · Developmental Cell · doi:10.1016/j.devcel.2008.07.017 · Cited by 402 · see citing works
The formation of mesodermal tissues in the mouse embryo during gastrulation and early organogenesis
Tam, P., & Beddington, R. S. P. (1987) · Development · doi:10.1242/dev.99.1.109 · Cited by 387 · see citing works
The emergent landscape of the mouse gut endoderm at single-cell resolution
Nowotschin, S., Setty, M., Kuo, Y.-Y., Liu, V., Garg, V., Sharma, R., Simon, C. S., Saiz, N., Gardner, R., Boutet, S. C., et al. (2019) · Nature · doi:10.1038/s41586-019-1127-1 · Cited by 383 · see citing works
Vertebrate Embryonic Cells Will Become Nerve Cells Unless Told Otherwise
Hemmati‐Brivanlou, A., & Melton, D. A. (1997) · Cell · doi:10.1016/s0092-8674(00)81853-x · Cited by 364 · see citing works
Molecular recording of mammalian embryogenesis
Chan, M. M., Smith, Z. D., Grosswendt, S., Kretzmer, H., Norman, T. M., Adamson, B., Jost, M., Quinn, J. J., Yang, D., Jones, M. G., et al. (2019) · Nature · doi:10.1038/s41586-019-1184-5 · Cited by 364 · see citing works
Developmental barcoding of whole mouse via homing CRISPR
Kalhor, R., Kalhor, K., Mejia, L., Leeper, K., Graveline, A., Mali, P., & Church, G. M. (2018) · Science · doi:10.1126/science.aat9804 · Cited by 363 · see citing works
Gastrulation in the mouse : Growth and regionalization of the epiblast
Mh, S. (1977) · Development · doi:10.1242/dev.42.1.293 · Cited by 353 · see citing works
Bowling, S., Sritharan, D., Osorio, F. G., Nguyen, M., Cheung, P., Rodriguez-Fraticelli, A., Patel, S. H., Yuan, W.-C., Fujiwara, Y., Li, B. E., et al. (2020) · Cell · doi:10.1016/j.cell.2020.04.048 · Cited by 345 · see citing works
Peitz, M., Pfannkuche, K., Rajewsky, K., & Edenhofer, F. (2002) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.032068699 · Cited by 340 · see citing works
Mohammed, H., Hernando-Herraez, I., Savino, A., Scialdone, A., Macaulay, I. C., Mulas, C., Chandra, T., Voet, T., Dean, W., Nichols, J., et al. (2017) · Cell Reports · doi:10.1016/j.celrep.2017.07.009 · Cited by 324 · see citing works
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
Resolving early mesoderm diversification through single-cell expression profiling
Scialdone, A., Tanaka, Y., Jawaid, W., Moignard, V., Wilson, N. K., Macaulay, I. C., Marioni, J. C., & Göttgens, B. (2016) · Nature · doi:10.1038/nature18633 · Cited by 293 · see citing works
Keren-Shaul, H., Kenigsberg, E., Jaitin, D. A., David, E., Paul, F., Tanay, A., & Amit, I. (2019) · Nature Protocols · doi:10.1038/s41596-019-0164-4 · Cited by 292 · see citing works
Self-citationDefining the earliest step of cardiovascular lineage segregation by single-cell RNA-seq
Lescroart, F., Wang, X., Lin, X., Swedlund, B., Gargouri, S., Sánchez‐Danés, A., Moignard, V., Dubois, C., Paulissen, C., Kinston, S., et al. (2018) · Science · doi:10.1126/science.aao4174 · Cited by 279 · see citing works
Single-cell analysis of cardiogenesis reveals basis for organ-level developmental defects
de Soysa, Y., Ranade, S. S., Okawa, S., Ravichandran, S., Huang, Y., Salunga, H. T., Schricker, A., del Sol, A., Gifford, C. A., & Srivastava, D. (2019) · Nature · doi:10.1038/s41586-019-1414-x · Cited by 269 · see citing works
Concepts and limitations for learning developmental trajectories from single cell genomics
Tritschler, S., Büttner, M., Fischer, D. S., Lange, M., Bergen, V., Lickert, H., & Theis, F. J. (2019) · Development · doi:10.1242/dev.170506 · Cited by 233 · see citing works
Molecular architecture of lineage allocation and tissue organization in early mouse embryo
Peng, G., Suo, S., Cui, G., Yu, F., Wang, R., Chen, J., Chen, S., Liu, Z., Chen, G., Qian, Y., et al. (2019) · Nature · doi:10.1038/s41586-019-1469-8 · Cited by 230 · see citing works
Rosenquist, T. A., & Martin, G. R. (1996) · Developmental Dynamics · doi:10.1002/(sici)1097-0177(199604)205:4 · Cited by 196 · see citing works
Winnier, G. E., Hargett, L. K., & Hogan, B. L. M. (1997) · Genes & Development · doi:10.1101/gad.11.7.926 · Cited by 194 · see citing works
Clonal Analysis of Cell Fate During Gastrulation and Early Neurulation in the Mouse
Lawson, K. A., & Pedersen, R. A. (2007) · Novartis Foundation symposium · doi:10.1002/9780470514221.ch2 · Cited by 177 · see citing works
EMAGE mouse embryo spatial gene expression database: 2014 update
Richardson, L., Venkataraman, S., Stevenson, P. L., Yang, Y., Moss, J. E., Graham, L., Burton, N., Hill, B., Rao, J., Baldock, R., et al. (2013) · Nucleic Acids Research · doi:10.1093/nar/gkt1155 · Cited by 161 · see citing works
Nervous System Regionalization Entails Axial Allocation before Neural Differentiation
Metzis, V., Steinhauser, S., Pakanavicius, E., Gouti, M., Stamataki, D., Ivanovitch, K., Watson, T., Rayón, T., Mousavy-Gharavy, S. N., Lovell-Badge, R. H., et al. (2018) · Cell · doi:10.1016/j.cell.2018.09.040 · Cited by 153 · see citing works
Head-tail patterning of the vertebrate embryo: one, two or many unresolved problems?
Stern, C. D., Charité, J., Deschamps, J., Duboule, D., Durston, A. J., Kmita, M., Nicolas, J.-F., Palmeirim, I., Smith, J. C., & Wolpert, L. (2005) · The International Journal of Developmental Biology · doi:10.1387/ijdb.052095cs · Cited by 150 · see citing works
Cheng, S., Pei, Y., He, L., Peng, G., Reinius, B., Tam, P., Jing, N., & Deng, Q. (2019) · Cell Reports · doi:10.1016/j.celrep.2019.02.031 · Cited by 141 · see citing works
Self-citationWhat does time mean in development?
Ebisuya, M., & Briscoe, J. (2018) · Development · doi:10.1242/dev.164368 · Cited by 136 · see citing works
Epigenetic regulator function through mouse gastrulation
Grosswendt, S., Kretzmer, H., Smith, Z. D., Kumar, A. S., Hetzel, S., Wittler, L., Klages, S., Timmermann, B., Mukherji, S., & Meissner, A. (2020) · Nature · doi:10.1038/s41586-020-2552-x · Cited by 132 · see citing works
Developmental plasticity, cell fate specification and morphogenesis in the early mouse embryo
Bedzhov, I., Graham, S. J. L., Leung, C. Y., & Zernicka‐Goetz, M. (2014) · Philosophical Transactions of the Royal Society B Biological Sciences · doi:10.1098/rstb.2013.0538 · Cited by 130 · see citing works
Ibarra-Soria, X., Jawaid, W., Pijuan-Sala, B., Ladopoulos, V., Scialdone, A., Jörg, D. J., Tyser, R. C. V., Calero‐Nieto, F. J., Mulas, C., Nichols, J., et al. (2017) · Nature Cell Biology · doi:10.1038/s41556-017-0013-z · Cited by 121 · see citing works
Inferring population dynamics from single-cell RNA-sequencing time series data
Fischer, D. S., Fiedler, A., Kernfeld, E. M., Genga, R. M. J., Bastidas-Ponce, A., Bakhti, M., Lickert, H., Hasenauer, J., Maehr, R., & Theis, F. J. (2019) · Nature Biotechnology · doi:10.1038/s41587-019-0088-0 · Cited by 116 · see citing works
Beckers, A., Alten, L., Viebahn, C., Andre, P., & Gossler, A. (2007) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0704344104 · Cited by 106 · see citing works
Costello, I., Nowotschin, S., Sun, X., Mould, A. W., Hadjantonakis, A., Bikoff, E. K., & Robertson, E. J. (2015) · Genes & Development · doi:10.1101/gad.268979.115 · Cited by 100 · see citing works
Foxc1 and Foxc2 deletion causes abnormal lymphangiogenesis and correlates with ERK hyperactivation
Fatima, A., Wang, Y., Uchida, Y., Norden, P. R., Liu, T., Culver, A. E., Dietz, W. H., Culver, F., Millay, M., Mukouyama, Y., et al. (2016) · Journal of Clinical Investigation · doi:10.1172/jci80465 · Cited by 79 · see citing works
Clonal and molecular analysis of the prospective anterior neural boundary in the mouse embryo
Cajal, M., Lawson, K. A., Hill, B., Moreau, A., Rao, J., Ross, A., Collignon, J., & Camus, A. (2011) · Development · doi:10.1242/dev.075499 · Cited by 68 · see citing works
The Cooperative Roles of Foxc1 and Foxc2 in Cardiovascular Development
Kume, T. (2009) · Advances in experimental medicine and biology · doi:10.1007/978-1-4419-1599-3_5 · Cited by 64 · see citing works
Notochord morphogenesis in mice: Current understanding & open questions
Balmer, S., Nowotschin, S., & Hadjantonakis, A. (2016) · Developmental Dynamics · doi:10.1002/dvdy.24392 · Cited by 63 · see citing works
Initiating head development in mouse embryos: integrating signalling and transcriptional activity
Arkell, R. M., & Tam, P. (2012) · Open Biology · doi:10.1098/rsob.120030 · Cited by 60 · see citing works
Location of transient ectodermal progenitor potential in mouse development
Li, L., Liu, C., Biechele, S., Zhu, Q., Song, L., Lanner, F., Jing, N., & Rossant, J. (2013) · Development · doi:10.1242/dev.092866 · Cited by 59 · see citing works
Cellular diversity and lineage trajectory: insights from mouse single cell transcriptomes
Tam, P., & Ho, J. W. K. (2020) · Development · doi:10.1242/dev.179788 · Cited by 43 · see citing works
Guiding embryonic stem cells towards differentiation: lessons from molecular embryology
Spagnoli, F. M., & Hemmati‐Brivanlou, A. (2006) · Current Opinion in Genetics & Development · doi:10.1016/j.gde.2006.08.004 · Cited by 35 · see citing works
Harvey, N. T., Hughes, J. N., Lonic, A., Yap, C., Long, C. E., Rathjen, P. D., & Rathjen, J. (2010) · Journal of Cell Science · doi:10.1242/jcs.047530 · Cited by 27 · see citing works
Suppressing Nodal Signaling Activity Predisposes Ectodermal Differentiation of Epiblast Stem Cells
Liu, C., Wang, R., He, Z., Osteil, P., Wilkie, E. E., Yang, X., Chen, J., Cui, G., Guo, W., Chen, Y., et al. (2018) · Stem Cell Reports · doi:10.1016/j.stemcr.2018.05.019 · Cited by 21 · see citing works
Flagged first, then by citations
1 of the 70 references couldn’t be matched to a known paper.
Research works printed but not linked: 1
- Bellomo D. Lander A. Harragan I. Brown N.A. Cell proliferation in mammalian gastrulation: the ventral node and notochord are relatively quiescent Dev. Dyn. 205 1996 471 485 8901057
Cited by
Sorted by citations
Inferring and perturbing cell fate regulomes in human brain organoids
Fleck, J. S., Jansen, S. M. J., Wollny, D., Zenk, F., Seimiya, M., Jain, A., Okamoto, R., Santel, M., He, Z., Camp, J. G., et al. (2023) · Nature · doi:10.1038/s41586-022-05279-8 · Cited by 315 · see citing works
Post-gastrulation synthetic embryos generated ex utero from mouse naive ESCs
Tarazi, S., Aguilera-Castrejon, A., Joubran, C., Ghanem, N., Ashouokhi, S., Roncato, F., Wildschutz, E., Haddad, M., Oldak, B., Gomez-Cesar, E., et al. (2022) · Cell · doi:10.1016/j.cell.2022.07.028 · Cited by 246 · see citing works
Herring, C. A., Simmons, R. K., Freytag, S., Poppe, D., Moffet, J. J. D., Pflueger, J., Buckberry, S., Vargas-Landín, D. B., Clément, O., Goñi, E., et al. (2022) · Cell · doi:10.1016/j.cell.2022.09.039 · Cited by 226 · see citing works
High-throughput total RNA sequencing in single cells using VASA-seq
Salmén, F., Jonghe, J. D., Kamiński, T. S., Alemany, A., Parada, G. E., Verity-Legg, J., Yanagida, A., Kohler, T. N., Battich, N., van den Brekel, F., et al. (2022) · Nature Biotechnology · doi:10.1038/s41587-022-01361-8 · Cited by 233 · see citing works
A single-cell time-lapse of mouse prenatal development from gastrula to birth
Qiu, C., Martin, B., Welsh, I. C., Daza, R. M., Le, T.-M., Huang, X., Nichols, E. K., Taylor, M. L., Fulton, O., O’Day, D. R., et al. (2024) · Nature · doi:10.1038/s41586-024-07069-w · Cited by 199 · see citing works
A reference cell tree will serve science better than a reference cell atlas
Domcke, S., & Shendure, J. (2023) · Cell · doi:10.1016/j.cell.2023.02.016 · Cited by 110 · see citing works
Lau, K. Y. C., Rubinstein, H., Gantner, C. W., Hadas, R., Amadei, G., Stelzer, Y., & Zernicka‐Goetz, M. (2022) · Cell stem cell · doi:10.1016/j.stem.2022.08.013 · Cited by 113 · see citing works
Self-citationFei, L., Chen, H., Ma, L., Weigao, E., Wang, R., Fang, X., Zhou, Z., Sun, H., Wang, J., Jiang, M., et al. (2022) · Nature Genetics · doi:10.1038/s41588-022-01118-8 · Cited by 107 · see citing works
Primate gastrulation and early organogenesis at single-cell resolution
Zhai, J., Guo, J., Wan, H., Qi, L. Q. L., Liu, L., Xiao, Z., Long, Y., Schmitz, D. A., Xu, Y., Yu, D., et al. (2022) · Nature · doi:10.1038/s41586-022-05526-y · Cited by 103 · see citing works
The continuum of Drosophila embryonic development at single-cell resolution
Calderon, D., Blecher‐Gonen, R., Huang, X., Secchia, S., Kentro, J. A., Daza, R. M., Martin, B., Dulja, A., Schaub, C., Trapnell, C., et al. (2022) · Science · doi:10.1126/science.abn5800 · Cited by 96 · see citing works
Deep-tissue transcriptomics and subcellular imaging at high spatial resolution
Gandin, V., Kim, J., Yang, L.-Z., Lian, Y., Kawase, T., Hu, A., Rokicki, K., Fleishman, G. M., Tillberg, P. W., Aguilera-Castrejon, A., et al. (2025) · Science · doi:10.1126/science.adq2084 · Cited by 100 · see citing works
Connecting past and present: single-cell lineage tracing
Chen, C., Liao, Y., & Peng, G. (2022) · Protein & Cell · doi:10.1007/s13238-022-00913-7 · Cited by 93 · see citing works
Modelling post-implantation human development to yolk sac blood emergence
Hislop, J., Song, Q., Kamyar Keshavarz, F., Alavi, A., Schoenberger, R., LeGraw, R., Velazquez, J. J., Mokhtari, T., Taheri, M. N., Rytel, M., et al. (2023) · Nature · doi:10.1038/s41586-023-06914-8 · Cited by 96 · see citing works
Hallmarks of totipotent and pluripotent stem cell states
Du, P., & Wu, J. (2024) · Cell stem cell · doi:10.1016/j.stem.2024.01.009 · Cited by 92 · see citing works
Pera, M. F., & Rossant, J. (2021) · Cell stem cell · doi:10.1016/j.stem.2021.10.001 · Cited by 86 · see citing works
Optimal transport for single-cell and spatial omics
Bunne, C., Schiebinger, G., Krause, A., Regev, A., & Cuturi, M. (2024) · Nature Reviews Methods Primers · doi:10.1038/s43586-024-00334-2 · Cited by 71 · see citing works
Advances and applications in single-cell and spatial genomics
Wang, J., Ye, F., Chai, H., Jiang, Y., Wang, T., Ran, X., Xia, Q., Xu, Z., Fu, Y., Zhang, G., et al. (2024) · Science China Life Sciences · doi:10.1007/s11427-024-2770-x · Cited by 69 · see citing works
Neurulation of the cynomolgus monkey embryo achieved from 3D blastocyst culture
Zhai, J., Xu, Y., Wan, H., Yan, R., Guo, J., Skory, R. M., Long, Y., Wu, X., Sun, F., Chen, G., et al. (2023) · Cell · doi:10.1016/j.cell.2023.04.019 · Cited by 63 · see citing works
Precise and scalable self-organization in mammalian pseudo-embryos
Merle, M., Friedman, L., Chureau, C., Shoushtarizadeh, A., & Gregor, T. (2024) · Nature Structural & Molecular Biology · doi:10.1038/s41594-024-01251-4 · Cited by 53 · see citing works
Murphy, D., Salataj, E., Giammartino, D. C. D., Rodriguez-Hernaez, J., Kloetgen, A., Garg, V., Char, E., Uyehara, C. M., Ee, L.-S., Lee, U., et al. (2023) · Nature Structural & Molecular Biology · doi:10.1038/s41594-023-01130-4 · Cited by 47 · see citing works
Thompson, J. J., Lee, D. J., Mitra, A., Frail, S., Dale, R., & Rocha, P. P. (2022) · Nature Communications · doi:10.1038/s41467-022-31938-5 · Cited by 47 · see citing works
Mapping cells through time and space with moscotPreprint
Klein, D., Palla, G., Lange, M., Klein, M., Piran, Z., Gander, M., Meng-Papaxanthos, L., Sterr, M., Bastidas-Ponce, A., Tarquis-Medina, M., et al. (2023) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2023.05.11.540374 · Cited by 49 · see citing works
H3K36 methylation maintains cell identity by regulating opposing lineage programmes
Hoetker, M. S., Yagi, M., Stefano, B. D., Langerman, J., Cristea, S., Wong, L. P., Huebner, A. J., Charlton, J., Deng, W., Haggerty, C., et al. (2023) · Nature Cell Biology · doi:10.1038/s41556-023-01191-z · Cited by 42 · see citing works
The transcriptional portraits of the neural crest at the individual cell level
Erickson, A. G., Kameneva, P., & Adameyko, I. I. (2022) · Seminars in Cell and Developmental Biology · doi:10.1016/j.semcdb.2022.02.017 · Cited by 45 · see citing works
The Intrinsic and Extrinsic Effects of Tet Proteins During Gastrulation
Cheng, S., Mittnenzweig, M., Mayshar, Y., Lifshitz, A., Dunjić, M., Rais, Y., Ben-Yair, R., Gehrs, S., Chomsky, E., Mukamel, Z., et al. (2021) · Cell · doi:10.1016/j.cell.2022.06.049 · Cited by 44 · see citing works
Self-citationFang, W., Bell, C. M., Sapirstein, A., Asami, S., Leeper, K., Zack, D. J., Ji, H., & Kalhor, R. (2022) · Cell · doi:10.1016/j.cell.2022.10.028 · Cited by 42 · see citing works
Single-cell, whole-embryo phenotyping of mammalian developmental disorders
Huang, X., Henck, J., Qiu, C., Sreenivasan, V. K. A., Balachandran, S., Amarie, O. V., de Angelis, M. H., Behncke, R. Y., Chan, W.-L., Despang, A., et al. (2023) · Nature · doi:10.1038/s41586-023-06548-w · Cited by 45 · see citing works
Imaz-Rosshandler, I., Rode, C., Guibentif, C., Harland, L. T. G., Ton, M.-L. N., Dhapola, P., Keitley, D., Argelaguet, R., Calero‐Nieto, F. J., Nichols, J., et al. (2023) · Development · doi:10.1242/dev.201867 · Cited by 41 · see citing works
The heart field transcriptional landscape at single-cell resolution
Kelly, R. G. (2023) · Developmental Cell · doi:10.1016/j.devcel.2023.01.010 · Cited by 39 · see citing works
Pajanoja, C., Hsin, J., Olinger, B., Schiffmacher, A. T., Yazejian, R. M., Abrams, S. R., Dapkunas, A., Zainul, Z., Doyle, A. D., Martı́n, D., et al. (2023) · Nature Communications · doi:10.1038/s41467-023-41384-6 · Cited by 37 · see citing works
The Advancement and Application of the Single-Cell Transcriptome in Biological and Medical Research
Huang, K., Xu, Y., Feng, T., Lan, H., Ling, F., Xiang, H., & Liu, Q. (2024) · Biology · doi:10.3390/biology13060451 · Cited by 41 · see citing works
López-Anguita, N., Gassaloglu, S. I., Stötzel, M., Typou, M., Virta, I., Hetzel, S., Buschow, R., Koksal, B., Atilla, D., Maitschke-Rajasekharan, R., et al. (2022) · Development · doi:10.1242/dev.200679 · Cited by 37 · see citing works
Single-cell transcriptomic characterization of sheep conceptus elongation and implantation
Jia, G., Ma, W., Wu, Z.-B., Li, S., Zhang, X., He, Z., Wu, S., Tao, H.-P., Fang, Y., Song, Y.-W., et al. (2023) · Cell Reports · doi:10.1016/j.celrep.2023.112860 · Cited by 38 · see citing works
Quantifying cell-state densities in single-cell phenotypic landscapes using Mellon
Otto, D. J., Jordan, C., Dury, B., Dien, C., & Setty, M. N. (2024) · Nature Methods · doi:10.1038/s41592-024-02302-w · Cited by 38 · see citing works
Vianello, S., & Lütolf, M. P. (2020) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2020.06.07.138883 · Cited by 38 · see citing works
Cell lineage-specific mitochondrial resilience during mammalian organogenesis
Burr, S. P., Klimm, F., Glynos, A., Prater, M., Sendon, P., Nash, P. A., Powell, C. A., Simard, M., Bonekamp, N. A., Charl, J., et al. (2023) · Cell · doi:10.1016/j.cell.2023.01.034 · Cited by 36 · see citing works
Time-aligned hourglass gastrulation models in rabbit and mouse
Mayshar, Y., Raz, O., Cheng, S., Ben-Yair, R., Hadas, R., Reines, N., Mittnenzweig, M., Ben-Kiki, O., Lifshitz, A., Tanay, A., et al. (2023) · Cell · doi:10.1016/j.cell.2023.04.037 · Cited by 34 · see citing works
Self-citationSpatial molecular anatomy of germ layers in the gastrulating cynomolgus monkey embryo
Cui, G., Feng, S., Yan, Y., Wang, L., He, X., Li, X., Duan, Y., Chen, J., Tang, K., Zheng, P., et al. (2022) · Cell Reports · doi:10.1016/j.celrep.2022.111285 · Cited by 35 · see citing works
Inferring and perturbing cell fate regulomes in human cerebral organoidsPreprint
Fleck, J. S., Jansen, S. M. J., Wollny, D., Seimiya, M., Zenk, F. L., Santel, M., He, Z., Camp, J. G., & Treutlein, B. (2021) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2021.08.24.457460 · Cited by 35 · see citing works
Single-cell multi-omics and lineage tracing to dissect cell fate decision-making
Haghverdi, L., & Ludwig, L. S. (2023) · Stem Cell Reports · doi:10.1016/j.stemcr.2022.12.003 · Cited by 35 · see citing works
Li, T., Zou, Y., Liu, S., Yang, Y. A., Zhang, Z., & Zhao, Y. (2022) · Cell Regeneration · doi:10.1186/s13619-021-00105-4 · Cited by 33 · see citing works
Approaches for single-cell RNA sequencing across tissues and cell types
Sant, P., Rippe, K., & Mallm, J. (2023) · Transcription · doi:10.1080/21541264.2023.2200721 · Cited by 34 · see citing works
The development of the amnion in mice and other amniotes
Lopes, S. M. C. D. S., Roelen, B. A. J., Lawson, K. A., & Zwijsen, A. (2022) · Philosophical Transactions of the Royal Society B Biological Sciences · doi:10.1098/rstb.2021.0258 · Cited by 31 · see citing works
Temporal BMP4 effects on mouse embryonic and extraembryonic development
Hadas, R., Rubinstein, H., Mittnenzweig, M., Mayshar, Y., Ben-Yair, R., Cheng, S., Aguilera-Castrejon, A., Reines, N., Orenbuch, A.-H., Lifshitz, A., et al. (2024) · Nature · doi:10.1038/s41586-024-07937-5 · Cited by 32 · see citing works
Self-citationRosen, L. U., Stapel, L. C., Argelaguet, R., Barker, C. G., Yang, A., Reik, W., & Marioni, J. C. (2022) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2022.09.27.509783 · Cited by 30 · see citing works
Yang, X. H., Goldstein, A., Sun, Y., Wang, Z., Wei, M., Moskowitz, I. P. G., & Cunningham, J. M. (2022) · Nucleic Acids Research · doi:10.1093/nar/gkac452 · Cited by 28 · see citing works
Maizels, R. J., Snell, D. M., & Briscoe, J. (2024) · Cell Systems · doi:10.1016/j.cels.2024.04.004 · Cited by 35 · see citing works
Juvenile hormone as a key regulator for asymmetric caste differentiation in ants
Li, R., Dai, X., Zheng, J., Larsen, R. S., Qi, Y., Zhang, X., Vizueta, J., Boomsma, J. J., Liu, W., & Zhang, G. (2024) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.2406999121 · Cited by 29 · see citing works
A single-cell atlas of pig gastrulation as a resource for comparative embryology
Simpson, L., Strange, A., Klisch, D., Kraunsoe, S., Azami, T., Goszczynski, D. E., Minh, T. L., Planells, B., Holmes, N., Sang, F., et al. (2024) · Nature Communications · doi:10.1038/s41467-024-49407-6 · Cited by 29 · see citing works
Proks, M., Salehin, N., & Brickman, J. M. (2024) · Nature Methods · doi:10.1038/s41592-024-02511-3 · Cited by 27 · see citing works
Fetal Leydig cells: What we know and what we don't
Jiang, K., & Jorgensen, J. S. (2024) · Molecular Reproduction and Development · doi:10.1002/mrd.23739 · Cited by 27 · see citing works
Tyshkovskiy, A., Kholdina, D., Ying, K., Davitadze, M., Molière, A., Tongu, Y., Kasahara, T., Kats, L., Vladimirova, A., Moldakozhayev, A., et al. (2024) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2024.07.04.601982 · Cited by 30 · see citing works
Actin polymerization and depolymerization in developing vertebrates
Bai, Y., Zhao, F., Wu, T., Chen, F., & Pang, X. (2023) · Frontiers in Physiology · doi:10.3389/fphys.2023.1213668 · Cited by 26 · see citing works
Thowfeequ, S., Fiorentino, J., Hu, D., Solovey, M., Ruane, S., Whitehead, M. A., Zhou, F., Godwin, J., Mateo‐Otero, Y., Vanhaesebroeck, B., et al. (2024) · Developmental Cell · doi:10.1016/j.devcel.2024.05.014 · Cited by 25 · see citing works
Dissecting mammalian reproduction with spatial transcriptomics
Zhang, X., Cao, Q., Rajachandran, S., Grow, E. J., Evans, M., & Chen, H. (2023) · Human Reproduction Update · doi:10.1093/humupd/dmad017 · Cited by 24 · see citing works
Hopkins, B. R., Barmina, O. Y., & Kopp, A. (2023) · PLoS Biology · doi:10.1371/journal.pbio.3002148 · Cited by 23 · see citing works
Atoh8 in Development and Disease
Divvela, S. S. K., Saberi, D., & Brand‐Saberi, B. (2022) · Biology · doi:10.3390/biology11010136 · Cited by 22 · see citing works
Balanced gene dosage control rather than parental origin underpins genomic imprinting
Weinberg‐Shukron, A., Ben-Yair, R., Takahashi, N., Dunjić, M., Shtrikman, A., Edwards, C. A., Ferguson‐Smith, A. C., & Stelzer, Y. (2022) · Nature Communications · doi:10.1038/s41467-022-32144-z · Cited by 21 · see citing works
Self-citationCohesin prevents cross-domain gene coactivation
Dong, P., Zhang, S., Gandin, V., Xie, L., Wang, L., Lemire, A. L., Li, W., Otsuna, H., Kawase, T., Lander, A. D., et al. (2024) · Nature Genetics · doi:10.1038/s41588-024-01852-1 · Cited by 23 · see citing works
Three‐dimensional stem cell models of mammalian gastrulation
Turner, D. A., & Arias, A. M. (2024) · BioEssays · doi:10.1002/bies.202400123 · Cited by 21 · see citing works
Swift, J., Greenham, K., Ecker, J. R., Coruzzi, G. M., & McClung, C. R. (2021) · The Plant Journal · doi:10.1111/tpj.15589 · Cited by 20 · see citing works
Digital reconstruction of full embryos during early mouse organogenesis
Xie, P., Shen, J., Yang, Y., Wang, X., Liu, W., Cao, H., Zheng, Y., Wu, C., Mao, G., He, J., et al. (2025) · Cell · doi:10.1016/j.cell.2025.05.035 · Cited by 20 · see citing works
Nox4 promotes endothelial differentiation through chromatin remodeling
Hahner, F., Moll, F., Warwick, T., Hebchen, D. M., Buchmann, G., Epah, J., Abplanalp, W. T., Schader, T., Günther, S., Gilsbach, R., et al. (2022) · Redox Biology · doi:10.1016/j.redox.2022.102381 · Cited by 19 · see citing works
LoxCode in vivo barcoding reveals epiblast clonal fate bias to fetal organs
Weber, T., Biben, C., Miles, D. C., Glaser, S. P., Tomei, S., Lin, C., Kueh, A. J., Pál, M., Zhang, S., Tam, P., et al. (2025) · Cell · doi:10.1016/j.cell.2025.04.026 · Cited by 18 · see citing works
Guo, X., Ning, J., Chen, Y., Liu, G., Zhao, L., Fan, Y., & Sun, S. (2023) · Briefings in Functional Genomics · doi:10.1093/bfgp/elad011 · Cited by 18 · see citing works
Building and analyzing metacells in single-cell genomics data
Bilous, M., Hérault, L., Gabriel, A. A., Teleman, M., & Gfeller, D. (2024) · Molecular Systems Biology · doi:10.1038/s44320-024-00045-6 · Cited by 18 · see citing works
Yılmaz, A., Gurhan, G., Comar, M.-Y., Viukov, S. V., Serfaty, I., Gayretli, M., Golenchenko, S., Lokshtanov, D., Ashouokhi, S., Polanco, A., et al. (2025) · Cell Stem Cell · doi:10.1016/j.stem.2025.07.005 · Cited by 15 · see citing works
Self-citationQi, S., Wang, W., Xue, X., Zhuo, L., Yan, J., Li, Y., Zhang, Y., Shu, M., Song, C., Wang, Q., et al. (2022) · PLoS Biology · doi:10.1371/journal.pbio.3001741 · Cited by 17 · see citing works
The extended analogy of extraembryonic development in insects and amniotes
Panfilio, K. A., & Lopes, S. M. C. D. S. (2022) · Philosophical Transactions of the Royal Society B Biological Sciences · doi:10.1098/rstb.2021.0268 · Cited by 17 · see citing works
exFINDER: identify external communication signals using single-cell transcriptomics data
He, C., Zhou, P., & Nie, Q. H. (2023) · Nucleic Acids Research · doi:10.1093/nar/gkad262 · Cited by 17 · see citing works
Zhang, H., Nie, J., Bao, Z., Shi, Y., Gong, J., & Li, H. (2025) · Cellular Signalling · doi:10.1016/j.cellsig.2025.111680 · Cited by 16 · see citing works
Oka, S., Tsuzuki, T., Hidaka, M., Ohno, M., Nakatsu, Y., & Sekiguchi, M. (2022) · Cell Death Discovery · doi:10.1038/s41420-022-00961-2 · Cited by 16 · see citing works
Icaritin inhibits endometrial carcinoma cells by suppressing O-GlcNAcylation of FOXC1
Wang, Y., Wang, G., Liu, Y., Yang, F., Zhang, H., & Kong, Y. (2023) · Phytomedicine · doi:10.1016/j.phymed.2023.155062 · Cited by 16 · see citing works
A synthetic differentiation circuit in Escherichia coli for suppressing mutant takeover
Glass, D. S., Bren, A., Vaisbourd, E., Mayo, A., & Alon, U. S. (2024) · Cell · doi:10.1016/j.cell.2024.01.024 · Cited by 14 · see citing works
Chugunov, A. O., Potapova, N. A., Klimenko, N. S., Tatarskiy, V. V., Georgieva, S. G., & Soshnikova, N. V. (2021) · International Journal of Molecular Sciences · doi:10.3390/ijms222011134 · Cited by 15 · see citing works
Gene regulatory networks: from correlative models to causal explanations
Maizels, R. J., & Briscoe, J. (2026) · Nature Reviews Genetics · doi:10.1038/s41576-026-00939-1 · Cited by 18 · see citing works
Guan, G., Li, Z., Ma, Y., Ye, P., Cao, J., Wong, M., Ho, V. W. S., Chan, L.-Y., Yan, H., Tang, C., et al. (2025) · Nature Communications · doi:10.1038/s41467-025-58878-0 · Cited by 14 · see citing works
Harland, L. T. G., Lohoff, T., Koulena, N., Pierson, N. G., Pape, C., Ameen, F., Griffiths, J. A., Theeuwes, B., Wilson, N. K., Kreshuk, A., et al. (2025) · Cell Reports · doi:10.1016/j.celrep.2025.116047 · Cited by 14 · see citing works
Stem Cell and Synthetic Embryo Models: Advances, Applications, and Ethical Considerations
Marei, H. E. S. (2025) · Stem Cell Reviews and Reports · doi:10.1007/s12015-025-10890-z · Cited by 14 · see citing works
Dissecting the Complexity of Early Heart Progenitor Cells
Sendra, M., Dominguez, J. N., Torres, M., & Ocaña, O. H. (2021) · Journal of Cardiovascular Development and Disease · doi:10.3390/jcdd9010005 · Cited by 14 · see citing works
Transient upregulation of IRF1 during exit from naive pluripotency confers viral protection
Romeike, M., Spach, S., Huber, M. L., Feng, S., Vainorius, G., Elling, U., Versteeg, G. A., & Buecker, C. (2022) · EMBO Reports · doi:10.15252/embr.202255375 · Cited by 12 · see citing works
van der Veer, B. K., Chen, L., Custers, C., Athanasouli, P., Schroiff, M., Cornelis, R., Chui, J. S., Finnell, R. H., Lluı́s, F., & Koh, K. P. (2023) · Nucleic Acids Research · doi:10.1093/nar/gkad231 · Cited by 14 · see citing works
The evolving definition of plant cell type
Amini, S., Doyle, J. J., & Libault, M. (2023) · Frontiers in Plant Science · doi:10.3389/fpls.2023.1271070 · Cited by 13 · see citing works
A dynamical perspective: moving towards mechanism in single-cell transcriptomics
Maizels, R. J. (2024) · Philosophical Transactions of the Royal Society B Biological Sciences · doi:10.1098/rstb.2023.0049 · Cited by 15 · see citing works
Origin, fate and function of extraembryonic tissues during mammalian development
Thowfeequ, S., Hanna, C. W., & Srinivas, S. (2024) · Nature Reviews Molecular Cell Biology · doi:10.1038/s41580-024-00809-w · Cited by 13 · see citing works
A single-cell atlas of spatial and temporal gene expression in the mouse cranial neural platePreprint
Brooks, E., Moorman, A. R., Bhattacharya, B., Prudhomme, I. S., Land, M., Alcorn, H. L., Sharma, R., Pe’er, D., & Zallen, J. A. (2024) · eLife · doi:10.7554/elife.102819 · Cited by 13 · see citing works
Technical Advances and Applications of Spatial Transcriptomics
Liang, G., Yin, H. Z., & Ding, F. (2023) · GEN Biotechnology · doi:10.1089/genbio.2023.0032 · Cited by 12 · see citing works
Bieker, J. J., & Philipsen, S. (2024) · Advances in experimental medicine and biology · doi:10.1007/978-3-031-62731-6_10 · Cited by 12 · see citing works
Multi-batch single-cell comparative atlas construction by deep learning disentanglement
Lynch, A. W., Brown, M. A., & Meyer, C. A. (2023) · Nature Communications · doi:10.1038/s41467-023-39494-2 · Cited by 11 · see citing works
Eldeeb, D., Ikeda, Y., Hojo, H., & Ohba, S. (2024) · Regenerative Therapy · doi:10.1016/j.reth.2024.03.023 · Cited by 11 · see citing works
Mapping Cell Atlases at the Single‐Cell Level
Ye, F., Wang, J., Li, J., Mei, Y., & Guo, G. (2023) · Advanced Science · doi:10.1002/advs.202305449 · Cited by 11 · see citing works
Pluripotency Dynamics during Embryogenesis and in Cell Culture
Gordeev, M. N., Bakhmet, E. I., & Tomilin, A. N. (2021) · Russian Journal of Developmental Biology · doi:10.1134/s1062360421060059 · Cited by 10 · see citing works
Multi-layered transcriptional control of cranial neural crest development
Candido-Ferreira, I., Lukoseviciute, M., & Sauka‐Spengler, T. (2022) · Seminars in Cell and Developmental Biology · doi:10.1016/j.semcdb.2022.07.010 · Cited by 8 · see citing works
Interspecies control of development during mammalian gastrulation
Simpson, L., & Alberio, R. (2023) · Emerging Topics in Life Sciences · doi:10.1042/etls20230083 · Cited by 10 · see citing works
Wu, Y., Devotta, A., José‐Edwards, D. S., Kugler, J. E., Negrón-Piñeiro, L. J., Braslavskaya, K., Addy, J., Saint‐Jeannet, J., & Gregorio, A. D. (2022) · eLife · doi:10.7554/elife.73992 · Cited by 10 · see citing works
Salehin, N., Knowles, H., Masamsetti, V. P., & Tam, P. (2022) · Biochemical Society Transactions · doi:10.1042/bst20220256 · Cited by 10 · see citing works
Golomb, S. M., Guldner, I. H., Aleksandrovic, E., Fross, S. R., Liu, X., Diao, L., Liang, K., Wu, J., Wang, Q., Lopez, J. A., et al. (2025) · Cell Reports · doi:10.1016/j.celrep.2025.115356 · Cited by 9 · see citing works
DNA methyltransferases 3A and 3B target specific sequences during mouse gastrulation
Mukamel, Z., Lifshitz, A., Mittnenzweig, M., Chomsky, E., Schwartzman, O., Ben-Kiki, O., Zerbib, M., & Tanay, A. (2022) · Nature Structural & Molecular Biology · doi:10.1038/s41594-022-00885-6 · Cited by 8 · see citing works
Self-citationEpigenetic priming of embryonic lineages in the mammalian epiblastPreprint
Sendra, M., McDole, K., Jiménez‐Carretero, D., Hourcade, J. D. D., Temiño, S., Raiola, M., Guignard, L., Keller, P., Sánchez‐Cabo, F., Dominguez, J. N., et al. (2024) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2024.01.11.575188 · Cited by 9 · see citing works
Time-resolved single-cell transcriptomic sequencing
Xu, X., Wen, Q. J., Lan, T., Zeng, L., Zeng, Y., Lin, S., Qiu, M., Na, X., & Yang, C. J. (2024) · Chemical Science · doi:10.1039/d4sc05700g · Cited by 10 · see citing works
- Authors
- Mittnenzweig, M., Mayshar, Y., Cheng, S., Ben-Yair, R., Hadas, R., Rais, Y., Chomsky, E., Reines, N., Uzonyi, A., Lumerman, L., Lifshitz, A., Mukamel, Z., Orenbuch, A.-H., Tanay, A., & Stelzer, Y.
- Affiliations
- Weizmann Institute of Science (IL)
- Corresponding author
- Tanay, Amos
- Stelzer, Yonatan
- ORCID
- Venue
- Cell
- Publisher
- Elsevier BV
- Published
- 2021-05
- Volume
- 184
- Issue
- 11
- Pages
- 2825-2842.e22
- ISSN
- 0092-8674 (ISSN-L)
- PMC
- PMC8162424
- OpenAlex
- W3159883015
- Cited by
- 214
- References
- 70
- Citations by year
- 2026: 33 · 2025: 39 · 2024: 52 · 2023: 40 · 2022: 37 · 2021: 12 · 2020: 1
- FWCI
- 11.07
- Type
- journal article
- Language
- en
- Open access
- hybrid
- doi.org
- Licence
- Locations
- Cell (publishedVersion, cc-by-nc-nd)
- PubMed Central (publishedVersion, cc-by-nc-nd)
- PubMed (publishedVersion)
- MDC Repository (Max-Delbrueck-Center for Molecular Medicine) (acceptedVersion)
- Funders
- ERC
- Weizmann Institute of Science
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Single-cell and spatial transcriptomics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Developmental Biology and Gene Regulation
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Pluripotent Stem Cells Research
- Keywords
- mouse gastrulation, single-cell transcriptomics, lineage specification, mesoderm differentiation, FOXC1, FOXC2, chimeric embryos, embryonic development
- MeSH terms
- Mouse Embryonic Stem Cells, Animals, Cell Differentiation, Embryo, Mammalian, Female, Mice, Inbred C57BL, Pregnancy, Gene Expression, Sequence Analysis, RNA, Cell Lineage, Embryonic Development, Mice, Gastrulation, Single-Cell Analysis
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