Publications

Doostdar, P., Hawley, J., Marinopoulou, E., Lea, R., Biga, V., Papalopulu, N., & Soto, X. (2022). Cell coupling compensates for changes in single-cell Her6 dynamics and provides phenotypic robustness. bioRxiv.

Soto, X., Burton, J., Manning, C. S., Minchington, T., Lea, R., Lee, J., … & Papalopulu, N. (2022). Sequential and additive expression of miR-9 precursors control timing of neurogenesis. Development, 149(19), dev200474.

Hawley, J., Manning, C., Biga, V., Glendinning, P., & Papalopulu, N. (2022). Dynamic switching of lateral inhibition spatial patterns. Journal of the Royal Society Interface, 19(193), 20220339.

Rowntree, A., Sabherwal, N., & Papalopulu, N. (2022). Bilateral Feedback in Oscillator Model Is Required to Explain the Coupling Dynamics of Hes1 with the Cell Cycle. Mathematics, 10(13), 2323.

Sabherwal, N., Rowntree, A., Marinopoulou, E., Pettini, T., Hourihane, S., Thomas, R., … & Papalopulu, N. (2021). Differential phase register of Hes1 oscillations with mitoses underlies cell-cycle heterogeneity in ER+ breast cancer cells. Proceedings of the National Academy of Sciences, 118(45).

Marinopoulou, E., Biga, V., Sabherwal, N., Miller, A., Desai, J., Adamson, A. D., & Papalopulu, N. (2021). HES1 protein oscillations are necessary for neural stem cells to exit from quiescence. Iscience, 24(10), 103198.

Burton, J., Manning, C. S., Rattray, M., Papalopulu, N., & Kursawe, J. (2021). Inferring kinetic parameters of oscillatory gene regulation from single cell time-series data. Journal of the Royal Society Interface, 18(182), 20210393.

Biga, V., Hawley, J., Soto, X., Johns, E., Han, D., Bennett, H., … & Papalopulu, N. (2021). A dynamic, spatially periodic, micro‐pattern of HES5 underlies neurogenesis in the mouse spinal cord. Molecular systems biology, 17(5), e9902.

Soto, X., Biga, V., Kursawe, J., Lea, R., Doostdar, P., Thomas, R., & Papalopulu, N. (2020). Dynamic properties of noise and Her6 levels are optimized by miR-9, allowing the decoding of the Her6 oscillator. The EMBO Journal, DOI:10. 15252/embj.2019103558

Cutillo, L., Boukouvalas, A., Marinopoulou, E., Papalopulu, N., & Rattray, M.(2020).  OscoNet: inferring oscillatory gene networks. BMC Bioinformatics 21, 351 (2020). https://doi.org/10.1186/s12859-020-03561-y

Minchington, TG., Griffiths-Jones, S., & Papalopulu, N (2020). Dynamical gene regulatory networks are tuned by transcriptional autoregulation with microRNA feedback. Scientific Reports, Sci Rep 10, 12960 (2020). https://doi.org/10.1038/s41598-020-69791-5

Manning, C. S., Biga, V., Boyd, J., Kursawe, J., Ymisson, B., Spiller, D. G., … & Papalopulu, N. (2019). Quantitative single-cell live imaging links HES5 dynamics with cell-state and fate in murine neurogenesis. Nature Communications, 10(1), 2835.

Phillips, NE., Manning, C., Papalopulu, N., and Rattray, M. (2017). Identifying stochastic oscillations in single-cell live imaging time series using Gaussian processes. PLoS Comput Biol 13(5):e1005479.

Phillips, NE., Manning, C., Pettini, T., Biga, V., Marinopoulou, E., Stanley, P., Boyd, J., Bagnall, J., Paszek, P., Spiller, D., White, M., Goodfellow, M., Galla, T., Rattray. M. and Papalopulu, N. (2016). Stochasticity in the microRNA/Hes1 oscillatory network accounts for clonal heterogeneity in the timing of differentiation. eLife 2016;5:e16118.

Thuret, R., Auger, H. and Papalopulu, N. (2015). Analysis of neural progenitors from embryogenesis to juvenile adult in Xenopus laevis reveals biphasic neurogenesis and continuous lengthening of the cell cycle. Biology Open 4(12):1772-81.

Sabherwal, N., Thuret, R., Lea R. and Papalopulu, N. (2014). aPKC phosphorylates p27Xic1, providing a mechanistic link between apicobasal polarity and cell-cycle control. Dev Cell 8(5): 559-71.

Jones, LA., Villemant, C., Starborg, T., Salter, A., Woodman, PG., Papalopulu, N., Woolner, S. and Allan, VJ. (2014). Dynein light intermediate chains are required to maintain spindle bipolarity by functioning in centriole cohesion. Journal of Cell Biol 207(4): 499-516.

Goodfellow, M., Phillips, N., Manning, C., Galla, T., and Papalopulu, N. (2014). microRNA input into a neural ultradian oscillator provides a mechanism for the timing of differentiation and the emergence of alternative cells states. Nature Communications 4; 5:3399.

Dubaissi, E., Rousseau, K., Lea, R., Soto, X., Nardeosingh, S., Amaya, E., Thornton, DJ. and Papalopulu, N. (2014). A secretory cell type develops alongside ionocytes, goblet and multiciliated cells and provides a protective, anti-infective, function in the frog embryonic mucociliary epidermis. Development 41(7): 1514-25.

Tian, H., Fletcher, JS., Thuret, R., Henderson, A., Papalopulu, N., Vickerman, JC. and Lockyer, NP. (2014). Spatiotemporal Lipid profiling during early embryo development of Xenopus laevis using dynamic ToF-SIMS imaging. J Lipid Res 55 (9) 1970-80.

Saiz, N., Grabarek, JB., Sabherwal, N., Papalopulu, N. and Plusa, B. (2013). Atypical protein kinase C couples cell sorting with primitive endoderm maturation in the mouse blastocyst. Development 40(21): 4311-22.

Soto, X., Li, J., Lea, R., Dubaissi, E., Papalopulu, N. and Amaya, E. (2013). An inositol kinase and its product accelerate wound healing by modulating calcium levels, Rho GTPases and F-actin assembly. PNAS 110(27): 11029-34.

Bonev, B., Stanley, P. and Papalopulu, N. (2012). miR-9 modulates Hes1 ultradian oscillations by forming a double negative-feedback loop. Cell Reports 2:10-8.

Dajas-Bailador, F., Bonev B., Garcez P., Stanley P., Guillemot F. and Papalopulu, N. (2012). microRNA-9 regulates axon extension and branching by targeting Map1b in mouse cortical neurons. Nature Neuroscience 15: 697-699.

Woolner, S. and Papalopulu, N. (2012). Spindle position in symmetric cell divisions during epiboly is controlled by opposing and dynamic apicobasal forces. Dev Cell 22:775-87.

Sabherwal, N. and Papalopulu, N. (2012) Apicobasal polarity and proliferation during development. Invited peer-reviewed review for ‘Cell polarity and cancer’, Essays in Biochemistry, eds Chalmers A. and Whitley, P.

Love, NR., Thuret, R., Chen, Y., Ishibashi, S., Lea, R., Paredes, R., Poulin, G., Noble, AM., Guille, MJ., Sasai, Y., Papalopulu , N. and Amaya, E. (2011). pTransgenesis: A modular cloning approach that expedites the creation of novel transgenic lines. Development, 38:5451-8.

Bonev, B., Pisco, A. and Papalopulu, N. (2011). microRNA-9 reveals regional diversity of neural progenitors along the anterior-posterior axis. Dev. Cell 18:19-32.

Dubaissi, E. and Papalopulu, N. (2011) Embryonic frog epidermis: a model for the study of cell-cell interactions in the development of mucociliary disease. Disease, Models and Mechanisms 4:179-92.

Panagiotaki, N., Dajas-Bailador, F., Amaya, E., Papalopulu, N.* and Dorey, K. (2010). Characterisation of a new regulator of BDNF signalling, Sprouty3, involved in axonal morphogenesis in vivo. Development 137:4005-15.
*co-corresponding author.

Roth, M., Bonev, B., Lindsay,J., Lea, R., Panagiotaki, N., Houart, C. and Papalopulu, N. (2010). FoxG1 with TLE2 act cooperatively to regulate ventral telencephalon formation. Development 137:1553-62.

Saberwhal, N., Tsutsui, A., Hodge, S., Wei, J., Chalmers, AD. and Papalopulu, N. (2009). The apical-basal polarity kinase aPKC functions as a nuclear determinant and regulates cell proliferation and fate during Xenopus neurogenesis. Development 136: 2767-77.

Danesin, C., Peres, J. N., Johansson, M., Snowden, V., Coding, A., Papalopulu, N. and Houart, C. (2009). Integration of telencephalic Wnt and Hedgehog signaling centre activities by Foxg1. Dev. Cell 16: 576-87.

Lea, R., Papalopulu, N., Amaya, E. and Dorey, K. (2009). Temporal and spatial expression of FGF ligands and receptors during Xenopus development. Dev. Dynamics 238:1467-79.

Gilchrist, MJ., Christensen, MB., Harland, R., Pollet, N., Smith J.C., Ueno, N. and Papalopulu, N. (2008). Evading the Annnotation Bottleneck: using sequence similarity to search non-sequence gene data. BMC Bioinformatics 9: 442.

Regad, T., Roth, M., Bredenkamp, N., Illing, N. and Papalopulu, N. (2007). The neural progenitor specifying activity of the forebrain transcription factor FoxG1 is regulated by CKI and FGF in opposite directions. Nature Cell Biology 9: 531-40.

Park, M., Serpinskaya, AS., Papalopulu, N. and Gelfand, VI. (2007). Rab32 regulates melanosome transport in Xenopus melanophores by Protein Kinase A recruitment. Curr. Biol. 17:2030-4.

Strauss, B., Adams, RJ. and Papalopulu, N. (2006). A default mechanism of spindle orientation based on cell shape is sufficient to generate cell fate diversity in polarised Xenopus blastomeres. Development 133: 3883-3893.

Voigt, J. and Papalopulu, N (2006). A dominant negative Cullin-1, an E3 ubiquitin ligase, disrupts the correct allocation of cell fate in the neural crest lineage. Development 559-68.

Chalmers, A., Goldstone, K., Shin, Y., Cho, K. and Papalopulu, N. (2006). Grainyhead like 3, a transcription factor identified in a microarray screen, promotes the specification of the superficial layer of the embryonic epidermis. Mech. Dev. 123: 702-18.

Chalmers, A., Pambos, M., Lang, S., Wylie, C. and Papalopulu, N. (2005) aPKC, crumbs3 and Lgl –2 control apical/basal polarity in early vertebrate development. Development 132: 977-986.

Plusa, B., Frankenberg, S., Chalmers, A., Hadjantonakis, A-K., Moore, C., Papalopulu, N., Papaioannou, VE., Glover, DM. and Zernicka-Goetz, M. (2005). Downregulation of Par3 and aPKC function directs cells towards an ICM fate in the preimplanation mouse embryo. Journal of Cell Science 118, 505-515.

Voigt, J., Chen, JA., Gilchrist, M., Amaya, E. and Papalopulu, N. (2005) Expression cloning screening of a unique and full-length set of cDNA clones is an efficient method to identify gene function in Xenopus neurogenesis. Mech. Dev. 122: 289-306.

Chalmers, AD., Goldstone, K., Smith, JC., Gilchrist, M., Amaya, E. and Papalopulu, N. (2005) A Xenopus tropicalis oligonucleotide microarray works across species using RNA from Xenopus laevis. Mech. Dev. 122:355-63.

Chen, J-A., Voigt, J., Gilchrist, M., Papalopulu, N. and Amaya, E. (2005) Identification of Novel Genes Affecting Mesoderm Formation and Morphogenesis through an Enhanced Large Scale Functional Screen in Xenopus. Mech. Dev. 122:307-331.

Gilchrist, M*., Zorn, AM., Voigt, J., Smith, JC., Papalopulu, N*. and Amaya, E*. (2004). Defining a large set of full length clones from a Xenopus tropicalis EST project. Dev. Biol. 271:498-516.
*corresponding authors.

Kenwrick, S., Amaya, E. and Papalopulu, N. (2004). A pilot morpholino screen in Xenopus tropicalis identifies a novel gene involved in head development. Dev. Dyn. 229:289-299.

Chalmers AD., Strauss, B. and Papalopulu, N. (2003). Oriented cell divisions asymmetrically segregate aPKC and generate cell fate diversity in the early Xenopus embryo. Development 130:2657-68.

Carruthers, S., Mason, J. and Papalopulu, N. (2003). Depletion of a cell cycle inhibitor, p27 Xic1, prevents neuronal differentiation and increases the number of neural progenitor cells in Xenopus tropicalis. Mech Dev. 120:607-16.

D’Souza, A., Lee, M., Taverner, N., Mason, J., Carruthers, S., Smith, JC., Amaya, E., Papalopulu, N. and Zorn, AM. (2003). Molecular components of the endoderm specification pathway in Xenopus tropicalis. Dev Dyn. 226:118-27.

Khokha, M. K., Chung, C., Bustamante, EL., Gaw, LWK., Trott, KA., Yeh, J., Lim, N., Lin, J., Taverner, N., Amaya, E., Papalopulu, N., Smith, JC., Zorn, A., Harland, RM. and Grammer, TC. (2002). Techniques and probes for the study of Xenopus tropicalis development. Dev. Dyn. 225: 499-510.

Chalmers, A., Welchman, D. and Papalopulu, N. (2002). Intrinsic differences between the superficial and deep layers of the Xenopus ectoderm control primary neuronal differentiation. Dev. Cell 2:171-182.

Hartley, KO., Hardcastle, Z., Amaya, E. and Papalopulu, N. (2001). Transgenic Xenopus embryo reveal that anterior neural development requires continued suppression of BMP signalling after gastrulation. Dev. Biol. 238, 168-184.

Hardcastle, Z., Chalmers A. and Papalopulu, N. (2000). FGF-8 stimulates neurogenesis through the FGF receptor 4 (FGFR4) and interferes with mesoderm induction in Xenopus embryos. Current Biology 10:1511-1514.

Hardcastle, Z. and Papalopulu, N. (2000). Distinct effects of XBF-1 in regulating the cell cycle inhibitor p27(Xic1) and imparting a neural fate. Development 127:1303-1314.

Xia, Y., Papalopulu, N., Vogt, PK. and Li, J. (2000). The oncogenic potential of the high mobility group box protein Sox3. Cancer Res. 22:6303-6.

Bang, AG., Papalopulu, N., Goulding, MD. and Kintner, C. (1999). Expression of Pax-3 in the lateral neural plate is dependent on a Wnt-mediated signal from posterior non-axial mesoderm. Dev. Biol. 212:366-380.

Bourguignon, C., Li, J. and Papalopulu, N. (1998). XBF-1, a winged helix transcription factor with dual activity, has a role in positioning neurogenesis in Xenopus competent ectoderm. Development 125:4889-4900.

Bellefroid, EJ., Kobbe, A., Gruss, P., Pieler, T., Gurdon, J. and Papalopulu, N. (1998). Xiro3 encodes a Xenopus homolog of the Drosophila Iroquois genes and functions in neural specification. EMBO Journal 17:191-203.

Blumberg, B., Bolado, J. Jr., Moreno, T., Kintner, C., Evans, R. and Papalopulu, N. (1997). An essential role for retinoid signalling in anteroposterior neural patterning. Development 124:373-379.

Bang, A., Papalopulu, N., Kintner, C. and Goulding, M. (1997). Expression of Pax-3, a marker for dorsal and posterior neural tube, is initiated by posteriorizing signals produced by the organizer and by non-axial mesoderm. Development 124:2075-2085.

Papalopulu, N. and Kintner, C. (1996). A posteriorising factor, retinoic acid, reveals that anteroposterior patterning controls the timing of neuronal differentiation in Xenopus neuroectoderm. Development 122:3409-3418.

Papalopulu, N. and Kintner, C. (1996). A novel Xenopus homeobox gene, Xbr-1 idefines a novel class of homeobox genes and is expressed in the dorsal ciliary margin of the eye. Dev. Biol. 173:104-114.

Evans, S., Yan, W., Murillo, MP., Ponce, J. and Papalopulu, N. (1995). Tinman, a Drosophila homeobox gene required for heart and visceral mesoderm specification, may be represented by a family of genes in vertebrates: XNkx-2.3, a second vertebrate homologue of Tinman. Development 121:3889-3899.

Papalopulu, N. (1995). Regionalization of the forebrain: from neural plate to neural tube. In Perspectives on Developmental Neurobiology 3:39-52.

Papalopulu, N. and Kintner, C. (1994). Molecular genetics of neurulation. In Neural Tube Defects, CIBA Research Foundation, pp 90-102.

Papalopulu, N. and Kintner, C. (1993). Xenopus Distal-less related homeobox genes are expressed in the developing forebrain and are induced by planar signals. Development 117:961-975.

Krumlauf, R., Hunt, P., Sham, M-H., Whiting, J., Nonchev., S., Marshall, H., Graham, A., Papalopulu, N., Cook, M., Boncinelli, E. and Wilkinson, D. (1993). Hox genes: a molecular code for patterning regional diversity in the nervous system and branchial structures. In: Restorative Neurology and Neuroscience pp 17-19.

Papalopulu, N. and Kintner, C. (1992). Induction and patterning of the neural plate. In: Seminars in Neurosciences 4:295-306.

Papalopulu, N., Clarke, JDW., Bradley, L., Wilkinson, D., Krumlauf, R. and Holder, N. (1991). Retinoic acid causes abnormal development and segmental patterning of the anterior hindbrain in Xenopus embryos. Development 113:1145-1158.

Papalopulu, N., Lovell-Badge, R. and Krumlauf, R. (1991). The expression of murine Hox-2 genes is dependent on the differentiation pathway and displays a collinear sensitivity to retinoic acid. Nucleic Acids Research 19:5497-5506.

Sham, MH., Hunt, P., Nochev, S., Papalopulu, N., Graham, A., Boncinelli, E. and Krumlauf, R. (1992). Analysis of the murine Hox 2.7 gene: conserved alternative transcripts with differential distributions in the nervous system and the potential for shared regulatory regions. EMBO J. 11:1825-1836.

Sham, M-H., Nochev, S., Whiting, J., Papalopulu, N., Marshall, H., Hunt, P., Muchamore, I., Cook, M. and Krumlauf, R. (1991). Hox-2: Gene regulation and segmental patterning in the vertebrate head. In: Cell-cell Interactions in Early Development. Wiley-Liss Inc, pp 129-143.

Krumlauf, R., Papalopulu, N., Clarke, JDW. and Holder, N. (1991). Retinoic acid and the Xenopus hindbrain. In Seminars in Developmental Biology 2:181-188.

Papalopulu, N., Hunt, P., Wilkinson, D., Graham, A. and Krumlauf, R. (1990). Hox-2 homeobox genes and retinoic acid: potential roles in patterning the vertebrate nervous system. In Advances in Neural Regeneration Research. Wiley-Liss Inc., pp 291-307.

Rubock, M., Larin, Z., Cook, M., Papalopulu, N., Krumlauf, R. and Lehrach, H. (1990). A yeast artificial chromosome containing the mouse homeobox cluster Hox-2. Proc. Natl. Acad. Sci. 87:4751-4755.

Graham A., Papalopulu, N. and Krumlauf, R. (1989). The murine and Drosophila homeobox gene networks have common features of organisation and expression. Cell 57:367-378.

Papalopulu N., Graham A., Lorimer J., Kenny R., McVey J. and Krumlauf R. (1989). Structure, expression and evolutionary relationships of murine homeobox genes in the Hox 2 cluster. In: Cell to Cell Signalling in Mammalian Development NATO ASI series, vol. 26, (eds. S.W. deLatt.). Springer-Verlag, Berlin, pp 9-22.

Graham A., Papalopulu N., Lorimer J., McVey J., Tuddenham EGD. and Krumlauf R. (1988) Characterisation of a murine homeobox gene, Hox 2.6, related to the Drosophila Deformed gene. Genes and Development 2:1424-1438.

METHODS CHAPTERS

Dubaissi, E., Panagiotaki, N., Papalopulu, N. and Vize, PD. (2012). Antibody development and use in chromogenic and fluorescent immunostaining. In Hoppler, S and Vize, P.D. (Editors). Xenopus Protocols, Second Edition. Methods in Molecular Biology series, Springer 2012.

Lea, R., Bonev, B., Dubaissi, E., Vize, PD. and Papalopulu, N. (2012). Triple fluorescent in situ hybridization (FISH) on whole mounts and sections. In Hoppler, S and Vize, P.D. (Editors). Xenopus Protocols, Second Edition. Methods in Molecular Biology series, Springer 2012.

Dubaissi, E., Panagiotaki, N., Papalopulu, N. and Vize, PD. (2012). Antibody Development and use in Chromogenic and Fluorescent Immunostaining. Methods in Molecular Biology, Xenopus Chapters, Post-genome approaches in Xenopus. Springer Science, Humana Press.

Auger, H., Thuret, R., Papalopulu, N. (2012). A Bromodeoxyuridine (BrdU) based protocol for characterizing proliferating progenitors in Xenopus embryos, MMB Xenopus chapters, Post-genome approaches in Xenopus. Springer Science, Humana Press.

Thuret, R. and Papalopulu, N. (2012). Following the fate of neural progenitors by homotopic/homochronic grafts in Xenopus embryos. Methods in Molecular Biology, Progenitor Cells: Methods and Protocols, 916:203-15.