Physics and data-based modelling of cellular decision making


Griffiths JA, Scialdone A, Marioni JC. (2018) Using single-cell genomics to understand developmental processes and cell fate decisions. Mol Syst Biol 14(4):e8046. doi: 10.15252/msb.20178046.

Ibarra-Soria X, Jawaid W, Pijuan-Sala B, Ladopoulos V, Scialdone A, Jörg DJ, Tyser RCV, Calero-Nieto FJ, Mulas C, Nichols J, Vallier L, Srinivas S, Simons BD, Göttgens B, Marioni JC., 2018, Defining murine organogenesis at single-cell resolution reveals a role for the leukotriene pathway in regulating blood progenitor formation. Nat Cell Biol. 2018 Feb;20(2):127-134. doi: 10.1038/s41556-017-0013-z. Epub 2018 Jan 8.

Sarrach S, Huang Y, Niedermeyer S, Hachmeister M, Fischer L, Gille S, Pan M, Mack B, Kranz G, Libl D, Merl-Pham J, Hauck SM, Paoluzzi Tomada E, Kieslinger M, Jeremias I, Scialdone A, Gires O., 2018, Spatiotemporal patterning of EpCAM is important for murine embryonic endo- and mesodermal differentiation, Nature Scientific Reports volume 8, Article number: 1801 (2018), 10.1038/s41598-018-20131-8


Mohammed H, Hernando-Herraez I, Savino A, Scialdone A, Macaulay I, Mulas C, Chandra T, Voet T, Dean W, Nichols J, Marioni JC, Reik W. (2017) Single-Cell Landscape of Transcriptional Heterogeneity and Cell Fate Decisions during Mouse Early Gastrulation. Cell Reports. 20(5):1215-1228. doi: 10.1016/j.celrep.2017.07.009.

C.A. Vallejos*, D. Risso*, A. Scialdone*, S. Dudoit, J.C. Marioni (2017) Normalizing single-cell RNA sequencing data: challenges and opportunities, Nature Methods, 14:565
*joint first authors

R. A. Beagrie*, A. Scialdone*, M. Schueler, D.C.A. Kraemer, M. Chotalia, S.Q. Xie, M. Barbieri, I. de Santiago, L.-M. Lavitas, M.R. Branco, J. Fraser, J. Dostie, L. Game, N. Dillon, P.A.W. Edwards, M. Nicodemi and A. Pombo, (2017) Complex multi-enhancer contacts captured by Genome Architecture Mapping (GAM), Nature, 543:519
* joint first authors

T. H. Ambrosi, A. Scialdone, A. Graja, S. Gohlke, A.-M. Jank, L. Woelk,H. Fan, D.W. Logan, A. Schurmann, L.R. Saraiva and T.J. Schulz (2017) Adipocyte accumulation in the bone marrow during obesity and aging impairs stem cell-based hematopoietic and bone regeneration, Cell Stem Cell 20:739

Shahbazi MN, Scialdone A, Skorupska N, Weberling A, Recher G, Zhu M, Jedrusik A, Devito LG, Noli L, Macaulay IC, Buecker C, Khalaf Y, Ilic D, Voet T, Marioni JC, Zernicka-Goetz M. (2017) Pluripotent state transitions coordinate morphogenesis in mouse and human embryos. Nature 552(7684):239-243. doi: 10.1038/nature24675.

Griffiths JA, Scialdone A, Marioni JC. (2017) Mosaic autosomal aneuploidies are detectable from single-cell RNAseq data, BMC Genomics, 18(1):904. doi: 10.1186/s12864-017-4253-x.


A. Scialdone*, Y. Tanaka*, W. Jawaid*, V. Moignard*, N.K. Wilson, I.C.Macaulay, J.C. Marioni and B. Gottgens (2016) Resolving early mesoderm diversification through single-cell expression profiling, Nature, 535:289
* joint first authors

M. Goolam*, A. Scialdone*, S.J.L. Graham*, I.C. Macaulay, A. Jedrusik, A. Hupalowska, T. Voet, J.C. Marioni and M. Zernicka-Goetz, (2016) Heterogeneity in Oct4 and Sox2 targets biases cell fate in four-cell mouse embryos, Cell, 165:61,
* joint first authors


L. Saraiva, X. Ibarra-Soria, M. Khan, M. Omura, A. Scialdone, P. Mombaerts, J.C. Marioni and D. Logan (2015) Hierarchical deconstruction of mouse olfactory sensory neurons: from whole mucosa to single-cell RNA-seq, Scientific Reports, 5:18178

A. Scialdone, K.N. Natarajan, L.R. Saraiva, V. Proserpio, S.A. Teichmann, O. Stegle, J.C. Marioni and F. Buettner, (2015) Computational assignment of cell-cycle stage from single-cell transcriptome data, Methods, 85:54

F. Buettner, K.N. Natarajan, F.P. Casale, V. Proserpio, A. Scialdone, F.J. Theis, S.A. Teichmann, J.C. Marioni and O. Stegle, (2015) Computational analysis of cell-to-cell heterogeneity in single-cell RNA-sequencing data reveals hidden subpopulations of cells, Nature Biotechnology, 33:155

A. Scialdone and M. Howard, (2015) How plants manage food reserves at night: quantitative models and open questions, Frontiers in Plant Science, 6:204


M. Barbieri, A. Scialdone, A. Gamba, A. Pombo and M. Nicodemi, (2013) Polymer physics, scaling and heterogeneity in the spatial organisation of chromosomes in the cell nucleus, Soft Matter , 9:8631

M. Barbieri, A. Scialdone, A. Piccolo, A.M. Chiariello, C. di Lanno, A. Prisco, A. Pombo and M. Nicodemi, (2013) Polymers models of chromatin organization, Frontiers in Genetics, 4:113

A. Scialdone*, S.T. Mugford*, D. Feike, A. Ske_ngton, P. Borrill, A. Graf, A. M. Smith and M. Howard, (2013) Arabidopsis plants perform arithmetic division to prevent starvation at night, eLife, e00669,
* joint first authors


V. Bianco, A. Scialdone and M. Nicodemi, (2012) Colocalization of multiple DNA loci: a physical mechanism, Biophysical Journal, 103:2223


A. Scialdone, I. Cataudella, M. Barbieri, A. Prisco and M. Nicodemi, (2011) Conformation regulation of the X Chromosome Inactivation Center: a model, PloS Computational Biology, 7:e1002229

A. Scialdone, M. Barbieri, D. Pallotti and M. Nicodemi, (2011) Mean-field theory of the symmetry breaking model for X Chromosome Inactivation, Progress of Theoretical Physics Supplement, 191:40


A. Scialdone and M. Nicodemi, (2010) Passive DNA-shuttling, Europhysics Letters, 92:20002

A. Scialdone and M. Nicodemi, (2010) Diffusion-based DNA target colocalization by thermodynamic mechanisms, Development, 137:3877,

A. Scialdone and M. Nicodemi, (2010) Statistical Mechanics models for X Chromosome inactivation, Advances in Complex Systems, 13:367


A. Scialdone and M. Nicodemi, (2009) DNA loci cross-talk through thermodynamics, Journal of Biomedicine and Biotechnology, 2009:516723


A. Scialdone and M. Nicodemi, (2008) Mechanics and dynamics of X Chromosome pairing at X Chromosome Inactivation, PloS Computational Biology, 4:e10000244