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


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