Publications

2017

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

2016

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

2015

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

2013

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

2012

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

2011

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

2010

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

2009

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

2008

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