Physics and data-based modelling of cellular decision making

2021

Tyser RCV, Mahammadov E, Nakanoh S, Vallier L, Scialdone A, Srinivas S. (2021) . Single-cell transcriptomic characterization of a gastrulating human embryo. Nature. DOI: 10.1038/s41586-021-04158-y.  PMID: 34789876.

Lima A, Lubatti G, Burgstaller J, Hu D, Green AP, Di Gregorio A, Zawadzki T, Pernaute B, Mahammadov E, Perez-Montero S, Dore M, Sanchez JM, Bowling S, Sancho M, Kolbe T, Karimi MM, Carling D, Jones N, Srinivas S, Scialdone A, Rodriguez TA. (2021). Cell competition acts as a purifying selection to eliminate cells with mitochondrial defects during early mouse development. Nat MetabPMID: 34253906. DOI: 10.1038/s42255-021-00422-7. PMID: 34253906.

Iturbide A, Ruiz Tejeda Segura ML, Noll C, Schorpp K, Rothenaigner I, Ruiz-Morales ER, Lubatti G, Agami A, Hadian K, Scialdone A, Torres-Padilla ME. (2021). Retinoic acid signaling is critical during the totipotency window in early mammalian development. Nat Struct Mol BiolPMID: 34045724. DOI: 10.1038/s41594-021-00590-w. 

Tyser RCV, Ibarra-Soria X, McDole K, Arcot Jayaram S, Godwin J, van den Brand TAH, Miranda AMA, Scialdone A, Keller PJ, Marioni JC, Srinivas S. (2021). Characterization of a common progenitor pool of the epicardium and myocardium. SciencePMID: 33414188. DOI: 10.1126/science.abb2986. 

2020

Fiorentino J.Torres-Padilla M.E., Scialdone A. (2020). Measuring and Modeling Single-Cell Heterogeneity and Fate Decision in Mouse Embryos. Annu Rev Genet. PMID: 32867543. DOI: 10.1146/annurev-genet-021920-110200.

Huang, S., Makhlouf, M., AbouMoussa, E. H., Ruiz Tejada Segura, M. L., Mathew, L. S., Wang, K., Leung, M. C., Chaussabel, D., Logan, D. W., Scialdone, A., Garand, M., & Saraiva, L. R. (2020). Differential regulation of the immune system in a brain-liver-fats organ network during short-term fasting. Mol Met. PMID: 32526449. DOI: 10.1016/j.molmet.2020.101038.

Solovey, M. , Scialdone, A. (2020). COMUNET: A tool to explore and visualize intercellular communication. Bioinformatics. DOI: 10.1093/bioinformatics/btaa482.

Angerer, P. , Fischer, D.S. , Theis, F.J. , Scialdone, A.**Marr, C.**. (2020). Automatic identification of relevant genes from low-dimensional embeddings of single cell RNAseq data. Bioinformatics. PMID: 32207520  DOI: 10.1093/bioinformatics/btaa198. **joint senior authors.

2019

Mrozek-Gorska P, Buschle A, Pich D, Schwarzmayr T, Fechtner R, Scialdone A**, Hammerschmidt W** (2019). Epstein-Barr virus reprograms human B lymphocytes immediately in the prelatent phase of infection. Proc Natl Acad Sci U S A. PMID: 31341086. DOI: 10.1073/pnas.1901314116. **joint senior authors

Manoel D, Makhlouf M, Scialdone A, Saraiva LR (2019). Interspecific variation of olfactory preferences in flies, mice, and humans. Chem Senses. PMID: 30445540. DOI: 10.1093/chemse/bjy074.

2018

Griffiths JA, Scialdone A, Marioni JC. (2018). Using single-cell genomics to understand developmental processes and cell fate decisionsMol Syst Biol. PMID: PMID: 29661792. 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. PMID: 29311656. DOI: 10.1038/s41556-017-0013-z.

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 differentiationNature Scientific Reports. PMID: 29379062. DOI: 10.1038/s41598-018-20131-8.

2017

Shahbazi, M.N. , Scialdone, A. , Skorupska, N. , Weberling, A. , Recher, G. , Zhu, M. , Jedrusik, A. , Devito, L.G. , Noli, L. , Macaulay, I.C. , Buecker, C. , Khalaf, Y. , Ilic, D. , Voet, T. , Marioni, J.C. , Zernicka-Goetz, M. (2017). Pluripotent state transitions coordinate morphogenesis in mouse and human embryos. Nature. PMID: 29186120.  DOI: 10.1038/nature24675

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 GastrulationCell Reports. PMID: 28768204. 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 opportunitiesNature Methods. PMID: 28504683. DOI: 10.1038/nmeth.4292.

Beagrie, R. A., Scialdone, A., Schueler, M., Kraemer, D. C., Chotalia, M., Xie, S. Q., Barbieri, M., de Santiago, I., Lavitas, L. M., Branco, M. R., Fraser, J., Dostie, J., Game, L., Dillon, N., Edwards, P. A., Nicodemi, M., & Pombo, A. (2017). Complex multi-enhancer contacts captured by genome architecture mapping. Nature. PMID: 28273065. DOI: 10.1038/nature21411. 

Ambrosi, T. H., Scialdone, A., Graja, A., Gohlke, S., Jank, A. M., Bocian, C., Woelk, L., Fan, H., Logan, D. W., Schürmann, A., Saraiva, L. R., & Schulz, T. J. (2017). Adipocyte accumulation in the bone marrow during obesity and aging impairs stem cell-based hematopoietic and bone regenerationCell Stem Cell. PMID: 28330582. DOI: 10.1016/j.stem.2017.02.009.

Griffiths JA, Scialdone A, Marioni JC. (2017) Mosaic autosomal aneuploidies are detectable from single-cell RNAseq dataBMC Genomics. PMID: 29178830. DOI: 10.1186/s12864-017-4253-x.

2016

Scialdone, A., Tanaka, Y., Jawaid, W., Moignard, V., Wilson, N. K., Macaulay, I. C., Marioni, J. C., & Göttgens, B. (2016). Resolving early mesoderm diversification through single-cell expression profiling. Nature. PMID: 27383781. DOI: 10.1038/nature18633.

2015

Scialdone, A., Natarajan, K. N., Saraiva, L. R., Proserpio, V., Teichmann, S. A., Stegle, O., Marioni, J. C., & Buettner, F. (2015). Computational assignment of cell-cycle stage from single-cell transcriptome data. Methods. PMID: 26142758.  DOI: 10.1016/j.ymeth.2015.06.021.

Buettner, F., Natarajan, K. N., Casale, F. P., Proserpio, V., Scialdone, A.Theis, F. J., Teichmann, S. A., Marioni, J. C., & Stegle, O. (2015). Computational analysis of cell-to-cell heterogeneity in single-cell RNA-sequencing data reveals hidden subpopulations of cellsNature biotechnology. PMID: 25599176. DOI: 10.1038/nbt.3102.

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

Pre-print publications

Tyser R.C.V, Mahammadov E., Nakanoh S., Vallier L, Scialdone A, Srinivas S. (2020). A spatially resolved single cell atlas of human gastrulation. bioRxiv 2020.07.21.213512; DOI: https://doi.org/10.1101/2020.07.21.213512

Lima A., Lubatti G., Burgstaller J., Hu D., Green A., Di Gregorio A., Zawadzki T., Pernaute B., Mahammadov E., Perez Montero S., Dore M., Sanchez J.M., Bowling S., Sancho M., Karimi M., Carling D., Jones N., Srinivas S., Scialdone A., Rodriguez T.A. (2020). Cell competition acts as a purifying selection to eliminate cells with mitochondrial defects during early mouse development. bioRxiv 2020.01.15.900613; DOI: https://doi.org/10.1101/2020.01.15.900613


Beagrie R.A., Thieme C.J., Annunziatella C., Baugher C., Zhang Y., Schueler M., Kramer D.C.A.,Chiariello A.M., Bianco S., Kukalev A., Li Y., Kempfer R., Scialdone A., Welch L.R., Nicodemi M., Pombo A. (2020). Multiplex-GAM: genome-wide identification of chromatin contacts yields insights not captured by Hi-C. bioRxiv 2020.07.31.230284; DOI: https://doi.org/10.1101/2020.07.31.230284