The Institute of Epigenetics and Stem Cells was established in 2016.  Publication lists for each of the research teams can be found in the Research section.


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.

Rodriguez-Terrones D, Gaume X, Ishiuchi T, Weiss A, Kopp A, Kruse K, Penning A, Vaquerizas JM, Brino L, Torres-Padilla ME. (2018) A molecular roadmap for the emergence of early-embryonic-like cells in culture, Nature Genetics, 50(1):106-119>

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


Jachowicz JW, Bing X, Pontabry J, Boskovic A, Rando OJ, Torres-Padilla ME, 2017, LINE-1 activation after fertilization regulates global chromatin accessibility in the early mouse embryo, Nature Genetics, 49, 1502-1510 doi: 10.1038/ng.3945

Izzo A, Ziegler-Birling C, Hill PWS, Brondani L, Hajkova P, Torres-Padilla ME, Schneider R (2017) Dynamic changes in H1 subtype composition during epigenetic reprogramming, Journal of Cell Biology, DOI: 10.1083/jcb.201611012.

Iturbide A and Torres-Padilla ME (2017) Starting embryonic transcription for the first time. Nature Genetics  49,820–821, doi:10.1038/ng.3880

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, 565-571
*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: 519-524
* 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.


Eid A, Rodriguez-Terrones D, Burton A, Torres-Padilla ME. 2016. SUV4-20 activity in the preimplantation mouse embryo controls timely replication. Genes and Development, doi: 10.1101/gad.288969.116

Burton A, Torres-Padilla ME. 2016. A Pluripotency Platform for Prdm14. Developmental Cell, 38(1): 3-5

Vaquerizas JM, Torres-Padilla ME. 2016. Developmental Biology: Panoramic views of the early epigenome. Nature doi:10.1038/nature19468

Eid A, Torres-Padilla ME. 2016. Characterization of non-canonical Polycomb Repressive Complex 1 subunits during early mouse embryogenesis. Epigenetics, 1-9

Borsos M, Torres-Padilla ME. 2016. Building up the nucleus: nuclear organization in the establishment of totipotency and pluripotency during mammalian development. Genes and Development 30(6): 611-621.