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.


Millán-Zambrano G, Burton A, Bannister AJ, Schneider R. (2022). Histone post-translational modifications - cause and consequence of genome function. Nat Rev Genet. PMID: 35338361.

Eve A. (2022). Transitions in development - an interview with Antonio Scialdone. Development. PMID: 35315485.

Fiorentino JScialdone A. (2022). The role of cell geometry and cell-cell communication in gradient sensing. PLoS Comput Biol. PMID: 35286298.

Ruiz Tejada Segura ML, Abou Moussa E, Garabello E, Nakahara TS, Makhlouf M, Mathew LS, Wang L, Valle F, Huang SSY, Mainland JD, Caselle M, Osella M, Lorenz S, Reisert J, Logan DW, Malnic B, Scialdone A•**, Saraiva LR**. (2022). A 3D transcriptomics atlas of the mouse nose sheds light on the anatomical logic of smell. Cell Rep. DOI: 10.1016/j.celrep.2022.110547. PMID: 35320714.

**joint corresponding author

•Fiorentino J••Scialdone A•. (2022). The role of cell geometry and cell-cell communication in gradient sensing. PLoS Comput Biol. DOI: 10.1371/journal.pcbi.1009552. PMID: 35286298. 

Nakatani T•, Lin J, Ji F, •Ettinger A•, Pontabry J, Tokoro M, •Altamirano-Pacheco L••Fiorentino J••Mahammadov E•, Hatano Y, Van Rechem C, Chakraborty D, Ruiz-Morales ER, Arguello Pascualli PY, •Scialdone A•, Yamagata K, Whetstine JR, Sadreyev RI, Torres-Padilla ME. (2022). DNA replication fork speed underlies cell fate changes and promotes reprogramming. Nat Genet. DOI: 10.1038/s41588-022-01023-0. PMID: 35256805.

•Helmholtz Munich Authors


Canat A & Torres-Padilla ME. (2021). Retrotransposing a promoter for development. Nat Cell Bio. DOI: 10.1038/s41556-021-00806-7. 

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.

*joint first author; **joint corresponding author

Burton A, Torres-Padilla ME. (2021). Deconfining heterochromatin for expression. Nat Cell Biol. DOI: 10.1038/s41556-021-00726-6. PMID: 34354235.

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 Metab. PMID: 34253906. DOI: 10.1038/s42255-021-00422-7. PMID: 34253906.

*joint first author; **joint corresponding author

Chanou AHamperl S. (2021). Single-Molecule Techniques to Study Chromatin. Front Cell Dev Bio. PMID: 34291054. DOI: 10.3389/fcell.2021.699771.

Antonio Urrutia G, Ramachandran H, Cauchy P, Boo K, Ramamoorthy S, Boller S, Dogan E, Clapes T, Trompouki E, Torres-Padilla ME, Palvimo JJ, Pichler A, Grosschedl R. (2021). ZFP451-mediated SUMOylation of SATB2 drives embryonic stem cell differentiation. Genes Dev. PMID: 34244292. DOI: 10.1101/gad.345843.120. 

Lalonde MTrauner MWerner MHamperl S. (2021). Consequences and Resolution of Transcription–Replication ConflictsLife. DOI: 10.3390/life11070637.

Pinheiro I, Torres-Padilla ME, Almouzni G. (2021). Epigenomics in the single cell era, an important read out for genome function and cell identity. Epigenomics. PMID: 34114476. DOI: 10.2217/epi-2021-0153.

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 Biol. PMID: 34045724. DOI: 10.1038/s41594-021-00590-w. 

Kruse, E, Hamperl, S. (2021). Dem Anfang auf der Spur — die Suche nach DNA-Replikationsursprüngen. Biospektrum. DOI: 10.1007/s12268-021-1562-z.

Hörmanseder E. (2021). Epigenetic memory in reprogrammingCurr Opin Genet Dev. PMID: 34058535. DOI: 10.1016/j.gde.2021.04.007.

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. Science. PMID: 33414188. DOI: 10.1126/science.abb2986. 

Hermant C, Torres-Padilla ME. (2021). TFs for TEs: the transcription factor repertoire of mammalian transposable elements. Genes Dev. PMID: 33397727. DOI: 10.1101/gad.344473.120. 


Pal M., Kind J., Torres-Padilla M.E. (2020). DamID to Map Genome-Protein Interactions in Preimplantation Mouse Embryos. Methods Mol Biol. PMID: 32944916. DOI: 10.1007/978-1-0716-0958-3_18. 

Ancelin K., Miyanari Y., Leroy O., Torres-Padilla M.E., Heard E. (2020). Mapping of Chromosome Territories by 3D-Chromosome Painting During Early Mouse Development. Methods Mol Biol. PMID: 32944910. DOI: 10.1007/978-1-0716-0958-3_12. 

Rajewsky N., Almouzni G., Gorski SA., Aerts S., Amit I., Bertero M.G., Bock C., Bredenoord A.L., Cavalli G., Chiocca S., Clevers H., De Strooper B., Eggert A., Ellenberg J., Fernández X.M., Figlerowicz M., Gasser S.M., Hubner N., Kjems J., Knoblich J.A., Krabbe G., Lichter P., Linnarsson S., Marine J.C., Marioni J., Marti-Renom M.A., Netea M.G., Nickel D., Nollmann M., Novak H.R., Parkinson H., Piccolo S., Pinheiro I., Pombo A., Popp C., Reik W., Roman-Roman S., Rosenstiel P., Schultze J.L., Stegle O., Tanay A., Testa G., Thanos D., Theis F.J., Torres-Padilla M.E., Valencia A., Vallot C., van Oudenaarden A., Vidal M., Voet T.; LifeTime Community. (2020). LifeTime and improving European healthcare through cell-based interceptive medicine. Nature. PMID: 32894860. DOI: 10.1038/s41586-020-2715-9. 

Torres-Padilla M.E., Bredenoord A.L., Jongsma K.R., Lunkes A., Marelli L., Pinheiro I., Testa G. (2020). Thinking "ethical" when designing an international, cross-disciplinary biomedical research consortium. EMBO J. PMID: 32894572. DOI: 10.15252/embj.2020105725.

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.

Genet M., Torres-Padilla M.E. (2020). The molecular and cellular features of 2-cell-like cells: a reference guide. Development. PMID: 32847823. DOI: 10.1242/dev.189688. 

Burton, A., Brochard, V., Galan, C., Ruiz-Morales, E. R., Rovira, Q., Rodriguez-Terrones, D., Kruse, K., Le Gras, S., Udayakumar, V. S., Chin, H. G., Eid, A., Liu, X., Wang, C., Gao, S., Pradhan, S., Vaquerizas, J. M., Beaujean, N., Jenuwein, T., & Torres-Padilla, M. E. (2020). Heterochromatin establishment during early mammalian development is regulated by pericentromeric RNA and characterized by non-repressive H3K9me3. Nat Cell Bio. PMID: 32601371. DOI; 10.1038/s41556-020-0536-6.

Iturbide, A., & Torres-Padilla, M. E. (2020). A cell in hand is worth two in the embryo: recent advances in 2-cell like cell reprogramming. Curr Opin Genetic Dev. PMID: 32599301. DOI: 10.1016/j.gde.2020.05.038.

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.

Ummethum, H. Hamperl, S. (2020). Proximity labeling techniques to study chromatin. Front Genet.  PMID: 32477404. DOI: 10.3389/fgene.2020.00450.

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

Torres-Padilla, M.E. (2020). On transposons and totipotency. Philos Trans R Soc B - Biol Sci. PMID: 32075562. DOI: 10.1098/rstb.2019.0339.

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

Cebrià-Costa, J.P. , Pascual-Reguant, L. , Gonzalez-Perez, A. , Serra-Bardenys, G. , Querol, J. , Cosín, M. , Verde, G. , Cigliano, R.A. , Sanseverino, W. , Segura-Bayona, S. , Iturbide Martinez De Albeniz, A. , Andreu, D. , Nuciforo, P. , Bernado-Morales, C. , Rodilla, V. , Arribas, J. , Yelamos, J. , de Herreros, A.G. , Stracker, T.H. , Peiró, S. (2020). LOXL2-mediated H3K4 oxidation reduces chromatin accessibility in triple-negative breast cancer cells. Oncogene. PMID: 31462706. DOI: 10.1038/s41388-019-0969-1.

Rodriguez-Terrones, D. , Hartleben, G. , Gaume, X. , Eid, A. , Guthmann, M. , Iturbide Martinez De Albeniz, A. , Torres-Padilla, M.E. (2020). A distinct metabolic state arises during the emergence of 2-cell-like cellsEMBO RepPMID: 31849178. DOI: 10.15252/embr.201948354.  


Guthmann M, Burton A, Torres-Padilla ME (2019). Expression and phase separation potential of heterochromatin proteins during early mouse development. EMBO Rep. PMID: 31701657. DOI: 10.15252/embr.201947952.

Jansz N (2019). DNA methylation dynamics at transposable elements in mammalsEssays Biochem. PMID: 31654072. DOI: 10.1042/EBC20190039.

Bruneau BG, Koseki H, Strome S, Torres-Padilla ME (2019). Chromatin and epigenetics in development: a Special Issue. Development. PMID: 31601561. PII: dev185025. DOI: 10.1242/dev.185025.

Pich D, Mrozek-Gorska P, Bouvet M, Sugimoto A, Akidil E, Grundhoff A, Hamperl S, Ling PD, Hammerschmidt W (2019). First Days in the Life of Naive Human B Lymphocytes Infected with Epstein-Barr Virus. Mbio. PMID: 31530670. PII: e01723-19. DOI: 10.1128/mBio.01723-19.

Ragazzini R, Pérez-Palacios R, Baymaz IH, Diop S, Ancelin K, Zielinski D, Michaud A, Givelet M, Borsos M, Aflaki S, Legoix P, Jansen PWTC, Servant N, Torres-Padilla ME, Bourc'his D, Fouchet P, Vermeulen M, Margueron R (2019). EZHIP constrains Polycomb Repressive Complex 2 activity in germ cells. Nat Commun. PMID: 31451685. DOI: 10.1038/s41467-019-11800-x.

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. PII: 201901314. DOI: 10.1073/pnas.1901314116. **joint senior authors

Borsos M*, Perricone SM*, Schauer T, Pontabry J, de Luca KL, de Vries SS, Ruiz-Morales ER, Torres-Padilla ME**, Kind J** (2019). Genome-lamina interactions are established de novo in the early mouse embryo. Nature. PMID: 31118510. DOI: 10.1038/s41586-019-1233-0. *joint first authors **joint senior authors

Jansz N, Torres-Padilla ME (2019). Genome activation and architecture in the early mammalian embryo. Curr Opin Genet Dev. PMID: 31128483. DOI: 10.1016/j.gde.2019.04.011.

Fissore RA, Burton A, Lykke-Hartmann K (2019). Editorial: Molecular and Cellular Mechanisms in Reproduction and Early Development. Front Cell Dev Biol. PMID: 30949478DOI: 10.3389/fcell.2019.00036.

Huang Y, Chanou A, Kranz G, Pan M, Kohlbauer V, Ettinger A, Gires O (2019). Membrane-associated epithelial cell adhesion molecule is slowly cleaved by γ-secretase prior to efficient proteasomal degradation of its intracellular domain. J Biol Chem. PMID: 30598504. DOI: 10.1074/jbc.RA118.005874.

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.


Cossec JA, Theurillat I, Chica C, Búa Aguín S, Gaume X, Andrieux A, Iturbide A, Jouvion G, Li H, Bossis G, Seeler JB, Torres-Padilla ME, Dejean A. (2018). SUMO Safeguards Somatic and Pluripotent Cell Identities by Enforcing Distinct Chromatin States. Cell Stem Cell.

Marti-Renom MA, Almouzni G, Bickmore WA, Bystricky K, Cavalli G, Fraser P, Gasser SM, Giorgetti L, Heard E, Nicodemi M, Nollmann M, Orozco M, Pombo A, Torres-Padilla ME (2018).Challenges and guidelines toward 4D nucleome data and model standards. Nat Genet. doi: 10.1038/s41588-018-0236-3. Review.

Rodriguez-Terrones D, Torres-Padilla ME (2018) Nimble and ready to mingle: Transposon outbursts of early development, Trends in Genetics, doi: 10.1016/j.tig.2018.06.006

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 opportunitiesNature Methods. PMID: 28504683. DOI: 10.1038/nmeth.4292.

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.