Publications
Nitsch, S. ; Coraor, A.E. ; Schauer, T. ; Wu, Y. ; Sun, J. ; Möritz, N. ; Funke, J.J. ; Nagpal, H. ; Chua, G.N.L. ; Battistini, F. ; Lauberth, S.M. ; Richard, E.M. ; Orozco, M. ; Liu, S. ; Desviat, L.R. ; Fierz, B. ; Dietz, H. ; Roeder, R.G. ; de Pablo, J.J. ; Schneider, R.
H4K16 acylations destabilize chromatin architecture and facilitate transcriptional response during metabolic perturbations.Oak, M.S. ; Stock, M. ; Janeva, A. ; Mezes, M. ; Hynes-Allen, A.M. ; Straub, T. ; Forné, I. ; Ettinger, A. ; Hamperl, S. ; Imhof, A. ; van den Ameele, J. ; Scialdone, A. ; Hörmanseder, E.
Pre-marking chromatin with H3K4 methylation is required for accurate zygotic genome activation and development.Ummethum, H. ; Murriello, A.C. ; Werner, M. ; Márquez-Gómez, E. ; König, A.-C. ; Kruse, E. ; Lalonde, M. ; Trauner, M. ; Chanou, A. ; Weiß, M. ; Lee, C.S.K. ; Ettinger, A. ; Erhard, F. ; Hauck, S.M. ; Hamperl, S.
The CGG triplet repeat binding protein 1 counteracts R-loop induced transcription-replication stress.Wagner, C.B. ; Longaretti, M. ; Sergi, S.G. ; Singh, N. ; Tsirkas, I. ; Bento, F. ; Wong, R.P. ; Wilkens, M. ; Hamperl, S. ; Butter, F. ; Aharoni, A. ; Ulrich, H.D. ; Luke, B.
Rad53 regulates RNase H1, which promotes DNA replication through sites of transcription-replication conflict.Apostolou, Z. ; Venkatasubramani, A.V. ; Kopp, L.C. ; Kars, G. ; Scacchetti, A. ; Campos-Sparr, A. ; Schauer, T. ; Imhof, A. ; Becker, P.B.
The Tip60 acetylome is a hallmark of the proliferative state in Drosophila.Ewe, C.K. ; Farnworth, M.S. ; Miller, A. ; Navajas Acedo, J. ; Oomen, M.E. ; Paci, G. ; Widen, S.A. ; Yamada, T.
Pathway to Independence: A forecast for the future of developmental biology.Stock, M.
Incorporation of prior knowledge to improve gene regulatory network inference from single-cell transcriptomics data.Iturbide Martinez De Albeniz, A. ; Ruiz Tejada Segura, M.L. ; Noll, C. ; Schorpp, K.K. ; Rothenaigner, I. ; Ruiz-Morales, E.R. ; Lubatti, G. ; Agami, A. ; Hadian, K. ; Scialdone, A. ; Torres-Padilla, M.E.
Addendum: Retinoic acid signaling is critical during the totipotency window in early mammalian development.Fukagawa, T. ; Torres-Padilla, M.E.
Exploring the cell nucleus: From chromosome structure to single-cell omics.Hains, A.E. ; Marques, J.G. ; Chetal, K. ; Nakatani, T. ; Ettinger, A. ; Biagi, C.A.O.d. ; Gonzalez‐Sandoval, A. ; Pillai, R. ; Gatto, A. ; Torres-Padilla, M.E. ; Sadreyev, R.I. ; Filbin, M.G. ; Rechem, C.V.
Abstract SY23-01: Diffuse midline gliomas: From cell cycle to therapeutic opportunities.Nakatani, T.
Dynamics of replication timing during mammalian development.Zikmund, T. ; Fiorentino, J. ; Penfold, C. ; Stock, M. ; Shpudeiko, P. ; Agarwal, G. ; Langfeld, L. ; Petrova, K. ; Peshkin, L. ; Hamperl, S. ; Scialdone, A. ; Hörmanseder, E.
Differentiation success of reprogrammed cells is heterogeneous in vivo and modulated by somatic cell identity memory.Neupane, J. ; Lubatti, G. ; Gross-Thebing, T. ; Ruiz Tejada Segura, M.L. ; Butler, R.H. ; Gross-Thebing, S. ; Dietmann, S. ; Scialdone, A. ; Surani, M.A.
The emergence of human primordial germ cell-like cells in stem cell-derived gastruloids.Burton, A. ; Torres-Padilla, M.E.
Epigenome dynamics in early mammalian embryogenesis.Nakatani, T. ; Schauer, T. ; Pal, M. ; Ettinger, A. ; Altamirano-Pacheco, L. ; Zorn, J. ; Gilbert, D.M. ; Torres-Padilla, M.E.
RIF1 controls replication timing in early mouse embryos independently of lamina-associated nuclear organization.Pal, M. ; Schauer, T. ; Burton, A. ; Nakatani, T. ; Pecori, F. ; Hernández-Giménez, A. ; Nadelson, I. ; Marti-Renom, M.A. ; Torres-Padilla, M.E.
The establishment of nuclear organization in mouse embryos is orchestrated by multiple epigenetic pathways.Götz, M. ; Torres-Padilla, M.E.
Stem cells as role models for reprogramming and repair.Stock, M. ; Losert, C. ; Zambon, M. ; Popp, N. ; Lubatti, G. ; Hörmanseder, E. ; Heinig, M. ; Scialdone, A.
Leveraging prior knowledge to infer gene regulatory networks from single-cell RNA-sequencing data.Toghani, D. ; Gupte, S.C. ; Zeng, S. ; Mahammadov, E. ; Crosse, E.I. ; Seyedhassantehrani, N. ; Burns, C. ; Gravano, D. ; Radtke, S. ; Kiem, H.P. ; Rodriguez, S. ; Carlesso, N. ; Pradeep, A. ; Georgiades, A. ; Lucas, F. ; Wilson, N.K. ; Kinston, S.J. ; Göttgens, B. ; Zong, L. ; Beerman, I. ; Park, B. ; Janssens, D.H. ; Jones, D. ; Toghani, A. ; Nerlov, C. ; Pietras, E.M. ; Mesnieres, M. ; Maes, C. ; Kumanogoh, A. ; Worzfeld, T. ; Cheong, J.G. ; Josefowicz, S.Z. ; Kharchenko, P.V. ; Scadden, D.T. ; Scialdone, A. ; Spencer, J.A. ; Silberstein, L.
Niche-derived Semaphorin 4A safeguards functional identity of myeloid-biased hematopoietic stem cells.Oomen, M.E. ; Rodriguez-Terrones, D. ; Kurome, M. ; Zakhartchenko, V. ; Mottes, L. ; Simmet, K. ; Noll, C. ; Nakatani, T. ; Mourra-Díaz, D.M. ; Aksoy, I. ; Savatier, P. ; Goke, J. ; Wolf, E. ; Kaessmann, H. ; Torres-Padilla, M.E.
An atlas of transcription initiation reveals regulatory principles of gene and transposable element expression in early mammalian development.Werner, M. ; Trauner, M. ; Schauer, T. ; Ummethum, H. ; Márquez-Gómez, E. ; Lalonde, M. ; Lee, C.S.K. ; Tsirkas, I. ; Sajid, A. ; Murriello, A.C. ; Längst, G. ; Hamperl, S.
Transcription-replication conflicts drive R-loop-dependent nucleosome eviction and require DOT1L activity for transcription recovery.Hermant, C. ; Mourra-Díaz, D.M. ; Oomen, M.E. ; Altamirano-Pacheco, L. ; Pal, M. ; Nakatani, T. ; Torres-Padilla, M.E.
The transcription factor SRF regulates MERVL retrotransposons and gene expression during zygotic genome activation.Toghani, D. ; Gupte, S.C. ; Zeng, S. ; Mahammadov, E. ; Crosse, E.I. ; Seyedhassantehrani, N. ; Burns, C. ; Gravano, D. ; Radtke, S. ; Kiem, H.P. ; Rodriguez, S. ; Carlesso, N. ; Pradeep, A. ; Georgiades, A. ; Lucas, F. ; Wilson, N.K. ; Kinston, S.J. ; Göttgens, B. ; Zong, L. ; Beerman, I. ; Park, B. ; Janssens, D.H. ; Jones, D. ; Toghani, A. ; Nerlov, C. ; Pietras, E.M. ; Mesnieres, M. ; Maes, C. ; Kumanogoh, A. ; Worzfeld, T. ; Cheong, J.G. ; Josefowicz, S.Z. ; Kharchenko, P.V. ; Scadden, D.T. ; Scialdone, A. ; Spencer, J.A. ; Silberstein, L.
Author Correction: Niche-derived Semaphorin 4A safeguards functional identity of myeloid-biased hematopoietic stem cells.Hains, A.E. ; Chetal, K. ; Nakatani, T. ; Marques, J.G. ; Ettinger, A. ; Junior, C.A.O.B. ; Gonzalez-Sandoval, A. ; Pillai, R. ; Filbin, M.G. ; Torres-Padilla, M.E. ; Sadreyev, R.I. ; Van Rechem, C.
Multi-omics approaches reveal that diffuse midline gliomas present altered DNA replication and are susceptible to replication stress therapy.Arner, A. ; Ettinger, A. ; Blaser, B.W. ; Schmid, B. ; Jeremias, I. ; Rostam, N. ; Binder-Blaser, V.
In vivo monitoring of leukemia-niche interactions in a zebrafish xenograft model.Schauer, T.
Bioinformatics core workflow for ChIP-seq data analysis.Ebisuya, M. ; Rayon, T. ; Diaz-Cuadros, M. ; Chalut, K.J. ; Wu, G. ; Dodd, A.N. ; Torres-Padilla, M.E. ; Levine, M.E. ; Gladyshev, V.N.
Understanding how cells and organisms keep time during development.Pereira, A. ; Diwakar, S.J. ; Masserdotti, G. ; Beşkardeş, S. ; Simon, T. ; So, Y. ; Martín-Loarte, L. ; Bergemann, F. ; Vasan, L. ; Schauer, T. ; Danese, A. ; Bocchi, R. ; Colomé-Tatché, M. ; Schuurmans, C. ; Philpott, A. ; Straub, T. ; Bonev, B. ; Götz, M.
Direct neuronal reprogramming of mouse astrocytes is associated with multiscale epigenome remodeling and requires Yy1.Liu, B. ; He, Y. ; Wu, X. ; Lin, Z. ; Ma, J. ; Qiu, Y. ; Xiang, Y. ; Kong, F. ; Lai, F. ; Pal, M. ; Wang, P. ; Ming, J. ; Zhang, B. ; Wang, Q. ; Wu, J. ; Xia, W. ; Shen, W. ; Na, J. ; Torres-Padilla, M.E. ; Li, J. ; Xie, W.
Mapping putative enhancers in mouse oocytes and early embryos reveals TCF3/12 as key folliculogenesis regulators.Thowfeequ, S. ; Fiorentino, J. ; Hu, D. ; Solovey, M. ; Ruane, S. ; Whitehead, M. ; Zhou, F. ; Godwin, J. ; Mateo-Otero, Y. ; Vanhaesebroeck, B. ; Scialdone, A. ; Srinivas, S.
An integrated approach identifies the molecular underpinnings of murine anterior visceral endoderm migration.Stock, M. ; Popp, N. ; Fiorentino, J. ; Scialdone, A.
Topological benchmarking of algorithms to infer Gene Regulatory Networks from Single-Cell RNA-seq Data.Chen, Y.-L. ; Jones, A. ; Crawford, A. ; Sattler, M. ; Ettinger, A. ; Torres-Padilla, M.E.
Determinants of minor satellite RNA function in chromosome segregation in mouse embryonic stem cells.Oomen, M.E. ; Torres-Padilla, M.E.
Jump-starting life: balancing transposable element co-option and genome integrity in the developing mammalian embryo.Werner, M. ; Hamperl, S.
A quick restart: RNA polymerase jumping onto post-replicative chromatin.Mahammadov, E.
Elucidating cell-fate decision-making of mammalian pluripotent cells through single-cell transcriptomics.Nakatani, T. ; Schauer, T. ; Altamirano-Pacheco, L. ; Klein, K.N. ; Ettinger, A. ; Pal, M. ; Gilbert, D.M. ; Torres-Padilla, M.E.
Emergence of replication timing during early mammalian development.Pal, M. ; Altamirano-Pacheco, L. ; Schauer, T. ; Torres-Padilla, M.E.
Reorganization of lamina-associated domains in early mouse embryos is regulated by RNA polymerase II activity.Chanou, A. ; Weiß, M. ; Holler, K. ; Sajid, A. ; Straub, T. ; Krietsch, J. ; Sanchi, A. ; Ummethum, H. ; Lee, C.S.K. ; Kruse, E. ; Trauner, M. ; Werner, M. ; Lalonde, M. ; Lopes, M. ; Scialdone, A. ; Hamperl, S.
Single molecule MATAC-seq reveals key determinants of DNA replication origin efficiency.Sajid, A. ; Hamperl, S.
Single-copy gene locus chromatin purification in Saccharomyces cerevisiae.Lalonde, M. ; Ummethum, H. ; Trauner, M. ; Ettinger, A. ; Hamperl, S.
An automated image analysis pipeline to quantify the coordination and overlap of transcription and replication activity in mammalian genomes.Beagrie, R.A. ; Thieme, C.J. ; Annunziatella, C. ; Baugher, C. ; Zhang, Y. ; Schueler, M. ; Kukalev, A. ; Kempfer, R. ; Chiariello, A.M. ; Bianco, S. ; Li, Y. ; Davis, T. ; Scialdone, A. ; Welch, L.R. ; Nicodemi, M. ; Pombo, A.
Multiplex-GAM: genome-wide identification of chromatin contacts yields insights overlooked by Hi-C.Cossec, J.C. ; Traboulsi, T. ; Sart, S. ; Loe-Mie, Y. ; Guthmann, M. ; Hendriks, I.A. ; Theurillat, I. ; Nielsen, M.L. ; Torres-Padilla, M.E. ; Baroud, C.N. ; Dejean, A.
Transient suppression of SUMOylation in embryonic stem cells generates embryo-like structures.Bell, O. ; Burton, A. ; Dean, C. ; Gasser, S.M. ; Torres-Padilla, M.E.
Heterochromatin definition and function.Pecori, F. ; Torres-Padilla, M.E.
Dynamics of nuclear architecture during early embryonic development and lessons from liveimaging.Guthmann, M. ; Qian, C. ; Gialdini, I. ; Nakatani, T. ; Ettinger, A. ; Schauer, T. ; Kukhtevich, I. ; Schneider, R. ; Lamb, D.C. ; Burton, A. ; Torres-Padilla, M.E.
A change in biophysical properties accompanies heterochromatin formation in mouse embryos.Bamezai, S. ; Pulikkottil, A.J. ; Yadav, T. ; Vegi, N.M. ; Mueller, J. ; Mark, J. ; Mandal, T. ; Feder, K. ; Ihme, S. ; Song, C. ; Rosler, R. ; Wiese, S. ; Hoell, J.I. ; Kloetgen, A. ; Karsan, A. ; Kumari, A. ; Wojenski, L. ; Sinha, A.U. ; González-Menéndez, I. ; Quintanilla-Martinez, L. ; Donato, E. ; Trumpp, A. ; Kruse, E. ; Hamperl, S. ; Zou, L. ; Rawat, V.P.S. ; Buske, C.
A noncanonical enzymatic function of PIWIL4 maintains genomic integrity and leukemic growth in AML.Lubatti, G. ; Stock, M. ; Iturbide Martinez De Albeniz, A. ; Ruiz Tejada Segura, M.L. ; Riepl, M. ; Tyser, R.C.V. ; Danese, A. ; Colomé-Tatché, M. ; Theis, F.J. ; Srinivas, S. ; Torres-Padilla, M.E. ; Scialdone, A.
CIARA: A cluster-independent algorithm for identifying markers of rare cell types from single-cell sequencing data.Lazzardi, S. ; Valle, F. ; Mazzolini, A. ; Scialdone, A. ; Caselle, M. ; Osella, M.
Emergent statistical laws in single-cell transcriptomic data.Lee, C.S.K. ; Weiß, M. ; Hamperl, S.
Where and when to start: Regulating DNA replication origin activity in eukaryotic genomes.Canat, A. ; Atilla, D. ; Torres-Padilla, M.E.
Hyperosmotic stress induces 2-cell-like cells through ROS and ATR signaling.Nakatani, T. ; Torres-Padilla, M.E.
Regulation of mammalian totipotency: A molecular perspective from in vivo and in vitro studies.Collins, A. ; Møller, P. ; Gajski, G. ; Vodenková, S. ; Abdulwahed, A. ; Anderson, D. ; Bankoglu, E.E. ; Bonassi, S. ; Boutet-Robinet, E. ; Brunborg, G. ; Chao, C. ; Cooke, M.S. ; Costa, C. ; Costa, S. ; Dhawan, A. ; de Lapuente, J. ; Bo', C.D. ; Dubus, J. ; Dusinska, M. ; Duthie, S.J. ; Yamani, N.E. ; Engelward, B. ; Gaivão, I. ; Giovannelli, L. ; Godschalk, R. ; Guilherme, S. ; Gutzkow, K.B. ; Habas, K. ; Hernandez, A. ; Herrero, O. ; Isidori, M. ; Jha, A.N. ; Knasmüller, S. ; Kooter, I.M. ; Koppen, G. ; Kruszewski, M. ; Ladeira, C. ; Laffon, B. ; Larramendy, M. ; Hégarat, L.L. ; Lewies, A. ; Lewinska, A. ; Liwszyc, G.E. ; de Cerain, A.L. ; Manjanatha, M. ; Marcos, R. ; Milić, M. ; de Andrade, V.M. ; Moretti, M. ; Muruzabal, D. ; Novak, M. ; Oliveira, R. ; Olsen, A.K. ; Owiti, N. ; Pacheco, M. ; Pandey, A.K. ; Pfuhler, S. ; Pourrut, B. ; Reisinger, K. ; Rojas, E. ; Rundén-Pran, E. ; Sanz-Serrano, J. ; Shaposhnikov, S. ; Sipinen, V. ; Smeets, K. ; Stopper, H. ; Teixeira, J.P. ; Valdiglesias, V. ; Valverde, M. ; van Acker, F. ; van Schooten, F.J. ; Vasquez, M. ; Wentzel, J.F. ; Wnuk, M. ; Wouters, A. ; Žegura, B. ; Zikmund, T. ; Langie, S.A.S. ; Azqueta, A.
Measuring DNA modifications with the comet assay: A compendium of protocols.Weiß, M. ; Chanou, A. ; Schauer, T. ; Tvardovskiy, A. ; Meiser, S. ; König, A.-C. ; Schmidt, T. ; Kruse, E. ; Ummethum, H. ; Trauner, M. ; Werner, M. ; Lalonde, M. ; Hauck, S.M. ; Scialdone, A. ; Hamperl, S.
Single-copy locus proteomics of early- and late-firing DNA replication origins identifies a role of Ask1/DASH complex in replication timing control.Abe, K. ; Schauer, T. ; Torres-Padilla, M.E.
Distinct patterns of RNA polymerase II and transcriptional elongation characterize mammalian genome activation.Tessier, S. ; Ferhi, O. ; Geoffroy, M.C. ; González-Prieto, R. ; Canat, A. ; Quentin, S. ; Pla, M. ; Niwa-Kawakita, M. ; Bercier, P. ; Rérolle, D. ; Therizols, P. ; Fabre, E. ; Vertegaal, A.C.O. ; de Thé, H. ; Lallemand-Breitenbach, V.
Exploration of nuclear body-enhanced sumoylation reveals that PML represses 2-cell features of embryonic stem cells.Scialdone, A. ; Rivron, N.
In preprints: Improving and interrogating embryo models.Kukhtevich, I. ; Rivero-Romano, M. ; Rakesh, N. ; Bheda, P. ; Chadha, Y. ; Rosales-Becerra, P. ; Hamperl, S. ; Bureik, D. ; Dornauer, S. ; Dargemont, C. ; Kirmizis, A. ; Schmoller, K.M. ; Schneider, R.
Quantitative RNA imaging in single live cells reveals age-dependent asymmetric inheritance.Beer, S. ; Wange, L.E. ; Zhang, X. ; Kuklik-Roos, C. ; Enard, W. ; Hammerschmidt, W. ; Scialdone, A. ; Kempkes, B.
EBNA2-EBF1 complexes promote MYC expression and metabolic processes driving S-phase progression of Epstein-Barr virus-infected B cells.Werner, M. ; Dyas, A. ; Parfentev, I. ; Schmidt, G.E. ; Mieczkowska, I.K. ; Mueller-Kirschbaum, L.C. ; Müller, C. ; Kalkhof, S. ; Reinhardt, O. ; Urlaub, H. ; Alves, F. ; Gallwas, J. ; Prokakis, E. ; Wegwitz, F.
ROBO3s: A novel ROBO3 short isoform promoting breast cancer aggressiveness.Fiorentino, J. ; Scialdone, A.
The role of cell geometry and cell-cell communication in gradient sensing.Thakur, S. ; Cahais, V. ; Turkova, T. ; Zikmund, T. ; Renard, C. ; Stopka, T. ; Korenjak, M. ; Zavadil, J.
Chromatin remodeler smarca5 is required for cancer-related processes of primary cell fitness and immortalization.Ruiz Tejada Segura, M.L. ; Abou Moussa, E. ; Garabello, E. ; Nakahara, T.S. ; Makhlouf, M. ; Mathew, L.S. ; Wang, L. ; Valle, F. ; Huang, S.S.Y. ; Mainland, J.D. ; Caselle, M. ; Osella, M. ; Lorenz, S. ; Reisert, J. ; Logan, D.W. ; Malnic, B. ; Scialdone, A. ; Saraiva, L.R.
A 3D transcriptomics atlas of the mouse nose sheds light on the anatomical logic of smell.Iturbide Martinez De Albeniz, A. ; Ruiz Tejada Segura, M.L. ; Noll, C. ; Schorpp, K.K. ; Rothenaigner, I. ; Lubatti, G. ; Agami, A. ; Hadian, K. ; Scialdone, A. ; Torres-Padilla, M.E.
Author Correction: Retinoic acid signaling is critical during the totipotency window in early mammalian development.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, E.R. ; Scialdone, A. ; Yamagata, K. ; Whetstine, J.R. ; Sadreyev, R.I. ; Torres-Padilla, M.E.
DNA replication fork speed underlies cell fate changes and promotes reprogramming.Canat, A. ; Torres-Padilla, M.E.
Retrotransposing a promoter for development.Tyser, R.C.V. ; Mahammadov, E. ; Nakanoh, S. ; Vallier, L. ; Scialdone, A. ; Srinivas, S.
Single-cell transcriptomic characterization of a gastrulating human embryo.Klanova, M. ; Kazantsev, D. ; Pokorna, E. ; Zikmund, T. ; Karolova, J. ; Behounek, M. ; Renesova, N. ; Sovilj, D. ; Kelemen, C.D. ; Helman, K. ; Jaksa, R. ; Havranek, O. ; Andera, L. ; Trneny, M. ; Klener, P.
Anti-apoptotic MCL1 protein represents critical survival molecule for most Burkitt lymphomas and BCL2-negative diffuse large B-cell lymphomas.Burton, A. ; Torres-Padilla, M.E.
Deconfining heterochromatin for expression.Chanou, A. ; Hamperl, S.
Single-molecule techniques to study chromatin.Antonio Urrutia, G. ; Ramachandran, H. ; Cauchy, P. ; Boo, K. ; Ramamoorthy, S. ; Boller, S. ; Dogan, E. ; Clapes, T. ; Trompouki, E. ; Torres-Padilla, M.E. ; Palvimo, J.J. ; Pichler, A. ; Grosschedl, R.
ZFP451-mediated SUMOylation of SATB2 drives embryonic stem cell differentiation.Lalonde, M. ; Trauner, M. ; Werner, M. ; Hamperl, S.
Consequences and resolution of transcription-replication conflicts.Lima, A. ; Lubatti, G. ; Burgstaller, J. ; Hu, D. ; Green, A.P. ; di Gregorio, A. ; Zawadzki, T. ; Pernaute, B. ; Mahammadov, E. ; Perez-Montero, S. ; Dore, M. ; Sanchez, J.M. ; Bowling, S. ; Sancho, M. ; Kolbe, T. ; Karimi, M.M. ; Carling, D. ; Jones, N. ; Srinivas, S. ; Scialdone, A. ; Rodriguez, T.A.
Cell competition acts as a purifying selection to eliminate cells with mitochondrial defects during early mouse development.Iturbide Martinez De Albeniz, A. ; Ruiz Tejada Segura, M.L. ; Noll, C. ; Schorpp, K.K. ; Rothenaigner, I. ; Ruiz-Morales, E.R. ; Lubatti, G. ; Agami, A. ; Hadian, K. ; Scialdone, A. ; Torres-Padilla, M.E.
Retinoic acid signaling is critical during the totipotency window in early mammalian development.Pinheiro, I. ; Torres-Padilla, M.E. ; Almouzni, G.
Epigenomics in the single cell era, an important read out for genome function and cell identity.Kruse, E. ; Hamperl, S.
Dem Anfang auf der Spur — die Suche nach DNA-Replikationsursprüngen.Buschle, A. ; Mrozek-Gorska, P. ; Cernilogar, F.M. ; Ettinger, A. ; Pich, D. ; Krebs, S. ; Mocanu, B. ; Blum, H. ; Schotta, G. ; Straub, T. ; Hammerschmidt, W.
Epstein-Barr virus inactivates the transcriptome and disrupts the chromatin architecture of its host cell in the first phase of lytic reactivation.Rajewsky, N. ; Almouzni, G. ; Gorski, S.A. ; 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.C. ; 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 (Schiller, H. B. ; Ziegler, A.-G.)
Publisher Correction: LifeTime and improving European healthcare through cell-based interceptive medicine (Nature, (2020), 587, 7834, (377-386), 10.1038/s41586-020-2715-9).Pal, M. ; Kind, J. ; Torres-Padilla, M.E.
DamID to map genome-protein interactions in preimplantation mouse embryos.Tyser, R.C.V. ; Ibarra-Soria, X. ; McDole, K. ; A Jayaram, S. ; Godwin, J. ; van den Brand, T.A.H. ; Miranda, A.M.A. ; Scialdone, A. ; Keller, P.J. ; Marioni, J.C. ; Srinivas, S.
Characterization of a common progenitor pool of the epicardium and myocardium.Hermant, C. ; Torres-Padilla, M.E.
TFs for TEs: The transcription factor repertoire of mammalian transposable elements.Ancelin, K. ; Miyanari, Y. ; Leroy, O. ; Torres-Padilla, M.E. ; Heard, E.
Mapping of chromosome territories by 3D-chromosome painting during early mouse development.Torres-Padilla, M.E. ; Bredenoord, A.L. ; Jongsma, K.R. ; Lunkes, A. ; Marelli, L. ; Pinheiro, I. ; Testa, G.
Thinking "ethical" when designing an international, cross-disciplinary biomedical research consortium.Kraus, A.J. ; Vanselow, J.T. ; Lamer, S. ; Brink, B.G. ; Schlosser, A. ; Siegel, T.N.
Distinct roles for H4 and H2A.Z acetylation in RNA transcription in African trypanosomes.Fischbeck, A. ; Ruehland, S. ; Ettinger, A. ; Paetzold, K. ; Masouris, I. ; Nößner, E. ; Mendler, A.N.
Tumor lactic acidosis: Protecting tumor by inhibiting cytotoxic activity through motility arrest and bioenergetic silencing.Fiorentino, J. ; Torres-Padilla, M.E. ; Scialdone, A.
Measuring and modeling single-cell heterogeneity and fate decision in mouse embryos.Monteagudo-Sánchez, A. ; Hernandez Mora, J.R. ; Simon, C. ; Burton, A. ; Tenorio, J. ; Lapunzina, P. ; Clark, S. ; Esteller, M. ; Kelsey, G. ; López-Siguero, J.P. ; de Nanclares, G.P. ; Torres-Padilla, M.E. ; Monk, D.
The role of ZFP57 and additional KRAB-zinc finger proteins in the maintenance of human imprinted methylation and multi-locus imprinting disturbances.Rajewsky, N. ; Almouzni, G. ; Gorski, S.A. ; 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 (Schiller, H. B.) ; LifeTime Community (Ziegler, A.-G.)
LifeTime and improving European healthcare through cell-based interceptive medicine.Genet, M. ; Torres-Padilla, M.E.
The molecular and cellular features of 2-cell-like cells: a reference guide.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.
Heterochromatin establishment during early mammalian development is regulated by pericentromeric RNA and characterized by non-repressive H3K9me3.Iturbide Martinez De Albeniz, A. ; Torres-Padilla, M.E.
A cell in hand is worth two in the embryo: Recent advances in 2-cell like cell reprogramming.Huang, S.S.Y. ; 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.
Differential regulation of the immune system in a brain-liver-fats organ network during short-term fasting.Ummethum, H. ; Hamperl, S.
Proximity labeling techniques to study chromatin.Solovey, M. ; Scialdone, A.
COMUNET: A tool to explore and visualize intercellular communication.Torres-Padilla, M.E.
On transposons and totipotency.Angerer, P. ; Fischer, D.S. ; Theis, F.J. ; Scialdone, A. ; Marr, C.
Automatic identification of relevant genes from low-dimensional embeddings of single-cell RNA-seq data.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.
LOXL2-mediated H3K4 oxidation reduces chromatin accessibility in triple-negative breast cancer cells.Rodriguez-Terrones, D. ; Hartleben, G. ; Gaume, X. ; Eid, A. ; Guthmann, M. ; Iturbide Martinez De Albeniz, A. ; Torres-Padilla, M.E.
A distinct metabolic state arises during the emergence of 2-cell-like cells.Jansz, N.
DNA methylation dynamics at transposable elements in mammals.Guthmann, M. ; Burton, A. ; Torres-Padilla, M.E.
Expression and phase separation potential of heterochromatin proteins during early mouse development.Bruneau, B.G. ; Koseki, H. ; Strome, S. ; Torres-Padilla, M.E.
Chromatin and epigenetics in development: A Special Issue.Pich, D. ; Mrozek-Gorska, P. ; Bouvet, M. ; Sugimoto, A. ; Akidil, E. ; Grundhoff, A. ; Hamperl, S. ; Ling, P.D. ; Hammerschmidt, W.
First days in the life of naïve human B-lymphocytes infected with Epstein-Barr Virus.Ragazzini, R. ; Pérez-Palacios, R. ; Baymaz, I.H. ; Diop, S. ; Ancelin, K. ; Zielinski, D. ; Michaud, A. ; Givelet, M. ; Borsos, M. ; Aflaki, S. ; Legoix, P. ; Jansen, P.W.T.C. ; Servant, N. ; Torres-Padilla, M.E. ; Bourc'his, D. ; Fouchet, P. ; Vermeulen, M. ; Margueron, R.
EZHIP constrains Polycomb Repressive Complex 2 activity in germ cells.Mrozek-Gorska, P. ; Buschle, A. ; Pich, D. ; Schwarzmayr, T. ; Fechtner, R. ; Scialdone, A. ; Hammerschmidt, W.
Epstein-Barr virus reprograms human B lymphocytes immediately in the prelatent phase of infection.Jansz, N. ; Torres-Padilla, M.E.
Genome activation and architecture in the early mammalian embryo.Borsos, M. ; Perricone, S.M. ; Schauer, T. ; Pontabry, J. ; de Luca, K.L. ; de Vries, S.S. ; Ruiz-Morales, E.R. ; Torres-Padilla, M.E. ; Kind, J.
Genome-lamina interactions are established de novo in the early mouse embryo.Huang, Y. ; Chanou, A. ; Kranz, G. ; Pan, M. ; Kohlbauer, V. ; Ettinger, A. ; Gires, O.
Membrane-associated epithelial cell adhesion molecule is slowly cleaved by -secretase prior to efficient proteasomal degradation of its intracellular domain.Fissore, R.A. ; Burton, A. ; Lykke-Hartmann, K.
Editorial: Molecular and cellular mechanisms in reproduction and early development.Manoel, D. ; Makhlouf, M. ; Scialdone, A. ; Saraiva, L.R.
Interspecific variation of olfactory preferences in flies, mice, and humans.Cossec, J.C. ; Theurillat, I. ; Chica, C. ; Búa Aguín, S. ; Gaume, X. ; Andrieux, A. ; Iturbide Martinez De Albeniz, A. ; Jouvion, G. ; Li, H. ; Bossis, G. ; Seeler, J.S. ; Torres-Padilla, M.E. ; Dejean, A.
SUMO safeguards somatic and pluripotent cell identities by enforcing distinct chromatin states.Marti-Renom, M.A. ; Almouzni, G. ; Bickmore, W.A. ; Bystricky, K. ; Cavalli, G. ; Fraser, P. ; Gasser, S.M. ; Giorgetti, L. ; Heard, E. ; Nicodemi, M. ; Nollmann, M. ; Orozco, M. ; Pombo, A. ; Torres-Padilla, M.E.
Challenges and guidelines toward 4D nucleome data and model standards.Rodriguez-Terrones, D. ; Torres-Padilla, M.E.
Nimble and ready to mingle: Transposon outbursts of early development.Griffiths, J.A. ; Scialdone, A. ; Marioni, J.C.
Using single-cell genomics to understand developmental processes and cell fate decisions.van Flaxen, J. ; Charafeddine, R.A. ; Ettinger, A. ; Wang, H. ; Hahn, K.M. ; Wittmann, T.
Optical control of EB1 reveals local functions of the microtubule plus TIP complex during cell migration and division.Conic, S. ; Desplancq, D. ; Ferrand, A. ; Fischer, V. ; Heyer, V. ; Martin, B.R.S. ; Pontabry, J. ; Oulad-Abdelghani, M. ; Babu, K.N. ; Wright, G.D. ; Molina, N. ; Weiss, E. ; Tora, L.
Imaging of native transcription factors and histone phosphorylation at high resolution in live cells.van Haren, J. ; Charafeddine, R.A. ; Ettinger, A. ; Wang, H. ; Hahn, K.M. ; Wittmann, T.
Local control of intracellular microtubule dynamics by EB1 photodissociation.Sarrach, S. ; Huang, Y. ; Niedermeyer, S. ; Hachmeister, M. ; Fischer, L. ; Gille, S. ; Pan, M. ; Mack, B. ; Kranz, G. ; Libl, D. ; Merl-Pham, J. ; Hauck, S.M. ; Paoluzzi Tomada, E. ; Kieslinger, M. ; Jeremias, I. ; Scialdone, A. ; Gires, O.
Spatiotemporal patterning of EpCAM is important for murine embryonic endo-And mesodermal differentiation.van Haren, J. ; Ettinger, A. ; Charafeddine, R.A. ; Wang, H. ; Hahn, K.M. ; Wittmann, T.
Controlling cytoskeletal organization and cellular dynamics by localized optical modulation of microtubule dynamics.Rodriguez-Terrones, D. ; Gaume, X. ; Ishiuchi, T. ; Weiss, A.R. ; Kopp, A. ; Kruse, K. ; Penning, A. ; Vaquerizas, J.M. ; Brino, L. ; Torres-Padilla, M.E.
A molecular roadmap for the emergence of early-embryonic-like cells in culture.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.
Pluripotent state transitions coordinate morphogenesis in mouse and human embryos.Izzo, A. ; Ziegler-Birling, C. ; Hill, P.W.S. ; Brondani, L. ; Hajkova, P. ; Torres-Padilla, M.E. ; Schneider, R.
Dynamic changes in H1 subtype composition during epigenetic reprogramming.Müller, R. ; Hanson, C. ; Hanson, M.S. ; Penkler, M. ; Samaras, G. ; Chiapperino, L. ; Dupré, J. ; Kenney, M. ; Kuzawa, C.W. ; Latimer, J. ; Lloyd, S. ; Lunkes, A. ; MacDonald, M. ; Meloni, M. ; Nerlich, B. ; Panese, F. ; Pickersgill, M. ; Richardson, S.D. ; Rüegg, J. ; Schmitz, S. ; Stelmach, A. ; Villa, P.I.
The biosocial genome? Interdisciplinary perspectives on environmental epigenetics, health and society.Jachowicz, J.W. ; Bing, X. ; Pontabry, J. ; Bošković, A. ; Rando, O.J. ; Torres-Padilla, M.E.
LINE-1 activation after fertilization regulates global chromatin accessibility in the early mouse embryo.Iturbide Martinez De Albeniz, A. ; Torres-Padilla, M.E.
Starting embryonic transcription for the first time.Eid, A. ; Rodriguez-Terrones, D. ; Burton, A. ; Torres-Padilla, M.E.
SUV4-20 activity in the preimplantation mouse embryo controls timely replication.Vaquerizas, J.M. ; Torres-Padilla, M.E.
Developmental biology: Panoramic views of the early epigenome.Pontabry, J. ; Rousseau, F. ; Studholme, C. ; Koob, M. ; Dietemann, J.L.
A discriminative feature selection approach for shape analysis: Application to fetal brain cortical folding.Ettinger, A. ; van Haren, J. ; Ribeiro, S.A. ; Wittmann, T.
Doublecortin is excluded from growing microtubule ends and recognizes the GDP-microtubule lattice.Eid, A. ; Torres-Padilla, M.E.
Characterization of non-canonical polycomb repressive complex 1 subunits during early mouse embryogenesis.Jachowicz, J.W. ; Torres-Padilla, M.E.
LINEs in mice: Features, families, and potential roles in early development.Borsos, M. ; Torres-Padilla, M.E.
Building up the nucleus: Nuclear organization in the establishment of totipotency and pluripotency during mammalian development.Ziegler-Birling, C. ; Daujat, S. ; Schneider, R. ; Torres-Padilla, M.E.
Dynamics of histone H3 acetylation in the nucleosome core during mouse pre-implantation development.Gaume, X. ; Torres-Padilla, M.E.
Regulation of reprogramming and cellular plasticity through histone exchange and histone variant incorporation.Dang-Nguyen, T.Q. ; Torres-Padilla, M.E.
How cells build totipotency and pluripotency: Nuclear, chromatin and transcriptional architecture.Bošković, A. ; Torres-Padilla, M.E.
Histone variants and reprogramming in early development.Burton, A.S. ; Torres-Padilla, M.E.
Chromatin dynamics in the regulation of cell fate allocation during early embryogenesis.Saksouk, N. ; Barth, T.K. ; Ziegler-Birling, C. ; Olova, N. ; Nowak, A. ; Rey, E. ; Mateos-Langerak, J. ; Urbach, S. ; Reik, W. ; Torres-Padilla, M.E. ; Imhof, A. ; Déjardin, J. ; Simboeck, E.
Redundant mechanisms to form silent chromatin at pericentromeric regions rely on BEND3 and DNA methylation.Ishiuchi, T. ; Torres-Padilla, M.E.
LINEing germ and embryonic stem cells' silencing of retrotransposons.Bošković, A. ; Eid, A. ; Pontabry, J. ; Ishiuchi, T. ; Spiegelhalter, C. ; Raghu Ram, E.V. ; Meshorer, E. ; Torres-Padilla, M.E.
Higher chromatin mobility supports totipotency and precedes pluripotency in vivo.Torres-Padilla, M.E. ; Chambers, I.
Transcription factor heterogeneity in pluripotent stem cells: A stochastic advantage.Almouzni, G. ; Altucci, L. ; Amati, B. ; Ashley, N. ; Baulcombe, D. ; Beaujean, N. ; Bock, C. ; Bongcam-Rudloff, E. ; Bousquet, J. ; Braun, S. ; de Paillerets, B.B. ; Bussemakers, M. ; Clarke, L. ; Conesa, A. ; Estivill, X. ; Fazeli, A. ; Grgurevi, N.A. ; Gut, I. ; Heijmans, B.T. ; Hermouet, S. ; Houwing Duistermaat, J. ; Iacobucci, I. ; Ila, J. ; Kandimalla, R. ; Krauss-Etschmann, S. ; Lasko, P. ; Lehmann, S. ; Lindroth, A. ; Majdi, G. ; Marcotte, E. ; Martinelli, G. ; Martinet, N. ; Meyer, E. ; Miceli, C. ; Mills, K. ; Moreno-Villanueva, M. ; Morvan, G. ; Nickel, D. ; Niesler, B. ; Nowacki, M. ; Nowak, J. ; Ossowski, S. ; Pelizzola, M. ; Pochet, R. ; Poto Nik, U. ; Radwanska, M. ; Raes, J. ; Rattray, M. ; Robinson, M.D. ; Roelen, B. ; Sauer, S. ; Schinzer, D. ; Slagboom, E. ; Spector, T. ; Stunnenberg, H.G. ; Tiligada, E. ; Torres-Padilla, M.E. ; Tsonaka, R. ; van Soom, A. ; Vidakovi, M. ; Widschwendter, M.
Relationship between genome and epigenome - challenges and requirements for future research.Jachowicz, J.W. ; Santenard, A. ; Bender, A. ; Müller, J. ; Torres-Padilla, M.E.
Heterochromatin establishment at pericentromeres depends on nuclear position.Burton, A.S. ; Müller, J. ; Tu, S. ; Padilla-Longoria, P. ; Guccione, E. ; Torres-Padilla, M.E.
Single-cell profiling of epigenetic modifiers identifies PRDM14 as an inducer of cell fate in the mammalian embryo.Miyanari, Y. ; Ziegler-Birling, C. ; Torres-Padilla, M.E.
Live visualization of chromatin dynamics with fluorescent TALEs.Bošković, A. ; Torres-Padilla, M.E.
How mammals pack their sperm: A variant matter.Ishiuchi, T. ; Torres-Padilla, M.E.
Towards an understanding of the regulatory mechanisms of totipotency.Lange, U.C. ; Siebert, S. ; Wossidlo, M. ; Weiss, T. ; Ziegler-Birling, C. ; Walter, J. ; Torres-Padilla, M.E. ; Daujat, S. ; Schneider, R.
Dissecting the role of H3K64me3 in mouse pericentromeric heterochromatin.Fadloun, A. ; Le Gras, S. ; Jost, B. ; Ziegler-Birling, C. ; Takahashi, H. ; Gorab, E. ; Carninci, P. ; Torres-Padilla, M.E.
Chromatin signatures and retrotransposon profiling in mouse embryos reveal regulation of LINE-1 by RNA.Torres-Padilla, M.E. ; Ciosk, R.
A germline-centric view of cell fate commitment, reprogramming and immortality.Fadloun, A. ; Eid, A. ; Torres-Padilla, M.E.
Mechanisms and dynamics of heterochromatin formation during mammalian development: closed paths and open questions.Beck, D.B. ; Burton, A.S. ; Oda, H. ; Ziegler-Birling, C. ; Torres-Padilla, M.E. ; Reinberg, D.
The role of PR-Set7 in replication licensing depends on Suv4-20h.Bošković, A. ; Bender, A. ; Gall, L. ; Ziegler-Birling, C. ; Beaujean, N. ; Torres-Padilla, M.E.
Analysis of active chromatin modifications in early mammalian embryos reveals uncoupling of H2A.Z acetylation and H3K36 trimethylation from embryonic genome activation.Talbert, P.B. ; Ahmad, K. ; Almouzni, G. ; Ausió, J. ; Berger, F. ; Bhalla, P.L. ; Bonner, W.M. ; Cande, W.Z. ; Chadwick, B.P. ; Chan, S.W. ; Cross, G.A. ; Cui, L. ; Dimitrov, S.I. ; Doenecke, D. ; Eirin-López, J.M. ; Gorovsky, M.A. ; Hake, S.B. ; Hamkalo, B.A. ; Holec, S. ; Jacobsen, S.E. ; Kamieniarz, K. ; Khochbin, S. ; Ladurner, A.G. ; Landsman, D. ; Latham, J.A. ; Loppin, B. ; Malik, H.S. ; Marzluff, W.F. ; Pehrson, J.R. ; Postberg, J. ; Schneider, R. ; Singh, M.B. ; Smith, M.M. ; Thompson, E.E. ; Torres-Padilla, M.E. ; Tremethick, D.J. ; Turner, B.M. ; Waterborg, J.H. ; Wollmann, H. ; Yelagandula, R. ; Zhu, B.M. ; Henikoff, S.
A unified phylogeny-based nomenclature for histone variants.Miyanari, Y. ; Torres-Padilla, M.E.
Control of ground-state pluripotency by allelic regulation of Nanog.Burton, A.S. ; Torres-Padilla, M.E.
Epigenetic reprogramming and development: A unique heterochromatin organization in the preimplantation mouse embryo.Miyanari, Y. ; Torres-Padilla, M.E.
Epigenetic regulation of reprogramming factors towards pluripotency in mouse preimplantation development.Santenard, A. ; Ziegler-Birling, C. ; Koch, M. ; Tora, L. ; Bannister, A.J. ; Torres-Padilla, M.E.
Heterochromatin formation in the mouse embryo requires critical residues of the histone variant H3.3.