Scialdone Lab Publications
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.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.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.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.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.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.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.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.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.Scialdone, A. ; Rivron, N.
In preprints: Improving and interrogating embryo models.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.Fiorentino, J. ; Scialdone, A.
The role of cell geometry and cell-cell communication in gradient sensing.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.Tyser, R.C.V. ; Mahammadov, E. ; Nakanoh, S. ; Vallier, L. ; Scialdone, A. ; Srinivas, S.
Single-cell transcriptomic characterization of a gastrulating human embryo.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.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.Fiorentino, J. ; Torres-Padilla, M.E. ; Scialdone, A.
Measuring and modeling single-cell heterogeneity and fate decision in mouse embryos.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.Solovey, M. ; Scialdone, A.
COMUNET: A tool to explore and visualize intercellular communication.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.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.Manoel, D. ; Makhlouf, M. ; Scialdone, A. ; Saraiva, L.R.
Interspecific variation of olfactory preferences in flies, mice, and humans.Griffiths, J.A. ; Scialdone, A. ; Marioni, J.C.
Using single-cell genomics to understand developmental processes and cell fate decisions.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.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.Scialdone, A. ; Natarajan, K.N. ; Saraiva, L.R. ; Proserpio, V. ; Teichmann, S.A. ; Stegle, O. ; Marioni, J.C. ; Buettner, F.
Computational assignment of cell-cycle stage from single-cell transcriptome data.Buettner, F. ; Natarajan, K.N. ; Casale, F.P. ; Proserpio, V. ; Scialdone, A. ; Theis, F.J. ; Teichmann, S.A. ; Marioni, J.C. ; Stegle, O.
Computational analysis of cell-to-cell heterogeneity in single-cell RNA-sequencing data reveals hidden subpopulations of cells.