Scialdone Lab Publications

2025 Nature Aging Nature Aging, DOI: 10.1038/s43587-025-00837-x (2025)

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.

2024 Scientific Article in Developmental Cell Dev. Cell 59, 2347-2363.e9 (2024)

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.

2024 Scientific Article in Bioinformatics Bioinformatics 40:btae267 (2024)

Stock, M. ; Popp, N. ; Fiorentino, J. ; Scialdone, A.

Topological benchmarking of algorithms to infer Gene Regulatory Networks from Single-Cell RNA-seq Data.

2023 Scientific Article in Nucleic Acids Research Nucleic Acids Res. 51, 12303-12324 (2023)

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.

2023 Scientific Article in Nature Methods Nat. Methods 20, 1037-1047 (2023)

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.

2023 Scientific Article in Development / Company of Biologists Development 150:12 (2023)

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.

2023 Scientific Article in Physical Review E Phys. Rev. E 107:044403 (2023)

Lazzardi, S. ; Valle, F. ; Mazzolini, A. ; Scialdone, A. ; Caselle, M. ; Osella, M.

Emergent statistical laws in single-cell transcriptomic data.

2023 Scientific Article in Cell Reports Cell Rep. 42:112045 (2023)

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.

2022 Letter to the Editor in Development / Company of Biologists Development 149:dev201404 (2022)

Scialdone, A. ; Rivron, N.

In preprints: Improving and interrogating embryo models.

2022 Scientific Article in Proceedings of the National Academy of Sciences of the United States of America Proc. Natl. Acad. Sci. U.S.A. 119:e2200512119 (2022)

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.

2022 Scientific Article in PLoS Computational Biology PLoS Comput. Biol. 18:e1009552 (2022)

Fiorentino, J. ; Scialdone, A.

The role of cell geometry and cell-cell communication in gradient sensing.

2022 Scientific Article in Cell Reports Cell Rep. 38:110547 (2022)

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.

2022 Nature Structural & Molecular Biology Nat. Struct. Mol. Biol. 29:282 (2022)

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.

2022 Scientific Article in Nature Genetics Nat. Genet. 54, 318–327 (2022)

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.

2021 Scientific Article in Nature Nature 600, 285-289 (2021)

Tyser, R.C.V. ; Mahammadov, E. ; Nakanoh, S. ; Vallier, L. ; Scialdone, A. ; Srinivas, S.

Single-cell transcriptomic characterization of a gastrulating human embryo.

2021 Scientific Article in Nature metabolism Nat. Metab. 3, 1091-1108 (2021)

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.

2021 Scientific Article in Nature Structural & Molecular Biology Nat. Struct. Mol. Biol. 28, 521-532 (2021)

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.

2021 Scientific Article in Science Science 371:eabb2986 (2021)

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.

2020 Review in Annual Review of Genetics Annu. Rev. Genet. 54, 167-187 (2020)

Fiorentino, J. ; Torres-Padilla, M.E. ; Scialdone, A.

Measuring and modeling single-cell heterogeneity and fate decision in mouse embryos.

2020 Scientific Article in Molecular Metabolism Mol. Metab. 40:101038 (2020)

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.

2020 Scientific Article in Bioinformatics Bioinformatics 36, 4296-4300 (2020)

Solovey, M. ; Scialdone, A.

COMUNET: A tool to explore and visualize intercellular communication.

2020 Scientific Article in Bioinformatics Bioinformatics 36, 4291-4295 (2020)

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.

2019 Scientific Article in Proceedings of the National Academy of Sciences of the United States of America Proc. Natl. Acad. Sci. U.S.A. 116, 16046-16055 (2019)

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.

2018 Scientific Article in Chemical senses Chem. Senses 44, 7-9 (2018)

Manoel, D. ; Makhlouf, M. ; Scialdone, A. ; Saraiva, L.R.

Interspecific variation of olfactory preferences in flies, mice, and humans.

2018 Review in Molecular Systems Biology Mol. Syst. Biol. 14:e8046 (2018)

Griffiths, J.A. ; Scialdone, A. ; Marioni, J.C.

Using single-cell genomics to understand developmental processes and cell fate decisions.

2018 Scientific Article in Scientific Reports Sci. Rep. 8:1801 (2018)

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.

2017 Scientific Article in Nature Nature 552, 239-243 (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.

Pluripotent state transitions coordinate morphogenesis in mouse and human embryos.

2015 Scientific Article in Methods Methods 85, 54-61 (2015)

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.

2015 Scientific Article in Nature Biotechnology Nat. Biotechnol. 33, 155-160 (2015)

Buettner, F. ; Natarajan, K.N. ; Casale, F.P. ; Proserpio, V. ; Scialdone, A. ; Theis, F.J. ; Teichmann, S.A. ; Marioni, J.C. ; Stegle, O.