Publications | Gioele La Manno

Fusar Bassini L, Schede HH, Capolupo L, Alieh LHA, Venturi F, Valente A, Droin C, Trejo Banos D, Khven I, Asirim EZ, Nasrallah A, Kaysudu I, Krymova E, D’Angelo G, La Manno G. The Lipidomics Architecture of the Mouse Brain. bioRxiv, 2025.

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Skoufa E, Zhong J, Kahre O, Hu K, Tsissios G, Carrau L, Herrera A, Dominguez Mantes A, Castilla-Ibeas A, Jang H, Weigert M, La Manno G, Lutolf M, Ros M, Aztekin C. Specialized signaling centers direct cell fate and spatial organization in a limb organoid model. Science Advances (In Press), 2025.

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Halima H. Schede, Leila H. A. Alieh, Laurie A. Rohde, Antonio Herrera, Anjalie Schlaeppi, Guillaume Valentin, Alireza Gargoorimothlag, Albert Dominguez Mantes, Celine Jollivet, Julijana Paz-Montoya, Lucile Capolupo, Irina Khven, Andrew C. Oates, Giovanni D’Angelo, Gioele La Manno. Unified Mass Imaging Maps the Lipidome of Vertebrate Development. Nature Methods, 2025.

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Albert Dominguez Mantes, Antonio Herrera, Irina Khven, Anjalie Schlaeppi, Eftychia Kyriacou, Georgios Tsissios, Evangelia Skoufa, Luca Santangeli, Ekaterina Buglakova, Emine Berna Durmus, Suliana Manley, Anna Kreshuk, Detlev Arendt, Can Aztekin, Joachim Lingner, Gioele La Manno, Martin Weigert. Spotiflow: accurate and efficient spot detection for fluorescence microscopy with deep stereographic flow regression. Nature Methods, 2025.

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Asgrímsdóttir ES, Fusar Bassini L, Rivetti di Val Cervo P, Gyllborg D, Puigsasllosas Pastor C, Lee K, Grigsby C, Islam S, Lönneberg P, Villaescusa C, Saltó C, Linnarsson S, Castelo-Branco G, La Manno G, Toledo EM, Arenas E. Midbrain Dopaminergic Neuron Development is Regulated by Two Molecularly Distinct Subtypes of Radial Glia Cells. Nature Neuroscience (In Press), 2025.

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Yu T, Ekbote C, Morozov N, Herrera A, Fan J, Dominguez Mantes A, Novello S, Lashuel HA, Frossard P, D’Ascoli S, La Manno G, Brbić M. Tissue Reassembly with Generative AI. bioRxiv (in revision at Nature Methods), 2025.

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Alex R. Lederer, Maxime Leonardi, Lorenzo Talamanca, Antonio Herrera, Colas Droin, Irina Khven, Hugo J. F. Carvalho, Alessandro Valente, Albert Dominguez Mantes, Pau Mulet Arabí, Luca Pinello, Felix Naef, Gioele La Manno. Statistical inference with a manifold-constrained RNA velocity model uncovers cell cycle speed modulations. Nature Methods, 2024.

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Giovanni D’Angelo, Gioele La Manno. The Lipotype hypothesis. Nature Reviews MCB, 2022.

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Capolupo L, Khven I, Lederer AR, Mazzeo L, Glousker G, Ho S, Russo F, Montoya JP, Bhandari DR, Bowman AP, Ellis SR, Guiet R, Burri O, Detzner J, Muthing J, Homicsko K, Kuonen F, Gilliet M, Spengler B, Heeren RMA, Dotto GP, La Manno G, D’Angelo G. Sphingolipids Control Dermal Fibroblast Heterogeneity. Science, 2022.

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Jeongsik Park, Howin Hsiung, Irina Khven, Gioele La Manno, Matthias Lutolf. Self-organizing in vitro mouse neural tube organoids mimic embryonic development. Development, 2022.

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Sandra Petrus-Reurer, Alex R Lederer, Laura Baqué-Vidal, Iyadh Douagi, Belinda Pannagel, Irina Khven, Monica Aronsson, Hammurabi Bartuma, Magdalena Wagner, Andreas Wrona, Paschalis Efstathopoulos, Elham Jaberi, Hanni Willenbrock, Yutaka Shimizu, J Carlos Villaescusa, Helder André, Erik Sundstrӧm, Aparna Bhaduri, Arnold Kriegstein, Anders Kvanta, Gioele La Manno, Fredrik Lanner. Molecular profiling of stem cell-derived retinal pigment epithelial cell differentiation established for clinical translation. Stem Cell Reports, 2022.

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Ratz M, von Berlin L, Larsson L, Martin M, Orzechowski Westholm J, La Manno G, Lundeberg J, Frisén J. Clonal relations in the mouse brain revealed by single-cell and spatial transcriptomics. Nature Neuroscience, 2022.

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Jordan W. Squair, Matthieu Gautier, Claudia Kathe, Mark A. Anderson, Nicholas D. James, Thomas H. Hutson, Rémi Hudelle, Taha Qaiser, Kaya J.E. Matson, Quentin Barraud, Ariel J. Levine, Gioele La Manno, Michael A. Skinnider, Grégoire Courtine. Confronting false discoveries in single-cell differential expression. Nature Communications, 2021.

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Halima Hannah Schede, Christian G Schneider, Johanna Stergiadou, Lars E Borm, Anurag Ranjak, Tracy M Yamawaki, Fabrice P A David, Peter Lönnerberg, Maria Antonietta Tosches, Simone Codeluppi, Gioele La Manno. Spatial tissue profiling by imaging-free molecular tomography. Nature Biotechnology, 2021.

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Gioele La Manno, Kimberly Siletti, Alessandro Furlan, Daniel Gyllborg, Elin Vinsland, Alejandro Mossi Albiach, Christoffer Mattsson Langseth, Irina Khven, Alex R. Lederer, Lisa M. Dratva, Anna Johnsson, Mats Nilsson, Peter Lönnerberg, Sten Linnarsson. Molecular architecture of the developing mouse brain. Nature, 2021.

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Michael A. Skinnider, Jordan W. Squair, Claudia Kathe, Mark A. Anderson, Matthieu Gautier, Kaya J.E. Matson, Marco Milano, Thomas H. Hutson, Quentin Barraud, Aaron A. Phillips, Leonard J. Foster, Gioele La Manno, Ariel J. Levine, Grégoire Courtine. Cell type prioritization in single-cell data. Nature Biotechnology, 2020.

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Alex R. Lederer, Gioele La Manno. The emergence and promise of single-cell temporal-omics approaches. Curr Opin Biotechnol, 2020.

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Gioele La Manno, Ruslan Soldatov, Amit Zeisel, Emelie Braun, Hannah Hochgerner, Viktor Petukhov, Katja Lidschreiber, Maria E. Kastriti, Peter Lönnerberg, Alessandro Furlan, Jean Fan, Lars E. Borm, Zehua Liu, David van Bruggen, Jimin Guo, Xiaoling He, Roger Barker, Erik Sundström, Gonçalo Castelo-Branco, Patrick Cramer, Igor Adameyko, Sten Linnarsson & Peter V. Kharchenko. RNA velocity in single cells. Nature, 2018.

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Amit Zeisel, Hannah Hochgerner, Peter Lonnerberg, Anna Johnsson, Fatima Memic, Job van der Zwan, Martin Haring, Emelie Braun, Lars Borm, Gioele La Manno, Simone Codeluppi, Alessandro Furlan, Nathan Skene, Kenneth D Harris, Jens Hjerling Leffler, Ernest Arenas, Patrik Ernfors, Ulrika Marklund, Sten Linnarsson. Molecular architecture of the mouse nervous system. Cell, 2018.

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Simone Codeluppi, Lars E Borm, Amit Zeisel, Gioele La Manno, Josina A van Lunteren, Camilla I Svensson, Sten Linnarsson. Spatial organization of the somatosensory cortex revealed by cyclic smFISH. Nature Methods, 2018.

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Hannah Hochgerner, Peter Lännerberg, Rebecca Hodge, Jaromir Mikes, Abeer Heskol, Herman Hubschle, Philip Lin, Simone Picelli, Gioele La Manno, Michael Ratz, Jude Dunne, Syed Husain, Ed Lein, Maithreyan Srinivasan, Amit Zeisel, Sten Linnarsson. STRT-seq-2i: dual-index 5ʹ single cell and nucleus RNA-seq on an addressable microwell array. Scientific Reports, 2017.

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Enrique M Toledo, Gioele La Manno, Pia Rivetti di Val Cervo, Daniel Gyllborg, Saiful Islam, Carlos Villaescusa, Sten Linnarsson, Ernest Arenas. Molecular analysis of the midbrain dopaminergic niche during neurogenesis. biorxiv, 2017.

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Pia Rivetti di Val Cervo, Roman A Romanov, Giada Spigolon, Débora Masini, Elisa Martín-Montañez, Enrique M Toledo, Gioele La Manno, Michael Feyder, Christian Pifl, Yi-Han Ng, Sara Padrell Sánchez, Sten Linnarsson, Marius Wernig, Tibor Harkany, Gilberto Fisone, Ernest Arenas. Induction of functional dopamine neurons from human astrocytes in vitro and mouse astrocytes in a Parkinson's disease model. Nature Biotechnology, 2017.

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Gioele La Manno, Daniel Gyllborg, Simone Codeluppi, Kaneyasu Nishimura, Carmen Salto, Amit Zeisel, Lars E Borm, Simon RW Stott, Enrique M Toledo, J Carlos Villaescusa, Peter Lönnerberg, Jesper Ryge, Roger A Barker, Ernest Arenas, Sten Linnarsson. Molecular diversity of midbrain development in mouse, human, and stem cells. Cell, 2016.

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Alessandro Furlan, Gioele La Manno, Moritz Lübke, Martin Häring, Hind Abdo, Hannah Hochgerner, Jussi Kupari, Dmitry Usoskin, Matti S Airaksinen, Guillermo Oliver, Sten Linnarsson, Patrik Ernfors. Visceral motor neuron diversity delineates a cellular basis for nipple-and pilo-erection muscle control. Nature Neuroscience, 2016.

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Simon Joost, Amit Zeisel, Tina Jacob, Xiaoyan Sun, Gioele La Manno, Peter Lönnerberg, Sten Linnarsson, Maria Kasper. Single-cell transcriptomics reveals that differentiation and spatial signatures shape epidermal and hair follicle heterogeneity. Cell Systems, 2016.

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Sueli Marques, Amit Zeisel, Simone Codeluppi, David van Bruggen, Ana Mendanha Falcão, Lin Xiao, Huiliang Li, Martin Häring, Hannah Hochgerner, Roman A Romanov, Daniel Gyllborg, Ana B Muñoz-Manchado, Gioele La Manno, Peter Lönnerberg, Elisa M Floriddia, Fatemah Rezayee, Patrik Ernfors, Ernest Arenas, Jens Hjerling-Leffler, Tibor Harkany, William D Richardson, Sten Linnarsson, Gonçalo Castelo-Branco. Oligodendrocyte heterogeneity in the mouse juvenile and adult central nervous system. Science, 2016.

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Amit Zeisel, Ana B Muñoz-Manchado, Simone Codeluppi, Peter Lönnerberg, Gioele La Manno, Anna Juréus, Sueli Marques, Hermany Munguba, Liqun He, Christer Betsholtz, Charlotte Rolny, Gonçalo Castelo-Branco, Jens Hjerling-Leffler, Sten Linnarsson. Cell types in the mouse cortex and hippocampus revealed by single-cell RNA-seq. Science, 2015.

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Saiful Islam, Amit Zeisel, Simon Joost, Gioele La Manno, Pawel Zajac, Maria Kasper, Peter Lönnerberg, Sten Linnarsson. Quantitative single-cell RNA-seq with unique molecular identifiers. Nature methods, 2014.

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