Discovering the cellular landscape of the airways and the lung

Risultati finali

Publications in at least 12 peer-reviewed scientific publications

Publications in at least 12 peerreviewed scientific publications

Description of knowledge exchange and best practices from coordination meetings

Protocol for computational methods for spatial cell mapping

Extension of pipeline on spatial data sets development of a framework for analysis and presentation of single cell information in a spatial context

Protocols.io collection of tissue acquisition and processing methods

Protocolsio or similar platform collection of tissue acquisition and processing methods from discovAIR

Protocol for computational methods for microscopy-based single cell detection and phenotyping

Improvement of framework to create a lung cell annotated single cell database for nuclei and extending with cytoplasm segmentation

Integrated spatial maps

Integrated spatial maps of the cell types in each patient cohort based on ChloFISH Data from each disease cohort will be compared to the corresponding data from the deep dive and to each other

Github collection of discovAIR computational methods

Github collection of computational methods developed within discovAIR

Project website

Project website online continuously updated with news progress reports and links to published papers datasets and information about upcoming meetings of discovAIR and HCA

Portal prototype

Portal prototype developed for the scientific community for data handling data analysis and interactive presentation of the accumulated single cell information in a spatiotemporal context

Position paper on user groups perspective on discovAIR platform

Position paper on Human Lung Cell Atlas requirements from user groups perspective

Software application for annotation & visualization of multimodal data

Software application for annotation and visualisation of multimodal singlecell feature datasets

Pubblicazioni

The local and systemic response to SARS-CoV-2 infection in children and adults

Autori: Masahiro Yoshida, Kaylee B. Worlock, Ni Huang, Rik G.H. Lindeboom, Colin R. Butler, Natsuhiko Kumasaka, Cecilia Dominguez Conde, Lira Mamanova, Liam Bolt, Laura Richardson, Krzysztof Polanski, Elo Madissoon, Josephine L. Barnes, Jessica Allen-Hyttinen, Eliz Kilich, Brendan C. Jones, Angus de Wilton, Anna Wilbrey-Clark, Waradon Sungnak, J. Patrick Pett, Elena Prigmore, Henry Yung, Puja
Pubblicato in: Nature, Numero 602, 2022, Pagina/e 321-327, ISSN 0028-0836
Editore: Nature Publishing Group
DOI: 10.1038/s41586-021-04345-x

Squidpy: a scalable framework for spatial single cell analysis

Autori: Giovanni Palla, Hannah Spitzer, Michal Klein, David Fischer, Anna Christina Schaar, Louis Benedikt Kuemmerle, Sergei Rybakov, Ignacio L. Ibarra, Olle Holmberg, Isaac Virshup, Mohammad Lotfollahi, Sabrina Richter & Fabian J. Theis
Pubblicato in: Nature Methods, Numero 19(2), 2022, Pagina/e 171-178, ISSN 1548-7091
Editore: Nature Publishing Group
DOI: 10.1038/s41592-021-01358-2

Integrative analysis of cell state changes in lung fibrosis with peripheral protein biomarkers

Autori: Christoph H Mayr, Lukas M Simon, Gabriela Leuschner, Meshal Ansari, Janine Schniering, Philipp E Geyer, Ilias Angelidis, Maximilian Strunz, Pawandeep Singh, Nikolaus Kneidinger, Frank Reichenberger, Edith Silbernagel, Stephan Böhm, Heiko Adler, Michael Lindner, Britta Maurer, Anne Hilgendorff, Antje Prasse, Jürgen Behr, Matthias Mann, Oliver Eickelberg, Fabian J Theis, Herbert B Schiller
Pubblicato in: EMBO Molecular Medicine, Numero 13/4, 2021, ISSN 1757-4676
Editore: John Wiley & Sons Ltd.
DOI: 10.15252/emmm.202012871

Multiparametric platform for profiling lipid trafficking in human leukocytes

Autori: Simon G. Pfisterer, Ivonne Brock, Kristiina Kanerva, Iryna Hlushchenko, Lassi Paavolainen, Pietari Ripatti, Mohammad Majharul Islam, Aija Kyttälä, Maria D. Di Taranto, Annalisa Scotto di Frega, Giuliana Fortunato, Johanna Kuusisto, Peter Horvath, Samuli Ripatti, Markku Laakso, Elina Ikonen
Pubblicato in: Cell Reports Methods, Numero Volume 2 issue 2, 2022, Pagina/e 100166, ISSN 2667-2375
Editore: Elsevier
DOI: 10.1016/j.crmeth.2022.100166

Mapping single-cell data to reference atlases by transfer learning

Autori: Mohammad Lotfollahi, Mohsen Naghipourfar, Malte D. Luecken, Matin Khajavi, Maren Büttner, Marco Wagenstetter, Žiga Avsec, Adam Gayoso, Nir Yosef, Marta Interlandi, Sergei Rybakov, Alexander V. Misharin & Fabian J. Theis
Pubblicato in: Nature Biotechnology, Numero 40, 2022, Pagina/e 121-130, ISSN 1087-0156
Editore: Nature Publishing Group
DOI: 10.1038/s41587-021-01001-7

A Single-Cell Atlas of the Human Healthy Airways

Autori: Marie Deprez, Laure-Emmanuelle Zaragosi, Marin Truchi, Christophe Becavin, Sandra Ruiz García, Marie-Jeanne Arguel, Magali Plaisant, Virginie Magnone, Kevin Lebrigand, Sophie Abelanet, Frédéric Brau, Agnès Paquet, Dana Pe’er, Charles-Hugo Marquette, Sylvie Leroy, Pascal Barbry
Pubblicato in: American Journal of Respiratory and Critical Care Medicine, Numero 202/12, 2020, Pagina/e 1636-1645, ISSN 1073-449X
Editore: American Thoracic Society
DOI: 10.1164/rccm.201911-2199oc

Single-cell meta-analysis of SARS-CoV-2 entry genes across tissues and demographics

Autori: Christoph Muus, Malte D. Luecken, Gökcen Eraslan, Lisa Sikkema, Avinash Waghray, Graham Heimberg, Yoshihiko Kobayashi, Eeshit Dhaval Vaishnav, Ayshwarya Subramanian, Christopher Smillie, Karthik A. Jagadeesh, Elizabeth Thu Duong, Evgenij Fiskin, Elena Torlai Triglia, Meshal Ansari, Peiwen Cai, Brian Lin, Justin Buchanan, Sijia Chen, Jian Shu, Adam L. Haber, Hattie Chung, Daniel T. Montoro, Taylor
Pubblicato in: Nature Medicine, Numero 27/3, 2021, Pagina/e 546-559, ISSN 1078-8956
Editore: Nature Publishing Group
DOI: 10.1038/s41591-020-01227-z

The discovAIR project: a roadmap towards the Human Lung Cell Atlas

Autori: Malte D. Luecken, Laure-Emmanuelle Zaragozi, Elo Madissoon, Lisa Sikkema, Alexandra B. Firsova, Elena De Domenico, Louis Kümmerle, Adem Saglam, Marijn Berg, Aurore C.A. Gay, Janine Schniering, Christoph H. Mayr, Xesús M. Abalo, Ludvig Larsson, Alexandros Sountoulidis, Sarah Teichmann, Karen van Eunen, Gerard H. Koppelman, Kourosh Saeb-Parsy, Sylvie Leroy, Pippa Powell, Ugis Sarkans, Wim Timens,
Pubblicato in: European Respiratory Journal, Numero Feb 3, 2022, 2022, ISSN 0903-1936
Editore: European Respiratory Society
DOI: 10.1183/13993003.02057-2021

SARS-CoV-2 infection triggers profibrotic macrophage responses and lung fibrosis

Autori: Daniel Wendisch, Oliver Dietrich, Tommaso Mari, Saskia von Stillfried, Ignacio L. Ibarra, Mirja Mittermaier, Christin Mache, Robert Lorenz Chua, Rainer Knoll, Sara Timm, Sophia Brumhard, Tobias Krammer, Henrik Zauber, Anna Luisa Hiller, Anna Pascual-Reguant, Ronja Mothes, Roman David Bülow Jessica Schulze, Alexander M. Leipold, Sonja Djudjaj, Florian Erhard, Robert Geffers, Fabian Pott, Julia Kaz
Pubblicato in: Cell, Numero Volume 184, Numero 26, 2021, Pagina/e 6243*6261, ISSN 0092-8674
Editore: Cell Press
DOI: 10.1016/j.cell.2021.11.033

Determinants of expression of SARS-CoV-2 entry-related genes in upper and lower airways

Autori: Hananeh Aliee,Florian Massip,Cancan Qi,Maria Stella de Biase,Jos van Nijnatten,Elin T. G. Kersten,Nazanin Z. Kermani,Basil Khuder,Judith M. Vonk,Roel C. H. Vermeulen,U-BIOPRED study group,Cambridge Lung Cancer Early Detection Programme,INER-Ciencias Mexican Lung Program,Margaret Neighbors,Gaik W. Tew,Michele A. Grimbaldeston,Nick H. T. ten Hacken,Sile Hu,Yike Guo,Xiaoyu Zhang,Kai Sun,Pieter S. Hie
Pubblicato in: Allergy, Numero Volume 77, Numero 2, 2021, Pagina/e 690-694, ISSN 1398-9995
Editore: John Wiley and Sons, Ltd
DOI: 10.1111/all.15152

Periostin: contributor to abnormal airway epithelial function in asthma?

Autori: Janette K. Burgess, Marnix R. Jonker, Marijn Berg, Nick T.H. ten Hacken, Kerstin B. Meyer, Maarten van den Berge, Martijn C. Nawijn, Irene H. Heijink
Pubblicato in: European Respiratory Journal, Numero 57/2, 2021, Pagina/e 2001286, ISSN 0903-1936
Editore: European Respiratory Society
DOI: 10.1183/13993003.01286-2020

Single-cell RNA sequencing reveals ex vivo signatures of SARS-CoV-2-reactive T cells through 'reverse phenotyping'.

Autori: David S. Fischer; Meshal Ansari; Karolin I. Wagner; Sebastian Jarosch; Yiqi Huang; Christoph H. Mayr; Maximilian Strunz; Niklas J. Lang; Elvira D’Ippolito; Monika Hammel; Laura Mateyka; Simone Weber; Lisa S. Wolff; K. Witter; Isis E. Fernandez; Gabriela Leuschner; Katrin Milger; Marion Frankenberger; Lorenz Nowak; Katharina Heinig-Menhard; Ina Koch; Mircea Gabriel Stoleriu; Anne Hilgendorff; Jü
Pubblicato in: Nature Communications, Numero 12(1), 2021, Pagina/e 4515, ISSN 2041-1723
Editore: Nature Publishing Group
DOI: 10.1038/s41467-021-24730-4

Where Is the Cystic Fibrosis Transmembrane Conductance Regulator?

Autori: Pascal Barbry, Brice Marcet, Ignacio Caballero
Pubblicato in: American Journal of Respiratory and Critical Care Medicine, Numero 203/10, 2021, Pagina/e 1214-1216, ISSN 1073-449X
Editore: American Thoracic Society
DOI: 10.1164/rccm.202012-4434ed

Expression Atlas update: gene and protein expression in multiple species

Autori: Pablo Moreno, Silvie Fexova, Nancy George, Jonathan R Manning, Zhichiao Miao, Suhaib Mohammed, Alfonso Muñoz-Pomer, Anja Fullgrabe, Yalan Bi, Natassja Bush, Haider Iqbal, Upendra Kumbham, Andrey Solovyev, Lingyun Zhao, Ananth Prakash, David García-Seisdedos, Deepti J Kundu, Shengbo Wang, Mathias Walzer, Laura Clarke, David Osumi-Sutherland, Marcela Karey Tello-Ruiz, Sunita Kumari, Doreen Ware, J
Pubblicato in: Nucleic Acid Research, Numero volume 50, issue D1, 2021, Pagina/e D129-D140, ISSN 0305-1048
Editore: Oxford University Press
DOI: 10.1093/nar/gkab1030

Neuropilin-1 is a host factor for SARS-CoV-2 infection

Autori: James L. Daly, Boris Simonetti, Katja Klein, Kai-En Chen, Maia Kavanagh Williamson, Carlos Antón-Plágaro, Deborah K. Shoemark, Lorena Simón-Gracia, Michael Bauer, Reka Hollandi, Urs F. Greber, Peter Horvath, Richard B. Sessions, Ari Helenius, Julian A. Hiscox, Tambet Teesalu, David A. Matthews, Andrew D. Davidson, Brett M. Collins, Peter J. Cullen, Yohei Yamauchi
Pubblicato in: Science, Numero 370/6518, 2020, Pagina/e 861-865, ISSN 0036-8075
Editore: American Association for the Advancement of Science
DOI: 10.1126/science.abd3072

Computationally prioritized drugs inhibit SARS-CoV-2 infection and syncytia formation

Autori: Angela Serra, Michele Fratello, Antonio Federico, Ravi Ojha, Riccardo Provenzani, Ervin Tasnadi, Luca Cattelani, Giusy del Giudice, Pia A S Kinaret, Laura A Saarimäki, Alisa Pavel, Suvi Kuivanen, Vincenzo Cerullo, Olli Vapalahti, Peter Horvath, Antonio Di Lieto, Jari Yli-Kauhaluoma, Giuseppe Balistreri, Dario Greco
Pubblicato in: Briefings in Bioinformatics, Numero Volume 23, Numero 1, 2022, ISSN 1467-5463
Editore: Oxford University Press
DOI: 10.1093/bib/bbab507

Human airway mast cells proliferate and acquire distinct inflammation-driven phenotypes during type 2 inflammation

Autori: Daniel F. Dwyer, Jose Ordovas-Montanes, Samuel J. Allon, Kathleen M. Buchheit, Marko Vukovic, Tahereh Derakhshan, Chunli Feng, Juying Lai, Travis K. Hughes, Sarah K. Nyquist, Matthew P. Giannetti, Bonnie Berger, Neil Bhattacharyya, Rachel E. Roditi, Howard R. Katz, Martijn C. Nawijn, Marijn Berg, Maarten van den Berge, Tanya M. Laidlaw, Alex K. Shalek, Nora A. Barrett, Joshua A. Boyce
Pubblicato in: Science Immunology, Numero 6/56, 2021, Pagina/e eabb7221, ISSN 2470-9468
Editore: American Association for the Advancement of Science
DOI: 10.1126/sciimmunol.abb7221

Seamless integration of image and molecular analysis for spatial transcriptomics workflows

Autori: Joseph Bergenstråhle, Ludvig Larsson, Joakim Lundeberg
Pubblicato in: BMC Genomics, Numero 21/1, 2020, ISSN 1471-2164
Editore: BioMed Central
DOI: 10.1186/s12864-020-06832-3

AnnotatorJ: an ImageJ plugin to ease hand annotation of cellular compartments

Autori: Réka Hollandi, Ákos Diósdi, Gábor Hollandi, Nikita Moshkov, Péter Horváth
Pubblicato in: Molecular Biology of the Cell, Numero 31/20, 2020, Pagina/e 2179-2186, ISSN 1059-1524
Editore: American Society for Cell Biology
DOI: 10.1091/mbc.e20-02-0156

Cell lines and clearing approaches: a single-cell level 3D light-sheet fluorescence microscopy dataset of multicellular spheroids

Autori: Akos Diosdi, Dominik Hirling, Maria Kovacs, Timea Toth, Maria Harmati, Krisztian Koos, Krisztina Buzas, Filippo Piccinini, Peter Horvath
Pubblicato in: Data in Brief, Numero 36, 2021, Pagina/e 107090, ISSN 2352-3409
Editore: Elsevier BV
DOI: 10.1016/j.dib.2021.107090

SCRINSHOT enables spatial mapping of cell states in tissue sections with single-cell resolution

Autori: Alexandros Sountoulidis, Andreas Liontos, Hong Phuong Nguyen, Alexandra B. Firsova, Athanasios Fysikopoulos, Xiaoyan Qian, Werner Seeger, Erik Sundström, Mats Nilsson, Christos Samakovlis
Pubblicato in: PLOS Biology, Numero 18/11, 2020, Pagina/e e3000675, ISSN 1545-7885
Editore: Public Library of Science
DOI: 10.1371/journal.pbio.3000675

Regression plane concept for analysing continuous cellular processes with machine learning

Autori: Abel Szkalisity, Filippo Piccinini, Attila Beleon, Tamas Balassa, Istvan Gergely Varga, Ede Migh, Csaba Molnar, Lassi Paavolainen, Sanna Timonen, Indranil Banerjee, Elina Ikonen, Yohei Yamauchi, Istvan Ando, Jaakko Peltonen, Vilja Pietiäinen, Viktor Honti, Peter Horvath
Pubblicato in: Nature Communications, Numero 12/1, 2021, ISSN 2041-1723
Editore: Nature Publishing Group
DOI: 10.1038/s41467-021-22866-x

A quantitative metric for the comparative evaluation of optical clearing protocols for 3D multicellular spheroids

Autori: Akos Diosdi, Dominik Hirling, Maria Kovacs, Timea Toth, Maria Harmati, Krisztian Koos, Krisztina Buzas, Filippo Piccinini, Peter Horvath
Pubblicato in: Computational and Structural Biotechnology Journal, Numero 19, 2021, Pagina/e 1233-1243, ISSN 2001-0370
Editore: Elsevier
DOI: 10.1016/j.csbj.2021.01.040

Deep Visual Proteomics defines single-cell identity and heterogeneity

Autori: Andreas Mund, Fabian Coscia, András Kriston, Réka Hollandi, Ferenc Kovács, Andreas-David Brunner, Ede Migh, Lisa Schweizer, Alberto Santos, Michael Bzorek, Soraya Naimy, Lise Mette Rahbek-Gjerdrum, Beatrice Dyring-Andersen, Jutta Bulkescher, Claudia Lukas, Mark Adam Eckert, Ernst Lengyel, Christian Gnann, Emma Lundberg, Peter Horvath & Matthias Mann
Pubblicato in: Nature Biotechnology, 2022, ISSN 1087-0156
Editore: Nature Publishing Group
DOI: 10.1038/s41587-022-01302-5

Benchmarking atlas-level data integration in single-cell genomics

Autori: Malte D. Luecken, M. Büttner, K. Chaichoompu, A. Danese, M. Interlandi, M. F. Mueller, D. C. Strobl, L. Zappia, M. Dugas, M. Colomé-Tatché & Fabian J. Theis
Pubblicato in: Nature Methods, Numero 19, 2022, Pagina/e 41-50, ISSN 1548-7091
Editore: Nature Publishing Group
DOI: 10.1038/s41592-021-01336-8

Genome-wide spatial expression profiling in formalin-fixed tissues

Autori: Eva Gracia Villacampa, Ludvig Larsson, Reza Mirzazadeh, Linda Kvastad, Alma Andersson, Annelie Mollbrink, Georgia Kokaraki, Vanessa Monteil, Niklas Schultz, Karin Sofia Appelberg, Nuria Montserrat, Haibo Zhang, Josef M. Penninger, Wolfgang Miesbach, Ali Mirazimi, Joseph Carlson, JoakimLundeberg
Pubblicato in: Cell Genomics, Numero Volume 1 Isuue 3, 2021, Pagina/e 100065, ISSN 2666-979X
Editore: Elsevier
DOI: 10.1016/j.xgen.2021.100065

SARS-CoV-2 entry factors are highly expressed in nasal epithelial cells together with innate immune genes

Autori: Waradon Sungnak, Ni Huang, Christophe Bécavin, Marijn Berg, Rachel Queen, Monika Litvinukova, Carlos Talavera-López, Henrike Maatz, Daniel Reichart, Fotios Sampaziotis, Kaylee B. Worlock, Masahiro Yoshida, Josephine L. Barnes
Pubblicato in: Nature Medicine, Numero 26/5, 2020, Pagina/e 681-687, ISSN 1078-8956
Editore: Nature Publishing Group
DOI: 10.1038/s41591-020-0868-6

SpheroidPicker: An Automated 3D cell culture manipulator robot using deep learning

Autori: Istvan Grexa, Akos Diosdi, Andras Kriston, Nikita Moshkov, Maria Harmati, Krisztina Buzas, Vilja Pietiainen, Krisztian Koos, Peter Horvath
Pubblicato in: Scientific Reports, Numero 11(1), 2021, Pagina/e 14813, ISSN 2045-2322
Editore: Nature Publishing Group
DOI: 10.1038/s41598-021-94217-1

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