Deliverables
Publications in at least 12 peerreviewed scientific publications
Best practices reportDescription of knowledge exchange and best practices from coordination meetings
Protocol for computational methods for spatial cell mappingExtension 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 methodsProtocolsio or similar platform collection of tissue acquisition and processing methods from discovAIR
Protocol for computational methods for microscopy-based single cell detection and phenotypingImprovement of framework to create a lung cell annotated single cell database for nuclei and extending with cytoplasm segmentation
Integrated spatial mapsIntegrated 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 methodsGithub collection of computational methods developed within discovAIR
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 prototypePortal 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 platformPosition paper on Human Lung Cell Atlas requirements from user groups perspective
Software application for annotation & visualization of multimodal dataSoftware application for annotation and visualisation of multimodal singlecell feature datasets
Publications
Author(s):
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
Published in:
Nature, Issue 602, 2022, Page(s) 321-327, ISSN 0028-0836
Publisher:
Nature Publishing Group
DOI:
10.1038/s41586-021-04345-x
Author(s):
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
Published in:
Nature Methods, Issue 19(2), 2022, Page(s) 171-178, ISSN 1548-7091
Publisher:
Nature Publishing Group
DOI:
10.1038/s41592-021-01358-2
Author(s):
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
Published in:
EMBO Molecular Medicine, Issue 13/4, 2021, ISSN 1757-4676
Publisher:
John Wiley & Sons Ltd.
DOI:
10.15252/emmm.202012871
Author(s):
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
Published in:
Cell Reports Methods, Issue Volume 2 issue 2, 2022, Page(s) 100166, ISSN 2667-2375
Publisher:
Elsevier
DOI:
10.1016/j.crmeth.2022.100166
Author(s):
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
Published in:
Nature Biotechnology, Issue 40, 2022, Page(s) 121-130, ISSN 1087-0156
Publisher:
Nature Publishing Group
DOI:
10.1038/s41587-021-01001-7
Author(s):
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
Published in:
American Journal of Respiratory and Critical Care Medicine, Issue 202/12, 2020, Page(s) 1636-1645, ISSN 1073-449X
Publisher:
American Thoracic Society
DOI:
10.1164/rccm.201911-2199oc
Author(s):
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
Published in:
Nature Medicine, Issue 27/3, 2021, Page(s) 546-559, ISSN 1078-8956
Publisher:
Nature Publishing Group
DOI:
10.1038/s41591-020-01227-z
Author(s):
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,
Published in:
European Respiratory Journal, Issue Feb 3, 2022, 2022, ISSN 0903-1936
Publisher:
European Respiratory Society
DOI:
10.1183/13993003.02057-2021
Author(s):
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
Published in:
Cell, Issue Volume 184, Issue 26, 2021, Page(s) 6243*6261, ISSN 0092-8674
Publisher:
Cell Press
DOI:
10.1016/j.cell.2021.11.033
Author(s):
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
Published in:
Allergy, Issue Volume 77, Issue 2, 2021, Page(s) 690-694, ISSN 1398-9995
Publisher:
John Wiley and Sons, Ltd
DOI:
10.1111/all.15152
Author(s):
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
Published in:
European Respiratory Journal, Issue 57/2, 2021, Page(s) 2001286, ISSN 0903-1936
Publisher:
European Respiratory Society
DOI:
10.1183/13993003.01286-2020
Author(s):
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
Published in:
Nature Communications, Issue 12(1), 2021, Page(s) 4515, ISSN 2041-1723
Publisher:
Nature Publishing Group
DOI:
10.1038/s41467-021-24730-4
Author(s):
Pascal Barbry, Brice Marcet, Ignacio Caballero
Published in:
American Journal of Respiratory and Critical Care Medicine, Issue 203/10, 2021, Page(s) 1214-1216, ISSN 1073-449X
Publisher:
American Thoracic Society
DOI:
10.1164/rccm.202012-4434ed
Author(s):
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
Published in:
Nucleic Acid Research, Issue volume 50, issue D1, 2021, Page(s) D129-D140, ISSN 0305-1048
Publisher:
Oxford University Press
DOI:
10.1093/nar/gkab1030
Author(s):
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
Published in:
Science, Issue 370/6518, 2020, Page(s) 861-865, ISSN 0036-8075
Publisher:
American Association for the Advancement of Science
DOI:
10.1126/science.abd3072
Author(s):
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
Published in:
Briefings in Bioinformatics, Issue Volume 23, Issue 1, 2022, ISSN 1467-5463
Publisher:
Oxford University Press
DOI:
10.1093/bib/bbab507
Author(s):
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
Published in:
Science Immunology, Issue 6/56, 2021, Page(s) eabb7221, ISSN 2470-9468
Publisher:
American Association for the Advancement of Science
DOI:
10.1126/sciimmunol.abb7221
Author(s):
Joseph Bergenstråhle, Ludvig Larsson, Joakim Lundeberg
Published in:
BMC Genomics, Issue 21/1, 2020, ISSN 1471-2164
Publisher:
BioMed Central
DOI:
10.1186/s12864-020-06832-3
Author(s):
Réka Hollandi, Ákos Diósdi, Gábor Hollandi, Nikita Moshkov, Péter Horváth
Published in:
Molecular Biology of the Cell, Issue 31/20, 2020, Page(s) 2179-2186, ISSN 1059-1524
Publisher:
American Society for Cell Biology
DOI:
10.1091/mbc.e20-02-0156
Author(s):
Akos Diosdi, Dominik Hirling, Maria Kovacs, Timea Toth, Maria Harmati, Krisztian Koos, Krisztina Buzas, Filippo Piccinini, Peter Horvath
Published in:
Data in Brief, Issue 36, 2021, Page(s) 107090, ISSN 2352-3409
Publisher:
Elsevier BV
DOI:
10.1016/j.dib.2021.107090
Author(s):
Alexandros Sountoulidis, Andreas Liontos, Hong Phuong Nguyen, Alexandra B. Firsova, Athanasios Fysikopoulos, Xiaoyan Qian, Werner Seeger, Erik Sundström, Mats Nilsson, Christos Samakovlis
Published in:
PLOS Biology, Issue 18/11, 2020, Page(s) e3000675, ISSN 1545-7885
Publisher:
Public Library of Science
DOI:
10.1371/journal.pbio.3000675
Author(s):
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
Published in:
Nature Communications, Issue 12/1, 2021, ISSN 2041-1723
Publisher:
Nature Publishing Group
DOI:
10.1038/s41467-021-22866-x
Author(s):
Akos Diosdi, Dominik Hirling, Maria Kovacs, Timea Toth, Maria Harmati, Krisztian Koos, Krisztina Buzas, Filippo Piccinini, Peter Horvath
Published in:
Computational and Structural Biotechnology Journal, Issue 19, 2021, Page(s) 1233-1243, ISSN 2001-0370
Publisher:
Elsevier
DOI:
10.1016/j.csbj.2021.01.040
Author(s):
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
Published in:
Nature Biotechnology, 2022, ISSN 1087-0156
Publisher:
Nature Publishing Group
DOI:
10.1038/s41587-022-01302-5
Author(s):
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
Published in:
Nature Methods, Issue 19, 2022, Page(s) 41-50, ISSN 1548-7091
Publisher:
Nature Publishing Group
DOI:
10.1038/s41592-021-01336-8
Author(s):
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
Published in:
Cell Genomics, Issue Volume 1 Isuue 3, 2021, Page(s) 100065, ISSN 2666-979X
Publisher:
Elsevier
DOI:
10.1016/j.xgen.2021.100065
Author(s):
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
Published in:
Nature Medicine, Issue 26/5, 2020, Page(s) 681-687, ISSN 1078-8956
Publisher:
Nature Publishing Group
DOI:
10.1038/s41591-020-0868-6
Author(s):
Istvan Grexa, Akos Diosdi, Andras Kriston, Nikita Moshkov, Maria Harmati, Krisztina Buzas, Vilja Pietiainen, Krisztian Koos, Peter Horvath
Published in:
Scientific Reports, Issue 11(1), 2021, Page(s) 14813, ISSN 2045-2322
Publisher:
Nature Publishing Group
DOI:
10.1038/s41598-021-94217-1
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