Learning and modeling the molecular response of single cells to drug perturbations

Project Information

DeepCell

Grant agreement ID: 101054957

DOI

10.3030/101054957

EC signature date 28 November 2022

Start date 1 January 2023

End date 31 December 2027

Funded under

• European Research Council (ERC)

Total cost

€ 2 497 298,00

EU contribution

€ 2 497 298,00

Coordinated by

HELMHOLTZ ZENTRUM MUENCHEN DEUTSCHES FORSCHUNGSZENTRUM FUER GESUNDHEIT UND UMWELT GMBH
Germany

CORDIS provides links to public deliverables and publications of HORIZON projects.

Links to deliverables and publications from FP7 projects, as well as links to some specific result types such as dataset and software, are dynamically retrieved from OpenAIRE .

Deliverables

Documents, reports (1)

Data Management Plan

The Data Management Plan describes the data management life cycle for all data sets that will be collected processed or generated by the action It is a document describing what data will be collected processed or generated and following what methodology and standards whether and how this data will be shared andor made open and how it will be curated and preserved

Publications

Peer reviewed articles (15)

GraphCompass: spatial metrics for differential analyses of cell organization across conditions

Author(s): Mayar Ali; Merel Kuijs; Soroor Hediyeh-zadeh; Tim Treis; Karin Hrovatin; Giovanni Palla; Anna C. Schaar; Fabian J. Theis
Published in: Bioinformatics, 2024, ISSN 1367-4811
Publisher: Oxford University Press
DOI: 10.1101/2024.02.02.578605

An open-source framework for end-to-end analysis of electronic health record data

Author(s): Lukas Heumos; Philipp Ehmele; Tim Treis; Julius Upmeier zu Belzen; Eljas Roellin; Lilly May; Altana Namsaraeva; Nastassya Horlava; Vladimir A. Shitov; Xinyue Zhang; Luke Zappia; Rainer Knoll; Niklas J. Lang; Leon Hetzel; Isaac Virshup; Lisa Sikkema; Fabiola Curion; Roland Eils; Herbert B. Schiller; Anne Hilgendorff; Fabian J. Theis
Published in: Nature Medicine, 2024, ISSN 1548-7105
Publisher: Springer Nature
DOI: 10.1038/s41591-024-03214-0

Nature

Author(s): Zhisong He; Leander Dony; Jonas Simon Fleck; Artur Szałata; Katelyn X. Li; Irena Slišković; Hsiu-Chuan Lin; Malgorzata Santel; Alexander Atamian; Giorgia Quadrato; Jieran Sun; Sergiu P. Pașca; Neal D. Amin; Kevin W. Kelley; Taylor Bertucci; Sally Temple; Kathryn R. Bowles; Nicolò Caporale; Emanuele Villa; Giuseppe Testa; Cristiana Cruceanu; Elisabeth B. Binder; J. Gray Camp; Fabian J. Theis; Barbara Treutlein
Published in: Nature, 2023, ISSN 0028-0836
Publisher: Springer Nature
DOI: 10.1038/S41586-024-08172-8

Delineating the effective use of self-supervised learning in single-cell genomics

Author(s): Till Richter; Mojtaba Bahrami; Yufan Xia; David S. Fischer; Fabian J. Theis
Published in: Nature Machine Intelligence, 2024, ISSN 2522-5839
Publisher: Springer Nature
DOI: 10.1101/2024.02.16.580624

Mapping lineage-traced cells across time points with moslin

Author(s): Marius Lange; Zoe Piran; Michal Klein; Bastiaan Spanjaard; Dominik Klein; Jan Philipp Junker; Fabian J. Theis; Mor Nitzan
Published in: Genome Biology, 2024, ISSN 1474-760X
Publisher: BioMed Central
DOI: 10.1101/2023.04.14.536867

Transformers in single-cell omics: a review and new perspectives

Author(s): Artur Szałata; Karin Hrovatin; Sören Becker; Alejandro Tejada-Lapuerta; Haotian Cui; Bo Wang; Fabian J. Theis
Published in: Nature Methods, 2024, ISSN 1548-7105
Publisher: Springer Nature
DOI: 10.1038/S41592-024-02353-Z

Modeling fragment counts improves single-cell ATAC-seq analysis

Author(s): Laura D. Martens; David S. Fischer; Vicente A. Yépez; Fabian J. Theis; Julien Gagneur
Published in: Nature Methods, 2023, ISSN 1548-7105
Publisher: Springer Nature
DOI: 10.1038/S41592-023-02112-6

CellRank 2: unified fate mapping in multiview single-cell data

Author(s): Philipp Weiler; Marius Lange; Michal Klein; Dana Pe’er; Fabian Theis
Published in: Nature Methods, 2024, ISSN 1548-7105
Publisher: Springer Nature
DOI: 10.3929/ETHZ-B-000681242

Nature Genetics

Author(s): Alejandro Tejada-Lapuerta; Paul Bertin; Stefan Bauer; Hananeh Aliee; Yoshua Bengio; Fabian J. Theis
Published in: Nature Genetics, 2025, ISSN 1061-4036
Publisher: Springer Nature
DOI: 10.48550/ARXIV.2310.14935

scooby: Modeling multi-modal genomic profiles from DNA sequence at single-cell resolution

Author(s): Johannes C. Hingerl; Laura D. Martens; Alexander Karollus; Trevor Manz; Jason D. Buenrostro; Fabian J. Theis; Julien Gagneur
Published in: bioRxiv, 2024, ISSN 2692-8205
Publisher: bioRxiv
DOI: 10.1101/2024.09.19.613754

Population-level integration of single-cell datasets enables multi-scale analysis across samples

Author(s): Carlo De Donno; Soroor Hediyeh-Zadeh; Amir Ali Moinfar; Marco Wagenstetter; Luke Zappia; Mohammad Lotfollahi; Fabian J. Theis
Published in: Nature Methods, 2022, ISSN 1548-7105
Publisher: Springer Nature
DOI: 10.1101/2022.11.28.517803

Mapping cells through time and space with moscot

Author(s): Dominik Klein, Giovanni Palla, Marius Lange, Michal Klein, Zoe Piran, Manuel Gander, Laetitia Meng-Papaxanthos, Michael Sterr, Lama Saber, Changying Jing, Aimée Bastidas-Ponce, Perla Cota, Marta Tarquis-Medina, Shrey Parikh, Ilan Gold, Heiko Lickert, Mostafa Bakhti, Mor Nitzan, Marco Cuturi, Fabian J. Theis
Published in: Nature, Issue 638, 2025, ISSN 0028-0836
Publisher: Springer Science and Business Media LLC
DOI: 10.1038/S41586-024-08453-2

Delineating mouse β-cell identity during lifetime and in diabetes with a single cell atlas

Author(s): Karin Hrovatin; Aimée Bastidas-Ponce; Mostafa Bakhti; Luke Zappia; Maren Büttner; Ciro Salinno; Michael Sterr; Anika Böttcher; Adriana Migliorini; Heiko Lickert; Fabian J. Theis
Published in: Nature Metabolism, 2023, ISSN 2522-5812
Publisher: Springer Nature
DOI: 10.1101/2022.12.22.521557

Nature Methods

Author(s): Karin Hrovatin; Lisa Sikkema; Vladimir A. Shitov; Graham Heimberg; Maiia Shulman; Amanda J. Oliver; Michaela F. Mueller; Ignacio L. Ibarra; Hanchen Wang; Ciro Ramírez-Suástegui; Peng He; Anna C. Schaar; Sarah A. Teichmann; Fabian J. Theis; Malte D. Luecken
Published in: Nature Methods, 2024, ISSN 1548-7091
Publisher: Nature Publishing Group
DOI: 10.1038/S41592-024-02532-Y

Nature Genetics

Author(s): Quan Xu; Lennard Halle; Soroor Hediyeh-zadeh; Merel Kuijs; Rya Riedweg; Umut Kilik; Timothy Recaldin; Qianhui Yu; Isabell Rall; Tristan Frum; Lukas Adam; Shrey Parikh; Raphael Kfuri-Rubens; Manuel Gander; Dominik Klein; Fabiola Curion; Zhisong He; Jonas Simon Fleck; Koen Oost; Maurice Kahnwald; Silvia Barbiero; Olga Mitrofanova; Grzegorz Jerzy Maciag; Kim B. Jensen; Matthias Lutolf; Prisca Liberali; Jason R. Spence; Nikolche Gjorevski; Joep Beumer; Barbara Treutlein; Fabian J. Theis; J. Gray Camp
Published in: Nature Genetics, 2025, ISSN 1061-4036
Publisher: Nature Publishing Group
DOI: 10.1038/S41588-025-02182-6

Conference proceedings (1)

A benchmark for prediction of transcriptomic responses to chemical perturbations across cell types

Author(s): Artur Szałata, Andrew Benz, Robrecht Cannoodt, Mauricio Cortes, Jason Fong, Sunil Kuppasani, Richard Lieberman, Tianyu Liu, Javier Mas-Rosario, Rico Meinl, Jalil Nourisa, Jared Tumiel, Tin M. Tunjic, Mengbo Wang, Noah Weber, Hongyu Zhao, Benedict Anchang,
Published in: 2024
Publisher: MIT Press

Other (5)

Integrating single-cell RNA-seq datasets with substantial batch effects

Author(s): Karin Hrovatin; Amir Ali Moinfar; Luke Zappia; Alejandro Tejada Lapuerta; Ben Lengerich; Manolis Kellis; Fabian J. Theis
Published in: bioRxiv, 2024
Publisher: Cold Spring Harbor Laboratory
DOI: 10.1101/2023.11.03.565463

TNF-<i>α</i>disrupts the malate-aspartate shuttle, driving metabolic rewiring in iPSC-derived enteric neural lineages from Parkinson’s Disease patients

Author(s): Bruno Ghirotto; Luís Eduardo Gonçalves; Vivien Ruder; Christina James; Elizaveta Gerasimova; Tania Rizo; Holger Wend; Michaela Farrell; Juan Atilio Gerez; Natalia Cecilia Prymaczok; Merel Kuijs; Maiia Shulman; Anne Hartebrodt; Iryna Prots; Arne Gessner; Friederike Zunke; Jürgen Winkler; David B. Blumenthal; Fabian J. Theis; Roland Riek; Claudia Günther; Markus Neurath; Pooja Gupta; Beate Winner
Published in: bioRxiv, 2025
Publisher: bioRxiv
DOI: 10.1101/2025.03.25.644826

Predicting cell morphological responses to perturbations using generative modeling

Author(s): Alessandro Palma; Fabian J. Theis; Mohammad Lotfollahi
Published in: Nature Communications, 2023
Publisher: Springer Nature
DOI: 10.1101/2023.07.17.549216

A multimodal cross-species comparison of pancreas development

Author(s): Heiko Lickert; Kyong-Wol Yang; Hannah Spitzer; Michael Sterr; Karin Hrovatin; Sean de la O; Xinghao Zhang; Eunike S.A. Setyono; Minhaz Ud-Dean; Thomas Walzthoeni; Krzysztof Flisikowski; Tatiana Flisikowska; Angelika Schnieke; Katharina Scheibner; James M. Wells; Julie B. Sneddon; Barbara Keßler; Eckhard Wolf; Elisabeth Kemter; Fabian J. Theis
Published in: Research Square, 2024
Publisher: Springer Nature
DOI: 10.60692/1JM7F-D8256

An integrated transcriptomic cell atlas of human endoderm-derived organoids

Author(s): Quan Xu, Lennard Halle, Soroor Hediyeh-zadeh, Merel Kuijs, Umut Kilik, Qianhui Yu, Tristan Frum, Lukas Adam, Shrey Parikh, Manuel Gander, Raphael Kfuri-Rubens, Dominik Klein, Zhisong He, Jonas Simon Fleck, Koen Oost, Maurice Kahnwald, Silvia Barbiero, Olga Mitrofanova, Grzegorz Maciag, Kim B. Jensen, Matthias Lutolf, Prisca Liberali, Joep Beumer, Jason R. Spence, Barbara Treutlein, Fabian J. Theis, J. Gray Camp
Published in: 2023
Publisher: Cold Spring Harbor Laboratory
DOI: 10.1101/2023.11.20.567825