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

Informations projet

DeepCell

N° de convention de subvention: 101054957

DOI

10.3030/101054957

Date de signature de la CE 28 Novembre 2022

Date de début 1 Janvier 2023

Date de fin 31 Decembre 2027

Financé au titre de

• European Research Council (ERC)

Coût total

€ 2 497 298,00

Contribution de l’UE

€ 2 497 298,00

Coordonné par

HELMHOLTZ ZENTRUM MUENCHEN DEUTSCHES FORSCHUNGSZENTRUM FUER GESUNDHEIT UND UMWELT GMBH
Germany

CORDIS fournit des liens vers les livrables publics et les publications des projets HORIZON.

Les liens vers les livrables et les publications des projets du 7e PC, ainsi que les liens vers certains types de résultats spécifiques tels que les jeux de données et les logiciels, sont récupérés dynamiquement sur OpenAIRE .

Livrables

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

Auteurs: Mayar Ali; Merel Kuijs; Soroor Hediyeh-zadeh; Tim Treis; Karin Hrovatin; Giovanni Palla; Anna C. Schaar; Fabian J. Theis
Publié dans: Bioinformatics, 2024, ISSN 1367-4811
Éditeur: Oxford University Press
DOI: 10.1101/2024.02.02.578605

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

Auteurs: 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
Publié dans: Nature Medicine, 2024, ISSN 1548-7105
Éditeur: Springer Nature
DOI: 10.1038/s41591-024-03214-0

Nature

Auteurs: 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
Publié dans: Nature, 2023, ISSN 0028-0836
Éditeur: Springer Nature
DOI: 10.1038/S41586-024-08172-8

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

Auteurs: Till Richter; Mojtaba Bahrami; Yufan Xia; David S. Fischer; Fabian J. Theis
Publié dans: Nature Machine Intelligence, 2024, ISSN 2522-5839
Éditeur: Springer Nature
DOI: 10.1101/2024.02.16.580624

Mapping lineage-traced cells across time points with moslin

Auteurs: Marius Lange; Zoe Piran; Michal Klein; Bastiaan Spanjaard; Dominik Klein; Jan Philipp Junker; Fabian J. Theis; Mor Nitzan
Publié dans: Genome Biology, 2024, ISSN 1474-760X
Éditeur: BioMed Central
DOI: 10.1101/2023.04.14.536867

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

Auteurs: Artur Szałata; Karin Hrovatin; Sören Becker; Alejandro Tejada-Lapuerta; Haotian Cui; Bo Wang; Fabian J. Theis
Publié dans: Nature Methods, 2024, ISSN 1548-7105
Éditeur: Springer Nature
DOI: 10.1038/S41592-024-02353-Z

Modeling fragment counts improves single-cell ATAC-seq analysis

Auteurs: Laura D. Martens; David S. Fischer; Vicente A. Yépez; Fabian J. Theis; Julien Gagneur
Publié dans: Nature Methods, 2023, ISSN 1548-7105
Éditeur: Springer Nature
DOI: 10.1038/S41592-023-02112-6

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

Auteurs: Philipp Weiler; Marius Lange; Michal Klein; Dana Pe’er; Fabian Theis
Publié dans: Nature Methods, 2024, ISSN 1548-7105
Éditeur: Springer Nature
DOI: 10.3929/ETHZ-B-000681242

Nature Genetics

Auteurs: Alejandro Tejada-Lapuerta; Paul Bertin; Stefan Bauer; Hananeh Aliee; Yoshua Bengio; Fabian J. Theis
Publié dans: Nature Genetics, 2025, ISSN 1061-4036
Éditeur: Springer Nature
DOI: 10.48550/ARXIV.2310.14935

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

Auteurs: Johannes C. Hingerl; Laura D. Martens; Alexander Karollus; Trevor Manz; Jason D. Buenrostro; Fabian J. Theis; Julien Gagneur
Publié dans: bioRxiv, 2024, ISSN 2692-8205
Éditeur: bioRxiv
DOI: 10.1101/2024.09.19.613754

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

Auteurs: Carlo De Donno; Soroor Hediyeh-Zadeh; Amir Ali Moinfar; Marco Wagenstetter; Luke Zappia; Mohammad Lotfollahi; Fabian J. Theis
Publié dans: Nature Methods, 2022, ISSN 1548-7105
Éditeur: Springer Nature
DOI: 10.1101/2022.11.28.517803

Mapping cells through time and space with moscot

Auteurs: 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
Publié dans: Nature, Numéro 638, 2025, ISSN 0028-0836
Éditeur: 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

Auteurs: Karin Hrovatin; Aimée Bastidas-Ponce; Mostafa Bakhti; Luke Zappia; Maren Büttner; Ciro Salinno; Michael Sterr; Anika Böttcher; Adriana Migliorini; Heiko Lickert; Fabian J. Theis
Publié dans: Nature Metabolism, 2023, ISSN 2522-5812
Éditeur: Springer Nature
DOI: 10.1101/2022.12.22.521557

Nature Methods

Auteurs: 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
Publié dans: Nature Methods, 2024, ISSN 1548-7091
Éditeur: Nature Publishing Group
DOI: 10.1038/S41592-024-02532-Y

Nature Genetics

Auteurs: 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
Publié dans: Nature Genetics, 2025, ISSN 1061-4036
Éditeur: 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

Auteurs: 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,
Publié dans: 2024
Éditeur: MIT Press

Other (5)

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

Auteurs: Karin Hrovatin; Amir Ali Moinfar; Luke Zappia; Alejandro Tejada Lapuerta; Ben Lengerich; Manolis Kellis; Fabian J. Theis
Publié dans: bioRxiv, 2024
Éditeur: 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

Auteurs: 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
Publié dans: bioRxiv, 2025
Éditeur: bioRxiv
DOI: 10.1101/2025.03.25.644826

Predicting cell morphological responses to perturbations using generative modeling

Auteurs: Alessandro Palma; Fabian J. Theis; Mohammad Lotfollahi
Publié dans: Nature Communications, 2023
Éditeur: Springer Nature
DOI: 10.1101/2023.07.17.549216

A multimodal cross-species comparison of pancreas development

Auteurs: 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
Publié dans: Research Square, 2024
Éditeur: Springer Nature
DOI: 10.60692/1JM7F-D8256

An integrated transcriptomic cell atlas of human endoderm-derived organoids

Auteurs: 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
Publié dans: 2023
Éditeur: Cold Spring Harbor Laboratory
DOI: 10.1101/2023.11.20.567825