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

Informazioni relative al progetto

DeepCell

ID dell’accordo di sovvenzione: 101054957

DOI

10.3030/101054957

Data della firma CE 28 Novembre 2022

Data di avvio 1 Gennaio 2023

Data di completamento 31 Dicembre 2027

Finanziato da

• European Research Council (ERC)

Costo totale

€ 2 497 298,00

Contributo UE

€ 2 497 298,00

Coordinato da

HELMHOLTZ ZENTRUM MUENCHEN DEUTSCHES FORSCHUNGSZENTRUM FUER GESUNDHEIT UND UMWELT GMBH
Germany

CORDIS fornisce collegamenti ai risultati finali pubblici e alle pubblicazioni dei progetti ORIZZONTE.

I link ai risultati e alle pubblicazioni dei progetti del 7° PQ, così come i link ad alcuni tipi di risultati specifici come dataset e software, sono recuperati dinamicamente da .OpenAIRE .

Risultati finali

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

Pubblicazioni

Peer reviewed articles (15)

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

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

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

Autori: 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
Pubblicato in: Nature Medicine, 2024, ISSN 1548-7105
Editore: Springer Nature
DOI: 10.1038/s41591-024-03214-0

Nature

Autori: 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
Pubblicato in: Nature, 2023, ISSN 0028-0836
Editore: Springer Nature
DOI: 10.1038/S41586-024-08172-8

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

Autori: Till Richter; Mojtaba Bahrami; Yufan Xia; David S. Fischer; Fabian J. Theis
Pubblicato in: Nature Machine Intelligence, 2024, ISSN 2522-5839
Editore: Springer Nature
DOI: 10.1101/2024.02.16.580624

Mapping lineage-traced cells across time points with moslin

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

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

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

Modeling fragment counts improves single-cell ATAC-seq analysis

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

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

Autori: Philipp Weiler; Marius Lange; Michal Klein; Dana Pe’er; Fabian Theis
Pubblicato in: Nature Methods, 2024, ISSN 1548-7105
Editore: Springer Nature
DOI: 10.3929/ETHZ-B-000681242

Nature Genetics

Autori: Alejandro Tejada-Lapuerta; Paul Bertin; Stefan Bauer; Hananeh Aliee; Yoshua Bengio; Fabian J. Theis
Pubblicato in: Nature Genetics, 2025, ISSN 1061-4036
Editore: Springer Nature
DOI: 10.48550/ARXIV.2310.14935

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

Autori: Johannes C. Hingerl; Laura D. Martens; Alexander Karollus; Trevor Manz; Jason D. Buenrostro; Fabian J. Theis; Julien Gagneur
Pubblicato in: bioRxiv, 2024, ISSN 2692-8205
Editore: bioRxiv
DOI: 10.1101/2024.09.19.613754

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

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

Mapping cells through time and space with moscot

Autori: 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
Pubblicato in: Nature, Numero 638, 2025, ISSN 0028-0836
Editore: 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

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

Nature Methods

Autori: 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
Pubblicato in: Nature Methods, 2024, ISSN 1548-7091
Editore: Nature Publishing Group
DOI: 10.1038/S41592-024-02532-Y

Nature Genetics

Autori: 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
Pubblicato in: Nature Genetics, 2025, ISSN 1061-4036
Editore: 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

Autori: 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,
Pubblicato in: 2024
Editore: MIT Press

Other (5)

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

Autori: Karin Hrovatin; Amir Ali Moinfar; Luke Zappia; Alejandro Tejada Lapuerta; Ben Lengerich; Manolis Kellis; Fabian J. Theis
Pubblicato in: bioRxiv, 2024
Editore: 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

Autori: 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
Pubblicato in: bioRxiv, 2025
Editore: bioRxiv
DOI: 10.1101/2025.03.25.644826

Predicting cell morphological responses to perturbations using generative modeling

Autori: Alessandro Palma; Fabian J. Theis; Mohammad Lotfollahi
Pubblicato in: Nature Communications, 2023
Editore: Springer Nature
DOI: 10.1101/2023.07.17.549216

A multimodal cross-species comparison of pancreas development

Autori: 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
Pubblicato in: Research Square, 2024
Editore: Springer Nature
DOI: 10.60692/1JM7F-D8256

An integrated transcriptomic cell atlas of human endoderm-derived organoids

Autori: 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
Pubblicato in: 2023
Editore: Cold Spring Harbor Laboratory
DOI: 10.1101/2023.11.20.567825