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

Información del proyecto

DeepCell

Identificador del acuerdo de subvención: 101054957

DOI

10.3030/101054957

Fecha de la firma de la CE 28 Noviembre 2022

Fecha de inicio 1 Enero 2023

Fecha de finalización 31 Diciembre 2027

Financiado con arreglo a

• European Research Council (ERC)

Coste total

€ 2 497 298,00

Aportación de la UE

€ 2 497 298,00

Coordinado por

HELMHOLTZ ZENTRUM MUENCHEN DEUTSCHES FORSCHUNGSZENTRUM FUER GESUNDHEIT UND UMWELT GMBH
Germany

CORDIS proporciona enlaces a los documentos públicos y las publicaciones de los proyectos de los programas marco HORIZONTE.

Los enlaces a los documentos y las publicaciones de los proyectos del Séptimo Programa Marco, así como los enlaces a algunos tipos de resultados específicos, como conjuntos de datos y «software», se obtienen dinámicamente de OpenAIRE .

Resultado final

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

Publicaciones

Peer reviewed articles (15)

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

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

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

Autores: 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
Publicado en: Nature Medicine, 2024, ISSN 1548-7105
Editor: Springer Nature
DOI: 10.1038/s41591-024-03214-0

Nature

Autores: 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
Publicado en: Nature, 2023, ISSN 0028-0836
Editor: Springer Nature
DOI: 10.1038/S41586-024-08172-8

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

Autores: Till Richter; Mojtaba Bahrami; Yufan Xia; David S. Fischer; Fabian J. Theis
Publicado en: Nature Machine Intelligence, 2024, ISSN 2522-5839
Editor: Springer Nature
DOI: 10.1101/2024.02.16.580624

Mapping lineage-traced cells across time points with moslin

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

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

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

Modeling fragment counts improves single-cell ATAC-seq analysis

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

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

Autores: Philipp Weiler; Marius Lange; Michal Klein; Dana Pe’er; Fabian Theis
Publicado en: Nature Methods, 2024, ISSN 1548-7105
Editor: Springer Nature
DOI: 10.3929/ETHZ-B-000681242

Nature Genetics

Autores: Alejandro Tejada-Lapuerta; Paul Bertin; Stefan Bauer; Hananeh Aliee; Yoshua Bengio; Fabian J. Theis
Publicado en: Nature Genetics, 2025, ISSN 1061-4036
Editor: Springer Nature
DOI: 10.48550/ARXIV.2310.14935

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

Autores: Johannes C. Hingerl; Laura D. Martens; Alexander Karollus; Trevor Manz; Jason D. Buenrostro; Fabian J. Theis; Julien Gagneur
Publicado en: bioRxiv, 2024, ISSN 2692-8205
Editor: bioRxiv
DOI: 10.1101/2024.09.19.613754

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

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

Mapping cells through time and space with moscot

Autores: 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
Publicado en: Nature, Edición 638, 2025, ISSN 0028-0836
Editor: 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

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

Nature Methods

Autores: 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
Publicado en: Nature Methods, 2024, ISSN 1548-7091
Editor: Nature Publishing Group
DOI: 10.1038/S41592-024-02532-Y

Nature Genetics

Autores: 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
Publicado en: Nature Genetics, 2025, ISSN 1061-4036
Editor: 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

Autores: 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,
Publicado en: 2024
Editor: MIT Press

Other (5)

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

Autores: Karin Hrovatin; Amir Ali Moinfar; Luke Zappia; Alejandro Tejada Lapuerta; Ben Lengerich; Manolis Kellis; Fabian J. Theis
Publicado en: bioRxiv, 2024
Editor: 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

Autores: 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
Publicado en: bioRxiv, 2025
Editor: bioRxiv
DOI: 10.1101/2025.03.25.644826

Predicting cell morphological responses to perturbations using generative modeling

Autores: Alessandro Palma; Fabian J. Theis; Mohammad Lotfollahi
Publicado en: Nature Communications, 2023
Editor: Springer Nature
DOI: 10.1101/2023.07.17.549216

A multimodal cross-species comparison of pancreas development

Autores: 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
Publicado en: Research Square, 2024
Editor: Springer Nature
DOI: 10.60692/1JM7F-D8256

An integrated transcriptomic cell atlas of human endoderm-derived organoids

Autores: 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
Publicado en: 2023
Editor: Cold Spring Harbor Laboratory
DOI: 10.1101/2023.11.20.567825