Decoding Context-Dependent Genetic Networks in vivo

Project Information

DECODE

Grant agreement ID: 810296

DOI

10.3030/810296

EC signature date 6 April 2019

Start date 1 July 2019

End date 30 June 2027

Funded under

• EXCELLENT SCIENCE - European Research Council (ERC)

Total cost

€ 10 625 000,00

EU contribution

€ 10 625 000,00

Coordinated by

DEUTSCHES KREBSFORSCHUNGSZENTRUM HEIDELBERG
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 .

Publications

Peer reviewed articles (30)

Aged intestinal stem cells propagate cell-intrinsic sources of inflammaging in mice

Author(s): Maja C. Funk, Jan G. Gleixner, Florian Heigwer, Dominik Vonficht, Erica Valentini, Zeynep Aydin, Elena Tonin, Stefania Del Prete, Sylvia Mahara, Yannick Throm, Jenny Hetzer, Danijela Heide, Oliver Stegle, Duncan T. Odom, Angelika Feldmann, Simon Haas, Mathias Heikenwalder, Michael Boutros
Published in: Developmental Cell, Issue 58, 2025, Page(s) 2914-2929.e7, ISSN 1534-5807
Publisher: Cell Press
DOI: 10.1016/j.devcel.2023.11.013

Principles and challenges of modeling temporal and spatial omics data

Author(s): Britta Velten, Oliver Stegle
Published in: Nature Methods, Issue 20, 2023, Page(s) 1462-1474, ISSN 1548-7091
Publisher: Nature Publishing Group
DOI: 10.1038/s41592-023-01992-y

The Hidden Architects: Nitric Oxide and Redox Dynamics in Plant Stem Cell Homeostasis

Author(s): Jian Zeng, Xin'Ai Zhao, Jan U. Lohmann
Published in: BioEssays, Issue 47, 2025, ISSN 0265-9247
Publisher: John Wiley & Sons Inc.
DOI: 10.1002/bies.70048

Chromatin accessibility illuminates single-cell regulatory dynamics of rice root tips

Author(s): Dan Feng, Zhe Liang, Yifan Wang, Jiaying Yao, Zan Yuan, Guihua Hu, Ruihong Qu, Shang Xie, Dongwei Li, Liwen Yang, Xinai Zhao, Yanfei Ma, Jan U Lohmann, Xiaofeng Gu
Published in: BMC Biology, Issue 20/1, 2022, Page(s) 274, ISSN 1471-2229
Publisher: BioMed Central
DOI: 10.1186/s12915-022-01473-2

Multiplexed conditional genome editing with Cas12a in Drosophila

Author(s): Fillip Port, Maja Starostecka, Michael Boutros
Published in: Proceedings of the National Academy of Sciences, Issue 117/37, 2020, Page(s) 22890-22899, ISSN 0027-8424
Publisher: National Academy of Sciences
DOI: 10.1073/pnas.2004655117

Deep-learning-based gene perturbation effect prediction does not yet outperform simple linear baselines

Author(s): Constantin Ahlmann-Eltze, Wolfgang Huber, Simon Anders
Published in: Nature Methods, Issue 22, 2025, Page(s) 1657-1661, ISSN 1548-7091
Publisher: Nature Publishing Group
DOI: 10.1038/s41592-025-02772-6

Tissue-Specific CRISPR-Cas9 Screening in Drosophila

Author(s): Fillip Port, Michael Boutros
Published in: Methods in Molecular Biology, Issue 19406029, 2022, Page(s) 157-176, ISSN 1940-6029
Publisher: Springer Nature
DOI: 10.1007/978-1-0716-2541-5_7

The Role of Organelles in Intestinal Function, Physiology, and Disease

Author(s): Siamak Redhai, Michael Boutros
Published in: Trends in Cell Biology, Issue 09628924, 2021, Page(s) 485-499, ISSN 0962-8924
Publisher: Elsevier BV
DOI: 10.1016/j.tcb.2021.01.003

Systematic discovery of biomolecular condensate-specific protein phosphorylation

Author(s): Sindhuja Sridharan, Alberto Hernandez-Armendariz, Nils Kurzawa, Clement M. Potel, Danish Memon, Pedro Beltrao, Marcus Bantscheff, Wolfgang Huber, Sara Cuylen-Haering, Mikhail M. Savitski
Published in: Nature Chemical Biology, Issue 18, 2022, Page(s) 1104-1114, ISSN 1552-4450
Publisher: Nature Publishing Group
DOI: 10.1038/s41589-022-01062-y

Comparison of transformations for single-cell RNA-seq data

Author(s): Constantin Ahlmann-Eltze, Wolfgang Huber
Published in: Nature Methods, Issue 20/5, 2023, Page(s) 665-672, ISSN 1548-7091
Publisher: Nature Publishing Group
DOI: 10.1038/s41592-023-01814-1

A global genetic interaction network by single-cell imaging and machine learning

Author(s): Florian Heigwer, Christian Scheeder, Josephine Bageritz, Schayan Yousefian, Benedikt Rauscher, Christina Laufer, Sergi Beneyto-Calabuig, Maja Christina Funk, Vera Peters, Maria Boulougouri, Jana Bilanovic, Thilo Miersch, Barbara Schmitt, Claudia Blass, Fillip Port, Michael Boutros
Published in: Cell Systems, Issue 14/5, 2023, Page(s) 346–362, ISSN 2405-4712
Publisher: Elsevier
DOI: 10.1016/j.cels.2023.03.003

CellRegMap: a statistical framework for mapping context-specific regulatory variants using scRNA-seq

Author(s): Anna S E Cuomo, Tobias Heinen, Danai Vagiaki, Danilo Horta, John C Marioni, Oliver Stegle
Published in: Molecular Systems Biology, Issue 17444292, 2022, Page(s) e10663, ISSN 1744-4292
Publisher: Nature Publishing Group
DOI: 10.15252/msb.202110663

A large-scale resource for tissue-specific CRISPR mutagenesis in Drosophila

Author(s): Fillip Port, Claudia Strein, Mona Stricker, Benedikt Rauscher, Florian Heigwer, Jun Zhou, Celine Beyersdörffer, Jana Frei, Amy Hess, Katharina Kern, Laura Lange, Nora Langner, Roberta Malamud, Bojana Pavlović, Kristin Rädecke, Lukas Schmitt, Lukas Voos, Erica Valentini, Michael Boutros
Published in: eLife, Issue 9, 2020, Page(s) e53865, ISSN 2050-084X
Publisher: eLife Sciences Publications
DOI: 10.7554/elife.53865

Metabolic balance in colorectal cancer is maintained by optimal Wnt signaling levels

Author(s): Katharina Imkeller; Giulia Ambrosi; Nancy Klemm; Ainara Claveras Cabezudo; Luisa Henkel; Wolfgang Huber; Michael Boutros
Published in: Molecular Systems Biology, Issue 17444292, 2022, Page(s) e10874, ISSN 1744-4292
Publisher: Nature Publishing Group
DOI: 10.15252/msb.202110874

Glyoxal as an alternative fixative for single-cell RNA sequencing

Author(s): Josephine Bageritz, Niklas Krausse, Schayan Yousefian, Svenja Leible, Erica Valentini, Michael Boutros
Published in: G3: Genes, Genomes, Genetics, Issue 13, 2023, Page(s) jkad160, ISSN 2160-1836
Publisher: Genetics Society of America
DOI: 10.1093/g3journal/jkad160

Cell2fate infers RNA velocity modules to improve cell fate prediction

Author(s): Alexander Aivazidis, Fani Memi, Vitalii Kleshchevnikov, Sezgin Er, Brian Clarke, Oliver Stegle, Omer Ali Bayraktar
Published in: Nature Methods, Issue 22, 2025, Page(s) 698-707, ISSN 1548-7091
Publisher: Nature Publishing Group
DOI: 10.1038/s41592-025-02608-3

Conditional CRISPR-Cas Genome Editing in Drosophila to Generate Intestinal Tumors

Author(s): Shivohum Bahuguna, Siamak Redhai, Jun Zhou, Tianyu Wang, Fillip Port, Michael Boutros
Published in: Cells, Issue 20734409, 2021, Page(s) 3156, ISSN 2073-4409
Publisher: MDPI
DOI: 10.3390/cells10113156

The dynamic genetic determinants of increased transcriptional divergence in spermatids

Author(s): Jasper Panten, Tobias Heinen, Christina Ernst, Nils Eling, Rebecca E. Wagner, Maja Satorius, John C. Marioni, Oliver Stegle, Duncan T. Odom
Published in: Nature Communications, Issue 15, 2024, ISSN 2041-1723
Publisher: Nature Publishing Group
DOI: 10.1038/s41467-024-45133-1

Identifying temporal and spatial patterns of variation from multimodal data using MEFISTO

Author(s): Britta Velten; Jana M. Braunger; Ricard Argelaguet; Damien Arnol; Jakob Wirbel; Danila Bredikhin; Georg Zeller; Oliver Stegle
Published in: Nature Methods, Issue 15487105, 2022, Page(s) 179-186, ISSN 1548-7105
Publisher: Springer Nature
DOI: 10.1038/s41592-021-01343-9

scDALI: modeling allelic heterogeneity in single cells reveals context-specific genetic regulation

Author(s): Tobias Heinen, Stefano Secchia, James P Reddington, Bingqing Zhao, Eileen E M Furlong, Oliver Stegle
Published in: Genome Biology, Issue 23/1, 2022, Page(s) 8, ISSN 1474-760X
Publisher: BioMed Central Ltd. Part of Springer Nature
DOI: 10.1186/s13059-021-02593-8

Analysis of multi-condition single-cell data with latent embedding multivariate regression

Author(s): Constantin Ahlmann-Eltze, Wolfgang Huber
Published in: Nature Genetics, Issue 57, 2025, Page(s) 659-667, ISSN 1061-4036
Publisher: Nature Publishing Group
DOI: 10.1038/s41588-024-01996-0

MicroRNA control of stem cell reconstitution and growth in root regeneration

Author(s): J. L. Baulies, R. E. Rodríguez, F. E. Lazzara, D. Liebsch, X. Zhao, J. Zeng, L. Bald, C. Schommer, J. U. Lohmann, J. F. Palatnik
Published in: Nature Plants, Issue 11, 2025, Page(s) 531-542, ISSN 2055-0278
Publisher: Springer Science and Business Media LLC
DOI: 10.1038/s41477-025-01922-0

A single-cell multi-omics atlas of rice

Author(s): Xiangyu Wang, Huanwei Huang, Sanjie Jiang, Jingmin Kang, Dongwei Li, Kailai Wang, Shang Xie, Cheng Tong, Chaofan Liu, Guihua Hu, Haoqian Li, Cong Li, Liwen Yang, Yike Ding, Shang-Tong Li, Faming Wang, Jan U. Lohmann, Zhe Liang, Xiaofeng Gu
Published in: Nature, Issue 644, 2025, Page(s) 722-730, ISSN 0028-0836
Publisher: Nature Publishing Group
DOI: 10.1038/s41586-025-09251-0

MUON: multimodal omics analysis framework

Author(s): Danila Bredikhin; Ilia Kats; Oliver Stegle
Published in: Genome Biology, Issue 23/1, 2022, Page(s) 42, ISSN 1474-760X
Publisher: BioMed Central Ltd. Part of Springer Nature
DOI: 10.1186/s13059-021-02577-8

glmGamPoi: fitting Gamma-Poisson generalized linear models on single cell count data

Author(s): Constantin Ahlmann-Eltze, Wolfgang Huber
Published in: Bioinformatics, Issue 36/24, 2020, Page(s) 5701-5702, ISSN 1367-4803
Publisher: Oxford University Press
DOI: 10.1093/bioinformatics/btaa1009

Transcriptional landscape of rice roots at the single-cell resolution

Author(s): Qing Liu, Zhe Liang, Dan Feng, Sanjie Jiang, Yifan Wang, Zhuoying Du, Ruoxi Li, Guihua Hu, Pingxian Zhang, Yanfei Ma, Jan U. Lohmann, Xiaofeng Gu
Published in: Molecular Plant, Issue 14/3, 2021, Page(s) 384-394, ISSN 1674-2052
Publisher: Oxford University Press
DOI: 10.1016/j.molp.2020.12.014

A temperature-tolerant CRISPR base editor mediates highly efficient and precise gene editing in Drosophila

Author(s): Roman M Doll, Michael Boutros, Fillip Port
Published in: Science Advances, Issue 9/35, 2023, Page(s) eadj1568, ISSN 2375-2548
Publisher: AAAS
DOI: 10.1126/sciadv.adj1568

FISHFactor: a probabilistic factor model for spatial transcriptomics data with subcellular resolution

Author(s): Florin C. Walter; Oliver Stegle; Britta Velten
Published in: Bioinformatics, Issue 39/5, 2023, Page(s) btad183, ISSN 1367-4811
Publisher: Oxford University Press
DOI: 10.1093/bioinformatics/btad183

Nitric oxide controls shoot meristem activity via regulation of DNA methylation.

Author(s): Jian Zeng, Xin’Ai Zhao, Zhe Liang, Inés Hidalgo, Michael Gebert, Pengfei Fan, Christian Wenzl, Sebastian G. Gornik, Jan U. Lohmann
Published in: Nature Communications, Issue 14/1, 2023, Page(s) 8001, ISSN 2041-1723
Publisher: Nature Publishing Group
DOI: 10.1038/s41467-023-43705-1

Best practices for the execution, analysis, and data storage of plant single-cell/nucleus transcriptomics

Author(s): Carolin Grones, Thomas Eekhout, Dongbo Shi, Manuel Neumann, Lea S. Berg, Yuji Ke, Rachel Shahan, Kevin L. Cox Jr, Fabio Gomez-Cano, Hilde Nelissen, Jan U. Lohmann, Stefania Giacomello, Olivier C. Martin, Benjamin Cole, Jia-Wei Wang, Kerstin Kaufmann, Michael T. Raissig, Gergo Palfalvi, Thomas Greb, Marc Libault, Bert De Rybel
Published in: Plant Cell, Issue 36/4, 2024, Page(s) 812-828, ISSN 1040-4651
Publisher: American Society of Plant Biologists
DOI: 10.1093/plcell/koae003