EMBL Interdisciplinary Postdoc Programme 4

Project Information

EIPOD4

Grant agreement ID: 847543

DOI

10.3030/847543

Project closed

EC signature date 7 May 2019

Start date 1 December 2019

End date 31 May 2025

Funded under

• EXCELLENT SCIENCE - Marie Skłodowska-Curie Actions

Total cost

€ 13 240 800,00

EU contribution

€ 6 620 400,00

Coordinated by

EUROPEAN MOLECULAR BIOLOGY LABORATORY
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 (35)

Mislocalization of pathogenic RBM20 variants in dilated cardiomyopathy is caused by loss-of-interaction with Transportin-3

Author(s): Julia Kornienko, Marta Rodríguez-Martínez, Kai Fenzl, Florian Hinze, Daniel Schraivogel, Markus Grosch, Brigit Tunaj, Dominik Lindenhofer, Laura Schraft, Moritz Kueblbeck, Eric Smith, Chad Mao, Emily Brown, Anjali Owens, Ardan M. Saguner, Benjamin Meder, Victoria Parikh, Michael Gotthardt, Lars M. Steinmetz
Published in: Nature Communications, Issue 14, 2023, ISSN 2041-1723
Publisher: Nature Publishing Group
DOI: 10.1038/s41467-023-39965-6

Chromatin enables precise and scalable gene regulation with factors of limited specificity

Author(s): Mindy Liu Perkins, Justin Crocker, Gašper Tkačik
Published in: Proceedings of the National Academy of Sciences, Issue 122, 2024, ISSN 0027-8424
Publisher: National Academy of Sciences
DOI: 10.1073/pnas.2411887121

MosaiCatcher v2: a single-cell structural variations detection and analysis reference framework based on Strand-seq

Author(s): Thomas Weber, Marco Raffaele Cosenza, Jan Korbel
Published in: Bioinformatics, Issue 39, 2023, ISSN 1367-4811
Publisher: Oxford University Press (OUP)
DOI: 10.1093/bioinformatics/btad633

Variable microtubule architecture in the malaria parasite

Author(s): Josie L. Ferreira, Vojtěch Pražák, Daven Vasishtan, Marc Siggel, Franziska Hentzschel, Annika M. Binder, Emma Pietsch, Jan Kosinski, Friedrich Frischknecht, Tim W. Gilberger, Kay Grünewald
Published in: Nature Communications, Issue 14, 2023, ISSN 2041-1723
Publisher: Nature Publishing Group
DOI: 10.1038/s41467-023-36627-5

A ubiquitin-specific, proximity-based labeling approach for the identification of ubiquitin ligase substrates

Author(s): Urbi Mukhopadhyay, Sophie Levantovsky, Teresa Maria Carusone, Sarah Gharbi, Frank Stein, Christian Behrends, Sagar Bhogaraju
Published in: Science Advances, Issue 10, 2024, ISSN 2375-2548
Publisher: American Association for the Advancement of Science (AAAS)
DOI: 10.1126/sciadv.adp3000

Decipher enzymes from human microbiota for drug discovery and development

Author(s): Mariia A. Beliaeva, Matthias Wilmanns, Michael Zimmermann
Published in: Current Opinion in Structural Biology, Issue 80, 2024, Page(s) 102567, ISSN 0959-440X
Publisher: Elsevier BV
DOI: 10.1016/j.sbi.2023.102567

Understanding the interplay of membrane trafficking, cell surface mechanics, and stem cell differentiation

Author(s): Jia Hui Li, Vikas Trivedi, Alba Diz-Muñoz
Published in: Seminars in Cell & Developmental Biology, Issue 133, 2024, Page(s) 123-134, ISSN 1084-9521
Publisher: Academic Press
DOI: 10.1016/j.semcdb.2022.05.010

A synthetic synthesis to explore animal evolution and development

Author(s): Mindy Liu Perkins, Lautaro Gandara, Justin Crocker
Published in: Philosophical Transactions of the Royal Society B: Biological Sciences, Issue 377, 2023, ISSN 0962-8436
Publisher: Royal Society of London
DOI: 10.1098/rstb.2020.0517

Sensing their plasma membrane curvature allows migrating cells to circumvent obstacles

Author(s): Ewa Sitarska, Silvia Dias Almeida, Marianne Sandvold Beckwith, Julian Stopp, Jakub Czuchnowski, Marc Siggel, Rita Roessner, Aline Tschanz, Christer Ejsing, Yannick Schwab, Jan Kosinski, Michael Sixt, Anna Kreshuk, Anna Erzberger, Alba Diz-Muñoz
Published in: Nature Communications, Issue 14, 2024, ISSN 2041-1723
Publisher: Nature Publishing Group
DOI: 10.1038/s41467-023-41173-1

A novel subgroup of light-driven sodium pumps with an additional Schiff base counterion

Author(s): E. Podoliak, G. H. U. Lamm, A. Alekseev, E. Marin, A. V. Schellbach, D. A. Fedotov, A. Stetsenko, N. Maliar, G. Bourenkov, T. Balandin, C. Baeken, R. Astashkin, T. R. Schneider, A. Bateman, J. Wachtveitl, I. Schapiro, V. Busskamp, A. Guskov, V. Gordeliy, K. Kovalev
Published in: Nature Communications, 2024, ISSN 2041-1723
Publisher: Nature Publishing Group
DOI: 10.1101/2023.10.11.561842

Randomly barcoded transposon mutant libraries for gut commensals II: Applying libraries for functional genetics

Author(s): Carlos Geert Pieter Voogdt, Surya Tripathi, Stefan Oliver Bassler, Saria A. McKeithen-Mead, Emma R. Guiberson, Alexandra Koumoutsi, Afonso Martins Bravo, Cullen Buie, Michael Zimmermann, Justin L. Sonnenburg, Athanasios Typas, Adam M. Deutschbauer, Anthony L. Shiver, Kerwyn Casey Huang
Published in: Cell Reports, Issue 43, 2024, Page(s) 113519, ISSN 2211-1247
Publisher: Cell Press
DOI: 10.1016/j.celrep.2023.113519

High-precision targeting workflow for volume electron microscopy

Author(s): Paolo Ronchi ORCID logo , Giulia Mizzon ORCID logo , Pedro Machado ORCID logo , Edoardo D’Imprima ORCID logo , Benedikt T. Best, Lucia Cassella ORCID logo , Sebastian Schnorrenberg, Marta G. Montero ORCID logo , Martin Jechlinger ORCID logo , Anne Ephrussi ORCID logo , Maria Leptin ORCID logo , Julia Mahamid ORCID logo , Yannick Schwab
Published in: Journal of Cell Biology, Issue June 23, 2021 220(9), 2021, Page(s) e202104069, ISSN 1540-8140
Publisher: Rockefeller University Press
DOI: 10.1083/jcb.202104069

Rapid response of fly populations to gene dosage across development and generations

Author(s): Xueying C. Li, Lautaro Gandara, Måns Ekelöf, Kerstin Richter, Theodore Alexandrov, Justin Crocker
Published in: Nature Communications, 2024, ISSN 2041-1723
Publisher: Nature Publishing Group
DOI: 10.1101/2022.09.28.509860

Flow in fetoplacental-like microvessels in vitro enhances perfusion, barrier function, and matrix stability

Author(s): Marta Cherubini, Scott Erickson, Prasanna Padmanaban, Per Haberkant, Frank Stein, Violeta Beltran-Sastre, Kristina Haase
Published in: Science Advances, Issue 9, 2024, ISSN 2375-2548
Publisher: American Association for the Advancement of Science (AAAS)
DOI: 10.1126/sciadv.adj8540

Modular control of vertebrate axis segmentation in time and space

Author(s): Ali Seleit, Ian Brettell, Tomas Fitzgerald, Carina Vibe, Felix Loosli, Joachim Wittbrodt, Kiyoshi Naruse, Ewan Birney, Alexander Aulehla
Published in: The EMBO Journal, Issue 43, 2024, Page(s) 4068-4091, ISSN 1460-2075
Publisher: Springer Science and Business Media LLC
DOI: 10.1038/s44318-024-00186-2

Systemic coordination of whole-body tissue remodeling during local regeneration in sea anemones

Author(s): Stephanie Cheung, Danila Bredikhin, Tobias Gerber, Petrus J. Steenbergen, Soham Basu, Richard Bailleul, Pauline Hansen, Alexandre Paix, Matthew A. Benton, Hendrik C. Korswagen, Detlev Arendt, Oliver Stegle, Aissam Ikmi
Published in: Developmental Cell, Issue 60, 2025, Page(s) 780-793.e7, ISSN 1534-5807
Publisher: Cell Press
DOI: 10.1016/j.devcel.2024.11.001

Enhancer architecture and chromatin accessibility constrain phenotypic space during Drosophila development

Author(s): Rafael Galupa, Gilberto Alvarez-Canales, Noa Ottilie Borst, Timothy Fuqua, Lautaro Gandara, Natalia Misunou, Kerstin Richter, Mariana R.P. Alves, Esther Karumbi, Melinda Liu Perkins, Tin Kocijan, Christine A. Rushlow, Justin Crocker
Published in: Developmental Cell, Issue 58, 2024, Page(s) 51-62.e4, ISSN 1534-5807
Publisher: Cell Press
DOI: 10.1016/j.devcel.2022.12.003

Structural basis of the Integrator complex assembly and association with transcription factors

Author(s): Michal Razew, Angelique Fraudeau, Moritz M. Pfleiderer, Romain Linares, Wojciech P. Galej
Published in: Molecular Cell, Issue 84, 2024, Page(s) 2542-2552.e5, ISSN 1097-2765
Publisher: Cell Press
DOI: 10.1016/j.molcel.2024.05.009

Light and electron microscopy continuum-resolution imaging of 3D cell cultures

Author(s): Edoardo D’Imprima, Marta Garcia Montero, Sylwia Gawrzak, Paolo Ronchi, Ievgeniia Zagoriy, Yannick Schwab, Martin Jechlinger, Julia Mahamid
Published in: Developmental Cell, 2024, ISSN 1534-5807
Publisher: Cell Press
DOI: 10.1101/2021.07.02.450855

Developmental phenomics suggests that H3K4 monomethylation confers multi-level phenotypic robustness

Author(s): Lautaro Gandara, Albert Tsai, Måns Ekelöf, Rafael Galupa, Ella Preger-Ben Noon, Theodore Alexandrov, Justin Crocker
Published in: Cell Reports, Issue 41, 2024, Page(s) 111832, ISSN 2211-1247
Publisher: Cell Press
DOI: 10.1016/j.celrep.2022.111832

The molecular dissection of TRIM25’s RNA-binding mechanism provides key insights into its antiviral activity

Author(s): Lucía Álvarez, Kevin Haubrich, Louisa Iselin, Laurent Gillioz, Vincenzo Ruscica, Karine Lapouge, Sandra Augsten, Ina Huppertz, Nila Roy Choudhury, Bernd Simon, Pawel Masiewicz, Mathilde Lethier, Stephen Cusack, Katrin Rittinger, Frank Gabel, Alexander Leitner, Gracjan Michlewski, Matthias W. Hentze, Frédéric H. T. Allain, Alfredo Castello, Janosch Hennig
Published in: Nature Communications, Issue 15, 2024, ISSN 2041-1723
Publisher: Nature Publishing Group
DOI: 10.1038/s41467-024-52918-x

USP7/Maged1-mediated H2A monoubiquitination in the paraventricular thalamus: an epigenetic mechanism involved in cocaine use disorder

Author(s): Julian Cheron, Leonardo Beccari, Perrine Hagué, Romain Icick, Chloé Despontin, Teresa Carusone, Matthieu Defrance, Sagar Bhogaraju, Elena Martin-Garcia, Roberto Capellan, Rafael Maldonado, Florence Vorspan, Jérôme Bonnefont, Alban de Kerchove d’Exaerde
Published in: Nature Communications, Issue 14, 2023, ISSN 2041-1723
Publisher: Nature Publishing Group
DOI: 10.1038/s41467-023-44120-2

Endogenous protein tagging in medaka using a simplified CRISPR/Cas9 knock-in approach

Author(s): Ali Seleit, Alexander Aulehla, Alexandre Paix
Published in: eLife, Issue 10, 2023, ISSN 2050-084X
Publisher: eLife Sciences Publications
DOI: 10.7554/elife.75050

Plasticity of the binding pocket in peptide transporters underpins promiscuous substrate recognition

Author(s): Vadim Kotov, Maxime Killer, Katharina E.J. Jungnickel, Jian Lei, Giada Finocchio, Josi Steinke, Kim Bartels, Jan Strauss, Florine Dupeux, Anne-Sophie Humm, Irina Cornaciu, José A. Márquez, Els Pardon, Jan Steyaert, Christian Löw
Published in: Cell Reports, Issue 42, 2025, Page(s) 112831, ISSN 2211-1247
Publisher: Cell Press
DOI: 10.1016/j.celrep.2023.112831

Randomly barcoded transposon mutant libraries for gut commensals I: Strategies for efficient library construction

Author(s): Surya Tripathi, Carlos Geert Pieter Voogdt, Stefan Oliver Bassler, Mary Anderson, Po-Hsun Huang, Nazgul Sakenova, Tümay Capraz, Sunit Jain, Alexandra Koumoutsi, Afonso Martins Bravo, Valentine Trotter, Michael Zimmerman, Justin L. Sonnenburg, Cullen Buie, Athanasios Typas, Adam M. Deutschbauer, Anthony L. Shiver, Kerwyn Casey Huang
Published in: Cell Reports, Issue 43, 2024, Page(s) 113517, ISSN 2211-1247
Publisher: Cell Press
DOI: 10.1016/j.celrep.2023.113517

Ribosomes hibernate on mitochondria during cellular stress

Author(s): Olivier Gemin, Maciej Gluc, Higor Rosa, Michael Purdy, Moritz Niemann, Yelena Peskova, Simone Mattei, Ahmad Jomaa
Published in: Nature Communications, Issue 15, 2024, ISSN 2041-1723
Publisher: Nature Publishing Group
DOI: 10.1038/s41467-024-52911-4

Pulsed stimulated Brillouin microscopy enables high-sensitivity mechanical imaging of live and fragile biological specimens

Author(s): Fan Yang, Carlo Bevilacqua, Sebastian Hambura, Ana Neves, Anusha Gopalan, Koki Watanabe, Matt Govendir, Maria Bernabeu, Jan Ellenberg, Alba Diz-Muñoz, Simone Köhler, Georgia Rapti, Martin Jechlinger, Robert Prevedel
Published in: Nature Methods, Issue 20, 2024, Page(s) 1971-1979, ISSN 1548-7091
Publisher: Nature Publishing Group
DOI: 10.1038/s41592-023-02054-z

Induction of territorial behavior and dominance hierarchies in laboratory mice

Author(s): Dorian Battivelli, Lucas Boldrini, Mohit Jaiswal, Pradnya Patil, Sofia Torchia, Elizabeth Engelen, Luca Spagnoletti, Sarah Kaspar, Cornelius T. Gross
Published in: Scientific Reports, 2024, ISSN 2045-2322
Publisher: Nature Publishing Group
DOI: 10.21203/rs.3.rs-4617383/v1

ColabSeg: An interactive tool for editing, processing, and visualizing membrane segmentations from cryo-ET data

Author(s): Marc Siggel, Rasmus K. Jensen, Valentin J. Maurer, Julia Mahamid, Jan Kosinski
Published in: Journal of Structural Biology, Issue 216, 2024, Page(s) 108067, ISSN 1047-8477
Publisher: Academic Press
DOI: 10.1016/j.jsb.2024.108067

Single-cell ultra-high-throughput multiplexed chromatin and RNA profiling reveals gene regulatory dynamics

Author(s): Sara Lobato-Moreno, Umut Yildiz, Annique Claringbould, Nila H. Servaas, Evi P. Vlachou, Christian Arnold, Hanke Gwendolyn Bauersachs, Víctor Campos-Fornés, Minyoung Kim, Ivan Berest, Karin D. Prummel, Kyung-Min Noh, Mikael Marttinen, Judith B. Zaugg
Published in: Nature Methods, Issue 22, 2025, Page(s) 1213-1225, ISSN 1548-7091
Publisher: Nature Publishing Group
DOI: 10.1038/s41592-025-02700-8

AlphaDesign: a de novo protein design framework based on AlphaFold

Author(s): Michael A Jendrusch, Alessio L J Yang, Elisabetta Cacace, Jacob Bobonis, Carlos G P Voogdt, Sarah Kaspar, Kristian Schweimer, Cecilia Perez-Borrajero, Karine Lapouge, Jacob Scheurich, Kim Remans, Janosch Hennig, Athanasios Typas, Jan O Korbel, S Kashif Sadiq
Published in: Molecular Systems Biology, 2025, ISSN 1744-4292
Publisher: Nature Publishing Group
DOI: 10.1038/s44320-025-00119-z

Glycolytic activity instructs germ layer proportions through regulation of Nodal and Wnt signaling

Author(s): Kristina S. Stapornwongkul, Elisa Hahn, Patryk Poliński, Laura Salamó Palau, Krisztina Arató, LiAng Yao, Kate Williamson, Nicola Gritti, Kerim Anlas, Mireia Osuna Lopez, Kiran R. Patil, Idse Heemskerk, Miki Ebisuya, Vikas Trivedi
Published in: Cell Stem Cell, Issue 32, 2025, Page(s) 744-758.e7, ISSN 1934-5909
Publisher: Cell Press
DOI: 10.1016/j.stem.2025.03.011

Mechanisms of inward transmembrane proton translocation

Author(s): Kirill Kovalev, Fedor Tsybrov, Alexey Alekseev, Vitaly Shevchenko, Dmytro Soloviov, Sergey Siletsky, Gleb Bourenkov, Michael Agthe, Marina Nikolova, David von Stetten, Roman Astashkin, Sergey Bukhdruker, Igor Chizhov, Antoine Royant, Alexander Kuzmin, Ivan Gushchin, Riccardo Rosselli, Francisco Rodriguez-Valera, Nikolay Ilyinskiy, Andrey Rogachev, Valentin Borshchevskiy, Thomas R. Schneider, Ernst
Published in: Nature Structural & Molecular Biology, Issue 30, 2023, Page(s) 970-979, ISSN 1545-9993
Publisher: Nature Publishing Group
DOI: 10.1038/s41594-023-01020-9

Direct observation of motor protein stepping in living cells using MINFLUX

Author(s): Takahiro Deguchi, Malina K. Iwanski, Eva-Maria Schentarra, Christopher Heidebrecht, Lisa Schmidt, Jennifer Heck, Tobias Weihs, Sebastian Schnorrenberg, Philipp Hoess, Sheng Liu, Veronika Chevyreva, Kyung-Min Noh, Lukas C. Kapitein, Jonas Ries
Published in: Science, Issue 379, 2024, Page(s) 1010-1015, ISSN 0036-8075
Publisher: American Association for the Advancement of Science
DOI: 10.1126/science.ade2676

A combinatorial approach to uncover an additional Integrator subunit

Author(s): Sarah R. Offley, Moritz M. Pfleiderer, Avery Zucco, Angelique Fraudeau, Sarah A. Welsh, Michal Razew, Wojciech P. Galej, Alessandro Gardini
Published in: Cell Reports, Issue 42, 2024, Page(s) 112244, ISSN 2211-1247
Publisher: Cell Press
DOI: 10.1016/j.celrep.2023.112244

Non-peer reviewed articles (1)

Zooming into lipid droplet biology through the lens of electron microscopy

Author(s): Wioleta Dudka, Veijo T. Salo, Julia Mahamid
Published in: FEBS Letters, Issue 598, 2025, Page(s) 1127-1142, ISSN 0014-5793
Publisher: Elsevier BV
DOI: 10.1002/1873-3468.14899