EMBL Interdisciplinary Postdoc Programme 4

Informazioni relative al progetto

EIPOD4

ID dell’accordo di sovvenzione: 847543

DOI

10.3030/847543

Progetto chiuso

Data della firma CE 7 Maggio 2019

Data di avvio 1 Dicembre 2019

Data di completamento 31 Maggio 2025

Finanziato da

• EXCELLENT SCIENCE - Marie Skłodowska-Curie Actions

Costo totale

€ 13 240 800,00

Contributo UE

€ 6 620 400,00

Coordinato da

EUROPEAN MOLECULAR BIOLOGY LABORATORY
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 .

Pubblicazioni

Peer reviewed articles (35)

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

Autori: 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
Pubblicato in: Nature Communications, Numero 14, 2023, ISSN 2041-1723
Editore: Nature Publishing Group
DOI: 10.1038/s41467-023-39965-6

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

Autori: Mindy Liu Perkins, Justin Crocker, Gašper Tkačik
Pubblicato in: Proceedings of the National Academy of Sciences, Numero 122, 2024, ISSN 0027-8424
Editore: 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

Autori: Thomas Weber, Marco Raffaele Cosenza, Jan Korbel
Pubblicato in: Bioinformatics, Numero 39, 2023, ISSN 1367-4811
Editore: Oxford University Press (OUP)
DOI: 10.1093/bioinformatics/btad633

Variable microtubule architecture in the malaria parasite

Autori: 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
Pubblicato in: Nature Communications, Numero 14, 2023, ISSN 2041-1723
Editore: Nature Publishing Group
DOI: 10.1038/s41467-023-36627-5

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

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

Decipher enzymes from human microbiota for drug discovery and development

Autori: Mariia A. Beliaeva, Matthias Wilmanns, Michael Zimmermann
Pubblicato in: Current Opinion in Structural Biology, Numero 80, 2024, Pagina/e 102567, ISSN 0959-440X
Editore: Elsevier BV
DOI: 10.1016/j.sbi.2023.102567

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

Autori: Jia Hui Li, Vikas Trivedi, Alba Diz-Muñoz
Pubblicato in: Seminars in Cell & Developmental Biology, Numero 133, 2024, Pagina/e 123-134, ISSN 1084-9521
Editore: Academic Press
DOI: 10.1016/j.semcdb.2022.05.010

A synthetic synthesis to explore animal evolution and development

Autori: Mindy Liu Perkins, Lautaro Gandara, Justin Crocker
Pubblicato in: Philosophical Transactions of the Royal Society B: Biological Sciences, Numero 377, 2023, ISSN 0962-8436
Editore: Royal Society of London
DOI: 10.1098/rstb.2020.0517

Sensing their plasma membrane curvature allows migrating cells to circumvent obstacles

Autori: 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
Pubblicato in: Nature Communications, Numero 14, 2024, ISSN 2041-1723
Editore: Nature Publishing Group
DOI: 10.1038/s41467-023-41173-1

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

Autori: 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
Pubblicato in: Nature Communications, 2024, ISSN 2041-1723
Editore: Nature Publishing Group
DOI: 10.1101/2023.10.11.561842

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

Autori: 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
Pubblicato in: Cell Reports, Numero 43, 2024, Pagina/e 113519, ISSN 2211-1247
Editore: Cell Press
DOI: 10.1016/j.celrep.2023.113519

High-precision targeting workflow for volume electron microscopy

Autori: 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
Pubblicato in: Journal of Cell Biology, Numero June 23, 2021 220(9), 2021, Pagina/e e202104069, ISSN 1540-8140
Editore: Rockefeller University Press
DOI: 10.1083/jcb.202104069

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

Autori: Xueying C. Li, Lautaro Gandara, Måns Ekelöf, Kerstin Richter, Theodore Alexandrov, Justin Crocker
Pubblicato in: Nature Communications, 2024, ISSN 2041-1723
Editore: Nature Publishing Group
DOI: 10.1101/2022.09.28.509860

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

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

Modular control of vertebrate axis segmentation in time and space

Autori: Ali Seleit, Ian Brettell, Tomas Fitzgerald, Carina Vibe, Felix Loosli, Joachim Wittbrodt, Kiyoshi Naruse, Ewan Birney, Alexander Aulehla
Pubblicato in: The EMBO Journal, Numero 43, 2024, Pagina/e 4068-4091, ISSN 1460-2075
Editore: 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

Autori: 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
Pubblicato in: Developmental Cell, Numero 60, 2025, Pagina/e 780-793.e7, ISSN 1534-5807
Editore: Cell Press
DOI: 10.1016/j.devcel.2024.11.001

Enhancer architecture and chromatin accessibility constrain phenotypic space during Drosophila development

Autori: 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
Pubblicato in: Developmental Cell, Numero 58, 2024, Pagina/e 51-62.e4, ISSN 1534-5807
Editore: Cell Press
DOI: 10.1016/j.devcel.2022.12.003

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

Autori: Michal Razew, Angelique Fraudeau, Moritz M. Pfleiderer, Romain Linares, Wojciech P. Galej
Pubblicato in: Molecular Cell, Numero 84, 2024, Pagina/e 2542-2552.e5, ISSN 1097-2765
Editore: Cell Press
DOI: 10.1016/j.molcel.2024.05.009

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

Autori: Edoardo D’Imprima, Marta Garcia Montero, Sylwia Gawrzak, Paolo Ronchi, Ievgeniia Zagoriy, Yannick Schwab, Martin Jechlinger, Julia Mahamid
Pubblicato in: Developmental Cell, 2024, ISSN 1534-5807
Editore: Cell Press
DOI: 10.1101/2021.07.02.450855

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

Autori: Lautaro Gandara, Albert Tsai, Måns Ekelöf, Rafael Galupa, Ella Preger-Ben Noon, Theodore Alexandrov, Justin Crocker
Pubblicato in: Cell Reports, Numero 41, 2024, Pagina/e 111832, ISSN 2211-1247
Editore: 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

Autori: 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
Pubblicato in: Nature Communications, Numero 15, 2024, ISSN 2041-1723
Editore: 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

Autori: 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
Pubblicato in: Nature Communications, Numero 14, 2023, ISSN 2041-1723
Editore: Nature Publishing Group
DOI: 10.1038/s41467-023-44120-2

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

Autori: Ali Seleit, Alexander Aulehla, Alexandre Paix
Pubblicato in: eLife, Numero 10, 2023, ISSN 2050-084X
Editore: eLife Sciences Publications
DOI: 10.7554/elife.75050

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

Autori: 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
Pubblicato in: Cell Reports, Numero 42, 2025, Pagina/e 112831, ISSN 2211-1247
Editore: Cell Press
DOI: 10.1016/j.celrep.2023.112831

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

Autori: 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
Pubblicato in: Cell Reports, Numero 43, 2024, Pagina/e 113517, ISSN 2211-1247
Editore: Cell Press
DOI: 10.1016/j.celrep.2023.113517

Ribosomes hibernate on mitochondria during cellular stress

Autori: Olivier Gemin, Maciej Gluc, Higor Rosa, Michael Purdy, Moritz Niemann, Yelena Peskova, Simone Mattei, Ahmad Jomaa
Pubblicato in: Nature Communications, Numero 15, 2024, ISSN 2041-1723
Editore: 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

Autori: 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
Pubblicato in: Nature Methods, Numero 20, 2024, Pagina/e 1971-1979, ISSN 1548-7091
Editore: Nature Publishing Group
DOI: 10.1038/s41592-023-02054-z

Induction of territorial behavior and dominance hierarchies in laboratory mice

Autori: Dorian Battivelli, Lucas Boldrini, Mohit Jaiswal, Pradnya Patil, Sofia Torchia, Elizabeth Engelen, Luca Spagnoletti, Sarah Kaspar, Cornelius T. Gross
Pubblicato in: Scientific Reports, 2024, ISSN 2045-2322
Editore: 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

Autori: Marc Siggel, Rasmus K. Jensen, Valentin J. Maurer, Julia Mahamid, Jan Kosinski
Pubblicato in: Journal of Structural Biology, Numero 216, 2024, Pagina/e 108067, ISSN 1047-8477
Editore: Academic Press
DOI: 10.1016/j.jsb.2024.108067

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

Autori: 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
Pubblicato in: Nature Methods, Numero 22, 2025, Pagina/e 1213-1225, ISSN 1548-7091
Editore: Nature Publishing Group
DOI: 10.1038/s41592-025-02700-8

AlphaDesign: a de novo protein design framework based on AlphaFold

Autori: 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
Pubblicato in: Molecular Systems Biology, 2025, ISSN 1744-4292
Editore: Nature Publishing Group
DOI: 10.1038/s44320-025-00119-z

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

Autori: 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
Pubblicato in: Cell Stem Cell, Numero 32, 2025, Pagina/e 744-758.e7, ISSN 1934-5909
Editore: Cell Press
DOI: 10.1016/j.stem.2025.03.011

Mechanisms of inward transmembrane proton translocation

Autori: 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
Pubblicato in: Nature Structural & Molecular Biology, Numero 30, 2023, Pagina/e 970-979, ISSN 1545-9993
Editore: Nature Publishing Group
DOI: 10.1038/s41594-023-01020-9

Direct observation of motor protein stepping in living cells using MINFLUX

Autori: 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
Pubblicato in: Science, Numero 379, 2024, Pagina/e 1010-1015, ISSN 0036-8075
Editore: American Association for the Advancement of Science
DOI: 10.1126/science.ade2676

A combinatorial approach to uncover an additional Integrator subunit

Autori: Sarah R. Offley, Moritz M. Pfleiderer, Avery Zucco, Angelique Fraudeau, Sarah A. Welsh, Michal Razew, Wojciech P. Galej, Alessandro Gardini
Pubblicato in: Cell Reports, Numero 42, 2024, Pagina/e 112244, ISSN 2211-1247
Editore: 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

Autori: Wioleta Dudka, Veijo T. Salo, Julia Mahamid
Pubblicato in: FEBS Letters, Numero 598, 2025, Pagina/e 1127-1142, ISSN 0014-5793
Editore: Elsevier BV
DOI: 10.1002/1873-3468.14899