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Prof. Dagmar Iber (ETH Zürich)02/03/2026, 17:20
Computational simulations have long been used to study emergent phenomena in biology. Data-driven in silico models of tissue behavior in development and disease now enable the creation of Digital Twins—virtual counterparts with applications in bioengineering and precision medicine. In this talk, I will present our simulation frameworks for high-resolution tissue modeling and parameter...
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Dr Max Bonomi (Institut Pasteur)02/03/2026, 18:05
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Prof. Stefan Knapp (Goethe University)03/03/2026, 09:00
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Dr Barak Raveh (The Hebrew University of Jerusalem)03/03/2026, 09:45
T cells respond swiftly, specifically, sensitively, and robustly to cognate antigens presented on the surface of antigen presenting cells. Existing microscopic models capture various aspects of early T-cell antigen receptor (TCR) signaling at the molecular level. However, none of these models account for the totality of the data, impeding our understanding of early T-cell activation. Here, we...
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Dr Sergio Cruz-Leon (Max Planck Institute of Biophysics)03/03/2026, 11:00
High-confidence 3D template matching (hcTM) turns in situ cryoET tomograms into simulation-ready subcellular segments. Multiscale simulations then make predictions later confirmed experimentally. For example, how mutations or composition changes propagate to mesoscale organization and biological function. Examples include human chromatin organization, viral transport and mutation-driven...
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Prof. Lukas Stelzl (Johannes Gutenberg University Mainz & IMB)03/03/2026, 11:20
Cellular processes are organized by the phase separation of proteins into biomolecular condensates. These condensates are regulated by post-translational modifications, most notably phosphorylation. Phosphorylation of proteins is catalysed by kinases which consumes the chemical fuel ATP. While the phosphorylation of TDP-43 is closely linked to neurodegenerative disease, how TDP-43 is...
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Stephan Preibisch (HHMI Janelia)03/03/2026, 11:45
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Dr Andrej Sali (UCSF)03/03/2026, 14:00
Integrative modeling is an increasingly important tool in structural biology, providing structures by combining data from varied experimental methods and prior information. As a result, molecular architectures of large, heterogeneous, and dynamic systems, such as the ~52 MDa Nuclear Pore Complex, can be mapped with useful accuracy, precision, and completeness. Key challenges in improving...
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Dr Florian Wilfing (Max Planck Institute of Biophysics)03/03/2026, 14:45
Biomolecular condensates organise cellular biochemistry, yet their molecular architecture in situ remains poorly understood. During selective autophagy, macromolecules frequently accumulate into biomolecular condensates, forming discrete entities for autophagic engulfment and degradation – ideal systems for structural analysis. We employed in situ cryo-electron tomography to determine the...
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Dr Karen Palacio-Rodriguez (Max Planck Institute of Biophysics)03/03/2026, 16:00
During mitotic exit, the nuclear envelope seals spindle‑microtubule holes in a process mediated via LEM2‑ESCRT. Cryo-electron tomography (Cryo-ET) shows LEM2-ESCRT filament architecture but not the sealing mechanism. We built a digital twin by integrating Cryo‑ET with multiscale molecular dynamics simulations of filaments in a 90 nm membrane hole, capturing conformational changes, showing how...
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Dr Soumaya Zaghbani (Max Planck Institute of Biophysics)03/03/2026, 16:20
Correlative light and electron microscopy (CLEM) links dynamic functional imaging with ultrastructural detail, yet automated correlation remains unresolved due to the difficulty of bridging two fundamentally different microscopy modalities. Current approaches either bypass segmentation or rely on generic models, leading to poor or inconsistent alignment. We present Deep-SegCLEM, a fully...
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Prof. Martin Beck (Max Planck Institute of Biophysics)03/03/2026, 16:45
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Prof. Samantha Wood (Indiana University Bloomington)04/03/2026, 09:00
The origins of perception and cognition have been debated for centuries, with ongoing disagreement about what knowledge and neural structure are hardwired at birth. A major obstacle to resolving this debate is that, until recently, it has been impossible to train formal computational models of intelligence on the same sensory experiences as developing animals. We address this limitation by...
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Ms Mara Müller (MPI for Brain Research)04/03/2026, 09:45
When stressed, all cells downregulate protein synthesis, to conserve energy and shift resources towards repair. Here, we show that in some mammalian cells, including neurons, stress also results in the formation of inactive ribosome-ribosome clusters (disomes). Using cryogenic electron tomography we visualized ribosomes in situ and observed that this dimerization is mediated by a homotypic...
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Mr Jonas Elpelt (FIAS)04/03/2026, 10:05
We study time-irreversibility in spontaneous neural activity as a multiscale dynamical phenomenon. Using large-scale Neuropixels recordings across mouse brain areas, we quantify temporal asymmetry from milliseconds to seconds (30–0.5 Hz) with complementary computational measures capturing population-level asymmetry, metastable state fluxes, and state-space divergence. This framework enables...
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Prof. Sasha van Albada (FZ Jülich)04/03/2026, 11:00
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Prof. Alexander Gottschalk (Goethe University)04/03/2026, 11:45
Gap junctions (GJs) are intercellular channels that mediate electrical signals and transfer of small molecules. They are crucial for brain, heart, and other organ functions. While molecular structures of purified homomeric GJs are available, information of in situ structures is lacking. In vivo, GJs can form heteromers with different functionalities and may associate with other proteins. Here,...
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Dr Veronika Thallmair (Philipps University Marburg)04/03/2026, 12:05
Membrane contact sites between the ER and the PM are site of non-vesicular lipid transport as they harbor various lipid transfer proteins. They are established by protein tethers among which Extended Synaptotagmins (E-Syts) are the most abundant family in mammals. E-Syts are ER-resident and regulate ER-PM connectivity via reversible association of their C2 domains with lipids at the PM. Here,...
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Prof. Liesbet Geris (University of Liège, KU Leuven, VPH society)04/03/2026, 14:00
In silico and in vitro technologies are complementary to traditional biological and biomedical tools, enabling the study of multifactorial processes under controlled conditions. In the first part of this talk, I will present examples from bone and joint degeneration and regeneration research, where we combine computer modeling and simulation with microphysiological systems to better understand...
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04/03/2026, 14:45
Panelists: Stefan Knapp, Jan Kosinski,
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Loic Royer, Stephan Preibisch,
Liesbet Geris and Sacha van Albada -
Dr Tim Liebisch (EMBL Barcelona)04/03/2026, 16:00
Limb development is regulated by feedback between the tissue-scale mechanics and cellular decisions–migration, contraction, division, and death–implemented through gene-regulatory networks. The dynamically changing states of these cellular networks reflect the decisions being made. To integrate these interactions across 3 scales: genes, cells, and tissues, we develop a 3D cell-based model in...
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Prof. Liangyi Chen (National Biomedical Imaging Center, Peking University)04/03/2026, 16:20
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Dr Loic Royer (Biohub)04/03/2026, 16:45
Imagine having an interactive digital twin of a developing embryo — one you could pause, rewind, or zoom into, exploring how every cell divides, moves, and differentiates. To make this vision real, we created Zebrahub, a dynamic atlas of zebrafish embryogenesis that combines cutting-edge microscopy, powerful computational lineage tracking (Ultrack), and precise molecular mapping into an...
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Dr Ramachandra M. Bhaskara (Goethe University)04/03/2026, 17:30
FAM134B drives selective ER-phagy to maintain ER homeostasis. Modeling, coarse-grained MD, and experiments capture RHD-driven curvature induction/sensing (isoform-specific), ubiquitination-triggered clustering, and IDR-amplified ER budding. These self-organizing principles inform a hierarchical digital twin of the ER–phagophore contact site linking membrane mechanics/curvature, FAM134B–LC3B...
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Prof. Birgit Strodel (FZ Jülich)04/03/2026, 17:50
This work explores digital twins for innate immunity, focusing on human guanylate-binding protein 1 (hGBP1) and its role in targeting intracellular pathogens. Using coarse-grained molecular dynamics simulations, we examine protein-membrane interfaces with realistic pathogen membranes. We find that hGBP1 interacts with various membrane types; negatively charged lipids enhance affinity, while...
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Dr Annalisa Marsico (Computational Health Center, Helmholtz Munich)05/03/2026, 09:00
Computational analysis of high-resolution CLIP-seq data has enabled precise mapping of RBP binding sites and cis-regulatory elements underlying post-transcriptional RNA regulation. Recently, the field has shifted with the emergence of RNA foundation models—self-supervised models trained on vast unlabeled RNA sequences—that enable holistic modeling of RNA function and in silico hypothesis...
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Dr Judith Zaugg (University of Basel)05/03/2026, 09:45
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Dr Josep BIayna (Goethe University)05/03/2026, 11:00
Intron retention (IR) is an important regulator of RNA fate, yet its spatial and temporal organization in human cells remains poorly understood. Here, we investigate the dynamics, localization, and regulation of intron-retained RNAs in pluripotent stem cells using compartment-resolved transcriptional shutdown, sequence-based modeling, and advanced RNA imaging. We focus on the relationship...
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Prof. Stefanie Kaiser (Goethe University)05/03/2026, 11:20
Digital twins in structural cell biology critically depend on experimental data quality and interpretability. RNA is a central molecular layer, yet its mass spectrometric analysis remains analytically fragile. I will discuss why RNA-MS cannot be treated as an extension of proteomics and how intrinsic ambiguity, redundancy, and modification complexity challenge confidence. I argue that explicit...
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Prof. Marcel Schulz (Goethe University and Uniklinikum Frankfurt)05/03/2026, 11:45
Modern applications of AI technologies have enabled to predict the expression of genes genome-wide in a cell-type specific way using DNA sequence or epigenetic information. In this talk I will explain how these methods can be used to build digital twins for modelling gene expression and introduce novel applications for associating genes with disease and suggest personalised drug treatments.
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Dr Fabio Lolicato (Heidelberg University)05/03/2026, 14:00
Fibroblast Growth Factor 2 (FGF2) is a key cell survival factor involved in tumor-induced angiogenesis. Unlike most secreted proteins, FGF2 lacks a signal peptide and is exported via unconventional protein secretion (UPS), bypassing the ER/Golgi. It translocates directly across the plasma membrane (Type I UPS), a process initiated by PI(4,5)P₂- mediated recruitment to the inner leaflet....
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Mr Lars Dingeldein (FIAS)05/03/2026, 14:20
Biomolecules are inherently flexible, continuously transitioning between conformations to carry out their cellular functions. Cryo–electron microscopy (cryo-EM) enables us to image individual biomolecules at near-atomic resolution. As a result, an image dataset can capture the entire biomolecular ensemble at once. By comparing cryo-EM images to structural hypotheses, one can identify the...
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Prof. Suliana Manley (EPFL - Laboratory of Experimental Biophysics Lausanne)05/03/2026, 14:45
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Ms Srilakshmi Kalathil (Goethe University)05/03/2026, 16:00
he p53 family member p63 exhibits multiple isoforms and functional domains, with ΔNp63α serving as a critical transcriptional regulator implicated in epithelial-mesenchymal transition. While the various domains of ΔNp63α have been extensively characterized, the precise function of its Sterile Alpha Motif (SAM) domain stays elusive. Mutations within the SAM domain are associated with...
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Mr Thilo Duve (FIAS)05/03/2026, 16:20
Molecular photoswitches are light-responsive compounds that undergo reversible conformational changes upon irradiation. We present Martini 3 coarse-grained models for seven photoswitches, parameterized using semi-empirical reference data and experimental water–octanol partitioning. These models enable the development of digital twins for light-controlled biological systems including membrane...
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Prof. Jeffery Hoch (UConn Health)05/03/2026, 16:45
Machine learning is impacting not just the natural sciences but also the social sciences, engineering, architecture, and the art world. In many fields an obstacle to the application of machine learning is the relative paucity of available training data. Other challenges
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include the problem of interpreting the results of a machine learning algorithms, incorporating machine learning into... -
Mr Jan Kosinski (EMBL)05/03/2026, 17:30
One of the central goals of computational biology is to build a realistic model of a cell – one that can simulate cellular processes, predict the effects of perturbations, and support rational drug design. This vision has gained new momentum through recent technological advances, for example, in single-cell omics, structural proteomics, and visual mapping of cells using in-cell cryo-electron...
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Prof. Volker Zickermann (Goethe University Medical School)
Cardiolipin (CL) is the signature phospholipid of mitochondria. CL is essential for cristae formation and the functionality of the enzyme complexes involved in biological energy conversion. The mitochondrial transacylase Tafazzin catalyses the obligatory remodeling of CL, a process in which the composition of the four CL acyl chains is altered. Tafazzin dysfunction causes Barth syndrome, a...
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Mr Harsh Oza (Max Planck Institute of Biophysics / Goethe University Frankfurt)
Harsh Vinodkumar Oza, Marius Wegener, Timur Makarov*, Jonas Busam, Kathi Zarnack# & Michaela Müller-McNicoll# A critical quality control step in gene expression is the coupling of pre-mRNA splicing to nuclear export, ensuring that only fully processed transcripts reach the cytoplasm. How splicing fidelity is monitored and translated into export competence, however, remains poorly understood....
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Dr Jürgen Köfinger (Max Planck Institute of Biophysics)
We combine experiments with molecular simulations to learn more about a biomolecular system than we could from the individual methods alone. Ensemble and force-field refinement provide consistent, reproducible, and robust ways to do so. Biophysical experiments like SAXS, FRET, NMR, PELDOR/DEER provide ensemble averaged information. Although valuable by themselves, such information can be of...
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Balázs Fábián (Max Planck Institute of Biophysics)
Membrane buckling simulations are routinely analysed using Fourier fits to estimate protein intrinsic curvature. We show that such fits introduce systematic artifacts, despite accurate height profiles. Fitting the analytical Helfrich buckle shape yields consistent curvature distributions and intrinsic curvatures. Applying this approach to Martini 3 simulations, we extract the intrinsic...
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Lucia Baltz (JGU Mainz)
Molecular dynamics (MD) simulations have been proven essential for elucidating the hierarchical interplay of molecular interaction patterns on different time and length scales. To study the material properties of biomolecular condensates and ultimately their biological function, simulations of large systems require a vast amount of computational resources. Gaining insight into minute details...
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Dr Caterina Merla (ENEA BIOTEC-RED)
Accurate evaluation of the delivered electric dose is a key challenge in therapeutic brain stimulation based on physical stimulation, as clinical effects depend on the spatial distribution of brain induced electric fields. Numerical simulations were developed to describe electric field distributions in the heads of patients using two modelling approaches: one simulating transcranial magnetic...
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Horacio V. Guzman (ICMAB-Consejo Superior de Inv. Científicas)
We are standing at a unique crossroads in the fabrication of nanoparticles in-house [1-6] and AI algorithms. A decade from now, we have seen computational power explode, giving us the tools to dream up new biocompatible materials as novel drugs and treatments, designed faster than ever before. However, in the high-stakes world of nanomedicine, simply having a 'black-box answer' from AI isn't...
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Mr Magnus Petersen (Frankfurt Institute for Advanced Studies)
Characterizing conformational transitions in physical systems remains a fundamental challenge, as traditional sampling methods struggle with the high-dimensional nature of molecular systems and high-energy barriers between stable states. These rare events often represent the most biologically significant processes, yet may require months of continuous simulation to observe. One way to...
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Anika Dolata (Goethe University Frankfurt)
In plant biology, functional imaging enables the visualization and quantitative analysis of molecular activities in living cells with high spatiotemporal resolution. It involves fluorescent protein (FP) tagging combined with advanced fluorescence microscopy techniques, such as laser-scanning confocal imaging, super-resolution Airyscan detection, Förster Resonance Energy Transfer (FRET) and...
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Dr Ali Eljebbawi (Goethe University Frankfurt)
In plant biology, functional imaging enables the visualization and quantitative analysis of molecular activities in living cells with high spatiotemporal resolution. It involves fluorescent protein (FP) tagging combined with advanced fluorescence microscopy techniques, such as laser-scanning confocal imaging, super-resolution Airyscan detection, Förster Resonance Energy Transfer (FRET) and...
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Dr Sergio Alejandro Alejandro Poveda (Goethe University)
We developed an integrative pipeline that combines multi-omics data, structural screening, AlphaFold2 modeling, and all-atom molecular dynamics to identify and characterize selective autophagy receptors (SARs). The framework enables rapid screening of canonical LIR-LDS interactions by scoring motif-based residue contacts and pocket occlusion across experimental structures, AF2 models, and MD...
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Dr Vladimir Despic (Goethe University Frankfurt)
UV-C crosslinking and immunoprecipitation (CLIP)–based methods are the gold standard for identifying direct RNA binding protein (RBP) interaction sites on cellular RNA in vivo. Here, we describe individual nucleotide resolution CLIP version 3 (iCLIP3), an optimized protocol for generating transcriptome-wide maps of RBP-RNA interaction sites at single-nucleotide resolution from low-input...
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Ms Rachita Sharma (Max Planck Institute for Biophysics)
Here, we investigate Caenorhabditis elegans gap junctions (GJs) using an integrative approach combining electron cryo-tomography and molecular dynamics (MD) simulations. Cryo-tomographic analysis of primary embryonic cells revealed hexagonally packed arrays of GJs at cell–cell junctions. Notably, we identified a previously uncharacterized cap-like cytosolic density occluding the channel pore....
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Ms Alina Leiss (Max Planck Institute for Human Cognitive and Brain Sciences)
Our sham-controlled TMS study causally investigated the Angular Gyrus (AG) and DLPFC's roles in language comprehension and particularly examines how their contributions change under varying cognitive loads via dual-task reading/n-back. This detailed empirical data could serve as a valuable foundation for cognitive Digital Twins in the future, enabling simulation of individual responses and...
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Ainara Claveras (Max Planck Institute of Biophysics)
Autophagy requires lipid transfer from the ER to growing phagophores. Using structural predictions, molecular dynamics simulations, and in vitro lipid transfer assays, we investigated how the lipid transfer protein ATG2A mediates this process. We identified a novel gating mechanism driven by conformational rearrangements of N-terminal amphipathic helices. Guided by this insight, we designed an...
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Ms Sirgrid Trägenap (Franfkurt Institute of Advanced Studies)
The highly recurrent networks of the cerebral cortex are thought to profoundly shape neural responses, amplifying certain patterns of activity over others. However, whether such selective amplification organizes network activity at the level of the millimeter-scale networks which underlie perception and behavior remains unknown. Here, we combine patterned optogenetic stimulation informed by a...
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Mr Julian von Ehr (Goethe University Frankfurt)
The human serine-arginine rich splicing factor 6 (SRSF6) is part of the SR-protein family consisting of 12 members and as such is involved in (alternative-) splicing regulation. It is composed of an N-terminal RRM domain, followed by a pseudo RRM and a C-terminal serine-arginine rich disordered domain. With SRSF6 being an integral part of the splicing machinery, all three domains have been...
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Mr Alberto Cristiani (Goethe University Frankfurt)
E3 ubiquitin ligases define the ubiquitin code, regulating protein degradation and non-degradative processes such as DNA repair, signaling, and immunity. We present a comprehensive classification of the human E3 ligome by integrating sequence, structural, functional, and expression data using a weakly supervised metric-learning framework. This approach captures relationships across E3...
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Dr Josep BIayna (Goethe University Frankfurt)
Intron retention (IR) is an important regulator of RNA fate, yet its spatial and temporal organization in human cells remains poorly understood. Here, we investigate the dynamics, localization, and regulation of intron-retained RNAs in pluripotent stem cells using compartment-resolved transcriptional shutdown, sequence-based modeling, and advanced RNA imaging. We focus on the relationship...
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Dr Anusha Chaudhuri (Goethe University Frankfurt)
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Dr Gabrijela Dumbovic (Goethe University Frankfurt)
Intron retention (IR) is an important regulator of RNA fate, yet its spatial and temporal organization in human cells remains poorly understood. Here, we investigate the dynamics, localization, and regulation of intron-retained RNAs in pluripotent stem cells using compartment-resolved transcriptional shutdown, sequence-based modeling, and advanced RNA imaging. We focus on the relationship...
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Mr Plamen Kondev (Goethe University Frankfurt)
Membrane remodeling underlies many eukaryotic processes and is presumed to have co-evolved with the ER. We characterize six protein families that contain the Reticulon and Reticulon-like domains across all sequenced genomes. We present a new sequence-based subfamily classification. Despite poor sequence conservation across various phyla, this classification correlates with distinct changes in...
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Dr Naresh Yandrapalli (Saarland University)
Synthetic cells are vital for modeling cellular complexity. We present a progressive inverted emulsion method that transitions from robust on-chip vesicle production to engineering complex bilayers with ~95% asymmetry. By integrating lateral phase-separation ($L_o$/$L_d$ domains) and domain-specific protein binding , we induce spontaneous curvature leading to autonomous budding and fission....
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Dr Kateryna Lohachova (IBCii)
Large-scale membrane remodeling events, such as budding, fusion, fission, and pore formation, help maintain cellular homeostasis. Integral and peripheral membrane proteins play crucial roles in these remodeling events. By using coarse-grained molecular dynamics simulations, we quantify the protein-induced membrane perturbation fields. By employing the continuum Helfrich model and incorporating...
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Ms Deyue Kong (Frankfurt Institute for Advanced Studies)
Cortical circuits are proposed to amplify weak sensory inputs but transition to feature competition during strong drive. However, the evidence for this is scarce in cortices with a functional, modular organization, such as in primates and carnivores, where neighboring excitatory and inhibitory cells share feature selectivity. Here, we demonstrate that networks in ferret primary visual cortex...
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Nora Blümel (Goethe University Frankfurt)
After completion of processing in the nucleus eukaryotic mRNAs are bound by the nuclear export factor NXF1 and are exported to the cytoplasm. For binding to mRNAs, NXF1 requires adapter proteins that recruit NXF1 to newly transcribed pre-mRNAs in a non-sequence-specific manner. To identify novel NXF1 adapter proteins for the selective export of specific transcript classes we developed a...
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Dr Hendrik Jung (Goethe University Frankfurt)
We used the AI for Molecular Mechanism Discovery to simulate and understand the activation cascade of the Ca(2+)-sensing stromal interaction molecule 1 (STIM1) dimer. The detailed atomistic insight into the dimerization pathways enabled us to shed light on the experimentally observed changes in dimerization propensities for four different mutants and to reconcile previous experimental results....
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