Program
Registration & Light Lunch
11:00-12:00 CEST
Opening of SBMI 2025
12:00-12:10 CEST
Session I:
12:10-13:30 CEST
Chair: Yann Bachelot
12:10-12:50 CEST
TBD
Emmanuel Saliba, University of Würzburg, Germany.
Abstract
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12:50-13:10 CEST
Pandemic preparedness: Individual-based modeling of day care centers predicts optimal surveillance strategies against pandemic viral diseases
Philipp Städter, Applied Systems Biology,Hans Knöll Institute, Jena, Germany
Abstract
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13:10-13:30 CEST
A model of Rtc-regulated RNA repair reveals heterogeneous responses to ribosome-targeting antibiotics and suggests molecular
targets to potentiate their effects
Hollie Hindley, University of Edinburgh, UK.
Abstract
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Coffee break
13:30-14:00 CEST
Session II:
14:00-15:40 CEST
Chair: Karoline Schied
14:00-14:40 CEST
Deterministic and Stochastic dynamics in Bacterial Persistence: Insights from Experiments and Minimal Models
Namiko Mitarai, University of Copenhagen, Denmark
Abstract
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14:40-15:10 CEST
Degradation of a plant defense metabolite by pathogenic Pseudomonas shapes the leaf microbiome and offers potential biocontrol strategies
Kerstin Unger & Marco Mauri, Friedrich Schiller University Jena, Jena, Germany.
Michael Reichelt, Jonathan Gershenzon, Rosalind J. Allen, Matthew T. Agler
Abstract
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15:10-15:40 CEST
The role of neutrophil-derived extracellular vesicles in promoting Candida albicans escape from phagocytosis
Anastasia Solomatina, Applied Systems Biology, Hans Knöll Institute, Jena, Germany.
Kerstin Hünniger-Ast, University of Würzburg, Institute for Hygiene and Microbiology, Würzburg & Fungal Septomics, Hans Knöll Institute, Jena, Germany
J. J. Patitz, N. E. Nieuwenhuizen, Y. Bachelot, A. K. Zimmermann, M. Blango, T. Krüger, O. Kniemeyer, A. A. Brakhage, O. Kurzai, M. T. Figge
Abstract
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Coffee break
15:40-16:10 CEST
Session III:
16:10-18:10 CEST
Chair: Parastoo Akbarimoghaddam
16:10-16:50 CEST
Physiological Heterogeneity and the Fate of Treatment: Single-Cell Insights into Bacterial Responses to Antibiotics and Phages
Somenath Bakshi, University of Cambridge, UK.
Abstract
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16:50-17:10 CEST
Viral lifecycle dynamics and spatial structure explain why pathogenicity is prophage-encoded
Sultan Ahmed Nazir, Utrecht University, Netherlands
Bram van Dijk
Abstract
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17:10-17:30 CEST
Function-specific epistasis alters otherwise repeatable evolutionary trajectories towards antibiotic resistance
Gabriela Petrungaro, Institute for biological physics, University of Cologne, Germany
Theresa Fink, Booshini Fernando, Gerrit Ansmann, Tobias Bollenbach
Abstract
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17:30-17:50 CEST
Bayesian mechanistic modelling of Candida auris optical density data to detect antifungal drug synergy
Tara Hameed, Imperial College London, UK
Larissa John, Elaine Bignell, Reiko J. Tanaka
Abstract
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17:50-18:10 CEST
Generative AI for Inverse Problems in Biomedical Computational Microscopy
Artur Yakimovich, Center for Advanced Systems Understanding, Helmholtz-Zentrum Dresden-Rossendorf e.V., Görlitz, Germany
Abstract
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Dinner
18:10-19:10 CEST
Poster Session
19:10-21:00 CEST
Most (tandem) talks will also be presented as posters.
Studying the Transition from Persister to Active Cells in Mycobacterium
Andreas Ulmer, Cluster of Excellence Balance of the Microverse, Friedrich Schiller University Jena, Jena, Germany
Vijay Srinivasan, Marco Mauri, Rosalind J. Allen,
Abstract
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Antibiotic exposure reveals differential susceptibility among human gut bacterial species
Pallabita Saha, Department of Microbiology, Immunology and Transplantation, Rega Institute, KU Leuven, Leuven, Belgium
Abstract
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Diversity and activity of microbial communities of the sea surface microlayer in the southern North Sea
Gurleen Singh, Carl von ozzietsky universität oldenburg, Germany
Isha Athale, Thorsten Brinkhoff
Abstract
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Antidepressants can induce antibiotic resistance and persistence in the gut microbiome of patients with major depression
Johanna Wallnisch, Theortical Microbial Ecology, Friedrich Schiller University Jena, Germany
Abstract
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Exploring the Spatial and Temporal Distribution of Biofilm Microbiomes on Endotracheal Tubes and their Role in Ventilator-Associated Pneumonia
Tia Wünschmann, Theortical Microbial Ecology, Friedrich Schiller University Jena, Germany
Abstract
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Exploring the Functional Role of Bacterial Aggregation in the Human Gut Microbiota
Stefanie Wagner, Theoretical Microbial Ecology Group & Cluster of Excellence ‘Balance of the Microverse’, Friedrich Schiller University Jena, Germany
Anne Busch, Rosalind J. Allen
Abstract
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DY-635 as a Ligand for Nanoparticle Hepatocyte-Targeting via OATP Selectivity
Paul Andrew Lee, Department of Anaesthesiology and Intensive Care Medicine, Universitat Klinikum Jena, Germany; SmartDyeLivery GmbH, Jena, Germany
Walter Hauswald, Julia Greiser, Marta Pomraenke, Zoltán Cseresnyés, Marc Thilo Figge, Ruman Gerst, Adrian T. Press
Abstract
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Virtual Phagocytosis Assays Resolve Ambiguities in Traditional Phagocytosis Measurements
Jana Wilms, Applied Systems Biology,Hans Knöll Institute, Jena, Germany
Sandra Timme, Simranpreet Kaur, Mohamed Hassan, Zoltán Cseresnyés, Kerstin Voigt, Marc Thilo Figge,
Abstract
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Modeling Candida albicans complex-mediated evasion and in silico treatment strategies: a systems biology approach
Yann Bachelot, Applied Systems Biology,Hans Knöll Institute, Jena, Germany
Carl-Magnus Svensson, Josephine Schötz, Anastasia Solomatina, Kerstin Hünniger-Ast, Oliver Kurzai, Marc Thilo Figge
Abstract
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Agent-based modeling of Organ-on-Chip experiments
Karoline Schied, Applied Systems Biology,Hans Knöll Institute, Jena, Germany
Abstract
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From Pixels to Insights: Image-based Analysis of Intestine-on-Chip Models
Parastoo Akbarimoghaddam, Applied Systems Biology,Hans Knöll Institute, Jena, Germany
Tim Kaden, Raquel Alonso-Roman, Manuel Allwang, Tobias Schaal, Johannes Stallhofer, Zoltan Cseresnyes, Mark S. Gresnigt, Bernhard Hube, Alexander S. Mosig, Marc Thilo Figge
Abstract
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Capturing Macromolecular Crowding effect in Biochemical Systems
Liliana Angeles-Martinez, Applied Systems Biology,Hans Knöll Institute, Jena, Germany
Marc Thilo Figge
Abstract
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High-Throughput Detection of Microbial Growth and Antibiotic Resistance using Scattered Light Imaging and Deep Learning
Arjun Sarkar, Applied Systems Biology,Hans Knöll Institute, Jena, Germany
Martina Graf, Carl-Magnus Svensson, Anne-Sophie Munser, Sven Schröder, Sundar Hengoju, Marc Thilo Figge, Miriam A. Rosenbaum
Abstract
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Quantitative Characterization of MoS₂-Coated Titanium Surfaces and Analysis of S. aureus Adherence Using JIPipe
Mounir Zerdani, Applied Systems Biology,Hans Knöll Institute, Jena, Germany
Bettina Löffler, Carl-Magnus Svensson, Andrey Turchanin, Christof Neumann, Rania Ennaciri, Marc Thilo Figge, Gaurvanshi Gupta
Abstract
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Hybrid Agent-Based Model of Human Alveolar Sac Predicts Intrinsic Behaviour of Innate Immune Response Against Aspergillus fumigatus
Simone Piccioni, Applied Systems Biology,Hans Knöll Institute, Jena, Germany
Abstract
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Immune response of the Monocytic Cell Line THP-1 against wild-type Staphylococcus aureus and small colony variants to monitor host-pathogen interaction
Sahar Hosseini Dehkordi, Theoretical Microbial Ecology/Bioinstrumentezentrum, Microbiology-Friedrich Schiller Universität Jena, Germany
Stefanie Wagner, Anne Busch, Elena Tiumina, Rosalind Allen
Abstract
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Real-time simultaneous monitoring of multiple analytes in bacterial cultures
Maggie Fink, University of Notre Dame; Indiana University South Bend, USA
Abstract
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Type I interferons restrict C. albicans translocation through the intestinal epithelial barrier
Saloni Saloni & Beatriz Cristóvão, Adaptive Pathogenicity Strategies, Hans Knöll Institute, Jena, Germany
Özlem Kirav, Marina Pekmezović, Sascha Schäuble, Mark S. Gresnigt
Abstract
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Learning hierarchically structured viral abundances from metagenomics data improves prediction for host-associated disease classification
Daniele Pugno, Helmholtz Munich, Germany
Abstract
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Session IV:
09:00-10:20 CEST
Chair: Simone Piccioni
09:00-09:40 CEST
TBD
Florence Bansept, Aix-Marseille Université, France
Abstract
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09:40-10:00 CEST
Predicting Microbial Interactions Using Graph Neural Networks
Elham Gholamzadeh, Max Planck Institute for Human Cognitive and Brain Sciences, Leipzig, Germany
Kajal Singla, Nico Scherf
Abstract
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10:00-10:20 CEST
Can Time-Dependent Optimal Interventions Effectively Reduce Microbial Pathogen Spread? A Case Study of Salmonella Transmission
Zubair Ahmad, University of Naples Federico II; University of Campania “Luigi Vanvitelli”, Caserta, Italy
Francesco Giannino, Gerardo Toraldo
Abstract
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Coffee break
10:20-10:50 CEST
Session V:
10:50-12:40 CEST
Chair: Philipp Städter
10:50-11:30 CEST
Individual-based modelling of microbial interactions: examples and lessons learnt
Jan-Ulrich Kreft, Institute of Microbiology and Infection & School of Biosciences, University of Birmingham, UK
Bastiaan J. R. Cockx, Tim Foster, Robert J. Clegg, Barth F. Smets
Abstract
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11:30-12:00 CEST
DPO (3,5-dimethylpyrazin-2-ol)-dependent quorum sensing modulates biofilm behavior of Vibrio cholerae in a 3D-intestine-on-chip infection model
Adrian Feile, University Hospital Jena, Germany
Zoltan Cseresnyes, Applied Systems Biology, Hans Knöll Institute Jena, Germany
Elisabeth Urbauer, Annika König, Valentin Wegner, Kerstin Thriene, Marc T. Figge, Kai Papenfort, Alexander S. Mosig
Abstract
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12:00-12:20 CEST
Effect of efflux-pump activity, cell density and population composition on antibiotic accumulation in bacterial biofilms
Silvia Vareschi, Friedrich Schiller University Jena, Germany
Marco Mauri, Rosalind J. Allen
Abstract
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12:20-12:40 CEST
Statistical end-to-end analysis of large-scale microbial growth data with DGrowthR
Medina Feldl, Institute of Computational Biology, Helmholtz Munich, Germany
Roberto Olayo-Alarcon, Martin K. Amstalden, Annamaria Zannoni, Stefanie Peschel, Ana Rita Brochado, Cynthia M Sharma, Christian L. Müller
Abstract
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Lunch break
12:40-13:30 CEST
Session VI:
13:30-15:10 CEST
Chair: Jana Wilms
13:30-14:00 CEST
Deciphering immune adaptations of an opportunistic fungal pathogen
Axel Dietschmann & Candela Fernández-Fernández, Adaptive Pathogenicity Strategies,Hans Knöll Institute, Jena, Germany.
Sude Dinçer, Thomas Krüger, Sascha Schäuble, Fay Bruggeman, Maximilian Himmel, Salomé LeibundGut-Landmann, Frank L. van de Veerdonk, Olaf Kniemeyer, Gianni Panagiotou, Axel A. Brakhage, Mark S. Gresnigt
Abstract
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14:00-14:20 CEST
DAP10-engineered Af-CAR-NK cells exert enhanced antifungal activity against A.fumigatus.
Matteo Mauget, Medizinische Klinik und Poliklinik II und Lehrstuhl für Zelluläre Immuntherapie, Universitätsklinikum, Würzburg, Germany
Anna-Lena Schmitt, Hermann Einsele, Michael Hudecek, Jürgen Löffler, Michelle Seif
Abstract
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14:20-14:50 CEST
Response prediction of lipopolysaccharide challenged healthy subjects and NETosis dynamics
Carl-Magnus Svensson, Applied Systems Biology, Hans-Knöll-Institute, Jena, Germany
Friedemann Börner,Institute for Clinical Chemistry and Laboratory Diagnostics, Jena University Hospital, Jena, Germany
Adrian Press, Marc Thilo Figge
Abstract
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14:50-15:10 CEST
Bordetella pertussis Toxins Drive the Emergence of a Unique CD8⁺ T Cell Subset in the Respiratory Tract
Peter Sebo, Institute of Microbiology of the CAS, Prague, Czech Republic
Anna Kratochvilova, Jana Holubova, Ondrej Stepanek, Ondrej Stanek
Abstract
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