Integrative Pathway Modelling in Systems Biology and Systems Medicine

April 18-20

Scientific organizer: Jan Hasenauer, University of Bonn

Mathematical models of cellular pathways are essential tools in systems biology and systems medicine. They contribute to an understanding of structure and dynamics of cellular processes far beyond their isolated parts, as well as the prevention, diagnosis and therapy of diseases. Yet, there are a variety of open questions.

The track on Integrative Pathway Modelling is part of the series of INCOME events. It will will gather experts on the topics:

  • Modelling of signalling, metabolic and gene regulatory pathways
  • Reuse, extension and integration of models and datasets
  • Parameter optimization, identifiability and uncertainty analysis
  • Mathematical analysis of model properties

Oral presentations will be delivered by invited speakers and selected from submitted abstracts. This includes short presentations on open problems and scientific questions. The discussion of open problems and possible solutions will be a core element.

The 2-day track on Integrative Pathway Modelling during the Bonn Conference on Mathematical Life Sciences is complemented by hackathon. The hackathon will provide participants with time and space to work on tool-based integration of models. A focus will be on computational pipelines, and it will include the AMICI developer meeting.

Invited speakers:
Marija Cvijovic - University of Gothenburg
Fabian Fröhlich - University Clinics Heidelberg
Mustafa Khammash - ETH Zurich
Ina Koch - University of Frankfurt
Clemens Kreutz - University of Freiburg
Ellen Kuhl - Stanford University

Mathematical Image Analysis

April 17-18

Scientific organizers: Alexander Effland (University of Bonn), Erich Kobler (University of Bonn)

Numerous mathematical imaging problems arise in life sciences, including detection, reconstruction, registration, segmentation, or tracking problems. These problems are typically hard to solve and require fast, robust, and accurate methods. Recently, data-driven methods have boosted various developments. However, there are still many open questions that are discussed in the track on mathematical imaging focusing on robustness and stability, structured modeling, and reconstruction problems. This track brings together experts investigating a variety of topics including:

  • Inverse problems and optimization
  • Mathematics of deep learning
  • Structured machine learning models and stability
  • Robustness and stability analysis of data-driven methods
  • Medical imaging and automated quality assessment

Invited speakers:
Martin Benning - Queen Mary University of London
Anna Breger - University of Cambridge
Martin Holler - University of Graz
Sebastian Neumayer - École polytechnique fédérale de Lausanne
Stefania Petra - University of Heidelberg

Computational Protein Modelling and Design

April 17

Scientific organizer: Alena Khmelinskaia (University of Bonn)

 The understanding of natural proteins, evolved over millions of years to perform the functions essential to life, enables harnessing the power of proteins to address the challenges of today. Mathematical modelling, structural prediction and de novo design of proteins, contribute with new insights into the folding of sophisticated protein structures, the rules guiding protein-protein interactions, interactions with other macromolecules and binding of metabolites, and the structural malleability of active sites.

Oral presentations will be delivered by invited speakers and selected from submitted abstracts. This includes short presentations on current scientific problems, open questions, and possible solutions.

Invited speakers:
Noelia Ferruz Capapey - Molecular Biology Institute of Barcelona
Reidun Twarock - University of York

Computational Immunology
April 18-19

Scientific organizers: Frederik Graw (University of Heidelberg), Eva Kiermaier (University of Bonn), Kevin Thurley (University of Bonn)

While research over the last decades has provided an enormous body of knowledge about immune-regulatory mechanisms, it is still difficult to assess the contribution of each individual process for disease progression or successful recovery solely with experimental methods. Efficient induction of the mammalian immune response depends on the orchestrated interaction and collaboration of heterogeneous cells. Cell-cell communication by diffusible ligands generates spatial signaling gradients; and diverse feedback mechanisms as well as complex cell migration dynamics provide additional layers of complexity, with all of these aspects being fully understood only in the light of evolutionary host-pathogen interactions.

The advance of mathematical methods as well as computational tools, incl. capacities for large-scale simulations and extensive machine-learning approaches, provide opportunities for a data-driven, integrated view on the complex processes of immune regulation. However, that field of research has only recently emerged and many open questions and challenges remain.

To this end, the track on Computational Immunology will gather experts on the following topics:

  • Immune cell proliferation and differentiation
  • Spatio-temporal dynamics of immune cell migration and cell-cell communication
  • Tissue dynamics
  • Evolutionary dynamics of host-pathogen interactions
  • Individual cell-based modelling and immunological data analysis

Invited speakers:
Carmen Molina-Paris – Los Alamos National Laboratory, U.S.A.
Michael Lässig – University of Cologne, Germany
Johannes Textor - Radboud University Nijmegen, The Netherlands

Chemoinformatics and Computational Drug Design

April 19

Scientific organizers: Jürgen Bajorath (University of Bonn) and Christa Müller (University of Bonn)

Chemoinformatics and computational drug design are overlapping yet distinct disciplines at the interface between computational science, medicinal chemistry, and further experimental drug discovery approaches. While drug design strongly focuses on the discovery of new bioactive compounds for pharmaceutical targets, chemoinformatics also encompasses chemical information science and the application of informatics methods to address chemical tasks outside drug discovery. In both disciplines, machine learning − as a part of artificial intelligence − plays an increasingly important role.

The session on Chemoinformatics and Computational Drug Design brings together experts investigating a variety of topics including:

  • Computational methods for medicinal chemistry
  • Machine learning models for molecular property prediction
  • Chemical reaction modelling
  • Computational structural biology

Oral presentations will be delivered by invited speakers and also selected from submitted abstracts. This includes short presentations on current scientific problems, open questions, and possible solutions.

Invited speakers:
Johannes Kirchmair - University of Vienna
Alexandre Varnek - University of Strasbourg
Rebecca Wade – University of Heidelberg

Single-Cell Analysis in Systems Biology and Systems Medicine

April 19-20

Scientific organizers: Anna Aschenbrenner (German Center for Neurodegenerative Diseases and University of Bonn) and Thomas Ulas (German Center for Neurodegenerative Diseases and University of Bonn)

By enabling the study of individual cells and the molecular changes that result in disease in unprecedented detail both in time and space, single-cell technologies are revolutionizing biomedical research. However, there are many obstacles to overcome and interdisciplinary collaborations between clinicians, data scientists, and biomedical researchers are crucial for the translation of basic discoveries into clinical practice for early diagnosis and personalized treatments.

Oral presentations will be delivered by invited speakers and selected from submitted abstracts. This includes short presentations on open problems and scientific questions. The discussion of open problems and possible solutions will be a core element.

Invited speakers:
Dvir Aran - Technion - Israel Institute of Technology
Nir Yosef - UC Berkeley
Lior Pachter - Caltech

Mathematical Biology

April 20

Scientific Organizers: Alexander Effland (University of Bonn), Juan José López Velázquez (University of Bonn)

The understanding of biological processes at different scales has greatly benefited from a rigorous mathematical modeling. The relatively diverse field of mathematical biology combines methods originating, for instance, from partial differential equations, functional analysis, or stochastic processes to model or predict these highly complex biological mechanisms. The session on Mathematical Biology covers several recent topics including

  • Coupling of cell processes
  • Amplification of chemical signals
  • Asymptotic reduction
  • Renewal equations
  • Models of cell growth.

Oral presentations will be delivered by invited and selected speakers, who will present scientific problems, open questions, and possible solutions.

Invited speaker:
Matthias Röger – TU Dortmund


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