112 citations
Counting papers with at most 25 authors, so collaboration author lists do not stand in for the people here.
- Leipzig UniversityDE15 papers
- University of ViennaAT6 papers
- Santa Fe InstituteUS5 papers
- Max Planck Institute for Mathematics in the SciencesDE4 papers
- Saarland UniversityDE3 papers
- University of Southern DenmarkDK3 papers
- University of the West of EnglandGB3 papers
- Center for Scalable Data Analytics and Artificial IntelligenceDE2 papers
- Heidelberg UniversityDE2 papers
- Max Planck Institute for MathematicsDE2 papers
- Memorial Sloan Kettering Cancer CenterUS2 papers
- National Center for Tumor DiseasesDE2 papers
18 papers
Unsupervised risk factor identification across cancer types and data modalities via explainable artificial intelligence
Maximilian Ferle, Jonas Ader, Thomas Wiemers +7
Risk stratification is a key tool in clinical decision-making, yet current approaches often fail to translate sophisticated survival analysis into actionable clinical criteria. We…
Privacy-Preserving Multi-Center Differential Protein Abundance Analysis with FedProt
Yuliya Burankova, Miriam Abele, Mohammad Bakhtiari +28
Quantitative mass spectrometry has revolutionized proteomics by enabling simultaneous quantification of thousands of proteins. Pooling patient-derived data from multiple institutio…
Predicting Progression Events in Multiple Myeloma from Routine Blood Work
Maximilian Ferle, Nora Grieb, Markus Kreuz +5
The ability to accurately predict disease progression is paramount for optimizing multiple myeloma patient care. This study introduces a hybrid neural network architecture, combini…
Measuring structural parameters of crosslinked and entangled semiflexible polymer networks with single-filament tracing
Tina Händler, Cary Tutmarc, Martin Glaser +3
Single-filament tracing has been a valuable tool to directly determine geometrical and mechanical properties of entangled polymer networks. However, systematically verifying how th…
Actin Networks Voltage Circuits
Stefano Siccardi, Andrew Adamatzky Jack Tuszyński, Florian Huber +1
Starting with an experimentally observed networks of actin bundles, we model their network structure in terms of edges and nodes. We then compute and discuss the main electrical pa…
Changing cell mechanics -- a precondition for malignant transformation of oral squamous carcinoma cells
Felix Meinhoevel, Roland Stange, Joerg Schnauss +3
Oral squamous cell carcinomas (OSCC) are the 6th most common cancer and the diagnosis is often belated for a curative treatment. The reliable and early differentiation between heal…
The Role of Stickiness in the Rheology of Semiflexible Polymers
Tom Golde, Martin Glaser, Cary Tutmarc +7
Semiflexible polymers form central structures in biological material. Modeling approaches usually neglect influences of polymer-specific molecular features aiming to describe semif…
Towards Cytoskeleton Computers. A proposal
Andrew Adamatzky, Jack Tuszynski, Joerg Pieper +6
We propose a road-map to experimental implementation of cytoskeleton-based computing devices. An overall concept is described in the following. Collision-based cytoskeleton compute…
Phylogenomics with Paralogs
Marc Hellmuth, Nicolas Wieseke, Marcus Lechner +3
Phylogenomics heavily relies on well-curated sequence data sets that consist, for each gene, exclusively of 1:1-orthologous. Paralogs are treated as a dangerous nuisance that has t…
Direct observation and rational design of nucleation behavior in addressable self-assembly
Martin Sajfutdinow, William M. Jacobs, Aleks Reinhardt +2
In order to optimize a self-assembly reaction, it is essential to understand the factors that govern its pathway. Here, we examine the influence of nucleation pathways in a model s…
A Survey on Hypergraph Products (Erratum)
Marc Hellmuth, Lydia Ostermeier, Peter F. Stadler
A surprising diversity of different products of hypergraphs have been discussed in the literature. Most of the hypergraph products can be viewed as generalizations of one of the fo…
An Intermediate Level of Abstraction for Computational Systems Chemistry
Jakob L. Andersen, Christoph Flamm, Daniel Merkle +1
Computational techniques are required for narrowing down the vast space of possibilities to plausible prebiotic scenarios, since precise information on the molecular composition, t…
Tuning Synthetic Semiflexible Networks by Bending Stiffness
Carsten Schuldt, Jörg Schnauß, Tina Händler +5
The mechanics of complex soft matter often cannot be understood in the classical physical frame of flexible polymers or rigid rods. The underlying constituents are semiflexible pol…
Task-related edge density (TED) - a new method for revealing large-scale network formation in fMRI data of the human brain
Gabriele Lohmann, Johannes Stelzer, Verena Zuber +4
The formation of transient networks in response to external stimuli or as a reflection of internal cognitive processes is a hallmark of human brain function. However, its identific…
A Simple Data-Adaptive Probabilistic Variant Calling Model
Steve Hoffmann, Peter F. Stadler, Korbinian Strimmer
Background: Several sources of noise obfuscate the identification of single nucleotide variation (SNV) in next generation sequencing data. For instance, errors may be introduced du…
Square Property, Equitable Partitions, and Product-like Graphs
Marc Hellmuth, Lydia Ostermeier, Peter F. Stadler
Equivalence relations on the edge set of a graph that satisfy restrictive conditions on chordless squares play a crucial role in the theory of Cartesian graph products and grap…
Maximizing Output and Recognizing Autocatalysis in Chemical Reaction Networks is NP-Complete
Jakob L. Andersen, Christoph Flamm, Daniel Merkle +1
Background: A classical problem in metabolic design is to maximize the production of desired compound in a given chemical reaction network by appropriately directing the mass flow…
Funnels in Energy Landscapes
Konstantin Klemm, Christoph Flamm, Peter F. Stadler
Local minima and the saddle points separating them in the energy landscape are known to dominate the dynamics of biopolymer folding. Here we introduce a notion of a "folding funnel…