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Gene regulatory networks can be successfully modeled as Boolean networks. A much discussed hypothesis says that such model networks reproduce empirical findings the best if they are tuned to operate at criticality, i.e. at the borderline…
Complex systems are successfully reduced to interacting elements via the network concept. Transport plays a key role in the survival of networks. For example the specialized signaling cascades of cellular networks filter noise and…
The olfactory system employs responses of an ensemble of odorant receptors (ORs) to sense molecules and to generate olfactory percepts. Here we hypothesized that ORs can be viewed as 3D spatial filters that extract molecular features…
Cellular decision-making based on information received from the external environment is frequently initiated by transmembrane receptors. These receptors are known to propagate such information by triggering a series of irreversible,…
Prior work has shown that text-conditioned diffusion models can learn to identify and manipulate primitive concepts underlying a compositional data-generating process, enabling generalization to entirely novel, out-of-distribution…
Gene Regulatory Network (GRN) inference is essential for understanding complex cellular mechanisms, rendered tractable through single-cell transcriptomic data. With the emergence of single-cell Foundation Models (scFMs), enhanced…
High-throughput data acquisition in synthetic biology leads to an abundance of data that need to be processed and aggregated into useful biological models. Building dynamical models based on this wealth of data is of paramount importance to…
Multicellular organisms contain a wide variety of highly specialized cell types. The consistency and robustness of developmental trajectories suggest that complex gene regulatory networks effectively act as low-dimensional cell fate…
We investigate the evolution of Boolean networks subject to a selective pressure which favors robustness against noise, as a model of evolved genetic regulatory systems. By mapping the evolutionary process into a statistical ensemble and…
Revealing how a biological network is organized to realize its function is one of the main topics in systems biology. The functional backbone network, defined as the primary structure of the biological network, is of great importance in…
This thesis develops the theory of whispering gallery modes, exploring under what conditions a micro or nanoscale device can sustain these resonances, and for which physical criteria the resonance conditions deteriorate. The study is then…
Gene regulatory networks (GRNs) orchestrate cellular decision making and survival strategies. Inferring the structure of these networks from high-dimensional transcriptomics data is a central challenge in systems biology. Traditional…
Studies of insect olfactory processing indicate that odors are represented by rich spatio-temporal patterns of neural activity. These patterns are very difficult to predict a priori, yet they are stimulus specific and reliable upon repeated…
A Boolean network model of the cell-cycle regulatory network of fission yeast (Schizosaccharomyces Pombe) is constructed solely on the basis of the known biochemical interaction topology. Simulating the model in the computer, faithfully…
The large-scale properties of chemical reaction systems, such as the metabolism, can be studied with graph-based methods. To do this, one needs to reduce the information -- lists of chemical reactions -- available in databases. Even for the…
Olfactory receptor usage is highly heterogeneous, with some receptor types being orders of magnitude more abundant than others. We propose an explanation for this striking fact: the receptor distribution is tuned to maximally represent…
Establishing sharp and correctly positioned boundaries in spatial gene expression patterns is a central task, both in developmental and synthetic biology. We consider situations where a global morphogen gradient provides positional…
Sorting is fundamental and ubiquitous in modern computing systems. Hardware sorting systems are built based on comparison operations with Von Neumann architecture, but their performance are limited by the bandwidth between memory and…
We present a comparative analysis of large-scale topological and evolutionary properties of transcription networks in three species, the two distant bacteria E. coli and B. subtilis, and the yeast S. cerevisiae. The study focuses on the…
The phenomenon of oral tolerance refers to a local and systemic state of tolerance, induced in the gut associated lymphoid tissues, after its exposure to innocuous antigens, such as food proteins. While recent findings shed light in the…