Molecular Networks
The hyperbolic dependence of catalytic rate on substrate concentration is a classical result in enzyme kinetics, quantified by the celebrated Michaelis-Menten equation. The ubiquity of this relation in diverse chemical and biological…
We propose novel chemical reaction networks to translate levels of concentration into unique DNA strand species, which we call concentration translators. Our design of the concentration translators is based on combination of two chemical…
Drug combinations are frequently used for the treatment of cancer patients in order to increase efficacy, decrease adverse side effects, or overcome drug resistance. Given the enormous number of drug combinations, it is cost- and…
Introduction. Can the infection due to the human immunodeficiency virus type 1 induce a change in the differentiation status or process in T cells?. Methods. We will consider two stochastic Markov chain models, one which will describe the…
For three typical sets of small reaction networks (networks with two reactions, one irreversible and one reversible reaction, or two reversible-reaction pairs), we completely answer the challenging question: what is the smallest subset of…
Natural selection has shaped the evolution of cells and multi-cellular organisms such that social cooperation can often be preferred over an individualistic approach to metabolic regulation. This paper extends a framework for dynamic…
Cell type-specific gene expression patterns are represented as memory states of a Hopfield neural network model. It is shown that order parameters of this model can be interpreted as concentrations of master transcription regulators that…
We present the second generation of a rule-based language called Biochemical Space Language (BCSL) that combines the advantages of different approaches and thus makes an effort to overcome several problems with existing solutions. The key…
Lck (lymphocyte-specific protein tyrosine kinase) is an enzyme which plays a number of important roles in the function of immune cells. It belongs to the Src family of kinases which are known to undergo autophosphorylation. It turns out…
Chemical reactions occur in energy, environmental, biological, and many other natural systems, and the inference of the reaction networks is essential to understand and design the chemical processes in engineering and life sciences. Yet,…
Graph theoretical analyses of nervous systems usually omit the aspect of connection polarity, due to data insufficiency. The chemical synapse network of Caenorhabditis elegans is a well-reconstructed directed network, but the signs of its…
Cells regulate themselves via dizzyingly complex biochemical processes called signaling pathways. These are usually depicted as a network, where nodes represent proteins and edges indicate their influence on each other. In order to…
Profiling of whole transcriptomes has become a cornerstone of molecular biology and an invaluable tool for the characterization of clinical phenotypes and the identification of disease subtypes. Analyses of these data are becoming ever more…
Gene expression (GE) is an inherently random or stochastic or noisy process. The randomness in different steps of GE, e.g., transcription, translation, degradation, etc., leading to cell-to-cell variations in mRNA and protein levels. This…
Quantitatively predictive models of biomolecular circuits are important tools for the design of synthetic biology and molecular communication circuits. The information content of typical time-lapse single-cell data for the inference of…
Corynebacterium glutamicum is a Gram-positive bacterium found in soil where the condition changes demand plasticity of the regulatory machinery. The study of such machinery at the global scale has been challenged by the lack of data…
Some organism-specific databases about regulation in bacteria have become larger, accelerated by high-throughput methodologies, while others are no longer updated or accessible. Each database homogenize its datasets, giving rise to…
A minimal model for gene expression, consisting of a switchable promoter together with the resulting messenger RNA, is equivalent to a Poisson channel with a binary Markovian input process. Determining its capacity is an optimization…
Protein synthesis is one of the most fundamental biological processes, which consumes a significant amount of cellular resources. Despite existence of multiple mathematical models of translation, varying in the level of mechanistical…
Biochemical reactions involving three or more reactants, called higher-molecular reactions, play an important role in theoretical systems and synthetic biology. In particular, such reactions underpin a variety of important bio-dynamical…