分子网络
Networks of genetic expression can be modelled by hypergraphs with the additional structure that real coefficients are given to each vertex-edge incidence. The spectra, i.e. the multiset of the eigenvalues, of such hypergraphs, are known to…
Networks are widely used in many fields for their powerful ability to provide vivid representations of relationships between variables. However, many of them may be corrupted by experimental noise or inappropriate network inference methods…
Cocaine addiction accounts for a large portion of substance use disorders and threatens millions of lives worldwide. There is an urgent need to come up with efficient anti-cocaine addiction drugs. Unfortunately, no medications have been…
Given that biochemical circuits can process information by using analog computation, a question is: What can biochemical circuits compute? This paper considers the problem of using biochemical circuits to distinguish persistent signals from…
A decomposition of a chemical reaction network (CRN) is produced by partitioning its set of reactions. The partition induces networks, called subnetworks, that are "smaller" than the given CRN which, at this point, can be called parent…
There are many mathematical models of biochemical cell signaling pathways that contain a large number of elements (species and reactions). This is sometimes a big issue for identifying critical model elements and describing the model…
We describe a mathematical model for the aggregation of starved first-stage C elegans larvae (L1s). We propose that starved L1s produce and respond chemotactically to two labile diffusible chemical signals, a short-range attractant and a…
Effective control of biological systems can often be achieved through the control of a surprisingly small number of distinct variables. We bring clarity to such results using the formalism of Boolean dynamical networks, analyzing the…
We explored the dynamical and structural effects of actin-related proteins 2/3 (Arp2/3) on actomyosin networks using mechanochemical simulations of active matter networks. At a nanoscale, the Arp2/3 complex alters the topology of actomyosin…
Living organisms must respond to environmental changes. Generally, accurate and rapid responses are provided by simple, unidirectional networks that connect inputs with outputs. Besides accuracy and speed, biological responses should also…
Native shortcut networks (SCN0) are sub-graphs of native protein residue networks (PRN0). In this paper, we propose the Network Dynamics (ND) model, which reconstructs a PRN0 by adding back its edges according to some recipe, while its…
The last decade has seen the advent and consolidation of ontology based tools for the identification and biological interpretation of classes of genes, such as the Gene Ontology. The information accumulated time-by-time and included in the…
In this technical report, we describe a new version of SimpleSBML which provides an easier to use interface to python-libSBML allowing users of Python to more easily construct, edit, and inspect SBML based models. The most commonly used…
Innovation in synthetic biology often still depends on large-scale experimental trial-and-error, domain expertise, and ingenuity. The application of rational design engineering methods promise to make this more efficient, faster, cheaper…
The investigation of topological properties of ovarian cancer network (OCN) and the roles of hubs involved in it by digging the network at various levels of organization are important to understand how OCN is organized to understand disease…
While atom tracking with isotope-labeled compounds is an essential and sophisticated wet-lab tool in order to, e.g., illuminate reaction mechanisms, there exists only a limited amount of formal methods to approach the problem. Specifically…
The identification of protein-ligand interaction plays a key role in biochemical research and drug discovery. Although deep learning has recently shown great promise in discovering new drugs, there remains a gap between deep learning-based…
The identification of essential genes/proteins is a critical step towards a better understanding of human biology and pathology. Computational approaches helped to mitigate experimental constraints by exploring machine learning (ML) methods…
The emerging field of Molecular Communication (MC) aims to characterize biological-based signaling environment through information that are encoded into molecules. Since the birth of this field, a number of different applications and…
Background: Gene regulatory networks coordinate the expression of genes across physiological states and ensure a synchronized expression of genes in cellular subsystems, critical for the coherent functioning of cells. Here we address the…