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The modeling of the spreading of communicable diseases has experienced significant advances in the last two decades or so. This has been possible due to the proliferation of data and the development of new methods to gather, mine and…
The complexity of the cells can be described and understood by a number of networks such as protein-protein interaction, cytoskeletal, organelle, signalling, gene transcription and metabolic networks. All these networks are highly dynamic…
Network analysis provides a powerful framework for the interpretation of genome-wide data. While static network approaches have proved fruitful, there is increasing interest in the insights gained from the analysis of cellular networks…
A new method for determining whether or not a mitrochondrial DNA (mtDNA) sequence belongs to a vertebrate is described and tested. This method only needs the mtDNA sequence of the organism in question, and unlike alignment based methods, it…
The unwelcome evolution of malignancy during cancer progression emerges through a selection process in a complex heterogeneous population structure. In the present work, we investigate evolutionary dynamics in a phenotypically heterogeneous…
Due to recent breakthroughs in state-of-the-art DNA sequencing technology, genomics data sets have become ubiquitous. The emergence of large-scale data sets provides great opportunities for better understanding of genomics, especially gene…
Metastasis is a leading cause of cancer-related mortality and remains challenging to detect during early stages. Accurate identification of cancers likely to metastasize can improve treatment strategies and patient outcomes. This study…
Genetic sequences are known to possess non-trivial composition together with symmetries in the frequencies of their components. Recently, it has been shown that symmetry and structure are hierarchically intertwined in DNA, suggesting a…
Based on a non-equilibrium mechanism for spatial pattern formation we study how position information can be controlled by locally coupled discrete dynamical networks, similar to gene regulation networks of cells in a developing…
Several networks occurring in real life have modular structures that are arranged in an hierarchical fashion. In this paper, we have proposed a model for such networks, using a stochastic generation method. Using this model we show that,…
An important goal of medical research is to develop methods to recover the loss of cellular function due to mutations and other defects. Many approaches based on gene therapy aim to repair the defective gene or to insert genes with…
Mutations in proteins can have deleterious effects on a protein's stability and function, which ultimately causes particular diseases. Genetically inherited muscular dystrophies (MDs) include several genetic diseases, which cause increasing…
The proper functioning of mitochondria requires that both the mitochondrial and the nuclear genome are functional. To investigate the importance of the mitochondrial genome, which encodes only 13 subunits of the respiratory complexes, the…
Pluripotent embryonic stem cells are of paramount importance for biomedical research thanks to their innate ability for self-renewal and differentiation into all major cell lines. The fateful decision to exit or remain in the pluripotent…
We investigate the impact of network heterogeneity on synergistic contagion dynamics. By extending a synergistic contagion model to diverse heterogeneous network topologies, we uncover the emergence of novel dynamical regimes characterized…
Movement behavior of biological entities plays a crucial role in their destiny through regulating their intraspecific and interspecific interactions as well as their interaction with surrounding environment. In spite of various models for…
There is a growing body of work considering the use of representations based upon genetic regulatory networks. This paper uses a recently presented abstract, tunable Boolean regulatory network model to explore aspects of mobile DNA, such as…
The PHASE software package allows phylogenetic tree construction with a number of evolutionary models designed specifically for use with RNA sequences that have conserved secondary structure. Evolution in the paired regions of RNAs occurs…
Rapidly mutating pathogens may be able to persist in the population and reach an endemic equilibrium by escaping hosts' acquired immunity. For such diseases, multiple biological, environmental and population-level mechanisms determine the…
Cancer has relational information residing at varying scales, modalities, and resolutions of the acquired data, such as radiology, pathology, genomics, proteomics, and clinical records. Integrating diverse data types can improve the…