Related papers: How T-cells use large deviations to recognize fore…
The diversity of T-cell receptors recognizing foreign pathogens is generated through a highly stochastic recombination process, making the independent production of the same sequence rare. Yet unrelated individuals do share receptors, which…
Cancer is a complex disease characterized by uncontrolled cell growth and proliferation. T cell receptors (TCRs) are essential proteins for the adaptive immune system, and their specific recognition of antigens plays a crucial role in the…
Cell differentiation in multicellular organisms is a complex process whose mechanism can be understood by a reductionist approach, in which the individual processes that control the generation of different cell types are identified.…
Immunology is the emerging research area which deals with the study of the immune system in any living organism. It is modelled through various computational and mathematical models to deal with the problem facing while to boost the immune…
The human adaptive immune response is known to weaken in advanced age, resulting in increased severity of pathogen-born illness, poor vaccine efficacy, and a higher prevalence of cancer in the elderly. Age-related erosion of the T-cell…
We present a stochastic model which describes fronts of cells invading a wound. In the model cells can move, proliferate, and experience cell-cell adhesion. We find several qualitatively different regimes of front motion and analyze the…
A model of bit-strings, that uses the technique of multi-spin coding, was previously used to study the time evolution of B-cell clone repertoire, in a paper by Lagreca, Almeida and Santos. In this work we extend that simplified model to…
Four reasons why you might wish to read this paper: 1. We have devised a new statistical T test to determine differentially expressed genes (DEG) in the context of microarray experiments. This statistical test adds a new member to the…
The immune response to a pathogen has two basic features. The first is the expansion of a few pathogen-specific cells to form a population large enough to control the pathogen. The second is the process of differentiation of cells from an…
Stochastic reaction network models are widely utilized in biology and chemistry to describe the probabilistic dynamics of biochemical systems in general, and gene interaction networks in particular. Most often, statistical analysis and…
We study a dynamical system model of an idiotypic immune network with a small number of degrees of freedom, mainly focusing on the effect of a threshold above which antibodies can recognise antibodies. The response of the system to…
Hypervariable T-cell receptors (TCR) play a key role in adaptive immunity, recognising a vast diversity of pathogen-derived antigens. High throughput sequencing of TCR repertoires (RepSeq) produces huge datasets of T-cell receptor sequences…
Diseases involve complex processes and modifications to the cellular machinery. The gene expression profile of the affected cells contains characteristic patterns linked to a disease. Hence, biological knowledge pertaining to a disease can…
In the immune system, T cells can quickly discriminate between foreign and self ligands with high accuracy. There is evidence that T-cells achieve this remarkable performance utilizing a network architecture based on a generalization of…
I revisit two theories of cell differentiation in multicellular organisms published a half-century ago, Stuart Kauffman's global gene regulatory dynamics (GGRD) model and Roy Britten's and Eric Davidson's modular gene regulatory network…
The adaptive immune system responds to foreign invaders by activating T cells. However, this response is perilous if T cells are activated by the wrong signal or if they remain activated unduly long after the threat has been eliminated. It…
We consider the general problem of sensitive and specific discrimination between biochemical species. An important instance is immune discrimination between self and not-self, where it is also observed experimentally that ligands just below…
From the response to external stimuli to cell division and death, the dynamics of living cells is based on the expression of specific genes at specific times. The decision when to express a gene is implemented by the binding and unbinding…
It is widely accepted that the immune system undergoes age-related changes correlating with increased disease in the elderly. T cell subsets have been implicated. The aim of this work is firstly to implement and validate a simulation of T…
Time-irreversible stochastic processes are frequently used in natural sciences to explain non-equilibrium phenomena and to design efficient stochastic algorithms. Our main goal in this thesis is to analyse their dynamics by means of large…