Related papers: How many different clonotypes do immune repertoire…
Whole exome sequencing was performed on HLA-matched stem cell donors and transplant recipients to measure sequence variation contributing to minor histocompatibility antigen differences between the two. A large number of nonsynonymous…
Accurate immunological models offer the possibility of performing highthroughput experiments in silico that can predict, or at least suggest, in vivo phenomena. In this chapter, we compare various models of immunological memory. We first…
Cancer arises from successive rounds of mutations which generate tumor cells with different genomic variation i.e. clones. For drug responsiveness and therapeutics, it is necessary to identify the clones in tumor sample accurately. Many…
We investigate 738 complete genomes of viruses to detect the presence of short inverted repeats. The number of inverted repeats found is compared with the prediction obtained for a Bernoullian and for a Markovian control model. We find as a…
Complete understanding of the mechanisms regulating the proliferation and differentiation that takes place during human immune CD8+ T cell responses is still lacking. Human clinical data is usually limited to blood cell counts, yet the…
Code clones are pairs of code snippets that implement similar functionality. Clone detection is a fundamental branch of automatic source code comprehension, having many applications in refactoring recommendation, plagiarism detection, and…
The article presents the theoretical foundations of the algorithm for calculating the number of different genomes in the medium under study and of two algorithms for determining the presence of a particular (known) genome in this medium.…
The composition of a polyclonal antibody response is hard to measure experimentally but contains vital information about the robustness of immunity. Here, we argue that the statistics of neutralization titers alone can be used to make…
Some cells have to take decision based on the quality of surroundings ligands, almost irrespective of their quantity, a problem we name "absolute discrimination". An example of absolute discrimination is recognition of not-self by immune T…
Due to their pivotal role in software engineering, considerable effort is spent on the quality assurance of software requirements specifications. As they are mainly described in natural language, relatively few means of automated quality…
Immunological self/not-self discrimination is conventionally seen as an extracellular event, involving interactions been receptors on T cells pre-educated to discriminate, and peptides bound to major histocompatibility complex proteins…
The ability of the adaptive immune system to discriminate between self and non-self mainly stems from the ontogenic clonal-deletion of lymphocytes expressing strong binding affinity with self-peptides. However, some self-directed…
Recent experimental evidence suggests that acute myeloid leukemias may originate from multiple clones of malignant cells. Nevertheless it is not known how the observed clones may differ with respect to cell properties such as proliferation…
We are interested in modeling theoretical immunology within a statistical mechanics flavor: focusing on the antigen-independent maturation process of B-cells, in this paper we try to revise the problem of self vs non-self discrimination by…
In this work we adopt a statistical mechanics approach to investigate basic, systemic features exhibited by adaptive immune systems. The lymphocyte network made by B-cells and T-cells is modeled by a bipartite spin-glass, where, following…
Human brain contains about 10 billion neurons, each of which has about 10~10,000 nerve endings from which neurotransmitters are released in response to incoming spikes, and the released neurotransmitters then bind to receptors located in…
A key challenge in molecular biology is to decipher the mapping of protein sequence to function. To perform this mapping requires the identification of sequence features most informative about function. Here, we quantify the amount of…
Some years ago a cellular automata model was proposed to describe the evolution of the immune repertoire of B cells and antibodies based on Jerne's immune network theory and shape-space formalism. Here we investigate if the networks…
Multicellular organisms comprise a diverse collection of stable tissues built from different cell types. It remains unclear how large numbers of interacting cells can precisely coordinate their gene expression during tissue…
We study some simple mathematical models designed to test the following hypothesis: can a pathogen escape the immune system only because of its high probability of mutation? We propose both spatial and non-spatial models. In all of our…