Related papers: Affinity maturation for an optimal balance between…
System dynamics and agent based simulation models can both be used to model and understand interactions of entities within a population. Our modeling work presented here is concerned with understanding the suitability of the different types…
Many biological networks have to filter out useful information from a vast excess of spurious interactions. We use computational evolution to predict design features of networks processing ligand categorization. The important problem of…
Given a network with an ongoing epidemic, the network immunization problem seeks to identify a fixed number of nodes to immunize in order to maximize the number of infections prevented. A fundamental computational challenge in network…
Liver transplantation continues to be the gold standard for treating patients with end-stage liver diseases. However, despite the huge success of liver transplantation in improving patient outcomes, long term graft survival continues to be…
A fundamental question in biology is how cell populations evolve into different subtypes based on homogeneous processes at the single cell level. Here we show that population bimodality can emerge even when biological processes are…
Degeneration and adaptation are two competing sides of the same coin called resilience in the progressive processes of brain aging or diseases. Degeneration accumulates during brain aging and other cerebral activities, causing structural…
Many biological populations exhibit diversity in their strategy for survival and reproduction in a given environment, and microbes are an example. We explore the fate of different strategies under sustained environmental change by…
The intratumor heterogeneity has been recognized to characterize cancer cells impairing the efficacy of cancer treatments. We here propose an extension of constraint-based modeling approach in order to simulate metabolism of cell…
Why, contrary to theoretical predictions, do marine microbe communities harbor tremendous phenotypic heterogeneity? How can so many marine microbe species competing in the same niche coexist? We discovered a unifying explanation for both…
Based on a recent model of evolving viruses competing with an adapting immune system [1], we study the conditions under which a viral quasispecies can maximize its growth rate. The range of mutation rates that allows viruses to thrive is…
Migration of immune cells within the human body allows them to fulfill their main function of detecting pathogens. Adopting an optimal navigation and search strategy by these cells is of crucial importance to achieve an efficient immune…
Affinity propagation is an exemplar-based clustering algorithm that finds a set of data-points that best exemplify the data, and associates each datapoint with one exemplar. We extend affinity propagation in a principled way to solve the…
When confronted with an undesired cell population, such as bacterial infections or tumors, we seek the most effective treatment, designed to eliminate the population as rapidly as possible. A common practice is to monitor the cells…
We consider a spatial stochastic model for a pathogen population growing inside a host that attempts to eliminate the pathogens through its immune system. The pathogen population is divided into different types. A pathogen can either…
Existing approaches to modelling antibody concentration data are mostly based on finite mixture models that rely on the assumption that individuals can be divided into two distinct groups: seronegative and seropositive. Here, we challenge…
This contribution is devoted to a new model of HIV multiplication motivated by the patent of one of the authors. We take into account the antigenic diversity through what we define "antigenicity", whether of the virus or of the adapted…
Memories are stored, retained, and recollected through complex, coupled processes operating on multiple timescales. To understand the computational principles behind these intricate networks of interactions we construct a broad class of…
We propose a new method to immunize populations or computer networks against epidemics which is more efficient than any method considered before. The novelty of our method resides in the way of determining the immunization targets. First we…
The process of identifying and characterizing B-cell epitopes, which are the portions of antigens recognized by antibodies, is important for our understanding of the immune system, and for many applications including vaccine development,…
Resource are often not uniformly distributed within a population. Spatial variations of concentration of a resource, change the fitness of competing strategies locally. The notion of fitness varying with respect to both genotype and…