Related papers: Statistical Mechanics of Horizontal Gene Transfer …
We study the statistics of ecosystems with a variable number of co-evolving species. The species interact in two ways: by prey-predator relationships and by direct competition with similar kinds. The interaction coefficients change slowly…
In higher organisms, all cells share the same genome, but every cell expresses only a limited and specific set of genes that defines the cell type. During cell division, not only the genome, but also the cell type is inherited by the…
Inferring the directionality of interactions between cellular processes is a major challenge in systems biology. Time-lagged correlations allow to discriminate between alternative models, but they still rely on assumed underlying…
Selection, mutation and random drift affect the dynamics of allele frequencies and consequently of quantitative traits. While the macroscopic dynamics of quantitative traits can be measured, the underlying allele frequencies are typically…
In bacterial populations, cells are able to cooperate in order to yield complex collective functionalities. Interest in population-level cellular behaviour is increasing, due to both our expanding knowledge of the underlying biological…
In this article, we investigate the evolution of sexual diploid populations which are hosts for active TE families. Our purpose is to explore the relationship between the environmental change, that influences such population and activity of…
Cooperation is a widespread natural phenomenon yet current evolutionary thinking is dominated by the paradigm of selfish competition. Recent advanced in many fronts of Biology and Non-linear Physics are helping to bring cooperation to its…
As a living information and communications system, the genome encodes patterns in single nucleotide polymorphisms (SNPs) reflecting human adaption that optimizes population survival in differing environments. This paper mathematically…
Transposable elements are DNA sequences that can move around to different positions in the genome. During this process, they can cause mutations, and lead to an increase in genome size. Despite representing a large genomic fraction,…
The human microbiome is the ensemble of genes in the microbes that live inside and on the surface of humans. Because microbial sequencing information is now much easier to come by than phenotypic information, there has been an explosion of…
Horizontal gene Transfer (HT) denotes the transmission of genetic material between two living organisms, while the vertical transmission refers to a DNA transfer from parents to their offspring. Consistent experimental evidence report that…
Historical sciences like evolutionary biology reconstruct past events by using the traces that the past has bequeathed to the present. The Markov Chain Convergence Theorem and the Data Processing Inequality describe how the mutual…
Most of the DNA that composes a complex organism is non-coding and defined as junk. Even the coding part is composed of genes that affect the phenotype differently. Therefore, a random mutation has an effect on the specimen fitness that…
How diversity is maintained in natural ecosystems is a long-standing question in Theoretical Ecology. By studying a system that combines ecological dynamics, heterogeneous interactions and spatial structure, we uncover a new mechanism for…
These are notes for a set of 7 two-hour lectures given at the 2010 Summer School on Quantitative Evolutionary and Comparative Genomics at OIST, Okinawa, Japan. The emphasis is on understanding how biological systems process information. We…
Most genes are part of larger families of evolutionary related genes. The history of gene families typically involves duplications and losses of genes as well as horizontal transfers into other organisms. The reconstruction of detailed gene…
With a view to connecting random mutation on the molecular level to punctuated equilibrium behavior on the phenotype level, we propose a new model for biological evolution, which incorporates random mutation and natural selection. In this…
Motivated by the results of recent laboratory experiments (Yoshida et al. Nature, 424, 303-306 (2003)) as well as many earlier field observations that evolutionary changes can take place in ecosystems over relatively short ecological time…
This study builds upon a model proposed by Joanny and collaborators that examines the dynamics of interfaces between two distinct cell populations, particularly during tumor growth in healthy tissues. This framework leads to the…
One of the main properties of biological systems is modularity, which manifests itself at all levels of their organization, starting with the level of molecular genetics, ending with the level of whole organisms and their communities. In a…