Related papers: Inferring evolutionary histories of pathway regula…

The regulation of a gene depends on the binding of transcription factors to specific sites located in the regulatory region of the gene. The generation of these binding sites and of cooperativity between them are essential building blocks…

Reconstructing transcriptional regulatory networks is an important task in functional genomics. Data obtained from experiments that perturb genes by knockouts or RNA interference contain useful information for addressing this reconstruction…

Phylogenetic networks represent evolutionary history of species and can record natural reticulate evolutionary processes such as horizontal gene transfer and gene recombination. This makes phylogenetic networks a more comprehensive…

Phylogenetics is a branch of computational biology that studies the evolutionary relationships among biological entities. Its long history and numerous applications notwithstanding, inference of phylogenetic trees from sequence data remains…

Populations of isogenic embryonic stem cells or clonal bacteria often exhibit extensive phenotypic heterogeneity which arises from stochastic intrinsic dynamics of cells. The internal state of the cell can be transmitted epigenetically in…

We propose a methodology for the identification of transcription factors involved in the deregulation of genes in tumoral cells. This strategy is based on the inference of a reference gene regulatory network that connects transcription…

Quantitatively predicting phenotype variables by the expression changes in a set of candidate genes is of great interest in molecular biology but it is also a challenging task for several reasons. First, the collected biological…

Evolution of genetic code is studied as the change in the choice of enzymes that are used to synthesize amino acids from the genetic information of nucleic acids. We propose the following theory: the differentiation of physiological states…

Survival analysis concerns the task of predicting the time until an event occurs. Often used in the medical field, survival analysis deals with incomplete (i.e., censored) data, for instance, from patients who did not experience the event…

The promise of discovering a functional blueprint of a cellular system from large-scale and high-throughput sequence and experimental data is predicated on the belief that the same top-down investigative approach that proved successful in…

Although the role of lateral gene transfer is well recognized in the evolution of bacteria, it is generally assumed that it has had less influence among eukaryotes. To explore this hypothesis we compare the dynamics of genome evolution in…

A long-standing goal of evolutionary biology is to decode how gene regulatory processes contribute to organismal diversity, both within and between species. This question has remained challenging to answer, due both to the difficulties of…

The inability to resolve deep node relationships of highly divergent/rapidly evolving protein families is a major factor that stymies evolutionary studies. In this manuscript, we propose a Multiple Sequence Alignment (MSA) independent…

An early burst of speciation followed by a subsequent slowdown in the rate of diversification is commonly inferred from molecular phylogenies. This pattern is consistent with some verbal theory of ecological opportunity and adaptive…

Causal discovery in multi-omic datasets is crucial for understanding the bigger picture of gene regulatory mechanisms, but remains challenging due to high dimensionality, differentiation of direct from indirect relationships, and hidden…

We describe the time evolution of gene expression levels by using a time translational matrix to predict future expression levels of genes based on their expression levels at some initial time. We deduce the time translational matrix for…

We develop a path-based approach to continuous-time random walks on networks with arbitrarily weighted edges. We describe an efficient numerical algorithm for calculating statistical properties of the stochastic path ensemble. After…

In this work we present a systematic mathematical approximation scheme that exposes the way that information, about the evolutionary forces of selection and random genetic drift, is encoded in gene-frequency trajectories. We determine…

We model the transcription factor based regulation network of yeast using a content-based network model that mimicks the recognition of binding motifs on the regulatory regions of the genes. We are thereby able to faithfully reproduce many…

In tumoral cells, gene regulation mechanisms are severely altered, and these modifications in the regulations may be characteristic of different subtypes of cancer. However, these alterations do not necessarily induce differential…