RAiSD: Selective Sweep Detection based on Multiple Signatures


SweeD: Selective Sweep Detection based on SFS


OmegaPlus: Selective Sweep Detection based on LD


Demography Inference (ABC)


SPS: Forward-Backward Spatial Simulator for Genetic Data


EVONET: Evolution of Gene Regulatory Networks

Evonet simulates the evolution of GRNs by means of genetic drift and selection. Based on the work of Dr. Andreas Wagner on boolean GRNs,  Evonet expands those ideas by implementing two regulatory regions on each network gene. Evonet is written in C to ensure maximum compatibility and permit faster execution times. Github + Readme:

Endogenous Virus Evolution

During a retrovirus infection, a DNA copy of the viral RNA genome is permanently integrated into the nuclear DNA of the host cell as a provirus. Endogenous retroviruses (ERVs) have contributed to more than 8% of the human genome.
This project’s goal is to locate endogenous retroviruses DNA copies into host’s genome and their lineage and then to consider whether is a mutation in genes close to and what the consequences are.

Mitochondrial-Nuclear genes Co-Evolution


HiC Data analysis — Evolution of DNA 3D Structure

In this project, we compare the binding sites of TFs from the ENCODE Consortium against random points and we perform hypothesis testing and statistical tests for the location of TFs and Histone Modifiers relative to the boundaries of LADs and TADs. Furthermore, we examine the distribution of Transcription Start Sites (TSS) from the GENCODE project within or outside TADs’ and LADs’ boundaries, and we measure the distance of the former from the latter, as well as from the center of each 3D DNA conformation.  Simultaneously, we address the type of transcript that arises from each TSS, with our focus being placed on protein coding genes. In addition, we identify the recent evolutionary forces that shape the patterns of polymorphisms in relation to LAD and TAD boundaries within Human and Mice populations. Thus, we provide insights into whether recent, within populations evolution acts on the 3D structures of DNA within the nucleus. Finally, using Dn/Ds measurements we examine whether older selective forces have been applied on genes located within or outside  TADs and LADs.

Population Metagenomics


Evolutionary models of amino acids substitutions based on their neighborhood tertiary structure

We have used the Protein Interaction Statistics (PrInS) algorithm to statistically describe interactions between amino acids using protein structures. PrInS produces a scoring matrix to describe the frequency of amino acid interactions in the protein structures. Then, this matrix was converted to several different types of matrices in order to be compared with the model substitution matrices, such BLOSUM62 and PAM120, in the prediction of protein evolution.

Analysis of RNA-Seq and Chip-Seq Data