Journal papers:

• IEEE/ACM TCBB :: 15 October 2020

  Evaluation of Existing Methods for High-Order Epistasis Detection

  Christian Ponte-Fernández Jorge González-Domínguez Antonio Carvajal-Rodríguez María J. Martín

  Finding epistatic interactions among loci when expressing a phenotype is a widely employed strategy to understand the genetic architecture of complex traits in GWAS. The abundance of methods dedicated to the same purpose, however, makes it increasingly difficult for scientists to decide which method is more suitable for their studies. This work compares the different epistasis detection methods published during the last decade in terms of runtime, detection power and type I error rate, with...

• BMC Bioinformatics :: 9 April 2020

  Toxo: a library for calculating penetrance tables of high-order epistasis models

  Christian Ponte-Fernández Jorge González-Domínguez Antonio Carvajal-Rodríguez María J. Martín

  Background
  Epistasis is defined as the interaction between different genes when expressing a specific phenotype. The most common way to characterize an epistatic relationship is using a penetrance table, which contains the probability of expressing the phenotype under study given a particular allele combination. Available simulators can only create penetrance tables for well-known epistasis models involving a small number of genes and under a large number of limitations.
  
  Results
  Toxo is a MATLAB library...

• IJHPCA :: 27 May 2019

  Fast search of third-order epistatic interactions on CPU and GPU clusters

  Christian Ponte-Fernández Jorge González-Domínguez María J. Martín

  Genome-Wide Association Studies (GWASs), analyses that try to find a link between a given phenotype (such as a disease) and genetic markers, have been growing in popularity in the recent years. Relations between phenotypes and genotypes are not easy to identify, as most of the phenotypes are a product of the interaction between multiple genes, a phenomenon known as epistasis. Many authors have resorted to different approaches and hardware architectures in order to mitigate the...

Conference papers:

• HPCS 2017 :: 17 July 2017

  Evaluation of OpenMP SIMD Directives on Xeon Phi Coprocessors

  Christian Ponte-Fernández Jorge González-Domínguez María J. Martín

  Nowadays, most of the available computer architectures include vector processing units. Therefore, exploiting this type of parallelism is fundamental to achieve the highest performance on modern systems. OpenMP is a parallel programming API based on a set of compiler directives. In its latest release (version 4) explicit vector programming through Single Instruction Multiple Data (SIMD) directives was added, among other features. This paper studies the ease of use and performance of these new SIMD directives,...