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

C Ponte-Fernández… - … Journal of High …, 2020 - journals.sagepub.com
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 …

Refining the genetic risk of breast cancer with rare haplotypes and pattern mining

W Letsou, F Wang, W Moon, C Im… - Life science …, 2023 - life-science-alliance.org
Hundreds of common variants have been found to confer small but significant differences in
breast cancer risk, supporting the widely accepted polygenic model of inherited …

CASMAP: detection of statistically significant combinations of SNPs in association map**

F Llinares-López, L Papaxanthos, D Roqueiro… - …, 2019 - academic.oup.com
Combinatorial association map** aims to assess the statistical association of higher-order
interactions of genetic markers with a phenotype of interest. This article presents …

Machine learning to reveal hidden risk combinations for the trajectory of posttraumatic stress disorder symptoms

Y Takahashi, K Yoshizoe, M Ueki, G Tamiya… - Scientific reports, 2020 - nature.com
The nature of the recovery process of posttraumatic stress disorder (PTSD) symptoms is
multifactorial. The Massive Parallel Limitless-Arity Multiple-testing Procedure (MP-LAMP) …

A fast and scalable workflow for SNPs detection in genome sequences using hadoop map-reduce

M Tahir, M Sardaraz - Genes, 2020 - mdpi.com
Next generation sequencing (NGS) technologies produce a huge amount of biological data,
which poses various issues such as requirements of high processing time and large …

Potential Misrepresentation of Inherited Breast Cancer Risk by Common Germline Alleles

W Letsou, F Wang, W Moon, C Im, Y Sapkota… - medRxiv, 2022 - medrxiv.org
Hundreds of common variants have been found to confer small but significant differences in
breast cancer risk, supporting the polygenic additive model of inherited risk. This widely …

[PDF][PDF] Significant Pattern Mining for Biomarker Discovery

F Llinares-López - 2018 - research-collection.ethz.ch
Biomarker discovery, the search for measurable biological indicators of a phenotypic trait of
interest, is a fundamental problem in healthcare and computational biology. Biomarkers help …

[PDF][PDF] Machine learning on molecular networks to decipher the genetics underlying complex traits

A Gum**er - 2020 - research-collection.ethz.ch
The past decades have been coined by technological advancements at remarkable rates,
leading to the generation and collection of unprecedented amounts of data. This is …

Summarizing significant subgraphs by probabilistic logic programming

E Bellodi, K Satoh, M Sugiyama - Intelligent Data Analysis, 2019 - content.iospress.com
Although recent advances of significant subgraph mining enable us to find subgraphs that
are statistically significantly associated with the class variable from graph databases, it is …

MotiMul: A significant discriminative sequence motif discovery algorithm with multiple testing correction

K Mori, H Ozaki, T Fukunaga - 2020 IEEE International …, 2020 - ieeexplore.ieee.org
Sequence motifs play essential roles in intermolecular interactions such as DNA-protein
interactions. The discovery of novel sequence motifs is therefore crucial for revealing gene …