Detecting gene–gene interactions that underlie human diseases

HJ Cordell - Nature Reviews Genetics, 2009 - nature.com
Following the identification of several disease-associated polymorphisms by genome-wide
association (GWA) analysis, interest is now focusing on the detection of effects that, owing to …

Prioritizing GWAS results: a review of statistical methods and recommendations for their application

RM Cantor, K Lange, JS Sinsheimer - The American Journal of Human …, 2010 - cell.com
Genome-wide association studies (GWAS) have rapidly become a standard method for
disease gene discovery. A substantial number of recent GWAS indicate that for most …

SHEsisPlus, a toolset for genetic studies on polyploid species

J Shen, Z Li, J Chen, Z Song, Z Zhou, Y Shi - Scientific reports, 2016 - nature.com
Currently, algorithms and softwares for genetic analysis of diploid organisms with bi-allelic
markers are well-established, while those for polyploids are limited. Here, we present …

Topological features of rugged fitness landscapes in sequence space

DA Kondrashov, FA Kondrashov - Trends in Genetics, 2015 - cell.com
The factors that determine the tempo and mode of protein evolution continue to be a central
question in molecular evolution. Traditionally, studies of protein evolution focused on the …

Information theory in computational biology: where we stand today

P Chanda, E Costa, J Hu, S Sukumar, J Van Hemert… - Entropy, 2020 - mdpi.com
“A Mathematical Theory of Communication” was published in 1948 by Claude Shannon to
address the problems in the field of data compression and communication over (noisy) …

Entropy‐based information gain approaches to detect and to characterize gene‐gene and gene‐environment interactions/correlations of complex diseases

R Fan, M Zhong, S Wang, Y Zhang… - Genetic …, 2011 - Wiley Online Library
For complex diseases, the relationship between genotypes, environment factors, and
phenotype is usually complex and nonlinear. Our understanding of the genetic architecture …

Gene-centric gene–gene interaction: A model-based kernel machine method

S Li, Y Cui - 2012 - projecteuclid.org
Much of the natural variation for a complex trait can be explained by variation in DNA
sequence levels. As part of sequence variation, gene–gene interaction has been …

A gene-based method for detecting gene–gene co-association in a case–control association study

Q Peng, J Zhao, F Xue - European Journal of Human Genetics, 2010 - nature.com
Association study (especially the genome-wide association study) now has a key function in
identification and characterization of disease-predisposing genetic variant (s), which …

A gene-based information gain method for detecting gene–gene interactions in case–control studies

J Li, D Huang, M Guo, X Liu, C Wang, Z Teng… - European Journal of …, 2015 - nature.com
Currently, most methods for detecting gene–gene interactions (GGIs) in genome-wide
association studies are divided into SNP-based methods and gene-based methods …

Bridging the gap between statistical and biological epistasis in Alzheimer's disease

MTW Ebbert, PG Ridge… - BioMed research …, 2015 - Wiley Online Library
Alzheimer's disease affects millions of people worldwide and incidence is expected to rise
as the population ages, but no effective therapies exist despite decades of research and …