Crop genome‐wide association study: a harvest of biological relevance

HJ Liu, J Yan - The Plant Journal, 2019 - Wiley Online Library
With the advent of rapid genotyping and next‐generation sequencing technologies, genome‐
wide association study (GWAS) has become a routine strategy for decoding genotype …

Reaching the end-game for GWAS: machine learning approaches for the prioritization of complex disease loci

HL Nicholls, CR John, DS Watson, PB Munroe… - Frontiers in …, 2020 - frontiersin.org
Genome-wide association studies (GWAS) have revealed thousands of genetic loci that
underpin the complex biology of many human traits. However, the strength of GWAS–the …

Recent advances in artificial intelligence, mechanistic models, and speed breeding offer exciting opportunities for precise and accelerated genomics‐assisted …

JA Bhat, X Feng, ZA Mir, A Raina… - Physiologia …, 2023 - Wiley Online Library
Given the challenges of population growth and climate change, there is an urgent need to
expedite the development of high‐yielding stress‐tolerant crop cultivars. While traditional …

The influence of higher-order epistasis on biological fitness landscape topography

DM Weinreich, Y Lan, J Jaffe… - Journal of statistical …, 2018 - Springer
The effect of a mutation on the organism often depends on what other mutations are already
present in its genome. Geneticists refer to such mutational interactions as epistasis. Pairwise …

Revisiting genome-wide association studies from statistical modelling to machine learning

S Sun, B Dong, Q Zou - Briefings in Bioinformatics, 2021 - academic.oup.com
Over the last decade, genome-wide association studies (GWAS) have discovered thousands
of genetic variants underlying complex human diseases and agriculturally important traits …

Niche harmony search algorithm for detecting complex disease associated high-order SNP combinations

S Tuo, J Zhang, X Yuan, Z He, Y Liu, Z Liu - Scientific reports, 2017 - nature.com
Genome-wide association study is especially challenging in detecting high-order disease-
causing models due to model diversity, possible low or even no marginal effect of the model …

Functional coding haplotypes and machine-learning feature elimination identifies predictors of Methotrexate Response in Rheumatoid Arthritis patients

AJW Lim, LJ Lim, BNS Ooi, ET Koh, JWL Tan… - …, 2022 - thelancet.com
Background Major challenges in large scale genetic association studies include not only the
identification of causative single nucleotide polymorphisms (SNPs), but also accounting for …

Discovering SNP-disease relationships in genome-wide SNP data using an improved harmony search based on SNP locus and genetic inheritance patterns

F Esmaeili, Z Narimani, M Vasighi - Plos one, 2023 - journals.plos.org
Advances in high-throughput sequencing technologies have made it possible to access
millions of measurements from thousands of people. Single nucleotide polymorphisms …

Deep mixed model for marginal epistasis detection and population stratification correction in genome-wide association studies

H Wang, T Yue, J Yang, W Wu, EP Xing - BMC bioinformatics, 2019 - Springer
Abstract Background Genome-wide Association Studies (GWAS) have contributed to
unraveling associations between genetic variants in the human genome and complex traits …

An empirical fuzzy multifactor dimensionality reduction method for detecting gene-gene interactions

S Leem, T Park - BMC genomics, 2017 - Springer
Background Detection of gene-gene interaction (GGI) is a key challenge towards solving the
problem of missing heritability in genetics. The multifactor dimensionality reduction (MDR) …