easyGWAS: a cloud-based platform for comparing the results of genome-wide association studies

DG Grimm, D Roqueiro, PA Salomé… - The Plant …, 2017 - academic.oup.com
The ever-growing availability of high-quality genotypes for a multitude of species has
enabled researchers to explore the underlying genetic architecture of complex phenotypes …

AraPheno and the AraGWAS Catalog 2020: a major database update including RNA-Seq and knockout mutation data for Arabidopsis thaliana

M Togninalli, Ü Seren, JA Freudenthal… - Nucleic acids …, 2020 - academic.oup.com
Genome-wide association studies (GWAS) are integral for studying genotype-phenotype
relationships and gaining a deeper understanding of the genetic architecture underlying trait …

Genetic architecture of nonadditive inheritance in Arabidopsis thaliana hybrids

DK Seymour, E Chae, DG Grimm… - Proceedings of the …, 2016 - National Acad Sciences
The ubiquity of nonparental hybrid phenotypes, such as hybrid vigor and hybrid inferiority,
has interested biologists for over a century and is of considerable agricultural importance …

Localized lasso for high-dimensional regression

M Yamada, T Koh, T Iwata… - Artificial Intelligence …, 2017 - proceedings.mlr.press
We introduce the localized Lasso, which learns models that both are interpretable and have
a high predictive power in problems with high dimensionality d and small sample size n …

BRANE Cut: biologically-related a priori network enhancement with graph cuts for gene regulatory network inference

A Pirayre, C Couprie, F Bidard, L Duval, JC Pesquet - BMC bioinformatics, 2015 - Springer
Background Inferring gene networks from high-throughput data constitutes an important step
in the discovery of relevant regulatory relationships in organism cells. Despite the large …

Predicting Gene Regulatory Interactions Using Natural Genetic Variation

M John, D Grimm, A Korte - Plant Gene Regulatory Networks: Methods and …, 2023 - Springer
Genome-wide association studies (GWAS) are a powerful tool to elucidate the genotype–
phenotype map. Although GWAS are usually used to assess simple univariate associations …

Spadis: An algorithm for selecting predictive and diverse snps in gwas

S Yilmaz, O Tastan, AE Cicek - IEEE/ACM transactions on …, 2019 - ieeexplore.ieee.org
Phenotypic heritability of complex traits and diseases is seldom explained by individual
genetic variants identified in genome-wide association studies (GWAS). Many methods have …

Transfer learning in information criteria-based feature selection

S Chen, NV Sahinidis, C Gao - Journal of Machine Learning Research, 2022 - jmlr.org
This paper investigates the effectiveness of transfer learning based on information criteria.
We propose a procedure that combines transfer learning with Mallows' Cp (TLCp) and prove …

Network-Guided Biomarker Discovery

CA Azencott - Machine Learning for Health Informatics: State-of-the …, 2016 - Springer
Identifying measurable genetic indicators (or biomarkers) of a specific condition of a
biological system is a key element of precision medicine. Indeed it allows to tailor diagnostic …

[PDF][PDF] Exploring the Genotype-Phenotype Relationship Using Big Data and Machine Learning

M Togninalli - 2020 - research-collection.ethz.ch
Biology is orchestrated by a myriad of beautifully complex phenomena. While scientists have
only been able to uncover a tiny part of all existing biological mechanisms, they have done …