The genetics of gaits in Icelandic horses goes beyond DMRT3, with RELN and STAU2 identified as two new candidate genes
status: published
Detecting gene-gene interactions from GWAS using diffusion kernel principal components
Genes and gene products do not function in isolation but as components of complex networks of macromolecules through physical or biochemical interactions. Dependencies of gene mutations on genetic background (i.e., epistasis) are believed to play a role in understanding molecular underpinnings of complex diseases such as inflammatory bowel disease ...
Development of a method for generating SNP interaction-aware polygenic risk scores for radiotherapy toxicity
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AIM: To identify the effect of single nucleotide polymorphism (SNP) interactions on the risk of toxicity following radiotherapy (RT) for prostate cancer (PCa) and propose a new method for polygenic risk score incorporating SNP-SNP interactions (PRSi). MATERIALS AND METHODS: Analysis included the REQUITE PCa cohort that received external beam RT and...
Development of a method for generating SNP interaction-aware polygenic risk scores for radiotherapy toxicity.
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Published in Radiotherapy and oncology : journal of the European Society for Therapeutic Radiology and Oncology
To identify the effect of single nucleotide polymorphism (SNP) interactions on the risk of toxicity following radiotherapy (RT) for prostate cancer (PCa) and propose a new method for polygenic risk score incorporating SNP-SNP interactions (PRSi). Analysis included the REQUITE PCa cohort that received external beam RT and was followed for 2 years. L...
Inheritance of Striga hermonthica adaptive traits in an earlymaturing white maize inbred line containing resistance gene...
Striga hermonthica can cause as high as 100% yield loss in maize depending on soil fertility level, type of genotype, severity of infestation and climatic conditions. Understanding the mode of inheritance of Striga resistance in maize is crucial for introgression of resistance genes into tropical germplasm and deployment of resistant varieties. Thi...
IAMBEE: a web-service for the identification of adaptive pathways from parallel evolved clonal populations
IAMBEE is a web server designed for the Identification of Adaptive Mutations in Bacterial Evolution Experiments (IAMBEE). Input data consist of genotype information obtained from independently evolved clonal populations or strains that show the same adapted behavior (phenotype). To distinguish adaptive from passenger mutations, IAMBEE searches for ...
IAMBEE : a web-service for the identification of adaptive pathways from parallel evolved clonal populations
IAMBEE is a web server designed for the Identification of Adaptive Mutations in Bacterial Evolution Experiments (IAMBEE). Input data consist of genotype information obtained from independently evolved clonal populations or strains that show the same adapted behavior (phenotype). To distinguish adaptive from passenger mutations, IAMBEE searches for ...
On the evolutionary ecology of multidrug resistance in bacteria
Resistance against different antibiotics appears on the same bacterial strains more often than expected by chance, leading to high frequencies of multidrug resistance. There are multiple explanations for this observation, but these tend to be specific to subsets of antibiotics and/or bacterial species, whereas the trend is pervasive. Here, we consi...
Variable prioritization in nonlinear black box methods: a genetic association case study
The central aim in this paper is to address variable selection questions in nonlinear and nonparametric regression. Motivated by statistical genetics, where nonlinear interactions are of particular interest, we introduce a novel and interpretable way to summarize the relative importance of predictor variables. Methodologically, we develop the “RelA...
Immunochip Analyses of Epistasis in Rheumatoid Arthritis Confirm Multiple Interactions within MHC and Suggest Novel Non-...
Published in The Journal of rheumatology
There are multiple but relatively weak interactions independent of the additive effects in RA and a larger sample number is required to confidently assign additional non-MHC epistasis.
