相关论文: Functional Mapping of Multiple Dynamic Traits
In many longitudinal microarray studies, the gene expression levels in a random sample are observed repeatedly over time under two or more conditions. The resulting time courses are generally very short, high-dimensional, and may have…
Complexity in biology is often described using a multi-map architecture, where the genotype, representing the encoded information, is mapped to the functional level, known as the phenotype, which is then connected to a latent phenotype we…
Clinical end-point traits are often characterized by quantitative or qualitative precursors and it has been argued that it may be statistically a more powerful strategy to analyze these precursor traits to decipher the genetic architecture…
Understanding how genetic variants influence cellular-level processes is an important step towards understanding how they influence important organismal-level traits, or "phenotypes", including human disease susceptibility. To this end…
Motivated by the genomic application of expression quantitative trait loci (eQTL) mapping, we propose a new procedure to perform simultaneous testing of multiple hypotheses using Bayes factors as input test statistics. One of the most…
Genome-wide experiments to map the DNA-binding locations of transcription-associated factors (TFs) have shown that the number of genes bound by a TF far exceeds the number of possible direct target genes. Distinguishing functional from…
Understanding which phenotypic traits are consistently correlated throughout evolution is a highly pertinent problem in modern evolutionary biology. Here, we propose a multivariate phylogenetic latent liability model for assessing the…
The twin crises of climate change and biodiversity loss define a strong need for functional diversity monitoring. While the availability of high-quality ecological monitoring data is increasing, the quantification of functional diversity so…
The genotype-phenotype map is an essential object in our understanding of organismal complexity and adaptive properties, determining at once genomic plasticity and those constraints that may limit the ability of genomes to attain…
In modern scientific studies, it is often imperative to determine whether a set of phenotypes is affected by a single factor. If such an influence is identified, it becomes essential to discern whether this effect is contingent upon…
Many complex disease syndromes such as asthma consist of a large number of highly related, rather than independent, clinical phenotypes, raising a new technical challenge in identifying genetic variations associated simultaneously with…
Methods to effectively detect multi-locus genetic association are becoming increasingly relevant in the genetic dissection of complex trait in humans. Current approaches typically consider a limited number of hypotheses, most of which are…
In a mouse intercross with more than 500 animals and genome-wide gene expression data on six tissues, we identified a high proportion (18%) of sample mix-ups in the genotype data. Local expression quantitative trait loci (eQTL; genetic loci…
Multi-task learning (MTL) is a learning paradigm that enables the simultaneous training of multiple communicating algorithms. Although MTL has been successfully applied to ether regression or classification tasks alone, incorporating mixed…
An expression quantitative trait locus (eQTL) is a chromosomal region where genetic variants are associated with the expression levels of certain genes that can be both nearby or distant. The identifications of eQTLs for different tissues,…
The discovery of genomic polymorphisms influencing gene expression (also known as expression quantitative trait loci or eQTLs) can be formulated as a sparse Bayesian multivariate/multiple regression problem. An important aspect in the…
This paper explores the genotype-phenotype relationship. It outlines conditions under which the dependence of a quantitative trait on the genome might be predictable, based on measurement of a limited subset of genotypes. It uses the theory…
Admixture mapping is a popular tool to identify regions of the genome associated with traits in a recently admixed population. Existing methods have been developed primarily for identification of a single locus influencing a dichotomous…
Genetic variation affecting gene regulation is a central driver of phenotypic differences between individuals and can be used to uncover how biological processes are organized in a cell. Although detecting cis-eQTLs is now routine,…
Post-genomic research deals with challenging problems in screening genomes of organisms for particular functions or potential for being the targets of genetic engineering for desirable biological features. 'Phenotyping' of wild type and…