Related papers: Bayesian Method for Disease QTL Detection and Mapp…
Identifying disease genes from human genome is an important and fundamental problem in biomedical research. Despite many publications of machine learning methods applied to discover new disease genes, it still remains a challenge because of…
Disease subtype identification (clustering) is an important problem in biomedical research. Gene expression profiles are commonly utilized to infer disease subtypes, which often lead to biologically meaningful insights into disease. Despite…
Expression quantitative trait loci (eQTL) mapping aims to determine genomic regions that regulate gene transcription. Expression QTL is used to study the regulatory structure of normal tissues and to search for genetic factors in complex…
Targeted therapies on the basis of genomic aberrations analysis of the tumor have shown promising results in cancer prognosis and treatment. Regardless of tumor type, trials that match patients to targeted therapies for their particular…
Background: Bayesian Networks (BNs) are probabilistic graphical models that leverage Bayes' theorem to portray dependencies and cause-and-effect relationships between variables. These networks have gained prominence in the field of health…
We develop statistically based methods to detect single nucleotide DNA mutations in next generation sequencing data. Sequencing generates counts of the number of times each base was observed at hundreds of thousands to billions of genome…
Genetic differences between individuals associated to quantitative phenotypic traits, including disease states, are usually found in non-coding genomic regions. These genetic variants are often also associated to differences in expression…
We propose a general method to carry out a valid Bayesian analysis of a finite-dimensional `targeted' parameter in the presence of a finite-dimensional nuisance parameter. We apply our methods to causal inference based on estimating…
Tumor samples are heterogeneous. They consist of different subclones that are characterized by differences in DNA nucleotide sequences and copy numbers on multiple loci. Heterogeneity can be measured through the identification of the…
Some methods aim to correct or test for relationships or to reconstruct the pedigree, or family tree. We show that these methods cannot resolve ties for correct relationships due to identifiability of the pedigree likelihood which is the…
The "rare type match problem" is the situation in which the suspect's DNA profile, matching the DNA profile of the crime stain, is not in the database of reference. The evaluation of this match in the light of the two competing hypotheses…
Variable selection has played a critical role in modern statistical learning and scientific discoveries. Numerous regularization and Bayesian variable selection methods have been developed in the past two decades for variable selection, but…
Many biological phenomena undergo developmental changes in time and space. Functional mapping, which is aimed at mapping genes that affect developmental patterns, is instrumental for studying the genetic architecture of biological changes.…
Expression quantitative trait loci (eQTL) analysis identifies genetic markers associated with the expression of a gene. Most existing eQTL analyses and methods investigate association in a single, readily available tissue, such as blood.…
A central part of population genomics consists of finding genomic regions implicated in local adaptation. Population genomic analyses are based on genotyping numerous molecular markers and looking for outlier loci in terms of patterns of…
Important objectives in cancer research are the prediction of a patient's risk based on molecular measurements such as gene expression data and the identification of new prognostic biomarkers (e.g. genes). In clinical practice, this is…
We present a Bayesian method for characterizing the mating system of populations reproducing through a mixture of self-fertilization and random outcrossing. Our method uses patterns of genetic variation across the genome as a basis for…
We provide a mathematical formulation and develop a computational framework for identifying multiple strains of microorganisms from mixed samples of DNA. Our method is applicable in public health domains where efficient identification of…
In this paper, a Bayesian approach is developed for simultaneously comparing multiple experimental treatments with a common control treatment in an exploratory clinical trial. The sample size is set to ensure that, at the end of the study,…
Studies of the genetic loci that contribute to variation in gene expression frequently identify loci with broad effect on gene expression: expression quantitative trait locus (eQTL) hotspots. We describe a set of exploratory graphical…