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Providing provenance in scientific workflows is essential for reproducibility and auditability purposes. Workflow systems model and record provenance describing the steps performed to obtain the final results of a computation. In this work,…

We consider the problem of detecting and estimating the strength of association between a trait of interest and alleles or haplotypes in a small genomic region (e.g. a gene or a gene complex), when no direct information on that region is…

While we once thought of cancer as single monolithic diseases affecting a specific organ site, we now understand that there are many subtypes of cancer defined by unique patterns of gene mutations. These gene mutational data, which can be…

Motivated by the important problem of detecting association between genetic markers and binary traits in genome-wide association studies, we present a novel Bayesian model that establishes a hierarchy between markers and genes by defining…

We introduce genetic algorithms as a means to estimate the accuracy required to discriminate among different models using experimental observables. We exemplify the technique in the context of the minimal supersymmetric standard model. If…

The increasing availability of time --and space-- resolved data describing human activities and interactions gives insights into both static and dynamic properties of human behavior. In practice, nevertheless, real-world datasets can often…

Ancestry-specific proteome-wide association studies (PWAS) based on genetically predicted protein expression can reveal complex disease etiology specific to certain ancestral groups. These studies require ancestry-specific models for…

Genotype networks are a method used in systems biology to study the "innovability" of a set of genotypes having the same phenotype. In the past they have been applied to determine the genetic heterogeneity, and stability to mutations, of…

In this paper we describe a new technique for the comparison of populations of DNA strands. Comparison is vital to the study of ecological systems, at both the micro and macro scales. Existing methods make use of DNA sequencing and cloning,…

The protection of privacy of individual-level information in genome-wide association study (GWAS) databases has been a major concern of researchers following the publication of "an attack" on GWAS data by Homer et al. (2008) Traditional…

Anomalies are strange data points; they usually represent an unusual occurrence. Anomaly detection is presented from the perspective of Wireless sensor networks. Different approaches have been taken in the past, as we will see, not only to…

Many forensic genetic trace samples are of too low quality to obtain short tandem repeat (STR) DNA profiles as the nuclear DNA they contain is highly degraded (e.g., telogen hairs). Instead, performing shotgun DNA sequencing of such samples…

Generative models are invaluable in many fields of science because of their ability to capture high-dimensional and complicated distributions, such as photo-realistic images, protein structures, and connectomes. How do we evaluate the…

Genome-wide association studies (GWAS) have identified thousands of genetic variants associated with complex traits, and some variants are shown to be associated with multiple complex traits. Genetic covariance between two traits is defined…

Observed differences in mean phenotypic values across human groups have attracted renewed interest with the rise of large-scale genomic studies and polygenic risk prediction. However, the genetic basis of these differences is far more…

This paper proposes a new method for determining similarity and anomalies between time series, most practically effective in large collections of (likely related) time series, by measuring distances between structural breaks within such a…

The evolutionary edit distance between two individuals in a population, i.e., the amount of applications of any genetic operator it would take the evolutionary process to generate one individual starting from the other, seems like a…

The advent of modern genome sequencing techniques allows for a more stringent test of the neutrality hypothesis of Darwinian evolution, where all individuals have the same fitness. Using the individual based model of Wright and Fisher, we…

This paper describes a Bayesian statistical method for determining the genetic basis of a complex genetic trait. The method uses a sample of unrelated individuals classified into two groups, for example cases and controls. Each group is…

Mendelian randomization (MR) is an epidemiological method that can be used to strengthen causal inference regarding the relationship between a modifiable environmental exposure and a medically relevant trait and to estimate the magnitude of…