BACKGROUND Hepatitis C virus (HCV) is a major cause of liver diseases worldwide. Due to its asymptomatic nature, screening is necessary for identification. Because screening of the total population is not cost effective, it is important to identify which risk factors for positivity characterize the key populations in which targeting of screening yields the highest numbers of HCV positives, and ...

Synthetic populations attempt to capture population dynamics of a geographic region and hence are widely used in large-scale multiagent applications simulating real-world phenomena. However, current synthetic populations are mostly static — individuals are assumed to perform same daily routine every day. My thesis aims at taking the first step towards making it a “live” synthetic population tha...

Respondent-Driven Sampling (RDS) is n approach to sampling design and inference in hard-to-reach human populations. It is often used in situations where the target population is rare and/or stigmatized in the larger population, so that it is prohibitively expensive to contact them through the available frames. Common examples include injecting drug users, men who have sex with men, and female s...

Hidden Markov Models are commonly trained using algorithms derived from gradient-based methods such as the Baum-Welch procedure. We describe a new representation of discrete observation HMMs that permits them to be trained using Population-Based Incremental Learning (PBIL), a variant of genetic learning that combines evolutionary optimization and hill-climbing Baluja and Caruana, 1995]. In this...

One of the most solid generalizations of transmission genetics is that the phenotypic variance of populations carrying a major mutation is increased relative to the wild type. At least some part of this higher variance is genetic and due to release of previously hidden variation. Similarly, stressful environments also lead to the expression of hidden variation. These two observations have been ...

We present GERMLINE, a robust algorithm for identifying segmental sharing indicative of recent common ancestry between pairs of individuals. Unlike methods with comparable objectives, GERMLINE scales linearly with the number of samples, enabling analysis of whole-genome data in large cohorts. Our approach is based on a dictionary of haplotypes that is used to efficiently discover short exact ma...

Several recent papers have argued that understanding of pathologic perinatal processes may be advanced by considering, in varying ways, the population of fetuses still in utero. Initially invoked by Yudkin et al. (Lancet 1987;1:1192-4) as the optimum denominator for intrapartum stillbirths, fetuses in utero (or "fetuses at risk") have also been of interest because of their patterns of growth, e...

The heritability of a trait is the proportion of its variance explained by genetic factors; it has historically been estimated using familial data. However, new methods have appeared for estimating heritabilities using genomewide data from unrelated individuals. A drawback of this strategy is that population stratification can bias the estimates. Indeed, an environmental factor associated with ...