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In the genomic era, the identification of gene signatures associated with disease is of significant interest. Such signatures are often used to predict clinical outcomes in new patients and aid clinical decision-making. However, recent…
Many aspects of the historical relationships between populations in a species are reflected in genetic data. Inferring these relationships from genetic data, however, remains a challenging task. In this paper, we present a statistical model…
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…
Maps of infectious disease---charting spatial variations in the force of infection, degree of endemicity, and the burden on human health---provide an essential evidence base to support planning towards global health targets. Contemporary…
Falciparum malaria is a major parasitic disease causing widespread morbidity and mortality globally. Artemisinin derivatives---the most effective and widely-used antimalarials that have helped reduce the burden of malaria by 60% in some…
The rise of antimicrobial drug resistance is an imminent threat to global health that has warranted, and duly received, considerable attention within the medical, microbiological and modelling communities. Outbreaks of drug-resistant…
Admixture models are a ubiquitous approach to capture latent population structure in genetic samples. Despite the widespread application of admixture models, little thought has been devoted to the quality of the model fit or the accuracy of…
Genomic signal processing has been used successfully in bioinformatics to analyze biomolecular sequences and gain varied insights into DNA structure, gene organization, protein binding, sequence evolution, etc. But challenges remain in…
The occurrence of multiple strains of a bacterial pathogen such as M. tuberculosis or C. difficile within a single human host, referred to as a mixed infection, has important implications for both healthcare and public health. However,…
Spatial transcriptomics is a modern sequencing technology that allows the measurement of the activity of thousands of genes in a tissue sample and map where the activity is occurring. This technology has enabled the study of the so-called…
Malaria is a major contributor to health burdens throughout the regions where it is endemic. Historically, it was believed that there was limited morbidity and essentially no mortality associated with Plasmodium vivax; however, evidence…
Accurate detection of Plasmodium falciparum in Giemsa-stained blood smears is an essential component of reliable malaria diagnosis, especially in developing countries. Deep learning-based object detection methods have demonstrated strong…
This work was motivated by a twin study with the goal of assessing the genetic control of immune traits. We propose a mixture bivariate distribution to model twin data where the underlying order within a pair is unclear. Though estimation…
Plasmodium vivax populations are more resistant to malaria control strategies than Plasmodium falciparum, maintaining high genetic diversity and gene flow even at low transmission. To quantify the impact of declining transmission on P.…
The var genes of the human malaria parasite Plasmodium falciparum present a challenge to population geneticists due to their extreme diversity, which is generated by high rates of recombination. These genes encode a primary antigen protein…
Understanding the relationship between genomic variation and variation in phenotypes for quantitative traits such as physiology, yield, fitness or behavior, will provide important insights for both predicting adaptive evolution and for…
The genetic structure of human populations is extraordinarily complex and of fundamental importance to studies of anthropology, evolution, and medicine. As increasingly many individuals are of mixed origin, there is an unmet need for tools…
Antimicrobial resistance is becoming a major threat to public health throughout the world. Researchers are attempting to contrast it by developing both new antibiotics and patient-specific treatments. In the second case, whole-genome…
Multitype branching processes with immigration in one type are used to model the dynamics of stage-structured plant populations. Parametric inference is first carried out when count data of all types are observed. Statistical…
Large-scale statistical analysis of data sets associated with genome sequences plays an important role in modern biology. A key component of such statistical analyses is the computation of $p$-values and confidence bounds for statistics…