Improvements in medical and genomic technologies have dramatically increased the production of electronic data over the last decade. As a result, data management is rapidly becoming a major determinant, and urgent challenge, for the development of Precision Medicine. Although su…
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Malaria caused an estimated 627, 000 deaths, mostly among African children in 2012. Anopheles gambiae is one of the most efficient vectors of malaria in the world. An. gambiae is highly anthropophilic, preferring the human host as a source of blood. An. gambiae enjoys an excepti…
Computational proteogenomic integrates proteomics with genomics and transcriptomics data and has emerged over the past decade as a useful discipline for functional annotation of genomes. It has been driven by high-throughput technologies from mass spectrometry and next generatio…
The common bean ( Phaseolus vulgaris L.) is consumed by millions of people worldwide and is a staple source of protein, starch and micronutrients. Common bean production across the world is affected by abiotic and biotic stresses that limit the growth and yield of this important…
Reef-building corals globally face an increasing assortment of existential threats, ranging from disease outbreaks to intensifying climate change, resulting in wide-scale population declines. Until recently, our understanding of coral evolutionary genetics, as well as any potent…
Modern machine learning methods have been widely applied in genomics and metagenomics data analysis. This dissertation focuses on the area of unsupervised machine learning and discusses community membership testing, matrix completion and generative adversarial nets with applicat…
Macrophages perform a wide variety of crucial, and sometimes contradictory, functions. While “pro-inflammatory” activities like fighting off infections and “anti-inflammatory” activities like wound-healing traditionally have been attributed to M1 and M2 macrophage subsets, studi…
Transcription factors (TFs) confer specificity to transcriptional regulation by binding specific DNA sequences and ultimately affecting the ability of RNA polymerase to transcribe a locus. The C2H2 zinc finger proteins (C2H2 ZFPs) are a TF class with the unique ability to divers…
The revolution in sequencing technologies has greatly advanced our understanding of genomes. Many regulatory elements lacking protein-coding ability, such as long non-coding RNAs have been identified and characterized in different biological contexts. However, functional interro…
Modern genomic sequencing technologies provide the opportunity to address long-standing questions in molecular evolution with empirical data. In this dissertation, I combine this new technology with advances in statistical population genetics to describe how deleterious mutation…
Cancer progression is an evolutionary process: somatic mutations can confer selective advantages to certain cells, eventually causing them to abnormally proliferate. Parallels can be drawn between the evolution of organismal populations and cancer cell populations. In both, sele…
The burgeoning frequency of genome sequencing in recent years is a testament to both the improvements in sequencing technologies and the utility of genomic analyses for biological discovery. The rapid proliferation in technological advancements and availability of complementary …
Viruses have been responsible for some of the most notorious outbreaks and pandemics in modern history. With increases in urbanization and global transportation we can expect viruses to remain a major concern both now and in the future. It is important to establish new ways to m…
Platanthera is one of the largest genera of temperate orchids and exemplifies a lineage that has adaptively radiated into diverse habitats within North America, Asia, Europe, North Africa, Borneo, and Sarawak. Major centers of diversity in this genus are western North America an…
Bacterial cells during many cell division cycles accumulate spontaneous mutations, which result in the birth of novel clones – cells that carry identical set of mutations. As a result of this clonal expansion, an evolving bacterial population has different clonal composition ove…
The modern synthesis was a critical development in evolutionary biology as it combined Darwinian evolution with Mendelian genetics. Today, we embark on a new revolution – the widespread availability of genomic data. In this dissertation, I use three applications of phylogenetic,…
The genus Amanita (Agaricomycetes) is an emerging non-model system for ecological population genomics. Amanita is a charismatic genus of beautiful and sometimes deadly poisonous mushrooms. Several Amanitae are invasive species, including the ectomycorrhizal A. phalloides and sap…
Aneuploidy can have contradictory effects on organisms and cells, from developmental disorders and cancer in humans to drug resistance and adaptive advantage in yeast. Despite a long history of involvement in human health and innumerable cases in other model organisms, how aneup…