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Genetics and Genomics

Genome Sequences of Eight Bacterial Species Found in Coculture with the Haptophyte <i>Chrysochromulina tobin</i> : TABLE 1 

Fixen KR, Starkenburg SR, Hovde BT, Johnson SL, Deodato CR, Daligault HE, Davenport KW, Harwood CS, Cattolico RAnn.  2016.  Genome Sequences of Eight Bacterial Species Found in Coculture with the Haptophyte Chrysochromulina tobin : TABLE 1 . Genome Announcements. 4(6):e01162-16.

Genomics-inspired biology: From genes to organisms, and beyond

Charles Darwin was a brilliant naturalist who recognized many biological connections through his observations of the natural world. Darwin would no doubt revel in our ability to draw biological inferences from DNA sequences. Of course, we also know that biological inference and biological content are easily conflated and that genomics can only take us so far without proper authentication via empirical biology.

History repeats itself: Using evolutionary convergence to reveal adaptations and genome-wide functional networks

Life is in a constant state of revision in response to evolutionary pressures such as environmental change. In the Clark lab we seek to understand these adaptive changes by studying evolutionary signatures in genes and regulatory sequences. Our computational methods leverage convergent evolution, in which independent phylogenetic lineages evolve the same phenotype, to discover the genetic changes underlying specific adaptations.

Evolution and ecology of cold-specialized insects in the Cascades Range

Montane ecosystems of the Cascades Range provide a simple, naturally replicated system to test a wide range of evolutionary and ecological processes, from the origin of cold-specialized species to the role of ecological diversification in community assembly. My research focuses on groups of insects that are dispersal limited microhabitat specialists of snowfield and riparian ecosystems. Based on extensive sampling and genetic data, I discuss biogeographic models that explain the origin, current distribution and pattern of endemism in these insects.

Color, structure and evolution of avian eggs: A multidisciplinary approach

Avian eggs are remarkably varied in their color, pattern, shape, size and ultrastructure. What evolutionary forces have affected their appearance and form? Using a multidisciplinary approach, I will explore the phenotypic diversity of avian eggs from functional and mechanistic perspectives, focusing on cuckoo egg mimicry, speckled songbird eggs, shorebird egg camouflage and nano-scale shell structure.

The Allen Institute of Cell Science – Integrated, multi-scale and spatial-temporal cell biology

The mission of the Allen Institute for Cell Science is to understand and predict cellular behaviors. Our initial project takes an integrative approach, developing high replicates of dynamic, visual data on cell organization and activities using endogenous fluorescently tagged human induced pluripotent stem cells. We are quantifying the relative locations and dynamics of the major cellular structures and activities as the stem cells go through the cell cycle and differentiate into cardiomyocytes andrespond to environmental perturbations and drugs.

Cachexia-like wasting in drosophila

During animal development, homeostasis, and aging, anything that grows eventually decays or undergoes consumption, which is known as atrophy or wasting. Thus, like growth, wasting is a fundamental biological process. Importantly, wasting is also part of a complex systemic disorder associated with many diseases. Cachexia, the wasting syndrome commonly observed in advanced cancer patients, affects approximately eight million people worldwide. Due to the complexity of the disease, it is challenging to dissect the molecular mechanisms of cachexia.

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