Despite a large and multifaceted effort to understand the vast landscape of phenotypic data, their current form inhibits productive data analysis. The lack of a community-wide, consensus-based, human- and machine-interpretable language for describing phenotypes and their genomic and environmental contexts is perhaps the most pressing scientific bottleneck to integration across...
Transcription of the VERNALIZATION1 gene (VRN1) is induced by prolonged cold
(vernalization) to trigger flowering of cereal crops, such as wheat and barley. VRN1 encodes a
MADS box transcription factor that promotes flowering by regulating the expression of other
genes. Here we use transcriptome sequencing (RNA-seq) and chromatin immunoprecipitation
sequencing...
Over 100 monthly bacterioplankton DNA samples, from each of the surface and 200 m depths at the Bermuda Atlantic Time-series Study (BATS) site, were analyzed for community assembly processes. Correlation networks, filtered for potential autocorrelation artifacts, were constructed for each depth. Network characteristics for the two depths were remarkably similar...
Despite knowledge that concerted evolution of high-copy loci is often imperfect,
studies that investigate the extent of intragenomic polymorphisms and comparisons
across a large number of species are rarely made. We present a bioinformatic pipeline
for characterizing polymorphisms within an individual among copies of a high-copy
locus. Results are presented...
This thesis presents two related studies on the methodology for creating, and
subsequently analyzing, an inverse food web model of an intertidal seagrass bed. The first study (Chapter 2) describes, for the first time in the literature, a method for incorporating isotopic information gained from Bayesian mixing models into an...