Analyses of large-scale datasets in diatoms, an essential group of photosynthetic organisms.

Year: 2017
Project Description:

The Wickett lab invites interested undergraduates to apply for an REU in computational bioinformatics and phylogenomics. We are currently investigating the nearly 200 million year history of diatoms, a fascinating group of unicellular organisms that number between 100-200,000 species, and account for around 1/5th of global photosynthesis. Our lab primarily utilizes cutting edge software for assembling and analyzing raw DNA and RNA sequence data at the genomic and transcriptomic levels. REU participants would have the opportunity to explore these datasets and software across a diversity of diatom lineages, and also gain experience leveraging large-scale DNA and protein databases as they perform an independent research project with a selected focus.

The REU intern will be based at the Chicago Botanic Garden, where s/he will utilize our two high performance computing clusters comprising over 72 processing units and 768 GB of RAM. Specifically, the intern will have the opportunity to:

- learn and/or further develop skills in both command-line computing and scripting in one or more computing languages (Perl, Python, Linux/Unix, R, etc.)

- gain skill in manipulating genome- and transcriptome-scale datasets generated from Illumina and Pacific Biosciences sequencing platforms

- utilize large database resources (NCBI, SwissProt, etc.) to assess quality of genomic and transcriptomic assemblies

- assemble and analyze chloroplast genomes and chloroplast-based evolutionary relationships

A specific project will be developed under the supervision of Norm Wickett and one or more Post Doctoral researchers; the exact nature of the project is flexible and will depend on the level of experience of the intern.


Key words:

Evolution, Genetics, Phylogenomics, Next Generation Sequencing


Fieldwork Conditions: