The Center for Life Beyond Reed is a great resource for both summer research and scholarships. This is a short list of opportunities that I have compiled, mostly relating to computational biology and computer science.

Student Research Opportunities

Summer 2018 Research in the Compbio Lab

I have many ongoing projects that students may contribute to over the summer. All projects involve a large computational component; programming experience is useful (e.g., Bio131, Math121,...). Keep an eye on the Applications page for summer undergraduate research fellowships in the Biology department. There are also post-bac summer research fellowships courtesy of the Stafford Fund.
  • Reconstruction of disease/dysregulated pathways. Previous work reconstructs canonical signaling pathways from large protein-protein interaction networks. We want to extend similar ideas to study signaling pathways that are known to be perturbed in cancer.
  • Signaling hypergraph algorithms. Signaling hypergraphs more faithfully reflect the organization of signaling pathway data as it is stored in pathway databases such as Reactome, KEGG, and NetPath. We are interested in extending well-studied graph algorithms to signaling hypergraphs and using them to analyze signaling pathways.
  • Graph and hypergraph visualization. Understanding algorithmic output is crucial when developing computational methods. GraphSpace is an interactive graph sharing and visualization tool that has been invaluable for analyzing protein-protein interaction networks. Can we develop algorithms for visualizing hypergraphs in the same tool?
  • Drug response in kidney cancer. We often measure response to a drug compared to a drug-free control with high-throughput methods such as gene expression, metabolomics, or phosphoproteomics. What can we learn by integrating these high-throughput assays of ACHN, a renal cell adenocarcinoma cell line, upon treatment of kidney cancer drugs?
  • Other projects. I am open to working on other projects, especially if the student secures external funding and/or the project involves collaboration with other faculty member at Reed.

Research During the Semester

  • Students interested in learning about ongoing research and thesis projects may join the weekly lab meetings. Students must commit to participating weekly one-hour meetings and leading discussion about one topic or paper in the semester.
  • In some circumstances, I may advise independent projects over the semester. These half-unit Bio481 courses require a petition that is approved by the Department and the Division.
  • Students who want to learn more about computational biology can independently solve problems on Rosalind,a bioinformatics education platform. The Bioinformatics Textbook track provides problems from the Bio131 textbook. I highly recommend this website.

Research at Other Institutions

The Biology Department provides a list of off-campus summer internships. Databases maintained by the Center for Life Beyond Reed (login required) may also have other research opportunities. Below are a few other programs that may be of interest.

Fellowships and Scholarships

Most of the funding opportunities listed here are intended for women in computer science or related fields. This list will get longer. If you know of other funding opportunities, please send them my way.

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Biology Department
Reed College
3203 SE Woodstock Blvd.
Portland, OR 97202-8199

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