Summer 2022 – Picking Back Up!

This summer is jam-packed with new research ideas and projects! Since the last posts in 2020, postdoctoral researcher Pramesh Singh has joined the group. We have also started some exciting collaborations with folks at UW-Madison, Tufts, and University of Florida. Here’s what we are up to for the next few weeks:

Streamlining pathway reconstruction algorithms with SPRAS. We are excited to continue working with Tony Gitter at UW-Madison to build SPRAS, a workflow to easily run multiple pathway reconstruction algorithms on multiple datasets. Nina Young is helping on this project as we add more downstream analysis functionality and incorporate new algorithms into the workflow.

Using networks to understand metal ion transport and homeostasis in bacteria. In this brand-new collaboration with Reed chemist Shivani Ahuja, Max Bennett and Henry Jacques are using network-based mapping, visualization, and analysis to identify conserved interactions that may be involved in regulating the ATP-binding cassette (ABC) transporter family, which are highly conserved in bacteria.

Studying the topology of disease genes using graphlets. Last year, we published a paper showing that using small, connected, induced subgraphs called graphlets to describe signaling pathways can compare these pathways across databases. Lixing Yi, Hannah Kuder, and Larry Zeng are working on related projects to implement a directed graphlet library, identify graphlet-enriched communities, and better understand graphlet-based measurements in networks. Pramesh is the research co-mentor on this project.

Tools to identify gendered language in student letters of recommendation. In a non-compbio project, post-baccalaureate Alex Richter is investigating existing methods to identify gendered language in evaluations, with a goal to build a tool to help faculty remove bias from their letters of recommendations. This project is funded by Reed’s Social Justice Research and Education Fund.

Stay tuned to hear more about these and other projects!