Summer Research Highlight

Orientation next week marks the true end of summer for Reed.  For a final summer highlight, Tunç Köse shares his perspective on directed acyclic graphs (DAGs) for signaling pathway reconstructions and comparing to a shortest-paths approach.  Read his post for more information: More about DAGs.

Thanks to all summer students, both returning and graduated!  Here’s to a wonderful academic 2019/20 year.


Summer Research Highlight

Jiarong Li, a Math/CS major, is third in our series of summer research highlights. She has teamed up with Tunç Köse to design and implement an algorithm that builds increasingly larger directed acyclic graphs (DAGs) within a protein-protein interactome.  We are looking to see how this algorithm reconstructs known signaling pathways.  Read Jiarong’s post for more info:

Reconstructing Signaling Pathways by DAGs

(If you want to learn a bit about all projects, read my summer kickstarter post).

Summer Research Highlight

Next up for summer highlights is Tayla Isensee, a rising Junior at Reed who is splitting her research time on computational and experimental sides of the same project -searching for targets of Retinoic Acid (RA) signaling in zebrafish retinal development.  This is a joint project with Kara Cerveny, whose work produces beautiful images of the zebrafish eye (images from her website):

In this project we’re going back to bioinformatics with motif-finding – read Tayla’s post for more info:

Retinoic Acid, Development, and Motif Finding

Summer Research Highlight

Seven fantastic undergrads & recent-grads are working with me this summer, and we’ve already made a ton of progress.  We have a separate student blog, The Pathway Not Taken, which was established as part of a Computing Research Association Collaborative REU grant (I hope that program comes back, it was great).

First up is Amy Rose Lazarte, who just graduated from Reed. Before heading to Puppet Labs as a software engineer, she’s working to build models of phytoplankton fitness in freshwater lakes.  Read her post for more info:

Ecology Modeling: Thermal Variation and Phytoplankton Fitness

(If you want to learn a bit about all projects, read my summer kickstarter post).

New Reed CompBio Blog

As part of a recently-funded collaborative REU (generously supported by the CRA-W), my colleague Derek Applewhite and I are working with undergraduates to study machine learning methods to predict genes that regulate cell movement patterns in schizophrenia.  The team will post their work on new a Reed College blog, The Pathway Not Taken, and I may re-post selected pieces here.  The first post gives a general idea of the problem we will work on, and how biology and computer science are intertwined in the project.

Congratulations Seniors

It’s been a long while since I posted, so I figured it’s appropriate to resume this blog by congratulating all the seniors at Reed who have labored over their theses throughout the year.  Now, they will ceremoniously burn all their drafts this afternoon at the bonfire.  Happy Renn Fayre!


Spotted outside my office door in the Biology building.