Pandemic Edition Part 1

My last post was in the fall, when I was transitioning from sabbatical research to teaching.  Since then, needless to say, much has happened.  Like all institutions that continued teaching, Reed College finished the semester completely online.  I managed to finish my classes and the semester has officially concluded. As for next fall, we will see, but one thing is crystal clear: even in-person teaching will not be like it was.

First, some congratulations are in order:

  • Congratulations to all Reed 2020 graduating seniors!  You finished your time at Reed under exceptional circumstances, and we will never fully know how hard that was for each one fo you.
  • Congratulations to all Reed faculty and staff who carried off a pretty much successful experience overall, given the situation.
  • Congratulations to anyone who completed this year in a way that was safe and kept others from getting sick.

Next, I’m excited to say that undergraduate research is continuing at Reed through remote fellowships, and I have a bunch of students and post-bacs doing computational biology research. Read more about their plans in my kickstarter post on the Reed Compbio blog: Summer 2020 Research | The Pathway Not Taken

Finally, I went back to my creative roots during the pandemic and designed a new compbio lab logo – expect to see it on future posters!

compbio-lab

There were numerous challenges this spring, many of which were shared by other colleagues. However, these comprised only a tiny sliver of the hardships that people have faced in the past months.  I’ll write more this summer about how the pandemic has affected research and teaching at Reed. But for now, I feel lucky to be safe and able to continue doing what I love.

 

Conferences, Conferences, Conferences

Thanksgiving break is quickly approaching, and it’s amazing how time flies — that goal of writing a blog post once a week?  Try once a semester!

Luckily, there has been one major theme since I’ve started teaching again – conference travel.  Undergraduate travel to conferences are a major part of my NSF grant, and I’ve also been making rounds on the conference circuit presenting work students and I conducted during my sabbatical last year.

ISMB/ECCB in Basel, Switzerland.  I’ve already talked about the heat wave & the wickelfisch, and I mentioned Ananthan Nambiar’s poster on NLP-based methods for protein family classification.  I also presented a poster on pathway connectivity with hypergraphs that has since been published in PLOS Computational Biology.   Ananthan was also featured in Reed Magazine’s annual “What is a Reedie?” 

Pacific Northwest Quantitative Biology (PacNoW QB) Symposium at OHSU in Portland, OR.  This one-day symposium focuses on quantitative and computational biology efforts in Oregon and Washington, encompassing different types of institutions and programs. Tunc Kose and Jiarong Li presented a poster on pathway reconstruction. (They also presented at the Pre-Inauguration Showcase at Reed College in honor of our new president Audrey Bilger).
 

ACM Conference on Bioinformatics, Computational Biology, and Health Informatics (BCB) in Niagara Falls, NY.  I was excited to meet the eight undergraduates from the New York area who received travel funds to attend ACM-BCB as part of my NSF grant.    The students came from institutions large and small, and got to learn a bit about computational biology.  My student Amy Rose Lazarte, who now works at Puppet, also presented a poster on her senior thesis research.

Murdock College Science Research Conference, Vancouver, WA. Tayla Isensee, who was co-advised by Kara Cerveny, presented a poster at the annual conference organized by the Murdock Charitable Trust that celebrates undergraduate research.  She also presented at the Pre-Inauguration Showcase earlier in the semester.

IEEE Conference on Bioinformatics and BioMedicine (BIBM) in San Diego, CA.  Finally, my upper-level Computational Systems Biology course just returned from sunny San Diego after attending part of BIBM.  I presented a workshop paper based on Alex King’s thesis and post-bac work, which should be out soon as an IEEE proceedings.  Remarkably, all ten students and I managed the travel with no large holdups!

Many of my summer students also presented posters at the Reed College Poster Session early in the semester (including Karl Young, Jiarong Li, Tunc Kose, and Tayla Isensee), which highlighted computational biology at Reed.  I’m looking forward to continuing the tradition of conference attendance and presentations of Reed student work!

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).