Summer Research Highlight

Our next summer highlight comes from Alex Richter, a rising Computer Science / Mathematics junior.  She has been working to integrate a recently published hypergraph algorithm into a large, community driven biological network visualization tool.  This has been an exciting collaboration with Dr. Guanming Wu from Medical Informatics and Clinical Epidemiology at OHSU.

Read Alex’s post on the Reed CompBio Blog: Hypergraph Algorithms.

(you can catch up with all summer research projects in my earlier Summer 2020 Research post)




Summer Research Highlight

Our first summer research highlight comes from Gabe Preising, who graduated from Reed in 2020 and is now working as a post-baccalaureate researcher with me and Suzy Renn to extend his undergrad thesis work.  Gabe is working as part of Suzy’s NIH award to study a species of fish where the females do not eat during early parental care because they hold eggs in their mouths (called mouth brooding).

Read Gabe’s post on the Reed CompBio Blog: Nets Full of Fish Brains.

You can read about all the summer research projects in my Summer 2020 Research post. Stay tuned for more highlights!


Black Lives Matter, and White People Need to Act

It has been a week since #ShutDownSTEM and #Strike4BlackLives on June 10, which was a day to give Black academics in STEM a brief rest and non-Black academics in STEM a time for reflection, education, and planning to eradicate anti-Black racism from our institutions.

Courtesy of header images from WeRepSTEM

Resources and personal experiences poured in through Twitter (especially the #BlackInTheIvory hashtag). The first thing that became immediate is that I have a lot of reading to do. The second thing is simply that reading is not enough. We cannot have this movement end in a day, in a week, in a month, in a year. We all need to work to disrupt the status quo of academia, and there have been calls to action (Michael Eisen’s editorial and Black in Computing’s open letter are just two of many examples). So, in my small way, I’ve made a plan of action.

Continue reading

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!


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.

Sabbatical Part 9

Summer students are finishing their ten-week research projects, we started receiving emails about the upcoming semester, and there’s a general buzz about campus.  Classes are fast approaching, and my year-long junior leave is (almost) over.

Wrapping Up with Wickelfisch

My final academic travel of sabbatical was to ISMB/ECCB 2019, which was held in Basel in July.  I presented a poster on hypergraph connectivity measures and my student Ananthan Nambiar presented a poster on NLP approaches for protein family classification before heading to a PhD program at UIUC (check out the posters page on my website).  It was also great to see work from my graduate group (Brown) and postdoc group (Virginia Tech) presented as posters, invited talks, and papers.

Basel was a beautiful city, though it was surprisingly easy to accidentally end up in France or Germany.  There was a heat wave, but we managed with extra servings of gelato and floating down the Rhine with our waterproof swim bags (a.k.a. wickelfisch):

Even though sabbatical is over, there will still be lots to write about! I’m excited to get back to teaching – I’m offering my upper-level computational systems biology course and a sophomore-level course on scientific literacy that will be team-taught with cell biologist superstar Derek Applewhite.

Stay tuned for more news about science, academia, and undergraduate education.

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