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.

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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

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).

Sabbatical Part 8

It’s summer, and faculty have submitted their grades, attended their last faculty meeting, and have gleefully moved on to full-time summer research.  Faculty on sabbatical have a few more precious months to wrap up the year’s worth of research projects before returning to teaching.  Sabbatical is not over, but the end is in sight.

The last few weeks were a whirlwind of meetings – first to Memphis, TN to the NCWIT Summit, where I received an Undergraduate Research Mentoring award.  I ate some hot chicken, saw the Grand Ole Opry, and did some novice line dancing.

summitemail_messagingsmcard

I then flew to Madison, WI for the Great Lakes Bioinformatics conference.  It was a great meeting – the talks presented new and innovative ideas in bioinformatics and computational biology.  I gave two talks — a research talk on hypergraph connectivity measures for signaling pathway analysis and an education talk on undergraduate engagement in computational biology through conference attendance.  Materials related to these talks will be posted on my website in the next few weeks.

Madison and the University’s campus has changed a lot since I was a kid, but I was excited to introduce the Great Dane Pub to some folks.  I also probably talked about cheese curds more than I should have.  I also caught up with other liberal arts computational biology faculty: Layla Oesper from Carleton, Catie Welsh from Rhodes, and Getiria Onsongo from Macalester.  Undergraduate institutions in the midwest are certainly stepping up their computational biology game!

Summer research is now in full swing, with three students and two post-bacs working on a bunch of different projects.  I’ve also taken advantage of the outstanding (dry!) Portland weather to get back into playing ultimate frisbee – my last sabbatical goal is to not get (too) injured.

 

Sabbatical Part 7

Preprints and Pasta

I have finally joined the preprint bandwagon (which is embarrassingly late, given how much I am in support of open science).  Here are four recent preprints that are finally free to the public.  Congratulations and thanks go to the four other PIs, one postdoc, one grad student, and six undergraduates who contributed to these papers.

Integrating Protein Localization with Automated Signaling Pathway Reconstruction
Ibrahim Youssef, Jeffrey Law, Anna Ritz
Full version of BIBM 2018 conference paper, under review
Big Question: When we hunt for protein interactions that are potentially involved in cellular signaling responses, can we use information about where the proteins are localized in the cell?
Short Answer: Yep.  We modify an existing algorithm to find paths within large protein protein interaction networks that respect where we expect proteins to be expressed in the cell.

Distance Measures for Tumor Evolutionary Trees
Zach DiNardo, Kiran Tomlinson, Anna Ritz, and Layla Oesper
RECOMB-CCB 2019 conference paper
Big Question: Suppose we have two “options” for how an individual’s tumor has evolved, in terms of the order of acquired mutations.  How should we compare these options?
Short Answer: We need to compare both the grouping (labeling) and the relative order of acquired mutations in evolutionary time – our distances account for these features.

Connectivity Measures for Signaling Pathway Topologies
Nicholas Franzese, Adam Groce, T. M. Murali, and Anna Ritz
GLBio 2019 conference paper
Big Question:Signaling pathways are inherently more complicated than their graph representations, and many other representations have been proposed to capture the complexity of signaling pathway topologies (e.g. compound graphs, bipartite graphs, and hypergraphs).  In these representations, what does it mean for two molecules to be “connected,” and is connectivity a useful measure?
Short Answer: We show that “connectivity” highly depends on the data representation, and we propose a parameterized measure that switches from connectivity in graphs to connectivity in hypergraphs.  This measure can capture the “influence” of one signaling pathway on another better than other connectivity measures.

Improved Differentially Private Analysis of Variance
PETS 2019 conference paper
Marika Swanberg, Ira Globus-Harris, Iris Griffith, Anna Ritz, Adam Groce, Andrew Bray
Big Question: The Analysis of Variance (ANOVA) statistic is heavily used in contexts where user privacy is imperative (biomedicine, sociology, and business).  We already developed an algorithm with differential privacy guarantees on datasets of a certain size – can we improve the method so we get this guarantee with fewer data points?
Short Answer: Yep.  In fact, we define variants of the ANOVA statistic with good differential privacy guarantees.

…and the pasta. In non-work-related news, I just returned from a family vacation in Italy! We saw great architecture and art (in addition to the pasta, wine, and gelato), walking about 10 miles a day on cobblestones.

The History of Science Museum (Museo Galileo) in Florence was fantastic, displaying scientific instruments big and small.

 

Finally, good luck Reed thesis students as they wrap up their senior theses!  Only a few short weeks until Renn Fayre….