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….


Sabbatical Part 6

Early Spring Edition: From Sun to Snow

We are now well into the New Year, and I’ve spent a fair amount of it on the road.  Here’s an update:

  1. I got out of the Pacific Northwest gray winter and headed south to California, where I spent nearly a month working remotely.  Work was interspersed with rainbow-filled short hikes around the central coast.

    I was also at the Polar Bear Plunge in Cayucos, CA (as an observer, obviously).

  2. During my time in California, I had a quick trip to visit biology and CS faculty at Harvey Mudd College.  I then drove up north to Portland, stopping in San Fransisco & the Shasta Lake caverns for some sightseeing.
  3. I returned to a bunch of research projects in full swing.   My postdoc’s BIBM 2018 paper on localized PathLinker was invited to be in a special issue of BMC Systems Biology.  The differential privacy crew (led by computer scientist Adam Groce and statistician Andrew Bray) had a paper on differentially private ANOVA officially accepted to PETS.  We also submitted a paper (with a former student as first author) on signaling pathway connectivity using directed hypergraphs.  I also started some brand-new collaborations with Layla Oesper at Carleton College, and wrapped up a project with Ali Bashir at the Icahn School of Medicine and Mt. Sinai.


    Minneapolis, MN

  4. I then flew to Rhodes College in Memphis, TN, where I gave a talk on signaling pathway analysis and caught up with colleagues and good friends Catie Welsh in Computer Science and Dan Blustein in Neuroscience.
  5. Finally, I trekked to snowy Minneapolis, MN, for the 50th SIGCSE conference, where I saw colleagues from undergrad, grad school, and the Pacific Northwest.  What a great meeting – it was worth the cold.

Here’s hoping for warm weather soon.

Sabbatical Part 5

The winter edition:  posters, presentations, and pastries

Yes, you read that right.  First, though, thanks to Romel Hernandez and Reed’s Public Affairs staff for the article on my NSF CAREER award!


four Reed students and alums presented posters on their recent work.  See some of these posters and others on the updated posters page on my website.

  • Current students Sol Taylor-Brill and Kathy Thompson presented their work on CancerLinker – a method to integrate gene expression data from cancer patients in signaling pathway analysis.  They gave a poster at the 2018 Murdock College Science Research Conference in Vancouver, WA.
  • Current student Mattie O’Kelley-Bangsberg presented work from Derek Applewhite’s and my collaboration to find potential regulators of non-muscle myosin II, a protein known to be involved in cellular constriction.  This project involved students from two upper-level biology courses, contributing to both the computational predictions and the experimental validations.  She presented a poster at ASCB/EMBO in San Diego, CA; you can read more in the list of poster abstracts (P3219).
  • Post-baccalaureate Amy Platenkamp presented her work in Derek Applewhite’s lab investigating the regulatory role of the RN-tre protein in non-muscle myosin II’s localization and function.  She also presented a poster at ASCB/EMBO in San Diego, P1104 in the list of poster abstracts.


I gave a talk at BIBM 2018 on my postdoc’s work that integrates protein localization information in signaling pathway analysis.  Our previous work computed many short paths within a protein-protein interaction network to automatically reconstruct a signaling pathway of interest. While this worked better than other methods, we found that some of the paths were not starting at the membrane of the cell and ending in the nucleus — an assumption we impose on intracellular signaling pathways.  In this paper, we show that constraining the paths with proteins that are in the expected place in the cell produces more accurate pathway reconstructions.

Also, Carleton student Kiran Tomlinson gave an excellent talk on his work with CS professor Layla Oesper on the effect of noise in tumor evolution reconstructions.


BIBM 2018 was in Madrid, which was a fantastic place to visit over Spain’s Constitution Day.  The food was amazing – the baked clams at the oldest continuously-operating restaurant in the world, paella Thursday, and the grilled octopus were top-notch.  Then there were the pastries (photos from Mercado de San Miguel):

An adventure to El Escorial also led us to the local chocolate bizcotelas (photo from this blog post, which includes the recipe):

This trip was sabbatical-approved.

View from my office

The weather in Portland is bonkers — low-seventies and sunny for days.  I took a moment to capture the view from my spot in the brand-new Knight Cancer Research Building, where I’m a visiting scientist with Emek Demir’s group in the Computational Biology program at OHSU.  Photo of the pedestrian-and-bus-only Tillikum Bridge with Mt. Hood in the background.


But wait let’s not forget the tree turning colors outside my office window at Reed College:


The rubber chicken has a beautiful view.

Sabbatical Part 4

This fall has has been filled with meetings of all types:

Meeting 1: Pacific Northwest Quantitative Biology (PacNow QB) Meeting
Who: Organized by yours truly and Derek Applewhite.
What: Regional meeting for faculty, researchers, and students interest in quantitative, data-driven biology.
Where: Hosted at Lewis & Clark College (thanks Clarkies!).
When: September 22
Interested? The meeting has been held annually, and includes a student poster session and faculty/researcher invited talks.

Meeting 2: Computational Biology Workshop
Who: Organized by kick-ass computer scientist Layla Oesper.
What: Undergraduate workshop that brought together faculty from five liberal arts institutions to introduce computer science students to applications in biology.
Where: Hosted at Carleton College in Northfield, Minnesota (proudly known as the city of “Cows, Colleges, and Contentment”).
When: September 29-30
Interested? No immediate plans for a future workshop of this type, but all the materials are freely available online.

Meeting 3: Consortium for Computing Sciences in Colleges (CCSC-NW) Regional Meeting
Who: Organized by Kelvin Sung and others, including pretty fantastic women in CS: Tammy VanDeGrift, Haiyan Cheng, and Shereen Khoja.
What: Regional meeting for computer science educators at colleges in the Pacific Northwest, with a focus on CS education.
Where: Hosted at University of Washington, Bothell.
When: October 12-13
Interested? This was my first time and I loved meeting new colleagues.  CCSC-NW is usually held in early October every year, and will be held in the Portland area next year.

And then there’s the crazy beautiful weather here in Portland – fantastic view of St. John’s Bridge in North Portland during a hike in Forest Park:


CMU professors resign due to sexism in the workplace

Yet another example of how sexism can creep into academia: as CMU’s business incubator became more prestigious, its female founder’s role became marginalized.

Read an interview with Dr. Blum in NEXT Pittsburgh: Lenore Blum shocked the community with her sudden resignation from CMU. Here she tells us why.

Coverage from the Pittsburgh Post-Gazette: 2 CMU computer science professors — including founder of Project Olympus incubator — resign

Sabbatical Part 3

After a jaunt to the midwest for ISMB, I spent some weeks with friends and family hiking to waterfalls near Mount Hood and getting excellent views of the Columbia River Gorge.


Columbia River Gorge, from the Washington side (Cape Horn Trail)

Next up was a trip to the Bay area  – the free Cable Car museum was cool to see.


The semester’s in full swing now, with everyone returning to classes (except for the lucky few on sabbatical).  I flew to Washington, D.C. with some undergraduates and gave a talk at the CNB-MAC workshop, a precursor to the ACM-BCB conference.


After some delays getting home, Mt. Hood welcomed me back to PDX.


P.S. I also updated the header image from my July trip back home to Wisconsin – that was a lot of lawn to mow during my high school years.