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.
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.
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:
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.
We are right smack in the middle of summer — my undergraduate research group is doing great as they wrap up the last few weeks of their projects, with plans to present work at conferences. Keep an eye out for posters (and even papers!) at some of these venues:
Last week I had the chance to attend ISMB in Chicago, where I met with old and new colleagues in computational biology. My postdoc Ibrahim Youssef also presented a poster on his recent work on signaling pathway reconstruction algorithms. The weather cooperated and Chicago was wonderful.
View from Michigan Avenue – the ISMB venue location was fantastic.
Sabbatical, you do not disappoint.
It’s official — my junior sabbatical (technically “junior leave”) has begun. I’m free from teaching, college service, and academic advising for a whole year. I’m being paid part-time, but it’s worth it!
In addition to the mountain of research-related goals I’ve set for myself, I also want to get outside and explore more of the area. I’ve succeeded so far, spending the first weekend visiting colleagues at UC Merced and hiking in Yosemite.
Ok, so not every weekend’s going to get views like this one. I’ve been also doing some long bike rides in Portland (long for me, at least) — part of the 10 best rides in Portland, a map that has quickly become my go-to guide. Last weekend I biked to the summit of McKenzie Pass — the views were as good as I had heard, including the vast lava fields near the top.
So far, the start of sabbatical has been great.
P.S. My summer students are maintaining a blog of their research – The Pathway Not Taken – check it out!