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!

Posters2018-thompson-taylor_brill-cancerlinker

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.

Presentationsinvalid-paths

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.

Pastries

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.

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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:

20181014_102423

Time-to-parity for women publishing in STEM fields

A recent paper by Holman et al. in PLOS Biology presents a new look at the gender gap in publications for millions of authors from over one hundred countries in over six thousand journals.  You can interact with the data through their  web app.

The gender gap in science: How long until women are equally represented?
Luke Holman, Devi Stuart-Fox, Cindy E. Hauser, PLOS Biology 2018.

The authors present the current author gender ratio, its rate of change per year, and the estimate number of years until the gender ratio comes with 5% of parity.  A few notes below the image…

Here are the first things I noticed:

  1. The estimated percent of women authors “maxes out” at 50% (there’s a Figure 2 that includes fields with a higher percentage of women).
  2. arXiv.org – the preprint server that began as a mathematics and physics venue – has particularly poor percent of women authors.
  3. First author percentages tend to be “ahead of the curve” for each discipline, while last authors lag behind the numbers for all authors.  In many fields, first authors denote who did the most work, and last authors denote who funded the work.  My hunch is that a higher proportion of women get papers as graduate students and postdocs, whereas fewer women make it to senior-level faculty as heads of a lab.
  4. On a positive note, more women are publishing in the fields than before (the rate of change is mostly positive).

The paper’s supplementary figure S3 shows data for Computer Science (from arXiv).  Based on current trajectories, only two sub-categories (Information Theory and Robotics) hope to see gender parity within the next 50-100 years.  We still have a long way to go.

New Reed CompBio Blog

As part of a recently-funded collaborative REU (generously supported by the CRA-W), my colleague Derek Applewhite and I are working with undergraduates to study machine learning methods to predict genes that regulate cell movement patterns in schizophrenia.  The team will post their work on new a Reed College blog, The Pathway Not Taken, and I may re-post selected pieces here.  The first post gives a general idea of the problem we will work on, and how biology and computer science are intertwined in the project.

Field Trip! Computational Biology on the Road

A few weeks ago I took my students to the Association Computing Machinery Conference on Bioinformatics, Computational Biology, and Health Informatics (ACM-BCB) in Seattle, WA.  It was a fantastic experience for everyone involved – the organizers did an excellent job running the conference.  I asked my students to reflect on the conference, and I figured I should do the same.

With such a large cohort of undergraduates at a scientific conference, my role shifted to encompass one of an educator as well as a researcher.  I honed in on the accessibility of the material in talks, feeling a bit of pride when the speakers showed an image or mentioned a topic I have taught in class.  I also had some moments of “wow, should have taught them that” when a speaker presented a fundamental concept we have not yet covered.  Many of my students came out of sessions excited about what they had just learned – they talked with the speakers, asked for their papers, and are now delving into this new material.  Graduate student attendees became mentors, fielding questions about why they went to graduate school and how they picked their research topic.

ACM-BCB was an ideal size – the conference had compelling talks and tutorials while being small enough to chat with the keynote speakers and conference organizers.  I caught up with existing colleagues and met some potential collaborators in the Pacific Northwest.  I also found myself in discussions with  graduate students about my position in a liberal arts environment.  Reed had a research presence, since three Reed students submitted posters to the poster session.  My students had garnered enough research experience — either through their thesis, summer research, or independent projects in class — to have engaging conversations with other attendees.

Finally, the trip to ACM-BCB as a class taught everyone (including me) the importance of logistics.  Some gems:

  1. Make sure the taxi to the train station can fit the entire group.
  2. Remember who you gave the posters to in your mad dash to find parking before your train departs (see #1).
  3. Make sure your PCard credit limit is set so it’s not declined at the hotel.
  4. Tell your students the correct time of the first keynote.

And the question of the day: is a (very detailed) receipt for a can of soda written on a napkin by a bartender reimbursable?

My Dream Job, Part 4

As of August, I am an Assistant Professor of Biology at Reed College.  In this series of blog posts, I will explain why I chose this environment as my academic landing pad (or launching pad).

Part 4:  Being in a Biology Department changes my perspective.

With one semester under my belt, I took some time this break to reflect on my position at Reed.*  As I begin teaching another round of Introduction to Computational Biology, I will try to articulate why I find my position so exciting.

The students who are taking my classes have had a mixture of backgrounds, but most of them major in the natural sciences.  Up to this point, I have been surrounded by people with strong backgrounds in math and computer science.  As a result, students ask questions that have a completely different underlying motivation than the questions I’ve received in talks and research meetings.  I walk a fine line between oversimplifying the biology in order to describe a problem in computational terms and oversimplifying an algorithm in order to describe how it is applied to a biological concept.  In some ways, this makes teaching class hard.  Talk about inviting the imposter syndrome to step in when you have to answer “I don’t know” in class more than once.  Yet it also makes class engaging, unexpected, and fun.  Add to that an occasional power pose, and teaching is very satisfying.

so-try-that-power-pose

Screenshot from Amy Cuddy’s TED Talk (provided from a blog post by Amy Neuzil)

I am currently one of two tenure-track computer scientists at Reed.  We are at the cusp of establishing a computer science program: students are excited, funds have been acquired, and an active search is underway. I feel like much of the incredibly hard work has been done, and I get to show up for the fun part.**  This momentum has trickled over to the Biology Department through the students I advise and teach.

The other computer scientists at Reed are affiliated with the Math Department.  One might think that being in a different department from the faculty who are “most like me” may make my research life isolating.  Instead, I may just have the best of both worlds.  I get to sit in the same department as my biological collaborators, while networking with faculty in the Math Department to establish computational research collaborations.  Put simply, I love being interdisciplinary.  I deeply appreciate the flexibility that Reed offers in designing my courses to be hybrids of two fields.

My professional identity is quickly becoming steeped in teaching interdisciplinary courses and conducting research across departments.  Over the next few years, my research will undoubtedly become more applications-focused as I co-advise more student projects with Biology faculty. Yet there is enough interest at Reed, from both faculty and students, for me to continue algorithmic research.

*It’s been a while since I posted. Consider it a Spring semester resolution to start posting more.

**This might be naive, but hey, I’m an optimist.