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!

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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.

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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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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.

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

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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:

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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.

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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.

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

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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.

NIH Funding by Gender – A Rollercoaster Ride

Nature came out with a News article reporting that, for women who land a large NIH grant, their mid- and late-career funding tracks about the same as men.

Leaky pipeline for women scientists dries up after they win first big grant

Sounds promising, right?  But there’s more to the story.  The original article published in PNAS by Lisa A. Hechtman et al, gives more details (including those listed below).

Good news: women now earn more doctorates in the life sciences, comprising 55% of the recipients in 2016.  This trend has held since 2006, according to the NSF’s statistics.

Bad news: according to the same table, the gender gaps are still large for physical & earth sciences, math & CS, and engineering.

But that’s for another post.

Bad news: despite the gender parity in doctorate recipients, women are underrepresented among assistant professors (even accounting for a postdoctoral research delay).

Bad news: women submit less than one-third of NIH research proposals, according to the NIH.

 

Good news: women who do submit NIH research proposals are as successful as men in obtaining first-time grants.

Good news: the paper studied “funding longevity” among first-time grant awardees between 1991 and 2010, and found that women’s success in securing funding over their careers in this cohort were nearly as good as men (there’s still a gender gap, but it’s small).

Bad news: other gender differences exist when comparing men and women in this cohort of investigators, though the differences are smaller than the previous numbers.  For example, women are less likely to attempt to renew grants and are less successful in the NIH grant renewal process, which is a factor that leads to sustained funding for both genders.

So a mix of good news and bad news, some signs of progress, and indications of where career support may stop the “leaky pipeline.”