Our next summer highlight comes from Maham Zia, a recent Reed Physics graduate who has spent time working with cells and cell images in Derek Applewhite’s lab. Maham worked to automate cell density calculations from microscopy images. She’s now a research assistant at the University of Minnesota.
Read Maham’s post on the Reed CompBio Blog: Automate Image analysis using Matlab
If you missed it, read about the Summer 2020 Recap.
Our first summer research highlight comes from Gabe Preising, who graduated from Reed in 2020 and is now working as a post-baccalaureate researcher with me and Suzy Renn to extend his undergrad thesis work. Gabe is working as part of Suzy’s NIH award to study a species of fish where the females do not eat during early parental care because they hold eggs in their mouths (called mouth brooding).
Read Gabe’s post on the Reed CompBio Blog: Nets Full of Fish Brains.
You can read about all the summer research projects in my Summer 2020 Research post. Stay tuned for more highlights!
Thanksgiving break is quickly approaching, and it’s amazing how time flies — that goal of writing a blog post once a week? Try once a semester!
Luckily, there has been one major theme since I’ve started teaching again – conference travel. Undergraduate travel to conferences are a major part of my NSF grant, and I’ve also been making rounds on the conference circuit presenting work students and I conducted during my sabbatical last year.
ISMB/ECCB in Basel, Switzerland. I’ve already talked about the heat wave & the wickelfisch, and I mentioned Ananthan Nambiar’s poster on NLP-based methods for protein family classification. I also presented a poster on pathway connectivity with hypergraphs that has since been published in PLOS Computational Biology. Ananthan was also featured in Reed Magazine’s annual “What is a Reedie?”
Pacific Northwest Quantitative Biology (PacNoW QB) Symposium at OHSU in Portland, OR. This one-day symposium focuses on quantitative and computational biology efforts in Oregon and Washington, encompassing different types of institutions and programs. Tunc Kose and Jiarong Li presented a poster on pathway reconstruction. (They also presented at the Pre-Inauguration Showcase at Reed College in honor of our new president Audrey Bilger).
Such a wonderful, stimulating day of research at the 2019 #PacNowQB conference! PacNow brings together Pacific Northwest colleges and universities and highlights quantitative research across disciplines. @anna_m_ritz @GalbraithLab pic.twitter.com/L3h9k0oFSy
— Derek Applewhite (@ApplewhiteDerek) August 23, 2019
ACM Conference on Bioinformatics, Computational Biology, and Health Informatics (BCB) in Niagara Falls, NY. I was excited to meet the eight undergraduates from the New York area who received travel funds to attend ACM-BCB as part of my NSF grant. The students came from institutions large and small, and got to learn a bit about computational biology. My student Amy Rose Lazarte, who now works at Puppet, also presented a poster on her senior thesis research.
Murdock College Science Research Conference, Vancouver, WA. Tayla Isensee, who was co-advised by Kara Cerveny, presented a poster at the annual conference organized by the Murdock Charitable Trust that celebrates undergraduate research. She also presented at the Pre-Inauguration Showcase earlier in the semester.
IEEE Conference on Bioinformatics and BioMedicine (BIBM) in San Diego, CA. Finally, my upper-level Computational Systems Biology course just returned from sunny San Diego after attending part of BIBM. I presented a workshop paper based on Alex King’s thesis and post-bac work, which should be out soon as an IEEE proceedings. Remarkably, all ten students and I managed the travel with no large holdups!
Many of my summer students also presented posters at the Reed College Poster Session early in the semester (including Karl Young, Jiarong Li, Tunc Kose, and Tayla Isensee), which highlighted computational biology at Reed. I’m looking forward to continuing the tradition of conference attendance and presentations of Reed student work!
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:
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).
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….
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.
Data plotted from NSF Table 14: Doctorate recipients, by broad field of study and sex
Bad news: according to the same table, the gender gaps are still large for physical & earth sciences, math & CS, and engineering.
Data plotted from NSF Table 14: Doctorate recipients, by broad field of study and sex
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.”
An online presence has become an important professional networking tool, and offers a low-stakes way to connect with the public. The social media giant Twitter has been leveraged for this purpose, and articles at venues such as PLOS Biology and AAAS have promoted Twitter and other social media for use by scientists. At a time where we increasingly emphasize Open Science and Open Data and manuscript preprints are becoming commonplace (even in biology), Twitter is yet another way to communicate your research quickly.
Me, crawling out from under a rock.
So, I decided to join Twitter (@anna_m_ritz). I know, I’m slow to the game. Joining is like jumping off the high dive — social media is something I was used to doing a long time ago, and something I can do again but it’s going to take some work. I’m getting the hang of it — the following, the liking, the retweeting, the tweeting — and I was struck by some immediate reactions. Naturally, I thought I’d write a blog post.
I immediately felt more connected to my scientific community. Reading tweets about scientific accomplishments (preprints, talks, posters, publications, grants, awards) and frustrations (data availability, proposal rejections, sexism in STEM) put these ideas in the context of happening right now.
Twitter is the place to advertise, even in science. This means tweeting your recent manuscript, a new postdoctoral position in your lab, or an upcoming talk at a meeting.
There is so much to catch up on. My list of bookmarked tweets of relevant preprints grows by the day. I’m comforted by the fact that these preprints are papers I’d see months from now and need to read then. So I’m saving my future self time…?
Most of the people I follow are men. For now. This is depressing, and came about because I started with following my computer science colleagues who are, let’s face it, mostly men. I’ve been seeking out women in the field to follow, and hope to achieve a better balance here.
I always love a good photograph…and here’s Nature‘s 2018 #ScientistsAtWork winner.
More information and other amazing runner-up photos are in the full article: A photo celebration of scientists at work by Jack Leeming.
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:
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.
Ritz Bits 
