Rich Abdill

Bioinformatics person

About

Who I am

My name is Rich. I live in New Jersey. I hang out with two cats, two dogs and a lovely woman named Lauren. My hobbies include genealogy and ruining home improvement projects. My favorite color is green, but it used to be blue. My favorite book is Catch-22, and my favorite sport is spreadsheets (so... baseball).

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Illustration by Ethan Kocak

What I do

I'm currently a PhD candidate at the University of Minnesota studying bioinformatics and computational biology under Dr. Ran Blekhman, whose research focus is on the human gut microbiome—in short, studying the bacteria that colonize the human body (there are... a lot of them in there), how they affect human health, and what role our DNA plays in managing the whole process. My current research is about how we can apply machine learning techniques to large collections of metagenomic data to measure hard-to-find ecological patterns that may be linked to disease.

I am also a senior software engineer at Dimensions, where I build reporting and visualization tools for bibliometrics data. Previously, I worked as a system programmer at the Minnesota Supercomputing Institute, and before that as a developer or consultant at companies including USA Today, Target and Amazon Web Services, with a focus on infrastructure automation and cloud architecture.

Research

Publications: Meta-research

I'm very interested in the "science of science," particularly the dynamics of the scientific publishing system. All my publications are on my Google Scholar page, but here are my first-author papers:

Tracking the popularity and outcomes of all bioRxiv preprints

Abdill RJ & Blekhman R
eLife (2019). doi: 10.7554/eLife.45133

The growth of preprints in the life sciences has been reported widely and is driving policy changes for journals and funders, but little quantitative information has been published about preprint usage. Here, we report how we collected and analyzed data on all 37,648 preprints uploaded to bioRxiv.org, the largest biology-focused preprint server, in its first five years. The rate of preprint uploads to bioRxiv continues to grow (exceeding 2,100 in October 2018), as does the number of downloads (1.1 million in October 2018). We also find that two-thirds of preprints posted before 2017 were later published in peer-reviewed journals, and find a relationship between the number of downloads a preprint has received and the impact factor of the journal in which it is published. We also describe Rxivist.org, a web application that provides multiple ways to interact with preprint metadata.

Rxivist.org: Sorting biology preprints using social media and readership metrics

Abdill RJ & Blekhman R
PLOS Biology (2019). doi: 10.1371/journal.pbio.3000269

Preprints have arrived. In increasing numbers, researchers across the life sciences are embracing the once-niche practice, shaking off decades of reluctance and posting hundreds of papers per week to preprint servers, sharing their findings with the community before embarking on the weary march through peer review. However, there are limited methods for individuals sifting through this avalanche of research to identify the preprints that are most relevant to their interests. Here, we describe Rxivist.org, a website that indexes all preprints posted to bioRxiv.org, the largest preprint server in the life sciences, and allows users to filter and sort papers based on download metrics and Twitter activity over a variety of categories and time periods. In this work, we hope to make it easier for readers to find relevant research on bioRxiv and to improve the visibility of preprints currently being read and discussed online.

International authorship and collaboration across bioRxiv preprints

Abdill RJ, Adamowicz EM & Blekhman R
eLife (2020). doi: 10.7554/eLife.58496

Preprints are becoming well established in the life sciences, but relatively little is known about the demographics of the researchers who post preprints and those who do not, or about the collaborations between preprint authors. Here, based on an analysis of 67,885 preprints posted on bioRxiv, we find that some countries, notably the United States and the United Kingdom, are overrepresented on bioRxiv relative to their overall scientific output, while other countries (including China, Russia, and Turkey) show lower levels of bioRxiv adoption. We also describe a set of ‘contributor countries’ (including Uganda, Croatia and Thailand): researchers from these countries appear almost exclusively as non-senior authors on international collaborations. Lastly, we find multiple journals that publish a disproportionate number of preprints from some countries, a dynamic that almost always benefits manuscripts from the US.

Tools and projects

Writing

Get in touch

Email is best: rabdill@umn.edu.

Public key

(Verifiable at keybase.io)

Ephemera

Fun with networks

My Erdős–Bacon number is 8.

My Erdős number is 4:

  1. I co-authored a paper with Eleazar Eskin,
  2. who co-authored a paper with Eran Halperin,
  3. who co-authored a paper with Noga Alon,
  4. who co-authored a paper with Paul Erdős.

My Bacon number is 4, if you allow a TV appearance as the origin node:

  1. I was on the Nancy Grace Show with Nancy Grace,
  2. who appeared in A Lawyer Walks into a Bar with Robert Shapiro,
  3. who appeared in Burn Hollywood Burn with Billy Bob Thornton,
  4. who appeared in Jayne Mansfield's Car with Kevin Bacon.