As is always the case when I do this exercise, I can’t help but reflect back on 2022 (and 2021) with gratitude and appreciation for my amazing collaborators. It was my first year on the tenure-track and hours that normally would have been spent pushing research forward were instead spent getting my feet under me, taking on new students, hiring new postdocs, building up some community partnerships, shuffling through administrative tasks, etc. There’s a lot of things I enjoy about the job but by far the most enjoyable thing is working on things I think are interesting and important with people I like.

Below is a plot of collaborations (circles) over time (x-axis) by collaborator (y-axis). The grey ones are collaborators I’ve never actually met in person while the black ones are collaborators I’ve met in person. I had assumed COVID would have impacted collaborations such that there would be many more collaborators I’ve never met in person but that doesn’t seem to be the case.

Here is a set plot of my top ten collaborators (in terms of numbers of collaborations) and their different sets. Surprisingly, this list has changed pretty substantially since 2020 with a core group of UCSF researchers (Kirsten, Maria, and Yea-Hung) shooting up the list. 

Conditional on having more than one collaboration, who are my “most efficient” collaborators in terms of average number of citations per project?

And lastly, do COVID-19-related papers get more citations than non-COVID papers? Below I plot all papers published since 2020 along with their annual citations. The ribbons and bold lines represent the linear fit. As you can see, COVID papers have both a higher intercept (they get more immediate citations) and a slightly higher slope (they are cited more over time) that is probably not statistically significant. 

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A couple related items:

• Our (fully reproducible) code is available on Github.
• The data we used for all simulations is too large for Github but is available on OSF.
• The published version is substantially improved (thanks to six very thorough peer reviewers), but here’s the original pre-print.
• UCSF put out a press release here.
• Nathan’s informative tweetorial about the paper is here.
• SF Chronicle coverage.
• The correction notice resulting from Dr. Lee Altenberg’s letter which pointed out an error in how we calculated the post-quarantine infectious days. We thank Dr. Lee Altenberg for finding and reporting this error.
• Our reply to both Dr. Altenberg’s letter and Dr. Mohammad Shahid’s letter.

In addition to (hopefully) being useful, this project was a lot of fun — especially considering the urgency. A lot of time was saved because it was built on open-source code from another paper. Still, this one went from an idea Nathan and I chatted about to a pre-print in a little over a month, went through expedited review (fun fact: that’s what the little bird icon is on the top of some Lancet papers) in a month, then returned back to the journal with revisions and accepted in about another month, and finally went through a couple rounds of super helpful editorial revisions and proofing in a month.

When it was all said and done, we went from an idea to a published manuscript in just under 5 months. I’ve literally had other papers under review for that entire duration — The Lancet journals are not messing around when they call it expedited review. Special thanks to Elizabeth Chin for help with the coding infrastructure and Nathan Lo for supervising the whole thing.

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