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Clif McKee

@clifmckee.bsky.social
213 followers 106 following 13 posts

research associate @ Johns Hopkins | ecology of 🦇 and their 🦠, runner 👟, birder 🐦, he/him

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Reposted by Clif McKee
Justine Debelius @jwoodelius.bsky.social · 11/08/2026
How do people combine their 16S human microbiome studies and what do they call them? Check out our scoping review in AJE advances. @ajeadvances.bsky.social academic.oup.com/ajeadvances/... TL;DR: Lots of heterogeneity in methods, analysis, reporting: we need field standards (1/7)
academic.oup.com
In harmony? A scoping review of methods to combine multiple 16S amplicon datasets
Abstract. Robust evidence on relationships between the human microbiome and health is critical for understanding and improving the human condition. However
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Clif McKee @clifmckee.bsky.social · 04/05/2026
Students who take this intensive two-week course say they were immediately able to start working with some of their own research data by the end of the sessions. The course runs June 8-19, 2026. Hope to see some of you there! 👉 Registration is now open. publichealth.jhu.edu/academics/gr...
publichealth.jhu.edu
Graduate Summer Institute of Epidemiology and Biostatistics | Johns Hopkins Bloomberg School of Public Health
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Clif McKee @clifmckee.bsky.social · 04/05/2026
I’ll be teaching our Intro to R course at the Summer Institute of Epidemiology & Biostatistics in June. The course focuses on the basics of data wrangling, analysis & visualization and is designed for students, clinicians & public health professionals who want hands-on, real-world training.
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Clif McKee @clifmckee.bsky.social · 16/02/2026
And Brent Jones' paper in Parasites & Vectors showed that bat fly populations in Australia have consistent seasonal population changes with peaks in summer and decreases during winter, though changes in Bartonella prevalence were asynchronous and less pronounced. doi.org/10.1186/s130...
doi.org
Asynchronous seasonal dynamics of nycteribiid bat flies and Bartonella spp. in Australian flying foxes (Pteropus spp.) - Parasites & Vectors
Background Bat flies are ubiquitous ectoparasites of bats, recognised as potential vectors for viral and bacterial transmission between individual bats within a roost. Despite this, little is known ab...
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Clif McKee @clifmckee.bsky.social · 16/02/2026
Dan Crowley's paper in Journal of Animal Ecology showed that Bartonella infection rates were consistent across birth cohorts of immature flying foxes, indicating that opportunities for pathogen transmission remained consistent over time. doi.org/10.1111/1365...
doi.org
Cohorts of immature Pteropus bats show interannual variation in Hendra virus serology
Pteropus bat with offspring, photo taken by Manuel Ruiz-Aravena.
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Clif McKee @clifmckee.bsky.social · 16/02/2026
This paper came out concurrently with a few others that I coauthored with colleagues in the BatOneHealth group that include related data on Bartonella and bat flies in Australian bats. Really interesting to see how ubiquitous and prevalent these bacteria are across multiple bat species!
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Clif McKee @clifmckee.bsky.social · 16/02/2026
The paper sat on bioRxiv for a few years while I tried to carve time out to revise the paper to send to another journal. Definitely not ideal and there are lots of things I would do differently 😅 But a good lesson in persistence! Get those old papers off the back burner and send them out again!
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Clif McKee @clifmckee.bsky.social · 16/02/2026
I started on this project in 2013 during my Master's, but decided to hold it for my PhD. I then finished all the lab work in 2017 and the data analysis in 2019. Drafting the manuscript took a few more years after I had started my postdoc, then it got rejected from the first journal I sent it to 🫠
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Clif McKee @clifmckee.bsky.social · 16/02/2026
The study provides some of the first experimental evidence that bat flies are vectors of Bartonella, which we had long suspected based on observational studies. The study also turned into a neat opportunity to investigate some of the ecological forces that shape communities of parasites over time.
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Clif McKee @clifmckee.bsky.social · 16/02/2026
I'm so excited to have the last chapter of my PhD OUT!! Based on a longitudinal study of captive fruit bats in Ghana, we show that a decline in the population density of bat flies resulted in decreased Bartonella prevalence, which then rebounded when flies were restocked. doi.org/10.1017/s003...
doi.org
Manipulating vector transmission reveals local processes in Bartonella communities of bats | Parasitology | Cambridge Core
Manipulating vector transmission reveals local processes in Bartonella communities of bats
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Clif McKee @clifmckee.bsky.social · 16/02/2026
If you’re looking to strengthen your skills in data wrangling and analysis, I’d love to have you join my course. 👉 Registration is now open. publichealth.jhu.edu/academics/gr...
publichealth.jhu.edu
Graduate Summer Institute of Epidemiology and Biostatistics | Johns Hopkins Bloomberg School of Public Health
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Clif McKee @clifmckee.bsky.social · 16/02/2026
I’m excited to be teaching “Introduction to R for Public Health Researchers” at the 44th Summer Institute of Epidemiology & Biostatistics this June! 🗓️ June 8-19, 2026 📊 Short, intensive course with practical, applied skills 🌍 Online Hybrid
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Clif McKee @clifmckee.bsky.social · 23/10/2025
As a long-time Zotero user, this feels illegal. How did I not know you could do this?!
blog.stephenturner.us
Switching word processors with Zotero
Moving from Google Docs to Word will break your Zotero citations/bibliography linkages unless you do this first.
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Clif McKee @clifmckee.bsky.social · 25/07/2025
Say hello to my little friends.
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Reposted by Clif McKee
Jane Qiu, PhD @janeqiu.bsky.social · 08/04/2025
Mpox has inflicted Africa since 1970 but its origins remain a mystery Thanks to long-term surveillance, scientists were able to pinpoint a squirrel species as the source of mpox outbreak But is it the reservoir? Or is it part of a network of reservoirs? My latest in @nature.com shorturl.at/lY7Kf
shorturl.at
An animal source of mpox emerges — and it’s a squirrel
Researchers solve the mystery of a disease outbreak through long-term surveillance of wildlife in Africa.
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Reposted by Clif McKee
Benny Borremans 🇧🇪🇺🇸 @bennyborremans.wildlifehero.org · 27/12/2024
Disease ecologist starter pack -- reply with people/organizations to be added or with related lists/feeds #diseaseecology 🦠🐀🦠🦇🦠🦭🦠🦆🦠 go.bsky.app/RwAuiNT
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Reposted by Clif McKee
Bat1K Genome Project @bat1kgenomes.bsky.social · 29/01/2025
🚨Bat1K Paper Alert🚨There couldn’t be a better first post for us on this app - excited to share 10 new bat genomes and groundbreaking insights into bat immunity and viral resistance! 🌍🔬 www.nature.com/articles/s41...
nature.com
Bat genomes illuminate adaptations to viral tolerance and disease resistance - Nature
A systematic analysis of 115 mammalian genomes, including 10 new bat genomes, reveals prevalent positive selection in immune genes in bats and shows key adaptations in the antiviral gene ISG15 that ai...
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