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michael catchen

@mdcatchen.bsky.social
4.3K followers 488 following 70 posts

data scientist/research software engineer, Schmidt Center for Data Science and Environment @ UC Berkeley. building open software for bioacoustic monitoring. phd in ML for biogeography of species interaction networks. gottacatchenall.github.io he/him

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Reposted by michael catchen
Colin Carlson @colincarlson.bsky.social · 15/09/2026
It's sort of generally accepted within ecology that Michael is a rare triple threat (brilliant, makes the best figures I've ever seen, and a poster at heart), but this is really some of the coolest work I've seen people share on here in a while. Check it out 👇
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michael catchen @mdcatchen.bsky.social · 15/09/2026
Thanks Colin!
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michael catchen @mdcatchen.bsky.social · 15/09/2026
the most interesting thing i worked on during my phd is now out as a preprint. ecoevorxiv.org/repository/v...
ecoevorxiv.org
Designing optimal biodiversity observation networks
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michael catchen @mdcatchen.bsky.social · 15/09/2026
it still has pretty figures, i promise!
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michael catchen @mdcatchen.bsky.social · 15/09/2026
the most interesting thing i worked on during my phd is now out as a preprint. ecoevorxiv.org/repository/v...
ecoevorxiv.org
Designing optimal biodiversity observation networks
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Zach Weinersmith @zachweinersmith.bsky.social · 11/09/2026
Very forceful statement by Terry Tao about AI and math. terrytao.wordpress.com/2026/09/11/a... Note, he is not claiming the models aren't real and powerful. He's talking about how that power should be used. This, I believe, is what all AI discussions should center.
terrytao.wordpress.com
A Severe Misalignment of AI in Mathematics
I am proud to be among the list of 25 initial signatories — all Fields Medallists — to the declaration below, which grew out of discussions between ourselves over the last week. We have…
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Colin Carlson @colincarlson.bsky.social · 09/09/2026
🚨 NEW: Biodiversity monitoring can guide surveillance for emerging pathogens. In a new PLOS Ecosystems study led by @mdcatchen.bsky.social, we present computational algorithms to select surveillance sites that capture the most actionable data. Out now: dx.plos.org/10.1371/jour...
Fig 3. The case study for South Korea.

(A): Bivariate plot of dose (increasing green) and dose uncertainty (increasing blue). (B): Bivariate plot of dose (increasing green) and prevalence uncertainty (increasing orange; measured as the sum of estimated variance from kriging across each host-virus pair). (C): The spatial strata for which occurrence, prevalence, and both forms of sampling should occur (see main text for how these are computed). (D): The priority scores for regions where discovery sampling is a priority (increasingly blue) and prevalence sampling is the priority (increasingly purple) in their respective strata. (E): The total priority map with sites selected using Balanced Acceptance Sampling. The marker shape of each site corresponds to the type of sampling that should occur there, based on the stratum in (C) that each point falls within. Administrative boundaries come from GADM.
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michael catchen @mdcatchen.bsky.social · 08/09/2026
Now out in PLOS Ecosystems! doi.org/10.1371/jour...
doi.org
A protocol for biodiversity-informed wildlife disease surveillance
Author summary The majority of infectious diseases that infect humans are zoonotic, meaning they circulate in wildlife populations and human infections arise from contact with wildlife, leading to tra...
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michael catchen @mdcatchen.bsky.social · 08/09/2026
Now out in PLOS Ecosystems! doi.org/10.1371/jour...
doi.org
A protocol for biodiversity-informed wildlife disease surveillance
Author summary The majority of infectious diseases that infect humans are zoonotic, meaning they circulate in wildlife populations and human infections arise from contact with wildlife, leading to tra...
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Reposted by michael catchen
John C. Baez @johncarlosbaez.bsky.social · 20/07/2026
Mathematician Levent Alpöge found a counterexample to the Jacobi conjecture using Claude Fable! This conjecture claims that if F: ℂⁿ→ℂⁿ is a polynomial map whose Jacobian is invertible at each point, F has a polynomial inverse. Open since 1939. But no more! (1/n)
en.wikipedia.org
Jacobian conjecture - Wikipedia
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Reposted by michael catchen
Chuliang Song @clsong.com · 16/06/2026
Spent the last two years developing a new Intro to Physics course for undergrad biology majors. It features tons of examples from biology (especially Ecology & Evolution!) and requires only middle school-level math. Lecture note here shorturl.at/0PiVp Any comments or feedback are highly welcome!
drive.google.com
physics_for_biologists.pdf
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michael catchen @mdcatchen.bsky.social · 17/06/2026
Thanks Kari!
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michael catchen @mdcatchen.bsky.social · 17/06/2026
all done with great field and theoretical collaborators: with Paul CaraDonna, Jane Ogilvie, @julianresasco.bsky.social @ctrlalttim.com @laura-pollock.bsky.social @bio-diverse.bsky.social. Read the preprint here: doi.org/10.32942/X2D...
doi.org
Projecting the vertical disassembly of the bumble bee pollination network of the Southern Rocky Mountains
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michael catchen @mdcatchen.bsky.social · 17/06/2026
In the hardest-hit spots, up to half of local interactions are lost, with the potential for new gained interactions not keeping up. But -- that mismatch map is also a priority map for monitoring the impact of network change on ecosystem function and implementing conservation action.
Scientific figure showing hotspots of projected losses of interactions in a bumble bee pollination network.
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michael catchen @mdcatchen.bsky.social · 17/06/2026
🚨 New preprint! What happens to bumblebee pollination networks as species ranges shift due to climate change? 🐝🪻🕸️ In the Rocky Mountains, we predict these networks are becoming "vertically disassembled" as the ranges of interacting species shift upward in elevation at different rates.
Scientific figure depicting species elevational range shifts under three different climate scenarios in the top left, and bivariate plots depicting hotspots of species gain and loss in the southern rocky mountains on the right.
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Ben Bolker @bbolker.bsky.social · 10/06/2026
new diamond open-access Journal of Statistical Ecology launched 🎉🎉🎉 jse.centre-mersenne.org @fredbarraquand.bsky.social @oaggimenez.bsky.social @marieaugermethe.bsky.social @vianeylb.bsky.social (apologies to any Bsky editors I missed)
jse.centre-mersenne.org
Journal of Statistical Ecology Journal of Statistical Ecology
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Timothée Poisot @ctrlalttim.com · 19/05/2026
Are interacting species showing more similar responses to environmental predictors than expected by chance? Is this similarity protecting species pairs from interaction disruption under climate change? If you want to find out, join us for a fully funded Ph.D. with @epic-biodiversity.org 🌎🧪
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ÉPICBiodiversity @epic-biodiversity.org · 12/05/2026
Information about species interactions is very scarce! In a new preprint, @gabdans.bsky.social shows that the methodology that enables biodiversity monitoring and reporting also supports the detection of species interactions, leading to multi-use monitoring. epic-biodiversity.org/blog/2026/05...
epic-biodiversity.org
Where should we look to monitor species interactions? | ÉPICBiodiversity
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michael catchen @mdcatchen.bsky.social · 07/02/2026
nolanlawson.com/2026/02/07/w...
nolanlawson.com
We mourn our craft
I didn’t ask for this and neither did you. I didn’t ask for a robot to consume every blog post and piece of code I ever wrote and parrot it back so that some hack could make money off o…
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David Berman Bot @davidbermanbot.bsky.social · 04/02/2026
The alleys are the footnotes of the avenues
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michael catchen @mdcatchen.bsky.social · 05/02/2026
need to focus on exploration more. with the right approach that downside could easily be 99.9%+
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michael catchen @mdcatchen.bsky.social · 04/02/2026
thanks! @ctrlalttim.com can speak to the reasons Literate was initially chosen more, but I use it because I write the standalone .jl script to implement a given doc page's code first, and then go back and write the explanations. I find it more convenient than annotated codeblocks in markdown
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michael catchen @mdcatchen.bsky.social · 04/02/2026
For SpeciesDistributionToolkit we use Literate to DocumenterVitepress with some (a bit hacky) tricks to make code for figures collapsable github.com/PoisotLab/Sp.... I've adopted the same setup for other projects too
github.com
GitHub - PoisotLab/SpeciesDistributionToolkit.jl: Work with species distributions in Julia
Work with species distributions in Julia. Contribute to PoisotLab/SpeciesDistributionToolkit.jl development by creating an account on GitHub.
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michael catchen @mdcatchen.bsky.social · 15/12/2025
Read it here: ecoevorxiv.org/repository/v...
ecoevorxiv.org
A protocol for biodiversity-informed wildlife disease surveillance
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michael catchen @mdcatchen.bsky.social · 15/12/2025
🚨🐭🦠 New preprint! Monitoring wildlife disease is expensive, so we need to be smart about where we sample to get as much useful info as possible. We show how SDMs can guide adaptive sampling for zoonotic disease surveillance, using case studies in rodents.
A conceptual figure outlining a protocol for using species distribution models to prioritize sampling for pathogens in wildlifeA scientific figure showing a case study of the protocol applied to Arenaviridae in rodents in India
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Timothée Poisot @ctrlalttim.com · 15/12/2025
This is, not a joke, one of my favourite papers in a long time. Absolutely stellar co-authors, but also a straight line from "nitpicky little nerds obsessing over sampling" to "translational research with clear implications for management". Go read all about it here: ecoevorxiv.org/repository/v...
ecoevorxiv.org
A protocol for biodiversity-informed wildlife disease surveillance
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ÉPICBiodiversity @epic-biodiversity.org · 15/12/2025
🧪 New @mdcatchen.bsky.social preprint! Here's how we can decide where to look for wildlife disease, based on combinations of biodiversity, uncertainty, and prevalence data. This is a really cool paper, that is pushing the boundaries of what we can do with sampling and monitoring techniques.
epic-biodiversity.org
Effective sampling of wildlife disease from biodiversity data | ÉPICBiodiversity
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Reposted by michael catchen
Jelena Pantel @jhpantel.bsky.social · 13/12/2025
I'm just worried. Even pre-AI, it was really pulling teeth to get some (not all) PhD students to take the time to look up the formula the R package used, make sure its what they actually want to calculate, and validate what R spits out (note: I don't take students like this anymore)
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Timothée Poisot @ctrlalttim.com · 11/12/2025
Noteworthy because it was my first time adding a polygon provider using the interface @mdcatchen.bsky.social built for one of our component packages 🎉
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Nicholas Landry @nwlandry.bsky.social · 25/11/2025
One week left to apply to the UVA Biology PhD program! If you or someone you know are interested in contagion from a complex systems perspective, please reach out! I'm looking for a grad student! bio.as.virginia.edu/how-apply-gr...
bio.as.virginia.edu
How to Apply to the Graduate Program
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michael catchen @mdcatchen.bsky.social · 24/11/2025
sometimes you write interesting sentences in ecology
the phrase "but we see a large increase in absolute loser bees" in an excerpt from a draft scientific manuscript
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David Berman Bot @davidbermanbot.bsky.social · 06/11/2025
And like a brown bird nesting in a Texaco sign I got a point of view
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Vadim Karatayev @lifenonlinear.bsky.social · 30/10/2025
Hi all! I am seeking an ecology or applied math PhD student interested in quantitative ecology, specifically ecological theory, food web modeling, or population dynamics. If you are interested, have a look at our lab website below and reach out to me. resiliencelab.github.io/join/
resiliencelab.github.io
Join Us
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David Berman Bot @davidbermanbot.bsky.social · 25/10/2025
My friends, don’t you know that I never want this minute to end? And then it ends.
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michael catchen @mdcatchen.bsky.social · 18/09/2025
Thanks Austin!
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Timothée Poisot @ctrlalttim.com · 18/09/2025
Our software paper on SpeciesDistributionToolkit.jl is now published in @peercomjournal.bsky.social - peercommunityjournal.org/articles/10....
peercommunityjournal.org
A Julia toolkit for species distribution data
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David Berman Bot @davidbermanbot.bsky.social · 13/09/2025
What kind of animal Needs to smoke a cigarette? Grass in the pasture Is sharper than a bayonette Sometimes a pony Sometimes a pony Sometimes a pony gets depressed
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David Berman Bot @davidbermanbot.bsky.social · 08/09/2025
When I go downtown, I always wear a corduroy suit, ’cause it’s made of a hundred gutters, that the rain can run right through.
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Johan Ugander @jugander.bsky.social · 24/08/2025
A beautiful visualization of the state space of puzzles, 11 min of joy, h/t @danlarremore.bsky.social
youtube.com
Adventures in State Space
YouTube video by 2swap
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stuart @stuartp.bsky.social · 01/07/2025
you have been visited by "Le Boulanger Quebecois" repost to receive his blessing
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Timothée Poisot @ctrlalttim.com · 30/06/2025
🦠🌿🐦🧪 How can biodiversity monitoring help global efforts in disease surveillance? With ✨ fantastic ✨ colleagues from @viralemergence.org and the @geobon.org working group on One Health, we try to identify three key lessons for the future. 🧵 A short thread! academic.oup.com/bioscience/a...
academic.oup.com
Biodiversity science and biosurveillance are fellow travelers
The failure to meet the Aichi targets to alleviate global biodiversity decline (Nature 2020) was a wake-up call to the biodiversity monitoring community (T
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David Berman Bot @davidbermanbot.bsky.social · 25/06/2025
Poor as a mouse every morning Rich as a cat every night
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Verena @viralemergence.org · 02/06/2025
An update from the team on the uncertain future of our program and the impact of NSF budget cuts. Please share and reach out 🦠
Some difficult news from the team:

In NSF's FY25-26 Budget Request to Congress, we learned that our program will take a whopping 50% cut - meaning that in September, we'll be $1.25m short of an operating budget that currently supports a cohort of seven PhD students, four postdocs, and three full-time staff.

Verena is one of the largest and last pandemic prevention-focused programs in the United States: since 2020, we've supported the training of over 60 postdocs, graduate students, and undergraduates. Our researchers have established unique laboratory resources for studying animal immune systems, and discovered new antiviral immune adaptations in bats; developed risk assessment algorithms for wildlife and livestock viruses, and diagnostic algorithms for viruses like dengue, Ebola, and Zika; and quantified the effects of climate change, deforestation, and factory farming on spillover risk. Everything we develop is 100% open source, and our data has supported the research of nearly 150 external researchers in 21 countries to date.

We have three months to make up our budget shortfall. Every dollar spent on Verena supports not just our team, but the community of researchers who use our data, code, and resources. You can help us by sharing this post, and reaching out if you're able to support a unique and vulnerable program. Or just head over to viralemergence.org, and take a look at what we do. 🦟 🦇 🦠
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Katherine Hébert @katherinehebert.bsky.social · 26/05/2025
One week until Blitz the Gap (www.blitzthegap.org) starts - a Canada-wide event to fill biodiversity data gaps with iNaturalist! @laura-pollock.bsky.social
blitzthegap.org
Blitz the Gap 2025
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David Berman Bot @davidbermanbot.bsky.social · 14/05/2025
There were no new ways to understand the world, only new days to set our understanding against.
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CSEE | SCEE Meetings @csee-sceemtgs.bsky.social · 09/05/2025
🐾 #CSEE2025 Workshop Highlight 🐾 "Interpretable machine learning for species distribution modelling" 💻 Discover how to use reproducible ML tools to tackle diverse ecological questions! 🔗 Register here: event.fourwaves.com/scee2025/reg...
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David Berman Bot @davidbermanbot.bsky.social · 09/05/2025
What kind of animal Needs to smoke a cigarette? Grass in the pasture Is sharper than a bayonette Sometimes a pony Sometimes a pony Sometimes a pony gets depressed
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David Berman Bot @davidbermanbot.bsky.social · 29/04/2025
Boy wants a car from his dad Dad says, "First, you got to cut that hair" Boy says, "Hey, Dad, Jesus had long hair" And Dad says, "That's right, son, Jesus walked everywhere"
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michael catchen @mdcatchen.bsky.social · 23/04/2025
only if the title is: okay, this is epic
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