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augustuspendle1.bsky.social
Augustus (Gus) Pendleton
@augustuspendle1.bsky.social
480 followers 1K following 53 posts
Microbes 🤝 Lakes 🤝 Computers. Schmidt Lab @ Cornell. 🏳️‍🌈Scientist, 🇮🇪Fulbright, NOAA Davidson Fellow. Code-obsessed cat owner who likes to be outside.
https://gus-pendleton.github.io/
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augustuspendle1.bsky.social
Augustus (Gus) Pendleton @augustuspendle1.bsky.social · Apr 30
New blog post from the Schmidt Lab! Play around with environmental and microbial data from Lake Ontario, and make some pretty maps!

marschmilab.github.io/blog/microbe...

#rstats #microbiology #ecology #limnology #shiny
Our new interactive tool: MicrobeMapper – Schmidt Lab
Play with microbial data from Lake Ontario!
marschmilab.github.io
Reposted by Augustus (Gus) Pendleton
lanelaburi.bsky.social
Marine Ecologist tenure track job, here at URI. Come join a thriving research environment with a major focus on all things marine!

jobs.uri.edu/postings/15960
Assistant Professor in Marine Ecology
The search will remain open until the position has been filled. First consideration will be given to applications received by December 12, 2025. Applications received after December 12, 2025 may be re...
jobs.uri.edu
November 13, 2025 at 2:26 PM
Reposted by Augustus (Gus) Pendleton
jakubnowosad.com
tmap or ggplot2 for maps? 🗺️

David O’Sullivan breaks down the trade-offs in a blog post.

URL: dosull.github.io/posts/2024-1...

#RStats #RSpatial #Maps #tmap #ggplot2
tmap vs. ggplot2 for mapping – Geospatial Stuff
For me at least the choice between ggplot2 and tmap is an ongoing question. Here are my latest thoughts on the subject (with code).
dosull.github.io
November 12, 2025 at 2:02 PM
augustuspendle1.bsky.social
This paper combines so many things I love! Community assembly, an appreciation for absolute abundance, and carefully selected (and interpreted!) alpha and beta diversity. Fun to see generalized concepts we're measuring in freshwater systems also get their due in host-associated microbiomes.
November 10, 2025 at 6:59 PM
Reposted by Augustus (Gus) Pendleton
beatekraft.bsky.social
Please apply if you are interested in marine biogeochemistry and microbial dark oxygen production. Deadline: November 17th.
beatekraft.bsky.social Beate Kraft @beatekraft.bsky.social · 22d
📣Postdoc opportunity @nordcee.bsky.social , University of Southern Denmark! 📣

Join us and work with Bo Thamdrup and me on microbial dark oxygen production in marine oxygen minimum zones!

Please share widely!

Deadline: 17 November

More information can be found here:
tinyurl.com/2vuur3wh
Postdoc on microbial oxygen production in marine oxygen minimum zones
Application deadline: 17 November 2025 at 23:59 hours local Danish time
fa-eosd-saasfaprod1.fa.ocs.oraclecloud.com
November 10, 2025 at 12:06 AM
augustuspendle1.bsky.social
Pitchfork is down...quick everyone just enjoy the music you like without feeling judged
October 31, 2025 at 3:39 PM
Reposted by Augustus (Gus) Pendleton
gretelwaugh.bsky.social
Prospective PhD students - here is a brilliant opportunity to explore how bacteria and viruses evolve in liquid environments like the ocean 🌊

The LSI is a great place to explore microbial evolution, and you'll be working with fantastic, interdisciplinary supervisors. Email Wolfram if interested 👇
wolframmoebius.bsky.social Wolfram Moebius @wolframmoebius.bsky.social · 16d
Even more biased: I'm excited about the project 'Turbulent Partners: Unravelling Host-Virus Coevolution in Dynamic Environments' with Adam Monier and Daniel Kattnig. Drop me an email if interested! www.exeter.ac.uk/v8media/rese...
October 28, 2025 at 2:40 PM
augustuspendle1.bsky.social
Too cool!!
ryanziels.bsky.social Ryan Ziels @ryanziels.bsky.social · 23d
I’m very happy this is finally out! Here, we showcase the combination of BONCAT and SIP metaproteomics to uncover rare and active microbes driving anaerobic acetate turnover. We are excited to see what other microbial metabolisms and ecosystems this approach can help to illuminate! 🦠
natmicrobiol.nature.com Nature Microbiology @natmicrobiol.nature.com · 23d
OUT NOW Activity-targeted metaproteomics uncovers rare syntrophic bacteria central to anaerobic community metabolism by @ryanziels.bsky.social www.nature.com/articles/s41...
October 21, 2025 at 5:30 PM
augustuspendle1.bsky.social
Dream job alert 🚨🚨
roeyangel.bsky.social Roey Angel @roeyangel.bsky.social · Oct 13
📣 New PhD student position opening in my lab!
Soils are full of microbes, but how many are active?
Surprisingly, we still lack reliable methods to answer this.
If you are interested in microbial dormancy and are fascinated by the Alps and glacier forefields, contact me.
🏔️ 🦠 💤 🧬 🎓
The team at our research site in the alps
October 13, 2025 at 10:42 PM
augustuspendle1.bsky.social
Anyone have access to this article and would like to share it as a gift link? It's a topic near-and-dear to my heart 😅
www.nytimes.com/2025/10/08/n...
Why Is This Lake ‘Burping’?
www.nytimes.com
October 8, 2025 at 8:03 PM
augustuspendle1.bsky.social
Anyone have access to this and might be willing to send me a pdf?
academic.oup.com/etc/article-...
Environmental factors affecting the formation of methylmercury in low pH lakes
Abstract. Recent studies have demonstrated elevated levels of mercury in fish from remote, low alkalinity and low pH lakes. The mechanisms of this enhanced
academic.oup.com
September 18, 2025 at 9:03 PM
Reposted by Augustus (Gus) Pendleton
drfishsg.bsky.social
Yesterday I headed over to Fremont, WI on the Wolf River to help prep for wild rice seeding that the Brothertown Indian Nation is doing. We collected some sediment at two sites, mixed up seeds for several sources, and made mud balls for seeding. They are seeding today and tomorrow! #restoration
A pontoon boat loaded with two canoes cruises across a calm Lake Poygon. Two hands in pink gloves mix a large pile of mayom/manoomin/Zizania/wild rice seed.
September 11, 2025 at 4:41 PM
Reposted by Augustus (Gus) Pendleton
peteecology.bsky.social
3 year Postdoctoral Research Fellow position in Landscape Multifunctionality here in beautiful Bergen jobbnorge.no/en/available... please repost
September 8, 2025 at 10:54 AM
Reposted by Augustus (Gus) Pendleton
olivia.science
Finally! 🤩 Our position piece: Against the Uncritical Adoption of 'AI' Technologies in Academia:
doi.org/10.5281/zeno...

We unpick the tech industry’s marketing, hype, & harm; and we argue for safeguarding higher education, critical
thinking, expertise, academic freedom, & scientific integrity.
1/n
Abstract: Under the banner of progress, products have been uncritically adopted or even imposed on users — in past centuries with tobacco and combustion engines, and in the 21st with social media. For these collective blunders, we now regret our involvement or apathy as scientists, and society struggles to put the genie back in the bottle. Currently, we are similarly entangled with artificial intelligence (AI) technology. For example, software updates are rolled out seamlessly and non-consensually, Microsoft Office is bundled with chatbots, and we, our students, and our employers have had no say, as it is not considered a valid position to reject AI technologies in our teaching and research. This is why in June 2025, we co-authored an Open Letter calling on our employers to reverse and rethink their stance on uncritically adopting AI technologies. In this position piece, we expound on why universities must take their role seriously toa) counter the technology industry’s marketing, hype, and harm; and to b) safeguard higher education, critical thinking, expertise, academic freedom, and scientific integrity. We include pointers to relevant work to further inform our colleagues. Figure 1. A cartoon set theoretic view on various terms (see Table 1) used when discussing the superset AI (black outline, hatched background): LLMs are in orange; ANNs are in magenta; generative models are in blue; and finally, chatbots are in green. Where these intersect, the colours reflect that, e.g. generative adversarial network (GAN) and Boltzmann machine (BM) models are in the purple subset because they are both generative and ANNs. In the case of proprietary closed source models, e.g. OpenAI’s ChatGPT and Apple’s Siri, we cannot verify their implementation and so academics can only make educated guesses (cf. Dingemanse 2025). Undefined terms used above: BERT (Devlin et al. 2019); AlexNet (Krizhevsky et al. 2017); A.L.I.C.E. (Wallace 2009); ELIZA (Weizenbaum 1966); Jabberwacky (Twist 2003); linear discriminant analysis (LDA); quadratic discriminant analysis (QDA). Table 1. Below some of the typical terminological disarray is untangled. Importantly, none of these terms are orthogonal nor do they exclusively pick out the types of products we may wish to critique or proscribe. Protecting the Ecosystem of Human Knowledge: Five Principles
September 6, 2025 at 8:13 AM
Reposted by Augustus (Gus) Pendleton
chenxinli2.bsky.social
Please share! I'm looking for a postdoc. The position is to lead one of the following projects: 1) regulation of plant specialized metabolism by cell fate, or 2) foliar embryogenesis in the succulent plant Kalanchoe.

Learn more abt projects: cxli233.github.io/cxLi_lab/res...
Plant cells are totipotent, meaning individual cells have the potential to develop into a full organism, a property unique to the zygote for animals. However, in most species for most cells, plant cells are not spontaneously totipotent, since they must be treated with specific hormone combinations to unlock their totipotency. Species within the Kalanchoe genus is unique as they spontaneously develop foliar embryos that are fully realized plantlets with shoot and root from notches along the edges of leaves. We speculate that the progenitor cells that give rise to these foliar embryos are totipotent, and we are using single cell techniques to identify & characterize them. In addition to being a fundamental process for plant biology, we foresee unlocking totipotency has many biotechnological applications, such as faciliating genetic transformation and the development of synthetic organs of biomanufacturing.
cxli233.github.io
September 4, 2025 at 2:00 PM
Reposted by Augustus (Gus) Pendleton
msbr89.bsky.social
www.nature.com/articles/nme...
Mapping quantitative data to color - Nature Methods
Data structure informs choice of color maps.
www.nature.com
September 6, 2025 at 12:26 PM
Reposted by Augustus (Gus) Pendleton
jeffwwhite.bsky.social
New open access paper out! We evaluated the population structure and conservation needs for 3 crested penguin species in NZ. Read it here: journals.plos.org/plosone/arti...
August 28, 2025 at 9:09 PM
Reposted by Augustus (Gus) Pendleton
biorxiv-evobio.bsky.social
Leaving Academia: Insights from Evolutionary Biologists on Their Career Transitions and Job Satisfaction https://www.biorxiv.org/content/10.1101/2025.08.19.671061v1
August 20, 2025 at 9:32 PM
augustuspendle1.bsky.social
This is what's held me back - amazing to see!
emilhvitfeldt.bsky.social Emil Hvitfeldt @emilhvitfeldt.bsky.social · Aug 20
Happy to announce ✨quarto-revealjs-editable✨

This fully supersedes the imagemover extension, as I back then didn't realize the potential. You can now also move, resize, change font size and alignment for text in your slides

github.com/EmilHvitfeld...
#quarto #slidecrafting
August 20, 2025 at 7:35 PM
augustuspendle1.bsky.social
Looking for potential fellowship opportunities for final-year writing funding (I understand this might be a moonshot at the moment). Just stipend (no research costs). I'm in the environmental/life sciences, and grateful if there are any directions people could point me towards!
August 20, 2025 at 5:55 PM
Reposted by Augustus (Gus) Pendleton
gibbological.bsky.social
You can get an accurate estimate of total bacterial biomass from stool metagenomes by simply normalizing by host read count, without needing any additional measurements.

Excellent work by UW Master's student Gechlang Tang in @asm.org #mSystems Journal.

journals.asm.org/doi/10.1128/...
🧵
Metagenomic estimation of absolute bacterial biomass in the mammalian gut through host-derived read normalization | mSystems
In this study, we asked whether normalization by host reads alone was sufficient to estimate absolute bacterial biomass directly from stool metagenomic data, without the need for synthetic spike-ins, ...
journals.asm.org
July 31, 2025 at 3:33 PM
Reposted by Augustus (Gus) Pendleton
mikeblazanin.bsky.social
A new version of gcplyr (1.12.0) has just been released and is available now from CRAN and github. This update fixes a handful of bugs along with some improvements to the documentation

mikeblazanin.github.io/gcplyr/
Wrangle and Analyze Growth Curve Data
Easy wrangling and model-free analysis of microbial growth curve data, as commonly output by plate readers. Tools for reshaping common plate reader outputs into tidy formats and merging them with desi...
mikeblazanin.github.io
July 29, 2025 at 5:00 PM
augustuspendle1.bsky.social
This reminds me when I was just messing around with codon usage in Julia and I found this out on my own - look at those AT-rich codons!!

gus-pendleton.github.io/CUBScout_Rel...
July 24, 2025 at 4:19 PM
augustuspendle1.bsky.social
Microbial ecologists! Do you use Unifrac distances? Are you curious about absolute abundances? Then I’ve got a paper for you!
www.biorxiv.org/content/10.1... (1/4)
Interpreting UniFrac with Absolute Abundance: A Conceptual and Practical Guide
Microbial ecologists routinely use β-diversity metrics to compare communities, yet these metrics vary in the ecological dimensions they capture. Popular for incorporating phylogenetic relationships, U...
www.biorxiv.org
July 19, 2025 at 5:25 PM
augustuspendle1.bsky.social
Amazing opportunity! 👇
jkpritch.bsky.social Jonathan Pritchard @jkpritch.bsky.social · Jul 7
Staff scientist position (computational):

I am looking for a computational scientist to join my genomics lab at Stanford. They should have an outstanding skillset in ML/statistical methods for genomic applications, postdoc experience and a strong publication record.
#sciencejobs
July 12, 2025 at 1:06 PM
Reposted by Augustus (Gus) Pendleton
sauerscientist.bsky.social
I'm recruiting a 2-yr postdoc to start in October or November of 2025! I'm looking for applicants interested in exploring amphibian disease ecology as it relates to climate change. Strong quantitative skills preferred, interviews start late July. More info: erinsauer.com
July 7, 2025 at 6:55 PM