Augustus (Gus) Pendleton
Microbes 🤝 Lakes 🤝 Computers. Schmidt Lab @ Cornell. 🏳️🌈Scientist, 🇮🇪Fulbright, NOAA Davidson Fellow. Code-obsessed cat owner who likes to be outside.
gus-pendleton.github.io
- Reposted by Augustus (Gus) PendletonFirst paper of my PhD @doerrlab.bsky.social is up! We characterized meropenem tolerance in Enterobacterales species, and then further dissected tolerance mechanisms in Klebsiella pneumoniae. journals.plos.org/plospathogen...
- Reposted by Augustus (Gus) Pendleton“We found that using AI assistance led to a statistically significant decrease in mastery.” Props to Anthropic for studying the effects of their creation and reporting results that are not probably what they wished for www.anthropic.com/research/AI-...
- Reposted by Augustus (Gus) PendletonWe are thrilled to announce the first official release (v0.1.8) of #𝗯𝗲𝗱𝗱𝗲𝗿, the successor to one of our flagship tool, #𝗯𝗲𝗱𝘁𝗼𝗼𝗹𝘀! Based on ideas we conceived of long ago (!), this was achieved thanks to the dedication of Brent Pedersen. 1/n
- Reposted by Augustus (Gus) PendletonWe have an open position for a bioinformatics/theoretical microbial ecology PhD student to study viral strategies in the global Microverse! Join us at the @microverse.bsky.social at @uni-jena.de, please apply through this link: jobs.uni-jena.de/jobposting/9...
- I am having fun with networks!
- Ecologists 🗣️ I want to study cooccurence of abundant ASVs (~1000) with a subset of abundant ASVs (~100). Tons of tools for this, with a specific corrections for sparsity and compositionality. But my data aren't sparse (all have high prevalence) nor compositional (absolute-abundance corrected). (1\2)
- I feel like I can use more classical/macroecology methods of calculating correlations/networks, but still want to control for false discovery rate. I'm having difficulty finding ideas/examples since most microbe-tools assume compositionality. Ideas? (2/2)
- Reposted by Augustus (Gus) PendletonThe Department of Homeland Security is refusing to release information on 3 detained Oglala Lakota tribal members who are being held at Fort Snelling, a former concentration camp for Native people, unless the tribe enters into an immigration agreement with ICE.
- Reposted by Augustus (Gus) PendletonThis is a vetted fundraiser for the family of Renee Good, the woman who was killed by ICE in Minneapolis. www.gofundme.com/f/support-fo...
- Reposted by Augustus (Gus) PendletonLatest work on the Diadema pathogen and its seasonal occurrence at a time series site
- Host-independent persistence of the Diadema antillarum Scuticociliatosis Philaster clade in coastal environments biorxiv.org/content/10.64898/20…
- Reposted by Augustus (Gus) PendletonNew paper up on bioRxiv! This is my third and hopefully final paper on rarefaction. It's still better than the other available methods. www.biorxiv.org/content/10.6...
- Reposted by Augustus (Gus) PendletonWe are recruiting several PhD students. If you are interested in conservation conflicts, population ecology, quantitative ecology, or biodiversity, check these projects out (links in the thread, feel free to reach out):
- Reposted by Augustus (Gus) PendletonThe sporulation phosphorelay protein Spo0B is membrane localized in Paenibacillus! The transmembrane domain appears to increase interaction with relay partners. Congrats to former lab undergrad @isabellalin.bsky.social and her grad mentor @cassidyprints.bsky.social journals.asm.org/doi/10.1128/...
- Reposted by Augustus (Gus) PendletonThis work was also our first time doing membrane localization (way to go Cassidy)! And so proud of Bella’s gorgeous Paenibacillus tree showing the distribution of the transmembrane containing Spo0B! Also it’s the lab’s first paper without ribosomes 🫨, but don’t worry - the ribosomes made the Spo0B!
- The sporulation phosphorelay protein Spo0B is membrane localized in Paenibacillus! The transmembrane domain appears to increase interaction with relay partners. Congrats to former lab undergrad @isabellalin.bsky.social and her grad mentor @cassidyprints.bsky.social journals.asm.org/doi/10.1128/...
- Looking for advice: we’re trying to extract HMW DNA from PES filters, so no bead beating. Pretty low biomass. Troubleshooting phenol-chloroform extractions right now but would love any advice or protocols if people are willing to share!
- Reposted by Augustus (Gus) PendletonLove aquatic research, teaching, and outreach? Want to join us at our terrific field station and live on Yellow Bay, Montana? University of Montana seeks a new Director for Flathead Lake Biological Station. Position details here: apply.interfolio.com/178916
- My family split it up and baked all of the NYT cookie week cookies. Here are our rankings, if helpful: 1. Dark 'n' Stormy - showstoppers, delicious 2. Vietnamese Coffee Brownies - tasty and easy 3. Coconut Snowballs - yummy and colorful 4. Creme de Menthe - okay flavor, not favorite texture cont...
- 5. Mortadella shortbreads - look fabulous, but overwhelmingly almond-y 6. Popcorn Candy Cookies - bad, popcorn adds nothing 7. Brown/Butter Peanut Cookies - dried very hard, too many nuts, worse than a normal peanut butter cookie.
- Very cool work!
- Ecologists recognize the importance of integrating across scales, yet our models often target specific scales. Our new paper presents models of population growth that scale up to explain community-level patterns, including interactions of temperature, light & nutrients. doi.org/10.1002/ecm....
- Looking for ideas: I have both sequencing data (relative abundances of cyanobacteria in a sample) as well as flow cytometry data (autofluorescence in multiple channels) for many mixed, environmental samples. I want to find fluorescence signatures for a few specific genera.
- I know this is a dimension reduction problem, but don't know where to start! Open to any ideas
- Reposted by Augustus (Gus) Pendletonvery cool: hydroacoustics shows "daily migration of both fish and mysid shrimps spanning several hundred meters throughout Lake Superior" -- in the Fall IAGLR Lakes Letter iaglr.org/ll/2025-4_Fa... 👏
- Reposted by Augustus (Gus) PendletonStarting at 7pm Central I will be streaming from the bottom of the ocean off the coast of Uruguay! Feel free to join and ask questions. www.youtube.com/@SchmidtOcean
- Reposted by Augustus (Gus) PendletonLove to see community action against this AI nonsense! neighborhoodview.org/2025/11/13/d...
- Reposted by Augustus (Gus) PendletonExcited to recruit a new PhD student for Fall 2026 in my lab at Cornell! Looking for someone interested in evolutionary genomics + fisheries/conservation applications. Quick timeline this year—reach out soon. More details: www.therkildsenlab.org/join-us.html
- Reposted by Augustus (Gus) Pendleton“The prohibited activities would include joint research, co-authorship on papers, and advising a foreign graduate student or postdoctoral fellow. The language is retroactive, meaning any interactions during the previous 5 years could make a scientist ineligible for future federal funding.”
- Reposted by Augustus (Gus) PendletonMarine 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
- Reposted by Augustus (Gus) Pendletontmap 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
- 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.
- New paper showing how immigration alters the ecological processes structuring the assembly and variation in #Monarch caterpillar gut #microbiomes. w/ @jaapderoode.bsky.social, @gabe-dubose.bsky.social, Joselyne Chavez, Lydia Fuller-Hall Ecology Letters onlinelibrary.wiley.com/doi/10.1111/...
- Reposted by Augustus (Gus) PendletonPlease apply if you are interested in marine biogeochemistry and microbial dark oxygen production. Deadline: November 17th.
- 📣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
- Pitchfork is down...quick everyone just enjoy the music you like without feeling judged
- Reposted by Augustus (Gus) PendletonProspective 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 👇
- Too cool!!
- Dream job alert 🚨🚨
- 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...
- Anyone have access to this and might be willing to send me a pdf? academic.oup.com/etc/article-...
- Reposted by Augustus (Gus) PendletonYesterday 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
- Reposted by Augustus (Gus) Pendleton3 year Postdoctoral Research Fellow position in Landscape Multifunctionality here in beautiful Bergen jobbnorge.no/en/available... please repost
- Reposted by Augustus (Gus) PendletonFinally! 🤩 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
- Reposted by Augustus (Gus) PendletonPlease 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...
- Reposted by Augustus (Gus) Pendleton
- Reposted by Augustus (Gus) PendletonNew 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...
- Reposted by Augustus (Gus) PendletonLeaving Academia: Insights from Evolutionary Biologists on Their Career Transitions and Job Satisfaction biorxiv.org/content/10.1101/202…
- This is what's held me back - amazing to see!
- 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
- 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!
- Reposted by Augustus (Gus) PendletonYou 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/... 🧵
- Reposted by Augustus (Gus) PendletonA 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/
- 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...
- TIL: A/T content of first few codons in a protein dramatically impacts translation efficiency "A short translational ramp determines the efficiency of protein synthesis" (2019) www.nature.com/articles/s41...
- 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)
- Choosing metrics for beta-diversity is important, and interpreting them is non-trivial! But we haven’t seen anyone discussing how phylogenetic similarity, composition, and absolute abundance intersect when calculating Weighted Unifrac. (2/4)
- In fact, most tools to calculate Weighted Unifrac will convert your counts to relative abundance under the hood! (3/4)
- This paper is a short, good read, even for those using relative or compositional approaches, who want a clear demonstration of how different distance metrics can be interpreted and how they discern differences between communities. Please reach out to us if you have comments! (4/4)
- Amazing opportunity! 👇
- 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
- Reposted by Augustus (Gus) PendletonI'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
- Excited to share the news that I have accepted a TT assistant professor position at @rutgersuniversity.bsky.social in the Dept of Ecology, Evolution, and Natural Resources! I will be recruiting a postdoc and grad students soon for my wildlife disease ecology lab, so check back in here!
- This seems awesome!
- 🌈 🌐 rainbowR conference: online, early 2026 🌐 🌈 Are you LGBTQIA+, do you code in R, and would you like to get involved in rainbowR’s first-ever conference? We are looking for people to join our conference organising committee! ➡️ rainbowr.org/conference 🗓️ 1st meeting: July 9, 4pm UTC
- New and MUCH improved - we've updated our work on Lake Ontario's microbial communities by linking in physical processes (upwellings propagated via Kelvin waves). Nearshore zones hold microbes and metabolisms EXCLUSIVE to the temporary upwelling niche! www.biorxiv.org/content/10.1...
- So exciting to see this work out! Looking forward to sharing our own work using 3-domain universal primers in the Laurentian Great Lakes!
- So excited to announce the GRUMP paper is published! This global dataset provides relative abundances for plankton spanning Archaea to Zooplankton from unfractionated (>0.2µm) water samples using 3-domain universal primers that amplify 16S and 18S in one PCR reaction. www.nature.com/articles/s41...
- Reposted by Augustus (Gus) PendletonIAGLR values a just, equitable, and inclusive culture that removes barriers to participation in our activities and embraces people from diverse identities, perspectives, and experiences. This Pride Month, we honor the LGBTQ+ large lake science community.
- Reposted by Augustus (Gus) PendletonTime for Episode 95 of #MattersMicrobial! This time, Dr. Tory Hendry of Cornell University joins the #QualityQuorum to discuss aphids, symbiosis, and fluorescent bacteria. Please spread the #GoodMicrobialWord? microbe.tv youtu.be/i9xoWApANNM?...
- Um, dream job alert!!
- Are you a recent PhD (or soon to be PhD) from outside Canada looking to do a postdoc in Quebec? Get in touch if you are excited about microbes, evolution, ecology, genomics (or all of the above!) and I'd be happy to help develop a project together! www.mcgill.ca/gps/funding/...
- BIG news for Superior Cyanobacteria!!
- PhD student researcher Abby Smason, supported by #Minnesota Sea Grant, presented this week at #IAGLR25 on preliminary findings of a breakthrough discovery that identifies the bacteria behind toxins in the St. Louis River estuary. 🧪 📢 Get the full story: z.umn.edu/mnsg_25cyano... #GreatLakes
- Reposted by Augustus (Gus) PendletonMore exciting lab news from the @iaglr.bsky.social conference. @hjesparra91.bsky.social received the Student Presenter IDEA+ Award for his impactful research on how road salt affects freshwater systems. Critical work for the health of our lakes! 👏 @waynestateresearch.bsky.social
- Where do we fall on memes in presentations? Corny? Fun?
- Reposted by Augustus (Gus) PendletonThe Milwaukee Public Museum seeks a postdoctoral fellow in Invertebrate Paleontology to assist with an NSF-funded project on W. Atlantic Mollusks. The position is dependent upon continued NSF support and will have a duration of two years. www.indeed.com/viewjob?jk=7...
- Reposted by Augustus (Gus) Pendletonwww.nytimes.com/interactive/... 🧪🔭⭐🌌😭😰🤬
- Reposted by Augustus (Gus) PendletonThis looks like a fabulous opportunity to share the deep value science has for society in a non-partisan way. A collective effort put together by graduate students. blogs.cornell.edu/asap/events-...
- Reposted by Augustus (Gus) PendletonGFW needs your help! We have too much data and not enough researchers to investigate all the possibilities. So today we're piloting a new research grant program to encourage researchers to do novel things with our data. Find out more here buff.ly/MDL4xLE #OceanScience #Fisheries #ResearchFunding
- Reposted by Augustus (Gus) PendletonOn this day, 10 years ago, my lab published the @nature.com paper reporting the discovery of the Asgard archaea (Lokiarchaeota at the time), revealing the archaeal nature of eukaryotic cells, and reshaping the Tree of Life. What a ride it has been since then... www.nature.com/articles/nat...
- Please share this letter written in collaboration with other NOAA Davidson Fellows. The National Estuarine Research Reserve System (NERRS) is a precious resource which directly benefits coastal communities. Projected budget cuts would destroy this system - please don't let it die in silence!
- Reposted by Augustus (Gus) PendletonVim is the original escape room
- Reposted by Augustus (Gus) PendletonNEW: The Trump administration’s slashing of budgets and staff have Great Lakes scientists concerned that they have lost the ability to protect the public from toxic algal blooms, which can kill animals and sicken people. By @annaleighclark.bsky.social
- I feel like an old grump refusing to use these tools but then I see people show me nonsensical code they don't understand in the first place...cover letters that are so anonymous they mean nothing...art that's cool if your only metric is "vaguely recognizable"...it frustrates me
- This article is so important. AI will *always* make mistakes. The best and newest LLMs are even hallucinating more than before. People are using these tools for serious decisions and may not always notice the mistake. 🚨AI does not "know" or "understand" ANYTHING!🚨 www.nytimes.com/2025/05/05/t...
- Had an amazing run at the Syracuse Mountain Goat 10-miler! New PR of 64:45 at 6:29 pace 🚗💨
- Shameless husband appreciation post 😍
- 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
- I solemnly swear to never mess with combining cloud storage and git repos again 🤬
- Reposted by Augustus (Gus) PendletonThis week, I’ll be curating the #RLadies bluesky account. Be sure to follow @weare.rladies.org to learn more about the Data Science Learning Community @dslc.io, our book clubs, recent workshops we’ve hosted, new developments with #TidyTuesday, and more!
- This week’s #RLadies curator is @lydz-gibby.bsky.social.
- Reposted by Augustus (Gus) PendletonNEW: The total loss of NOAA’s office of Oceanic and Atmospheric Research —a nerve center of global climate science, data collection and modeling — represents a setback for climate preparedness that experts warn the nation may never recover from. By @abrahm.bsky.social
- #Ecology Bluesky! I need some advice. Let's say I have many species (bacterial ASVs, in this case) over ten timepoints in the summer. I want to classify these ASVs as having different time trends over the season (e.g. consistent, linearly increasing, parabolic, etc.). 1/2
- I want something similar to fitting species abundance curves, but instead fitting different models for their abundance over time. There are too many species to do this by eye. Any statistical recommendations I should check out? 2/2
- Last note! These ASVs are in absolute abundance (which is important for these time series and relaxes some of the assumptions of compositionality across samples)
