Augustus (Gus) Pendleton

I always try and present like I'm about to tell you the juiciest gossip about bacteria

WOAH!! Catherine Lozupone and Rob Knight cited my paper!! this is actually mind blowing to the microbial ecologist nerd that I am 🤯🥳🤓 Huge credit to Jianshu Zhao for an incredible innovation

www.biorxiv.org/content/10.6...

I take data types very seriously

I‘m sure there‘s a #rstats or #stats person who can tell me why I would want to apply canonical correlation analysis (CCA)?

I finally spent some time sprucing up my personal website. Feel free to see what I've been up to!
gus-pendleton.github.io

A Shapiro-Wilk test of the response variable concludes very significant deviation of Normality. But residuals of linear model consistent with Normal distribution.

Visual check of the linear model with DHARMa

Periodic reminder that we should avoid testing the Normality of the response variable.

For a linear model, what matters is the Normality of residuals (and not that much). Visual checks better than test. #statistics

Where I ended up instead is binarizing the two variables and testing the probability of them both "peaking" together against a set of permuted datasets

I stumbled into defining a variable ("Active" vs. "Inactive") defined by high X OR high Y, and we get a beautiful example of anticorrelation in the "active" group. Of course, even in random data like above, you get great anticorrelation when you "cut the corner" like this (glad I checked!)

Yup - self-imposed! The real data (above is a simulation) is characterized by mostly low levels of both variables, with periods of "peaky" highs. Those peaks look anti-correlated, but the two variable have an overall positive correlation! ...

Learned a very painful statistics lesson today (after investing a whole day of analysis)

I am seeking a postdoc to join my group at UCLA -- ideally the candidate would have some experience in either population genetics or microbes/microbiome (computational background needed). We have a range of projects and are happy to tailer to your interests. Please dm/email me if interested.

Survived the 50km Winona Tourathon last Saturday, all in sub-zero temps! Skied an hour longer than planned but super happy with my 5th-place finish.

Prevalence and mechanisms of high-level carbapenem antibiotic tolerance in clinical isolates of Klebsiella pneumoniae Author summary Bacteria can survive exposure to antibiotics by constantly repairing cellular damage induced by the drug. This “antibiotic tolerance” enables diverse bacteria to survive long enough to ...

First 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...

How AI assistance impacts the formation of coding skills Anthropic is an AI safety and research company that's working to build reliable, interpretable, and steerable AI systems.

“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-...

We 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

We 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...

Network diagram showing correlations between cyanobacterial taxa. Microcystis forms a cluster, Pseudanabaena and Dolichospermum form a cluster, and Cyanobium forms a cluster.

Network diagram showing correlations between cyanobacterial taxa. Microcystis forms a cluster, Pseudanabaena and Dolichospermum form a cluster, and Cyanobium forms a cluster.

I am having fun with networks!

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)

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)

Oglala Sioux Tribe accuses federal authorities of treaty violation after four members detained by ICE “Members of the Oglala Sioux Tribe are United States citizens. We are the first Americans.”

The 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.

Donate to Support for Renee Good’s wife and son, organized by Mattie Weiss Please support the wife and son of Renee Good as they grapple with the devastating … Mattie Weiss needs your support for Support for Renee Good’s wife and son

This 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...

Latest work on the Diadema pathogen and its seasonal occurrence at a time series site

Rarefaction is better than robust Aitchison PCA and other compositional data analysis methods at controlling for uneven sequencing effort Amplicon sequencing typically results in a wide distribution in the number of sequences obtained from each sample. How best to account for this variation has been a persistent problem in the microbial...

New 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...

We 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):

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/...

This 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!

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!

Love 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

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.

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...