Jessica Bernardin

Introducing Causion: A web app for playing with DAGs | Peder M. Isager Personal website of Dr. Peder M. Isager

#statstab #482 Introducing Causion: A web app for playing with DAGs

Thoughts: A very cool app. Let's you see exactly what your assumptions and DGP mean for your causal model.

#causal #causalinference #DAG #DAGs #dgp #tutorial #guide #education #pedagogy

pedermisager.org/blog/causion...

Bacterial Strain Identity and Community Composition Drive the Seed-to-Seedling Microbiota Assembly https://www.biorxiv.org/content/10.64898/2026.02.02.703190v1

DeepKOALA: A Fast and Accurate Deep Learning Framework for KEGG Orthology Assignment www.biorxiv.org/content/10.6... #jcampubs

Approaches for accelerating microbial gene function discovery using artificial intelligence - Nature Microbiology In this Review, the authors discuss how artificial intelligence can aid microbial gene function discovery.

Approaches for accelerating microbial gene function discovery using artificial intelligence www.nature.com/articles/s41... #jcampubs

Every time I catch academic dishonesty, I require a re-write/re-do. Not only does this give students a chance to make up for their mistake, but they get a chance to see what they can do when they are held accountable. It's more work & stress on me but IMO it's worth it. 1/4

Localized nutrient colimitation of phytoplankton growth rates across the subtropical South Pacific Ocean | PNAS The simultaneous depletion of multiple nutrients in seawater potentially leads to colimitation of phytoplankton growth across large oceanic extents...

Localized nutrient colimitation of phytoplankton growth rates across the subtropical South Pacific Ocean www.pnas.org/doi/abs/10.1... #jcampubs 🌊

Comparison of short-read and long-read metagenome assemblies in a natural soil community highlights systematic bias in recovery of high-diversity populations Abstract. Comparisons of long-read and short-read (meta)genome assemblies typically show that short-read sequence assemblies are less error-prone, but stru

🧬🦠🚨 Another new paper alert, this time led by @maureenbug.bsky.social ! In collaboration with the Emerson lab and
@titus.idyll.org lab (@taylorreiter.bsky.social), both at UC Davis. Asking the question: what are we missing in short-read metagenome assembly, and why ?

doi.org/10.1093/narg...

Inside the World of Pitcher Plants: How Tiny Ecosystems Reveal Big Insights on Biodiversity YouTube video by Cal Poly Humboldt SPF

A little video of our work with pitcher plant microbial communities. www.youtube.com/watch?v=7EvI...

#statstab #471 Give Your Hypotheses Space!

Thoughts: "each hypothesis requires its own model" + "Only interpret the output for your exposure of interest"

#causalinference #modelling #hypothesis #tutorial #confounding #mbias

brian-lookabaugh.github.io/website-bria...

Models and co-culture experiments assess four mechanisms of phytoplankton–bacteria interactions - Nature Microbiology Mathematical representations of overflow metabolism, mixotrophy, exoenzymes and reactive oxygen species detoxification recapitulate dynamics in co-cultures of Prochlorococcus and eight heterotrophic b...

#NewResearch

Mathematical representations of overflow metabolism, mixotrophy, exoenzymes and reactive oxygen species detoxification recapitulate dynamics in co-cultures of Prochlorococcus and eight heterotrophic bacteria.

#MicroSky 🦠

www.nature.com/articles/s41...

📅Our speaker next week is Ágnes Móréh (HUN-REN Centre for Ecological Research, Hungary) presenting:

⭐Simultaneous invasion by two species: consequences for their success and for the resident community⭐

Zoom Link: iite.info/seminar/
Global times: www.timeanddate.com/worldclock/f...

See you there!

Plotting pp_check interactions I am trying to model ordinal data with an interaction of two predictors. However, I have issues with plotting interactions and individual data with the BRMS functions. My model is of the type ratin...

#statstab #464 Plotting p-check interaction {brms}

Thoughts: Annoyingly #brms doesn't natively allow plotting for interactions (that I know of). The forum has a solution.

#ppc #posterior #bayesian #modelfit #diagnostic #rstats #r #stan

discourse.mc-stan.org/t/plotting-p...

News & Views out now - Entomopathogenic fungi bait and kill insects with longifolene

By Thiago Luiz Alves e Silva & Joel Vega-Rodriguez

#microsky #malaria

www.nature.com/articles/s41...

Come be our colleague! We are looking for a tenure track cell / molecular biologist with focus on biochemical sciences. Strong bio department, lovely rural communities and living among the redwoods! Ask me questions !

careers.humboldt.edu/mob/hm/en-us...

Metagenomic editing of commensal bacteria in vivo using CRISPR-associated transposases Although metagenomic sequencing has revealed a rich microbial biodiversity in the mammalian gut, methods to genetically alter specific species in the microbiome are highly limited. Here, we introduce ...

#NatMicroPicks

CRISPR Metagenome Engineering! 🦠🔧🧬

MetaEdit enables precise genetic editing of native gut bacteria in mice.

#MicroSky #SynBio

www.science.org/doi/10.1126/...

Ep. 551 - Sagebrush, Pitcher Plants, & Leaf Microbiomes — In Defense of Plants In Defense of Plants' Matt Candeias talks with Microbial Ecologist Dr. Leonora Bittleston about the leaf microbiomes of sagebrush (Artemisia tridentat) and pitcher plants (Sarracenia, Nepenthes, and C...

I was thrilled to be interviewed by Matt Candeias for his cool podcast In Defense of Plants! Check it out if you want to hear about sagebrush, pitcher plants and leaf microbiomes!
www.indefenseofplants.com/podcast/2025...

Munching a baby butterfinger as we speak :)

Ecological coherence in abundance dynamics across terrestrial and marine assemblages https://www.biorxiv.org/content/10.1101/2025.11.05.686795v1

Precipitation legacy effects on soil microbiota facilitate adaptive drought responses in plants - Nature Microbiology Metagenomes from prairie soils in Kansas, USA, show how historical exposure to water stress impacts soil microorganisms and subsequently drought responses in plants.

#NewResearch

Precipitation legacy effects on soil microbiota facilitate adaptive drought responses in plants

#microsky

www.nature.com/articles/s41...

This was such a neat study it got posted twice on our 'cool papers' channel in lab slack 😅

#ProtistsonSky

An artistic reconstruction of the fossil lichen Spongiophyton.

Through an extensive investigation using over 20 complementary analytical techniques, researchers identify Spongiophyton as one of the earliest undisputed lichens in the fossil record.

Learn more in this week’s issue of #ScienceAdvances: https://scim.ag/4oHMxeU

The average nucleotide identity (ANI) underpins how we map microbial diversity, compare species, and connect genomes to ecology.
I wrote a short piece reflecting on the discovery and significance of this metric (and really enjoyed digging into the context and story behind it!) #microsky 🧬

Whoa—my book is up for pre-order!

𝐌𝐨𝐝𝐞𝐥 𝐭𝐨 𝐌𝐞𝐚𝐧𝐢𝐧𝐠: 𝐇𝐨𝐰 𝐭𝐨 𝐈𝐧𝐭𝐞𝐫𝐩𝐫𝐞𝐭 𝐒𝐭𝐚𝐭 & 𝐌𝐋 𝐌𝐨𝐝𝐞𝐥𝐬 𝐢𝐧 #Rstats 𝐚𝐧𝐝 #PyData

The book presents an ultra-simple and powerful workflow to make sense of ± any model you fit

The web version will stay free forever and my proceeds go to charity.

tinyurl.com/4fk56fc8

New @exeter.ac.uk reveals how cilia choreograph their “Mexican wave”, enabling marine creatures to swim!

Full paper in Science Advances - www.science.org/doi/10.1126/...

🦑🌊🌍🧪🐟 #AcademicSky
@micromotility.bsky.social

The best scientific talk advice that gets ignored Here are some prescriptions for a case of UCPS (Unengaging Conference Presentation Syndrome).

I find there's a huge mismatch between the standard advice that people give about scientific conference talks, and how people actually give talks.

So I picked out the most important pieces of advice that are most often ignored. 🧪

A "methods primer" article in the journal "BMJ Medicine", titled "Factors associated with: problems of using exploratory multivariable regression to identify causal risk factors"

We wrote an article explaining why you shouldn't put several variables into a regression model and report which are statistically significant - even as exploratory research. bmjmedicine.bmj.com/content/4/1/.... How did we do?

Long-read metagenomics for strain tracking after faecal microbiota transplant - Nature Microbiology A long-read metagenomics method empowers faecal microbiota transplantation studies by precisely tracking bacteria from donors to recipients, distinguishing co-existing strains and revealing genomic ch...

OUT NOW - Long-read metagenomics method for strain tracking after FMT #microsky www.nature.com/articles/s41...

Identifying rare and active species that drive carbon turnover in complex microbiotas - Nature Microbiology By combining bioorthogonal non-canonical amino acid tagging, metaproteomics and stable isotope probing, we identified a rare and uncharacterized bacterium with a glycine-mediated metabolism for syntro...

Our latest Research Briefing is out, on using metaproteomics and stable isotope labelling to uncover rare species involved in carbon turnover www.nature.com/articles/s41...

📣Tomorrow our next series of online seminars restarts: Chris Klausmeier (MSU) will present:

⭐Microbial cross-feeding: coexistence and collapse, spatial patterns and population cycles⭐

Free and open to all:
Zoom link: iite.info/seminar/
Global Times: www.timeanddate.com/worldclock/f...