Assistant Professor of Plant Pathology & Fungal Biology, UC Davis. 🍄🌱 recruit.ucdavis.edu/JPF07339 Deadline Dec 1, 2025. 👀 "Primary teaching responsibilities will be teaching Introductory Mycology, an upper-division lab class, and SAS 30, Mushroom, Molds & Society"

📊 Interactive visualizations with Plotly: Multivariate plots with outlier detection Wright's ENC plots (ENC vs GC3s) GC content comparisons RSCU heatmaps CAI distribution plots Custom scatter plots of any metrics. 7/25

🎯 Multivariate analysis is where GCUA really shines! Perform Correspondence Analysis (CA) or Principal Component Analysis (PCA) on RSCU values or amino acid usage. Identify patterns and group genes by expression levels or evolutionary pressures. 6/25

📈 Key metrics GCUA calculates: ENC (Effective Number of Codons) - measures codon bias strength CAI (Codon Adaptation Index) - gene expression optimization Fop (Frequency of Optimal Codons) - adaptation to preferred codons SCUO (Synonymous Codon Usage Order) - information theory approach 5/25

💾 Getting started is simple: Load your FASTA file of coding sequences and GCUA automatically calculates codon frequencies, RSCU values (Relative Synonymous Codon Usage), amino acid composition, and base composition statistics. 4/25

🔬 GCUA supports ALL major genetic codes! From the standard universal code to vertebrate mitochondrial, yeast mitochondrial, bacterial/archaeal, and 30+ specialized codes. Perfect for comparative genomics across domains of life. 3/25

What is codon usage analysis? Different organisms (and even genes within organisms) prefer certain codons over others for the same amino acid. This "codon bias" reveals insights about gene expression, evolution, and optimal protein production strategies. 2/25

MMseqs2-GPU sets new standards in single query search speed, allows near instant search of big databases, scales to multiple GPUs and is fast beyond VRAM. It enables ColabFold MSA generation in seconds and sub-second Foldseek search against AFDB50. 1/n 📄 www.nature.com/articles/s41... 💿 mmseqs.com

📦 epfml / ML_course ⭐ 1,373 (+11) 🗒 Jupyter Notebook EPFL Machine Learning Course, Fall 2025

Job Alert! The University of Tübingen is hiring a FULL PROFESSOR (W3) in FUNCTIONAL ECOLOGY! Come and join our institute, and maybe our new excellence clusters @terra-cluster.org and @greenrobust.de. @gfoesoc.bsky.social @britishecologicalsociety.org @ecologicalsociety.bsky.social Please repost!

oooh, nice one @official-smbe.bsky.social "Title: Classifying Convergences in the Light of Horizontal Gene Transfer: Epaktovars and Xenotypes Dear Dr. McInerney, [...]we are pleased to inform you that your manuscript has been accepted for publication in Molecular Biology and Evolution."

📢 The Call for Symposia for SMBE2026 is now open. We warmly invite you to submit a symposium proposal and help shape the scientific content of our annual meeting. 🗓️ Key dates Call for symposia: Sep. 1 - Oct. 15 Announcement of accepted symposia: Nov. 3 More information: smbe2026.org/symposia

I’ll be advertising a post-doc position (up to 3 year) soon. It will be for somebody that is a good programmer, interested in evolution & is keen to learn new machine learning & AI approaches. I don’t have a link to a job advertisement yet. The post will be hybrid working and based at U of Liverpool

Extraordinary paper. I LOVE this sentence: “This translates to a net lateral gene transfer rate of ~250 genes L−1 seawater day−1 and involves both “flexible” and “core” genes. “ Must read in detail, but these numbers are amazing. academic.oup.com/ismej/advanc...

Would he prefer to fly in an aeroplane built by expert engineers, or one built by a “citizen that had done their own research” and had come to a very different opinion on how flight should work and built a very different plane? Experts are expert for a reason.

New preprint reveals bacteria can't just collect all resistance genes like Pokemon cards. We found mutually exclusive evolutionary pathways to multidrug resistance in E. coli & P. aeruginosa - some resistance mechanisms actively prevent others from coexisting www.biorxiv.org/content/10.1...

Is there only one "path" that evolution tends to take when a new trait arises? Or can the trait arise in more than one way? In other words, walking back from a particular evolutionary "destination", do we always take the same path? The answer might be "no", at least some of the time. In fact... 1/n

New preprint from the group: @lucydillon.bsky.social analysis of 16,000+ genomes finds Bacteria cannot combine certain resistance genes as they are mutually exclusive, forcing them down incompatible evolutionary paths. biorxiv.org/content/10.1101/2025.08.20.671315v1 @jomcinerney.bsky.social

GCUA has been updated to v2.5.1. It has some nice visualisations and the menu system got overhauled. It will do some parallelisations- particularly when reading in big files and if the dataset is big, then it only holds codon counts in memory, not sequences. See here: github.com/mol-evol/gcua

Named and shamed. www.nature.com/articles/d41...

This version has very targeted updates, particularly optimizations for large file handling. Retaining only codon counts is indeed more suitable for large-scale analysis

MMseqs2 v18 is out - SIMD FW/BW alignment (preprint soon!) - Sub. Mat. λ calculator by Eric Dawson - Faster ARM SW by Alexander Nesterovskiy - MSA-Pairformer’s proximity-based pairing for multimer prediction (www.biorxiv.org/content/10.1...; avail. in ColabFold API) 💾 github.com/soedinglab/M... & 🐍

Credit to the BBC’s Jeremy Bowen. Defying the Israeli ban on filming Gaza from above, Bowen instead describes the carnage & genocide he can see: “I can tell you that communities in the north of Gaza that I knew well…with tens of thousands of people…are flat. There’s nothing left of them.”

Take a look at our work on miRNAs and their involvement with placental phenotypes. It's great to see this work finally see the light of day - huge thanks to everyone involved with the manuscript.

How did mammal placental diversity evolve? miRNAs play a significant role - indeed their repertoire is predictive of phenotype. Congrats to all: esp 1st author @jfennbio.bsky.social & all in @niamhforde.bsky.social group. Thanks to @ukri.org and @leverhulme.ac.uk. www.biorxiv.org/content/10.1...

Happy to have contributed to this paper!!! Convergent placental phenotypes are mechanistically shaped by the same regulators

When you see convergent phenotypes do u wonder about their genetic basis? Did they re-invent some genetic element to construct the phenotype? The mammal placenta-a pretty important organ-has a lot of convergent phenotypes & this paper helps explain how they come about www.biorxiv.org/content/10.1...

GCUA has been updated to v2.5.1. It has some nice visualisations and the menu system got overhauled. It will do some parallelisations- particularly when reading in big files and if the dataset is big, then it only holds codon counts in memory, not sequences. See here: github.com/mol-evol/gcua

Jay, please stop gaslighting early career researchers.

Not my field, so I cannot judge, but this trade-off is something I always assumed was true. Anybody got comments on it? Lucy A Winder, et al (2025) No evidence for a trade-off between reproduction and survival in a meta-analysis across birds eLife 12:RP87018 doi.org/10.7554/eLif...

SIB Executive Director @dessimoz.bsky.social‬ highlights Switzerland’s opportunity to invest in science where others are retreating, arguing for: 🇨🇭strengthened ERI funding & international collaboration; 🚀 funding for data infrastructure as a driver of innovation. See more👇

Had a terrible day (lost all of yesterdays work), then I had a great day (got something to work that has been brewing for months).

One obvious economic implication of the latest travel ban is that genuinely international conferences will no longer be held in the U.S.

URGENT: FlyBase has lost practically all its funding overnight; even user fees are tied up in denied grant funding. 🤬🤯 Any lab using @flybase.bsky.social please donate using the link in post below. This incredible community, on whose backs our #Drosophila labs depend, can't be left out to dry.

Watched Yoshua Bengio’s TED talk recently and it was super interesting. Now he is doing this: www.theguardian.com/technology/2...

YUP. Made an error in the very first post. Correct link is: github.com/mol-evol/gcua

Thread: Introducing GCUA v2.0 (General Codon Usage Analysis) - a Python tool for analysing codon usage patterns in DNA sequences! Originally developed in 1998, now completely rewritten with modern features. Let me walk you through what I like about this version (PLS RT) github.com/mol-evol/gcu...

Over a long career it would be strange not to pivot. I suspect a lot will depend on the degree of pivot, the extent to which the research has shifted (e.g. if disruptive tech changed your field). I hope the message is not to keep people doing the same thing because they fear change will be bad

The Spectator doing Spectator things. www.spectator.co.uk/article/brit...

A new crop of artificial-intelligence models allows users to create, manipulate and learn about biology using ordinary language. www.nature.com/articles/d41...

ok. I just broke all the code, so I now must go for a walk. #python #bioinformatics #phylogeny

About a year ago I finished writing panGPT and I made a video about it. Just re-upping it here in case you missed it. Go on - make your own genomic model. youtu.be/cRSAhyTzg6Q?...

A pangenome influence graph. How much does the presence or absence of a gene influence the presence or absence of another in a genome? Somewhere in here is some of the answer.

“The visa fees are so exceedingly high that it makes coming here very difficult for some people. We are fishing for the best scientists in the world. They want to come and work here because we are such an effective country at science, but if we have these high costs, they can and will go elsewhere.”

Choose Science. Choose Europe. A new Marie Skłodowska-Curie Actions Postdoctoral Fellowships 2025 call is now open. With a budget of €404.3 million, it will support around 1,650 researchers from Europe and beyond. Apply by 10 September → europa.eu/!fBTMgF

installing dependencies of various kinds all morning. How's your day going?

Hard to believe....and yet, it has happened. www.nytimes.com/2025/05/05/u...

Interesting. A 57-codon genome. www.biorxiv.org/content/10.1...

This meeting will be great! Abstract submission open now See you 26-27 Nov in Liverpool microbiologysociety.org/event/societ...