James McInerney

The job is still open. Get your application in ASAP. Or just pass it on to somebody that might be interested.

That’s my bet. Remains to be proven though. Working on it.

The job is still open. Get your application in ASAP. Or just pass it on to somebody that might be interested.

That’s super, Hannah.

🌍🦋 Across 6 continents, 21 sites & 15,000 paper moths, we joined a worldwide experiment led by @wlallen.bsky.social & Iliana Medina, showing how ecological context shapes the evolution of animal colouration.

Proud to be part of this global team effort: doi.org/10.1126/scie...

Ooooh. Thats awesome news. Go you!!

hahaha

or even ALLLLMs (All LLMs). Acronyms don't have nearly enough Ls in them :)

PLEASE RETWEET.

Postdoctoral Research Associate - Grade 7 at University of Liverpool Apply now for the Postdoctoral Research Associate - Grade 7 role on jobs.ac.uk - the leading job board for higher education jobs. View details.

The lab github is here: github.com/mol-evol/ so you can get an idea of what we have been working on recently (several projects are private at the moment, so this will be bigger soon) and the job ad is here: www.jobs.ac.uk/job/DOU184/p...

You don't have to be an expert in AI, but you need to be able to program and do some bioinformatics. You also need to be interested in Evolution. The job is hybrid, so we would need to meet regularly, but working from home or from the university are equally good. 3/4

The focus is on Evolutionary history, but we might end up venturing into Synthetic biology as well - predicting genome constructs and that kind of thing. We will be using Transformers (like a ChatGPT for genomes..but a bit different). 2/4

OK, here it is. Come work with me at the University of Liverpool making ALL THE AI models from ALL THE prokaryote pangenome data. Heck, we will make models from ALL the pangenomes, even eukaryotes!!! (link below👇) 1/4

I have to agree!!

Huntington's disease successfully treated for first time One of the most devastating diseases finally has a treatment that can slow its progression and transform lives, tearful doctors tell BBC.

This is just amazing. I'm flabbergasted. I have lectured about Huntington's for years. I first heard about it as a student 30+ years ago. I never thought we would see progress like this. Science works!! www.bbc.co.uk/news/article...

Assistant Professor of Plant Pathology University of California, Davis is hiring. Apply now!

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

GitHub - mol-evol/gcua: GCUA - General Codon Usage Analysis (v2.0) GCUA - General Codon Usage Analysis (v2.0). Contribute to mol-evol/gcua development by creating an account on GitHub.

github.com/mol-evol/gcua

GPU-accelerated homology search with MMseqs2 - Nature Methods Graphics processing unit-accelerated MMseqs2 offers tremendous speedups for homology retrieval from metagenomic databases, query-centered multiple sequence alignment generation for structure predictio...

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

This looks amazing. I’m planning on using it to construct a very large prokaryotic pangenome in the next few weeks on the Isambard-AI machine here in the uk. The machine is in testing phase, so I’m very pleased that so many things have come together at once (data/mmseqs2/computer).

GitHub - epfml/ML_course: EPFL Machine Learning Course, Fall 2025 EPFL Machine Learning Course, Fall 2025. Contribute to epfml/ML_course development by creating an account on GitHub.

📦 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."

SMBE2026 - Call for Symposia Proposals

📢 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