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James McInerney @jomcinerney.bsky.social · 21h

Just one week to go until the deadline. www.jobs.ac.uk/job/DOU184/p... #ai #pangenome #genomics #evolution #microbiology

Postdoctoral Research Associate - Grade 7 at University of Liverpool

Apply for the Postdoctoral Research Associate - Grade 7 role on jobs.ac.uk, the top job board for academic positions in higher education. View details and apply now.

www.jobs.ac.uk

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Reposted by James McInerney

James McInerney @jomcinerney.bsky.social · 7d

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

James McInerney @jomcinerney.bsky.social · 13d

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

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James McInerney @jomcinerney.bsky.social · 6d

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

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James McInerney @jomcinerney.bsky.social · 7d

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

James McInerney @jomcinerney.bsky.social · 13d

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

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James McInerney @jomcinerney.bsky.social · 12d

That’s super, Hannah.

Reposted by James McInerney

Dr Hannah M. Rowland @hannahmrowland.bsky.social · 12d

🌍🦋 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...

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James McInerney @jomcinerney.bsky.social · 12d

Ooooh. Thats awesome news. Go you!!

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James McInerney @jomcinerney.bsky.social · 13d

hahaha

James McInerney @jomcinerney.bsky.social · 13d

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

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James McInerney @jomcinerney.bsky.social · 13d

PLEASE RETWEET.

James McInerney @jomcinerney.bsky.social · 13d

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...

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.

www.jobs.ac.uk

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James McInerney @jomcinerney.bsky.social · 13d

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...

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.

www.jobs.ac.uk

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James McInerney @jomcinerney.bsky.social · 13d

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

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James McInerney @jomcinerney.bsky.social · 13d

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

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James McInerney @jomcinerney.bsky.social · 13d

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

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James McInerney @jomcinerney.bsky.social · 13d

I have to agree!!

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James McInerney @jomcinerney.bsky.social · 14d

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...

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.

www.bbc.co.uk

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Jason Stajich @hyphaltip.bsky.social · 15d

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"

Assistant Professor of Plant Pathology

University of California, Davis is hiring. Apply now!

recruit.ucdavis.edu

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Reposted by James McInerney

James McInerney @jomcinerney.bsky.social · Jun 1

📊 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

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Reposted by James McInerney

James McInerney @jomcinerney.bsky.social · Jun 1

🎯 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

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Reposted by James McInerney

James McInerney @jomcinerney.bsky.social · Jun 1

📈 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

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Reposted by James McInerney

James McInerney @jomcinerney.bsky.social · Jun 1

💾 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

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Reposted by James McInerney

James McInerney @jomcinerney.bsky.social · Jun 1

🔬 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

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Reposted by James McInerney

James McInerney @jomcinerney.bsky.social · Jun 1

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

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Reposted by James McInerney

James McInerney @jomcinerney.bsky.social · Jun 1

github.com/mol-evol/gcua

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

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Reposted by James McInerney

Martin Steinegger 🇺🇦 @martinsteinegger.bsky.social · 17d

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

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...

www.nature.com

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