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Laurie Belcher @lauriebelch.bsky.social · Aug 18

Super interesting session on post-phylogenomics this morning at #eseb2025

I have a poster on the new version of Orthofinder - there will be a suggestion box 🎁

P03.076 on Thursday

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Laurie Belcher @lauriebelch.bsky.social · Aug 12

Is there a single PDF with a list of talks/times for #ESEB2025 ? I don't get on well with conference apps

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Laurie Belcher @lauriebelch.bsky.social · Jul 16

Get OrthoFinder here github.com/OrthoFinder/...

Read the preprint here www.biorxiv.org/content/10.1...

Millions of species here we come!

(10/10)

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Laurie Belcher @lauriebelch.bsky.social · Jul 16

OrthoFinder is not only fast and accurate, it's easy to use

Just provide the complete set of amino acid sequences for your species

If you prefer a specific tree or alignment tool, it's easy to customise

We also provide rich outputs like gene duplications and comparative genomics stats (9/10)

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Laurie Belcher @lauriebelch.bsky.social · Jul 16

What else is new?

We now use gene tree–species tree reconciliation to refine orthogroups

This catches cases where distinct orthogroups were mistakenly fused (8/10)

figure showing how orthogroups are now phylogenetically delineated in orthofinder 3

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Laurie Belcher @lauriebelch.bsky.social · Jul 16

What about ortholog accuracy?

We tested using the gold standard Quest for Orthologs benchmarking service

OrthoFinder scored highly across the board (7/10)

figure showing ortholog benchmarking of various orthology inference tools

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Laurie Belcher @lauriebelch.bsky.social · Jul 16

But is it still accurate?

We benchmarked orthogroups using the OrthoBench dataset

OrthoFinder came out on top (6/10)

orthogroup benchmarking figure, using orthobench data

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Laurie Belcher @lauriebelch.bsky.social · Jul 16

So is it scalable?

We benchmarked OrthoFinder against other widely used orthology tools

OrthoFinder is the only method able to analyse >1000 species within our time cutoff (5/10)

image showing scalability of orthology inference tools on large datasets

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Laurie Belcher @lauriebelch.bsky.social · Jul 16

Our trick: run OrthoFinder on a small subset of species first

Next, we sample representative sequences from each orthogroup to build profiles

Genes from new species are then matched to these profiles to assign them to orthogroups

We avoid the costly all-vs-all step that kills scalability (4/10)

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Laurie Belcher @lauriebelch.bsky.social · Jul 16

Most tools rely on all-versus-all comparisons between species

This becomes painfully slow as datasets grow

We needed a better way (3/10)

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Laurie Belcher @lauriebelch.bsky.social · Jul 16

Millions of species are being sequenced

That’s a huge opportunity, but also a major challenge
How can we ramp up scalability without compromising accuracy?

That’s exactly what we set out to solve in this update (2/10)

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Laurie Belcher @lauriebelch.bsky.social · Jul 16

OrthoFinder just dropped a major update

It’s faster, more accurate, and ready for thousands of genomes

Let’s break it down (1/10)

github.com/OrthoFinder/...
www.biorxiv.org/content/10.1...

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Laurie Belcher @lauriebelch.bsky.social · Jun 2

I'll do the top row!

Buff tip, peach blossom, brimstone!

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Laurie Belcher @lauriebelch.bsky.social · Mar 31

Evolution of cooperation is well represented at #Microbio25 by Rosie's first ever conference poster - definitely worth a visit!

Rosie Randall @rosierand.bsky.social · Mar 30

Very excited to be in Liverpool for #Microbio25 ! I'll be presenting a poster on bacterial cooperation and antibiotic resistance in Block A on Tuesday. Come and check out poster A098 to hear more! 🧬🧫🦠

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Reposted by Laurie Belcher

Jamie Hall @jpjhall.bsky.social · Feb 18

I'm delighted to announce that the 2025 @microbiologysociety.org meeting on "Understanding and predicting microbial evolutionary dynamics" will be held in Liverpool 26-27 November 2025! Abstract submission will open soon... #microsky 🧪🧫🦠 microbiologysociety.org/event/societ...

Understanding and predicting microbial evolutionary dynamics - 2025 meeting

microbiologysociety.org

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Laurie Belcher @lauriebelch.bsky.social · Jan 22

screenshot from the movie 'Johnny English', showing the villain's plan to turn Britain into a giant prison

Laurie Belcher @lauriebelch.bsky.social · Jan 8

Hopefully this will be useful for anyone doing comparative genomics! In Box 1 we show some case studies where controlling for phylogenetic non-independance can reverse a result

Anna Dewar @annadewar.bsky.social · Jan 8

Our review is out in Nature Reviews Genetics! rdcu.be/d5AY2

We show how phylogeny-based methods can resolve the problem of non-independence in genomic datasets.

These methods must be considered an essential part of the comparative genomics toolkit.

@lauriebelch.bsky.social @stuwest.bsky.social

A phylogenetic approach to comparative genomics

Nature Reviews Genetics - Controlling for phylogeny is essential in comparative genomics studies, because species, genomes and genes are not independent data points within statistical tests. The...

rdcu.be

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Reposted by Laurie Belcher

Anna Dewar @annadewar.bsky.social · Jan 8

Our review is out in Nature Reviews Genetics! rdcu.be/d5AY2

We show how phylogeny-based methods can resolve the problem of non-independence in genomic datasets.

These methods must be considered an essential part of the comparative genomics toolkit.

@lauriebelch.bsky.social @stuwest.bsky.social

A phylogenetic approach to comparative genomics

Nature Reviews Genetics - Controlling for phylogeny is essential in comparative genomics studies, because species, genomes and genes are not independent data points within statistical tests. The...

rdcu.be

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Reposted by Laurie Belcher

Rachel M. Wheatley @rachelmwheatley.bsky.social · Dec 30

Sharing three fully funded PhD opportunities to join my lab at Queen’s to work on topics spanning bacterial pathogens, antibiotic resistance, microbial interactions, & mobile genetic elements 🦠. Closing dates in January and February, and open to international candidates 🌍 Projects detailed below ⬇️

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Laurie Belcher @lauriebelch.bsky.social · Dec 6

When you are a millenial but you want to connect with your students

a slide from a powerpoint presentation that reads "Genes? Total ✨pick-me✨ energy. They’re out here being selfish AF, chasing their own clout, even if it wrecks the whole genome vibe 💀. If they get too bold (like distorting phenotypes and being ✨that✨ guy), the ‘parliament of genes’ 👩‍⚖️ pulls up like, “Not on my watch, bestie,” and shuts it all the way down. 🚨
Basically, selfish genes either: 1️⃣ cause low-key drama 😬, or 2️⃣ get cancelled harder than a mid influencer scandal. The parliament? Straight-up GOAT 🐐 for keeping our genomes from turning into a hot mess express."

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Reposted by Laurie Belcher

Eduardo Rocha @epcrocha.bsky.social · Apr 4

New job offer: we search a postdoc (bioinformatics) to work on mobile genetic elements and gene flow in bacteria, with a focus on antibiotic resistance within a consortium including bioinformatics, synthetic biology, epidemiology & biochemistry. See research.pasteur.fr/en/job/postd... #MicroSky

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Laurie Belcher @lauriebelch.bsky.social · Nov 29

Post a photo of yourself from a different era.

Piazza San Marco, Venice

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Laurie Belcher @lauriebelch.bsky.social · Nov 27

go.bsky.app/QKajPgc
A starter pack for social evolution! Lots of space left for anyone who would like to be added

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Laurie Belcher @lauriebelch.bsky.social · Nov 1

Yep! Will also sadly not be going this year due to no option to go for two days. Hopefully there are more of the smaller meetings, like the evolutionary dynamics one in Manchester a few years ago

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Reposted by Laurie Belcher

Mike Blazanin @mikeblazanin.bsky.social · Oct 20

Tried to put together a Microbial Evolution starter pack, but there were so many great people I didn't want to leave out it turned into 3 starter packs

Comment or DM me if you were missed or would like to be added!

A thread (1/3)

go.bsky.app/6pkuYhi

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