Jeffrey Vedanayagam

Confused by all the histones that are cropping up in organisms that are decidedly NOT eukaryotes? check out our review - fantastic work by team NucEvo in the #Lugerlab
The Expanding Histone Universe: Histone-Based DNA Organization in Noneukaryotic Organisms - www.annualreviews.org/content/jour...

Targeted sequencing and iterative assembly of near-complete genomes - Nature Communications Long-read sequencing enables high-quality genome assemblies, but challenges remain. Here, the authors introduce Cornetto, a method that improves assembly quality, enables genome sequencing from saliva...

Our cornetto work is now published at www.nature.com/articles/s41...

It can do near-T2T assembly using @nanoporetech.com adaptive sampling
- with less 💸
- reference agnostic, so works for non-humans
- not just blood, even saliva

Just presented at #abacbs2025 yesterday.

Systematic analysis of noncanonical ribosomal protein paralogs does not provide evidence for specialized functions in Drosophila

So excited to finally be able to share my first paper and the culmination of my PhD work with @felipekteixeira.bsky.social 🪰🔬

www.pnas.org/doi/10.1073/...

a life changing opportunity made possible by the Nobel Prize funds awarded to John Sulston -- the @sangerinstitute.bsky.social runs the Sanger Prize scheme, open to an undergrad from any LMIC to spend 3 months here learning all about genomics. more details here www.sanger.ac.uk/about/study/...

🪱 Selfish genes are everywhere and drive some of biology’s biggest innovations (CRISPR, antibody recombination, epigenetics). Yet almost no one asks the obvious question: how does a selfish gene begin? Our new manuscript uncovers how selfishness can emerge directly from the host genome.

Helixer: ab initio prediction of primary eukaryotic gene models combining deep learning and a hidden Markov model - Nature Methods By leveraging both deep learning and hidden Markov models, Helixer achieves broad taxonomic coverage for ab initio gene annotation of eukaryotic genomes from fungi, plants, vertebrates and invertebrat...

We all wish peer review to be rapid and professional: doesn’t always go like that. But I am relieved to finally see Helixer by @alisandra-denton.bsky.social and team published in Nature Method. Congratulations! www.nature.com/articles/s41...

Today in @nature.com, in work led by @adititm.bsky.social, we report the ability to prompt Evo to generate functional de novo genes.

You shall know a gene by the company it keeps!

GitHub - alanrogers/popgen: A course on population genetics A course on population genetics. Contribute to alanrogers/popgen development by creating an account on GitHub.

I taught (and co-taught) a course on human population genetics from 2000-2024. Having retired, I'm now making all the course materials public: github.com/alanrogers/p... #popgen #evbio

Rapid compensatory evolution within a multiprotein complex preserves telomere integrity Intragenomic conflict with selfish genetic elements spurs adaptive changes in subunits of essential multiprotein complexes. Whether and how these adaptive changes disrupt interactions within such comp...

How to keep in step when your (protein) partner speeds up…

Here we investigated the adaptive remodeling of a protein-protein interaction surface essential for telomere protection.

Congrats to whole team!

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

Heterochromatin boundaries maintain centromere position, size and number - Nature Structural & Molecular Biology Carty et al. identify the H3K9 methyltransferases that restrict the size and position of the centromere protein A chromatin domain, maintaining functional centromeres.

Very proud to have our latest work now online in
@natsmb.nature.com. A wonderful team effort across the centromere community, across @jansenlab.bsky.social @naltemose.bsky.social @dfachinetti.bsky.social and Giunta labs. Happy reading! 1/4

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

An infographic describing the drain of scientific publishing

In general, let's just stop paying companies that host this BS.

Fight the drain of scientific publishing.

arxiv.org/abs/2511.04820

Functions of RNA m6A methylation at the molecular, genomic and organismal level: go.nature.com/484M6pB
Free to read here: rdcu.be/eR4zx

Happy to share that my PhD project is finally published!🪱✨
Selfish genes are found across the tree of life. They can disrupt inheritance patterns and at the same time act as units for molecular innovation. Here we tried to answer one big question: how do selfish genes emerge in the first place?

Revised evolutionary relationships within Brachycera and the early origin of bicoid in flies Mulhair et al. uncover a functional bicoid in non-cyclorrhaphan flies, pushing the gene's origin back by ∼20 million years. Reassessing the Diptera phylogeny using the largest dataset to date permits ...

Latest work out today in @currentbiology.bsky.social

We find the fly development gene bicoid is much older than previously thought (~20 million yrs older!) 🪰🧬

To pinpoint its origins we tackled the Diptera phylogeny, providing some resolution (many open questions remain).

🔗 tinyurl.com/2vyuevpy

CRISPR-Cas–mediated heritable chromosome fusions in Arabidopsis The genome of Arabidopsis thaliana consists of 10 chromosomes. By inducing CRISPR-Cas–mediated breaks at subcentromeric and subtelomeric sequences, we fused entire chromosome arms, obtaining two eight...

And now we have Arabidopsis plants with 8 chromosomes instead of 10 and no obvious phenotypic differences, this week in @science.org
#PlantScience
Paper here: www.science.org/doi/10.1126/...

Perspective here:
www.science.org/doi/10.1126/...

Sharing this important article... for no reason whatsoever.

"We must also continue to deepen and refine our understanding of fundamental biological processes because these details frequently hold the keys to major advances in applied research."

elifesciences.org/articles/102...

Finally out in @nature.com! We uncovered a mechanistic framework for a general and conserved mRNA nuclear export pathway. www.nature.com/articles/s41.... 1/

Excited to share our new @narjournal.bsky.social paper!

Using ReLo and AlphaFold, we described a network of interactions between Drosophila piRNA pathway factors suggesting new links how they coordinate to ensure transposon silencing and genome integrity.

academic.oup.com/nar/article/...

A few py2Dmol updates 🧬

py2dmol.solab.org
Integration with AlphaFoldDB (will auto fetch results). Drag and drop results from AF3-server or ColabFold for interactive experience! (1/4)

GBE | De Novo Gene Emergence: Summary, Classification, and Challenges of Current Methods

Grandchamp, @drdomain.bsky.social et al. publish a new Review on commonly used methods for de novo gene detection, address the limitations of nomenclature and detection methods, and establish a de novo gene annotation format to standardize reporting

🔗 doi.org/10.1093/gbe/evaf197

#genome #evolution

Summer Undergraduate Research Experience | HHMI The Cech Fellows Program is a paid, nine-week summer research experience empowering the next generation of scientific leaders.

Calling all rising juniors & seniors: Interested in biological or biomedical research? Applications for our ’26 Summer Undergraduate Research Experience Program are now open! Nine weeks, hands-on research, & mentorship from some of the nation’s top scientists — learn more: bit.ly/CechFellows

An advertisement for the project Cryptc consequences of a selfish X chromosome. It shows chromosome mapping indicating many inversions, flies with eye colour phenotypes (wild-type brighter than selfish X), and sections of testes that show ordered (wild-type) or deformed structure (selfish X).

We have a funded NERC PhD studentship!

Selfish X chromosomes are these bizarre things where males carrying the selfish X suffer from imploding testes. Lots to do in this space, especially in evolutionary, stress, and infection biology.

Please share!

#PhDchat #AcademicSky @uniexecec.bsky.social

Check this out. @artermeret.bsky.social and @spo11rulz.bsky.social cleverly used protein structural information to pinpoint the action of selection and evolutionary constraints in 3D space on meiotic recombination proteins.

#GI2025 Vikram Shivakumar from Ben Langmead's lab (@benlangmead.bsky.social) presents "MumemtoM - partitioned Multi-MUM finding for scalable pangenomics ". Now published in Genome Research @genomeresearch.bsky.social. Read full text here ➡️ tinyurl.com/Genome-Res-2...

Required reading for cell biologists to get a sense of basic statistical principles!

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

Choose your human genome reference wisely - Nature Methods Scientists can choose between multiple human genome references, and a pangenome reference is coming. Deciding what to use when is not quite straightforward.

As new human assemblies become available on beta.ensembl.org - which human reference genome will you choose? This article explores the question with insights from Ensembl’s own Fergal Martin - www.nature.com/articles/s41...

#HumanGenomics #Pangenomes #ReferenceGenomes

🐸 Xenopus laevis 💚 The frog that shaped modern developmental biology! ✨ Xenopus embryos have revealed how the body axis forms, cells choose their fate, and tissues self-organize during early development 📹 Video by Bioquest Sudio and Xenbase #ModelMonday #DevBio

a, Next-generation sequencing (NGS)-based methods require pretreatment or pre-labelling of the nucleic acid with antibodies (left), restriction enzymes or endonucleases (middle), or chemicals (right) before sequencing, so that modified and unmodified bases can be distinguished during NGS sequencing. b, Long-read sequencing (LRS)-based methods can directly detect modified bases. In single-molecule, real-time (SMRT) sequencing (left), a DNA polymerase (or reverse transcriptase for RNA) is bound within the zero-mode waveguide (ZMW). When a dNTP is incorporated at the polymerase active site, it will emit a fluorescent pulse in the corresponding colour channel. The order of pulses provides the read sequence and inter-pulse duration (IPD) between base incorporation events indicates the presence of a covalent modification in the DNA or RNA template. Nanopore sequencing (right) relies on engineered biological nanopores embedded in a lipid membrane to sequence single-stranded DNA (ssDNA) or RNA. The ionic current measured as DNA or RNA gets ratcheted through the nanopore depends on the precise set of nucleotides occupying the constriction point. Modified nucleotides in the ssDNA or RNA introduce distinct current patterns, making it possible to detect the existence of modified bases relative to non-modified nucleotides.

DNA and RNA modification mapping methods based on next-generation sequencing and long-read sequencing technologies
go.nature.com/47yAbPc

For over 20 years, the mouse model organism has helped scientists uncover the biology behind human health and disease.

But the mouse reference genomes still have missing pieces.
The first collection of telomere-to-telomere mouse genomes are now available for two key mouse strains.
🧬💻

General framework for centromere organisation built on a model of the internal stratification of the Earth

Special issue: The discovery of CENP-A, the centromere-specific histone H3 variant turns 40 years!
Sam Corless @scorless.bsky.social and Goks Thangaval @gokilavani.bsky.social are Revisiting the question: When is a centromere not a kinetochore? Check it out. rdcu.be/eMJkd