Elias Dohmen

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

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YouTube video by ERGA - European Reference Genome Atlas What is ERGA? - European Reference Genome Atlas

Sign up today to receive the monthly newsletter from the ERGA European Reference Genome Atlas to learn about #biodiversy #genomics initiatives in #Europe, courses, jobs, conferences, & more www.youtube.com/watch?v=kYL9...

check out the accompanying paper doi.org/10.1093/gbe/... as well!

check out the accompanying paper doi.org/10.1093/bioi... as well!

Grateful to my co-authors @anna-grandchamp.bsky.social , @margaubel.bsky.social , @lacholt.bsky.social, Victor Luria and Amir Karger — great teamwork all around! 🙌

Let’s keep the conversation going — what questions does this raise for your own research? 🔍

🧬 Read more: doi.org/10.1093/gbe/...

🧩 Thrilled to share our new paper in @genomebiolevol.bsky.social !

We present a comprehensive review of de novo gene emergence — providing a classification of current detection methods and a roadmap for addressing major challenges in the field of gene birth from non-genic sequences.

Big thanks to @anna-grandchamp.bsky.social , @margaubel.bsky.social , @lacholt.bsky.social and many others for making this happen!

We’d love to hear from the community — how could this be most useful in your workflows? 💬

📄 Read it: doi.org/10.1093/bioi...
💻Try it: github.com/EDohmen/denofo

🚀We’re excited to share our new paper in Bioinformatics!

We introduce a user-friendly toolkit that implements our novel DeNoFo file-format for standardised annotation of de novo gene detection workflows — enabling reproducible methodology descriptions and easier dataset comparison across studies.

PhD position available in evolutionary genomics/bioinformatics (hoehnalab.github.io/job_adverts/...). Topic: analyzing gene expression evolution across several firefly species and linking expression changes to genomic architecture. The position is jointly supervised with @anaevolcatalan.bsky.social

The DeNoFo format & toolkit for annotating, assessing and comparing the tools and tresholds used in studies of de novo evolved genes is out now in Bioinformatics! Great effort led by @drdomain.bsky.social and Anna Grandchamp!

academic.oup.com/bioinformati...

BIG ANNOUNCEMENT📣: I haven’t been this excited to be part of something new in 15 years… Thrilled to reveal the passion project I’ve been working on for the past year and a half!🙀🥳 (thread 👇)

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

Going into my last week @uni-muenster.de and was really happy to have a final meeting with so many awesome people from @gevol.bsky.social . Good luck to all of you for your second phase projects, a great time and hopefully I'm crossing paths with some of you in the future! ☺️

Only 10 days left to apply:

We are searching for a senior postdoc (3 +3 years) in the field of theoretical ecology and evolution.

The position provides the opportunity to closely interact with experimentalists and develop own research projects.

Please RT.

Details 👇:
shorturl.at/iiiOv

Robert Waterhouse at #ESEB2025 - PIs/Profs please give your students a break when they're doing orthology, ancestral state reconstruction, gene/species tree reconciliation work - it's not an overnight process, there are no push-button tools, and fast doesn't equal correct! Love this :-)

Detect de novo expressed ORFs in transcriptomes with DESwoMAN Motivation De novo gene emergence refers to the process by which new genes arise from mutations in previously non-coding genomic regions. Prior to becoming fixed in a species, newly expressed open rea...

Grantham is Grandchamp actually (doi.org/10.1101/2025... ), but really nice to get some updates of the ESEB and what's happening although I can't be there, thanks! ☺️

Me and my group are searching for a senior postdoc (3 +3 years) in the field of theoretical/ computational biology.

The position provides the opportunity to closely interact with experimentalists and develop own research projects.

Please RT.

Deadline: 11/09/2025

Details 👇:
shorturl.at/iiiOv

If you want to discuss #networks in #evo-devo, you should join this year's satellite symposium of the @dzg2025berlin.bsky.social organized by the developmental biology section (@marketa-kau.bsky.social, Benjamin Naumann, Alexander Klimovich). I will talk about gene regulatory networks.

I am excited to announce that the position of a senior postdoc (3 +3 years) in the field of theoretical biology is available in my group.

The position provides the opportunity to closely interact with experimentalists and develop own research projects.

Please RT.

Details 👇:
shorturl.at/iiiOv

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...

BUSCO v6.0.0 has been released. busco.ezlab.org

🚨 Abstract deadline approaching!
🧬 Are you passionate about decoding life through genomics and cutting-edge science?
📅 Don’t delay—register today and submit your abstract!
🚨LINK to apply 👉 bit.ly/4n9AuqN

🧬 Reports mutations that give rise to coding potential & key properties of neORFs.
🛠️ Developed by Anna Grandchamp
🐳 Easy to run via Docker or Apptainer — no messy installs!

📄 Preprint: doi.org/10.1101/2025...
💻 GitHub: github.com/AnnaGrBio/DE...
🐋 DockerHub: hub.docker.com/r/edohmen/de...

🚨 New preprint alert! 🚨

🔬 Ever wondered how new genes emerge from scratch? Meet DESwoMAN, a fully automated pipeline to detect and analyze newly expressed ORFs (neORFs) from transcriptome data — giving us a window into the earliest stages of de novo gene emergence!

(Thread 🧵👇)

📖 SMBE journals on Bluesky

Interested in learning the latest advances in evolutionary biology, genomics, and molecular biology? Follow the SMBE sister journals MBE and GBE here on Bluesky and get updates on new articles coming out.

MBE: @molbioevol.bsky.social
GBE: @genomebiolevol.bsky.social

GitHub - harvardinformatics/cactus-snakemake: Snakemake workflows for performing whole genome alignment with Cactus efficiently on SLURM clusters Snakemake workflows for performing whole genome alignment with Cactus efficiently on SLURM clusters - harvardinformatics/cactus-snakemake

Recently I developed several Snakemake workflows for tasks related to Cactus and HAL files, including whole genome alignment and pangenome inference. The goal was to perform these tasks efficiently on SLURM-based (or possibly other) clusters. I hope they are useful!

github.com/harvardinfor...

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

WorkflowHub: a registry for computational workflows - Scientific Data Scientific Data - WorkflowHub: a registry for computational workflows

The WorkflowHub registry has a global reach, with hundreds of research organisations involved, and more than 800 workflows registered. www.nature.com/articles/s41... #bioinformatics #FAIR

Welcoming @lassemiddendorf.bsky.social as Mayor of iGEM’s Biomanufacturing Village.

This Village explores how we can grow the medicines, materials and commodities of the future using synthetic biology- powered by shared tools, scalable ideas and practical roadmaps.

villages.igem.org