Elias Dohmen

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

Release RAxML-NG v2.0-beta2 · amkozlov/raxml-ng Main new features Adaptive tree search heuristic (Togkousidis 2023) , (Togkousidis 2024) Multiple fast branch support measures Integrated model testing Full Changelog: 1.2.2...2.0-beta2

RAxML-NG v2.0 beta is here

github.com/amkozlov/rax...
Features
1. Difficulty prediction
academic.oup.com/mbe/article/...
2. Adaptive search academic.oup.com/mbe/article/...
3. Early Stop
www.biorxiv.org/content/10.1...
4. Model selection
5. Rapid bootstrapping academic.oup.com/mbe/article/...

We are pleased to announce that the next speaker in the ProSE seminar series will be Dr. Klara Hlouchova with a talk on "Protein Structure Before LUCA"
May 13, 4PM CET
Registration link: tinyurl.com/prose-seminar4
Please share!

Could you elaborate what InterPro-N matches are or point me to where I find more info about it? I associated it first with the former DL-based Pfam-N motifs, which don't exist anymore I guess...?

F1000Research Article: Recommendations for connecting molecular sequence and biodiversity research infrastructures through ELIXIR. Read the latest article version by Robert M. Waterhouse, Anne-Françoise Adam-Blondon, Donat Agosti, Petr Baldrian, Bachir Balech, Erwan Corre, Robert P. Davey, Henrik Lantz, Graziano Pesole, Christian...

⏩ Is your institute part of the @elixir-europe.org Network?
⏩ Do you work with #biodiversity #data?

The ELIXIR #Biodiversity Community
🟢 Recommendations: f1000research.com/articles/10-...
🟦 Goals: elixir-europe.org/communities/...
🟢 Community: f1000research.com/articles/12-...

🎓 #PhD in Evolutionary Ecology @UniBayreuth 🇩🇪

Parental care vs microbe communities in burying beetles 🪲🧫
ERC-funded | 3 years | behavioral ecology & metabarcoding

Details: tinyurl.com/CareVsMicrobes

Apply by May 16, start in September

#AcademicSky #Microbiome #SocialEvolution #Insects

Darwin Tree of Life Impact Assessment This form is used to share information within DToL about case studies, ongoing research, and funding awards that demonstrate the impact the Darwin Tree of Life consortium project has had on Global and...

Do you use Darwin Tree of Life (DToL) genomes for your work or grant applications? If so, can you please fill out this form? docs.google.com/forms/d/e/1F... We are gathering info on how DToL genomes are used. It will help us raise money to continue producing publicly available high-quality genomes.

Unravelling termite evolution with 47 high-resolution genome assemblies Termites are a lineage of social cockroaches abundant in tropical ecosystems where they are key decomposers of organic matter from wood to soil. Despite their ecological significance, only a handful o...

A trove of new termite genomes www.biorxiv.org/content/10.1... #biodiversity #genomics

Genomic divergence across the tree of life | PNAS Nucleotide sequence data are being harnessed to identify species, even in cases in which organisms themselves are neither in hand nor witnessed. Bu...

How #genome-wide sequence divergence maps to species status www.pnas.org/doi/10.1073/... #biodiversity #genomics

Happy to see this work out (with @margaubel.bsky.social and @lacholt.bsky.social )! 🥳
We're curious about your feedback! 🔬 (3/3)

We collected a lot of feedback from the community and developed not only a standardised, still flexible annotation format, but as well a toolkit to annotate, convert and compare studies in this format in a quick and easy way without reading long papers or manuals beforehand. (2/3)

De novo genes research community 🧬 - please consider using for your future or past work our new methodology annotation format for better comparability of studies and higher reproducibility. (1/3)

Dear Blueskye-verse, I have a question:

We are about to buy a new 96-well microplate-reader that we want to use for measuring OD and fluorescence in long-term-cultivation experiments inside the platereader (to e.g. measure growth rate). Which instruments/ brand can you recommend?

Genome sequencing, assembly, curation, and downstream analyses Advances in long-read sequencing methods such as Pacific Biosciences (PacBio) and Oxford Nanopore Technologies (ONT) and scaffolding approaches using chromosome conformation capture have significantl…

🧪📣Course alert!📣🧪

Applications are open for the new edition of the @EMBO.org course on Genome assembly and downstream analysis in Florence 🇮🇹. We can’t wait to welcome a new group of participants after the success of🇧🇪 & 🇪🇸 editions.

🗓️ Apply by May 31.

🧪🧬🖥️ #EMBOgenomeSeq #ScienceTraining

Maintenance of long-term transposable element activity through regulation by nonautonomous elements Abstract. Transposable elements are DNA sequences that can move and replicate within genomes. Broadly, there are 2 types: autonomous elements, which encode

Check out the recent "Genetics" paper by our Gevol members Pete Czuppon and Daniel Omole: "Maintenance of long-term transposable element activity through regulation by nonautonomous elements" doi.org/10.1093/gene...

ESEB2025 "The Future Meets the Beginning: Synthetic Biology, evolution & origin of Life" symposium flyer, which features Klara Hlouchova and Ryo Mizuuchi as featured speakers, and is organized by Bruno Cuevas-Zuviría, Katsumi Hagino, and Evrim Fer.

Join us this August in Barcelona for the @eseb2025.bsky.social. In "The Future Meets The Beginning: Synthetic Biology, Evolution & Origin of Life," we will explore the connections between these topics. Submit your abstract before the 25th of April! #evolution #science #synthetic_biology

Marie, Sarah, Bharat and Lars (@lacholt.bsky.social) presented their research last week at the Münster Evolution Meeting 2025!

We are looking forward to your abstracts for our Syposium #29 Genomic Basis of Evolutionary Innovations @eseb2025.bsky.social in 🌞Barcelona this August ➡️ eseb2025.com/list-of-symp...

Excellent first day (and finish) at MEM25 :) with @drdomain.bsky.social and @joskramer.bsky.social & @kathrinaotte

Scientists use AI to design life-like enzymes from scratch Combined approach takes AI-engineered enzymes one step closer to practical applications.

The AI tools in the study could one day be used to design enzymes capable of entirely new chemical reactions that do not exist in nature, says @noeliaferruz.bsky.social in @nature.com. “The limitations are just basically your imagination; you can design anything.”

I am trying to find everyone working on plant genomics:
go.bsky.app/NqARJ7V
Please let me know who is already on @bsky.app, but missing in this #PlantGenomics starter pack