iiinova — where your digital self keeps evolving

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

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

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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/...

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🧩 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.

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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

academic.oup.com

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Sebastian Höhna @hoehna.bsky.social · 11/11/2025

🚀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.

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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

hoehnalab.github.io

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Lars Eicholt @lacholt.bsky.social · 03/11/2025

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...

academic.oup.com

DeNoFo: a file format and toolkit for standardized, comparable de novo gene annotation

AbstractMotivation. De novo genes emerge from previously non-coding regions of the genome, challenging the traditional view that new genes primarily arise

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Oded Rechavi @odedrechavi.bsky.social · 15/10/2025

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 👇)

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James McInerney @jomcinerney.bsky.social · 09/09/2025

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

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Elias Dohmen @drdomain.bsky.social · 08/09/2025

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! ☺️

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Christian Kost @kostchristian.bsky.social · 01/09/2025

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

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Kelsey J.R.P. Byers @plantpollinator.bsky.social · 19/08/2025

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 :-)

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Christian Kost @kostchristian.bsky.social · 18/08/2025

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

shorturl.at

116 FB 5 Research Assistant (m/f/d) field of Theoretical Ecology and Evolution or Computational Biology: Uni Osnabrück

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Nico Posnien @posnienlab.bsky.social · 08/08/2025

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.

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Christian Kost @kostchristian.bsky.social · 08/08/2025

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

shorturl.at

116 FB 5 Research Assistant (m/f/d) field of Theoretical Ecology and Evolution or Computational Biology: Uni Osnabrück

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Laurie Belcher @lauriebelch.bsky.social · 16/07/2025

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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Earth BioGenome Project 🌍 @ebpgenome.bsky.social · 23/06/2025

🚨 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

bit.ly

Understanding Life: Using Largescale Biodiversity Reference Genomes — 20251027

Understanding life: Using largescale biodiversity reference genomes

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Elias Dohmen @drdomain.bsky.social · 12/06/2025

🧬 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...

Elias Dohmen @drdomain.bsky.social · 12/06/2025

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🚨 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 🧵👇)

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Society for Molecular Biology and Evolution @official-smbe.bsky.social · 18/04/2025

📖 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

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Gregg Thomas @gwct.bio · 05/06/2025

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...

github.com

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

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Rob Waterhouse @rmwaterhouse.bsky.social · 24/05/2025

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

nature.com

WorkflowHub: a registry for computational workflows - Scientific Data

Scientific Data - WorkflowHub: a registry for computational workflows

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Alexis Stamatakis @stamatak.bsky.social · 15/05/2025

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/...

github.com

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

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Claudia Alvarez Carreño @claudiaalcar.bsky.social · 01/05/2025

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!

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Elias Dohmen @drdomain.bsky.social · 25/04/2025

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...?

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Jos Kramer @joskramer.bsky.social · 24/04/2025

🎓 #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

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Joana Meier @joanameier.bsky.social · 24/02/2025

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.

docs.google.com

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...

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Elias Dohmen @drdomain.bsky.social · 03/04/2025

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

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Elias Dohmen @drdomain.bsky.social · 03/04/2025

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)

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Elias Dohmen @drdomain.bsky.social · 03/04/2025

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)

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Christian Kost @kostchristian.bsky.social · 03/04/2025

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?

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Silvia Manrique @tank-silvia.bsky.social · 02/04/2025

🧪📣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

meetings.embo.org

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…

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SPP 2349 Gevol @gevol.bsky.social · 02/04/2025

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...