Elias Dohmen
@drdomain.bsky.social
Bioinformatician & Evolutionary Biologist
https://edohmen.github.io/
Protein Domains, De novo genes, Insects, Python, Machine Learning, ...
https://edohmen.github.io/
Protein Domains, De novo genes, Insects, Python, Machine Learning, ...
Reposted by Elias Dohmen
The PSF's 2025 end-of-year fundraiser is live 🐍🚀
#Python is for everyone—and it takes everyone to keep it thriving. Support the PSF, the Python community, and the language we love.
Join in today 💛💙 donate.python.org
#PythonForEveryone
#Python is for everyone—and it takes everyone to keep it thriving. Support the PSF, the Python community, and the language we love.
Join in today 💛💙 donate.python.org
#PythonForEveryone
PSF Fundraiser 2025
The Python Software Foundation is the charitable organization behind the Python programming language.
donate.python.org
November 12, 2025 at 5:06 PM
The PSF's 2025 end-of-year fundraiser is live 🐍🚀
#Python is for everyone—and it takes everyone to keep it thriving. Support the PSF, the Python community, and the language we love.
Join in today 💛💙 donate.python.org
#PythonForEveryone
#Python is for everyone—and it takes everyone to keep it thriving. Support the PSF, the Python community, and the language we love.
Join in today 💛💙 donate.python.org
#PythonForEveryone
Reposted by Elias Dohmen
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...
What is ERGA? - European Reference Genome Atlas
YouTube video by ERGA - European Reference Genome Atlas
www.youtube.com
September 27, 2025 at 2:27 PM
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...
🧩 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.
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.
November 12, 2025 at 3:42 PM
🧩 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.
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.
🚀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.
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.
November 12, 2025 at 12:41 PM
🚀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.
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.
Reposted by Elias Dohmen
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
November 11, 2025 at 9:00 AM
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
Reposted by Elias Dohmen
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/bioinformati...
November 3, 2025 at 7:47 PM
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/bioinformati...
Reposted by Elias Dohmen
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 👇)
October 15, 2025 at 12:22 PM
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 👇)
Reposted by Elias Dohmen
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
September 9, 2025 at 2:25 PM
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! ☺️
Many thanks to all GEvol members for a truly wonderful annual meeting. It was really great to catch up with you all again.
September 8, 2025 at 8:39 AM
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! ☺️
Reposted by Elias Dohmen
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
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
September 1, 2025 at 5:54 AM
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
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
Reposted by Elias Dohmen
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 :-)
August 19, 2025 at 12:10 PM
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 :-)
Reposted by Elias Dohmen
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
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
116 FB 5 Research Assistant (m/f/d) field of Theoretical Ecology and Evolution or Computational Biology: Uni Osnabrück
shorturl.at
August 18, 2025 at 5:35 AM
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
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
Reposted by Elias Dohmen
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.
August 8, 2025 at 6:50 AM
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.
Reposted by Elias Dohmen
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
The position provides the opportunity to closely interact with experimentalists and develop own research projects.
Please RT.
Details 👇:
shorturl.at/iiiOv
116 FB 5 Research Assistant (m/f/d) field of Theoretical Ecology and Evolution or Computational Biology: Uni Osnabrück
shorturl.at
August 8, 2025 at 10:09 AM
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
The position provides the opportunity to closely interact with experimentalists and develop own research projects.
Please RT.
Details 👇:
shorturl.at/iiiOv
Reposted by 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...
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...
July 16, 2025 at 5:51 PM
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...
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...
Reposted by Elias Dohmen
BUSCO v6.0.0 has been released. busco.ezlab.org
BUSCO - from QC to gene prediction and phylogenomics
from QC to gene prediction and phylogenomics
busco.ezlab.org
July 11, 2025 at 9:29 PM
BUSCO v6.0.0 has been released. busco.ezlab.org
Reposted by Elias Dohmen
🚨 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
🧬 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
June 23, 2025 at 3:32 PM
🚨 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
🧬 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
🚨 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 🧵👇)
🔬 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 🧵👇)
June 12, 2025 at 9:50 AM
🚨 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 🧵👇)
🔬 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 🧵👇)
Reposted by Elias Dohmen
📖 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
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
April 18, 2025 at 7:32 AM
📖 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
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
Reposted by Elias Dohmen
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/harvardinfor...
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
github.com
June 4, 2025 at 11:15 PM
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/harvardinfor...
Reposted by Elias Dohmen
YUP. Made an error in the very first post. Correct link is: github.com/mol-evol/gcua
June 1, 2025 at 7:31 PM
YUP. Made an error in the very first post. Correct link is: github.com/mol-evol/gcua
Reposted by Elias Dohmen
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
WorkflowHub: a registry for computational workflows - Scientific Data
Scientific Data - WorkflowHub: a registry for computational workflows
www.nature.com
May 24, 2025 at 12:02 PM
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
Reposted by Elias Dohmen
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
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
May 16, 2025 at 9:52 AM
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
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
Reposted by Elias Dohmen
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/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/...
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
github.com
May 15, 2025 at 5:35 AM
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/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/...
Reposted by Elias Dohmen
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!
May 13, 4PM CET
Registration link: tinyurl.com/prose-seminar4
Please share!
May 1, 2025 at 7:32 AM
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!
May 13, 4PM CET
Registration link: tinyurl.com/prose-seminar4
Please share!