Katharina Hoff
@katharinahoff.bsky.social
Genome annotation geek at University of Greifswald, always interested in friendly scientific collaboration. Developer of BRAKER, GALBA, MakeHub and other Gaius-Augustus tools.
Pinned
Katharina Hoff
@katharinahoff.bsky.social
· Oct 24
Release v1.1.7 · Gaius-Augustus/Tiberius
⚠️ New Models available:
Diatoms
Eudicotyledons
Lepidoptera
Monocotyledonae
Mucoromycota
Saccharomycota
Sordariomycota
Several bugfixes.
github.com
With help of international colleagues at @jgi.doe.gov, @oregonstate.edu, and @stockholm-uni.bsky.social, we are relasing new parameters for Tiberius. Thx to Lars Gabriel, @tomasbruna.bsky.social, Samuel Talbot, @chriswheat.bsky.social, @masta.bsky.social - and many others. github.com/Gaius-August...
What has to change in the German academic system? In my opinion, achievements should be rewarded. Some countries have criteria for in-house promotions & tenure in place. In Germany, that is very difficult. Our anti nepotism laws make it hard. www.nature.com/articles/d41...
How to stop the revolving door of German academia
Germany is one of the most popular destinations for students and scholars worldwide, but those pursuing academic careers face significant hurdles to success.
www.nature.com
November 29, 2025 at 9:46 AM
What has to change in the German academic system? In my opinion, achievements should be rewarded. Some countries have criteria for in-house promotions & tenure in place. In Germany, that is very difficult. Our anti nepotism laws make it hard. www.nature.com/articles/d41...
Reposted by Katharina Hoff
Corinna and I were awarded the “FAIR Software Award Lower Saxony 2025” on Monday at TU Braunschweig!
We are thrilled that our bHLH_annotator tool convinced the jury.
Check it out here: doi.org/10.1186/s128...
#OpenScience #FAIR #Python @puckerlab.bsky.social
We are thrilled that our bHLH_annotator tool convinced the jury.
Check it out here: doi.org/10.1186/s128...
#OpenScience #FAIR #Python @puckerlab.bsky.social
November 28, 2025 at 5:41 AM
Corinna and I were awarded the “FAIR Software Award Lower Saxony 2025” on Monday at TU Braunschweig!
We are thrilled that our bHLH_annotator tool convinced the jury.
Check it out here: doi.org/10.1186/s128...
#OpenScience #FAIR #Python @puckerlab.bsky.social
We are thrilled that our bHLH_annotator tool convinced the jury.
Check it out here: doi.org/10.1186/s128...
#OpenScience #FAIR #Python @puckerlab.bsky.social
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...
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...
www.nature.com
November 28, 2025 at 4:58 AM
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...
Reposted by Katharina Hoff
📢 Job alert: Post-Doc Position in the project "Functional annotation of genomic🧬 innovations in a densely populated clade🪰 with deep learning 💻" Join the GEvol community in a collaborative project between @bornberglab.bsky.social and @katharinahoff.bsky.social lab.
👉 bornberglab.org/post-doc-pos...
👉 bornberglab.org/post-doc-pos...
Post-Doc – bornberglab.org
bornberglab.org
November 26, 2025 at 10:09 AM
📢 Job alert: Post-Doc Position in the project "Functional annotation of genomic🧬 innovations in a densely populated clade🪰 with deep learning 💻" Join the GEvol community in a collaborative project between @bornberglab.bsky.social and @katharinahoff.bsky.social lab.
👉 bornberglab.org/post-doc-pos...
👉 bornberglab.org/post-doc-pos...
Reposted by Katharina Hoff
PhD position available for theoretical and statistical modeling in my joint @gevol.bsky.social project with @luisapallares.bsky.social on the evolution of transcriptional variability and its role in adaptation and evolutionary innovation.
See
job-portal.lmu.de/jobposting/6...
See
job-portal.lmu.de/jobposting/6...
PhD candidate in biology — theoretical and statistical modeling (m/f/x)
job-portal.lmu.de
November 26, 2025 at 2:37 PM
PhD position available for theoretical and statistical modeling in my joint @gevol.bsky.social project with @luisapallares.bsky.social on the evolution of transcriptional variability and its role in adaptation and evolutionary innovation.
See
job-portal.lmu.de/jobposting/6...
See
job-portal.lmu.de/jobposting/6...
Reposted by Katharina Hoff
🎉We are happy to announce that our wonderful GEvol SPP will be funded by @dfg.de for another 3 years. Included are 17 great projects all over Germany with amazing people. You want to be part of this fantastic community? Soon you can find new PhD/Post-Doc positions here & on our website. Stay tuned🎉
November 10, 2025 at 11:39 AM
🎉We are happy to announce that our wonderful GEvol SPP will be funded by @dfg.de for another 3 years. Included are 17 great projects all over Germany with amazing people. You want to be part of this fantastic community? Soon you can find new PhD/Post-Doc positions here & on our website. Stay tuned🎉
Reposted by Katharina Hoff
🚀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 Katharina Hoff
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 Katharina Hoff
🧩 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.
Reposted by Katharina Hoff
📢 Check out our GEvol inspired Special Issue in JEZ-B:
onlinelibrary.wiley.com/toc/15525015... 🚨
onlinelibrary.wiley.com/toc/15525015... 🚨
Genomic Basis of Evolutionary Innovations in Insects: Journal of Experimental Zoology Part B: Molecular and Developmental Evolution: Vol 344, No 7
The Journal of Experimental Zoology – B (JEZ-B): Molecular and Developmental Evolution covers the structure & evolution of animal & non-animal organisms.
onlinelibrary.wiley.com
November 3, 2025 at 7:41 AM
📢 Check out our GEvol inspired Special Issue in JEZ-B:
onlinelibrary.wiley.com/toc/15525015... 🚨
onlinelibrary.wiley.com/toc/15525015... 🚨
Reposted by Katharina Hoff
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 Katharina Hoff
Es ist soweit – mit Eurer Hilfe haben wir die 2k Unterschriften geknackt! 🥳
Die Kampagne wird fortgeführt, der Brief kann weiterhin hier unterzeichnet werden: ✍️ c.org/mvvg2V2nND
Wir freuen uns über jede weitere Verbreitung unseres offenen Briefs!! 🙏💪
#PDprekär #IchBinHanna #IchBinReyhan
Die Kampagne wird fortgeführt, der Brief kann weiterhin hier unterzeichnet werden: ✍️ c.org/mvvg2V2nND
Wir freuen uns über jede weitere Verbreitung unseres offenen Briefs!! 🙏💪
#PDprekär #IchBinHanna #IchBinReyhan
November 6, 2025 at 1:48 PM
Es ist soweit – mit Eurer Hilfe haben wir die 2k Unterschriften geknackt! 🥳
Die Kampagne wird fortgeführt, der Brief kann weiterhin hier unterzeichnet werden: ✍️ c.org/mvvg2V2nND
Wir freuen uns über jede weitere Verbreitung unseres offenen Briefs!! 🙏💪
#PDprekär #IchBinHanna #IchBinReyhan
Die Kampagne wird fortgeführt, der Brief kann weiterhin hier unterzeichnet werden: ✍️ c.org/mvvg2V2nND
Wir freuen uns über jede weitere Verbreitung unseres offenen Briefs!! 🙏💪
#PDprekär #IchBinHanna #IchBinReyhan
The best part of 2025 is that, unexpectedly, Lucy became part of our family. She brings us so much joy.
November 1, 2025 at 11:05 AM
The best part of 2025 is that, unexpectedly, Lucy became part of our family. She brings us so much joy.
Reposted by Katharina Hoff
Beam Danneels continues at the #biodiversity25 with a presentation about resistant chemical pollutants and induced defenses in #marine_mammals (#chemical_defensome, Chad). Cetaceans lost 2 keys TF involved in the ChD. They have developed a different path. Comparative genomics gave us some insights.
October 29, 2025 at 10:41 AM
Beam Danneels continues at the #biodiversity25 with a presentation about resistant chemical pollutants and induced defenses in #marine_mammals (#chemical_defensome, Chad). Cetaceans lost 2 keys TF involved in the ChD. They have developed a different path. Comparative genomics gave us some insights.
Reposted by Katharina Hoff
Sam Speak closes the session at the #biodiversity25 with a presentation about #tilapia and the gene positive #selection for saline environments. There are 70 tilapia species with variation in saline tolerance. They sequenced several genomes within this group finding twelve positive selected genes.
October 29, 2025 at 10:55 AM
Sam Speak closes the session at the #biodiversity25 with a presentation about #tilapia and the gene positive #selection for saline environments. There are 70 tilapia species with variation in saline tolerance. They sequenced several genomes within this group finding twelve positive selected genes.
Reposted by Katharina Hoff
We close the #biodiversity25 conference with a keynote presentation by Ute Hentschel Humeida about the basis of #sponge #symbiosis. “Life has evolved in a sea of microbes”. Microbial diversity already existed before the diversification of Eukaryotes. Host-microbes symbiosis appeared early in time.
October 29, 2025 at 12:02 PM
We close the #biodiversity25 conference with a keynote presentation by Ute Hentschel Humeida about the basis of #sponge #symbiosis. “Life has evolved in a sea of microbes”. Microbial diversity already existed before the diversification of Eukaryotes. Host-microbes symbiosis appeared early in time.
Reposted by Katharina Hoff
Elisa Ramos brings us a presentation about #gulls at the #biodiversity25. The large white-headed gulls lineage has one of the faster #radiation processes of the birds of the northern hemisphere. LarOmics project aims to elucidate the genetic base of the gull #evolution.
October 28, 2025 at 2:56 PM
Elisa Ramos brings us a presentation about #gulls at the #biodiversity25. The large white-headed gulls lineage has one of the faster #radiation processes of the birds of the northern hemisphere. LarOmics project aims to elucidate the genetic base of the gull #evolution.
Reposted by Katharina Hoff
Niklas Wahlberg opens last day session at the #biodiversity25 with a wonderful presentation about diversification in #Lepidoptera. More than 1000 Lepidoptera #genomes have been sequenced! Some families have more than 100 reference genomes. They have been able to learn many things from them.
October 29, 2025 at 9:57 AM
Niklas Wahlberg opens last day session at the #biodiversity25 with a wonderful presentation about diversification in #Lepidoptera. More than 1000 Lepidoptera #genomes have been sequenced! Some families have more than 100 reference genomes. They have been able to learn many things from them.
Reposted by Katharina Hoff
Amanda Gardiner follows at the #biodiversity25 with a presentation about #genetic_diversity in sharks, rays and other vertebrates. She analyzed ROH, homozygous regions in vertebrates genomes produced by the VGP. Critically endangered species have more frequently long ROH than other species.
October 29, 2025 at 10:15 AM
Amanda Gardiner follows at the #biodiversity25 with a presentation about #genetic_diversity in sharks, rays and other vertebrates. She analyzed ROH, homozygous regions in vertebrates genomes produced by the VGP. Critically endangered species have more frequently long ROH than other species.
Reposted by Katharina Hoff
Ashwini V. Mohan follows at the #biodiversity25 presenting about the #limbless Layard’s snake skink. Snakes and caecilians lost their limbs due variations in one gene, but limbless #lizards have multiple evolutionary paths. They sequenced the Nessia layardi genome (1.55Gb) native to SriLanka.
October 29, 2025 at 10:25 AM
Ashwini V. Mohan follows at the #biodiversity25 presenting about the #limbless Layard’s snake skink. Snakes and caecilians lost their limbs due variations in one gene, but limbless #lizards have multiple evolutionary paths. They sequenced the Nessia layardi genome (1.55Gb) native to SriLanka.
Reposted by Katharina Hoff
Jeden Mittwoch stellen wir ein Mitglied von PD Prekär im Kurzinterview vor. Heute: die Bioinformatikerin PD Dr. Katharina Hoff.
Seit wann bist Du PD?
Ich habe meine Habilitationsschrift im Sommer 2020 eingereicht und bin seit Februar 2022 Privatdozentin.
Seit wann bist Du PD?
Ich habe meine Habilitationsschrift im Sommer 2020 eingereicht und bin seit Februar 2022 Privatdozentin.
October 29, 2025 at 7:05 AM
Jeden Mittwoch stellen wir ein Mitglied von PD Prekär im Kurzinterview vor. Heute: die Bioinformatikerin PD Dr. Katharina Hoff.
Seit wann bist Du PD?
Ich habe meine Habilitationsschrift im Sommer 2020 eingereicht und bin seit Februar 2022 Privatdozentin.
Seit wann bist Du PD?
Ich habe meine Habilitationsschrift im Sommer 2020 eingereicht und bin seit Februar 2022 Privatdozentin.
Reposted by Katharina Hoff
Simona Buonanno closes the 2nd day session at #biodiversity25 presenting benthic genomes in #ascidians. Botryllus schlosseri is a #species_complex. They sequenced 9 ascidian species, including 2 clades of B. schlosseri. BUSCO was higher than 90% for all the genomes.
October 28, 2025 at 3:14 PM
Simona Buonanno closes the 2nd day session at #biodiversity25 presenting benthic genomes in #ascidians. Botryllus schlosseri is a #species_complex. They sequenced 9 ascidian species, including 2 clades of B. schlosseri. BUSCO was higher than 90% for all the genomes.
Reposted by Katharina Hoff
Claire Merot opens the afternoon session at the #biodiversity25 with a presentation about the structural genetic diversity across the tree of life. Structural variants (SVs) are in order de magnitude higher than SNPs. TEs accounts for many SVs. SVs are different across different lineages.
October 28, 2025 at 2:13 PM
Claire Merot opens the afternoon session at the #biodiversity25 with a presentation about the structural genetic diversity across the tree of life. Structural variants (SVs) are in order de magnitude higher than SNPs. TEs accounts for many SVs. SVs are different across different lineages.