KatharinaHoff<p>My colleague Joscha Diehl in Greifswald is hiring an AI/XR research assistant. Applicants from Poland are particularly encouraged to apply: <a href="https://bazaogloszen.nauka.gov.pl/oferta/assistant-60/" target="_blank" rel="nofollow noopener noreferrer" translate="no"><span class="invisible">https://</span><span class="ellipsis">bazaogloszen.nauka.gov.pl/ofer</span><span class="invisible">ta/assistant-60/</span></a></p>
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KatharinaHoff@KatharinaHoff@fosstodon.org
Genome Annotation Geek, @unigreifswald , always interested in friendly scientific collaboration
- Joined
- Nov 09, 2022
KatharinaHoff<p>Are you at <a href="https://fosstodon.org/tags/PAG32" class="mention hashtag" rel="tag">#<span>PAG32</span></a>? Don’t miss the talk by Lars Gabriel on our new gene finder Tiberius on Tue at 11:50 in Pacific A! He also presents 2 posters on Tiberius. P102 is on diatom genome annotation.</p>
KatharinaHoff<p>My colleagues acquired funding for an amazing large research consortium: Wetscapes. They are now hiring. Please have a look at the open positions at <a href="https://botanik.uni-greifswald.de/experimentelle-pflanzenoekologie/wetscapes2/open-positions/" target="_blank" rel="nofollow noopener noreferrer" translate="no"><span class="invisible">https://</span><span class="ellipsis">botanik.uni-greifswald.de/expe</span><span class="invisible">rimentelle-pflanzenoekologie/wetscapes2/open-positions/</span></a></p>
KatharinaHoff<p>Big news! Tiberius, our new deep learning tool for genome annotation has been accepted for publication at Bioinformatics :-) <a href="https://doi.org/10.1093/bioinformatics/btae685" target="_blank" rel="nofollow noopener noreferrer" translate="no"><span class="invisible">https://</span><span class="ellipsis">doi.org/10.1093/bioinformatics</span><span class="invisible">/btae685</span></a></p>
KatharinaHoff
KatharinaHoff<p>Congratulations to the OrthoDB team to the paper <a href="https://doi.org/10.1093/nar/gkae987" target="_blank" rel="nofollow noopener noreferrer" translate="no"><span class="invisible">https://</span><span class="">doi.org/10.1093/nar/gkae987</span><span class="invisible"></span></a> . We are now hosting the partitions v12 files at <a href="https://bioinf.uni-greifswald.de/bioinf/partitioned_odb12/" target="_blank" rel="nofollow noopener noreferrer" translate="no"><span class="invisible">https://</span><span class="ellipsis">bioinf.uni-greifswald.de/bioin</span><span class="invisible">f/partitioned_odb12/</span></a> for BRAKER users.</p>
KatharinaHoff<p>Interested in genome annotation? Listen up! There will be several interesting talks during the BG24 Genomics Technologies Session on Tuesday Oct 29 from 20-22 CET. For example, Mario Stanke will talk about Tiberius and Pooja Strope will talk about EGAPx. Don't miss it, it's free. BG24 program: biodiversitygenomicsconference.org/programme</p>
KatharinaHoff<p>And while I am happy for one grant being funded, my career grant application failed. But whoever you are, R1, I really appreciate the thoroughness and attention to detail in your reviewer comments. Thinking about it!</p>
KatharinaHoff<p>I am thrilled that the German Research Foundation will fund the further development of our AI-based genome annotation methods! And so grateful to actually have the best possible team for this challenge!</p>
KatharinaHoff<p>We spent a large part of our summer on annotating protein coding genes in 49 diatom genomes. A joint effort of <br />@jillwegrzyn.bsky.social 's team at UConn, @miamynta.bsky.social and my own team UG. Preprint: <a href="https://arxiv.org/abs/2410.05467" target="_blank" rel="nofollow noopener noreferrer" translate="no"><span class="invisible">https://</span><span class="">arxiv.org/abs/2410.05467</span><span class="invisible"></span></a><br />Data is currently on Zenodo.</p>
KatharinaHoff<p>Inspired by Helixer (by <span class="h-card" translate="no"><a href="https://genomic.social/@Alisandra" class="u-url mention">@<span>Alisandra</span></a></span> ), we explore the potential of deep learning for genome annotation. We introduce Tiberius for highly accurate ab initio prediction of protein coding genes in mammals. Tiberius beats Augustus, BRAKER3, and Galba. <a href="https://doi.org/10.1101/2024.07.21.604459" target="_blank" rel="nofollow noopener noreferrer" translate="no"><span class="invisible">https://</span><span class="ellipsis">doi.org/10.1101/2024.07.21.604</span><span class="invisible">459</span></a></p>
KatharinaHoff<p>We had a productive meeting discussing strategies to develop digitalization in agriculture at the FLI Riems, today. <a href="https://fosstodon.org/tags/artifarm" class="mention hashtag" rel="tag">#<span>artifarm</span></a> <a href="https://fosstodon.org/tags/AI" class="mention hashtag" rel="tag">#<span>AI</span></a> <a href="https://fosstodon.org/tags/MV" class="mention hashtag" rel="tag">#<span>MV</span></a></p>
KatharinaHoff<p>Have you heard? </p><p>The <a href="https://fosstodon.org/tags/BG24" class="mention hashtag" rel="tag">#<span>BG24</span></a> abstract deadline has been extended. 🗓️</p><p> Abstracts due July 7th! ⏰ Submit here: <a href="https://biodiversitygenomicsconference.org" target="_blank" rel="nofollow noopener noreferrer" translate="no"><span class="invisible">https://</span><span class="ellipsis">biodiversitygenomicsconference</span><span class="invisible">.org</span></a></p><p>Don't miss out - share your research. 📢 </p><p>Please re-share to your networks to help spread the word.</p>
KatharinaHoff<p>This morning, I discussed the application of BRAKER2 to marine eukaryotic metagenomes. Slides are available at ResearchGate: <a href="https://doi.org/10.13140/RG.2.2.23455.78246" target="_blank" rel="nofollow noopener noreferrer" translate="no"><span class="invisible">https://</span><span class="ellipsis">doi.org/10.13140/RG.2.2.23455.</span><span class="invisible">78246</span></a></p>
KatharinaHoff<p>BRAKER3 is setting a new standard in genome annotation accuracy in eukaryotes. We proudly present joint work of the teams of @mborodovsky and @Goemario, appearing in @genomeresearch <a href="http://m.genome.cshlp.org/content/early/2024/05/28/gr.278090.123" target="_blank" rel="nofollow noopener noreferrer" translate="no"><span class="invisible">http://</span><span class="ellipsis">m.genome.cshlp.org/content/ear</span><span class="invisible">ly/2024/05/28/gr.278090.123</span></a></p>
KatharinaHoff<p>Lese-Empfehlung: <a href="https://open.substack.com/pub/arbeitinderwissenschaft/p/weil-du-eine-frau-bist-zum-stand?utm_campaign=post&utm_medium=web" target="_blank" rel="nofollow noopener noreferrer" translate="no"><span class="invisible">https://</span><span class="ellipsis">open.substack.com/pub/arbeitin</span><span class="invisible">derwissenschaft/p/weil-du-eine-frau-bist-zum-stand?utm_campaign=post&utm_medium=web</span></a></p>
KatharinaHoff<p>Navigating Eukaryotic Genome Annotation Pipelines: A Route Map to BRAKER, Galba, and TSEBRA, a book chapter with Tomas Bruna and Lars Gabriel, now on arXiv: <a href="https://arxiv.org/abs/2403.19416" target="_blank" rel="nofollow noopener noreferrer" translate="no"><span class="invisible">https://</span><span class="">arxiv.org/abs/2403.19416</span><span class="invisible"></span></a></p>
KatharinaHoff<p>My colleague Stefan Simm (stefan.simm@uni-greifswald.de) is looking for a PhD student with a keen interest in AI (e.g. pytorch, tensorflow) and image as well as NGS analysis. If you are interested, I will be happy to e-mail you the full job description PDF. Nice Group!</p>
KatharinaHoff<p>Cool paper lead by the team of <br />@miamynta<br /> : <a href="https://doi.org/10.1093/femsec/fiae037" target="_blank" rel="nofollow noopener noreferrer" translate="no"><span class="invisible">https://</span><span class="">doi.org/10.1093/femsec/fiae037</span><span class="invisible"></span></a> It's cool because we did not previously know that sulfate reducing bacteria play a role in diatom blooms.</p>
KatharinaHoff<p>I worked on visualizing the BRAKER and Galba input files and their formats, today. Sharing the fun.</p>
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