Katharina Hoff

Haha, ok. Es war tatsächlich bisher in allen BKs, an denen ich bisher beteiligt war, am Anfang völlig unklar, wie die Liste aussehen soll… aber das mag anderswo anders sein.

PhD position open! Bioinformatics | Python | Phytoplankton genomics | Deep learning. Funded until 2029. If you love code AND biology, we want to hear from you. Deadline: March 15! www.uni-greifswald.de/en/universit...

Alisandra Denton invented the first deep learning gene finder that achieved impressive accuracy, the Helixer.

Jill L. Wegrzyn develops annotation evaluation standards and pipelines for structural & functional annotation of large plant genomes.

Suzanna Lewis led the fruit fly genome annotation. She played an important role in the GASP assessment that benchmarked genome annotation tools, and led the development of the original GBrowse genome browser.

Margaret Dayhoff invented the one letter amino acid code and created early sequence databases & developed tools to query them. We today still teach about PAM substitution matrices that she invented.

As genome annotation scientist, I want on woman’s day draw your attention to women who impact(-ed) eukaryotic genome annotation:

Excited to share this preprint that describes my latest work on using GPUs to accelerate processing of RNA-seq data.

The title says it all: "RNA-seq analysis in seconds using GPUs" now on biorxiv www.biorxiv.org/content/10.6... and github github.com/pachterlab/k...

Figure 1 shows they key result

Es gibt stark beschleunigte Berufungsverfahren, wenn jemand einen Ruf nach außen hat, oder dieser unmittelbar bevorsteht, und die Heimatuni die Person unbedingt halten will. Und es gibt personengebundene Drittmittelprofessuren.

Involuntarily learnt a lot about xylitol induced insulin secretion jn dogs during the weekend. Luckily the little patient is recovering well. (We will never know what she ate… but a chewing gum seems realistic.)

So how many of my colleagues are PAYING OpenAI to use their LLM again???? You see where your money is going?

Und dann bewirbt frau sich mal in Norwegen oder NL - holla, das geht zackig! Es könnte durchaus anders laufen 🙄

Hey #Physco sphere! What's your favorite protocol for purifying total RNA (or mRNA) from moss gametophores?

Marnix Medema appointed chair of Bioinformatics at WUR Marnix Medema has been appointed Chair of the Bioinformatics Group at Wageningen University & Research as of 1 February. He aims to further strengthen bioinformatics as a connecting discipline within ...

Our chairgroup Bioinformatics at Wageningen University changed leadership: prof. Dick de Ridder (@dickderidder.bsky.social) moved on to become Dean of Education and is now followed up by prof. Marnix Medema. Congrats @marnixmedema.bsky.social! www.wur.nl/en/news/marn...

PhD position open! Bioinformatics | Python | Phytoplankton genomics | Deep learning. Funded until 2029. If you love code AND biology, we want to hear from you. Deadline: March 15! www.uni-greifswald.de/en/universit...

Daylight during our morning walk 😁

New paper alert! The latest from my lab describing atypicalities in the processing of cues in the PFC and V1 of preterm mice trained on a visual discrimination task: www.nature.com/articles/s41...

#IchbinHanna-Gründerin schmeißt hin: Amrei Bahr wurde Juniorprofessorin – und verlässt die Wissenschaft Mit ihrem Einsatz für bessere Arbeitsbedingungen an Unis wurde Amrei Bahr bekannt und löste eine Bewegung aus, die das Wissenschaftssystem ändern will. Jetzt gab die Juniorprofessorin ihren Ausstieg a...

Gestern hab ich bekannt gegeben, dass ich spätestens 2028 aus der Wissenschaft aussteigen werd — darüber schreibt @evamurasov.bsky.social nun im @tagesspiegel.de. Zig Kommentare & Nachrichten zeigen mir: Sehr viele Wissenschaftler_innen hadern. Bedingungen müssen dringend besser werden! #IchBinHanna

do nextflow pipeline developers consider temporary storage needs when developing pipelines?

I love nextflow, but I feel like the modular structure encourages design choices that cause temporary storage to explode.

Scientists have seen Asgard archaea crawling for the first time. When it comes to the origin of eukaryotes, this is like seeing a feathered dinosaur in the wild. (Video courtesy of Philipp Ralder)

Congratulations to @stepbystepsolution.bsky.social to the manuscript on genome annotation of 200 insect genomes, a result his work within of @gevol.bsky.social ! doi.org/10.1038/s415...

Genome Annotation Workshop 2026 Providing scientists with a comprehensive overview of eukaryotic genome annotation approaches.

💻🧬 Keen to learn about eukaryotic genome annotation?

Registration is now open for our 2026 online #genomeannotation course, led by our core #bioinformatics team.

➡️ buff.ly/sonWCgT

Unmasked model for all genomes unless you are sure you masked exactly like the training data was masked (which varies).

The new diatom Tiberius parameters for unmasked genomes illustrate the gain in accuracy that we often observe compared to parameters for unmasked genomes. #geneprediction #genomeannotation #diatoms #bacillariophyta github.com/Gaius-August...

GitHub - Gaius-Augustus/Tiberius: Tiberius is a deep learning gene finder. Tiberius is a deep learning gene finder. Contribute to Gaius-Augustus/Tiberius development by creating an account on GitHub.

We have a new insect parameter set for unmasked genomes and a new fungal parameter set for unmasked genomes. Both deliver accuracy superior to previous models for insects and fungi. #genomeannotation #geneprediction github.com/Gaius-August...

GitHub - Gaius-Augustus/Tiberius: Tiberius is a deep learning gene finder. Tiberius is a deep learning gene finder. Contribute to Gaius-Augustus/Tiberius development by creating an account on GitHub.

What we more recently learnt about Tiberius: the models trained on softmasked genomes are very sensitive to how the genome was masked for inference. It seems safer to use models trained on unmasked genomes. #genomeannotation #geneprediction github.com/Gaius-August...

I am very, very happy! I got a pull up bar for x-mas, and today, my dear husband installed it. It’s so much easier to grip than those cheap gymnastics rings that I have used until now. Can I do a pull up? No. But the pathetic-looking attempts have changed my life. Pain is gone since I started trying

This article is now published! academic.oup.com/nargab/artic...
We’ve added a few new analyses. First off, we show that, while gene presence absence variation (PAV) scales with evolutionary distance in both plants and animals, the base level and rate of accrual are both twice as high in plants.

#ProtistsOnSky
no 'swimming' by 𝘝𝘢𝘮𝘱𝘺𝘳𝘦𝘭𝘭𝘢, definitively no 'staying still'. just a relaxed walk towards the lunch...