de.NBI & ELIXIR GermanyDec 8

🚀 Big news in genome annotation! The latest @naturemethods paper presents Helixer, a new deep learning tool that predicts eukaryotic gene structures directly from DNA—no RNAseq needed. Developed as part of the @deNBI infrastructure, Helixer makes high-quality genome annotations more accessible and efficient for the community.
🔗 nature.com/articles/s41592-025-02939-1

#Bioinformatics #DeepLearning #GenomeAnnotation #OpenScience

galaxyprojectOct 21

My internship experience with assembling genomes and annotating them during a 6 week internship at Freiburg Galaxy.
https://galaxyproject.org/news/2025-07-22-ming-li-internship/

@galaxyfreiburg
#UseGalaxy #GalaxyProject #EOSC #Bioinformatics #Genomics #GenomeAssembly #GenomeAnnotation #TrainingProgram #Internship #Journey #internship #OpenScience #ComputationalBiology #DataScience #ResearchExperience #NextGenScientists

Exploring Genomics with Galaxy: A Six-Week Internship Journey

My internship experience with assembling genomes and annotating them during a 6 week internship

Galaxy-Team der Uni FreiburgOct 21

My internship experience with assembling genomes and annotating them during a 6 week internship at Freiburg Galaxy.
https://galaxyproject.org/news/2025-07-22-ming-li-internship/

@galaxyproject
#UseGalaxy #GalaxyProject #EOSC #UniFreiburg #Bioinformatics #Genomics #GenomeAssembly #GenomeAnnotation #TrainingProgram #Internship #Journey #internship #OpenScience #ComputationalBiology #DataScience #ResearchExperience #NextGenScientists

Exploring Genomics with Galaxy: A Six-Week Internship Journey

My internship experience with assembling genomes and annotating them during a 6 week internship

Nikos Tsardakas RenhuldtSep 11, 2024

I’m looking for databases similar to #TAIR but for #plants that aren’t #arabidopsis. Or rather, I want to understand what some set of “standard annotations” are - what would be the go-to annotation for a given plant species? Any recommendations? Had a look at #GDR #GenomeDatabaseForRosaceae but couldn’t get my head around which of these are considered standard to use. Mostly interested in #protein sequences.

#GenomeAnnotation #genomics #PlantGenomics

Nikos Tsardakas RenhuldtJan 10, 2024
Seems like it's time for a new #introduction! I've just started a postdoc with Colin Olito and Bengt Hansson at #LundUniversity. I'll be working with #SexChromosome #evolution in Wikstroemia, doing #genomics, #GenomeAnnotation, and other #bioinformatics things related to that. I'm an avid #tidyverse and #RStats user, but with a ton of #python background. I did my PhD on #oat genomics with #ScanOats. I'm really into #visualization, and I want to learn more about statistical modelling.
KatharinaHoffDec 8, 2023
Looking forward to PAG in January! We will bring exciting news about BRAKER with different types and amounts of extrinsic evidence 😀 #genomeannotation #bioinformatics
Show threadNikos Tsardakas RenhuldtApr 23, 2023
Oh, and obviously I've done a ton of work on #oats and #GenomeAnnotation and #GeneMapping, and looked at at bunch of different types of data from #PlantGenomes - this ended up in a Nature publication on the oat genome with me as one of the first authors: https://www.nature.com/articles/s41586-022-04732-y. #GenomicPrediction and #PlantBreeding are things I'm interested in. I've also dabbled in #DeepLearning, mainly #ConvNets for protein contact prediction and image segmentation.
The mosaic oat genome gives insights into a uniquely healthy cereal crop - Nature

Assembly of the hexaploid oat genome and its diploid and tetraploid relatives clarifies the evolutionary history of oat and allows mapping of genes for agronomic traits.

Nature
Ian HolmesApr 18, 2023

#JBrowse2 has been a long time coming - seven years in development, ten if you count the first rumblings from Rob Buels. The payoff is an amazingly versatile, fast, and beautiful suite of programs for visualizing general genome annotations, relationships between genomes, and genomic evidence: https://rdcu.be/c98wf

#JBrowse #GenomeBrowser #Genomics #Bioinformatics #GenomeAnnotation #Genome #Genomes

JBrowse 2: a modular genome browser with views of synteny and structural variation

TAIRFeb 23, 2023
Latest #ArabidopsisV12 news: Automated annotation pipeline has begun at NCBI. Looking forward to reviewing the initial results by the end of March. #CommunityProject #GenomeAnnotation #GeneStructure
Show threadGallantries ProjectJan 27, 2023
@gtn Thanks to funding from Erasmus+, we'll be supporting this event with tutorials covering #GenomeAnnotation, #Oncology, #Transcriptomics, and #DataScience!