Dear @anthropic.com, my lab builds a lot of OSS for genomics (github.com/COMBINE-lab). While we lack the widespread OSS market of popular NPM packages, pieces of our software are critical in biomedical research. Please consider extending your Claude Max offer to such labs!
Hannah
We are delighted to welcome Hannah to our group. She will conduct long-read sequencing to explore plant genomes. We are excited to have her on board and look forward to amazing discoveries ahead!
www.izmb.uni-bonn.de/en/pbb/team
#PlantGenomics #LongReadSequencing #Bioinformatics #Nanopore
This is an amazing piece of scientific satire by @russcd.bsky.social. The first sentence alone is a banger:
"The defining goal of the academic endeavor is to establish a single perfect value that completely summarizes entire careers’ achievements."
academic.oup.com/mbe/article/...
A molecular 'gatekeeper' in plants opens the door for beneficial microbes
Congratulations, @ottlab.bsky.social on a great paper in Science.
www.cibss.uni-freiburg.de/news/a-molec...
On one hand I am really excited to try running kallisto using GPUs and do 50 sec/sample; on the other hand I am very bad at remembering how to submit GPU jobs on the cluster. 😅
Purple flowers with long red filaments and light orange anthers
Amorpha canescens, our Lead Plant, blooming at Rocky Mountain Arsenal National Wildlife Refugee #nativeplants
#FallBackFlowers #FallBack to Sep. 7 🌿
Amorpha means ‘without form’ since this genus’ flowers have only one petal, unlike most "pea-shaped" flowers, missing the wing and keel petals.
Begonia manicata plant with red, soft outgrowths emerging from the leaf and stems. Photo credit: Jakob Maximilian Horz. Source: https://doi.org/10.64898/2026.02.26.708300
🌿 New preprint: Genome sequence of Begonia manicata and genes responsible for striking red color of its leaf/stem outgrowths. Pigmentation appears linked to anthocyanin biosynthesis genes that are strongly expressed in the red tissues
📄 doi.org/10.64898/202...
#PlantGenomics @puckerlab.bsky.social
Summary of our "Plant Bioinformatics" course content. Generated with ChatGPT. Details: https://github.com/bpucker/PlantBioinformatics
This week in our "Plant Bioinformatics" course: students practice critically evaluating scientific papers. We check: data availability, reproducibility, and whether claims are supported by evidence. Teaching reproducible science 🌱
github.com/bpucker/Plan...
#RNAseq #Bioinformatics #OpenScience
A general evolutionary model for the emergence of novel characters from serial homologs
doi.org/10.1101/2025...
DupyliCate: mining, classifying, and characterizing gene duplications
doi.org/10.1101/2025...
#Bioinformatics #Genomics
A comprehensive assessment of tandem repeat genotyping methods for Nanopore long-read genomes
doi.org/10.64898/202...
Large scale genomic rearrangements in selected Arabidopsis thaliana T-DNA lines are caused by T-DNA insertion mutagenesis
doi.org/10.1101/2021...
#Genomics #Bioinformatics
BOTANIC-0: a series of foundation models for plant genomic data
doi.org/10.64898/202...
Cookbook for plant genome sequences
doi.org/10.1186/s128...
#PlantGenomics #LongRead #Bioinformatics #AI
How many bromeliads are there?
doi.org/10.64898/202...
Tracing the evolutionary and genetic footprints of atmospheric tillandsioids transition from land to air
doi.org/10.1038/s414...
Jan Malik's photos of carnivorous plants in New York and New Jersey.
whyevolutionistrue.com/2026/03/02/r...
Pangenomes, really?
Most early “pangenomes” = oligogenomes (oligo, Gr., few).
More recent “pangenomes” generally = poligenomes (polis, Gr., many).
True pangenomes (pas, Gr., every/all) would be rare indeed.
🙏🏼 @zbao.bsky.social for pointing out his review.
www.nature.com/articles/s41...
Sequencing output per P2 flow cell. Details: https://www.izmb.uni-bonn.de/en/pbb/news#P2OS
We (Julie) are still very active in the long-read sequencing business. Please see an updated figure regarding the output per P2 flow cell below. Reach out if you would like to collaborate!
Details: www.izmb.uni-bonn.de/en/pbb/news#...
#PlantGenomics #LongReads @bpucker.bsky.social
Diversity of Asteraceae flower pictures. Source: https://commons.wikimedia.org/wiki/File:Asteracea_poster_3.jpg, CC BY-SA 3.0
Plants do not just turn red when stressed: pathogen-induced red pigmentation actively boosts disease resistance through protective anthocyanins in Asteraceae #FlavonoidFriday (doi.org/10.64898/202... & shorturl.at/TolZT)
Be part of OMGN! Open to all researchers with an interest in oomycetes, from molecular genetics & genomics to biology, population biology, and ecology, at either an experimental or a computational level. Investigators new to the field are always welcome oomycetes.com
Flowering desert lily underneath yesterday's spectacular sunset lenticular clouds. The lily sits on bare compact soil with rocks.
Flowering desert lily underneath yesterday's sunset lenticular clouds (Photo: Sicco Rood).
#ECR #PlantSciConfi
Please share with potentially interested colleagues :)
#Bioinformatics #Genomics #EvolutionaryBiology
Are you passionate about computational biology and the evolution of specialized plant metabolism? We invite highly motivated and experienced students and early-career researchers to join our group in Bonn for a visiting research stay. This is a great opportunity to gain hands-on experience, exchange ideas, and work in a collaborative and supportive scientific environment with excellent computational resources. We especially welcome colleagues with prior research experience in bioinformatics, phylogeny, evolutionary biology, or comparative genomics, and a strong interest in plant metabolism. Master’s students and candidates looking to strengthen their research profile are strongly encouraged to reach out. If you are proactive, curious, and eager to conduct your own research project, we would love to hear from you. More details and contact information: https://www.izmb.uni-bonn.de/en/pbb/contact#EBPCM #ComputationalBiology #Bioinformatics #EvolutionaryBiology #ComparativeGenomics #ResearchOpportunity #EarlyCareerResearchers #PhDOpportunity #ScientificCollaboration #ResearchInGermany
Are you passionate about computational biology and the evolution of specialized plant metabolism?
More details and contact information:
www.izmb.uni-bonn.de/en/pbb/conta...
#Bioinformatics #Genomics #ResearchInGermany @puckerlab.bsky.social
Yellow four-petal flower with red spots at petal bases
Eulobus californicus, the California Primrose, blooming in Anza-Borrego today #nativeplants 🌿
I wouldn’t put it this way for research, as science isn’t about winning. But I also returned last week from China with similar sentiments about Chinese prowess.
www.nytimes.com/2026/02/10/o...
Screenshots of slides of the Plant Bioinformatics lecture. More details & course materials: https://github.com/bpucker/PlantBioinformatics
🌿 Plant Bioinformatics! 💻🧬
How do we turn massive plant data into biological insight?
We cover genomics, transcriptomics, sequence analysis, phylogenetics, statistics, and reproducible research practices. Plant science is data science. 🌱
Materials:
github.com/bpucker/Plan...
@puckerlab.bsky.social
Spoiler: it's a 'yes, but...'
Is bee‐avoidance by bird‐pollinated flowers driven by nectar robbing in Erica? - Coetzee - Functional Ecology - Wiley Online Library besjournals.onlinelibrary.wiley.com/doi/10.1111/...
Two fern fronds #BlueSkyArtShow #Two #Photography #Flora #Macro #Oregon 📷
Ophrys bombyliflora (a first for me 💥) flowering today on Gran Canaria alongside Gennaria diphylla (and seeding Habenaria tridactylites) @1025m asl on a NW facing slope under pine & eucalyptus. Orchis canariensis in full bloom nearby. Happy days! 💜🇪🇸🌋 @ukorchids.bsky.social @orchidvinny.bsky.social
On the consistency of duplication, loss, and deep coalescence gene tree parsimony costs under the multispecies coalescent
doi.org/10.64898/202...
DupyliCate - mining, classifying, and characterizing gene duplications
doi.org/10.1101/2025...
Enhanced phenylalanine biosynthesis amplifies light-stress-driven phenylpropanoid production in Arabidopsis
doi.org/10.64898/202...
Diversity and ecological functions of anthocyanins
doi.org/10.1186/s128...
#Phenylpropanoids #Flavonoids #Anthocyanins
They are feeding our proposals to ChatGPT to ask "is this DEI" and then ChatGPT will use our proposals, which is supposed to be confidential and proprietary, to train its next model. Talking about breach of confidentiality and intellectual theft.
