Paired plus-minus sequencing is an ultra-high throughput and accurate method for dual strand sequencing of DNA molecules
doi.org/10.1101/2025...

Cookbook for plant genome sequences
doi.org/10.1186/s128...

#Genomics #Bioinformatics

COMBINE lab COMputational BIology and Network Evolution lab. COMBINE lab has 137 repositories available. Follow their code on GitHub.

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!

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

The core-pivotal index: a geometry-first approach to academic impact The defining goal of the academic endeavor is to establish a single perfect value that completely summarizes entire careers’ achievements. Such an index wo

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 CIBSS researchers at the University of Freiburg are part of an international team that sheds light on a crucial step in the initiation of the symbiosis between plants and soil bacteria.

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. 😅

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.

🌿 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

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...

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

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 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?

More details and contact information:
www.izmb.uni-bonn.de/en/pbb/conta...

#Bioinformatics #Genomics #ResearchInGermany @puckerlab.bsky.social

Eulobus californicus, the California Primrose, blooming in Anza-Borrego today #nativeplants 🌿

Opinion | I Just Returned From China. We Are Not Winning.

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...

🌿 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

Is bee‐avoidance by bird‐pollinated flowers driven by nectar robbing in Erica? Read the free Plain Language Summary for this article on the Journal blog.

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