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PuckerLab

@puckerlab.bsky.social
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Plant Biotechnology and Bioinformatics @unibonn.bsky.social. Hosting @igembonn.bsky.social. Contact: www.pbb.uni-bonn.de #PlantGenomics #SpecializedMetabolites #SynBio #Genomics #Bioinformatics #Biotech #Evolution #Flavonoids #Pigments

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Boas Pucker @bpucker.bsky.social · 27/09/2026
Human design or AI-generated? 🤖🎨 With AI-generated images everywhere, we get this question a lot! The figures in our publications are designed by a talented human: Marie. 🌱✨✏️🧠🌿 👉 See her work: www.izmb.uni-bonn.de/en/pbb/mh 📖 Example: doi.org/10.1111/tpj.... #SciArt #SciComm @puckerlab.bsky.social
Pathway illustration for the anthocyanin and carotenoid biosynthesis. Figure source and details: https://doi.org/10.1111/tpj.71136.
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Boas Pucker @bpucker.bsky.social · 26/09/2026
Excited to share our new paper is out in TPJ! 🌱 "Out of the blue: family-wide loss of anthocyanin biosynthesis in Cucurbitaceae" We explore the anthocyanin biosynthesis gene loss through comparative genomics: doi.org/10.1111/tpj.... @nancy-choudhary.bsky.social @puckerlab.bsky.social #Evolution
Synteny analysis supports the loss of crucial genes in the anthocyanin biosynthesis across Cucurbitaceae. Details and figure reference: https://doi.org/10.1111/tpj.71136
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Boas Pucker @bpucker.bsky.social · 14/09/2026
Julie just completed sequencing run 200 on our PromethION @puckerlab.bsky.social . Time to celebrate numerous successful plant genomics projects and to look for new challenges! www.izmb.uni-bonn.de/en/pbb/news#... #PlantGenomics #Bioinformatics #LongReads
Julie and P2 Solo
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Boas Pucker @bpucker.bsky.social · 10/09/2026
Next Botanik-Tagung is going to take place in Göttingen. Looking forward to the next meeting. Thank you, @jandevries.bsky.social ! #BT2028 @plantsciencedbg.bsky.social
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PlantEvolution 🌱🌾 @plantevolution.bsky.social · 07/09/2026
Please submit comments to the EU Commission’s Call for Evidence on how to implement the new rules for "Plants obtained by new genomic techniques (#NGT)". Submission deadline 28 Sept. Below what I submitted. #plantscience ec.europa.eu/info/law/bet... ec.europa.eu/info/law/bet...
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Boas Pucker @bpucker.bsky.social · 08/09/2026
Final talk of the session by Jakob Horz about the evolution of MYB transcription factors in plants #BT2026 #Botanik-Tagung2026 @puckerlab.bsky.social @plantsciencedbg.bsky.social
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Boas Pucker @bpucker.bsky.social · 08/09/2026
Please remember to visit our group members at their posters and attend their talks #BT2026 #Botanik-Tagung2026
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Boas Pucker @bpucker.bsky.social · 09/09/2026
You missed the talk or you would like to read about the details? Here is the corresponding preprint: doi.org/10.1101/2025... #evolution #pigments @nancy-choudhary.bsky.social @puckerlab.bsky.social
doi.org
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German Society for Plant Sciences (DBG) @plantsciencedbg.bsky.social · 11/09/2026
Review paper What we know, what we assume + what remains unknown from anthocyanin research. By @nancy-choudhary.bsky.social, N. Khatun, and @bpucker.bsky.social Read more #OpenAccess in our Journal #PlantBiology @Wileyplantsci #PlantSci DOI: doi.org/10.1111/plb....
doi.org
Almost 200 years of anthocyanin research: What we know, what we assume and what remains unknown
Nearly 200 years of anthocyanin research reveal a well-understood anthocyanin biosynthetic pathway. However, there are still open questions regarding its evolution, functions and ecological significa...
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Boas Pucker @bpucker.bsky.social · 11/09/2026
Activation of anthocyanin biosynthesis in Utricularia gibba depends on nitrogen starvation and light exposure #FlavonoidFriday doi.org/10.64898/202... & shorturl.at/Be9T2
Utricularia gibba traps exhibiting red coloration, presumably due to anthocyanin accumulation. Reference: https://doi.org/10.64898/2026.08.27.747637
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Boas Pucker @bpucker.bsky.social · 08/09/2026
Interested in long read sequencing of plant genomes? Visit Julie at her poster to learn how it is done and what is possible today #Botanik-Tagung2026 #BT2026 #genomics @puckerlab.bsky.social @plantsciencedbg.bsky.social
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Nancy Choudhary @nancy-choudhary.bsky.social · 08/09/2026
Having a great time at the Botanik-Tagung 2026 in Bochum! I’ll be presenting my work on Cucurbitaceae tomorrow (09.09.2026) at 16:30. Looking forward to an interesting discussion! #BT2026 #PlantScience #SpecializedMetabolism #PlantPigments #Anthocyanins #Carotenoids #Evolution #Cucurbitaceae
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Boas Pucker @bpucker.bsky.social · 09/09/2026
Here is a picture of @puckerlab.bsky.social at #Botanik-Tagung2026 @plantsciencedbg.bsky.social #BT2026 #Genomics #Evolution #PlantScience @nancy-choudhary.bsky.social
PuckerLab at Botanik-Tagung 2026
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Boas Pucker @bpucker.bsky.social · 09/09/2026
Now, @nancy-choudhary.bsky.social is presenting her exciting findings about the anthocyanin biosynthesis loss in the Cucurbitaceae #BT2026 #Botanik-Tagung2026 @puckerlab.bsky.social @plantsciencedbg.bsky.social
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Boas Pucker @bpucker.bsky.social · 10/09/2026
Good news: Amanda and Katharina just won poster prizes for their amazing work on MYB transcription factors and pigment biosynthesis at #Botanik-Tagung2026 #BT2026 @puckerlab.bsky.social @ruhr-uni-bochum.de @unibonn.bsky.social @plantsciencedbg.bsky.social
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PuckerLab @puckerlab.bsky.social · 05/09/2026
We are excited to share our research at Botanik-Tagung 2026. Looking forward to inspiring discussions and a great time in Bochum! www.izmb.uni-bonn.de/en/pbb/news#... #BT2026 #PlantSciences @nancy-choudhary.bsky.social @bpucker.bsky.social @plantsciencedbg.bsky.social
Title slides of two PBB talks that are going to be given by Nancy Choudhary and Jakob Horz at Botanik-Tagung 2026. Details: https://www.izmb.uni-bonn.de/en/pbb/news#BT2026
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Boas Pucker @bpucker.bsky.social · 04/09/2026
Why could this be useful? We see cross-species coexpression (as implemented in CoExpPhylo) as a very powerful tool for future discoveries in the specialized plant metabolism, but you need big data to run it: doi.org/10.1186/s128...
doi.org
Client Challenge
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Boas Pucker @bpucker.bsky.social · 02/09/2026
Today is the day! Your chance to learn about synthetic biology (iGEM). We will be sharing our experiences at 6 pm in SR2.007 (IZMB, Kirschallee 1). Interested students from the University of Bonn are invited! Details: www.izmb.uni-bonn.de/en/pbb/igem @puckerlab.bsky.social @igembonn.bsky.social
Illustration showing an iGEM team at work. Partially generated with AI support.
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PuckerLab @puckerlab.bsky.social · 02/09/2026
Are you interested in gene expression? We have just released PanXpresso - a large collection of precomputed gene expression datasets for plants, animals, fungi, bacteria, and archaea: doi.org/10.64898/202... #RNAseq #Transcriptomics #Python @shakunthalan.bsky.social @bpucker.bsky.social
Phylogenetic tree showing the distribution of gene expression datasets across plant families. Source: https://doi.org/10.64898/2026.08.27.747620
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Boas Pucker @bpucker.bsky.social · 30/08/2026
We went on a boat trip to collect samples of aquatic carnivorous plants (Utricularia). Excited to learn more about these fascinating plants? Check out our latest preprint: doi.org/10.64898/202... #PlantSciences #Genomics #TeamWork @puckerlab.bsky.social
PuckerLab boat trip 2026. Details about our research: https://doi.org/10.64898/2026.08.27.747637
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Rob Waterhouse @rmwaterhouse.bsky.social · 29/08/2026
Presentation at #Quest4Orthologues on DupyliCate from Shakunthala Natarajan, from lab of @bpucker.bsky.social, ERGA Council member for Germany @ergabiodiv.bsky.social
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Boas Pucker @bpucker.bsky.social · 19/08/2026
Having a busy day? Julie’s latest work might be just the thing to calm things down. 🌿 Genome sequence and annotation of Valeriana officinalis doi.org/10.64898/202... #Genomics #Bioinformatics #PlantSciences @puckerlab.bsky.social @unibonn.bsky.social @opensciene-unibonn.bsky.social
A: Valeriana officinalis, Bonn University Botanic Gardens. B: Close-up of V. officinalis flowers. Source: https://doi.org/10.64898/2026.08.14.744958
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Boas Pucker @bpucker.bsky.social · 11/08/2026
More information about this upcoming course on our website: www.izmb.uni-bonn.de/en/pbb/news#... #Bioinformatics #CloudComputing #Genomics #CLI @puckerlab.bsky.social @nancy-choudhary.bsky.social
izmb.uni-bonn.de
News
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Boas Pucker @bpucker.bsky.social · 10/08/2026
It was a pleasure to recently give talks and meet with researchers working on exciting questions in plant sciences. My talks included “Addressing the Functional Annotation Bottleneck in Plant Genomics” and “Evolutionary Ups and Downs of Anthocyanin Biosynthesis”. #Genomics #Bioinformatics #Evolution
Title slides of “Addressing the Functional Annotation Bottleneck in Plant Genomics” and “Evolutionary Ups and Downs of Anthocyanin Biosynthesis”. https://www.izmb.uni-bonn.de/en/pbb/news
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Boas Pucker @bpucker.bsky.social · 09/08/2026
🧬 Want to get started with bioinformatics and the command line? Join our de.NBI training course “CLI Basics for Life Scientists” in Bonn! www.denbi.de/training-cou... #Bioinformatics #Bonn #CloudComputing @puckerlab.bsky.social @denbi.bsky.social @nancy-choudhary.bsky.social
denbi.de
CLI Basics for Life Scientists
The 'German Network for Bioinformatics Infrastructure – de.NBI' is a national, academic and non-profit infrastructure supported by the Federal Ministry of Education and Research providing bioinformati...
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German Society for Plant Sciences (DBG) @plantsciencedbg.bsky.social · 15/07/2026
#PlantSci Review: Anthocyanins and betalains in evolution: Why mutual exclusion remains the best-supported model – contrary to recently published reports By @bpucker.bsky.social and MI Khan Read more #OpenAccess in our Journal #PlantBiology @Wileyplantsci DOI: doi.org/10.1111/plb....
doi.org
Anthocyanins and betalains in evolution: Why mutual exclusion remains the best‐supported model
Anthocyanins and betalains are plant pigments produced through different biosynthetic pathways and are generally considered mutually exclusive. We examine claims of their co-occurrence, arguing that ...
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Nancy Choudhary @nancy-choudhary.bsky.social · 14/06/2026
3. Poaceae: doi.org/10.1101/2025... @puckerlab.bsky.social @puckerlabpapers.bsky.social
doi.org
Evolutionary Rewiring of Anthocyanin Biosynthesis Pathway in Poaceae
Poaceae is a species-rich family of plants in the monocots harboring many important crop species. As grasses, these plants lack striking flowers that are typically pigmented by anthocyanins. Here, we...
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Nancy Choudhary @nancy-choudhary.bsky.social · 14/06/2026
2. Cucurbitaceae: doi.org/10.1101/2025...
doi.org
Out of the blue: Family-wide loss of anthocyanin biosynthesis in Cucurbitaceae
### Competing Interest Statement The authors have declared no competing interest.
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Nancy Choudhary @nancy-choudhary.bsky.social · 14/06/2026
Interested in learning more? Read about our work: 1. Withanolide-associated gene cluster discovery: doi.org/10.1038/s414...
doi.org
Phylogenomics and metabolic engineering reveal a conserved gene cluster in Solanaceae plants for withanolide biosynthesis - Nature Communications
Withanolides are plant steroids with potent bioactivities found in many medicinal plants including Withania somnifera, but their biosynthetic pathway is largely unknown. Here, the authors report the g...
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Nancy Choudhary @nancy-choudhary.bsky.social · 14/06/2026
Great week at #EMPSEB31 in Oberwiesenthal, Germany! I presented a poster on the evolution of a withanolide biosynthetic gene cluster in Solanaceae and gave a talk on contrasting evolutionary outcomes of anthocyanin biosynthesis: complete loss in Cucurbitaceae and pathway rewiring in Poaceae. 🌱🧬
Nancy Choudhary is presenting a poster at EMPSEB31 titled "Better Together: Evolution of a Withanolide Biosynthetic Gene Cluster in Solanaceae"Nancy Choudhary is presenting a talk at EMPSEB31 titled "Poaceae and Cucurbitaceae: Non-model model systems for studying pigment evolution"Nancy Choudhary is presenting a talk at EMPSEB31 that highlights two distinct evolutionary trajectories of the anthocyanin biosynthesis pathway across major plant families.
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Boas Pucker @bpucker.bsky.social · 03/07/2026
Just in time for the weekend: our latest paper is out in Plant Biology! Anthocyanins and betalains in evolution: Why mutual exclusion remains the best-supported model doi.org/10.1111/plb.... #PlantBiology #Evolution #Anthocyanins #Betalains @puckerlab.bsky.social @unibonn.bsky.social
doi.org
Anthocyanins and betalains in evolution: Why mutual exclusion remains the best‐supported model
Anthocyanins and betalains are plant pigments produced through different biosynthetic pathways and are generally considered mutually exclusive. We examine claims of their co-occurrence, arguing that ...
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Plant Science🍀🌱 @sciplant.bsky.social · 16/06/2026
#PlantSciJobs #PlantScienceJobs
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German Society for Plant Sciences (DBG) @plantsciencedbg.bsky.social · 15/06/2026
#bioinformatics #PlantSciJobs #PlantSciJob
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Boas Pucker @bpucker.bsky.social · 15/06/2026
We are looking for a Bachelor's or Master's student to develop a functional annotation tool for large plant gene families. If you are excited about this opportunity, please get in touch. Details are available here: www.izmb.uni-bonn.de/en/pbb/news#... #Python #Bioinformatics @puckerlab.bsky.social
Illustration showing the opportunity to develop a gene family annotation tool. Details: https://www.izmb.uni-bonn.de/en/pbb/news#GFA2026
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PuckerLab publications @puckerlabpapers.bsky.social · 14/06/2026
Please share with your network: Would you benefit from full plasmid sequencing? Check out this cost-effective solution via nanopore sequencing on old flow cells: doi.org/10.64898/202... #LongReads #Biotech #SynBio #Plasmids #iGEM @puckerlab.bsky.social @bpucker.bsky.social
doi.org
NanoPlasmiQC: Full plasmid sequencing with ONT long-reads and automatic data analysis
Long-read sequencing has shown a rapid technological development during the last years. It has been established as the standard method for the sequencing of plant genomes and has also gained importanc...
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PuckerLab @puckerlab.bsky.social · 11/06/2026
In Glasgow, Hannah presented our Cucurbitaceae resarch at EURO EVO DEVO 2026: Who stole the blue flowers? Cucurbitaceae lack genes required for anthocyanin biosynthesis. This is quite unusual, as these genes are conserved in most flowering plants. www.izmb.uni-bonn.de/en/pbb/news#... #Evolution
Hannah at EURO EVO DEVO 2026. Details: https://www.izmb.uni-bonn.de/en/pbb/news#evodevo2026
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PuckerLab @puckerlab.bsky.social · 06/06/2026
🧬 New paper! DupyliCate provides an automated solution for the identification and characterization of gene duplications. 📄 doi.org/10.1038/s415... #Bioinformatics #Genomics @shakunthalan.bsky.social @bpucker.bsky.social
doi.org
DupyliCate: mining, classifying, and characterizing gene duplications - Scientific Reports
Scientific Reports - DupyliCate: mining, classifying, and characterizing gene duplications
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Boas Pucker @bpucker.bsky.social · 13/06/2026
We are looking for a new group member (BSc/MSc student) to bring our full plasmid sequencing data analysis workflow (NanoPlasmiQC) to the next level: www.izmb.uni-bonn.de/en/pbb/news#... #Python #Genomics #LongReads #Biotech #SynBio #Bioinformatics @puckerlab.bsky.social
Project summary figure with the details about our full plasmid sequencing data analysis workflow and this opportunity for Bachelor or Master students. Parts of the figure were generated with the help of ChatGPT. Details:  https://www.izmb.uni-bonn.de/en/pbb/news#NPQCS
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PuckerLab @puckerlab.bsky.social · 11/06/2026
In Glasgow, Hannah presented our Cucurbitaceae resarch at EURO EVO DEVO 2026: Who stole the blue flowers? Cucurbitaceae lack genes required for anthocyanin biosynthesis. This is quite unusual, as these genes are conserved in most flowering plants. www.izmb.uni-bonn.de/en/pbb/news#... #Evolution
Hannah at EURO EVO DEVO 2026. Details: https://www.izmb.uni-bonn.de/en/pbb/news#evodevo2026
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PuckerLab @puckerlab.bsky.social · 06/06/2026
🧬 New paper! DupyliCate provides an automated solution for the identification and characterization of gene duplications. 📄 doi.org/10.1038/s415... #Bioinformatics #Genomics @shakunthalan.bsky.social @bpucker.bsky.social
doi.org
DupyliCate: mining, classifying, and characterizing gene duplications - Scientific Reports
Scientific Reports - DupyliCate: mining, classifying, and characterizing gene duplications
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Boas Pucker @bpucker.bsky.social · 05/06/2026
Dark pigmentation of blackberry can be explained by high amounts of cyanidin-3-O-glucosides #FlavonoidFriday doi.org/10.64898/202... & shorturl.at/bxQU9 @puckerlab.bsky.social
Picture of Rubus armeniacus fruits. Figure references: https://doi.org/10.64898/2026.05.05.723051
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Plant Science Spotlight @plant-sci.bsky.social · 26/05/2026
🌾🧬A practical cookbook for plant genome sequencing. Oxford Nanopore workflows. From project planning to data release. Helping newcomers enter the growing field of plant genomics. #plantscience @bpucker.bsky.social @puckerlab.bsky.social @puckerlabpapers.bsky.social link.springer.com/article/10.1...
link.springer.com
Cookbook for plant genome sequences - BMC Genomics
BMC Genomics - Access to genome sequences is crucial to investigate and engineer traits in plants, explore biodiversity, and support phylogenetic studies. Over the last decade, affordable...
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PuckerLab publications @puckerlabpapers.bsky.social · 26/05/2026
Interested in getting the genome sequence of your favourite plant? "Cookbook for plant genome sequences" doi.org/10.1186/s128... #Genomics #PlantSciences #Bioinformatics @puckerlab.bsky.social
"Cookbook for plant genome sequences"
https://doi.org/10.1186/s12864-026-12623-z
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Boas Pucker @bpucker.bsky.social · 18/05/2026
Have you ever touched Urtica dioica? It is a memorable experience. Beyond its sting, this plant has medicinal properties. To better understand the genetics underlying key traits, we sequenced and analyzed its genome: doi.org/10.64898/202... #Genomics #PlantScience @puckerlab.bsky.social
Urtica dioica plant. Picture source: https://doi.org/10.64898/2026.05.15.725508
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Boas Pucker @bpucker.bsky.social · 15/05/2026
Near-black flowers of Tacca chantrieri are connected to anthocyanin genes including a curious DFR twist #FlavonoidFriday doi.org/10.64898/202... & shorturl.at/SnbhQ @puckerlab.bsky.social
Picture of Tacca chantrieri. Figure source: https://doi.org/10.64898/2026.03.17.712415
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German Society for Plant Sciences (DBG) @plantsciencedbg.bsky.social · 12/05/2026
The preliminary programme of International Conference of our German Society for #PlantSci, the Botanik-Tagung, is online botanik-tagung.de/programme.html 📆 6-10 September 2026 📍Bochum, Germany Makes it easier to plan your participation. Register today! botanik-tagung.de/registration...
"From industrial Past to Green Future" written around an ancient industry tower typical for the region together with a plant changing colours from blue to green is the motto of the German Society for Plant Sciences international Conference, the Botanik-Tagung, 2026 in Bochum Germany, that brings together plant scientists from several scientific disciplines. The logo highlights the structural change of the Ruhr area, from coal mining + heavy industries to the increasingly important issues of climate protection, sustainability + preservation of biodiversity, with plant sciences at the forefront of this transformation.
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PuckerLab publications @puckerlabpapers.bsky.social · 12/05/2026
Planning to sequence the genome of your favourite plant? This workflow based on ONT sequencing comes with hands-on instructions: "Cookbook for plant genome sequences" doi.org/10.1186/s128... #Genomics #LongReads #PlantSciences #Bioinformatics
Plant genome sequencing and annotation workflow. Source: https://doi.org/10.1186/s12864-026-12623-z
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Boas Pucker @bpucker.bsky.social · 12/05/2026
Curious about the dark side of plant biology? Check out our latest preprint on the secrets of black pigmentation in Rubus: doi.org/10.64898/202... #Anthocyanins #Transcriptomics #PlantScience @puckerlab.bsky.social
Gene expression analysis during Rubus armeniacus berry ripening. Source: https://doi.org/10.64898/2026.05.05.723051
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Boas Pucker @bpucker.bsky.social · 10/05/2026
Looking for an excellent conference to present your latest plant research or to meet @puckerlab.bsky.social : International Conference of the German Society for Plant Sciences (DBG) 6–10 September 2026 botanik-tagung.de #PlantSciences #Conferences @plantsciencedbg.bsky.social
botanik-tagung.de
Welcome
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PuckerLab @puckerlab.bsky.social · 27/04/2026
We are pleased to join the TRA Modelling: Mathematics, Modelling and Simulation of Complex Systems. Looking forward to more transdisciplinary collaborations! www.izmb.uni-bonn.de/en/pbb/news #Modelling #ComplexSystems #Transdisciplinary #UniversityOfBonn #DataScience @bpucker.bsky.social
Screenshot of https://www.uni-bonn.de/en/research-and-teaching/research-profile/transdisciplinary-research-areas/tra-1-modelling
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