Alexander Wittenberg

New hifiasm-ONT assembly method delivers high-quality, cost-efficient near T2T assemblies using standard Oxford Nanopore Simplex reads, broadening access to comprehensive genome assemblies across research and clinical applications. https://bit.ly/4awzU15

#pangenome #breeding #haplotypes | Alexander H.J. Wittenberg Great achievement ! This is going to accelerate our understanding and breeding efforts. Thanks also Oxford Nanopore Technologies since without long reads this would not have been possible. 🍌 🍌 🍌 #pang...

Announcing the #banana pangenome generated by @keygene.com using @nanoporetech.com long PromethION read platform. www.linkedin.com/posts/alexan...

Single nuclei RNA sequencing for high resolution insights KeyGene developed a single-cell transcriptomics technology based on the Chromium X by 10 X Genomics to analyze the gene expression profiles

Looking forward to attending #PAG33 in San Diego (if flights allow…) to present @nanoporetech.com industry workshop. Some background in the link below. www.keygene.com/single-nucle...

Joint research by KeyGene and Ultima Genomics shows that single-pollen-nuclei sequencing provides better profiling of meiotic recombination. | KeyGene Joint research by KeyGene and Ultima Genomics shows that single-pollen-nuclei sequencing provides better profiling of meiotic recombination. It can help plant breeders to improve their breeding by bet...

Must read! Great technology for fast high resolution recombination breakpoint mapping as well as for phasing complex crop genomes. www.linkedin.com/posts/keygen...

Single nuclei RNA sequencing for high resolution insights KeyGene developed a single-cell transcriptomics technology based on the Chromium X by 10 X Genomics to analyze the gene expression profiles

Looking forward to attending #PAG33 in San Diego (if flights allow…) to present @nanoporetech.com industry workshop. Some background in the link below. www.keygene.com/single-nucle...

Join Alexander Wittenberg at #PAG to uncover how he is utilising Oxford Nanopore technology to develop high-quality reference genomes and uncover genetic and phenotypic variants, which will help develop methods to improve crops. https://bit.ly/48tzBDa

Microscopic picture of a leaf, showing bright red dots in the cells in which a certain gene is active. In this picture, the studied gene is mainly active in the stomata: cells in the outer layer of the leaf that are responsible for the regulation of gas exchange between the plant and the environment.

We're proud to share that we have incorporated a state-f-the-art 'spatial transcriptomics' platform in our research facilities: the Merscope by @vizgen.bsky.social. To be used in e.g. innovative research on the interaction between plants & fungi for crop improvement. www.keygene.com/keygene-to-d...

KeyGene to deploy Vizgen’s Merscope for spatial transcriptomics KeyGene first organization in the Netherlands to purchase Merscope from Vizgen for spatial transcriptomics.

www.keygene.com/keygene-to-d...

Long-read nucleosome mapping of single chromatin fibers using DNA methylation and Nanopore sequencing. #LongRead #Nanopore #Sequencing #Chromatin #DNAmethylation @biophysj.bsky.social 🧪 🧬
www.sciencedirect.com/science/arti...

Phased nanopore assembly with Shasta and modular graph phasing with GFAse Reference-free genome phasing is vital for understanding allele inheritance and the impact of single-molecule DNA variation on phenotypes. To achieve thorough phasing across homozygous or repetitive r...

A new method using the Shasta assembler and GFAse tool improves the phasing of Oxford Nanopore Technologies (ONT) sequence data, enabling chromosome-scale phasing with higher accuracy and reduced complexity.

Uncover the science behind it: pmc.ncbi.nlm.nih.gov/articles/PMC...

Photo of the Omnia building at Wageningen Campus

In 2026, CROP Innovation & Business (CropIB) will be held in Wageningen, the Netherlands, March 29 - 31.
Subscribe to the CropIB newsletter (see link below) to stay informed about the program and other details!
www.cropib.com/newsletter
Partners: @ceplas.bsky.social @wurplant.bsky.social & VIB

Online now - the Review "Advancing #nanopore technology toward protein identification and sequencing" from Verena Rukes and @chancao.bsky.social.

#proteomics #proteinsequencing #proteinanalysis #fingerprinting #singlemolecule

authors.elsevier.com/sd/article/S...

Now published! Note that since Vikram's original post (quoted here), he's made it easy to dynamically update a set of multi-MUMs (e.g. when more genomes are added to a pangenome) and to find multi-MUMs for huge collections like HPRCv2 genomebiology.biomedcentral.com/articles/10....

Preprint on "Improving spliced alignment by modeling splice sites with deep learning". It describes minisplice for modeling splice signals. Minimap2 and miniprot now optionally use the predicted scores to improve spliced alignment.
arxiv.org/abs/2506.12986

Single pollen nuclei sequencing: profiling of meiotic recombination KeyGene’s advanced protocols & smart bioinformatics + Ultima Genomics sequencing platform: better understanding DNA recombination in meiosis.

Joint research by @keygene.com & Ultima Genomics shows that single-pollen-nuclei sequencing can help plant breeders to improve their breeding by better understanding the recombination of the mother and father DNA during meiosis without raising and analysing an F2.
www.keygene.com/newsitem/sin...

Joint research by KeyGene and Ultima Genomics shows that single-pollen-nuclei sequencing provides better profiling of meiotic recombination. | KeyGene Joint research by KeyGene and Ultima Genomics shows that single-pollen-nuclei sequencing provides better profiling of meiotic recombination. It can help plant breeders to improve their breeding by bet...

Must read! Great technology for fast high resolution recombination breakpoint mapping as well as for phasing complex crop genomes. www.linkedin.com/posts/keygen...

Automated high throughput workflow for plant exome analysis KeyGene, Twist Bioscience and Beckman Coulter Life Sciences developed an ultra-high throughput workflow for plant exome analysis

@keygene.com, Twist Bioscience, and Beckman Coulter Life Sciences developed an ultra-high throughput workflow for plant exome analysis: characterizing more than 9,000 samples per day, reducing costs of detecting functional SNP variation in breeding and research.
www.keygene.com/newsitem/aut...

Much of biology remains hidden, especially the proteome. Jeff Nivala explores progress toward Oxford Nanopore-based single-molecule protein sensing — offering a path to decode proteins like DNA and transform our understanding of cellular machinery. #NanoporeConf

Oxford Nanopore sequencing will be ubiquitous for multiomics….and the next step is proteomics.

First panel-based proteomics assays, before driving towards full protein sensing in the future. #nanoporeconf

At London Calling, Rosemary Sinclair Dokos and Lakmal Jayasinghe shared how we’re doubling down on what matters: delivering a future-ready platform with proven performance across DNA, RNA, and now proteins. Click here to discover what’s new – and why it matters: nanoporetech.com/news/london-...

YouTube video by Oxford Nanopore Technologies London Calling 2025 tech update

m.youtube.com/watch?v=OYql... #nanoporecomf

Oxford Nanopore’s roadmap to proteomics Oxford Nanopore unveils its pioneering roadmap to full protein sequencing, advancing real-time, direct proteomics for transformative healthcare and research applications.

nanoporetech.com/blog/london-...

Call for postdoctoral candidates for a Marie Curie fellowship - KeyGene Marie Curie Fellowship opportunity for fresh PhD's to accelerate career & be part of groundbreaking research for the future of agriculture

'Fresh' PhD graduates who lived outside the Netherlands for at least 24 months during 36 months before September 10: there's less than a month to apply as candidate for a joint Marie Curie grant application for a 'PostDoc in industry' at KeyGene! Deadline is May 19 !
www.keygene.com/newsitem/cal...

Fruits of the grapevine ‘Mgaloblishvili’

The University of Milan published the genome of the downy mildew-resistant grapevine ‘Mgaloblishvili’. The research was boosted by the winning of a high-quality high-molecular-weight DNA extraction in KeyGene's DNA-Day contest of 2021. Check this post:
www.keygene.com/newsitem/geo...

Deep Learning-Based Classification of Peptide Analytes from Single-Channel Nanopore Translocation Events

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Deep Learning-Based Classification of Peptide Analytes from Single-Channel Nanopore Translocation Events [new]
Deep Learning Classifies Peptides from Nanopore Events via a Two-Stage Pipeline.

A Recipe for Complexity: Building the Potato Pan-Genome

Interested in hearing more about the story behind our latest paper?
Check out our blog post and the latest @naturepodcast.bsky.social episode!

📝 go.nature.com/3G73vT7

🎙️ www.nature.com/articles/d41...

Efficient near telomere-to-telomere assembly of Nanopore Simplex reads Telomere-to-telomere (T2T) assembly is the ultimate goal for de novo genome assembly. Existing algorithms capable of near T2T assembly all require Oxford Nanopore Technologies (ONT) ultra-long reads w...

Preprint on hifiasm Nanopore-only assembly. Led by Haoyu Cheng: www.biorxiv.org/content/10.1...

First of its kind skin-transplant potato variety obtained plant breeders’ rights The Netherlands' Board for Plant Varieties has approved a revolutionary potato variety developed by KeyGene using the 2S1 graft hybrid technique. This method merges traits from two existing varieties, Pimpernel's skin and Bintje's cell layers, enhancing features like drought tolerance and yield. The successful commercialization of this proof-of-concept signals significant potential for improving various crops through sustainable breeding practices, according to KeyGene's leaders.

First of its kind skin-transplant potato variety obtained plant breeders’ rights

The Netherlands' Board for Plant Varieties has approved a revolutionary potato variety developed by KeyGene using the 2S1 graft hybrid technique. This method merges traits from two existing varieties, Pimpernel's skin…

KeyGene kweekt roodschillig Bintje met nieuwe veredelingstechniek Onderzoeksbedrijf KeyGene heeft een veredelingstechniek ontwikkeld waarmee het mogelijk is om huidtransplantatie toe te passen bij aardappelen.

Het nieuwe aardappelras heeft de huid van het bestaande ras Pimpernel en de binnenkant van Bintje en is gekweekt met behulp van 2S1-techniek. Deze nieuwe technologie is door KeyGene. 🥔 #veredeling

Rene Hogers @keygene.com presented his work on establishing single-cell research for crop improvement at #RNGS25.
▶️Watch his video pitch to find out more.