Alexander Wittenberg
@awngs.bsky.social
New horizons. All omics. AgBio field NGS specialist. 🌱 🍌🌾🍉🌻🍓vegetables, field crops, berries and ornamentals. #DNA #RNA #protein
Pinned
Alexander Wittenberg
@awngs.bsky.social
· Jun 12
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...
www.linkedin.com
Must read! Great technology for fast high resolution recombination breakpoint mapping as well as for phasing complex crop genomes. www.linkedin.com/posts/keygen...
Reposted by Alexander Wittenberg
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...
October 16, 2025 at 11:29 AM
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...
Reposted by Alexander Wittenberg
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...
www.sciencedirect.com/science/arti...
October 6, 2025 at 3:03 PM
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...
www.sciencedirect.com/science/arti...
Reposted by Alexander Wittenberg
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...
Uncover the science behind it: pmc.ncbi.nlm.nih.gov/articles/PMC...
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...
pmc.ncbi.nlm.nih.gov
August 8, 2025 at 8:33 PM
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...
Uncover the science behind it: pmc.ncbi.nlm.nih.gov/articles/PMC...
Reposted by Alexander Wittenberg
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
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
July 7, 2025 at 9:42 AM
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
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
Reposted by Alexander Wittenberg
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...
#proteomics #proteinsequencing #proteinanalysis #fingerprinting #singlemolecule
authors.elsevier.com/sd/article/S...
June 18, 2025 at 8:43 PM
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...
#proteomics #proteinsequencing #proteinanalysis #fingerprinting #singlemolecule
authors.elsevier.com/sd/article/S...
Reposted by Alexander Wittenberg
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....
June 17, 2025 at 2:02 PM
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....
Reposted by Alexander Wittenberg
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
arxiv.org/abs/2506.12986
June 17, 2025 at 1:49 AM
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
arxiv.org/abs/2506.12986
Reposted by Alexander Wittenberg
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...
www.keygene.com/newsitem/sin...
Single pollen nuclei sequencing: profiling of meiotic recombination
KeyGene’s advanced protocols & smart bioinformatics + Ultima Genomics sequencing platform: better understanding DNA recombination in meiosis.
www.keygene.com
June 12, 2025 at 12:48 PM
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...
www.keygene.com/newsitem/sin...
Must read! Great technology for fast high resolution recombination breakpoint mapping as well as for phasing complex crop genomes. www.linkedin.com/posts/keygen...
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...
www.linkedin.com
June 12, 2025 at 4:44 PM
Must read! Great technology for fast high resolution recombination breakpoint mapping as well as for phasing complex crop genomes. www.linkedin.com/posts/keygen...
Reposted by Alexander Wittenberg
@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...
www.keygene.com/newsitem/aut...
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
www.keygene.com
June 5, 2025 at 1:11 PM
@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...
www.keygene.com/newsitem/aut...
Reposted by Alexander Wittenberg
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
May 23, 2025 at 4:26 PM
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
Reposted by Alexander Wittenberg
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
First panel-based proteomics assays, before driving towards full protein sensing in the future. #nanoporeconf
May 21, 2025 at 6:27 PM
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
First panel-based proteomics assays, before driving towards full protein sensing in the future. #nanoporeconf
Reposted by Alexander Wittenberg
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-...
May 21, 2025 at 8:36 PM
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-...
Reposted by Alexander Wittenberg
'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...
www.keygene.com/newsitem/cal...
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
www.keygene.com
April 29, 2025 at 1:53 PM
'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...
www.keygene.com/newsitem/cal...
Reposted by Alexander Wittenberg
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...
www.keygene.com/newsitem/geo...
May 19, 2025 at 1:06 PM
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...
www.keygene.com/newsitem/geo...
Reposted by Alexander Wittenberg
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.
Deep Learning Classifies Peptides from Nanopore Events via a Two-Stage Pipeline.
May 6, 2025 at 5:51 PM
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.
Deep Learning Classifies Peptides from Nanopore Events via a Two-Stage Pipeline.
Reposted by Alexander Wittenberg
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...
Check out our blog post and the latest @naturepodcast.bsky.social episode!
📝 go.nature.com/3G73vT7
🎙️ www.nature.com/articles/d41...
A Recipe for Complexity: Building the Potato Pan-Genome
go.nature.com
April 16, 2025 at 4:01 PM
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...
Check out our blog post and the latest @naturepodcast.bsky.social episode!
📝 go.nature.com/3G73vT7
🎙️ www.nature.com/articles/d41...
Reposted by Alexander Wittenberg
Preprint on hifiasm Nanopore-only assembly. Led by Haoyu Cheng: www.biorxiv.org/content/10.1...
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...
www.biorxiv.org
April 18, 2025 at 9:54 PM
Preprint on hifiasm Nanopore-only assembly. Led by Haoyu Cheng: www.biorxiv.org/content/10.1...
Reposted by Alexander Wittenberg
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…
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…
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.
www.potatonewstoday.com
April 1, 2025 at 9:02 AM
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…
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…
Reposted by Alexander Wittenberg
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
KeyGene kweekt roodschillig Bintje met nieuwe veredelingstechniek
Onderzoeksbedrijf KeyGene heeft een veredelingstechniek ontwikkeld waarmee het mogelijk is om huidtransplantatie toe te passen bij aardappelen.
www.nieuweoogst.nl
March 31, 2025 at 11:54 AM
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
Reposted by Alexander Wittenberg
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.
▶️Watch his video pitch to find out more.
March 24, 2025 at 1:36 PM
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.
▶️Watch his video pitch to find out more.
