Jakob Ørtvig
@rtvig-j.bsky.social
Oxford Nanopore employee, work related posts, views are my own
Reposted by Jakob Ørtvig
Our cornetto work is now published at www.nature.com/articles/s41...
It can do near-T2T assembly using @nanoporetech.com adaptive sampling
- with less 💸
- reference agnostic, so works for non-humans
- not just blood, even saliva
Just presented at #abacbs2025 yesterday.
It can do near-T2T assembly using @nanoporetech.com adaptive sampling
- with less 💸
- reference agnostic, so works for non-humans
- not just blood, even saliva
Just presented at #abacbs2025 yesterday.
Targeted sequencing and iterative assembly of near-complete genomes - Nature Communications
Long-read sequencing enables high-quality genome assemblies, but challenges remain. Here, the authors introduce Cornetto, a method that improves assembly quality, enables genome sequencing from saliva...
www.nature.com
November 26, 2025 at 4:12 AM
Our cornetto work is now published at www.nature.com/articles/s41...
It can do near-T2T assembly using @nanoporetech.com adaptive sampling
- with less 💸
- reference agnostic, so works for non-humans
- not just blood, even saliva
Just presented at #abacbs2025 yesterday.
It can do near-T2T assembly using @nanoporetech.com adaptive sampling
- with less 💸
- reference agnostic, so works for non-humans
- not just blood, even saliva
Just presented at #abacbs2025 yesterday.
Reposted by Jakob Ørtvig
Did not expect to see disk space become an issue but after a disk clean up and restart I ended up with 243 and 244 gbp for these two @nanoporetech.com flowcells 🎉🚀🧬 💚🟩💚🟩💚🟩
November 4, 2025 at 12:10 PM
Did not expect to see disk space become an issue but after a disk clean up and restart I ended up with 243 and 244 gbp for these two @nanoporetech.com flowcells 🎉🚀🧬 💚🟩💚🟩💚🟩
Reposted by Jakob Ørtvig
Our MARTi @nanoporetech.com paper is now out in @genomeresearch.bsky.social after several years of development (particularly Ned Peel and Sam Martin). We'd love to hear from users about how you're using it, or suggestions for new features. @earlhaminst.bsky.social
genome.cshlp.org/content/earl...
genome.cshlp.org/content/earl...
Real-time analysis and visualization of nanopore metagenomic samples with MARTi
An international, peer-reviewed genome sciences journal featuring outstanding original research that offers novel insights into the biology of all organisms
genome.cshlp.org
October 28, 2025 at 9:36 AM
Our MARTi @nanoporetech.com paper is now out in @genomeresearch.bsky.social after several years of development (particularly Ned Peel and Sam Martin). We'd love to hear from users about how you're using it, or suggestions for new features. @earlhaminst.bsky.social
genome.cshlp.org/content/earl...
genome.cshlp.org/content/earl...
Reposted by Jakob Ørtvig
Trio-barcoded @nanoporetech.com Adaptive Sampling (TBAS) to improve #RareDisease diagnostic at less than 1/2 the $$ & high cov: 76% solve rate across 13 trios inc. two corrections from prev. diagnosis. www.medrxiv.org/content/10.1...
@gregor-research.bsky.social @bcmhgsc.bsky.social
#Research
@gregor-research.bsky.social @bcmhgsc.bsky.social
#Research
October 27, 2025 at 1:05 PM
Trio-barcoded @nanoporetech.com Adaptive Sampling (TBAS) to improve #RareDisease diagnostic at less than 1/2 the $$ & high cov: 76% solve rate across 13 trios inc. two corrections from prev. diagnosis. www.medrxiv.org/content/10.1...
@gregor-research.bsky.social @bcmhgsc.bsky.social
#Research
@gregor-research.bsky.social @bcmhgsc.bsky.social
#Research
Reposted by Jakob Ørtvig
Overall we found more than 300 previously unreported RNA isoforms from 31 genes in brain. Some were highly abundant or even the dominant isoform, and we could show translation of novel RNAs into novel proteoforms, including new isoforms of the depression risk gene ITIH4 (see image).
October 3, 2025 at 4:18 AM
Overall we found more than 300 previously unreported RNA isoforms from 31 genes in brain. Some were highly abundant or even the dominant isoform, and we could show translation of novel RNAs into novel proteoforms, including new isoforms of the depression risk gene ITIH4 (see image).
Reposted by Jakob Ørtvig
Methylation goes beyond just 5mC, but legacy sequencing methods do not.
Join our CoLab at #ASHG to learn how Dr Leyland Taylor is unravelling the dynamic regulatory role of multiple RNA mods in type 2 diabetes using Oxford Nanopore sequencing. nanoporetech.com/about/events...
Join our CoLab at #ASHG to learn how Dr Leyland Taylor is unravelling the dynamic regulatory role of multiple RNA mods in type 2 diabetes using Oxford Nanopore sequencing. nanoporetech.com/about/events...
October 1, 2025 at 4:25 PM
Methylation goes beyond just 5mC, but legacy sequencing methods do not.
Join our CoLab at #ASHG to learn how Dr Leyland Taylor is unravelling the dynamic regulatory role of multiple RNA mods in type 2 diabetes using Oxford Nanopore sequencing. nanoporetech.com/about/events...
Join our CoLab at #ASHG to learn how Dr Leyland Taylor is unravelling the dynamic regulatory role of multiple RNA mods in type 2 diabetes using Oxford Nanopore sequencing. nanoporetech.com/about/events...
Reposted by Jakob Ørtvig
PhD opportunity available on epigenomics/trasncriptomics as part of the network of clinicians and researchers working in glioblastoma research at @uniofnottingham.bsky.social Using a wide range of tech and methods but definitely long reads @nanoporetech.com - more at lnkd.in/eBtrtZiM
LinkedIn
This link will take you to a page that’s not on LinkedIn
lnkd.in
September 25, 2025 at 5:42 PM
PhD opportunity available on epigenomics/trasncriptomics as part of the network of clinicians and researchers working in glioblastoma research at @uniofnottingham.bsky.social Using a wide range of tech and methods but definitely long reads @nanoporetech.com - more at lnkd.in/eBtrtZiM
Reposted by Jakob Ørtvig
Epigenetic diagnosis of acute leukemia within two hours from sample receipt 🚀
Very happy to share the results of a great collaboration between @hovestadt.bsky.social and Griffin Labs, I co-led with @sbenfatto.bsky.social, published today in @natgenet.nature.com
📄 www.nature.com/articles/s41...
🧵1/n
Very happy to share the results of a great collaboration between @hovestadt.bsky.social and Griffin Labs, I co-led with @sbenfatto.bsky.social, published today in @natgenet.nature.com
📄 www.nature.com/articles/s41...
🧵1/n
Rapid epigenomic classification of acute leukemia - Nature Genetics
The authors present a molecular classification of acute leukemia using 5-methylcytosine signatures, together with a neural network-based classifier for clinical use.
www.nature.com
September 22, 2025 at 8:41 PM
Epigenetic diagnosis of acute leukemia within two hours from sample receipt 🚀
Very happy to share the results of a great collaboration between @hovestadt.bsky.social and Griffin Labs, I co-led with @sbenfatto.bsky.social, published today in @natgenet.nature.com
📄 www.nature.com/articles/s41...
🧵1/n
Very happy to share the results of a great collaboration between @hovestadt.bsky.social and Griffin Labs, I co-led with @sbenfatto.bsky.social, published today in @natgenet.nature.com
📄 www.nature.com/articles/s41...
🧵1/n
Reposted by Jakob Ørtvig
Introducing our new Microbial Amplicon Barcoding Kit, which enhances microbial community profiling with an information-rich, rapid & accessible protocol for streamlined identification of bacteria, archaea & fungi — in one go. nanoporetech.com/news/oxford-...
September 18, 2025 at 11:12 AM
Introducing our new Microbial Amplicon Barcoding Kit, which enhances microbial community profiling with an information-rich, rapid & accessible protocol for streamlined identification of bacteria, archaea & fungi — in one go. nanoporetech.com/news/oxford-...
Reposted by Jakob Ørtvig
A postdoc position in genomics available at our infrastructure in Uppsala, Sweden! An interesting R&D role a bit outside the traditional academic environment, great colleagues, work at the forefront of (long-read) sequencing.
www.uu.se/en/about-uu/...
www.uu.se/en/about-uu/...
Postdoctoral position - Uppsala University
Postdoctoral position, Department of Immunology, Genetics and Pathology, Uppsala University
www.uu.se
August 19, 2025 at 1:21 PM
A postdoc position in genomics available at our infrastructure in Uppsala, Sweden! An interesting R&D role a bit outside the traditional academic environment, great colleagues, work at the forefront of (long-read) sequencing.
www.uu.se/en/about-uu/...
www.uu.se/en/about-uu/...
Reposted by Jakob Ørtvig
What if targeted sequencing actually meant targeted?
Uncover how Oxford Nanopore’s adaptive sequencing delivers high coverage, faster results & a more efficient workflow than WGS — all in our latest Nanopore Know-How post.
Read here: nanoporetech.com/blog/adaptiv...
Uncover how Oxford Nanopore’s adaptive sequencing delivers high coverage, faster results & a more efficient workflow than WGS — all in our latest Nanopore Know-How post.
Read here: nanoporetech.com/blog/adaptiv...
August 14, 2025 at 11:04 AM
What if targeted sequencing actually meant targeted?
Uncover how Oxford Nanopore’s adaptive sequencing delivers high coverage, faster results & a more efficient workflow than WGS — all in our latest Nanopore Know-How post.
Read here: nanoporetech.com/blog/adaptiv...
Uncover how Oxford Nanopore’s adaptive sequencing delivers high coverage, faster results & a more efficient workflow than WGS — all in our latest Nanopore Know-How post.
Read here: nanoporetech.com/blog/adaptiv...
Reposted by Jakob Ørtvig
Very excited to see our latest paper published!
Our paper using Oxford #Nanopore direct RNA sequencing to identify m6A modifications on RNA isoforms in human brain is now out in Science Advances. 🧪
www.science.org/doi/10.1126/...
www.science.org/doi/10.1126/...
Isoform-level profiling of m6A epitranscriptomic signatures in human brain
Direct RNA-seq in brain reveals RNA isoform and region-specific m6A modifications, highlighting their role in gene regulation.
www.science.org
August 12, 2025 at 9:52 AM
Very excited to see our latest paper published!
Reposted by Jakob Ørtvig
ELRIN completes two T2T human genomes — using only #Nanopore data.
As part of their mission to advance clinical diagnostics, ELRIN has released two complete, haplotype-phased genomes—enabling deeper insights into genetic variation that could inform future clinical research elrin-network.eu/t2t.html
As part of their mission to advance clinical diagnostics, ELRIN has released two complete, haplotype-phased genomes—enabling deeper insights into genetic variation that could inform future clinical research elrin-network.eu/t2t.html
June 26, 2025 at 4:08 PM
ELRIN completes two T2T human genomes — using only #Nanopore data.
As part of their mission to advance clinical diagnostics, ELRIN has released two complete, haplotype-phased genomes—enabling deeper insights into genetic variation that could inform future clinical research elrin-network.eu/t2t.html
As part of their mission to advance clinical diagnostics, ELRIN has released two complete, haplotype-phased genomes—enabling deeper insights into genetic variation that could inform future clinical research elrin-network.eu/t2t.html
Reposted by Jakob Ørtvig
Each year at @asm.org I'm blown away by the growing amount of presentations and posters leveraging @nanoporetech.com. This year we identified nearly 100 abstracts, ranging from clinical micro & public health applications to environmental research. See you there! nanoporetech.com/about/events...
June 16, 2025 at 6:53 PM
Each year at @asm.org I'm blown away by the growing amount of presentations and posters leveraging @nanoporetech.com. This year we identified nearly 100 abstracts, ranging from clinical micro & public health applications to environmental research. See you there! nanoporetech.com/about/events...
Reposted by Jakob Ørtvig
In this article, GenomeWeb explores Oxford Nanopore Technologies' collaboration with the ELRIN consortium and how they are researching the potential of Oxford Nanopore sequencing as a first-line diagnostic tool for #rarediseases and familial #cancers.
Read here: www.genomeweb.com/sequencing/e...
Read here: www.genomeweb.com/sequencing/e...
June 9, 2025 at 4:49 PM
In this article, GenomeWeb explores Oxford Nanopore Technologies' collaboration with the ELRIN consortium and how they are researching the potential of Oxford Nanopore sequencing as a first-line diagnostic tool for #rarediseases and familial #cancers.
Read here: www.genomeweb.com/sequencing/e...
Read here: www.genomeweb.com/sequencing/e...
Reposted by Jakob Ørtvig
Oxford Nanopore Tech Update LC2025. My full analysis of what this means for NGS and Multi-Omics, including the new Proteomics PoC. open.substack.com/pub/albertvi...
Oxford Nanopore Tech Update LC2025 highlights
My highlights from the LC2025 announcements
open.substack.com
May 27, 2025 at 6:45 AM
Oxford Nanopore Tech Update LC2025. My full analysis of what this means for NGS and Multi-Omics, including the new Proteomics PoC. open.substack.com/pub/albertvi...
Reposted by Jakob Ørtvig
Lennart Kester showcased their deep-learning tools, that combined with Oxford Nanopore sequencing, classify paediatric tumours in under two hours – potentially enabling same-day, cost-effective and intraoperative characterisation in the future. #NanoporeConf
May 22, 2025 at 2:15 PM
Lennart Kester showcased their deep-learning tools, that combined with Oxford Nanopore sequencing, classify paediatric tumours in under two hours – potentially enabling same-day, cost-effective and intraoperative characterisation in the future. #NanoporeConf
Reposted by Jakob Ørtvig
Very excited to present the Great Barrier Reef Microbial Genomes Database (GBR-MGD), a comprehensive DB of 1000s of high-quality prokaryote, virus, plasmid, and chromosome-level eukaryote MAGs using Nanopore long reads. Subthreads incoming. Please share widely. 🙂
www.biorxiv.org/content/10.1...
www.biorxiv.org/content/10.1...
The planktonic microbiome of the Great Barrier Reef
Large genome databases have markedly improved our understanding of marine microorganisms. Although these resources have focused on prokaryotes, genomes from many dominant marine lineages, such as Pela...
www.biorxiv.org
May 21, 2025 at 7:34 AM
Very excited to present the Great Barrier Reef Microbial Genomes Database (GBR-MGD), a comprehensive DB of 1000s of high-quality prokaryote, virus, plasmid, and chromosome-level eukaryote MAGs using Nanopore long reads. Subthreads incoming. Please share widely. 🙂
www.biorxiv.org/content/10.1...
www.biorxiv.org/content/10.1...
Reposted by Jakob Ørtvig
Really pleased that this paper is out - academic.oup.com/neuro-oncolo... thanks to all our collaborators far and wide who have helped and of course @nanoporetech.com
ROBIN: A unified nanopore-based assay integrating intraoperative methylome classification and next-day comprehensive profiling for ultra-rapid tumor diagnosis
academic.oup.com
May 21, 2025 at 9:26 AM
Really pleased that this paper is out - academic.oup.com/neuro-oncolo... thanks to all our collaborators far and wide who have helped and of course @nanoporetech.com
Reposted by Jakob Ørtvig
Welcome to London Calling 2025! #NanoporeConf
May 21, 2025 at 9:59 AM
Welcome to London Calling 2025! #NanoporeConf
Reposted by Jakob Ørtvig
Live from London Calling 2025!
Speakers, attendees and the Oxford Nanopore crew are starting to fill into Old Billingsgate!
Ready for Gordon to kick things off for the 11th time!
Make sure you keep your posts coming using: #nanoporeconf
Speakers, attendees and the Oxford Nanopore crew are starting to fill into Old Billingsgate!
Ready for Gordon to kick things off for the 11th time!
Make sure you keep your posts coming using: #nanoporeconf
May 21, 2025 at 8:14 AM
Live from London Calling 2025!
Speakers, attendees and the Oxford Nanopore crew are starting to fill into Old Billingsgate!
Ready for Gordon to kick things off for the 11th time!
Make sure you keep your posts coming using: #nanoporeconf
Speakers, attendees and the Oxford Nanopore crew are starting to fill into Old Billingsgate!
Ready for Gordon to kick things off for the 11th time!
Make sure you keep your posts coming using: #nanoporeconf
Reposted by Jakob Ørtvig
@lh3lh3.bsky.social's latest assembler has really pushed using "routine" ONT libraries (N50s 30KB ish) to get to near T2T assemblies, leveraging read length for (diploid) error correction. Heng continues to be the fountain of excellent sequence bioinformatics tools and it impressive to see.
May 20, 2025 at 8:04 AM
@lh3lh3.bsky.social's latest assembler has really pushed using "routine" ONT libraries (N50s 30KB ish) to get to near T2T assemblies, leveraging read length for (diploid) error correction. Heng continues to be the fountain of excellent sequence bioinformatics tools and it impressive to see.
Reposted by Jakob Ørtvig
This week is the gathering of the tribes around @nanoporetech.com, for their annual meeting, London Calling. It is a blend of tech announcements, product updates + scientific conference (posters and breakout talks). I am only there for the informatics day at the end sadly, but here are some thoughts
May 20, 2025 at 8:04 AM
This week is the gathering of the tribes around @nanoporetech.com, for their annual meeting, London Calling. It is a blend of tech announcements, product updates + scientific conference (posters and breakout talks). I am only there for the informatics day at the end sadly, but here are some thoughts
Reposted by Jakob Ørtvig
New paper! Most human DNA replication initiation is dispersed throughout the genome with only a minority within previously identified initiation zones
genomebiology.biomedcentral.com/articles/10....
Identifying human DNA replication initiation sites on single molecules by @nanoporetech.com 1/7
genomebiology.biomedcentral.com/articles/10....
Identifying human DNA replication initiation sites on single molecules by @nanoporetech.com 1/7
Most human DNA replication initiation is dispersed throughout the genome with only a minority within previously identified initiation zones - Genome Biology
Background The identification of sites of DNA replication initiation in mammalian cells has been challenging. Here, we present unbiased detection of replication initiation events in human cells using ...
genomebiology.biomedcentral.com
May 12, 2025 at 10:35 AM
New paper! Most human DNA replication initiation is dispersed throughout the genome with only a minority within previously identified initiation zones
genomebiology.biomedcentral.com/articles/10....
Identifying human DNA replication initiation sites on single molecules by @nanoporetech.com 1/7
genomebiology.biomedcentral.com/articles/10....
Identifying human DNA replication initiation sites on single molecules by @nanoporetech.com 1/7
Reposted by Jakob Ørtvig
High-quality metagenome assembly from nanopore reads with nanoMDBG https://www.biorxiv.org/content/10.1101/2025.04.22.649928v1
April 25, 2025 at 12:46 AM
High-quality metagenome assembly from nanopore reads with nanoMDBG https://www.biorxiv.org/content/10.1101/2025.04.22.649928v1