Warren Bach
@sciencedude.bsky.social
Retired, ex-Nanopore, 30 years supporting genomic technologies in ANZ. Love talking science, fishing, bonsai, cooking and good wine.
Reposted by Warren Bach
🚀 Our new preprint is now live on bioRxiv!
“A systematic benchmark of bioinformatics methods for single-cell and spatial RNA-seq Nanopore long-read data”
🔗 Read here: www.biorxiv.org/content/10.1...
🔬 About the study
We present the first comprehensive benchmark of bioinformatics tools 👇
“A systematic benchmark of bioinformatics methods for single-cell and spatial RNA-seq Nanopore long-read data”
🔗 Read here: www.biorxiv.org/content/10.1...
🔬 About the study
We present the first comprehensive benchmark of bioinformatics tools 👇
July 30, 2025 at 12:00 PM
🚀 Our new preprint is now live on bioRxiv!
“A systematic benchmark of bioinformatics methods for single-cell and spatial RNA-seq Nanopore long-read data”
🔗 Read here: www.biorxiv.org/content/10.1...
🔬 About the study
We present the first comprehensive benchmark of bioinformatics tools 👇
“A systematic benchmark of bioinformatics methods for single-cell and spatial RNA-seq Nanopore long-read data”
🔗 Read here: www.biorxiv.org/content/10.1...
🔬 About the study
We present the first comprehensive benchmark of bioinformatics tools 👇
Reposted by Warren Bach
Now that Long Covid has become the most common chronic health condition in children, many more children may require additional support in school. pizer.law/long-covid-n...
Long Covid Now Most Common Chronic Health Problem in Children
Now that Long Covid has become the most common chronic health condition in children, many more children may require additional support in school.
pizer.law
July 1, 2025 at 8:47 PM
Now that Long Covid has become the most common chronic health condition in children, many more children may require additional support in school. pizer.law/long-covid-n...
Congrats Hasindu and Nanopore Garvan team. This is an exciting development. I remember asking myself how AS might be used when it was first released. You have truely answered this 🙌🎉
Introducing cornetto, an adaptive genome assembly paradigm using @nanoporetech.com adaptive sampling.
- greatly reduces cost per genome assembly
- reference agnostic, so works for non-humans
- assembly just using saliva
- & many more
Relies on 2 excellent software #readfish & #hifiasm.
- greatly reduces cost per genome assembly
- reference agnostic, so works for non-humans
- assembly just using saliva
- & many more
Relies on 2 excellent software #readfish & #hifiasm.
Adaptively integrated sequencing and assembly of near-complete genomes https://www.biorxiv.org/content/10.1101/2025.03.31.646505v1
April 5, 2025 at 10:51 PM
Congrats Hasindu and Nanopore Garvan team. This is an exciting development. I remember asking myself how AS might be used when it was first released. You have truely answered this 🙌🎉
Reposted by Warren Bach
Because I recently stealth-shared this with the nanopore sequencing community, I figured I might as well post this here as well. This is a TEDx talk I gave in 2016, which I believe is the first public on-stage demonstration of nanopore sequencing:
www.youtube.com/watch?v=kQK3...
www.youtube.com/watch?v=kQK3...
Sequencing That Stimulates The Sensors - TEDx Presenter's Cut
YouTube video by David Eccles
www.youtube.com
February 18, 2025 at 8:20 PM
Because I recently stealth-shared this with the nanopore sequencing community, I figured I might as well post this here as well. This is a TEDx talk I gave in 2016, which I believe is the first public on-stage demonstration of nanopore sequencing:
www.youtube.com/watch?v=kQK3...
www.youtube.com/watch?v=kQK3...
Reposted by Warren Bach
🌟 Client Publication Highlight! 🌟 We're proud to share a little summary of a recent study by Furnell et al (2024) who used the Ramaciotti Centre's long read (ONT) sequencing and Sanger sequencing services🧬
February 11, 2025 at 5:30 AM
🌟 Client Publication Highlight! 🌟 We're proud to share a little summary of a recent study by Furnell et al (2024) who used the Ramaciotti Centre's long read (ONT) sequencing and Sanger sequencing services🧬
Reposted by Warren Bach
This week, we established a new Grant Programme to support researchers who are pursuing breakthrough science but may lack all the resources to access Oxford #Nanopore sequencing.
Find out more and how you can apply here: register.nanoporetech.com/grants-progr...
#AnythingAnyoneAnywhere
Find out more and how you can apply here: register.nanoporetech.com/grants-progr...
#AnythingAnyoneAnywhere
February 7, 2025 at 12:28 PM
This week, we established a new Grant Programme to support researchers who are pursuing breakthrough science but may lack all the resources to access Oxford #Nanopore sequencing.
Find out more and how you can apply here: register.nanoporetech.com/grants-progr...
#AnythingAnyoneAnywhere
Find out more and how you can apply here: register.nanoporetech.com/grants-progr...
#AnythingAnyoneAnywhere
Well I wasn’t expecting that! Another amazing application with @nanoporetech.com
I might have to review my personal use of the overused term “Multiomics” 😉
I might have to review my personal use of the overused term “Multiomics” 😉
Glycan Sequencing Based on Glycosidase-Assisted Nanopore Sensing #JACS #MassSpec pubs.acs.org/doi/10.1021/...
Glycan Sequencing Based on Glycosidase-Assisted Nanopore Sensing
Nanopores are promising sensors for glycan analysis with the accurate identification of complex glycans laying the foundation for nanopore-based sequencing. However, their applicability toward continu...
pubs.acs.org
January 3, 2025 at 10:28 PM
Well I wasn’t expecting that! Another amazing application with @nanoporetech.com
I might have to review my personal use of the overused term “Multiomics” 😉
I might have to review my personal use of the overused term “Multiomics” 😉
Reposted by Warren Bach
NanoTiming is now in Nature Communications! High-resolution DNA replication timing using nanopore sequencing shows that Rif1 regulates only specific telomeres: www.nature.com/articles/s41...
Telomere-to-telomere DNA replication timing profiling using single-molecule sequencing with Nanotiming - Nature Communications
Current temporal studies of DNA replication are either complex or low-resolution. Here, the authors introduce Nanotiming, a simple and inexpensive method producing high-resolution, telomere-to-telomer...
www.nature.com
January 3, 2025 at 8:22 AM
NanoTiming is now in Nature Communications! High-resolution DNA replication timing using nanopore sequencing shows that Rif1 regulates only specific telomeres: www.nature.com/articles/s41...
Reposted by Warren Bach
Investigating the performance of Oxford Nanopore long-read sequencing with respect to Illumina microarrays and short-read sequencing https://www.biorxiv.org/content/10.1101/2024.12.19.629409v1
December 22, 2024 at 7:47 PM
Investigating the performance of Oxford Nanopore long-read sequencing with respect to Illumina microarrays and short-read sequencing https://www.biorxiv.org/content/10.1101/2024.12.19.629409v1
Reposted by Warren Bach
Researchers using Oxford Nanopore Tech. long-read sequencing effectively identify pathogenic structural variants in the PRKN locus that were missed by conventional methods; They propose that it should be considered for unresolved early onset #Parkinsons cases
onlinelibrary.wiley.com/doi/10.1002/...
onlinelibrary.wiley.com/doi/10.1002/...
December 20, 2024 at 12:32 PM
Researchers using Oxford Nanopore Tech. long-read sequencing effectively identify pathogenic structural variants in the PRKN locus that were missed by conventional methods; They propose that it should be considered for unresolved early onset #Parkinsons cases
onlinelibrary.wiley.com/doi/10.1002/...
onlinelibrary.wiley.com/doi/10.1002/...
Reposted by Warren Bach
Our hitchhiking paper is out at genomebiology.biomedcentral.com/articles/10.... great collaborative effort with Prasad Sarashetti, @jlipovac.bsky.social, Filip Tomas and JJ Liu.
Briefly, the nanopore is enough for high-quality human genomes. Recently, HERRO showed that even UL is sufficient. 1/3
Briefly, the nanopore is enough for high-quality human genomes. Recently, HERRO showed that even UL is sufficient. 1/3
Evaluating data requirements for high-quality haplotype-resolved genomes for creating robust pangenome references - Genome Biology
Background Long-read technologies from Pacific Biosciences (PacBio) and Oxford Nanopore Technologies (ONT) have transformed genomics research by providing diverse data types like HiFi, Duplex, and ult...
genomebiology.biomedcentral.com
December 19, 2024 at 7:13 AM
Our hitchhiking paper is out at genomebiology.biomedcentral.com/articles/10.... great collaborative effort with Prasad Sarashetti, @jlipovac.bsky.social, Filip Tomas and JJ Liu.
Briefly, the nanopore is enough for high-quality human genomes. Recently, HERRO showed that even UL is sufficient. 1/3
Briefly, the nanopore is enough for high-quality human genomes. Recently, HERRO showed that even UL is sufficient. 1/3
Reposted by Warren Bach
🎄 New Dorado release (v0.9.0) – and it's big!
🚀 Dorado polish command (experimental) for improving draft assemblies – faster & more accurate than Medaka
⚡ Faster modified base calling models
🔧 Usability & accuracy improvements: PolyA, Barcoding, 6mA calling
github.com/nanoporetech...
🚀 Dorado polish command (experimental) for improving draft assemblies – faster & more accurate than Medaka
⚡ Faster modified base calling models
🔧 Usability & accuracy improvements: PolyA, Barcoding, 6mA calling
github.com/nanoporetech...
Release v0.9.0 · nanoporetech/dorado
[0.9.0] (16 Dec 2024)
This major release of Dorado introduces several new features and enhancements. The polish command, currently experimental, is optimised for refining draft assemblies of human ...
github.com
December 17, 2024 at 11:59 AM
🎄 New Dorado release (v0.9.0) – and it's big!
🚀 Dorado polish command (experimental) for improving draft assemblies – faster & more accurate than Medaka
⚡ Faster modified base calling models
🔧 Usability & accuracy improvements: PolyA, Barcoding, 6mA calling
github.com/nanoporetech...
🚀 Dorado polish command (experimental) for improving draft assemblies – faster & more accurate than Medaka
⚡ Faster modified base calling models
🔧 Usability & accuracy improvements: PolyA, Barcoding, 6mA calling
github.com/nanoporetech...
Reposted by Warren Bach
𝗖𝗲𝗹𝗲𝗯𝗿𝗮𝘁𝗶𝗻𝗴 𝗢𝗻𝗲 𝗬𝗲𝗮𝗿 𝗼𝗳 𝗜𝗺𝗽𝗮𝗰𝘁𝗳𝘂𝗹 𝗜𝗻𝗱𝗶𝗴𝗲𝗻𝗼𝘂𝘀 𝗚𝗲𝗻𝗼𝗺𝗶𝗰𝘀 𝗥𝗲𝘀𝗲𝗮𝗿𝗰𝗵 𝗮𝘁 𝗔𝗡𝗨 𝗡𝗖𝗜𝗚 - 𝗧𝘄𝗼 𝗟𝗮𝗻𝗱𝗺𝗮𝗿𝗸 𝗣𝘂𝗯𝗹𝗶𝗰𝗮𝘁𝗶𝗼𝗻𝘀 𝗶𝗻 𝙉𝙖𝙩𝙪𝙧𝙚 with nearly 50,000 accesses and rankings above the 98th percentile globally. Thank you to our collaborators and Indigenous communities for your trust. Details on ANU NCIG LinkedIn Page.
December 17, 2024 at 10:00 PM
𝗖𝗲𝗹𝗲𝗯𝗿𝗮𝘁𝗶𝗻𝗴 𝗢𝗻𝗲 𝗬𝗲𝗮𝗿 𝗼𝗳 𝗜𝗺𝗽𝗮𝗰𝘁𝗳𝘂𝗹 𝗜𝗻𝗱𝗶𝗴𝗲𝗻𝗼𝘂𝘀 𝗚𝗲𝗻𝗼𝗺𝗶𝗰𝘀 𝗥𝗲𝘀𝗲𝗮𝗿𝗰𝗵 𝗮𝘁 𝗔𝗡𝗨 𝗡𝗖𝗜𝗚 - 𝗧𝘄𝗼 𝗟𝗮𝗻𝗱𝗺𝗮𝗿𝗸 𝗣𝘂𝗯𝗹𝗶𝗰𝗮𝘁𝗶𝗼𝗻𝘀 𝗶𝗻 𝙉𝙖𝙩𝙪𝙧𝙚 with nearly 50,000 accesses and rankings above the 98th percentile globally. Thank you to our collaborators and Indigenous communities for your trust. Details on ANU NCIG LinkedIn Page.
Reposted by Warren Bach
It’s incredibly gratifying to see our work on Direct RNA sequencing getting recognised in this way. Congratulations to all the team at @oxfordnanopore.bsky.social who helped us to make it a reality!
www.the-scientist.com/2024-top-10-...
#RNASequencing #Innovation #NanoporeSequencing #RNAResearch
www.the-scientist.com/2024-top-10-...
#RNASequencing #Innovation #NanoporeSequencing #RNAResearch
2024 Top 10 Innovations
The latest group of winning technologies has a little something for everyone—from scientists at the lab bench to those in the clinic and even the classroom.
www.the-scientist.com
December 14, 2024 at 10:25 AM
It’s incredibly gratifying to see our work on Direct RNA sequencing getting recognised in this way. Congratulations to all the team at @oxfordnanopore.bsky.social who helped us to make it a reality!
www.the-scientist.com/2024-top-10-...
#RNASequencing #Innovation #NanoporeSequencing #RNAResearch
www.the-scientist.com/2024-top-10-...
#RNASequencing #Innovation #NanoporeSequencing #RNAResearch
We got there in the end 😁
Thanks for sticking with us 👍
Thanks for sticking with us 👍
We generate a Nanopore only assembly and use long-read cDNA sequencing for annotation. This give us >99.999% consensus accuracy... no need for short reads or PacBio anymore.
December 13, 2024 at 8:38 AM
We got there in the end 😁
Thanks for sticking with us 👍
Thanks for sticking with us 👍
Reposted by Warren Bach
Publication exploring the future potential of nanopore sequencing for clinical use.
What you're missing matters. #WYMM #SwitchON
What you're missing matters. #WYMM #SwitchON
This is an interesting article that has benchmarked the use of @nanoporetech.com for clinical diagnostics in New Zealand. Lots of people (including us) are looking to do the same so a timely publication.
Also, great to see my old colleague @polona.bsky.social on the author list 🙌
rdcu.be/d2UoA
Also, great to see my old colleague @polona.bsky.social on the author list 🙌
rdcu.be/d2UoA
Benchmarking nanopore sequencing and rapid genomics feasibility: validation at a quaternary hospital in New Zealand - npj Genomic Medicine
npj Genomic Medicine - Benchmarking nanopore sequencing and rapid genomics feasibility: validation at a quaternary hospital in New Zealand
www.nature.com
December 10, 2024 at 2:14 PM
Kia ora koutou! 👋
I’ve put together a starter pack of amazing people working in #Genomics across Aotearoa New Zealand.
If I’ve missed anyone, please let me know!
go.bsky.app/KhMbQxK
I’ve put together a starter pack of amazing people working in #Genomics across Aotearoa New Zealand.
If I’ve missed anyone, please let me know!
go.bsky.app/KhMbQxK
December 6, 2024 at 1:14 AM
Guess where I have been this week ?
(Yes they are cheese scones)
(Yes they are cheese scones)
December 4, 2024 at 8:02 AM
Guess where I have been this week ?
(Yes they are cheese scones)
(Yes they are cheese scones)
Reposted by Warren Bach
We are proud to announce a collaboration with UK Biobank to create the world’s first large-scale #epigenetic dataset of 50k participants. The dataset will unlock crucial insights into how #epigenetics drives disease & the breakthroughs to treat them.
Read more: nanoporetech.com/news/oxford-...
Read more: nanoporetech.com/news/oxford-...
November 27, 2024 at 9:16 AM
We are proud to announce a collaboration with UK Biobank to create the world’s first large-scale #epigenetic dataset of 50k participants. The dataset will unlock crucial insights into how #epigenetics drives disease & the breakthroughs to treat them.
Read more: nanoporetech.com/news/oxford-...
Read more: nanoporetech.com/news/oxford-...
Reposted by Warren Bach
Please register for the course on Transposable elements in #genomics and #datascience. We will be sharing the magic of #nanopore long reads for #transposon expression #tesky
November 19, 2024 at 8:15 AM
Please register for the course on Transposable elements in #genomics and #datascience. We will be sharing the magic of #nanopore long reads for #transposon expression #tesky