iiinova — where your digital self keeps evolving

Reposted by Matt Parker

Laura White @laurakwhite.bsky.social · 16/06/2025

One thing I didn’t appreciate until London Calling this year is that @nanoporetech.com is now releasing more technical documentation and datasets as blog posts.

195

Reposted by Matt Parker

Ryan Wick @rrwick.bsky.social · 27/05/2025

New blog post! In it, I benchmark the new version of Dorado from @nanoporetech.com, which comes with new DNA basecalling models. Short version: big accuracy gains for hac, small improvements for sup. Check it out for the full results: rrwick.github.io/2025/05/27/d...

rrwick.github.io

Dorado v1.0.0 and the v5.2.0 basecalling models

a blog for miscellaneous bioinformatics stuff

45830

Reposted by Matt Parker

Sean McKenzie @dorylophile.bsky.social · 18/04/2025

Exciting preprint from Haoyu Cheng (not on bluesky?) and @lh3lh3.bsky.social: building amazing Nanopore assemblies just got faster and more accessible! Thrilled to have played a small part in this work!

073

Reposted by Matt Parker

Anna Maria Niewiadomska @amnbio.bsky.social · 09/04/2025

Missed our knowledge exchange on Oxford #Nanopore comprehensive metagenomic sequencing for pathogen surveillance? Watch the recording here! buff.ly/IDhJt0S This approach allows for discovery of #bacteria, #fungi, and viruses directly from respiratory samples #metagenomics #viromics

nanoporetech.com

Metagenomics for pathogen surveillance

In this webinar, we learn how Oxford Nanopore sequencing can provide a rapid and comprehensive metagenomic approach for characterising bacteria, fungi, and viruses directly from respiratory samples.

002

Reposted by Matt Parker

Albert Vilella, PhD. @albertvilella.bsky.social · 01/04/2025

New version of Oxford @nanoporetech.com Dorado v0.9.5

0166

Reposted by Matt Parker

Edward Nirenberg @enirenberg.bsky.social · 29/03/2025

Peter Marks’s resignation letter. Everyone should read this.

Peter Marks, MD, PhD
Director, Center for Biologics Evaluation and Research U.S. Food and Drug Administration
10903 New Hampshire Avenue
Silver Spring, MD 20903
March 28, 2025
Sara Brenner, MD, MPH
Acting Commissioner of Food and Drugs
U.S. Food and Drug Administration
10903 New Hampshire Avenue
Silver Spring, MD 20903
Dear Dr. Brenner:
It is with a heavy heart that I have decided to resign from FDA and retire from federal service as Director of the Center for Biologics Evaluation and Research effective April 5, 2025. I leave behind a staff of professionals who are undoubtedly the most devoted to protecting and promoting the public health of any group of people that I have encountered during my four decades working in the public and private sectors. I have always done my best to advocate for their well-being and I would ask that you do the same during this very difficult time during which their critical importance to the safety and security of our nation may be underappreciated.
Over the past years I have been involved in enhancing the safety of our nation's blood supply, in advancing the field of cell and gene therapy, and in responding to public health emergencies. In the last of these, during the COVID-19 pandemic I had the privilege of watching the vision that I conceived for Operation Warp Speed in March 2020 in collaboration with Dr. Robert Kadlec become a reality under the leadership of HHS Secretary Azar and President Trump due to the unwavering commitment of public servants at FDA and elsewhere across the government. At FDA, the tireless efforts of staff across the agency resulted in remarkably expediting the development of vaccines against the virus, meeting the standards for quality, safety, and effectiveness expected by the American public. The vaccines undoubtedly markedly reduced morbidity and mortality from COVID-19 in the United States and elsewhere. Many of these same individuals applied learnings from the pandemic during a flawless response helping…

15620333

Reposted by Matt Parker

Rasmus Kirkegaard @kirk3gaard.bsky.social · 25/03/2025

Less than two months to @nanoporetech.com London calling. Anyone secretly testing new pores? Kit chemistry? Devices?

121

Reposted by Matt Parker

Oxford Nanopore @nanoporetech.com · 14/03/2025

This week we celebrated 20 years of innovation! To mark the occasion, we’re offering 20 complimentary in-person tickets to London Calling for researchers facing barriers to attendance. Apply here: share.hsforms.com/1rfrIYeGhTCG... #nanoporeconf

1145

Matt Parker @bioinfomatt.bsky.social · 27/02/2025

#AGBT2025 #AGBTGM has been incredible. Lucky to be part of the event with @nanoporetech.com - as always we were so looked after by our amazing events team! (Photo credit to @minomatt.bsky.social)

091

Matt Parker @bioinfomatt.bsky.social · 23/02/2025

Stop by the @nanoporetech.com Lanai suite #190 at #AGBT2025 #AGBTGM tonight after the welcome reception. We’re open from 7pm. We can’t wait to PORE you a beverage. 😂

1122

Reposted by Matt Parker

Martin Smith @martinalexsmith.bsky.social · 19/02/2025

Who's going to #AGBT next week?

021

Reposted by Matt Parker

Willem van Schaik @wvschaik.bsky.social · 18/02/2025

Landmark paper claxon! 'Evaluating the economic and health impact of proactive genomic epidemiology in a hospital setting' www.medrxiv.org/content/10.1... Significant savings associated with proactive genomic epidemiology.

Figure 6:
Overall annual potential savings and costs by use of the proactive genomic epidemiology approach
The health economic assessment uncovered yearly net cost savings of approximately € 1·25 million if initiated IPC measures completely halt transmission of clinical isolates after the second patient. The reduction in costs is due to a lower rate of costs for non-MDRO (red) and MDRO (blue) infections, respectively as well as colonization with MDRO (green). The costs for non-MDRO infections (red) are made up of the additional days a patient has to spend in hospital due to the infection (7·8 days), multiplied by the costs per patient for an additional day in hospital (€325). The costs for the colonization with MDRO (green) is composed of the average number of days a patient spends in the hospital (4·6 days), multiplied by the extra-costs incurred per patient per day for the isolation of the patient (€325). The cost for MDRO infections (blue) results from the average number of days a patient with an MDRO infection has to spend in hospital (7·8 days) multiplied by the additional costs incurred per day by a patient with an MDRO infection (€650).

44423

Reposted by Matt Parker

Oxford Nanopore @nanoporetech.com · 27/01/2025

Recent #birdflu cases highlight the need for proactive #pathogen monitoring. Read how researchers using nanopore sequencing in wastewater detected surges in #influenza A, showing its potential as an early warning system. Read here: www.the-microbiologist.com/news/sewage-... #H5N1

the-microbiologist.com

Sewage could act as early warning system for influenza A outbreaks

Researchers monitoring wastewater for avian and human influenza A virus have detected a surge in virus as the flu season got underway, showing that the technique could act as an early warning system f...

196

Matt Parker @bioinfomatt.bsky.social · 22/01/2025

My 1st “computer” - I remember that genesis motherboard being very in the way when we tried to upgrade the RAM!

010

Reposted by Matt Parker

Association for Molecular Pathology @ampath.bsky.social · 15/01/2025

Join us next week for a webinar on 🧬nanopore sequencing 🧬 featuring speaker Stephanie Chrysanthou of MSK Cancer Center. Learn about the fundamentals, applications and impacts — and earn CE/CMLE credits. educate.amp.org/local/catalo...

022

Reposted by Matt Parker

Aaron Pomerantz @aaronpomerantz.bsky.social · 15/01/2025

There were remarkable updates presented at #PAG32 on incredibly accurate @nanoporetech.com sequencing for applications ranging from telomere-to-telomere plant & animal genome assemblies, to amplicon sequencing at massive scale. Here are some highlights in case you missed them (thread)

1159

Reposted by Matt Parker

Stephen Turner @stephenturner.us · 15/01/2025

CompàreGenome: a command-line tool for genomic diversity estimation in prokaryotes and eukaryotes bmcbioinformatics.biomedcentral.com… 🧬🖥️🧪 #Rstats github.com/gmoro-bioecopest/Compare…

052

Reposted by Matt Parker

Oxford Nanopore @nanoporetech.com · 13/01/2025

Following the announcement of our first speaker Jeff Nivala, we’re happy to announce early bird tickets for London Calling 2025, are now available. Make sure to purchase before 19th Jan to avoid the price increase. Get your ticket here: nanoporetech.com/about/events... #nanoporeconf

nanoporetech.com

London Calling 2025

London Calling - Oxford Nanopore's annual conference

083

Reposted by Matt Parker

Oxford Nanopore @nanoporetech.com · 13/01/2025

1/ We’re excited to announce our first speaker of London Calling 2025 Jeff Nivala will share their groundbreaking ‘proof-of-concept' method showcasing the capability of #nanopore sequencing to read #polypeptide strands. Register here: nanoporetech.com/about/events... #nanoporeconf

3197

Reposted by Matt Parker

Albert Vilella, PhD. @albertvilella.bsky.social · 13/01/2025

Oxford @nanoporetech.com 2024 results: - Commercial performance accelerated in the second half in-line with guidance; underlying revenue growth in the second half was approximately 34% on a constant currency basis

121

Reposted by Matt Parker

Tue Sparholt Jørgensen @tuesparholt.bsky.social · 08/01/2025

new lab member and a bunch of workhorses (on their makeshift heat sink) @nanoporetech.com

192

Reposted by Matt Parker

KNCV TB Plus | KNCV Tuberculosis Foundation @kncvtbplus.bsky.social · 30/12/2024

Our research this year covered: 🔬 TB diagnostics and technological innovations 💉 TB vaccines and preventive strategies 💊 Drug resistant #TB (DR-TB) and treatment innovations 🙌 Post-TB care and person-centred approaches 💸 Economic and #PublicHealth impacts of TB Find them here:

kncvtbc.org

KNCV Publications - KNCV - Tuberculosefonds

On this page you can find the up-to-date list of KNCV publications, research conducted within KNCV and partner organizations.

011

Matt Parker @bioinfomatt.bsky.social · 25/12/2024

Merry Christmas! Smoked port old fashioned to finish me off 🥂

000

Reposted by Matt Parker

Veera Rajagopal @doctorveera.bsky.social · 23/12/2024

Due to the limitations of short read sequencing, this mutation has remained hidden for more than 25 years since ASPA mutations were first characterized in individuals Canavan disease. 2/

142

Matt Parker @bioinfomatt.bsky.social · 20/12/2024

I gave the @seqera.io @nextflow.io AI the challenge of writing me a workflow that produced a really grumpy Christmas message. Damn guys - what you been feeding this thing??

110

Reposted by Matt Parker

Ryan Wick @rrwick.bsky.social · 17/12/2024

New release of Canu - first one in over 3 years! github.com/marbl/canu/r... The notes say this will be the very last release. Many thanks to its devs Brian Walenz and @sergek.bsky.social. Canu may be a bit old and it's certainly not fast, but it makes good assemblies and so I still use it!

github.com

Release Canu v2.3 · marbl/canu

These are release notes for Canu version 2.3, which was released on December 17th, 2024. Canu is specialized for assembly of single-molecule sequences. Full documentation can be found at http://can...

14016

Reposted by Matt Parker

Mike Vella @vellamike.bsky.social · 17/12/2024

🎄 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...

github.com

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 ...

23825

Reposted by Matt Parker

Albert Vilella, PhD. @albertvilella.bsky.social · 17/12/2024

In #NextGenSequencing news, Oxford @nanoporetech.com has released a new version of their basecalling software with new functionalities. An explainer ow what the basecalling software is and what this new release brings for ONT users. github.com/nanoporetech...

github.com

Release v0.9.0 · nanoporetech/dorado

23613

Reposted by Matt Parker

The Tattooed Professor @schwessinger.bsky.social · 13/12/2024

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.

353

Matt Parker @bioinfomatt.bsky.social · 12/12/2024

The things you find around the @nanoporetech.com headquarters! #WYMM

000

Reposted by Matt Parker

Phillipa Burns @phillipaburns.bsky.social · 16/11/2024

Please share with your Biomedical & Clinical Science friends on 🦋 - let’s build our network up again❤️

284730

Matt Parker @bioinfomatt.bsky.social · 08/12/2024

Thought it was time I joined @nanoporetech.com on here - follow me for the latest #EPI2ME tweets… probably the odd smattering of trains and travel too.

110