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Laura White @laurakwhite.bsky.social · Jun 16

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.

Mike Vella @vellamike.bsky.social · Jun 16

In this blog post, we show how chromatin accessibility can be profiled with minimal processing using nanopore sequencing – preserving native structure and capturing rich signal.
Read it here: epi2me.nanoporetech.com/chromatin-ac...

Chromatin accessibility data and tool release

Functional epigenomics uses high-throughput sequencing data to study how epigenetic modifications…

epi2me.nanoporetech.com

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Ryan Wick @rrwick.bsky.social · May 27

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...

Dorado v1.0.0 and the v5.2.0 basecalling models

a blog for miscellaneous bioinformatics stuff

rrwick.github.io

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Matt Parker @bioinfomatt.bsky.social · May 3

The @nanoporetech.com #EPI2ME team is hiring!

If you want to build workflows to analyse @nanoporetech.com sequencing data for end to end applications then this job is for you!

ejnh.fa.em2.oraclecloud.com/hcmUI/Candid...

Bioinformatics Software Developer

We are looking for talented Bioinformatics Software Engineer to work within the Customer Analysis Workflows group who will be responsible for developing coherent bioinformatic software tools for end u...

ejnh.fa.em2.oraclecloud.com

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Sean McKenzie @dorylophile.bsky.social · Apr 18

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!

bioRxiv Bioinfo @biorxiv-bioinfo.bsky.social · Apr 18

Efficient near telomere-to-telomere assembly of Nanopore Simplex reads https://www.biorxiv.org/content/10.1101/2025.04.14.648685v1

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Anna Maria Niewiadomska @amnbio.bsky.social · Apr 9

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

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.

nanoporetech.com

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Albert Vilella, PhD. @albertvilella.bsky.social · Apr 1

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

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Edward Nirenberg @enirenberg.bsky.social · Mar 29

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…

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Rasmus Kirkegaard @kirk3gaard.bsky.social · Mar 25

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

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Matt Parker @bioinfomatt.bsky.social · Mar 18

Quick amplicon prep on an @nanoporetech.com sequencer. Loads of service providers out there doing amplicons - @plasmidsaurus.bsky.social do them very very cheaply plasmidsaurus.com

Much more accurate than a gel.

Plasmidsaurus :: Sequence everything.

plasmidsaurus.com

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Oxford Nanopore @nanoporetech.com · Mar 14

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

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Matt Parker @bioinfomatt.bsky.social · Feb 27

#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)

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Matt Parker @bioinfomatt.bsky.social · Feb 25

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Matt Parker @bioinfomatt.bsky.social · Feb 25

Lanai #190 from 9pm tonight for drinks and canopies with @nanoporetech.com #AGBT2025 #AGBTGM

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Matt Parker @bioinfomatt.bsky.social · Feb 24

Matt Parker @bioinfomatt.bsky.social · Feb 23

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. 😂

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Martin Smith @martinalexsmith.bsky.social · Feb 19

Who's going to #AGBT next week?

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Willem van Schaik @wvschaik.bsky.social · Feb 18

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).

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Oxford Nanopore @nanoporetech.com · Jan 27

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

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...

www.the-microbiologist.com

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Matt Parker @bioinfomatt.bsky.social · Jan 22

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

Alfred Hitchcock's Kevin Newburn @kevinnewburn.bsky.social · Jan 21

One of my favorite oddball formats the Sega Genesis found itself in was the Amstrad Mega PC. A 386sx PC that also had an entire genesis motherboard on a ISA card. I'm fascinated by this sort of console/pc hybrid concept.

A picture of the Amstrad Mega PC running Sonic the Hedgehog.

A picture of a Mega PC (sega genesis) controller for the Amstrad Mega PC. It's the most PC beige you've ever seen.

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Association for Molecular Pathology @ampath.bsky.social · Jan 15

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...

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Aaron Pomerantz @aaronpomerantz.bsky.social · Jan 15

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)

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Stephen Turner @stephenturner.us · Jan 15

CompàreGenome: a command-line tool for genomic diversity estimation in prokaryotes and eukaryotes https://bmcbioinformatics.biomedcentral.com/articles/10.1186/s12859-025-06036-0 🧬🖥️🧪 #Rstats https://github.com/gmoro-bioecopest/CompareGenome

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Oxford Nanopore @nanoporetech.com · Jan 13

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

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Oxford Nanopore @nanoporetech.com · Jan 13

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

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Albert Vilella, PhD. @albertvilella.bsky.social · Jan 13

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

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