Matt Parker
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bioinfomatt.bsky.social
Matt Parker
@bioinfomatt.bsky.social
450 followers 170 following 17 posts
Director, Clinical Bioinformatics Software at Oxford Nanopore in the EPI2ME team. Interested in regulated application of Nanopore sequencing. Also bikes, beers, trains, and the American Office.
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Reposted by Matt Parker
laurakwhite.bsky.social
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.
vellamike.bsky.social 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
June 16, 2025 at 4:54 PM
Reposted by Matt Parker
rrwick.bsky.social
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
May 27, 2025 at 7:02 AM
bioinfomatt.bsky.social
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
May 3, 2025 at 6:32 AM
Reposted by Matt Parker
dorylophile.bsky.social
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.bsky.social 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
April 18, 2025 at 12:52 PM
Reposted by Matt Parker
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
April 9, 2025 at 11:37 AM
Reposted by Matt Parker
albertvilella.bsky.social
New version of Oxford @nanoporetech.com Dorado v0.9.5
April 1, 2025 at 5:50 AM
Reposted by Matt Parker
enirenberg.bsky.social
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… ongoing multistate measles outbreak that is particularly severe in Texas reminds us of what happens when confidence in well-established science underlying public health and well-being is undermined. Measles, which killed more than 100,000 unvaccinated children last year in Africa and Asia owing to pneumonitis and encephalitis caused by the virus, had been eliminated from our shores. The two-dose measles, mumps, rubella vaccine regimen (MMR) using over the past decades has a remarkably favorable benefit-risk profile. The MMR vaccine is 97% or more effective in preventing measles following the two-dose series, and its safety has been remarkably well studied. Though rarely followed by a single fever-related seizure, or very rarely by allergic reactions or blood clotting disorders, the vaccine very simply does not cause autism, nor is it associated with encephalitis or death. It does, however, protect against a potential devasting consequence of prior measles infection, subacute sclerosing panencephalitis (SSPE), which is an untreatable, relentlessly progressive neurologic disorder leading to death in about 1 in 10,000 individuals infected with measles. Undermining confidence in well-established vaccines that have met the high standards for quality, safety, and effectiveness that have been in place for decades at FDA is irresponsible, detrimental to public health, and a clear danger to our nation's health, safety. and security. In the years following the pandemic, at the Center for Biologics Evaluation and Research we have applied the same unwavering commitment to public health priorities to the development of cell and gene therapies to address both hereditary and acquired rare diseases. During my tenure as Center Director we have approved 22 gene therapies, including the first gene therapy ever to be approved in the United States. However, we know that we must do better to expedite the development of treatments for those individual suffering from any one of the thousan…
March 29, 2025 at 2:29 AM
Reposted by Matt Parker
kirk3gaard.bsky.social
Less than two months to @nanoporetech.com London calling. Anyone secretly testing new pores? Kit chemistry? Devices?
March 25, 2025 at 8:29 AM
Reposted by Matt Parker
nanoporetech.com
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
March 14, 2025 at 5:53 PM
bioinfomatt.bsky.social
#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)
February 27, 2025 at 12:34 AM
bioinfomatt.bsky.social
Lanai #190 from 9pm tonight for drinks and canopies with @nanoporetech.com #AGBT2025 #AGBTGM
February 25, 2025 at 12:21 AM
bioinfomatt.bsky.social
February 24, 2025 at 12:03 AM
bioinfomatt.bsky.social
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. 😂
February 23, 2025 at 6:03 PM
Reposted by Matt Parker
martinalexsmith.bsky.social
Who's going to #AGBT next week?
February 19, 2025 at 10:01 AM
Reposted by Matt Parker
wvschaik.bsky.social
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).
February 18, 2025 at 9:27 AM
Reposted by Matt Parker
nanoporetech.com
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
January 27, 2025 at 6:08 PM
bioinfomatt.bsky.social
My 1st “computer” - I remember that genesis motherboard being very in the way when we tried to upgrade the RAM!
kevinnewburn.bsky.social The Get Up Kevins @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.
January 22, 2025 at 8:50 PM
Reposted by Matt Parker
ampath.bsky.social
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...
January 15, 2025 at 1:29 PM
Reposted by Matt Parker
aaronpomerantz.bsky.social
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)
January 15, 2025 at 8:38 PM
Reposted by Matt Parker
stephenturner.us
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
January 15, 2025 at 9:00 PM
Reposted by Matt Parker
nanoporetech.com
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
January 13, 2025 at 5:26 PM
Reposted by Matt Parker
nanoporetech.com
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
January 13, 2025 at 4:35 PM
Reposted by Matt Parker
albertvilella.bsky.social
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
January 13, 2025 at 8:05 AM
Reposted by Matt Parker
tuesparholt.bsky.social
new lab member and a bunch of workhorses (on their makeshift heat sink) @nanoporetech.com
January 8, 2025 at 1:40 PM
Reposted by Matt Parker
kncvtbplus.bsky.social
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:
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.
www.kncvtbc.org
December 30, 2024 at 10:40 AM