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Devon Ryan

@dpryan79.bsky.social
1.5K followers 146 following 37 posts

An American in Germany, an ion channel guy in bioinformatics, a proponent of scientific skepticism in an irrational world. @devon@genomic.social, @dpryan79 on twitter and github

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Reposted by Devon Ryan
Wouter De Coster @wdecoster.bsky.social · 28/09/2026
We, internationally, have failed so many people.
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Rob Patro @robp.bsky.social · 10/09/2026
The motivation was that, while I think short-read identification is "too hard" to justify an immense outpouring of continued effort, I think long-read identification is challenging but promising & deserves new ideas. 1/3
drops.dagstuhl.de
Exact Transcript Quantification Over Splice Graphs
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Devon Ryan @dpryan79.bsky.social · 10/09/2026
Short reads are highly over rated for this, your long read only approach makes much more sense.
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Devon Ryan @dpryan79.bsky.social · 10/09/2026
What was the motivation and what sort of input data does/will it take?
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Katie Mack @astrokatie.com · 14/08/2026
OMG. 😳 First a bomb, then an arson attack, all to try to stop the scientists from building a gravitational wave detector. “A local opposition group says a legally protected quiet zone for the project could constrain industrial development across central Sardinia”
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Rob Patro @robp.bsky.social · 29/07/2026
New preprint🚨(*long* time coming)! We introduce seqproc: an efficient, flexible, and concise tool for describing and transforming sequencing-read geometry. The aim: make complex protocols easy to specify & transform without giving up speed or accuracy. www.biorxiv.org/content/10.6... 🧵
Crop of the preprint's first page. The title is "seqproc: An
efficient, flexible, and concise tool for sequence geometry description and
transformation." Authors are Noah Cape, Elan Fisher, Daniel Liu, and Rob Patro.
The abstract introduces seqproc, EFGDL, and the antisequence execution engine.
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Devon Ryan @dpryan79.bsky.social · 23/07/2026
Merged. Feel free to poke me if you hit a snag like this again. I’m largely inactive on GitHub these days but I’m happy to jump in and unblock things when it helps :)
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Rob Patro @robp.bsky.social · 29/06/2026
Hey @nilshomer.com, you'd asked about this in the past: we finally got around to implementing byte-level determinism in salmon (github.com/COMBINE-lab/...). It turned out to require a lot of thought and changes, but it turns out we can do it elegantly (with RAD files) and fast (`--deterministic`)!
github.com
Release v2.2.1 · COMBINE-lab/salmon
salmon 2.2.1 The recommended 2.2.x release: it carries the full 2.2.0 feature set plus a security fix for a lz4_flex advisory pulled in by the new RAD compression. If you are on 2.2.0, upgrade. No ...
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Michael Caley @michaelcaley.bsky.social · 12/06/2026
doing some analytics on the Canadian Men's National Team (via the @doublepivotpodcast.bsky.social discord)
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Matt Cameron @mattcameron.bsky.social · 23/05/2026
IS USCIS REALLY GOING TO "FORCE" EVERYONE WHO COULD OTHERWISE GET A GREENCARD OUT OF THE COUNTRY? My law office is being flooded with questions about yesterday's stunning USCIS policy announcement. In Part I of the most thorough analysis yet published on it, I provide detailed answers with receipts
deportnation.substack.com
DID DHS JUST STOP PROCESSING GREENCARDS? A CLOSER LOOK
Someone who has been helping people through the immigration system for 20 years answers your questions about USCIS's stunning new policy announcement
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Devon Ryan @dpryan79.bsky.social · 22/04/2026
A very poor version that’s oddly biased toward random contributions that aren’t very important, yes. This is the email version of those AI images where people have extra legs and fingers and such.
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Devon Ryan @dpryan79.bsky.social · 22/04/2026
Tell me you're using AI to trawl for candidates and send them slop emails without telling me you're just using crappy AI.
A 100% AI slop email from a recruiter where the AI trawled Linked In, github, and some other sources to craft the most poorly written email you can possibly imagine. If you can't see it, consider yourself lucky, it's AI-sloppier than what you're likely imagining.
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Adam Phillippy @aphillippy.bsky.social · 20/04/2026
Friday was my last day at NHGRI. After 10 wonderful years, my lab is headed to Johns Hopkins University genomeinformatics.github.io/movingday/
genomeinformatics.github.io
We're moving!
Friday was my last day at NHGRI. After 10 wonderful years, my lab is headed one hour north on I-95 to set up shop at Johns Hopkins University. This is a very bittersweet move for me, as NHGRI has prov...
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Stephen Turner @stephenturner.us · 18/04/2026
Accelerated long-read variant calling with Clair3 for whole-genome sequencing academic.oup.com/bioinformati...
academic.oup.com
Accelerated long-read variant calling with Clair3 for whole-genome sequencing
AbstractSummary. The rapid growth of genomic data and increasing adoption of long-read sequencing technologies have rendered variant calling one of the mos
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emptywheel @emptywheel.bsky.social · 12/04/2026
Magyar's report of an Orbán concession in English.
Magyar Péter (Ne féljetek)
@magyarpeterMP
Prime Minister Viktor Orbán has just called to congratulate us on our victory.
8:19 PM · Apr 12, 2026
·
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Devon Ryan @dpryan79.bsky.social · 12/04/2026
Any educated guesses on when enough results will be in to project the outcome?
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Chris Ingraham @cingraham.bsky.social · 12/04/2026
Current status of the Strait of Hormuz dispute
In Bruges scene where Colin Farrell is pointing a gun at his head and Brendon Gleeson is also pointing a gun at Colin Farrell's head
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Devon Ryan @dpryan79.bsky.social · 31/03/2026
Once again KBJ seems like the most sensible person on the court.
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Aaron Quinlan (he/him) @aaronquinlan.bsky.social · 12/03/2026
Brent Pedersen, Mitchell Vollger and I have "posted" our preprint of the manuscript describing bedder, a complement to the functionality of bedtools. The "preprint server" we have chosen is google docs because it was rejected by biorxiv. docs.google.com/document/d/1...
docs.google.com
bedder-manuscript.v10
Bioinformatics, 2026, 0–0 doi: 10.1093/bioinformatics/xxxxx Advance Access Publication Date: DD Month YYYY Genome Analysis Genome Analysis bedder: flexible genome interval intersection with user-defi...
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Jonathan Eisen @phylogenomics.bsky.social · 09/03/2026
I cannot stop thinking of all the amazing and wonderful people I have known from Israel, Iran, Lebanon and other countries caught up in this war. It is people just like them who are being killed and harmed here.
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Páll Melsted @pmelsted.bsky.social · 06/03/2026
Excited to share this preprint that describes my latest work on using GPUs to accelerate processing of RNA-seq data. The title says it all: "RNA-seq analysis in seconds using GPUs" now on biorxiv www.biorxiv.org/content/10.6... and github github.com/pachterlab/k... Figure 1 shows they key result
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Joaquin Castro @joaquincastrotx.bsky.social · 01/02/2026
Yesterday, five-year-old Liam and his dad Adrian were released from Dilley detention center. I picked them up last night and escorted them back to Minnesota this morning. Liam is now home. With his hat and his backpack.
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Devon Ryan @dpryan79.bsky.social · 27/01/2026
You’ve opened Pandora’s box. We’ve been spending our weekends taking our kid to cubing competitions.
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David Ho @davidho.bsky.social · 21/01/2026
I really think the net benefit for society is greater if we banned social media for those over 16.
theguardian.com
Badenoch tells Starmer to ‘just get on’ with under-16s social media ban
Tory leader says delay will harm children’s mental health after No 10 said it would consult on policy by summer
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Nick @sregorn.bsky.social · 21/01/2026
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Torsten Seemann @torstenseemann.bsky.social · 15/12/2025
💾 Prokka 1.15.6 is released! This is the last major release of Prokka. But don't be sad, because @oschwengers.bsky.social already has an excellent replacement called Bakta you can migrate to. #bioinformatics #microbiology #genomics github.com/tseemann/pro...
github.com
Release Heading into the sunset · tseemann/prokka
The future This is probably the last release of Prokka. I won't be making any code changes except bug fixes. I will update the databases occasionally. I strongly recommend you use Bakta by @oschwen...
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Devon Ryan @dpryan79.bsky.social · 03/12/2025
Big news!
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Vijini Mallawaarachchi @vijinim.bsky.social · 25/11/2025
🧬 Come check out my poster on agtools, an open-source Python framework for analysing and manipulating assembly graphs at #ABACBS2025 Poster #106 • 💻 Github: github.com/Vini2/agtools 📄 Preprint: biorxiv.org/content/10.110…
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Rob Patro @robp.bsky.social · 29/10/2025
End qualified immunity.
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Stephen Turner @stephenturner.us · 22/10/2025
PubMed is running on autopilot during shutdown, but key independent committee has been abolished www.bmj.com/content/391/... 🧪
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Frank Cogliano @frankcogliano.bsky.social · 22/10/2025
Graduate seminar did a deep dive on Thomas Paine’s Common Sense yesterday. At the line, “in America the law is king,” they (14 students from 6 countries) burst out laughing. I've been doing this for 35 years and this is the first time that was a laugh line.
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Devon Ryan @dpryan79.bsky.social · 21/10/2025
You know you work for a software company when the description of meeting room names in your new office comes with regex that they will all follow.
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Christophe 🔬 Leterrier @christlet.bsky.social · 17/09/2025
Our new preprint is up! This is the main postdoc work of @wiesner-t.bsky.social focusing on exocytosis along the axon shaft and its regulation by the sub membrane actin-spectrin scaffold: www.biorxiv.org/content/10.1... Read the thread below for a summary of our findings 🧵1/11
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Heng Li @lh3lh3.bsky.social · 12/09/2025
New blog post – A quick look at Roche's SBX lh3.github.io/2025/09/11/a...
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Heng Li @lh3lh3.bsky.social · 04/09/2025
Now published in GigaScience with minor improvements: academic.oup.com/gigascience/... * Download: zenodo.org/records/1490... * More info: github.com/lh3/panmask
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Jean-François Cudennec @limpetnerd.eurosky.social · 27/08/2025
Plants phylogeny is a mess anyway Credit : @xkcd.com
"Did you know the mighty redwood is actually the same species as brocoli and kale ? it's just a different cultivar"

"Every year or two, botanists add another plant to Brassica oleracea and see if anyone calls them on it"
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Stephen Farrell @lutzie.bsky.social · 10/06/2025
Always relevant.
A picture of William Adams, from the TV show Battlestar Galactica, with the quote:
"There's a reason you separate military and the police. One fights the enemies of the state, the other serves and protects the people. When the military becomes both, then the enemies of the state tend to become the people."
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Devon Ryan @dpryan79.bsky.social · 27/05/2025
My 6th grader is doing a survey for ethics class on the concepts of happiness and luck (or Glück for the German speakers). If you have a few minutes to submit your thoughts she’d appreciate it. docs.google.com/forms/d/1y2b...
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Carl T. Bergstrom @carlbergstrom.com · 26/05/2025
These are VERY rough estimates, but here's life expectancy after diagnosis of type-I diabetes over the past 150 years. It was Banting and Best's discovery of how to isolate insulin in 1921 — not some fucking cooking class — that gave people including my daughter a new lease on life.
Plot of life expectancy after Type 1 diabetes diagnosis, 1850-2025. 

After the discovery of insulin in 1921, life expectancies go gradually from zero to seventy years.
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Carl T. Bergstrom @carlbergstrom.com · 30/04/2025
I’m overwhelmed by the expressions of sympathy and support. And still this pales in comparison to what they are doing to immigrants and to undermine the Bill of Rights. If you could do one thing for me, call your representatives and demand accountability for their white supremacist terrorism.
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Devon Ryan @dpryan79.bsky.social · 25/04/2025
This seems like a good thing. Are we aloud to have good things? I feel like this is going to turn into a Charlie Brown and Lucy with the football sort of situation.
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Devon Ryan @dpryan79.bsky.social · 16/04/2025
Were you able to screenshot that? All I see is „blocked“.
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Devon Ryan @dpryan79.bsky.social · 16/04/2025
Anyone want to go in on an industry collab to fund this?
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Congressman Shri Thanedar @shrithanedar.bsky.social · 16/04/2025
I've seen enough. Donald Trump is not abiding by a lawful Supreme Court ruling. As a member of Congress, I fully support impeaching him. NOW.
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Stephen Turner @stephenturner.us · 15/04/2025
How is this Python package real pypi.org/project/tari...
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Popehat @kenwhite.bsky.social · 13/04/2025
Cruel Fate, 1525: Our cow died during the night. We will surely perish. Cruel Fate, 2025: Our Keurig stopped working during the night. We will surely perish.
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Hilde Kuehne @hildekuehne.bsky.social · 13/04/2025
That’s a wild backdoor…
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Devon Ryan @dpryan79.bsky.social · 10/04/2025
Burn
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Devon Ryan @dpryan79.bsky.social · 03/04/2025
I have yet to see a boring thread from you…
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