Reposted by Devon RyanWouter De Coster @wdecoster.bsky.social · 28/09/2026We, internationally, have failed so many people. 111
Reposted by Devon RyanRob Patro @robp.bsky.social · 10/09/2026The 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. 1/3drops.dagstuhl.deExact Transcript Quantification Over Splice Graphs 121
Devon Ryan @dpryan79.bsky.social · 10/09/2026Short reads are highly over rated for this, your long read only approach makes much more sense. 010
Devon Ryan @dpryan79.bsky.social · 10/09/2026What was the motivation and what sort of input data does/will it take? 110
Reposted by Devon RyanKatie Mack @astrokatie.com · 14/08/2026OMG. 😳 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” 13387100
Reposted by Devon RyanRob Patro @robp.bsky.social · 29/07/2026New 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... 🧵 1369
Devon Ryan @dpryan79.bsky.social · 23/07/2026Merged. 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 :) 110
Reposted by Devon RyanRob Patro @robp.bsky.social · 29/06/2026Hey @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.comRelease v2.2.1 · COMBINE-lab/salmonsalmon 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 ... 1243
Reposted by Devon RyanMichael Caley @michaelcaley.bsky.social · 12/06/2026doing some analytics on the Canadian Men's National Team (via the @doublepivotpodcast.bsky.social discord) 5522
Reposted by Devon RyanMatt Cameron @mattcameron.bsky.social · 23/05/2026IS 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 receiptsdeportnation.substack.comDID DHS JUST STOP PROCESSING GREENCARDS? A CLOSER LOOKSomeone who has been helping people through the immigration system for 20 years answers your questions about USCIS's stunning new policy announcement 14272119
Devon Ryan @dpryan79.bsky.social · 22/04/2026A 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. 010
Devon Ryan @dpryan79.bsky.social · 22/04/2026Tell me you're using AI to trawl for candidates and send them slop emails without telling me you're just using crappy AI. 210
Reposted by Devon RyanAdam Phillippy @aphillippy.bsky.social · 20/04/2026Friday was my last day at NHGRI. After 10 wonderful years, my lab is headed to Johns Hopkins University genomeinformatics.github.io/movingday/genomeinformatics.github.ioWe'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... 1513719
Reposted by Devon RyanStephen Turner @stephenturner.us · 18/04/2026Accelerated long-read variant calling with Clair3 for whole-genome sequencing academic.oup.com/bioinformati...academic.oup.comAccelerated long-read variant calling with Clair3 for whole-genome sequencingAbstractSummary. The rapid growth of genomic data and increasing adoption of long-read sequencing technologies have rendered variant calling one of the mos 091
Reposted by Devon Ryanemptywheel @emptywheel.bsky.social · 12/04/2026Magyar's report of an Orbán concession in English. 18933209
Devon Ryan @dpryan79.bsky.social · 12/04/2026Any educated guesses on when enough results will be in to project the outcome? 000
Reposted by Devon RyanChris Ingraham @cingraham.bsky.social · 12/04/2026Current status of the Strait of Hormuz dispute 456322496458
Devon Ryan @dpryan79.bsky.social · 31/03/2026Once again KBJ seems like the most sensible person on the court. 000
Reposted by Devon RyanAaron Quinlan (he/him) @aaronquinlan.bsky.social · 12/03/2026Brent 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.combedder-manuscript.v10Bioinformatics, 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... 74118
Reposted by Devon RyanJonathan Eisen @phylogenomics.bsky.social · 09/03/2026I 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. 313019
Reposted by Devon RyanPáll Melsted @pmelsted.bsky.social · 06/03/2026Excited 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 618887
Reposted by Devon RyanJoaquin Castro @joaquincastrotx.bsky.social · 01/02/2026Yesterday, 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. 25306664815875
Devon Ryan @dpryan79.bsky.social · 27/01/2026You’ve opened Pandora’s box. We’ve been spending our weekends taking our kid to cubing competitions. 010
Reposted by Devon RyanDavid Ho @davidho.bsky.social · 21/01/2026I really think the net benefit for society is greater if we banned social media for those over 16.theguardian.comBadenoch tells Starmer to ‘just get on’ with under-16s social media banTory leader says delay will harm children’s mental health after No 10 said it would consult on policy by summer 824830
Reposted by Devon RyanTorsten 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.comRelease Heading into the sunset · tseemann/prokkaThe 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... 311959
Reposted by Devon RyanVijini 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… 12815
Reposted by Devon RyanStephen Turner @stephenturner.us · 22/10/2025PubMed is running on autopilot during shutdown, but key independent committee has been abolished www.bmj.com/content/391/... 🧪 079
Reposted by Devon RyanFrank Cogliano @frankcogliano.bsky.social · 22/10/2025Graduate 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. 9756301635
Devon Ryan @dpryan79.bsky.social · 21/10/2025You 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. 000
Reposted by Devon RyanChristophe 🔬 Leterrier @christlet.bsky.social · 17/09/2025Our 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 614149
Reposted by Devon RyanHeng Li @lh3lh3.bsky.social · 12/09/2025New blog post – A quick look at Roche's SBX lh3.github.io/2025/09/11/a... 25730
Reposted by Devon RyanHeng Li @lh3lh3.bsky.social · 04/09/2025Now published in GigaScience with minor improvements: academic.oup.com/gigascience/... * Download: zenodo.org/records/1490... * More info: github.com/lh3/panmask 13010
Reposted by Devon RyanJean-François Cudennec @limpetnerd.eurosky.social · 27/08/2025Plants phylogeny is a mess anyway Credit : @xkcd.com 10700146
Devon Ryan @dpryan79.bsky.social · 27/05/2025My 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... 131
Reposted by Devon RyanCarl T. Bergstrom @carlbergstrom.com · 26/05/2025These 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. 423873717
Reposted by Devon RyanCarl T. Bergstrom @carlbergstrom.com · 30/04/2025I’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. 751683
Devon Ryan @dpryan79.bsky.social · 25/04/2025This 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. 000
Devon Ryan @dpryan79.bsky.social · 16/04/2025Were you able to screenshot that? All I see is „blocked“. 120
Devon Ryan @dpryan79.bsky.social · 16/04/2025Anyone want to go in on an industry collab to fund this? 010
Reposted by Devon RyanCongressman Shri Thanedar @shrithanedar.bsky.social · 16/04/2025I'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. 621575308
Reposted by Devon RyanStephen Turner @stephenturner.us · 15/04/2025How is this Python package real pypi.org/project/tari... 2256
Reposted by Devon RyanPopehat @kenwhite.bsky.social · 13/04/2025Cruel 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. 852033131
Reposted by Devon RyanHilde Kuehne @hildekuehne.bsky.social · 13/04/2025That’s a wild backdoor… 47514