DNA Software - Open Source / https://teapawt.org/t.co/Fpek1LQEuD /[email protected]. Alter ego of @bert_hu_bert / @bert_hubert. Writing a book on DNA & life: https://teapawt.org/t.co/X1LgV1xbIG
Nootdorp, The Netherlands
Joined November 2013
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Bert Hubert (DNA) retweeted
Germany's Federal Agency for Disruptive Innovation @SPRIND supports #PandemicPPR with funding breakthrough tech for broad-spectrum anitivirals able to tackle future virus X.
Learn about the breakthroughs at ⏩sprind.org/en/challenges/ant… #PPRforum @BMG_Bund @BMZ_Bund @BMBF_Bund
Bert Hubert (DNA) retweeted
Which demonstrate the richness of genomi diversity better? a pangenome graph (left) or Shared Block View (right, through principal bundle decomposition)?
#genomics #visualization
Bert Hubert (DNA) retweeted
We managed to build a splice site predictor that beats SpliceAI, the current state-of-the-art. SPLAM uses a convolutional neural net but w/a different design. Preprint and code are out; paper is under review. Great work by @KuanHaoChao biorxiv.org/content/10.1101/…
Bert Hubert (DNA) retweeted
This is very cool!! The absolutely no known RNA viruses in archaea had never occurred to me since I chatted to @mkrupovic at a conference last year, and I've been fascinated ever since! (also need to get my hands on using Lucaprot soon! 👀👀)
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Bert Hubert (DNA) retweeted
Y chromosome being annoyingly proud of the many, many repetitive regions in its DNA sequence.
ALT Jake Wyler in "Not Another Teen Movie" is proudly looking at a photo of himself, and then looking at another photo where he is proudly looking at a photo of himself.
Bert Hubert (DNA) retweeted
A very intriguing result in the new Y chromosome paper, one that you might miss unless you read the paper closely... 1/6 nature.com/articles/s41586-0…
Bert Hubert (DNA) retweeted
It’s August 2023 and we can finally celebrate the *true* complete sequencing of the human genome 🥂 Only now we have end to end assemblies of the Y chromosome. Congrats to both teams, and thank you for citing the previous work of yr beloved @germcells 🤓 nature.com/articles/s41586-0…
Bert Hubert (DNA) retweeted
This preprint is now published @PLOSCompBiol: journals.plos.org/ploscompbi…
Thanks to many of you who provided suggestions / asked pertinent questions via this thread.
It's time to stop making t-SNE & UMAP plots. In a new preprint w/ Tara Chari we show that while they display some correlation with the underlying high-dimension data, they don't preserve local or global structure & are misleading. They're also arbitrary.🧵biorxiv.org/content/10.1101/…
Bert Hubert (DNA) retweeted
Hey #genetics instructors! Pam Kalas and I are trying to bring the teaching of mitosis and meiosis into the 21st century. Check out our videos on YouTube: youtube.com/watch?v=a_89IZjn… and youtube.com/watch?v=ZbV6xmLC…. Guides at usefulgenetics.com
Bert Hubert (DNA) retweeted
This is an excellent thread summarizing our paper about the flaws in a major cancer microbiome study; wish I'd written it myself. If you don't have time to read our paper, at least read this thread
I think we need to talk about how devastating this cancer microbiome refutation paper from
@StevenSalzberg1
and colleagues is. It really speaks to how devoid of critical thinking and intellectual depth our glam publishing ecosystem has become. 1/n
biorxiv.org/content/10.1101/…
Bert Hubert (DNA) retweeted
Farewell to Bram Moolenaar, genius behind the beloved Vim text editor. His legacy will endure through Vim's groundbreaking impact on coding. A visionary programmer and influential open-source advocate. Rest in peace, Bram. 🌹
#BramMoolenaar #Vim #OpenSource #RIP
Bert Hubert (DNA) retweeted
Random thoughts on this paper that I've spent way too much time on
Background: sequence alignment is a fundamental problem, lots of software use it to search through DNA/RNA and protein datasets, its been studied since forever, etc
new paper just dropped
“Block Aligner: an adaptive SIMD-accelerated aligner for sequences and position-specific scoring matrices”
work done with Martin Steinegger @thesteinegger
academic.oup.com/bioinformat…
