Are you the less lucky of the co-first or co-last authors? @shougroup.bsky.social makes the case for changes to the way that equal contribution information is sent to indexing sites such as #PubMed.
🧪 #AcademicSky #publishing
A poorly photoshopped version of the Nike "Runners welcome. Walkers tolerated." storefront reading "Nerds welcome. R tolerated."
Wow, Nike's got a spicy take on bioinformatics
My thesis also covers a bunch of this. Specifically the chapters introducing pairwise alignment and minimizers:
curiouscoding.nl/categories/t...
I just realized that and uploaded it to my ebook reader yesterday! 😅
Host read removal sounds simple. It's not. 🧫Ep. 151 of hashtag#microbinfie: we talk with Bede Constantinides about Deacon — why alignment-based approaches fall short, the sensitivity/specificity tradeoff, and what it takes to remove host reads at scale. Part 1 of 2 […]
Our last manuscript is out! 🚨
We identify double stranded RNAs in embryonic stem cells - full of transposons, especially young LINEs and LTRs 🧐
🧬Happy Friday Reading🧬
So begins a long but very sustainable journey to #ESCMIDGlobal2026
That's great, looking forward to read! (Actually got recommended before that PhD theses can often be great intros to fast moving fields)
Not nearly as polished, but I'm currently writing my thesis and it overlaps many of these topics
That is, with extremely nice explanations of the algorithms themselves, but also beautiful code examples in some nice language. #bioinformatics #genomics #algorithms #books
Who has, or will be, writing an awesome book like in the style of these ones: algorithmsbook.com ... but for modern #genomics algorithms, like k-mer methods, minimizers, advanced alignment methods etc etc? #bioinformatics #books
😳 I so much need this for the mobile app!
But yea, this is a huge boon indeed!
OMG! Gene Myers is giving a keynote at RECOMB!
How cool is that!
(early bird rates end in a few days ;)
📌 Upcoming Deadlines📌
🗒️ Late-breaking poster submissions: 15 April
⌛️ Early registration: 15 April
Visit recomb.org/recomb2026 for details.
#RECOMB2026 #registration #submissions #CallForPosters
Been impressed with Pimsleur for basic language learning. Does more than spaced repetition though like focusing on pronunciation early to more effectively learn by ear later. Bit on the pricey side so've used their recurring 50% discounts. Perhaps could replicate with bunch of AI apps today though..
France starts moving government systems from Windows to Linux
France is ditching US software for homegrown alternatives of Google Docs, Microsoft Office, Zoom, and Telegram
Libre Office is very good.
www.techspot.com/news/112032-...
> The effectiveness of LLMs in computing is partially (perhaps mostly!) an indictment of how *bad* our tools have been for so long.
Very much this! I've been telling this to some of my peers for quite some time.
Very very important initiative, check it out #bioinformaticians!
Super excited to be launching two things today: #RustQC 🦀🧬 and rewrites.bio 🚀
I used AI to rewrite 15 RNA-seq QC tools into a single Rust binary (I've never written any Rust). It ended up being over 60x faster. Here's the story 🧵
seqeralabs.github.io/RustQC/
It strikes me that the legal situation for completely AI-generated code is not discussed more among open source developers?!
The situation seems way more complicated than most folks seem to realize!
chatgpt.com/share/69d78f...
Our latest publication is now out at Genome Biology!
link.springer.com/article/10.1...
We uncover a unique association between a H3K27me3 reader complex and active transcription.
A thread with our key findings: (1/8)
#TEsky #Polycomb #transcription #smallRNAs
Illustration of a man analysing different data. Image from Getty Images.
The results of a major international collaboration on scientific reliability are presented in three articles in @nature.com. Around half of previously published research results in #SocialScience and #BehaviouralScience could not be replicated in new experiments 🧪 news.ki.se/half-of-soci...
So cool to hear my colleagues mentioned on my fav podcast 😎
This episode of the #MicroBinfie Podcast on tools for host DNA removal mentions the massive contributions from Sofia Stamouli, Lili Andersson-Li & others (incl Lauri Mesilaakso_, on the #TaxProfiler pipeline!
soundcloud.com/microbinfie/...
Now out!
We show that TEs can be horizontally transferred between fungal species via Starships. Once transferred, these TEs can become active, changing the genome organization and affecting the lifestyle of the recipient fungus.
www.nature.com/articles/s41...
@oggenfussursula.bsky.social #TEsky
Super Bloom: Fast and precise filter for streaming k-mer queries www.biorxiv.org/content/10.64898/2026.03...
It's a good day when the first item in your feed is your own work :)
@rickbitloo.bsky.social was annoyed that scanning reads for all 96 rapid kit barcodes is bottleneck in Barbell, so he made Sassy2: 13x (150bp) to 4.6x (8kbp) faster than v1 by batch-searching patterns, and >100Gbp/s on 16 threads!
Can't wait to release a 10-year-old birthday version for SeqKit!
- 10 years
- 2 papers, 3500 citations
- 20 contributors
- 40 subcommands
- 880 commits
- 500 issues
- 685.5K Bioconda total downloads
Thank you all, dear contributors and users!
I'll keep maintaining it.
github.com/shenwei356/s...
📢 We want your feedback on our new pilot project for sharing AI models in life science research.
Finding, reusing and citing machine learning models remains a major challenge in the life sciences.
BioAIrepo is here to help.
www.ebi.ac.uk/about/news/t...
SeqKit is the best!! Such a joy to use for all kinds of messing around with sequences. The thought and attention to detail that went into it is impressive to say the least. Huge congrats on the 10 year anniversary! 🙌🎉😎
