Blogpost: I took an oral probiotic for a month and did microbiome sequencing at @Plasmidsaurus. blog.booleanbiotech.com/oral-microbi...

The registration deadline is fast approaching for probgen 2026! Abstracts due by January 15, registration by January 31 probgen2026.github.io

ntSynt: multi-genome synteny detection using minimizer graph mappings doi.org/10.1186/s129...

From @jchowning.bsky.social & colleagues in @plos.org #Computational #Biology | Ten simple rules for running a virtual program to introduce computational biology at the high school level | #Education #Bioinformatics #PLOSCBTSR #OpenScience 🧬 🖥️ 🧪 🔓 ⬇️ journals.plos.org/ploscompbiol...

The #European Meeting for PhD students in #Evolutionary #Biology (EMPSEB) is a student-led annual conference that brings together PhD researchers from around the world. Germany, 8th to 12th of June, 2026 empsebconf.github.io

We have detected that you are currently in a State where we do not offer the following rights to residents: - Right to Know - Right to Delete [the account] Currently, we only offer these rights to residents of Virginia, Texas, New Jersey, Delaware, Nebraska, Iowa and California !!!

Thrilled to share our new review online with @scottvedwards.bsky.social in @Trends Ecol & Evo! “pangenomics is rapidly transforming our ability to dissect the genetic basis of ecological and evolutionary change in natural systems.”

The 2026 JASPAR NAR paper provides a very good overview of literature of Deep Learning-based transcription factor analysis. Manual curation of >11k profiles across different species is amazing! Paper: doi.org/10.1093/nar/... Platform: jaspar.elixir.no

Atlassian just sent a message that "Unused workspaces will be deleted. Action may be needed to keep your workspace". I guess Atlassian can't afford to be a code archive, but still this seems like a shame. #Atlassian #Bitbucket #OpenSource community.atlassian.com/forums/Bitbu...

Random side thought: I showed someone a few of the very basic #sourmash plots from betterplot that we use regularly to look at relationships between piles of genomes - basic dist matrix/dendrogram, upset, etc. - and they loved them. Sometimes it's the simplest things...

The SNSF is considering restrictions for its Project funding. Goal: to ensure the quality of evaluation & stable success rates despite an increasing number of applications and limited funding. The final decision will be made in January 2026. 👉 buff.ly/iGOCf7R #research #science

Is then the idea that you can start hiring 2-3 people teams a few years into your position (or 10 years into it) or just never do more complex projects? Again not a criticism but trying to understand what fits into the scope of an academic lab vs industry lab (like DeepMind) vs a startup.

Looking for talks for our zeavolution seminar in the spring. Sign up! docs.google.com/spreadsheets...

There's an opening in our CompBio group at #PacBio. Apply below if you're interested in method / tool development for long-read sequencing applications! #Bioinformatics pacbio.wd12.myworkdayjobs.com/PacBio-/job/...

We are hiring a PhD intern for Summer 2026 in ML for regulatory genomics at ReLU/BRAID/Genentech! Work on DNA sequence models for the noncoding genome (e.g. DNA design, models of MPRA and genetic variants)! 🥳

Come work with us at the Institute for Genome Sciences @medschool.umaryland.edu in #Baltimore! We're hiring an Assistant/Associate Professor of #Genomics & #Bioinformatics, #PhD, #MD, or both #Computational #Biology Learn more/Apply: bit.ly/GenoBioinfo

Research Briefing: Bird sternum evolution facilitated the origins of powered flight rdcu.be/eyTdn

1/9 Just out: k-mer indexes are the backbone of fast search in genomic data, but many degrade under small k, subsampling, or high diversity. With Ondřej Sladký and @pavelvesely.bsky.social we asked: can we build one that works efficiently for any k-mer set?

These are fun educational puzzles to improve debugging skills of students! thanks to @robert.bio for creating these sandbox.bio/puzzles

Are you interested in biodiversity genomics? Fantastic opportunity to join us as a Group Leader at the Tree of Life Programme, @sangerinstitute.bsky.social. 👇 sanger.wd103.myworkdayjobs.com/en-GB/Wellco...

@benlangmead.bsky.social giving a talk about rowing his boat and explaining pangenomes with that :). Amazing talk about reference biases and the future to avoid it. Fascinating talk at @bcmhgsc.bsky.social @riceuniversity.bsky.social ! @treangen.bsky.social

POSTDOCS: We're hosting our fourth-annual Next Wave of Faculty in Genomics symposium in beautiful Santa Cruz, CA, to showcase rising talent in genomics research. Travel expenses are covered for selected applicants ✈️😎🏖 APPLY BY JAN 15: genomics.wordpress.ucsc.edu/calendar_eve...

I'm excited to present this new model to detect positive selection on regulatory sequences, which has been 3 years in the making! Thanks to Alexandre Laverré and @phylogenetrips.bsky.social for their amazing work on this project. 😃 doi.org/10.1101/2025... Thread!

SPrUCE: Utilizing Ultraconserved Elements of DNA for Population-Level Genetic Diversity Estimation (2025) doi.org/10.1101/2025... Comparing Ultraconserved Elements and Exons for Phylogenomic Analyses of Middle American Cichlids: When Data Agree to Disagree (2021) academic.oup.com/gbe/article/...

Happy to see this work on IG light chains from @e-engelbrecht1.bsky.social in press www.nature.com/articles/s41... How else will germline variation impact the expressed repertoire? Can't wait to see! Thanks to awesome collabs: @williamlees.bsky.social @guryaari.bsky.social @ayeletperes.bsky.social

We’re preparing workshop materials on debugging and troubleshooting in bioinformatics and computational biology, aimed at audience with bio background. Is anyone aware of relevant courses, workshops, or resources?

PanSN-spec: Pangenome Sequence Naming github.com/pangenome/Pa...

Building better genome annotations across the tree of life genome.cshlp.org/content/35/5... TOGA, BRAKER3, and the RNA-seq assembler StringTie are top performers when benchmarking 12 different methods for 21 different species spanning vertebrates, plants, and insects.

RegEvol: detection of directional selection in regulatory sequences through phenotypic predictions and phenotype-to-fitness functions www.biorxiv.org/content/10.1... 🧬🖥️🧪 github.com/mrrlab/RegEvol

Helixer: ab initio prediction of primary eukaryotic gene models nature.com/articles/s41592-025-02939-1

Join us for our next Kipoi Seminar with Gonzalo Benegas, Yun S. Song group,UC Berkeley; Open Athena @gonzalobenegas.bsky.social 👉 Predicting functional constraints across evolutionary timescales with phylogeny-informed genomic language models 📅 Wed Dec 3, 5:30pmCET 🧬 kipoi.org/seminar

With @burgesslab.bsky.social, not one, but TWO freshly caught T2T zebrafish reference genomes for the Tübingen and AB strains 🎣 🎣 🎉

Looks interesting! they benefit from GC content for metagenomic abundance estimation!

Hey #microbialsky - anyone looking for a good PhD student this cycle? Ugrad from my lab is looking but no luck with the PIs she has contacted (no funding, no response). She worked in my lab for 1.5 years, now is a research tech at the FWC research institute. Excellent at the bench & super smart!

Help. Can anyone in my network (or outside) endorse me for arXiv q-bio? #breeding #breeding

popEVE is out in Nature Genetics! 🎉 We built a proteome-wide model that combines cross-species and human population variation to rank missense variants by disease severity and help diagnose rare genetic disorders. rdcu.be/eRu7K

Colored graphs (+abundances), low density minimizers and quick sequence parse 🚀

Happy to present TOGA2, developed by Yury Malovichko @ymalovichko.bsky.social, the faster, memory-efficient & more accurate TOGA1 successor (github.com/hillerlab/TO...). And annotations, orthologs & gene loss/dup data generated with 4 references for 883 placental mammal and with 5 refs for 676 ...

Our trilogy of orthology publications is online! Review on Hierarchical Orthologous Groups doi.org/10.1007/s00239-025-10277-1 OrthoXML-Tools doi.org/10.1007/s00239-025-10271-7 A great community effort on Quest for Orthologs in the era of Data Deluge and AI doi.org/10.1007/s00239-025-10272-6

Most courses in December are now fully booked or have only a few seats remaining. If you or your colleagues were planning to register, please secure your spot right away! www.physalia-courses.org/courses-work... #Phylogenomics #StructuralVariants #GAMs #Rstats #Genviz #MultiOmics #Bioinformatics

The giant wakes up: Illumina goes spatial www.batcheffect.com/p/the-giant-...

For years since the GPT-2 paper, emergent in-context learning (ICL) from 'next-token' training has been treated as something deeply tied to 𝐡𝐮𝐦𝐚𝐧 𝐥𝐚𝐧𝐠𝐮𝐚𝐠𝐞. But … is it?

Interested in the newest developments in orthology? Check out the last Quest for Orthologs (QfO9) meeting report: link.springer.com/article/10.1... #orthology #function #domains #AI #paralogy Thanks to @sinamajidian.bsky.social and all co-authors for their valuable contribution.

Honoured and quite blown-over to receive this award. I have been, and continue to be, very lucky - first with great mentors, and then really prodigious students, postdocs and collaborators. Working with them has been a joy.

Exciting symposium on AI and Biology at EMBO | EMBL in Heidelberg on 10-13 March 2026! Excellent lineup of invited speakers across various scales of biology! Deadline for abstract submission is coming up — Dec 2. 🔗 www.embl.org/about/info/c... #EESAIBio @EMBLEvents

From coffee-fueled coding marathons ☕ to new genomics tools: Our 2024 #Hackathon paper is out in @f1000publishing.bsky.social ! Huge thanks to everyone world wide who joined the @bcmhgsc.bsky.social madness 🎉 🔗 f1000research.com/articles/14-... @gregor-research.bsky.social @smahtnetwrk.bsky.social

Thank you folks for your feedback on our survey about Hash functions in genomic sequence analysis. We've updated the paper and you can see the new version here: tinyurl.com/4kk9ccmt.

Opportunity! Anybody knows of young marine ecologists (within 7 years from earned PhD) that would like to come to Gothenburg, Sweden, for a nationally funded Assistant Professorship? It is highly competitive but well funded. (1) of (3)

Specificity, length and luck drive gene rankings in association studies nature.com/articles/s41586-025-09703-7