Now out in @natcomms.nature.com :
versions 2.0 of both BiG-SCAPE and BiG-SLiCE! With significant speed and accuracy increases, as well as new interactive functionalities.
Read the full paper here #openaccess:
www.nature.com/articles/s41...
Check out our paper in @asm.org Applied and Environmental Microbiology 🍾
OSMAC guided bioprospecting of Atlantic sponges reveals novel bacterial species and the antimicrobial thiazole alkaloid agrochelin II | Applied and Environmental Microbiology journals.asm.org/doi/10.1128/...
#secmet #microsky
Research into filamentous actinomycetes, the antibiotic producers, is in steep decline. Loads of natural products chemistry research worldwide but not much aimed at understanding their biology and ecology. The latter is key to unlocking their specialised metabolism
link.springer.com/article/10.1...
Another example of a custom-made 3D-printed 96-well magnet bead purification device, triggered by a "pipette eject" event on the OpenTrons.
Essentially, if the OpenTrons is thought as a flexible pipetter, then @plasmidsaurus.bsky.social turn pipette events into other MolBio tasks.
Another interesting use of 3D printed plastic adapters, in this case to turn the OpenTrons bays into racks of Oxford @nanoporetech.com PromethION flowcells.
Time for a thread on our Christmas preprint “Origin and evolution of acrocentric chromosomes in human and great apes”. I had so much fun with this project and paper. It will be hard to summarize in a thread, but I’ll try www.biorxiv.org/content/10.6... [1/21]
🦠🧬🖥️ Bakta v1.12.0 is out
with tons of tiny improvements and bug fixes, too many to list all:
- partial genes on linear seqs
- improved errror handlings & runtimes
- support Python 3.12 & 3.13
- ...
A huge shout out and thank you to all bug reporters and contributors!
github.com/oschwengers/...
First fully phased reference genome for the Yarrowia liploytica type-strain is out! academic.oup.com/jimb/advance... Super fun project in collaboration with James Crill at Syracuse University as well. Important platform organism for industrial microbiology and biomanufacturing as well. #genomics
New tool from @alexsweeten.bsky.social to find and classify all your satellites: "AniAnn's: alignment-free annotation of tandem repeat arrays using fast average nucleotide identity estimates"
📄 www.biorxiv.org/content/10.6...
📦 github.com/marbl/anianns
Exploring #microbiome data? MetaTree makes statistically based hierarchical tree comparisons easy and accessible.
My understanding of MDPI as the biggest polluter of science gets some quantitative basis in this cool study. How about we as researchers stop publishing there and stop reading it leaving the special issues with another issue: absence of honest science.
ONT Axes P2 Solo, Roiling Community
🧬🖥️
omicsomics.blogspot.com/2026/01/ont-...
New blog post with some thoughts on @nanoporetech.com and their recent announcement that the P2 Solo will be discontinued:
rrwick.github.io/2026/01/21/p...
Ultra-high-throughput mapping of genetic design space www.nature.com/articles/s41... (read free: rdcu.be/eY6E2) 🧬🖥️🧪 github.com/cbashorlab/C...
Unpacking my stuff in my new @ssi-dk.bsky.social office, I came across this post which resonated enough that I printed it out and hung it up on my wall. It's going back up now. I think from @danpsimpson.bsky.social ?
clearest link between yield and anything would be pore occupancy? since pores degrade waiting for DNA/having to reverse current
Cool, thank you. So only a very weak connection between N50 and yield for these samples (of course different treatments could have different restraints). Since pore occupancy changes over time, I see that having a single number to describe it for a flowcell could be tricky, but I'd think the ...
Wonderful, thank you for posting these! Did you also look at N50 vs yield, pore occupancy vs yield, short sequences vs yield?
Been doing a lot of @nanoporetech.com sequencing for soil and sediment lately and it appears that no matter how much DNA or how little we still get decent yields. So pretty robust performance. Yield clearly depends on pore count.
Bacteria chromosomes contain Genomic Islands that provide virulence, antibiotic resistance, MGE-defence,... They transfer between cells, but the mechanism of most remains elusive.
Here we explore the conjugative capacity of these mysterious Genomic Islands.
www.biorxiv.org/content/10.6...
I am looking for a postdoc to develop high-performance algorithms in computational genomics. Email or DM me if interested. For more information, see hlilab.github.io/vacancies. RTs appreciated!
yes, it would be great to see hi-res versions, I can't read the clade names
How delightful to start the year with a neat overview of the sequencing field from the most capable watcher of the space.
Sequencing Instrumrnt Outlook 2026
My observations & predictions on sequencing instrument companies
🧬🖥️
omicsomics.blogspot.com/2026/01/sequ...
Staying Current in Data Science and Computational Biology: 2026 Edition. Part 3 in a series of posts going back 14 years. doi.org/10.59350/2na...
New preprint. Work led by @ainsley-beaton.bsky.social & Rebecca Devine.
They show the highly conserved Streptomyces MtrAB two component system activates ectoine production and triggers sporulation in response to osmotic stress in Streptomyces venezuelae
www.biorxiv.org/content/10.6...
sure if a contig is actually a complete plasmid, but the circular topology helps.
It's worth noting that the way I identify plasmids in both the G1034 and IIMENA projects have been using a list of plasmid related PFAMs at least one of which needs to be found on a contig to be called a plasmid. Because of the flexible gene content of plasmids, it is also really hard to know for...
Hi, I'm a bit late to the party, but the G1034 plasmids should be good, maybe supplemented with these 228 circular plasmids (2025)from Actinomaduro, Streptosporangium, Amycolatopsis etc, lots of funk there from such a cool collection @medinadiscovery.bsky.social www.ncbi.nlm.nih.gov/nuccore/?ter...
Esther Lederberg in the laboratory in the 1950's. Credit: Estherlederberg.com
Born #OnThisDay in 1922, Esther Lederberg was the first to isolate the lambda phage in 1951. She characterised the lysogenic phase, whereby the phage are able to integrate into the bacterial genome, staying dormant. This discovery made them a model tool of study, leading to many more breakthroughs.
