Lightnews — Scholar-powered news

Reposted by Ben Vezina

Kevin J. CREATURE @kevinjkircher.com · 10d

Research also shows that spreading smaller amounts of funding out over more researchers generally delivers better scientific outcomes per dollar spent than focusing bigger grants on fewer researchers.

journals.plos.org/plosone/arti...

Big Science vs. Little Science: How Scientific Impact Scales with Funding

Agencies that fund scientific research must choose: is it more effective to give large grants to a few elite researchers, or small grants to many researchers? Large grants would be more effective only...

journals.plos.org

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Oliver Schwengers @oschwengers.bsky.social · 9d

Unbelievable, Bakta reached its 1,000th citation!

A huge shout out and thank you to all Bakta users, bug reporters, those sharing ideas and suggesting features...

...just the entire incredibly supporting binfie community!

Without you, Bakta wouldn't be the same.

Thank you!

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Ben Vezina @bananabenana.bsky.social · 11d

reject chromatic aberration, embrace chromosomal aberration

Chromatic aberration filter on top of the 24 human chromosomes lined up

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Reposted by Ben Vezina

Kelly Wyres @kelwyres.bsky.social · Jul 22

Our new #klebsiella O type nomenclature, codesigned with Chris Whitfield, is now live in @pathogenwatch.bsky.social!

Need a quick explainer on the new names? Check out my blog post: tinyurl.com/y8yb3rbb (+link to full review article)

#MicroSky @klebnet.bsky.social @tomstantonmicro.bsky.social

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Ryan Wick @rrwick.bsky.social · 16d

Happy to share that the paper describing Autocycler is now 100% up:
doi.org/10.1093/bioi...
(1/3)

Autocycler: long-read consensus assembly for bacterial genomes

AbstractMotivation. Long-read sequencing enables complete bacterial genome assemblies, but individual assemblers are imperfect and often produce sequence-l

doi.org

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Philip Ball @philipcball.bsky.social · 18d

And as for writing, don't get me started. Most often, the process of writing is not a laborious business of transcription, but a process of thinking itself. I'm not about to outsource my thinking to a machine.

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Ben Vezina @bananabenana.bsky.social · 18d

Staggering analysis here linking ciprofloxacin resistance to specific mutations in #Klebsiella.

In short, using ONLY genotype, one can reasonably predict phenotypic CIP MICs! See Fig 3 (below).

Loving the splitting of MIC and disk diffusion data as well.

#AMR #MicroSky #IDSky

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Voilà: Francis Gagnon @chezvoila.com · 19d

Celia also wrote about how we fitted 4.5 billion years in one image, at scale.

chezvoila.com/blog/saguenay/

A data scale tested by time - Voilà:

Most of the time, the choice of scale is based on the data. Or not when the data you want to visualize are 4.5 billion years!

chezvoila.com

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Animalcules @bacteriophile.bsky.social · 19d

journals.plos.org/plosgenetics...

#MicroSky

Genomic profiling and experimental validation of type VI secretion system-associated proteins in Klebsiella

Klebsiella is widely distributed in nature and recognized for its dual role as a human commensal and an opportunistic pathogen capable of causing severe infections. Among its key virulence mechanisms,...

journals.plos.org

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Arc Institute @arcinstitute.org · 20d

In another preprint from the @brianhie.bsky.social Lab and @synbiogaolab.bsky.social, they introduce Germinal, a generative AI system for de novo antibody design.

Germinal produces functional nanobodies in just dozens of tests, making custom antibody design more accessible than ever before.

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Tamar Haspel @tamarhaspel.bsky.social · 20d

Terrific @scientificdiscovery.dev post on randomized controlled trials in @ourworldindata.org.

Including this important chart on the impact of pre-registration.

Magically, when people had to pre-register outcomes, many of the benefits disappeared.

ourworldindata.org/randomized-c...

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Ben Vezina @bananabenana.bsky.social · 22d

Hey I am not an author on this, best to contact Ryan Wick himself! Maybe the GitHub page would be the best place.

Ben Vezina @bananabenana.bsky.social · 22d

Automated, almost-error-free consensus #assemblies with Autocycler

Impressive benchmarks in Fig 2B (below): ≤10 median errors PER genome

Once again, incredible, landmark work from @rrwick.bsky.social

doi.org/10.1093/bioi...

Tool here: github.com/rrwick/Autoc...

#bioinformatics #genomics

Box and whisker plot of various assemblers and their number of errors per assembly. Autocycler outperforms all assemblers with the lowest median of <=10 errors per genome

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Martin Steinegger 🇺🇦 @martinsteinegger.bsky.social · 24d

MMseqs2-GPU sets new standards in single query search speed, allows near instant search of big databases, scales to multiple GPUs and is fast beyond VRAM. It enables ColabFold MSA generation in seconds and sub-second Foldseek search against AFDB50. 1/n
📄 www.nature.com/articles/s41...
💿 mmseqs.com

GPU-accelerated homology search with MMseqs2 - Nature Methods

Graphics processing unit-accelerated MMseqs2 offers tremendous speedups for homology retrieval from metagenomic databases, query-centered multiple sequence alignment generation for structure predictio...

www.nature.com

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Nature Methods @natmethods.nature.com · 28d

Spacedust: a tool for de novo identification of conserved gene clusters from metagenomic data.
@ruoshiz.bsky.social @milot.bsky.social

www.nature.com/articles/s41...

De novo discovery of conserved gene clusters in microbial genomes with Spacedust - Nature Methods

This work presents Spacedust, a tool for de novo identification of conserved gene clusters from metagenomic data.

www.nature.com

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Marit Hetland @genomarit.bsky.social · 29d

Thrilled to share this preprint on Klebsiella pneumoniae plasmids in a One Health setting 🦠 Fantastic work by @twinkler.bsky.social! 🎉 @irenlohr.bsky.social @margaretlam.bsky.social

bioRxiv Microbiology @biorxiv-microbiol.bsky.social · Sep 15

A One Health study of Klebsiella pneumoniae species complex plasmids shows a highly diverse and ecologically adaptable plasmidome https://www.biorxiv.org/content/10.1101/2025.09.14.676155v1

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Joe Wanford @jwanford.bsky.social · Sep 15

🎉 Delighted to share the first pre-print from my lab where we demonstrate that intergenic DNA repeats mediate phase variation of the mucoid phenotype in hypervirulent Klebsiella pneumoniae: www.biorxiv.org/content/10.1... #klebclub

Simple Sequence Repeats Mediate Phase Variation of the Mucoid Phenotype in Hypervirulent Klebsiella pneumoniae

Hypervirulent Klebsiella pneumoniae (HVKp) express a thick mucoid capsular polysaccharide which is essential for virulence and survival in the bloodstream but inhibits epithelial adhesion and invasion...

www.biorxiv.org

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Ben Vezina @bananabenana.bsky.social · 29d

"Paying the filter tax" - Honours student Josh on how volume is lost during syringe filtration.

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Zamin Iqbal @zaminiqbal.bsky.social · Sep 7

For anyone who has used pling for comparing plasmids using rearrangement distances ("how many structural events apart are these plasmids"), here's how to tweak parameters, and integrate it with typing info, and the host phylogeny
www.biorxiv.org/content/10.1...
github.com/iqbal-lab-or...

Clustering of plasmid genomes for genomic epidemiology by using rearrangement distances, with pling

Integration of plasmids into genomic epidemiology is challenging, because there are no clearly defined evolving-units (equivalent to species), and because plasmids appear to evolve as much by structur...

www.biorxiv.org

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A Page in your life 🍁📎 @sailorgirl2017.bsky.social · Aug 26

A deadly tropical disease known as sleeping sickness has been eliminated from Kenya in a significant public health triumph.
Uganda, Rwanda, Benin, Ghana, Cote d’Ivoire, Guinea, Equatorial Guinea, Chad, & Togo have also eliminated sleeping sickness.

www.goodnewsnetwork.org/who-declares...

WHO Declares Kenya Free of This Deadly Tropical Parasite After Decades of Suffering

Sleeping sickness is often fatal of untreated and in sub-Saharan Africa in the 1990s, 40,000 cases were being diagnosed in a year

www.goodnewsnetwork.org

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Ryan Wick @rrwick.bsky.social · Sep 4

New blog post!

I added a new feature to @gbouras13.bsky.social's Pypolca: homopolymer-only polishing. Potentially useful for cross-sample polishing - early test on Cryptosporidium looks promising.

Check it out here:
rrwick.github.io/2025/09/04/h...

Cross-sample homopolymer polishing with Pypolca

a blog for miscellaneous bioinformatics stuff

rrwick.github.io

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MicroSeq2025 @microseqasm.bsky.social · Sep 4

The people have spoken: Best Lightning Talk goes to @bananabenana.bsky.social and Best Medium Talk goes to @munazzahmaqbool.bsky.social. Congratulations winner and winner, it was a pleasure listening to your talks! #MicroSeq2025

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MicroSeq2025 @microseqasm.bsky.social · Sep 3

🌏Jocelyn Hume shows us how #sequencing was able to characterise the evolutionary trajectory and driving forces behind IMP-4 transmission. Delve into one of the largest global and regional #epidemiology studies of blaIMP-4 in #bacterial isolates! #MicroSeq2025 #plasmid

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Ben Vezina @bananabenana.bsky.social · Sep 3

What is the name of that database and how would one access it?

Ben Vezina @bananabenana.bsky.social · Sep 3

"For pathogen surveillance, we identify the trapped mosquitos morphologically, painstakingly individually" - Peter Mee
#MicroSeq2025

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