Lightnews — Scholar-powered news

Reposted by Tommi Mäklin

Matti Ruuskanen @begia.bsky.social · 1h

Our new systematic review is now out! Briefly, temporal multi-omic data and analyses are crucially needed to improve our understanding of microbiomes. Also, often the omics layers are not analyzed in an integrative way, even while such methods exist.
academic.oup.com/bib/article/...

Multi-omics time-series analysis in microbiome research: a systematic review

Abstract. Recent developments in data generation have opened up unprecedented insights into living systems. It has been recognized that integrating and cha

academic.oup.com

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Reposted by Tommi Mäklin

Josie Bryant @josiebryant.bsky.social · 19h

New respiratory 🫁 infection and microbiomes conference in Hinxton with stellar line up of speakers.

🚨 Submit your abstracts now! 🚨

Please RT

coursesandconferences.wellcomeconnectingscience.org/event/air-20...

AIR 2026: Genomic and Systems Approaches to Respiratory Infection, Microbiomes and Immunity — 20260211

Course exploring how genomics, microbiome profiling, and systems biology reshape our understanding of respiratory infections and immune dynamics.

coursesandconferences.wellcomeconnectingscience.org

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Ellinor Alseth @ellinoralseth.bsky.social · 1d

Obsessed with this Journal of Immaterial Science article 🔥

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Michael Brockhurst @brockhurstlab.bsky.social · 3d

New preprint!

Ever wondered why only a fraction of genomes encode CRISPR immunity? 🧬 🦠

Turns out CRISPR is rarely beneficial against virulent phages, being most beneficial against those for which resistance mutations are rare!

An epic effort by Rosanna Wright

www.biorxiv.org/content/10.1...

Resistance mutation supply modulates the benefit of CRISPR immunity against virulent phages

Only a fraction of bacterial genomes encode CRISPR-Cas systems but the selective causes of this variation are unexplained. How naturally virulent bacteriophages (phages) select for CRISPR immunity has...

www.biorxiv.org

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Teppo Hiltunen @teppo-h.bsky.social · 9d

Professor (full) or Associate Professor (tenure track) in Microbial Genetics of Health (U. Turku Finland). Competitive starting package included! Please share.

duunitori.fi/tyopaikat/ty...

Professor or Associate professor (Tenure Track/Full) in Microbial Genetics of Health - Turun yliopisto - Työpaikat - Duunitori

Avoin työpaikka: Professor or Associate professor (Tenure Track/Full) in Microbial Genetics of Health - Turun yliopisto, Turku. Duunitorilla lisäksi yli 30 000 muuta avointa työpaikkaa. Lue lisää nyt!

duunitori.fi

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Sam Horsfield @samuelhorsfield.bsky.social · 14d

A new ggCaller version is out! v1.4 includes tweaks to improve efficiency, outputs Panaroo-friendly GFFs, and enables iterative gene calling; if you have already called a gene set, you can now add more genomes either one by one or in batches github.com/bacpop/ggCal...

GitHub - bacpop/ggCaller: Bifrost graph gene caller.

Bifrost graph gene caller. Contribute to bacpop/ggCaller development by creating an account on GitHub.

github.com

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Michael Brockhurst @brockhurstlab.bsky.social · 13d

Now peer-reviewed, improved and published in @microbiologysociety.org Microbiology - thanks to editor and reviewers!

www.microbiologyresearch.org/content/jour...

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Tiedetäti (Dr. Laura Nissin) @tiedetati.bsky.social · 16d

"Suomen Akatemia varoittaa yliopistoja perussuomalaisista
Yliopistoihin lähetetyssä ”varautumisviestissä” annetaan ohjeistusta häirinnän, maalittamisen ja mustamaalauksen kohteeksi joutuneille tutkijoille."
www.is.fi/kotimaa/art-...

Suomen Akatemia varoittaa yliopistoja perussuomalaisista

Yliopistoihin lähetetyssä ”varautumisviestissä” annetaan ohjeistusta häirinnän, maalittamisen ja mustamaalauksen kohteeksi joutuneille tutkijoille.

www.is.fi

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Reposted by Tommi Mäklin

Marit Hetland @genomarit.bsky.social · 23d

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 · 24d

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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Tommi Mäklin @themaklin.bsky.social · 23d

Don't tell them about fastq

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Reposted by Tommi Mäklin

Zamin Iqbal @zaminiqbal.bsky.social · 29d

Sometimes you meet absolutely incredible bioinfo-magicians.
It was a huge privilege when @shenwei356.bsky.social
joined our group for a year on an @embl.org sabbatical.
While here, he developed a new way of aligning to
millions of bacteria, called LexicMap 1/n
www.nature.com/articles/s41...

Efficient sequence alignment against millions of prokaryotic genomes with LexicMap - Nature Biotechnology

LexicMap uses a fixed set of probes to efficiently query gene sequences for fast and low-memory alignment.

www.nature.com

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Vivek Mutalik @vivekmutalik.bsky.social · Sep 8

Phenotypic heterogeneity of capsule production across opportunistic pathogens | mBio

#microsky #phage #phagesky

journals.asm.org/doi/10.1128/...

Phenotypic heterogeneity of capsule production across opportunistic pathogens | mBio

The polysaccharidic capsule is present in ~50% of species across the bacterial phylogeny, including all ESKAPE microorganisms, the six most significant multidrug-resistant (MDR) nosocomial pathogens. ...

journals.asm.org

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Total Internal Reflection🇬🇧🇺🇸🇺🇦 @tirscienceblog.bsky.social · Aug 26

Powerful, typically eloquent, and deeply troubling editorial from @berndpulverer.bsky.social ( @embopress.org ) on the ongoing attacks on #academics and #academia itself in the USA. 👇
www.embopress.org/doi/full/10....

Student hostages in culture war | EMBO reports

EMBO Press is an editorially independent publishing platform for the development of EMBO scientific publications.

www.embopress.org

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Jim Shaw @jimshaw.bsky.social · Sep 7

Preprint out for myloasm, our new nanopore / HiFi metagenome assembler!

Nanopore's getting accurate, but

1. Can this lead to better metagenome assemblies?
2. How, algorithmically, to leverage them?

with co-author Max Marin @mgmarin.bsky.social, supervised by Heng Li @lh3lh3.bsky.social

1 / N

bioRxiv Bioinfo @biorxiv-bioinfo.bsky.social · Sep 7

High-resolution metagenome assembly for modern long reads with myloasm https://www.biorxiv.org/content/10.1101/2025.09.05.674543v1

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Kai Kupferschmidt @kakape.bsky.social · Sep 5

Sequence data from the new Ebola outbreak in DRC suggests it is indeed a new spillover.

And just incredible to see the virus sequenced and the data publicly shared less than 24 hours after confirmation of the outbreak.
#IDsky 🧪

virological.org/t/the-16th-e...

The 16th Ebola Virus Disease Outbreak in Bulape Health Zone, Kasai, Democratic Republic of the Congo: A new spillover event from an unknown reservoir host

Background The Democratic Republic of the Congo (DRC) is currently facing concurrent outbreaks including mpox, cholera and malaria (1-4). The Ministry of Public Health, DRC has declared the 16th Ebola...

virological.org

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Kansan Uutiset KU @ku.fi · Sep 5

Karkotus uhkaa useita Suomessa toimivia palestiinalaisia tutkijoita, kertoo Tieteentekijöiden liitto

Useat suomalaisissa yliopistoissa tohtorintutkintoa suorittavat palestiinalaiset tutkijat eivät voi enää uusia oleskelulupaansa.

www.ku.fi

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Ragnar {Groot Koerkamp} @curiouscoding.nl · Sep 4

Paraseq 0.4 is out now! With double the throughput for processing paired-end input :)

github.com/noamteyssier...

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Reposted by Tommi Mäklin

Carolin Wendling @ccwendling.bsky.social · Sep 4

Interested in exploring prophages in your (meta)genomes, but don't know how and where to start? We've put together a beginners guide to exploring viral diversity in prokaryotes @marievasse.bsky.social
@sebwielgoss.bsky.social
@oxunipress.bsky.social

Séb Wielgoss @sebwielgoss.bsky.social · Sep 4

Our new review is out in
Briefings in Bioinformatics

Phage quest: a beginner’s guide to explore viral diversity in the prokaryotic world

@ccwendling.bsky.social
@marievasse.bsky.social
@sebwielgoss.bsky.social
@oxunipress.bsky.social

doi.org/10.1093/bib/...

Phage quest: a beginner’s guide to explore viral diversity in the prokaryotic world

Abstract. The increasing interest in finding new viruses within (meta)genomic datasets has fueled the development of computational tools for virus detectio

doi.org

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EMBL-EBI @ebi.embl.org · Sep 4

Looking for a postdoc that combines wet and dry lab experience?

The EMBL-EBI-Sanger postdoctoral fellowships might be the thing for you!

Choose one of our pre-defined topics or propose your own.

www.ebi.ac.uk/research/pos...

@sangerinstitute.bsky.social

#postdoc #sciencecareers
🧬🖥️🔬

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Tommi Mäklin @themaklin.bsky.social · Sep 4

125 000 queries in 5h w/ 20 cores and 1.6GB mem (disk bounded!), always love discovering new tools that scale this well github.com/steineggerla...

GitHub - steineggerlab/foldmason: Multiple Protein Structure Alignment at Scale with FoldMason

Multiple Protein Structure Alignment at Scale with FoldMason - steineggerlab/foldmason

github.com

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Jessica Blair @jessicamablair.bsky.social · Sep 4

Assistant Prof post in bacterial genomics @unibirmingham.bsky.social Come and join us!!

@imibirmingham.bsky.social
www.jobs.ac.uk/job/DOO184/a...

Assistant Professor (Research and Education) in Bacterial Genomics at University of Birmingham

Looking for a new job opportunity in academia? Check out this job opening for a Assistant Professor (Research and Education) in Bacterial Genomics on jobs.ac.uk!

www.jobs.ac.uk

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Aude Bernheim @audeber.bsky.social · Sep 4

Thanks to the authors of this piece. I love reading about the work of inspiring pioneers in bacterial genetics. Crazy amount of discoveries!

Pioneer of bacterial genetics: the legacy of Esther Miriam Lederberg
academic.oup.com/genetics/adv...

Pioneer of bacterial genetics: the legacy of Esther Miriam Lederberg

Abstract. Esther Miriam Lederberg's brilliant scientific lifework, from the discovery of phage lambda, bacterial conjugation, and replica plating, provided

academic.oup.com

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Bart Penders 🟥 @penders.bsky.social · Sep 3

Our data stewards have started recommending that we no longer use US-based infrastructure for #openscience practices, given the risk of (near-future) censorship, from pre-print and data hosting to preregistration and more. That includes OSF.

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Stephanie Lo @stephlo.bsky.social · Sep 3

[New paper alert 🚨 ] What happens when pneumococci 'slip' and 'add' just one extra A in a promoter spacer of a sugar scavenging gene? 🧬

www.cell.com/cell-host-mi...

Naturally acquired promoter variation influences Streptococcus pneumoniae infection outcomes

Barton et al. identify Streptococcus pneumoniae promoters containing repetitive nucleotide sequences that promote DNA strand slippage and accumulation of promoter sequence mutations. This drives popul...

www.cell.com

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Reposted by Tommi Mäklin

Leonie Lorenz @leonielorenz.bsky.social · Sep 3

Very happy to announce that my first first-author paper just got published in Bioinformatics! We developed the web-application Menelmacar that displays differential equation models from @biomodels.bsky.social in the browser - it's beautiful and interactive!
doi.org/10.1093/bioi...

SBMLtoOdin and menelmacar: Interactive visualisation of systems biology models for expert and non-expert audiences

AbstractSummary. Computational models in biology can increase our understanding of biological systems, be used to answer research questions, and make predi

doi.org

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