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annizlab.bsky.social
AnniZLab: [🦠, 🧬 , ✨]
@annizlab.bsky.social
200 followers 200 following 71 posts
A microbiologist 🦠& bioinformatician 🧬 uncovering diverse microbial mechanisms via AI ✨. A rising assistant professor @NTU Singapore. With data in the cloud, the sky is the limit! Check out our lab website :) https://genomiverse.net/
genomiverse.net
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annizlab.bsky.social
AnniZLab: [🦠, 🧬 , ✨] @annizlab.bsky.social · 23d
X-Mapper 🦠🧬🧪 - a sequence aligner developed for microbes, now on Bioconda! 🚀
• 11–24× fewer suboptimal alignments (same for human genome)
• 3–579× lower inconsistency
• improves on ~30% of reads aligned to non-target species
github.com/mathjeff/map...
bioconda.github.io/recipes/x-ma...
#microsky
Alignment algorithms represent a balance between speed and accuracy. We evaluated this balance across aligners, with accuracy measured by suboptimal alignments. We found that the relationship between alignment time (with 30 threads) and suboptimal alignment rates exhibits diminishing returns, where X-Mapper stands out as an outlier, offering the highest accuracy with competitive speed.
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annizlab.bsky.social
AnniZLab: [🦠, 🧬 , ✨] @annizlab.bsky.social · 3d
BindCraft: an AlphaFold2-powered de novo protein binder design tool 🧬✨
Tested in some bacterial systems too! Designs so far are short peptides or mini-domains. Looking forward to long/full protein design ahead! 🧪 #microsky
www.nature.com/articles/s41...
One-shot design of functional protein binders with BindCraft - Nature
BindCraft, an open-source, automated pipeline for de novo protein binder design with experimental success rates of 10–100%, leverages AlphaFold2 weights to generate binders with nanomolar affinity without the need for high-throughput screening.
www.nature.com
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annizlab.bsky.social
AnniZLab: [🦠, 🧬 , ✨] @annizlab.bsky.social · 6d
Super helpful guidelines! Curious-how do we apply DRI tags to existing publications/datasets? Is the default that data creators should be contacted first before use? Thoughts? 🤔🧪
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annizlab.bsky.social
AnniZLab: [🦠, 🧬 , ✨] @annizlab.bsky.social · 9d
Fascinating! A clear microbiome phylogeny shaped by the host. I’m curious about clades with both human- and bovine-derived isolates. Can they colonize both hosts? Or HGT of host-specific genes? Thoughts? #microsky #microbiomesky 🧪
rhystwhite.bsky.social
Rhys White @rhystwhite.bsky.social · 9d
Where else is ST1 hiding?

We need to start thinking about environmental & farm worker sampling to map the spread & persistence of ST1

#AMR #Genomics #OneHealth #Staphylococcus #Biosecurity #NZ

🖥️🧬💻
#AcademicSky
#MicroSky
🧪🧫🦠
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Reposted by AnniZLab: [🦠, 🧬 , ✨]
campy-bara.bsky.social
Sarah Svensson @campy-bara.bsky.social · 12d
#microsky
campy-bara.bsky.social
Sarah Svensson @campy-bara.bsky.social · 12d
Dual transposon sequencing profiles the genetic interaction landscape in bacteria | Science www.science.org/doi/10.1126/...
Dual transposon sequencing profiles the genetic interaction landscape in bacteria
Gene redundancy complicates systematic characterization of gene function as single-gene deletions may not produce discernible phenotypes. We report dual transposon sequencing (dual Tn-seq), a platform...
www.science.org
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Reposted by AnniZLab: [🦠, 🧬 , ✨]
lalouxlab.bsky.social
Géraldine Laloux @lalouxlab.bsky.social · 13d
📝New preprint! #MicroSky

🕰️We chart the full, synchronized lifecycle of a predatory bacterium using Hi-C, RNA-seq, ChIP-seq & microscopy.

🧬We uncover dramatic shifts in nucleoid architecture & transcription, tightly coordinated with predation.

www.biorxiv.org/content/10.1...
Dynamics and interplay of gene expression and chromosome organization across a predatory lifecycle
The obligate predatory bacterium Bdellovibrio bacteriovorus alternates between a motile attack phase and a growth phase inside another bacterium, during which it undergoes multiple rounds of DNA repli...
www.biorxiv.org
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Reposted by AnniZLab: [🦠, 🧬 , ✨]
zaminiqbal.bsky.social
Zamin Iqbal @zaminiqbal.bsky.social · 13d
#microsky
zaminiqbal.bsky.social
Zamin Iqbal @zaminiqbal.bsky.social · 13d
Delighted to see our paper studying the evolution of plasmids over the last 100 years, now out! Years of work by Adrian Cazares, also Nick Thomson @sangerinstitute.bsky.social - this version much improved over the preprint. Final version should be open access, apols.
Thread 1/n
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annizlab.bsky.social
AnniZLab: [🦠, 🧬 , ✨] @annizlab.bsky.social · 13d
Multidrug resistance efflux pumps drive C. parvum virulence differences - showing how gut microbiome protects against pathogen colonization, and how antibiotics can disrupt this defense. 🦠💊 #microsky #microbiomesky #Mevosky 🧪 www.cell.com/cell-host-mi...
Cryptosporidium parvum multidrug resistance protein confers resistance to toxic gut microbial metabolite
Huang et al. identify a multidrug-resistance-associated ABC transporter, CpMRP1, as a genetic determinant of pathogenicity in Cryptosporidium parvum. Through genetic mapping and functional assays, the...
www.cell.com
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annizlab.bsky.social
AnniZLab: [🦠, 🧬 , ✨] @annizlab.bsky.social · 14d
It's 3D LED DNA Lamp with ABS Touch Base. It's not 3D thought haha it's a 2D plastic plate :)
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annizlab.bsky.social
AnniZLab: [🦠, 🧬 , ✨] @annizlab.bsky.social · 15d
A little touch of science to personalize my office (DNA + lab pens) 🧬 - any new idea would be appreciated! Curious, what makes your office feels like yours? 🧪
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annizlab.bsky.social
AnniZLab: [🦠, 🧬 , ✨] @annizlab.bsky.social · 16d
#microsky
rscmedchem.rsc.org
RSC Medicinal Chemistry @rscmedchem.rsc.org · 16d
Take a look at this Review article by Katrine Qvortrup & co discussing advances in developing small molecules targeting three virulence categories, a promising strategy to combat antibiotic resistant infections👀

pubs.rsc.org/en/content/articlelanding/2025/md/d5md00272a

📍Denmark TU 🧪
Small molecule antipathogenic agents against Staphylococcus aureus infections
Staphylococcus aureus, a Gram-positive bacterium, is a pathogen capable of infecting nearly all host tissues, causing severe morbidity and mortality. Antibiotic resistant S. aureus are abundant, and…
pubs.rsc.org
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Reposted by AnniZLab: [🦠, 🧬 , ✨]
vscooper.micropopbio.org
Vaughn Cooper @vscooper.micropopbio.org · 17d
Lineage tracking using methylation states from longitudinal bulk sampling. Sounds 🆒 and given recent work by @trevorgraham.bsky.social and colleagues, looks real.

Wondering about other applications like 🦠🧫

👉🏻News and views: www.nature.com/articles/d41...
👉🏻Paper
www.nature.com/articles/s41...
Epigenetic clues from cancer’s past foretell its future
An innovative method to trace tumour evolution using patterns of fluctuating DNA modifications could be implemented in the clinic to predict cancer progression.
www.nature.com
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annizlab.bsky.social
AnniZLab: [🦠, 🧬 , ✨] @annizlab.bsky.social · 17d
Good to know - thanks!
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annizlab.bsky.social
AnniZLab: [🦠, 🧬 , ✨] @annizlab.bsky.social · 17d
Super interesting! I’m curious what’s considered a “high-fiber” diet for people. Looks like the mice were tested on either no fiber or all carbs replaced with fiber? 🌾VS🍞 #microbiomesky 🧪🦠
fzmarques.bsky.social
Prof Francine Marques @fzmarques.bsky.social · 18d
If you missed Dr Chudan Xu's talk on what happens when we don't eat enough fibre, the preprint is now live 👇

www.medrxiv.org/content/10.1...

#EESMicrobiome @events.embl.org
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annizlab.bsky.social
AnniZLab: [🦠, 🧬 , ✨] @annizlab.bsky.social · 17d
#microsky 🧪
evgenii-protasov.bsky.social
Evgenii Protasov @evgenii-protasov.bsky.social · 17d
Host-specific microbiome and genomic signatures in Bifidobacterium reveal co-evolutionary and functional adaptations across diverse animal hosts
#microbiology #microbiome #bifidobacterium
@cp-cellhostmicrobe.bsky.social
www.sciencedirect.com/science/arti...
Host-specific microbiome and genomic signatures in Bifidobacterium reveal co-evolutionary and functional adaptations across diverse animal hosts
Animals harbor divergent microbiota, including various Bifidobacterium species, yet their evolutionary relationships and functional adaptations remain…
www.sciencedirect.com
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annizlab.bsky.social
AnniZLab: [🦠, 🧬 , ✨] @annizlab.bsky.social · 18d
A great example that uses LLMs on temporal data to predict the future! Using historical health data as input tokens to predict later tokens - future disease events. www.nature.com/articles/s41... 🧪✨ #AI4S
Learning the natural history of human disease with generative transformers - Nature
Delphi-2M forecasts a person’s future health, covering more than 1,000 diseases, provides insights into co-morbidity dynamics and generates synthetic data for the training of AI models that have never...
www.nature.com
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annizlab.bsky.social
AnniZLab: [🦠, 🧬 , ✨] @annizlab.bsky.social · 19d
Sounds like a lot of fun to meet the winners face to face! First stop @mitpress.bsky.social Videos will be posted later? 🧪 improbable.com/the-35th-fir...
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annizlab.bsky.social
AnniZLab: [🦠, 🧬 , ✨] @annizlab.bsky.social · 19d
YAY 🎉 our lab is exploring how large-scale sequencing data from these tiny powerhouses 🧬 🦠 can fuel AI models! ✨ #microsky
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annizlab.bsky.social
AnniZLab: [🦠, 🧬 , ✨] @annizlab.bsky.social · 19d
Fascinating! 🤔 I wonder whether bacteria with simpler single-membrane envelopes (like Chloroflexota) could be more “permissive” to HGT of membrane systems (from both bacteria and archaea)? 🦠🔀🧪 #microsky
natmicrobiol.nature.com
Nature Microbiology @natmicrobiol.nature.com · 20d
#NewResearch

Structure of a functional archaellum in Bacteria of the Chloroflexota phylum

@archaellum.bsky.social @sgribaldo.bsky.social & co

#microsky 🧪🦠

www.nature.com/articles/s41...
Structure of a functional archaellum in Bacteria of the Chloroflexota phylum - Nature Microbiology
Bona fide gene clusters for archaella are widespread across a bacterial phylum and encode functional motility machinery.
www.nature.com
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annizlab.bsky.social
AnniZLab: [🦠, 🧬 , ✨] @annizlab.bsky.social · 20d
QuickVariants 🦠🧬🧪- a genetic variant identification tool developed for microbes, now on Bioconda! 🚀
• 9× faster median speed vs bcftools
• Higher accuracy for both SNPs & indels
bioconda.github.io/recipes/quic...
bmcbiol.biomedcentral.com/articles/10....
#microsky #microbiomesky
Fast and accurate variant identification tool for sequencing-based studies - BMC Biology
Background Accurate identification of genetic variants, such as point mutations and insertions/deletions (indels), is crucial for various genetic studies into epidemic tracking, population genetics, a...
bmcbiol.biomedcentral.com
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annizlab.bsky.social
AnniZLab: [🦠, 🧬 , ✨] @annizlab.bsky.social · 21d
Cool! Some gut microbes make 2-MiCit from propionate. In vitro, it inhibits 3D colon tumor growth (and normal cells at high dose). Just a 'lucky' one among millions of microbial by-products? I haven't thought of any selective advantage 🤔 Thoughts? 🦠🧪 #microsky #microbiomesky doi.org/10.1016/j.ce...
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annizlab.bsky.social
AnniZLab: [🦠, 🧬 , ✨] @annizlab.bsky.social · 22d
That's awesome - thanks, Uri! Please feel free to reach out :)
annizlab.bsky.social
AnniZLab: [🦠, 🧬 , ✨] @annizlab.bsky.social · 22d
Thanks for sharing! Curious how it goes :) Please feel free to reach out if there are any questions!
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annizlab.bsky.social
AnniZLab: [🦠, 🧬 , ✨] @annizlab.bsky.social · 23d
#microbiomesky
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annizlab.bsky.social
AnniZLab: [🦠, 🧬 , ✨] @annizlab.bsky.social · 23d
Thank you! We put it in bioconda specifically for CoverM :) Please feel free to reach out if there are any questions.
annizlab.bsky.social
AnniZLab: [🦠, 🧬 , ✨] @annizlab.bsky.social · 23d
Thank you! Please feel free to reach out if there're any questions - we check our GitHub quite often too :)
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