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annizlab.bsky.social
AnniZLab: [🦠, 🧬 , ✨]
@annizlab.bsky.social
310 followers 270 following 110 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/
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annizlab.bsky.social
AnniZLab: [🦠, 🧬 , ✨] @annizlab.bsky.social · Sep 15
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.
annizlab.bsky.social
A structural database of ~2.7M predicted human gut microbial proteins + an alignment-free method by structure-encoded protein language models for fast and sensitive detection of remote homologs - really cool!
#microsky 🧪🧬🖥️🦠✨
www.cell.com/cell-host-mi...
Exploring functional insights into the human gut microbiome via the structural proteome
Liu et al. develop a structure database of human gut microbial proteins and a structure-aware AI model for remote homolog detection. They demonstrate the power of structure-guided approach in discover...
www.cell.com
January 26, 2026 at 7:24 AM
annizlab.bsky.social
A related study from Nandita’s group on gene-specific sweeps - a great idea to compare non-synonymous linkage disequilibrium (LD) vs synonymous LD! Gut microbiome show pervasive selective sweeps in carbohydrate metabolism - diet adaptation! #microsky #microbiomesky 🧪🦠
www.nature.com/articles/s41...
January 20, 2026 at 3:16 AM
Reposted by AnniZLab: [🦠, 🧬 , ✨]
stevensalzberg.bsky.social
very sad news. Peer Bork was one of the leaders of our field, a wonderful scientist, and he's much too young to be gone. www.embl.org/news/embl-an...
In remembrance of Peer Bork  | EMBL
EMBL and its community are deeply saddened by the death of Peer Bork, the organisation’s Interim Director General.
www.embl.org
January 16, 2026 at 6:33 PM
Reposted by AnniZLab: [🦠, 🧬 , ✨]
wkhuber.bsky.social
For many years, Peer Bork organised Bio-IT retreats to bring together the bioinformaticians across EMBL, in Garmisch-Partenkirchen and later Feldberg. Days out on the mountain followed by forward-looking and meta-science oriented sessions in the hut that fueled many projects and careers.
Peer Bork on top of Zugspitze, ready to race down Peer Bork, Jan Korbel, others at Sonnenkar ski lift at Zugspitze Après-Ski scientific sessions from 16:00 till very late.
January 17, 2026 at 10:22 AM
annizlab.bsky.social
So happy to host Dr. Xiaoqian (Annie) Yu - soon starting her lab at University of Montreal! She used population genomics and large data analysis to group gut microbiome into ecological units based on sweep events (major revision at Nature)!
www.biorxiv.org/content/10.1... #microsky #microbiomesky 🧪🦠
January 14, 2026 at 1:23 PM
annizlab.bsky.social
Happy New Year, everyone! First paper to share in 2026: (finally) a mechanistic study of cancer microbiome! pks+ E. coli's colibactin binds AT-rich DNA in minor groove and induces cross-links in colorectal cancer cells #microsky #microbiomesky 🧪🦠
www-science-org.remotexs.ntu.edu.sg/doi/10.1126/...
Structure and specificity of the colibactin-DNA interstrand cross-link. Characterization of DNA damage by the human gut bacterial genotoxin colibactin reveals a preference for alkylation at AT-rich DNA sequences and the importance of an unstable central α-ketoimine in mediating this specificity. These results help to explain the locations of cancer-linked mutations derived from colibactin exposure.
January 4, 2026 at 5:46 AM
annizlab.bsky.social
Prof. Howard Hang (Scripps) shared a great story on forward and reverse chemical microbiology using model organisms during his visit! A sneak peek: microbiota-derived secondary bile acids promote STING activation and antitumor activity #microsky #microbiomesky 🧪🦠
www.biorxiv.org/content/10.1...
Bile acids target at STING dimer-dimer interface. (a) HEK293T transfected with pMSCV-hygro-STING were treated with DCA-4 (10 µM) in presence of different concentrations of NVS-STG2 for 30 mins at 37 °C, followed by 365-nm light irradiation. The labeled proteins in cell lysis were reacted with az-biotin and enriched with streptavidin beads (‘pulldown’). Equal loading was validated by immunoblotting of input samples before enrichment (‘input’). (b) Quantification of binding efficiency in A by grayscale analysis (pull down/input) (n = 5 - 6 biologically independent samples.). Data were analyzed by unpaired two-sided t-test. (c) High-resolution cryo-EM map of the two STING dimer with highlight of dimer-dimer interfac molecular density. (d-f) HEK293T transfected with pMSCV-hygro-STING (WT and mutations), IFN-Beta_pGL3 and pRL-TK control plasmid were treated with diABZI (20 nM) in presence or absence of DCA (n = 5 biologically independent samples). A two-way ANOVA followed by Sidak’s multiple comparisons test was used to calculate adjusted P values. *P < 0.05, **P < 0.01, ***P < 0.001, ****P < 0.0001.
December 17, 2025 at 12:46 PM
annizlab.bsky.social
Our first year PhD student, Qiwen, presenting our work on biology-guided AI models to predict bacteria protein DNA binding, on BUG seminars! Great job! Thanks, @cwhitch.bsky.social for organizing this! 🧪🧬🖥️🦠✨
December 11, 2025 at 12:23 PM
annizlab.bsky.social
Reference genome choice compromises population genetic analyses - a problem for microbes too! Our lab is designing a tool to automatically choose references for input samples using features like phylogeny of reads to existing references. Any thoughts🤩? 🧪🦠🧬🖥️ #microsky
www.cell.com/cell/abstrac...
Reference genome choice compromises population genetic analyses
Using a species-specific reference genome significantly improves the accuracy of population genetic analyses, as exemplified by mapping gray fox sequence data to genomes of several canid species. Mapp...
www.cell.com
December 6, 2025 at 8:51 AM
annizlab.bsky.social
Using leave-one-out cross-validation to calculate metrics such as AUC and R^2 creates bias! This can be fixed by removing one of each class in the meanwhile to maintain the training data distribution - great work by Tal and his team 🧪🧬🖥️
tkorem.bsky.social Tal Korem @tkorem.bsky.social · Nov 28
Out after peer-review: www.science.org/doi/full/10....

Our bottom line stayed: never use leave-one-out cross-validation as it has inherent train-test leakage. Consider our Rebalanced version instead!

We now also account for regression and nested cross-validation, with more extensive benchmarking.
November 29, 2025 at 1:04 PM
annizlab.bsky.social
My pleasure to host Dr. Klas Udekwu's seminar on *Dissecting community alteration: a control theory–based approach to microbial community modulation* with @briefutopia.bsky.social Cool math modeling to guide sequential antibiotic or nutrient treatment to manipulate microbiomes! 🧪 🧬 🖥️ #microsky
November 28, 2025 at 4:34 AM
Reposted by AnniZLab: [🦠, 🧬 , ✨]
gibbological.bsky.social
We're at 735 registrants and counting! 🎉🦠

If you haven't registered yet, don't miss out on this exciting (free) symposium on gut microbial metabolites and their impacts on host health.

Please share with your networks. 🔗👇

isbscience.org/events/2025-...
November 26, 2025 at 5:19 PM
annizlab.bsky.social
Boltz-2: an AI model approaching free-energy perturbation accuracy for small-molecule–protein binding affinity!
It builds on Boltz-1, an open-source model from MIT that predicts the 3D structures of biomolecular complexes with AlphaFold3-level accuracy 🧪✨ 🧬 & 🖥️
www.biorxiv.org/content/10.1...
November 25, 2025 at 5:38 AM
annizlab.bsky.social
A great pleasure to speak at the SCELSE retreat today! Sharing how to uncover diverse microbial mechanisms via AI-powered computation: regulatory network evolution, environmental sensing, phage defence, and host–microbiome interactions 🧪 🧬 🖥️ ✨ @scelse.bsky.social #microsky #microbiomesky
November 19, 2025 at 1:00 PM
Reposted by AnniZLab: [🦠, 🧬 , ✨]
emmseveri.bsky.social
#microsky #phagesky

Predicting host- #phage interactions from genomics.

www.biorxiv.org/content/10.1...
Phylogeny-agnostic strain-level prediction of phage-host interactions from genomes
Bacteriophages offer promising alternatives to antibiotics for treating drug-resistant infections and engineering microbiomes, but applications are limited by inability to select phages infecting spec...
www.biorxiv.org
November 16, 2025 at 9:53 AM
Reposted by AnniZLab: [🦠, 🧬 , ✨]
micromaresca.bsky.social
Reposting because it’s Sunday and maybe people have time for a podcast today. It was really fun to with @markowenmartin.bsky.social about my group’s concrete project! (with bonus road salt content)
@sunyesf.bsky.social #microsky #concrete #builtenvironment
markowenmartin.bsky.social Mark O. Martin @markowenmartin.bsky.social · Nov 15
It’s Friday: a new episode of #MattersMicrobial! This week, Dr. Julie Maresca joins the #QualityQuorum to discuss microbes and concrete and road salt! Please spread the #GoodMicrobialWord? @ASMicrobiology @univpugetsound @microbe.tv

youtu.be/3JpbySeOO20?...
November 16, 2025 at 2:51 PM
annizlab.bsky.social
Really cool new tech to engineer native gut bacteria inside living animals using mobile CRISPR-associated transposases!
Non-engrafting donor E. coli + broad-host-range conjugation system + guide-RNA–directed targeting
www.science.org/doi/10.1126/...
#microsky #microbiomesky 🧪
Metagenomic editing of commensal bacteria in vivo using CRISPR-associated transposases
Although metagenomic sequencing has revealed a rich microbial biodiversity in the mammalian gut, methods to genetically alter specific species in the microbiome are highly limited. Here, we introduce ...
www.science.org
November 14, 2025 at 5:46 AM
annizlab.bsky.social
#microsky 🧪
asm.org ASM @asm.org · Nov 10
#MicrobiologyMonday: Bacteria swarm, but DYK they also "swash"? This flagella-independent movement is tied to fermentation: as cells ferment sugars, they create local osmolarity gradients, which generate a wave of fluid driving expansion. #JBacteriology: asm.social/2Gh
Propulsion-independent surface migration in S. enterica LT2 and E. coli.
November 11, 2025 at 7:55 AM
annizlab.bsky.social
OpenFold3: Open-source protein structure AI aims to match AlphaFold! Has anyone tried it yet? 🙌
www.nature.com/articles/d41...
github.com/aqlaboratory...
#microsky #bioinformatics
🧪 🧬 🖥️ ✨
Open-source protein structure AI aims to match AlphaFold
The developers of OpenFold3 have released an early version of the tool, which they hope will one day perform on par with DeepMind’s protein-structure model.
www.nature.com
November 6, 2025 at 5:25 AM
Reposted by AnniZLab: [🦠, 🧬 , ✨]
cotoorellana.bsky.social
The average nucleotide identity (ANI) underpins how we map microbial diversity, compare species, and connect genomes to ecology.
I wrote a short piece reflecting on the discovery and significance of this metric (and really enjoyed digging into the context and story behind it!) #microsky 🧬
Average nucleotide identity — the backbone of modern ecological genomics - Nature Reviews Genetics
In this Journal Club, Luis Orellana recalls a 2005 publication by Konstantinidis and Tiedje that introduced average nucleotide identity as a sequence-based metric to determine the relatedness between ...
www.nature.com
October 30, 2025 at 9:11 PM
annizlab.bsky.social
A brand-new Gordon Conference on Microbiomes!🦠 The opening session (Jan 2026) dives into microbiome editing - how fundamental research and new technologies can advance human health and environmental sustainability. Super looking forward!🧪 #microsky #microbiomesky #grc
www.grc.org/microbiome-e...
2026 Microbiome Editing Conference GRC
The 2026 Gordon Research Conference on Microbiome Editing will be held in Pomona, California. Apply today to reserve your spot.
www.grc.org
October 31, 2025 at 9:42 AM
annizlab.bsky.social
🧪✨
cstross.bsky.social Charlie Stross @cstross.bsky.social · Oct 23
LLMs can get "brain rot" if trained on junk Twitter/X social media threads: models truncate reasoning trains, exhibit reduced semantic quality, and exhibit "dark triad" traits: https://llm-brain-rot.github.io/
October 27, 2025 at 4:09 AM
annizlab.bsky.social
Cool enzyme specificity predictor🦠✨! Build on >300k enzyme-substrate pairs (UniProt, BRENDA, literature), combining ESM-2 embeddings and GNNs to model atom–residue interactions. In one test (34 E. coli metabolites × 860 enzymes), it correctly matched 10! #microsky 🧪 www.nature.com/articles/s41...
Enzyme specificity prediction using cross attention graph neural networks - Nature
Nature - Enzyme specificity prediction using cross attention graph neural networks
www.nature.com
October 23, 2025 at 9:48 AM
Reposted by AnniZLab: [🦠, 🧬 , ✨]
emmseveri.bsky.social
www.cell.com/cell-host-mi...

#microsky #microbiome
Amino acid competition shapes Acinetobacter baumannii gut carriage
Ren and Clark et al. show that Acinetobacter baumannii uses ornithine to compete with the resident microbiota and persist in the gut. Additional evidence demonstrates that amino acid supplementation a...
www.cell.com
October 21, 2025 at 5:12 AM
annizlab.bsky.social
After hours of sitting in the office, a standing desk feels like a life savor! why not upgrade meeting and classrooms with standing desks? What else could make our work more healthful (and fun)? 🧘‍♀️🧪
October 17, 2025 at 3:16 AM