iiinova — where your digital self keeps evolving

AnniZLab: [🦠, 🧬 , ✨] @annizlab.bsky.social · 28/09/2026

Results shared to your email - thank you, Stefan!

AnniZLab: [🦠, 🧬 , ✨] @annizlab.bsky.social · 16/09/2026

Great honor to be invited by Dr. Dori Deng to give a talk about @jgi.doe.gov and @kbase.us's Demystify AI and Data Management Seminar Series! Insightful and fun discussing our recent work on "uncovering microbial mechanisms via biology-informed AI". Photo taken in front of the famous JGI mural! 🧪🦠🧬

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AnniZLab: [🦠, 🧬 , ✨] @annizlab.bsky.social · 16/09/2026

Great, thank you! Will keep you updated, Stefan!

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AnniZLab: [🦠, 🧬 , ✨] @annizlab.bsky.social · 13/09/2026

Awesome - glad to see E. coli here, thank you! We found more E. coli TF-DNA binding sites (shared on genomiverse.net/DNAProteinBi...) than the ChIP-Seq data from www.nature.com/articles/s41.... We are building a regulatory network on our prediction and will keep you updated if you are interested!

genomiverse.net

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AnniZLab: [🦠, 🧬 , ✨] @annizlab.bsky.social · 13/09/2026

Great idea - thanks, Stefan! Any isolates/genomes you prefer? Would love to share predictions for those for validation!

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AnniZLab: [🦠, 🧬 , ✨] @annizlab.bsky.social · 13/09/2026

Which bacterial species would benefit most from a comprehensive regulatory network for you? We are validating our AI model for TF-DNA binding prediction and selecting priority species for wet-lab validation. Happy to share wet-lab results with participants who are interested - please stay tuned!🦠🧬🧪

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AnniZLab: [🦠, 🧬 , ✨] @annizlab.bsky.social · 26/08/2026

Interesting baby gut work! They tracked strains by a phylogeny tree with many isolate reference genomes on species-level genome bins (from metagenomes). I think their method would work best for species with single-strain colonization per person. What do you think? 🦠🧬🧪 www.nature.com/articles/s41...

nature.com

Baby-to-baby strain transmission shapes the developing gut microbiome - Nature

A metagenomic survey of babies attending the first year of nursery detected extensive baby-to-baby microbial strain transmission, pointing to social interactions in infancy as crucial drivers of infan...

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AnniZLab: [🦠, 🧬 , ✨] @annizlab.bsky.social · 07/08/2026

Thank you all for the TF-DNA binding test idea! Doing a gel shift assay by robots is hard, so we are considering alternatives. Add the TF to a reporter system (T7 promoter + predicted-positive or predicted-negative DNA + GFP reporter) and see how it changes reporter expression. What do you think?🦠🧬🧪

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AnniZLab: [🦠, 🧬 , ✨] @annizlab.bsky.social · 06/08/2026

A great tour and discussion at Ginkgo today - thank you so much, Austin and Swami! Super excited to try Ginkgo Cloud Labs cloud.ginkgo.bio on our protein-DNA binding project🙌🙌🙌🦠🧬🧪

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AnniZLab: [🦠, 🧬 , ✨] @annizlab.bsky.social · 06/08/2026

Thank you so much for the idea! I'll look into that 🙌🙌🙌

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AnniZLab: [🦠, 🧬 , ✨] @annizlab.bsky.social · 05/08/2026

Any ideas to test bacterial transcription factor-DNA binding in the wet lab? We are testing our AI model's predictions in 42 bacterial species, each with 5 proteins. We tried Twist's antibody platform + BLI (Bio-Layer Interferometry) assay, but all bindings (including ground truth) are weak.🙏 🦠🧪🧬🖥️✨

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Nature Portfolio @natureportfolio.nature.com · 30/05/2026

Two papers in Nature present AI systems that can assist throughout multiple processes involved in scientific research. The systems are designed to assist researchers in accelerating scientific discovery, not to replace them. go.nature.com/4tFHspz go.nature.com/3RQzXyL #Academicsky 🧪

This is figure 1, which shows Co-Scientist design, multi-agent architecture, and experimental validation summary.

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AnniZLab: [🦠, 🧬 , ✨] @annizlab.bsky.social · 27/05/2026

Check out our updated website - we would love new ideas! We used an LLM to restyle it and then spent a bunch of manual effort going through the results. We are now building checks to keep things organized - please talk to us if you are interested :) 🦠🧪🧬🖥️✨ genomiverse.net

genomiverse.net

We build AI from biological principles and generate training data from data we already have:

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AnniZLab: [🦠, 🧬 , ✨] @annizlab.bsky.social · 15/05/2026

Our knowledge graph does consider synonyms, but it's possible that some have been missed. Which ones do you have in mind? We don't see Pseudomonadota and Proteobacteria in the same figure. We've now fixed a different issue where searching for synonyms display duplicate content. Thanks a lot!

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AnniZLab: [🦠, 🧬 , ✨] @annizlab.bsky.social · 13/05/2026

New feature: querying multiple terms in our microbiome knowledge graph (143k papers)! Generated by LLM prompt engineering with > 96% accuracy (expect-check). Demo with 1% data: genomiverse.net/MicrobiomeCo... Feedback is super appreciated :) #microsky #microbiomesky 🦠🧪🧬🖥️✨

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AnniZLab: [🦠, 🧬 , ✨] @annizlab.bsky.social · 25/04/2026

1) DNA-protein binding prediction AI (40 species' bindings coming in v1 this summer; 6k+ species' bindings coming in v2 this year! 2) Microbiome knowledge graph based on 143k literature (100% data coming in v1 this summer)! Please reach out if you are interested :) #microsky #microbiomesky

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AnniZLab: [🦠, 🧬 , ✨] @annizlab.bsky.social · 25/04/2026

Speaking on Apr 29 at global-engage.com/product/micr... about latest work: 1) Biology-informed AI for bacterial DNA-protein binding prediction (demo: known + new bindings in E.coli); 2) microbiome knowledge graph for druggable target prediction (1% data demo)! genomiverse.net See you there :) 🦠🧪🧬🖥️✨

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AnniZLab: [🦠, 🧬 , ✨] @annizlab.bsky.social · 09/03/2026

And it didn't stop when the balance reached 0 (already $-300)! 🧪🧬🖥️✨

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AnniZLab: [🦠, 🧬 , ✨] @annizlab.bsky.social · 09/03/2026

Hi everyone, heads up that openAI API monthly limits appear to not work! We got an email that our jobs passed the limit and they're still going (already $900 with a $400 limit). gpt-5_1 also costs more than we expected - need more real-time math! 🧪🧬🖥️✨

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AnniZLab: [🦠, 🧬 , ✨] @annizlab.bsky.social · 02/03/2026

Babies sharing microbes is a leading factor in gut development! A study across infants, educators, and families finds extensive transmission between babies during the first nursery year - early social interactions greatly shape their microbiome! www.nature.com/articles/s41... 🧪🦠 #microbiomesky

nature.com

Baby-to-baby strain transmission shapes the developing gut microbiome - Nature

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ISME - International Society for Microbial Ecology @isme-microbes.bsky.social · 18/02/2026

It is with deep sadness that we share the passing of Professor Yehuda Cohen, a founding figure of the International Society for Microbial Ecology and one of the architects of modern microbial ecology. isme-microbes.org/in-memoriam-...

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AnniZLab: [🦠, 🧬 , ✨] @annizlab.bsky.social · 21/02/2026

AlphaFold shifts to Closed Science? AF4, from DeepMind drug spin-off, outperforms AF3 by 2.3x and Boltz-2 by 20x in antibody-antigen predictions. Strictly proprietary + technical report lacks details for outside scientists to replicate the results 🧪🧬🖥️🦠✨ www.isomorphiclabs.com/articles/the...

isomorphiclabs.com

The Isomorphic Labs Drug Design Engine unlocks a new frontier beyond AlphaFold - Isomorphic Labs

Today, we are excited to share an update on our progress towards a new frontier of drug design. We have unlocked a new paradigm of predictive accuracy in understanding our biomolecular world, allowing...

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Theo Sanderson @theo.io · 08/02/2026

I made a map of 3.4 million Bluesky users - see if you can find yourself! bluesky-map.theo.io I've seen some similar projects, but IMO this seems to better capture some of the fine-grained detail

bluesky-map.theo.io

Bluesky Map

Interactive map of 3.4 million Bluesky users, visualised by their follower pattern.

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AnniZLab: [🦠, 🧬 , ✨] @annizlab.bsky.social · 11/02/2026

AlphaGenome is out! Input 1 Mb DNA -> predict gene expression, transcription initiation, chromatin accessibility, histone modifications, transcription factor binding, chromatin contact maps, ..., up to single-base-pair resolution! Trained on human and mouse data 🧪🧬🖥️🦠✨ www.nature.com/articles/s41...

nature.com

Advancing regulatory variant effect prediction with AlphaGenome - Nature

AlphaGenome, a deep learning model that inputs 1-Mb DNA sequence to predict functional genomic tracks at single-base resolution across diverse modalities, outperforms existing models in variant effect...

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AnniZLab: [🦠, 🧬 , ✨] @annizlab.bsky.social · 26/01/2026

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...

cell.com

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...

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AnniZLab: [🦠, 🧬 , ✨] @annizlab.bsky.social · 20/01/2026

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...

nature.com

Gene-specific selective sweeps are pervasive across human gut microbiomes - Nature

Development and application of the integrated linkage disequilibrium score (iLDS) reveals both selective pressures impacting the human gut microbiome and the mechanisms by which gut bacteria adapt to ...

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Steven Salzberg @stevensalzberg.bsky.social · 16/01/2026

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...

embl.org

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.

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Wolfgang Huber @wkhuber.bsky.social · 17/01/2026

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.

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AnniZLab: [🦠, 🧬 , ✨] @annizlab.bsky.social · 14/01/2026

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 🧪🦠

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AnniZLab: [🦠, 🧬 , ✨] @annizlab.bsky.social · 04/01/2026

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.

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AnniZLab: [🦠, 🧬 , ✨] @annizlab.bsky.social · 17/12/2025

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.

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AnniZLab: [🦠, 🧬 , ✨] @annizlab.bsky.social · 11/12/2025

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! 🧪🧬🖥️🦠✨

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AnniZLab: [🦠, 🧬 , ✨] @annizlab.bsky.social · 07/12/2025

Also, our seq alignment tool Mapper can infer ancestor references and reduce the penalty for a basepair mismatching a ref but matching its ancestor.

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AnniZLab: [🦠, 🧬 , ✨] @annizlab.bsky.social · 07/12/2025

The main idea is about using phylogeny to give feedback to users about which parts of the reference tree lack important genomes. A secondary idea is that our seq alignment tool Mapper can infer ancestor references and reduce the penalty for a basepair mismatching a ref but matching its ancestor.

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AnniZLab: [🦠, 🧬 , ✨] @annizlab.bsky.social · 07/12/2025

YAY this tool might be able to use that information to give feedback about which part of the reference tree lack important genomes!

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AnniZLab: [🦠, 🧬 , ✨] @annizlab.bsky.social · 07/12/2025

YAY thanks! maybe we can even choose several least bad references and/or a pangenome.

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AnniZLab: [🦠, 🧬 , ✨] @annizlab.bsky.social · 06/12/2025

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...

cell.com

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...

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AnniZLab: [🦠, 🧬 , ✨] @annizlab.bsky.social · 01/12/2025

That's awesome - will share with my people :) Thank you, Sean!

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AnniZLab: [🦠, 🧬 , ✨] @annizlab.bsky.social · 29/11/2025

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 🧪🧬🖥️

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AnniZLab: [🦠, 🧬 , ✨] @annizlab.bsky.social · 28/11/2025

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

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Sean Gibbons 🦠💩 @gibbological.bsky.social · 26/11/2025

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-...

isbscience.org

2025 ISB Virtual Microbiome Symposium - Institute for Systems Biology (ISB)

The gut’s microbial ecosystem produces diverse metabolites that actively shape neural, immune, and endocrine function. Join leading researchers on December 12 as they share new discoveries into these ...

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AnniZLab: [🦠, 🧬 , ✨] @annizlab.bsky.social · 25/11/2025

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...

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AnniZLab: [🦠, 🧬 , ✨] @annizlab.bsky.social · 19/11/2025

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

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Julie Maresca @micromaresca.bsky.social · 16/11/2025

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

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