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🙌🙌🙌🦠🧬🧪

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.🙏 🦠🧪🧬🖥️✨

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 🧪

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

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

genomiverse.net

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 🦠🧪🧬🖥️✨

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

AnniZLab: [🦠, 🧬 , ✨]@annizlab.bsky.social · 3mo ago

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 :) 🦠🧪🧬🖥️✨

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 :) 🦠🧪🧬🖥️✨

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

AnniZLab: [🦠, 🧬 , ✨]@annizlab.bsky.social · 5mo ago

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! 🧪🧬🖥️✨

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! 🧪🧬🖥️✨

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

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...

nature.com

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-...

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...

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...

isomorphiclabs.com

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

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

bluesky-map.theo.io

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...

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...

nature.com

FMT before immune checkpoint inhibitors improves response in NSCLC and melanoma. E.citroniae, E.lavalensis, C.innocuum persist in non-responders: suppress ICI efficacy? FMT works by depleting harmful taxa. Next step: targeted MO depletion? #microsky #microbiomesky 🧪🦠 www.nature.com/articles/s41...

Fecal microbiota transplantation plus immunotherapy in non-small cell lung cancer and melanoma: the phase 2 FMT-LUMINate trial - Nature Medicine

In a phase 2 trial evaluating healthy donor fecal microbial transplantation plus either anti-PD-1 in patients with non-small cell lung cancer or anti-PD-1 and anti-CTLA-4 in patients with melanoma, en...

nature.com

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...

cell.com

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...

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 ...

nature.com

AnniZLab: [🦠, 🧬 , ✨]@annizlab.bsky.social · 7mo ago

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 🧪🦠

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.

embl.org

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.

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 🧪🦠

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/...

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...

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! 🧪🧬🖥️🦠✨

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...

cell.com

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 🧪🧬🖥️

Tal Korem@tkorem.bsky.social · 8mo ago

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.

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

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-...

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 ...

isbscience.org

Science in Seattle@scienceinseattle.com · 9mo ago

🦠 The @isbscience.org Virtual Microbiome Symposium is on December 12, 2025! This virtual symposium will dive into the influence of gut microbial metabolites on human #physiology. This event is perfect for everyone in academia, industry, and the clinic. Register now: https://bit.ly/4oe67iw

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...

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

#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...

biorxiv.org