@travis.gibsonlab.io
Assistant Professor - Harvard Medical School Principal Investigator - Brigham and Women’s Hospital Associate Member - Broad Institute of MIT and Harvard Gibson Lab Bluesky handle: @gibsonlab.io Gibson Lab website: gibsonlab.io
It's time for the 2025 Gibbons Lab Research Roundup!
Yeehaw! 🤠 @isbscience.org
In these dark times, let the joy of scientific discovery and trainee success be your balm ❤️🩹
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If you missed the 2025 @isbscience.org Virtual Microbiome Symposium (theme: how microbial metabolites influence the brain, the immune system, & metabolism), the videos of the talks and the panel discussion are now available here:
youtube.com/playlist?lis...
Thanks to all who helped make it happen!
You still have time to register for our @isbscience.org Virtual Microbiome Symposium (Dec. 12th), with 6 speakers discussing how microbial metabolites impact the nervous, immune, and endocrine systems.
It's free! Recordings of the talks will be available afterwards.
isbscience.org/events/2025-...
#Newresearch
This Bayesian statistical method uses timeseries microbiome data to infer interaction modules and is tested using a faecal transplant experiment in mice.
#MicroSky
www.nature.com/articles/s41...
Our paper demonstrating that within-species warfare interactions are ecologically important on human skin is now published in Nature Micro! www.nature.com/articles/s41...
A nice blog post about our work www.nature.com/articles/s41... can be found here mgriblog.org/2025/08/04/c...
Im working on something and I am reminded of one of the wildest correspondences ever published www.nature.com/articles/nbt...
The paper has the incorrect dynamics for gLV
The mbtransfer paper also has data leakage issues. In many of the results they apply DESeq2 Normalization in a pre-processing step (for all samples in a bulk process) and include samples which are later used as forecasting test samples when doing so.
The new version of MetaPhlAn v4.2.2 released!
📌taxonomic profiling of long-read metagenomes for the first time
📌new version of the MetaPhlAn db (vJan25_202503) containing >21k new SGBs
Try it out & @hutlab.bsky.social and we are looking forward to your feedback!
forum.biobakery.org/t/metaphlan-...
Our paper is now open access as well.
New paper in Genome Biology!
genomebiology.biomedcentral.com/articles/10....
We introduce scale models, a generalization of normalizations that explciitly account for uncertainty in biological system scale (e.g., microbial load).
This month's editorial is an invitation to submit papers on clinical and translational aspect of the microbiome.
This collection is a joint effort with @naturemedicine.bsky.social @natcomms.nature.com and @commsbio.nature.com
#MicroSky #MicrobiomeSky 🦠⚕️🧪⚕️
www.nature.com/articles/s41...
🚨 Out now!
Chronostrain - a method to profile low abundance strains in longitudinal microbiome samples 🦠💻
@travis.gibsonlab.io @younhk.bsky.social @gibsonlab.io @harvardmed.bsky.social @broadinstitute.org
#MicroSky 🦠 #MicrobiomeSky
www.nature.com/articles/s41...
reviewer 3 or 2?
"Longitudinal profiling of low-abundance strains in microbiomes with ChronoStrain" - Kim et al.
rdcu.be/ekTwf
It is a great pleasure to listen to @seppekuehnlab.bsky.social
His talk is about ´Learning microbiome design principles from natural variation ´.
Below, the #liveSketch painting during the seminar and given at the end!
#ArtAndScience #MediationScientifique
Several Postdoctoral Fellow openings. All fellows have triple appointment at HMS,BWH, and Broad
- Biological sequence models (theory, design, and application)
- Learning single cell dynamics
- Bacteriotherapy design, “bugs-as-drugs” (using control theory principles)
gibsonlab.io/openings/
We are still accepting registrations for this event! Please come join us and hear about cutting edge microbiome research.
A must-read for any microbiome researcher 🦠📐and a new addition to our #bestpractices series
Planning and describing a microbiome data analysis by @amydwillis.bsky.social and @davidandacat.bsky.social
www.nature.com/articles/s41...
Paper just accepted
Gibson et al. "On the stability of gradient descent with second order dynamics for time-varying cost functions" Transactions Machine Learning Research (2025)
openreview.net/forum?id=Hlz...
Happy to share our new paper in @naturemicrobiol.bsky.social on mapping spatial relationships of the human gut microbiome. We identified distinct spatial hubs between gut bacteria that reflect sub-community assemblies at the micron-scale. Led by Miles Richardson & co.
www.nature.com/articles/s41...
Are regret based adaptive control strategies deployable?
arxiv.org/abs/2501.04572
This post has saved hours when trying to get old x86 bioinformatics pipelines working on Mac arm64 (like pplacer)
stackoverflow.com/questions/64...
It’s easy to think this is about politics, but Ran’s actually just subtweeting my working style
As further evidence you should send them the @abrahamgihawi.bsky.social paper that invalidated and lead to the retraction of the Nature paper about a cancer microbiome.
