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travis.gibsonlab.io
Travis Gibson
@travis.gibsonlab.io
140 followers 110 following 27 posts
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
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travis.gibsonlab.io
Travis Gibson @travis.gibsonlab.io · Aug 5
A nice blog post about our work www.nature.com/articles/s41... can be found here mgriblog.org/2025/08/04/c...
How a Scientist Followed Curiosity (and Love) to Build an Innovative Tool to Track Changes in the Gut Microbiome
Despite how common they are, scientists still don’t fully understand why some people develop allergies while others don’t.
mgriblog.org
travis.gibsonlab.io
arxiv.org/abs/2509.16486
Comment on "mbtransfer: Microbiome intervention analysis using transfer functions and mirror statistics": Implementation errors, theoretical misapplication, and methodological flaws
There are a number of errors in "mbtransfer: Microbiome intervention analysis using transfer functions and mirror statistics" PLOS Comp Bio (2024) spanning multiple aspects of the paper. The wrong inp...
arxiv.org
September 24, 2025 at 1:00 AM
Reposted by Travis Gibson
natmicrobiol.nature.com
#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...
Learning ecosystem-scale dynamics from microbiome data with MDSINE2 - Nature Microbiology
This Bayesian statistical method uses timeseries microbiome data to infer interaction modules and is tested using a faecal transplant experiment in mice.
www.nature.com
September 12, 2025 at 3:51 PM
travis.gibsonlab.io
www.nature.com/articles/s41...
Learning ecosystem-scale dynamics from microbiome data with MDSINE2 - Nature Microbiology
This Bayesian statistical method uses timeseries microbiome data to infer interaction modules and is tested using a faecal transplant experiment in mice.
www.nature.com
September 9, 2025 at 11:36 AM
Reposted by Travis Gibson
contaminatedsci.bsky.social
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...
June 30, 2025 at 12:26 PM
travis.gibsonlab.io
A nice blog post about our work www.nature.com/articles/s41... can be found here mgriblog.org/2025/08/04/c...
How a Scientist Followed Curiosity (and Love) to Build an Innovative Tool to Track Changes in the Gut Microbiome
Despite how common they are, scientists still don’t fully understand why some people develop allergies while others don’t.
mgriblog.org
August 5, 2025 at 12:36 AM
travis.gibsonlab.io
Im working on something and I am reminded of one of the wildest correspondences ever published www.nature.com/articles/nbt...
Silence on the relevant literature and errors in implementation - Nature Biotechnology
Nature Biotechnology - Silence on the relevant literature and errors in implementation
www.nature.com
July 16, 2025 at 1:16 AM
Reposted by Travis Gibson
cibiocm.bsky.social
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-...
MetaPhlAn 4.2.2 release (initial long-read sequencing support and database update)
Announcement We are pleased to share that MetaPhlAn 4.2.2 is now available, which incorporates taxonomic profiling of long-read metagenomes for the first time and includes a new version of the MetaPhl...
forum.biobakery.org
June 11, 2025 at 6:15 AM
Reposted by Travis Gibson
gibsonlab.io
Our paper is now open access as well.
May 29, 2025 at 4:23 PM
Reposted by Travis Gibson
inschool4life.bsky.social
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).
Incorporating scale uncertainty in microbiome and gene expression analysis as an extension of normalization - Genome Biology
Statistical normalizations are used in differential analyses to address sample-to-sample variation in sequencing depth. Yet normalizations make strong, implicit assumptions about the scale of biologic...
genomebiology.biomedcentral.com
May 22, 2025 at 4:43 PM
Reposted by Travis Gibson
natmicrobiol.nature.com
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...
Call for papers on the clinical microbiome - Nature Microbiology
Nature Microbiology has launched a joint collection on the clinical microbiome with Nature Communications, Nature Medicine and Communications Medicine.
www.nature.com
May 6, 2025 at 7:37 PM
Reposted by Travis Gibson
natmicrobiol.nature.com
🚨 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...
Longitudinal profiling of low-abundance strains in microbiomes with ChronoStrain - Nature Microbiology
ChronoStrain accurately profiles low-abundance strains in longitudinal samples by jointly modelling nucleotide sequencing errors, strain presence/absence and the temporal information associated with e...
www.nature.com
May 6, 2025 at 6:54 PM
Reposted by Travis Gibson
gibsonlab.io
"Longitudinal profiling of low-abundance strains in microbiomes with ChronoStrain" - Kim et al.

rdcu.be/ekTwf
Longitudinal profiling of low-abundance strains in microbiomes with ChronoStrain
Nature Microbiology - ChronoStrain accurately profiles low-abundance strains in longitudinal samples by jointly modelling nucleotide sequencing errors, strain presence/absence and the temporal...
rdcu.be
May 6, 2025 at 4:28 PM
Reposted by Travis Gibson
gulliver-lab.bsky.social
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
May 5, 2025 at 10:30 AM
Reposted by Travis Gibson
gibsonlab.io
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/
Openings
Positions available in the Gibson Lab
gibsonlab.io
April 17, 2025 at 2:02 PM
Reposted by Travis Gibson
hutlab.bsky.social
We are still accepting registrations for this event! Please come join us and hear about cutting edge microbiome research.
hutlab.bsky.social Hutlab @hutlab.bsky.social · Feb 28
Come join us in Boston for this year's HCMPH Symposium on May 19th! This year's theme is "microbiome in food systems", however, any and all microbiome research is welcome!
March 17, 2025 at 8:05 PM
Reposted by Travis Gibson
natmicrobiol.nature.com
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...
Planning and describing a microbiome data analysis - Nature Microbiology
We provide guidance on the planning, execution and description of statistical analyses in microbiome studies.
www.nature.com
February 21, 2025 at 2:48 PM
Reposted by Travis Gibson
gibsonlab.io
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...
February 7, 2025 at 4:35 PM
Reposted by Travis Gibson
harriswang.bsky.social
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...
SAMPL-seq reveals micron-scale spatial hubs in the human gut microbiome - Nature Microbiology
Split-And-pool Metagenomic Plot-sampling sequencing (SAMPL-seq) can be applied to complex microbial communities to reveal spatial co-localization of microbes at the micron scale.
www.nature.com
February 3, 2025 at 2:46 PM
Reposted by Travis Gibson
abmilliken.bsky.social
Join us in LA this March!
Ethics of Caring - National Nursing Ethics Conference on LinkedIn: #nursing #ethics #nursingethics #clinicalethics #socialworkers #socialwork…
“We can’t underestimate the power of storytelling…stories have a way of speaking to the humanity within each of us and can help remind us of the humanity in…
www.linkedin.com
January 31, 2025 at 6:19 PM
travis.gibsonlab.io
Are regret based adaptive control strategies deployable?
arxiv.org/abs/2501.04572
January 9, 2025 at 2:38 PM
travis.gibsonlab.io
This post has saved hours when trying to get old x86 bioinformatics pipelines working on Mac arm64 (like pplacer)

stackoverflow.com/questions/64...
How can I run two isolated installations of Homebrew?
I want to install and run two versions of Homebrew simultaneously on an Apple Silicon Mac: an ARM64 version, and an Intel version running under Rosetta 2. I know I can prepend any brew command with...
stackoverflow.com
December 16, 2024 at 3:22 PM
Reposted by Travis Gibson
baym.lol
It’s easy to think this is about politics, but Ran’s actually just subtweeting my working style
blekhman.bsky.social Ran Blekhman @blekhman.bsky.social · Dec 8
"There are decades where nothing happens, and weeks where decades happen"
December 8, 2024 at 6:16 PM
Reposted by Travis Gibson
teorth.bsky.social
When can a sum of reciprocals of natural numbers sum to a rational number? There are many unsolved problems in this area, by Erdős and others. With Vjeko Kovac, we have been able to resolve some open questions and make progress on others: terrytao.wordpress.com/2024/11/27/o...
On several irrationality problems for Ahmes series
Vjeko Kovac and I have just uploaded to the arXiv our paper “On several irrationality problems for Ahmes series”. This paper resolves (or at least makes partial progress on) some open q…
terrytao.wordpress.com
November 29, 2024 at 9:28 PM
travis.gibsonlab.io
Congrats Robert
lulamaybelle.bsky.social Courtney Howard @lulamaybelle.bsky.social · Nov 28
#Nosferatu is a personal story for filmmaker Robert Eggers to bring to the screen with all his collaborators, from the actors to the craftspeople. I love this letter he sent to us CCA members, allowing us insight into all the intense work that went into its making. 🖤 @focusfeatures.bsky.social
November 28, 2024 at 4:20 PM
Reposted by Travis Gibson
jcamthrash.bsky.social
Retraction Note: Culture of previously uncultured members of the human gut microbiota by culturomics | Nature Microbiology www.nature.com/articles/s41...
Retraction Note: Culture of previously uncultured members of the human gut microbiota by culturomics - Nature Microbiology
Nature Microbiology - Retraction Note: Culture of previously uncultured members of the human gut microbiota by culturomics
www.nature.com
November 25, 2024 at 3:49 PM