Travis Gibson
@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
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
Pinned
Travis Gibson
@travis.gibsonlab.io
· Aug 5
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
A nice blog post about our work www.nature.com/articles/s41... can be found here mgriblog.org/2025/08/04/c...
Reposted by Travis Gibson
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 ❤️🩹
🧵...
Yeehaw! 🤠 @isbscience.org
In these dark times, let the joy of scientific discovery and trainee success be your balm ❤️🩹
🧵...
December 19, 2025 at 12:06 AM
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 ❤️🩹
🧵...
Yeehaw! 🤠 @isbscience.org
In these dark times, let the joy of scientific discovery and trainee success be your balm ❤️🩹
🧵...
Reposted by Travis Gibson
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!
youtube.com/playlist?lis...
Thanks to all who helped make it happen!
2025 ISB Microbiome Symposium - YouTube
The 2025 ISB Microbiome Symposium was a virtual scientific event hosted by the Institute for Systems Biology (ISB) on December 12, 2025. The symposium brough...
youtube.com
December 17, 2025 at 4:34 PM
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!
youtube.com/playlist?lis...
Thanks to all who helped make it happen!
Reposted by Travis Gibson
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-...
It's free! Recordings of the talks will be available afterwards.
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
December 10, 2025 at 4:50 PM
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-...
It's free! Recordings of the talks will be available afterwards.
isbscience.org/events/2025-...
Reposted by Travis Gibson
#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...
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
#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...
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...
Reposted by Travis Gibson
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
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...
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
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...
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
Im working on something and I am reminded of one of the wildest correspondences ever published www.nature.com/articles/nbt...
Reposted by Travis Gibson
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-...
📌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
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-...
📌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-...
Reposted by Travis Gibson
Our paper is now open access as well.
🚨 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...
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 29, 2025 at 4:23 PM
Our paper is now open access as well.
Reposted by Travis Gibson
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).
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
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).
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).
Reposted by Travis Gibson
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...
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
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...
This collection is a joint effort with @naturemedicine.bsky.social @natcomms.nature.com and @commsbio.nature.com
#MicroSky #MicrobiomeSky 🦠⚕️🧪⚕️
www.nature.com/articles/s41...
Reposted by Travis Gibson
🚨 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...
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
🚨 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...
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...
Reposted by Travis Gibson
"Longitudinal profiling of low-abundance strains in microbiomes with ChronoStrain" - Kim et al.
rdcu.be/ekTwf
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
"Longitudinal profiling of low-abundance strains in microbiomes with ChronoStrain" - Kim et al.
rdcu.be/ekTwf
rdcu.be/ekTwf
Reposted by Travis Gibson
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
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
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
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
Reposted by Travis Gibson
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/
- 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
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/
- Biological sequence models (theory, design, and application)
- Learning single cell dynamics
- Bacteriotherapy design, “bugs-as-drugs” (using control theory principles)
gibsonlab.io/openings/
Reposted by Travis Gibson
We are still accepting registrations for this event! Please come join us and hear about cutting edge microbiome research.
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
We are still accepting registrations for this event! Please come join us and hear about cutting edge microbiome research.
Reposted by Travis Gibson
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 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
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 by @amydwillis.bsky.social and @davidandacat.bsky.social
www.nature.com/articles/s41...
Reposted by Travis Gibson
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...
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
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...
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...
Reposted by Travis Gibson
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...
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
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...
www.nature.com/articles/s41...
Reposted by Travis Gibson
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
Join us in LA this March!
Are regret based adaptive control strategies deployable?
arxiv.org/abs/2501.04572
arxiv.org/abs/2501.04572
January 9, 2025 at 2:38 PM
Are regret based adaptive control strategies deployable?
arxiv.org/abs/2501.04572
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...
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
This post has saved hours when trying to get old x86 bioinformatics pipelines working on Mac arm64 (like pplacer)
stackoverflow.com/questions/64...
stackoverflow.com/questions/64...
Reposted by Travis Gibson
It’s easy to think this is about politics, but Ran’s actually just subtweeting my working style
"There are decades where nothing happens, and weeks where decades happen"
December 8, 2024 at 6:16 PM
It’s easy to think this is about politics, but Ran’s actually just subtweeting my working style