Gibson Lab
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gibsonlab.io
Gibson Lab
@gibsonlab.io
29 followers 2 following 5 posts
We leverage tools from machine learning and control theory to advance our understanding of biological systems. (Harvard Medical School | Brigham and Women's Hospital)
PI: @travis.gibsonlab.io
Website: gibsonlab.io
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Gibson Lab @gibsonlab.io · May 6
"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
Reposted by Gibson Lab
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
Reposted by Gibson Lab
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
gibsonlab.io
Our paper is now open access as well.
May 29, 2025 at 4:23 PM
Reposted by Gibson Lab
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
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
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
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