Gibson Lab

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.

A nice blog post about our work www.nature.com/articles/s41... can be found here mgriblog.org/2025/08/04/c...

05.08.2025 00:36 — 👍 1    🔁 1    💬 0    📌 0

If you have the slightest bit of trouble using this please reach out. Would also be cool to see if we can track phages, or incorporate de novo assembly of novel genes jointly with the rest of the model.

30.05.2025 14:36 — 👍 0    🔁 0    💬 0    📌 0

Our paper is now open access as well.

29.05.2025 16:23 — 👍 4    🔁 1    💬 0    📌 0

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...

🚨 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...

06.05.2025 18:54 — 👍 41    🔁 29    💬 0    📌 2

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...

"Longitudinal profiling of low-abundance strains in microbiomes with ChronoStrain" - Kim et al.

rdcu.be/ekTwf

06.05.2025 16:27 — 👍 1    🔁 1    💬 0    📌 0

Openings Positions available in the Gibson Lab

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/

17.04.2025 14:02 — 👍 2    🔁 1    💬 0    📌 0

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...

07.02.2025 16:35 — 👍 2    🔁 1    💬 0    📌 0