Gibson Lab @harvardmed & @brighamresearch | ML and control for biology | PI: @travisegibson
Boston, MA
Joined July 2015
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"Longitudinal profiling of low-abundance strains in microbiomes with ChronoStrain" - Kim et al.
rdcu.be/ekTwf
Gibson Lab retweeted
See you @iclr_conf , poster session 2, April 23rd in the afternoon
"On the stability of gradient descent with second order dynamics for time-varying cost functions"
"Learning ecosystem-scale dynamics from microbiome data with MDSINE2"
We have also included two of the densest longitudinal microbiome studies to date with "humanized" mice (healthy and UC human donor). 76 sample per mouse over 65 days. 16S and qPCR
nature.com/articles/s41564-0…
Gibson Lab retweeted
Out Now! Learning ecosystem-scale dynamics from microbiome data with MDSINE2 bit.ly/3K0yguN #Microbiome #BayesianStatistics #EcosystemDynamics
Gibson Lab retweeted
A nice blog post by MGB on our work nature.com/articles/s41564-0… can be found here mgriblog.org/2025/08/04/copy…
Our paper on strain tracking is now open access.
nature.com/articles/s41564-0…
Several Postdoc Fellow openings. All fellows have triple appointment at HMS,BWH, and Broad
- Biological sequence models
- Learning single cell dynamics
- Bacteriotherapy design, “bugs-as-drugs”
more details: gibsonlab.io/openings/
If you like our work and want to join please reach out!
Two abstracts #cshlmbiome @cshlmeetings
Dynamical systems inference for learning the rules of microbial colonization
-@dannnmacdonald
Oral: Thursday 9AM
Direct, noninvasive single molecule measurements reveal the gut microbiome to be a shock absorber
-Utkarsh Sharma
Poster #195
Two abstracts #cshlmbiome @cshlmeetings
Dynamical systems inference for learning the rules of microbial colonization
-@dannnmacdonald
Oral: Thursday 9AM
Direct, noninvasive single molecule measurements reveal the gut microbiome to be a shock absorber
-Utkarsh Sharma
Poster #195
Updated our pre-print: Strain tracking with uncertainty quantification
Better benchmarking- strains are mutated before including them in the database, comparator method added, real dataset added that has WGS isolates, and model improvements.
Take a look
doi.org/10.1101/2023.01.25.5…
New Pre-print📄
"On the stability of second order gradient descent for time varying convex functions"
arxiv.org/abs/2405.13765
New opening in the lab for postdoc interested in
"Designing microbial communities using control theory principles"
gibsonlab.io/controlmicrobio…
Congrats to @dannnmacdonald on his @NSERC_CRSNG Banting Postdoctoral Fellowship! banting.fellowships-bourses.…
Official Job Posting
partners.taleo.net/careersec…
We are hiring a wet-lab research associate to work on multiplexed error-robust fluorescence in situ hybridization (MERFISH) and ultrasensitive single molecule array (Simoa) assay development in conjunction with David Walt's lab wyss.harvard.edu/team/core-f…. Reach out if interested.
We are hiring a wet-lab research associate to work on multiplexed error-robust fluorescence in situ hybridization (MERFISH) and ultrasensitive single molecule array (Simoa) assay development in conjunction with David Walt's lab wyss.harvard.edu/team/core-f…. Reach out if interested.
We are excited to host Dr. @GorinGennady fresh PhD from @lpachter Lab - @Caltech.
"Stochastic foundations for single-cell RNA sequencing"
Today Nov 20th
4PM EST - Zoom
zoom link with ability to join email list on announcement page
comp-path.bwh.harvard.edu/ev…
Gibson Lab retweeted
“Microbial dynamics inference at ecosystem-scale” - just revised
We have provided both a (Bayesian) model and, as a resource to the community, the most densely sampled microbiome time series to date (that we are aware of) with “humanized” mice
biorxiv.org/content/10.1101/…
🧵
ABC Seminar today at 11 AM est. Hybrid - Duncan Reid conference room.
Dylan Cable, MIT – “A statistical framework for characterizing cellular behavior in spatial transcriptomics”
comp-path.bwh.harvard.edu/ev…