@GibsonLab

Gibson Lab @harvardmed & @brighamresearch | ML and control for biology | PI: @travisegibson

 Boston, MA
gibsonlab.io
Joined July 2015
  • Tweets115
  • Following2.3K
  • Followers691
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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"
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Out Now! Learning ecosystem-scale dynamics from microbiome data with MDSINE2 bit.ly/3K0yguN #Microbiome #BayesianStatistics #EcosystemDynamics
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A nice blog post by MGB on our work nature.com/articles/s41564-0… can be found here mgriblog.org/2025/08/04/copy…

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...

nature.com
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“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/… 🧵

Microbial dynamics inference at ecosystem-scale

Dynamical systems models are a powerful tool for analyzing interactions, stability, resilience, and other key properties in biomedically important microbial ecosystems, such as the gut microbiome....

biorxiv.org
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Gibson Lab retweeted
Lynn Bry@see_anemone21 May 2023
Just released a pre-print of our in vivo work on central metabolic pathways supporting early gut colonization by C. difficile. Thanks to a great team at #BWH in the Mass. Host-Microbiome Ctr, #InstitutPasteur and #I2BC at U. Paris Saclay. biorxiv.org/content/10.1101/…

Central in vivo mechanisms by which C. difficile’s proline reductase drives efficient metabolism,...

Clostridioides difficile (CD) is a sporulating and toxin-producing nosocomial pathogen that opportunistically infects the gut, particularly in patients with depleted microbiota after antibiotic...

biorxiv.org
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Really excited to be giving a talk tomorrow at @BrighamWomens! I will discuss spatial algorithms for modeling gene expression Come watch tomorrow (Monday 3/27) at 10:30am, either in person or on Zoom 😊 Details: comp-path.bwh.harvard.edu/ev…
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With all the tech layoffs I thought I would share this open position in our division. "Research Scientist, Machine Learning for Microbiome" @harvardmed @BWHPath gerber.bwh.harvard.edu/resea…
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Congratulations to BSL alum @dannnmacdonald (now @GibsonLab) on the publication of YAPFHT (yet another paper from his thesis ;-) doi.org/10.1007/s13239-022-0…

Aneurysm Neck Overestimation has a Relatively Modest Impact on Simulated Hemodynamics

Cardiovascular Engineering and Technology - Overestimation of intracranial aneurysm neck width by 3D angiography is a recognized clinical problem, and has long been a concern for image-based...

link.springer.com
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What are we plotting? Wrong answers only
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Gut metabolites predict Clostridioides difficile recurrence dlvr.it/SRysYZ
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Out now: Longitudinal multi-omics analyses link gut microbiome dysbiosis with recurrent urinary tract infections in women. By Scott Hultgren, Ashlee Earl & colleagues. @colinworby @broadinstitute @hultgrenlab Read it here: rdcu.be/cMCqa nature.com/articles/s41564-0…
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Hi, I recently finished my PhD and am looking for a job in field of metagenomics and microbial ecology. I specialized in microbial foodwebs including bacteria, phytoplankton and viruses and with the special focus on genomics analysis of microbial eukaryotes. Please retweet. – at Carouge (GE), Suisse
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People in control article about me! @CSSIEEE ieeexplore.ieee.org/stamp/st…
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Gibson Lab retweeted
Lynn Bry@see_anemone11 Oct 2021
Our two papers defining commensal mechanisms of action to prevent, or worsen, C. difficile disease came out today in Cell Host and Microbe. Thanks to an innovative team of international collaborators! #Cdiff #Microbiome sciencedirect.com/science/ar… sciencedirect.com/science/ar…
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Gibson Lab retweeted
sina
@sinabooeshaghi7 Jun 2021
I'm giving a talk today at 4pm ET / 1pm PT on #scRNAseq preprocessing and analysis for the folks @BrighamWomens @harvardmed. All are welcome to join - zoom link below. gibsonlab.io/booeshaghi_talk…
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🦠 Abstract submission deadline EXTENDED. 🦠 Get your abstracts in by Friday 03/05 to join us for our first-ever virtual microbiome symposium! 💩microbiome2021.wordpress.com…

Abstract Submission

Abstract submission is now closed. Applicants can expect to hear back about their submissions shortly.

microbiome2021.wordpress.com
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Last semester we had our first forum on #AI, #ML - #Fairness & #Ethics - #Healthcare. This semester we will have another forum on the same subject with more focus on Ethics and Law as they relate to AI in Healthcare. Recommendations for Ethicists and Lawyers as speakers wanted.
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