Gibson Lab

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

Our paper on strain tracking is now open access. nature.com/articles/s4156…

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

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/10.1101/2023.0…

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/controlmicrobi…

Congrats to @dannnmacdonald on his @NSERC_CRSNG Banting Postdoctoral Fellowship! banting.fellowships-bourses.gc.ca/en/app-dem_ove…

Official Job Posting partners.taleo.net/careersection/…

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-facu…. 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/events-all/gen…

New lab logo 𝔾 Thoughts?

“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/10.110… 🧵

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/events-all/dyl…

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/10.110…

ABC Seminar “Contamination and genomic variability in microbiome data” - @tkorem (Tal Korem) Today! April 24 @ 4:00 pm - 5:00 pm EST Follow link for zoom information and calendar reminder comp-path.bwh.harvard.edu/events-all/tal…

Happening in one hour

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/events-all/uth…