Samantha Graham
@samanthagraham.bsky.social
Postdoc at Brigham and Women's Hospital studying COPD | she/her | spgraham1.github.io
Pinned
Integration of 168,000 samples reveals global patterns of the human gut microbiome
The Human Microbiome Compendium is a unified database of publicly available human
gut microbiome 16S samples, built with the integrated data from hundreds of independent
projects. The compendium is us...
www.cell.com
We’re thrilled that our first paper on the Human Microbiome Compendium, an integrated dataset of over 168,000 uniformly processed human gut microbiome samples, is officially out today in Cell! @richabdill.com @blekhman.bsky.social www.cell.com/cell/fulltex...
why would I use snakemake when I can simply write a python script to write 51 job scripts and then write a for loop in bash to submit them?
November 11, 2025 at 9:07 PM
why would I use snakemake when I can simply write a python script to write 51 job scripts and then write a for loop in bash to submit them?
Reposted by Samantha Graham
🧬 🦠 🏙️
Urban vs rural lifestyles create dramatically different gut microbiomes. But how do these different gut microbiomes affect the host?
Excited to share our new paper: www.biorxiv.org/content/10.1...
Urban vs rural lifestyles create dramatically different gut microbiomes. But how do these different gut microbiomes affect the host?
Excited to share our new paper: www.biorxiv.org/content/10.1...
November 5, 2025 at 2:04 AM
🧬 🦠 🏙️
Urban vs rural lifestyles create dramatically different gut microbiomes. But how do these different gut microbiomes affect the host?
Excited to share our new paper: www.biorxiv.org/content/10.1...
Urban vs rural lifestyles create dramatically different gut microbiomes. But how do these different gut microbiomes affect the host?
Excited to share our new paper: www.biorxiv.org/content/10.1...
Reposted by Samantha Graham
Another review from my lab out this week, on analyzing gut microbiome data from global populations -- tackling computational challenges and providing practical frameworks and resources for the field
With Sabrina Arif, @richabdill.com, @samanthagraham.bsky.social
www.cell.com/trends/micro...
With Sabrina Arif, @richabdill.com, @samanthagraham.bsky.social
www.cell.com/trends/micro...
Analyzing human gut microbiome data from global populations: challenges and resources
Research on the human gut microbiome is expanding rapidly; yet, most published studies
focus on populations from high-income regions such as North America and Europe. Underrepresentation
of population...
www.cell.com
June 18, 2025 at 10:12 PM
Another review from my lab out this week, on analyzing gut microbiome data from global populations -- tackling computational challenges and providing practical frameworks and resources for the field
With Sabrina Arif, @richabdill.com, @samanthagraham.bsky.social
www.cell.com/trends/micro...
With Sabrina Arif, @richabdill.com, @samanthagraham.bsky.social
www.cell.com/trends/micro...
Reposted by Samantha Graham
Interested in microbiome GWAS and heritability studies? Check out our new Review in Nature Reviews Genetics! We explore key findings, challenges, and future directions of the field.
rdcu.be/epoRR
@blekhman.bsky.social @sambhawa.bsky.social and Dr. Kelsey Johnson.
rdcu.be/epoRR
@blekhman.bsky.social @sambhawa.bsky.social and Dr. Kelsey Johnson.
Genomics of host–microbiome interactions in humans
Nature Reviews Genetics - In this Review, Ferretti et al. discuss advances in our understanding of interactions between the human genome and the microbiome, including the effects of the microbiome...
rdcu.be
June 4, 2025 at 4:52 PM
Interested in microbiome GWAS and heritability studies? Check out our new Review in Nature Reviews Genetics! We explore key findings, challenges, and future directions of the field.
rdcu.be/epoRR
@blekhman.bsky.social @sambhawa.bsky.social and Dr. Kelsey Johnson.
rdcu.be/epoRR
@blekhman.bsky.social @sambhawa.bsky.social and Dr. Kelsey Johnson.
Reposted by Samantha Graham
We wrote up the process we've developed for processing microbiome data in bulk! Workflow management tools are miraculous for processing a project with lots of samples, but when you have lots of *projects* too, as we do when pulling data from NCBI databases, it gets hard to juggle. #microbiomesky
Compendium Manager: a tool for coordination of workflow management instances for bulk data processing in Python
Compendium Manager is a command-line tool written in Python to automate the provisioning, launch, and evaluation of bioinformatics pipelines. Although workflow management tools such as Snakemake and N...
arxiv.org
May 19, 2025 at 7:40 PM
We wrote up the process we've developed for processing microbiome data in bulk! Workflow management tools are miraculous for processing a project with lots of samples, but when you have lots of *projects* too, as we do when pulling data from NCBI databases, it gets hard to juggle. #microbiomesky
Reposted by Samantha Graham
Last week @richabdill.com and @samanthagraham.bsky.social's paper was featured on the cover of Cell!
The cover, portraying microbes on shelves shaped like a world map, was possible thanks to the amazing team of illustrators at SciStories ✏️🦠
The cover, portraying microbes on shelves shaped like a world map, was possible thanks to the amazing team of illustrators at SciStories ✏️🦠
February 26, 2025 at 3:37 AM
Last week @richabdill.com and @samanthagraham.bsky.social's paper was featured on the cover of Cell!
The cover, portraying microbes on shelves shaped like a world map, was possible thanks to the amazing team of illustrators at SciStories ✏️🦠
The cover, portraying microbes on shelves shaped like a world map, was possible thanks to the amazing team of illustrators at SciStories ✏️🦠
Reposted by Samantha Graham
These are challenging times for science, but I'm happy to share a bright moment: our work is on the cover of Cell today.
We built a compendium of human gut microbiomes integrating 168K worldwide samples, revealing patterns of microbiome variation across the globe
www.cell.com/cell/current...
We built a compendium of human gut microbiomes integrating 168K worldwide samples, revealing patterns of microbiome variation across the globe
www.cell.com/cell/current...
February 20, 2025 at 4:06 PM
These are challenging times for science, but I'm happy to share a bright moment: our work is on the cover of Cell today.
We built a compendium of human gut microbiomes integrating 168K worldwide samples, revealing patterns of microbiome variation across the globe
www.cell.com/cell/current...
We built a compendium of human gut microbiomes integrating 168K worldwide samples, revealing patterns of microbiome variation across the globe
www.cell.com/cell/current...
Reposted by Samantha Graham
Use the Human Microbiome Compendium data!
We made the data and code available, & created a website and R package to navigate the compendium. Links:
- Website: microbiomap.org
- Data: zenodo.org/records/1373...
- R package: blekhmanlab.github.io/MicroBioMap/
- Code: github.com/blekhmanlab/...
We made the data and code available, & created a website and R package to navigate the compendium. Links:
- Website: microbiomap.org
- Data: zenodo.org/records/1373...
- R package: blekhmanlab.github.io/MicroBioMap/
- Code: github.com/blekhmanlab/...
January 24, 2025 at 2:50 AM
Use the Human Microbiome Compendium data!
We made the data and code available, & created a website and R package to navigate the compendium. Links:
- Website: microbiomap.org
- Data: zenodo.org/records/1373...
- R package: blekhmanlab.github.io/MicroBioMap/
- Code: github.com/blekhmanlab/...
We made the data and code available, & created a website and R package to navigate the compendium. Links:
- Website: microbiomap.org
- Data: zenodo.org/records/1373...
- R package: blekhmanlab.github.io/MicroBioMap/
- Code: github.com/blekhmanlab/...
We’re thrilled that our first paper on the Human Microbiome Compendium, an integrated dataset of over 168,000 uniformly processed human gut microbiome samples, is officially out today in Cell! @richabdill.com @blekhman.bsky.social www.cell.com/cell/fulltex...
Integration of 168,000 samples reveals global patterns of the human gut microbiome
The Human Microbiome Compendium is a unified database of publicly available human
gut microbiome 16S samples, built with the integrated data from hundreds of independent
projects. The compendium is us...
www.cell.com
January 22, 2025 at 5:31 PM
We’re thrilled that our first paper on the Human Microbiome Compendium, an integrated dataset of over 168,000 uniformly processed human gut microbiome samples, is officially out today in Cell! @richabdill.com @blekhman.bsky.social www.cell.com/cell/fulltex...
attempting to start posting on here as I (hopefully) wrap up my PhD in the next several months, both about science and my one true passion--taking pictures of peanut butter sandwiches on hikes
December 6, 2024 at 1:55 AM
attempting to start posting on here as I (hopefully) wrap up my PhD in the next several months, both about science and my one true passion--taking pictures of peanut butter sandwiches on hikes