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?

🧬 🦠 🏙️ 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...

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...

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.

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

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 ✏️🦠

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...

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’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