I spend a lot of time thinking about this problem for myself--would adopting AI more broadly make me a more productive researcher, or would it keep me from developing the knowledge and skills I want to learn?

Ran Blekhman@blekhman.bsky.social · last mo.

"All of this is already happening. We’re seeing the leading edge of AI-native students who have produced a ton of papers but, when challenged intellectually at the interview, falter and ultimately don’t get hired" eytanadar.medium.com/ai-native-ph...

1. We—@eduede.bsky.social, @mjcrockett.bsky.social, Kevin Gross, and I—have a new preprint on the arXiv today, based on ideas that emerged during an @sfiscience.bsky.social workshop in November 2024: The unintended consequences of large language models as a labor-augmenting technology in science.

The unintended consequences of large language models as a labor-augmenting technology in science

As a labor-augmenting technology, large language models (LLMs) have the potential to accelerate scientific activity across the research pipeline. But even if LLMs perform on par with human experts at ...

arxiv.org

memorial day hike in the white mountains. The beautiful blue sky and views in the second pic lasted for all of 5 minutes of the 6+ hour hike 🙃

Excited to share our new study out in Nature Communications. We mapped the composition of the human breast #milk #microbiome and showed that microbes present in breast milk directly contribute to the assembly of the #infant gut microbiome in the first months of life. www.nature.com/articles/s41...

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...

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...

cell.com

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.

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

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

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/...

Human Microbiome Compendium

An ongoing project to build a dataset of the human microbiome at an unprecedented scale.

microbiomap.org

Ran Blekhman@blekhman.bsky.social · 2y ago

Today we report a new compendium of human gut microbiomes with >168,000 samples By analyzing this massive dataset, we discovered distinct microbiome patterns across the globe, and show we can predict where a person lives just from their gut bacteria Now out in Cell: www.cell.com/cell/fulltex...

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...

cell.com

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