Adarsh Singh

Thrilled to see this project come to fruition! It has been an outstanding collaboration, yielding numerous valuable findings. Congratulations to all involved!

Happy to share that our study on gut microbiome associations with colorectal cancer (CRC) is out in @NatureMedicine! (doi.org/10.1038/s41591…).

Immunoglobulin A controls intestinal virus colonization to preserve immune homeostasis @cellhostmicrobe cell.com/cell-host-micr… @BanaJabri

Congrats to @CornellEng @CornellBME faculty @ilanabrito123 , named a 2024 @pewhealth Innovation Fund Investigator, working with Gabriel Victoria, Ph.D. of The Rockefeller University to unravel interactions between immune cells and the gut. bme.cornell.edu/news/brito-nam…

"Gut #microbiome strain-sharing within isolated village social networks," a @Nature study @NAChristakis @chocophlan @mqdicer @ShivkumarVs @DrewPrinster @adarshsingh110 @eairoldi @ilanabrito123 #Microbiota👇 nature.com/articles/s4158…

In case you missed it - out now in @Nature: Gut microbiome strain-sharing within isolated village social networks @NAChristakis @chocophlan @JacksonPullman1 @mqdicer @ShivkumarVs @DrewPrinster @adarshsingh110 @eairoldi @ilanabrito123 nature.com/articles/s4158…

Ticks make their own bioglue in their saliva to help them attach to and seal skin! It's an IDP, like the freshwater mussel adhesive I previously posted. No data yet on how it compares in terms of performance, so I guess we'll have to make it! biorxiv.org/content/10.110…

The bacteria in your gut depend on where you are in the social network. And the microbes within us treat our social networks as the extended environment in which they thrive. They can spread from person to person. New #HNL work out today in @Nature. 1/

"Gut microbiome strain-sharing within isolated village social networks" nature.com/articles/s4158… with @chocophlan, @JacksonPullman1, @mqdicer, @ShivkumarVs, @DrewPrinster, @adarshsingh110, RM Juárez, @eairoldi, @ilanabrito123 #HNL 2/

Spatial structure shapes the host-microbiome interactome. Our new method to map the host-microbiome interface at high-res, now on bioRxiv! Co-led with @0707bibi & @dwmckellar collab between the @IwijnDeVlaminck & @ilanabrito123 labs doi.org/10.1101/2024.1… A thread⬇️

I had to write. It's been 2 years since I moved back to India. Here's I what I think about moving abroad. orkohunter.net/blog/why-dont-…

Looking for a postdoc position in nuclear #mechanobiology, with a strong interest in microfluidics, device design, fluorescence microscopy, and image analysis? Check out our opening: #lammerdinglabpostdoc" target="_blank" rel="nofollow noopener">bme.cornell.edu/bme/job-openin… If you are attending #BMES2024, we can meet there. Please RT.

A core microbiome signature as an indicator of health | Cell Metagenomics on a high-fiber dietary intervention plus reanalysis of 26 case-control studies. Identified a set of stably correlated genome pairs perturbed by interventions and diseases cell.com/cell/fulltext/…

It's Nobel week, so—after a break last year when this account became a Karikó stan account—I am reposting my annual plea to give Lipman and Myers a Nobel Prize for creating BLAST substack-proxy.glitch.me/articles/luisp…

Gut bacteria identified which can degrade IgA. Read more here science.org/doi/10.1126/sc… and in this Perspective science.org/doi/10.1126/sc…

🤩 Abstract submission and early registration for the #ISEV2025 Annual Meeting are now open! 🎼 Submit your abstracts before November 3rd: buff.ly/4e8W0Xu @albers_eva @AnHendrix2 @editbuzas @LLanguino @LeeRetinaLab

Why are bioinformatics results so full of false positives? I've been thinking about this for a few years: the incentives in the field are to produce false positives (link in next tweet)

Our team's efforts in bio-imaging in live animals has been published on Science. If you are interested in our work, feel free to reach out to me and I am happy to chat and discuss future potentials! science.org/doi/10.1126/sc…

I'm going to keep saying this until someone proves me otherwise: AlphaFold(2, 3, 10000, whatever) or any structure prediction tool will not generalize to protein conformations if its training is optimized to "ground truth" structures in the PDB! Crystallized or cryo-EM structures are NOT ground truth: they are artificially-constrained, single conformations in a physiologically irrelevant environment. 👎 Perturbing these structures via MD or diffusion won't magically generate possible alternate conformations either. Those resulting poses are also artificial and likely wrong. This amazing paper, I believe, supports my point. This is also my gripe about training language models with structural tokens -- those are biased pieces of knowledge that inhibit design and modeling of conformationally and functionally diverse proteins operating in complex cellular environments. 🙄 However, I have to give credit to the ESM3 team for balancing loss on sequence, structure, and function during training. If you want to work on static proteins, go ahead, use these tools, use structure -- you'll probably get some working designs or semi-trustworthy models. 🤷‍♂️But we need a more first-principle, unbiased approach to modeling conformationally dynamic structures. I know a lot of people disagree with me on this. I like pLMs because at least we're not making assumptions (MLM is as basic as you get), and some signal should be trustworthy if evolution is indeed meaningful, but I agree that we need better training paradigms that correct evolutionary inconsistencies (can't be using ESM-2 forever). We'll keep pushing on this for out-of-distribution but important target classes. 😬 Alright, that's my rant for the week. We have some exciting works coming out soon though, so hope you'll stay tuned to our work. 🤗 Paper: nature.com/articles/s4146… (Beautiful) Benchmarking Code/Results: github.com/ncbi/AF2_bench…

To help address the antimicrobial resistance crisis, there are hundreds of very promising antibiotic candidates found hiding in our microbiome cell.com/cell/fulltext/… @CellCellPress @delafuenteupenn