Always exciting to see new theories develop on the history of our planet and moon! Gabi Serrato Marks, PhD massivesci.com/articles/moon-… via Massive Science

Josh Moore's comments on the scientific burden of the proliferation of vendor specific file formats. Open file formats are crucial for open science. #ISMBECCB2019

I've said it time and again: I think better at chalkboards, and it seems most mathematicians agree with me: nytimes.com/2019/09/23/sci…

Technology may change the world, but it is art that shows us the reflection of what we've wrought. bbc.com/reel/video/p07…

A very long time in the process, but Sumaiya's work on metabolic functional profiling of metagenomic reads finally came out!

.Cristina Vanko 💘 and I put together a non-mathy, hopefully accessible, summary of some of the mathematical ideas behind #flattenthecurve link.medium.com/8fS3k9UrZ4

Quarantine could be beautiful, y'all! Yun William Yu and I reconnected (after not seeing eachother in 10 years since Indiana University!) to bring you this non-mathy, hopefully accessible, summary of some of the mathematical ideas behind Flattening the Curve: medium.com/@yun.william.y…

Contact tracing is a key tool for combating COVID-19. We should absolutely be creating phone apps to do this at scale, but it's important to know that with modern cryptographic tools, we can get contact tracing without giving up all of our privacy. arxiv.org/abs/2003.11511

Physical distance, not social distance, is what we need to fight COVID-19. link.medium.com/hsvIFR2Y94

Always important to remember that while a good story is compelling, those stories may not be true. theguardian.com/books/2020/may…

Check out our work on balancing accuracy and privacy using probabilistic sketches for federated medical records. jmir.org/2020/11/e18735

My brilliant student Jim Shaw's latest unification of theory and application: proving theorems about k-mer distributions can have a real practical impact on read alignment.

Congratulations to my undergrad Ziye Tao on her upcoming ISMB/ECCB proceedings presentation/Bioinformatics publication on the expected 10-anonymity of HyperLogLog sketches! doi.org/10.1093/bioinf…

By using the older LogLog sketch, modern lattice cryptography libraries like Palisade let us perform secure federated count-queries across a network of institutions. Work by Alex Leighton

"Man, these scoring rules are really complicated." "I wonder if it's NP-hard." 4 years later, we've proven it. Presenting my paper with Yun William Yu, "Skiing is Easy, Gymnastics is Hard: Complexity of Routine Construction in Olympic Sports", in FUN '22. jameskoppel.com/files/papers/G…

Mora: abundance aware metagenomic read re-assignment for disentangling similar strains biorxiv.org/cgi/content/sh… #biorxiv_bioinfo

When we don't understand why heuristics work empirically, that just means we don't have enough theory yet. Jim's latest work proves that seed-chain-extend alignment actually has rigorous asymptotic bounds under average-case analysis.

I'm happy to announce that our web app SlowMoMan for discovering important features along user-drawn paths in a 2D embedding was accepted for presentation at GIW/ISCB-Asia. Credit to Kiran Deol, who did most of the actual work. biorxiv.org/content/10.110…

Me and Yun William Yu's new preprint on skani, a new tool for calculating ANI for metagenomic assembled genomes, is out. It's available on GitHub here: github.com/bluenote-1577/… 1/6

Turns out that properly calibrated sparse chaining can give you nearly all the benefits of alignment at a fraction of the cost! Brilliant work as always by Jim Shaw (who will shortly be on the job market, as an aside)