FastGA: Fast Genome Alignment biorxiv.org/content/10.110…

🧵1/n Estimating mutation rates using k-mers is fast—but what happens when repeats dominate the genome? In a new preprint, Haonan Wu, Antonio Blanca, and myself propose a *repeat-aware* estimator that's accurate even in centromeres.

Preprint on "Finding easy regions for short-read variant calling from pangenome data": arxiv.org/abs/2507.03718

Interested in a tool that aligns millions of proteins in minutes with quality similar to or better than the state-of-the-art utilities? Please take a look at our FAMSA2 paper: biorxiv.org/content/10.110… and GH repo: github.com/refresh-bio/FA…

Ooh look, now I know what to get (((Dan Graur))) ダン דן גראור 🇮🇱🇺🇸🇺🇦✌️🖖 and Homolog.us for Christmas. academic.oup.com/book/60710

I started a Substack with a focus on literature and art. My first post there explains my reasons for doing this. For anyone interested, you can subscribe to it here lyongholson.substack.com/?r=1nn6o5&utm_…

Now published in GigaScience with minor improvements: academic.oup.com/gigascience/ar… * Download: zenodo.org/records/149035… * More info: github.com/lh3/panmask

minimap2.com is potentially a phishing site. Please don't use anything from that website. github.com/lh3/minimap2/i…

Now preprinted at arxiv.org/abs/2509.07357

New #metagenome assembly comparison of PacBio, ONT, and Illumina in gut #microbiomes. - "HiFi generated more cMAGs than ONT at every depth with either assembly method" - "HiFi cMAGs had significantly higher completeness and lower contamination than ONT" doi.org/10.1016/j.cell…

#1 New Release in Social Philosophy on amazon: Investing In Revolution amzn.to/48qqggX

Terence Tao is exaggerating his woes and making political statements - pointing to his suspended NSF grant covering summer salary as proof of collapse. It’s absurd that a university with billions in revenue can’t cover three months of pay for one of its employees. The

The damage to research and academic integrity at universities began long before Terence Tao started complaining. His silence then was complicity. I’ve received a lot of pushback for saying this — much of it mean-spirited and ad hominem — so I’ll simply ignore and block the

RIP Jim Watson. A reminder that even those who built the modern scientific enterprise are no longer protected by the institutions they helped create. I met Jim Watson a couple of times over the years as he became interested in some of the research I was doing. On every

I am looking for a postdoc to develop high-performance algorithms in computational genomics. Email or DM me if interested. For more information, see hlilab.github.io/vacancies. RTs appreciated!

what? Jay Bhattacharya, MD, PhD and NIAID director Jeff Taubenberger's "new vision" is published behind a paywall? After Jay Bhattacharya, MD, PhD announced last year that all NIH-funded work had to be immediately available and free?

Thrilled to share our labor of love over the last 5 years! Leveraging long-read metagenomics we identified several previously unknown phage families that are highly prevalent in the human gut microbiome. Lead by Hanrong Chen [1/5] biorxiv.org/content/10.648…

#icanhazpdf #canIhazpdf Please email [email protected]. Thanks in advance. nature.com/articles/s4158…

Coding with AI - It Speeds You Up and Then Slows You Down (homolog.us/blogs/bioinfo/…)

"Really good people are not motivated by a need for security. They’re motivated by making intellectual breakthroughs" hbr.org/2014/09/j-crai…