Adam M Novak

Awesome @humanpangenome.bsky.social workshop at #ASHG26 🎉Thank you to everyone who participated!

I’m hiring a postdoc at Cambridge again! Work on privacy-preserving human pangenomes at the intersection of statistics, graph algorithms, optimization, differential privacy & computational genomics. Please spread the word! www.jobs.cam.ac.uk/job/57231/

In human genomics we see Epstein-Barr Virus all the time. It's used to immortalize cell lines. It even gets a fake chromosome in the human reference to suck up DNA reads from the virus. I don't understand why we put up with this virus infecting everybody? We should stop it from doing that.

Shredtools is making it easier to explore regions across a pangenome by quickly finding matching genomic regions across hundreds of genomes. The tool can identify a gene region across 476 human genomes in approximately half a second.  Read more: www.biorxiv.org/content/10.6...

periodic reminder that Wizard Zines has an educational use policy if you want to use them in your university courses! wizardzines.com/education/

Always exciting to see software you work on mentioned in a sentence like "We were unable to identify the cause of these discrepancies". Congratulations and apologies to all the #vg users out there; we're so glad you manage exciting research like this because of/despite it.

Our article introducing Aardvark for variant benchmarking is now published in Genome Biology! “Aardvark: sifting through differences in a mound of variants” DOI: doi.org/10.1186/s130... GitHub: github.com/PacificBiosc... Follow along for some highlights… 1/N

Pangenome coordinates can be complex... Shredtools offers a new approach using exact matches to query pangenome data efficiently. Its tools can extract syntenic regions across hundreds of genomes, making pangenome-scale exploration more accessible. pubmed.ncbi.nlm.nih.gov/42465356/

Hello, human geneticist here. There is no scientific basis for attempts to define people in terms of “good” or “bad” genes - these are discredited views in service of racist ideologies. For consensus & concerns of experts in our field, see e.g. this 2020 statement from @geneticssociety.bsky.social:

We’ve sequenced a marmoset! Grad student @prajnahebbar.bsky.social & @benedictpaten.bsky.social led the effort, and expect it to enable scientists to learn more about genes that contribute to memory loss and Alzheimer's. 🔗https://news.ucsc.edu/2026/08/first-complete-marmoset-genome/

HPRC2: A human pangenome reference with near-complete coverage of common genetic variation https://www.biorxiv.org/content/10.64898/2026.07.21.739710v1

Since I only get a couple weeks to peer-review papers, what's happening to *my* papers for the several months they're in review at the journal?

🔥 Does switching to a pangenome reference actually improve your association study? We tested it, and the answer is yes, measurably. Our preprint is online now: "Pangenome-based human genome analysis improves trait association and genomic prediction": doi.org/10.64898/202...

Congratulations to Prof Richard Durbin, winner of the 2026 Genetics Society Medal! His pioneering work in computational genomics has transformed how we analyse and understand genome sequences.

Growing neurons from stem cells—in high school! 🧠 A Genomics Institute platform uses cloud-connected microscopes so students design real stem cell experiments remotely. New study shows it measurably boosts STEM identity, especially for Hispanic & first-gen students. news.ucsc.edu/2026/0...

This is awful to hear, describing how Sean Eddy (HMMER, infernal, pfam, rfam) has been defunded. The letter said his work "had been determined to be of absolutely no value to the US taxpayer, and therefore it was being specifically terminated," www.npr.org/2026/05/21/n...

“The message, very clearly, they’re sending is, do not speak out on behalf of Chinese postdocs. If you do, you’re going to pay a penalty...It seems pretty obvious that this is an attempt by the current administration to silence people that question their activities." — Roger Innes, IU AAUP member

#dna #captcha

We got "Help me write" in our #UCSC Google Docs and I really can't deal with its little text prompt flashing in and out at the cursor position whenever I stop typing in order to think. I told to our IT that it meaningfully interferes with my ability to write in Google Docs and they can't fix it.

I feel like this all the time when trying to generate code with Claude Code. I end up spending lots of time reviewing what are supposedly *my own* pull requests for terrible ideas. I want to be reading code written by people *better at it than I am*, and I'm definitely not.

Today, March 31st, is International Trans Day of Visibility. In an era of immense difficulty for the community, it can be hard to remember that Trans Day of Visibility is as much about positivity as it is about awareness and resistance.

Ever receive a BAM aligned to “GRCh38” and realize that could mean several different references? We just released ref-solver, a tool that identifies the reference genome behind BAM/CRAM/FASTA files by comparing sequence dictionaries to known builds. 🔗 whatsmygenome.fulcrumgenomics.com Read more 👇

it has been [0] days since I've tried to emulate 64-bit atomic operations using 32-bit atomic ops in a system with relaxed memory ordering

Bit different from our usual work A PhD applying metagenomics to identify microbial plastic degradation and metabolism, fully funded studentship (UK students only). www.findaphd.com/phds/project...

Our latest vg release introduces GBZ v2 with better compression for sequences. I originally assumed that the total sequence length in a pangenome graph would be similar to the size of the genome. This does not hold in the full HPRC graphs due to unaligned centromeres.

Looking for a postdoc to build my new lab at TGen (Phoenix, AZ) focused on pangenome methods for cancer and complex disease. Full stack — from pangenome assembly and compression to association studies and somatic variant discovery. Reach out if interested! guarracinolab.github.io#join

Native Bio has made the @nytimes.com for the second time. The #IDsov movement is a tidal wave....and a solution for these difficult times. “We are at a fork in the road. Do not choose hate & do not choose unsustainability.” ~ 21st Century Maxim, Author Unknown www.nytimes.com/2026/02/05/s...

Excellent piece about why race is not a biological category and how medical education needs to respond. www.bmj.com/content/392/...

Apply ASAP to be a "Genomics Senior Systems Architect" AKA Linux Herder at @ucscgenomics.bsky.social ! The first test is convincing www.ucsc.edu/careers/ to show you #job number 82880.

Are #redhat #quay.io Docker container builds down for anyone else? Mine are failing with no logs, and then my trigger gets "automatically disabled due to successive internal errors".

You find yourself in the middle of a fastq file. You see + and @ all over the place. How do you find the start of the current record?

Kiddo age 5: daddy you don't work, you just sit at the computer Kiddo age 12: dad you just write grants

SMBE2026 Symposium 21 | From genomic graphs to evolutionary insights: standardising pangenomes for population inference 📨 Abstract submission smbe2026.org/abstracts 📋 Programme details smbe2026.org/programme #SMBE2026

The scikit-bio paper in online in Nature Methods! Many thanks to our collaborators, community contributors and reviewers! We couldn’t have done it without you. www.nature.com/articles/s41... #Bioinformatics #OpenSource

I am just hearing that Rust contains a type `Infallible`. Its description, "The error type for errors that can never happen.", sounds like the tagline for someone's next startup. doc.rust-lang.org/std/convert/...

One day I will ... write out this database (in a graph orientated, Json compatible data format with Rust bindings). The one graph to rule them all (though @benedictpaten.bsky.social's Cactus graph is pretty darn close to the graph to rule them all from the genomics side)

I found a paper in the wild today where I couldn't click through to the cited references, because the DOIs for them appeared to have been sampled from a large language model instead of actually looked up, producing plausible-looking but wrong links.

SAVE THE DATE! Stoked to organize the 2026 Santa Cruz Developmental Biology Meeting with @rashmi-priya.bsky.social, @lowelab.bsky.social, and Shelbi Russell. Come learn about Biomedicine, Biomechanics, and the Biosphere, August 24-28, 2026. Registration dates, etc., coming soon! Please RT

Now available: vg 1.70.0 release, code name "Zebedassi," with a new "vg describe" tool for inspecting files. 🧪🧬🖥️ github.com/vgteam/vg/re...