Adam Phillippy

For the past 30 years, “whole-genome sequencing” has been a misnomer. Today the T2T Consortium publishes a dozen papers heralding a future of truly complete genomes for humans and nearly any vertebrate 👨‍🔬🐒🐦🐀🦒🐎🫏🐹🐟 (sorry, no salamanders): www.cell.com/consortium/t... 🧵[1/15]

Half a century ago, King & Wilson proposed that humans differ from chimpanzees mainly through changes in gene regulation. In our new preprint, we used AlphaGenome to map such changes genome-wide, across tissues of the human body! www.biorxiv.org/content/10.6...

My department (UMD Computer Science) is hiring! If you're on the market, you should apply. LMK if you have any questions not answered in the ad. umd.wd1.myworkdayjobs.com/en-US/UMCP/d...

Are you keen to explore algorithmic and informatics approaches strengthening studies into genome biology?🧬 Join us 2-4 December for #GenomeInformatics26 - an established meeting for building global connections. 📍Wellcome Genome Campus, UK Register by 2 November👉 bit.ly/4bexmoH #AIinBiology

A telomere-to-telomere map of somatic mutation burden and functional impact in a cancer www.cell.com/cell/fulltex...

Must-see new tool from me and Alex! I hurt my back a few weeks ago and was confined to the couch. I used my "break" to play around with webassembly and ended up vibe-coding an AMAZING interactive dotplotter. Passed my prototype to Alex to clean up and extend. Check out his release thread!

Sweden's long-read genomics ecosystem is here!🧬🇸🇪 Our new preprint demonstrates how population-scale sequencing can be combined with clinical diagnostics. Aggregated SNV, SV and TR frequency data based on 576 Swedish individuals now available here: swefreq.nbis.se/dataset/GoS

Johns Hopkins Biology is hiring a tenure-track Assistant Professor in computational genetics and genomics. Applications due Nov. 8th: apply.interfolio.com/194924 In my experience, this has been an incredibly supportive environment to build a lab. Please feel free to reach out with any questions.

Here's the ad for the Genome Sciences faculty positions ap.washington.edu/ahr/position...

Exciting news: @uwgenome.bsky.social will be hiring for two tenure-track faculty positions this year, one open rank and one assistant professor. Both are “Genome Sciences” interpreted broadly so we welcome applicants working in a variety of fields and methods. Ad will be out shortly.

Happy to share results of the @bat1kgenomes.bsky.social phase 1, providing reference genomes covering 21 bat families. New insights into bat phylogeny, ancestral genome reconstruction, European origin & ancestral echolocation. Great work by a team of 100+ colleagues www.nature.com/articles/s41...

“Complete, personalized genomes are now possible for anyone,” says senior author @aphillippy.bsky.social.

What can we learn about a single rare variant? Published today in Science: the 23andMe Research Institute and Dana-Farber studied the EGFR T790M in 10.1M 23andMe research participants. The variant has OR = 25.2 for lung cancer, rising to 61.7 in never-smokers(!). 🧵

It's time to bring complete genome sequencing to the clinic 🧬🩺 Less than 5 years after first sequencing a human genome from end to end, @khmiga.bsky.social, @aphillippy.bsky.social & the #T2T team are making complete sequencing practical for personalized medicine. 🔗 news.ucsc.edu/2026/09/brin...

Infertility affects ~1 in 6 people, and up to 30% of cases are unexplained. I am excited to present my postdoctoral work from @toddmacfarlan.bsky.social 's lab, now available as a preprint: tinyurl.com/yync6f2r addressing a possible role for the meiotic gene PRDM9 in infertility 🧵/1

Everything you wanted to know about single-molecule epigenomics but were too afraid to ask! Wonderful to co-write (h/t ENORMOUS lift by @arnaudkr.bsky.social) this primer on our nascent field. Also, a 💯 example of wonderful colleagues building something *together*, not in competition =)

Scientists including @aphillippy.bsky.social, @mikeschatz.bsky.social, & @stevensalzberg.bsky.social have reconstructed the complete genome of a real person, a breakthrough expected to advance research, improve the diagnosis of genetic diseases, & make personalized genomics routine in medical care.

Reposting this ongoing search (any discipline of biology) for an Assistant to Associate level colleague in the Division of Basic Sciences at Fred Hutch. Great city, great colleagues, great core facilities, great trainees.

Interested in pursuing a PhD in computer science? Join us next week for a virtual info session! Details here: www.cs.jhu.edu/event/phd-pr...

I am delighted to announce that The Department of Human Genetics at the University of Utah is continuing a multi-year recruiting initiative for multiple tenure-track faculty positions at the rank of Assistant Professor. Please share and consider applying! utah.peopleadmin.com/postings/208...

Dangit but sciencing is fun. Discovered a >>10Mb pericentromeric inversion that looks like it adaptively introgressed and is a massive QTL for disease resistance. Preliminary and could be totally wrong, but holy bleep it's been a fun 90 minutes working this out (we had suspected much of this).

If you are thinking of applying to the @uwgenome.bsky.social PhD program this fall, we have a couple of zoom info sessions set up for Oct 6 and Oct 22. Please register at the link. Our website also has a ton of useful information about crafting your application. www.gs.washington.edu/news/graduat...

🧬 Why do high-quality reference genomes matter? Draft genomes can contain gaps, errors and fragmented sequences — potentially hiding important biology. 💻🧬 High-quality references give us a clearer, more complete picture — and a stronger foundation for discovery. #Genomics #EarthBioGenomeProject

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/

Long-read sequencing reveals pre-meiotic gene conversion in sperm www.nature.com/articles/s41...

On our last day, the lab ran a pop-up coffee shop for our NHGRI colleagues, staffed by our own highly experienced baristas Suhani and Serge. Farewell NIH! Thanks for being a great home for the past 11 years 🥲 Watch for our next pop-up at Hopkins once we get properly equipped 😁

Biological Databases are critical infrastructure - not projects. As so much effort is put into harnessing AI to solve all our problems, we are allowing the foundational data resources crumble. Treat biological databases as infrastructure, not projects www.nature.com/articles/d41...

I am delighted to present with @hannespetur.bsky.social our new study on the Icelandic pangenome reference HPRC-ICE. This work goes all the way from pangenome construction to disease association! (1/7) www.nature.com/articles/s41...

Our vole preprint is officially published in Cell Genomics @cellpress.bsky.social as part of the T2T special issue! www.cell.com/cell-genomic... Lead author @mabuelanin.bsky.social also built this amazing website that we hope will be a useful resource to the vole community: voles.dennislab.org 🐭

📢 Applications are now open for the NIH Stadtman Tenure-Track Investigator Program! We're recruiting early-career scientists across all areas of biomedical research for tenure-track faculty positions in the NIH Intramural Research Program. Deadline: Sept 30, 2026. 🔗 tinyurl.com/stadtman26

NHGRI is recruiting genomics oriented researchers through the Stadtman mechanism. It is also open to any kind of research, the goal is to match your interests to an institute. The applications are now open until Oct. 1st. Details below:

🧬 The VGP Phase I preprint is out! 🎉 The Vertebrate Genomes Project has completed Phase I, delivering 816 of the highest-quality vertebrate reference genomes ever produced. Explore this major new resource for vertebrate genomics: 📄 tinyurl.com/VGPphase1 @vertebrategenomes.bsky.social #Genomics

new preprint from our group led by Talleh Almelli -- important for folks doing single cell on malaria parasites or other organisms with hyperdiverse gene families. www.biorxiv.org/content/10.6...

New issue alert👉https://cell.com/cell/current On the cover: The Telomere-to-Telomere Consortium has finished the complete, diploid genome of a person. The cover is inspired by a karyotype of the chromosomes in metaphase, representing the two haplotypes as different colors.

We are excited to officially share the first fully phased telomere-to-telomere (T2T) reference genome for a songbird! 🐦 www.cell.com/cell/fulltex...

📣😮BIG release in @cellpress.bsky.social today!!! When @khmiga.bsky.social and @aphillippy.bsky.social led the completion of a single human genome in 2022, it was a milestone. Completing them routinely is a revolution. Welcome to a new era for personalized medicine.

#zebrafish genome update. UCSC has added both GRCz12tu and GRCz12ab to the zebrafish pulldown menu making it much easier to find the new assemblies!

Here's a fact that may surprise you. Until recently, nobody had managed to sequence the complete genome of a human being. Then, a landmark paper in 2022 reported end-to-end (telomere-to-telomere) coverage of all chromosomes. The new era of T2T genomics is showcased today in @cp-cell.bsky.social: 🧬🧪👇

I was honoured to make a small contribution to this paper published today in Cell, detailing the first T2T genome assembly of the zebra finch, a crucial model species for neurobiology: tinyurl.com/tguttata

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/