Adam Phillippy

With @burgesslab.bsky.social, not one, but TWO freshly caught T2T zebrafish reference genomes for the Tübingen and AB strains 🎣 🎣 🎉

Baym continues to make freakin' art. Must see thread/paper

Long-Read Sequencing Workshop The program will involve sessions on Genome Evolution, Genome Regulation, Transcriptomics, Rare Diseases, Common Diseases, and Viral and Microbial Genomes. Committed speakers include Adam Phillipy (NH...

Join us at this exciting Workshop on #LongReads with keynotes from @aphillippy.bsky.social @mydennis.bsky.social
co-organized by @christinebeck.bsky.social and Mark Adams @jacksonlab.bsky.social Register www.jax.org/longread
#RNA #genomics #bioinformatics #cancer #medicine #evolution #neuroscience

Congrats Zam! You should wear it around at conferences! If the royals do it, why not you? 😆🏅

Thanks for sharing, Erick!

‼️ There are an unprecedented number of Institute Director vacancies at the NIH and many of the application windows close this week or next, including ones that are essential to genomics research in the US including NHGRI, NLM/NCBI, and NIGMS. Please spread the word: hr.nih.gov/careers/open...

Was an abstract-selected talk on new work, rather than an invitation. Super bummed not to be there :(

Dozens of board members resign from big-data journal after mass staff firings More than three-fifths of the editorial board of a biomedical sciences journal resigned after the publication’s operations moved from Hong Kong to Shenzhen, China, and the editors and software team…

I was one of the Editorial Board Members at @gigascience.bsky.social who resigned from the Editorial Board.
🧪 🔓
⬇️
retractionwatch.com/2025/11/03/d...

Remembering Hamilton O. Smith Hamilton O. Smith August 31, 1931 – October 25, 2025 It is with profound sorrow that we announce the loss of Hamilton O. Smith, M.D., a...

My former mentor, colleague, and friend Hamilton Smith passed away this week. He was a giant in science, a Nobel Laureate, but also one of the nicest people you could ever meet. He will be missed by many. www.jcvi.org/media-center...

Editorial_Board Editorial Team Editor-in-Chief Xun Xu, PhD; BGI Research, Shenzhen, China Executive Editor Hongling Zhou; GigaScience Press, BGI Shenzhen, China Edito

About half the GigaScience editorial board (incl me) just resigned (academic.oup.com/gigascience/... is not yet updated). I resigned because it is very unclear what is happening and why - see @scedmunds.bsky.social blog post gigasciencejournal.com/blog/and-its..., for eg

Whole-genome sequencing reveals individual and cohort level insights into chromosome 9p syndromes - Genome Medicine Background Previous genomic efforts on chromosome 9p deletion and duplication syndromes have utilized low-resolution strategies (i.e., karyotypes, chromosome microarrays). These studies have provided ...

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WashU research news; excited to share our new paper on Chromosome 9p Syndromes 🧬 Hope you take the time to read it. Here is the link:
link.springer.com/article/10.1...

@washugenetics.bsky.social

Staff Scientist About EMBL-EBI EMBL’s European Bioinformatics Institute is a data powerhouse, utilised on a global scale to advance scientific discovery through bioinformatics and solutions to some of the world’s mos...

I am hiring! - looking for a Staff Scientist to co-run my research group with me. Staff Scientist is a senior professional scientist role at EMBL. Please forward to people you might know who could be interested! embl.wd103.myworkdayjobs.com/en-US/EMBL/j...

GitHub - lh3/dipcall: Reference-based variant calling pipeline for a pair of phased haplotype assemblies Reference-based variant calling pipeline for a pair of phased haplotype assemblies - lh3/dipcall

Here I am! Looks like you’re missing an L. Are you thinking of Heng’s dipcall? github.com/lh3/dipcall

Constellation illuminates rare disease genetics Despite significant advances in genomic sequencing, the resolution of many rare disease cases is still hindered by variant detection limitations. Short reads struggle in homologous regions, and long r...

We investigated Constellation from Illumina @bcmhgsc.bsky.social for rare disease cases @gregor-research.bsky.social from @bcmhouston.bsky.social.
We tested HG002-4 & sequenced 21 families. We could detangle complex SV & other interesting findings described here: www.medrxiv.org/content/10.1...

Population-scale Long-read Sequencing in the All of Us Research Program The All of Us Research Program (AoU) is a national biobank seeking to enroll one million individuals in the United States to link genomic and biomedical data, including short- and long-read whole-geno...

Read the preprint here with all the details, plus lots of other long-read powered analysis! www.medrxiv.org/content/10.1...

The T2T zebra finch genome has hatched! 🐣 🧬 @vertebrategenomes.bsky.social

For those interested in #Indigenous #Genomics and #ASHG25 in Boston, here are some interested posters/talks/events coming out of the Tsosie Lab, @nativebio.bsky.social, and @d4itdr.bsky.social. For those looking for Friday plans, attend our Ancillary Event, debuting a #Tribal #data repository!

Congrats Krystal and co!

Out today via @natgenet.nature.com, the first federally funded #Tribal #data repository, a revolutionary approach to data management and applied/operationalization of IDSov @d4itdr.bsky.social. Also, if you are at #ASHG25, come see us this morning in 205ABC
www.nature.com/articles/s41...

Human contamination in bacterial genomes has created thousands of spurious proteins - PubMed Contaminant sequences that appear in published genomes can cause numerous problems for downstream analyses, particularly for evolutionary studies and metagenomics projects. Our large-scale scan of com...

actually it reminds me more of finding 1000s of human contaminants annotated as proteins within draft bacterial genomes in GenBank, which we published in 2018 (and @aphillippy.bsky.social knows this work): pubmed.ncbi.nlm.nih.gov/31064768/

A telomere-to-telomere map of somatic mutation burden and functional impact in cancer https://www.biorxiv.org/content/10.1101/2025.10.10.681725v1

Predicting dynamic expression patterns in budding yeast with a fungal DNA language model Predicting gene expression from DNA sequence remains challenging due to complex regulatory codes. We introduce a masked DNA language model pretrained on 165 fungal genomes closely related to budding y...

Excited to share our new paper on predicting gene expression in yeast! We introduce "Shorkie," a supervised ML model that builds off a self-supervised foundation to interpret regulatory DNA.
Preprint: www.biorxiv.org/content/10.1...

A complete diploid human genome benchmark for personalized genomics Human genome resequencing typically involves mapping reads to a reference genome to call variants; however, this approach suffers from both technical and reference biases, leaving many duplicated and ...

The pangenome resources and genome assembly/inference approaches we are building will eventually enable complete, personalized “T2T” genomes for everyone. This is the thesis of the Q100 project (www.biorxiv.org/content/10.1...) and what my group is currently working towards. Stay tuned... [10/10]

Each genome is unique and should be treated as such. Analyzing the complete, personalized genome of an individual (yes, with the help of AI) will reduce reference bias and allow for the deep characterization of rare and novel structural variants that are the basis of many genetic diseases [9/10]

“I am suggesting we should flip that model, and we should map the metadata to the sequence of the patient, meaning we complete the patient’s genome, and then we take all of that metadata and we annotate it onto the personalized reference.” [8/10]

By sampling the pangenome to build good priors on what a typical genome looks like, you can do a much better job of inferring a patient’s genome “Perhaps, in the future, scientists can depart from the approach of mapping sequencing reads ... and accessing data in the context of the reference” [7/10]

And there is A LOT more structural variation in a typical human genome than most people realize, even between the two haplotypes of a single person’s genome, that can have big effects but are rarely captured, e.g. recurrent inversions doi.org/10.1016/j.ce... [6/10]

This point is often lost. One enormous benefit of the Human Pangenome Project is that it improves our general understanding of natural human variation. It’s like the 1000 Genomes Project, but inclusive of ALL variation, not just the variants you can see with short-read variant calling [5/10]

When [Phillippy] hears scientists say: “Oh, the pangenome is not for me,” he tells them, “You’re using it.” Illumina’s DRAGEN software already calls variants using graph genomes. Approaches related to graph genomes are, he says, “happening behind the scenes.” [4/10]

“Conceptually, the pangenome represents all of humankind’s genetic information ... Population projects cannot sample each individual in the world, so the idea is to represent the population’s multitude.” This cannot be done with singular references, enter the HPRC @humanpangenome.bsky.social [3/10]