Adam Phillippy

taxburst v0.3.0 is now released - this is an update of the Krona visualization system for microbiome/metagenome taxonomy analyses. Enjoy!

🚨 Our parent-of-origin study is out in Nature! 🧬
Maternal and paternal alleles can have distinct — even opposite — effects on human traits, revealing a hidden layer of genetic architecture that standard GWAS miss.
🔗 www.nature.com/articles/s41...

Highlights below!

Pospelova et al. present a comparative analysis of adaptive immune loci across diverse mammalian species, uncovering relationships between locus architecture, characteristics of immune genes, and population dynamics. The artwork illustrates how the structure of immunoglobulin heavy chain loci influences gene variability in three representative species from the study – the mountain lion, the ring-tailed lemur, and European hedgehog.

Pospelova et al. present a comparative analysis of full-length sequences of IG/TR loci across 46 mammalian species, demonstrating these as rapidly evolving genomic regions, with implications for immunogenomics.

🔗 doi.org/10.1093/molbev/msaf152

#evobio #molbio

Dynamics of Ribosomal RNA Transcription and Abundance in Normal and Leukemic Hematopoiesis Transcription of ribosomal RNAs (rRNAs) from rDNA repeats is the first step of ribosome biogenesis, accounting for a major portion of all cellular transcription. Often regarded as a housekeeping proce...

📣 New preprint 📣

We present a detailed map of nascent and mature ribosomal RNAs in mouse hematopoiesis and AML (including absolute rRNA molecule numbers), and outline principles of rDNA regulation.

Work by Eleanor Sams (@eleanor44.bsky.social) & Victoria Feist (@victoriafeist.bsky.social). (1/x)

After 10 years of work, a complete telomere-to-telomere gap-free genome for C. elegans finally exists: it has 106 Mb rather than the textbook 100.3 Mb, and up to 366 additional genes.
genome.cshlp.org/content/35/8...

It's exciting to see the continuing legacy of T2T sequencing methods being discussed on @scifri.bsky.social ! 🧬
Complete genomes are helping us understand more and more about genetic function and diversity in areas of our DNA that were unreadable just a few years ago.

This was both fun and terrifying to tape! Awesome to talk with @glennislogsdon.bsky.social and @aphillippy.bsky.social about our sequencing data / paper, the improvements to large-scale sequencing projects, and what this means for our understanding of our DNA!

I did not do the heavy lifting on this one, hat off to Glennis, Christine, and many others of the HGSVC ... I am just the color commentator. But it is super gratifying to see our "T2T" methods (Verkko in this case) enabling such studies! Onwards to our next goal of 1,000 T2T human haplotypes 🧬

65 Genomes Expand Our Picture Of Human Genetics Researchers closely examined the genomes of 65 individuals to paint a more complex, and more complete, picture of human genetic diversity.

Complete genomes alert! @glennislogsdon.bsky.social, @christinebeck.bsky.social, and I were on @scifri.bsky.social today talking about "Complex genetic variation in nearly complete human genomes"
📄 www.nature.com/articles/s41...
📻 www.sciencefriday.com/segments/65-...

🚨 📣 Deadline Alert!
Submit your talk or poster abstract by Friday, August 15, to be part of the 🧬 VGP In-Person Conference 2025

Don’t miss your chance to share your research with the global genomics community! 🌍🧬 @vertebrategenomes.bsky.social @rockefelleruniv.bsky.social

🧬 Vertebrate Genomes Project In-Person Conference 2025
📍 New York, NY
📅 September 30 (9AM) – October 1 (8PM EDT)
Join top researchers to explore the cutting edge of vertebrate genome science—from assembly to conservation genomics. 🌍
Register: bit.ly/VGP-register

@vertebrategenomes.bsky.social

I will talk about those papers in my Hitseq keynote tomorrow at #ISMBECCB2025, so if you are in Liverpool don't miss it.

Complex genetic variation in nearly complete human genomes - Nature Using sequencing and haplotype-resolved assembly of 65 diverse human genomes, complex regions including the major histocompatibility complex and centromeres are analysed.

Two papers in today's issue of @nature.com ‬: 1) we assemble 65 genomes to near completion, including centromeres and the MHC. tinyurl.com/3huhax6w. 2) we sequence 1,019 genomes from the 1kGP with long reads, revealing SVs down to low allele frequencies tinyurl.com/wbx3we9x.

Hooray for something to celebrate! Congrats @benlangmead.bsky.social ! 🎉

Ben Langmead promoted to full professor. Computer science.

Congratulations to @benlangmead.bsky.social on his promotion to full professor! 🎉 Prof. Langmead is recognized across the computational and life sciences fields for his innovative methods helping to transform how biomedical researchers and other life scientists access and use DNA sequencing data. 🧬

If you’re in Liverpool, stop by my poster A217 at ISMB/EECB 2025, and chat about all things pangenomes, MUMs, and alignment (and the Beatles or Oasis-mania)

Thrilled that our study on human gene duplications and brain evolution is out! It was a true labor of love, with special shout-outs to my co-first author @jmuribescr.bsky.social and my PhD mentor @mydennis.bsky.social. Huge thanks as well to @aidaandres.bsky.social for all the popgen wisdom!

Postdoc position opening in my group! Research projects: pangenomes for diverse organisms, genome evolution, biocomputing, language models. Please reach out if interested!

Accurate diagram 😂

Graphical overview of the biological foundations of the proposed approach.

Application of SCINKD to identify XY chromosomes in the Christmas island skink

Application of SCINKD to identify previously unannotated sex chromosomes in the Lesser electric ray.

🚨Preprint🚨

Sex chromosome identification & genome curation from a single individual with SCINKD
www.biorxiv.org/content/10.1...

Incredible work led by @drpintothe2nd.bsky.social in collaboration w/ @drsimonegable.bsky.social @stuartvnielsen.bsky.social @tonygamble.bsky.social SE Keating & CH Smith

Really excited to see this published! To more mum-finding 🍻

As just one example, Verkko2 allowed us to assemble the first T2T Robertsonian chromosomes and pinpoint a particular SST1 satellite repeat array as the fusion site of most ROBs: www.biorxiv.org/content/10.1...

Congrats to @dantipov.bsky.social et al. on the publication of Verkko2! The team put a ton of work into this making it the first assembler that deals with the complexity of human acrocentric chromosomes. Lots of interesting discoveries to come! genome.cshlp.org/content/earl...

Lossless Pangenome Indexing Using Tag Arrays Pangenome graphs represent the genomic variation by encoding multiple haplotypes within a unified graph structure. However, efficient and lossless indexing of such structures remains challenging due t...

A new preprint on indexing pangenome graphs using an FM-index of the haplotypes and a tag array. Joint work with Parsa Eskandar and @benedictpaten.bsky.social.

I remember chatting with @sergek.bsky.social and intentionally calling this a "golden threshold" so that it would be a brainworm. Glad our strategy worked and you still remember it 12 years later 😁 This was the original figure from doi.org/10.1186/gb-2...

Some exciting news! NCBI has finished the annotation pipeline for our new #zebrafish reference sequence GRCz12tu:
www.ncbi.nlm.nih.gov/refseq/annot...

This is a big step up in data depth and quality and should be super helpful going forward.

NIH is allowing us to recruit postbacs and postdocs again. Please reach out if you are interested in working with us! Ad: genomeinformatics.github.io/jobs2025/

Best practices for improving alignment and variant calling on human sex chromosomes Sex chromosome complement is the largest karyotypic variation observed in humans. X and Y chromosomes were once a pair of homologous autosomes. Although chromosome X and Y differentiated from one anot...

Our work looking at the effects of using autosomal assumptions for calling variation on X and Y. We used simulated data to compare to a ground truth.

Tldr: Accurate ploidy is important for reducing false positives; appropriate alignment reduces false negatives.

www.biorxiv.org/content/10.1...

The human pangenome continues to grow and improve! Release 2 is here! Click through for the details, but this is a pretty amazing dataset including not just the phased assemblies, but PacBio HiFi, ONT Ultralong, Dovetail/Illumina Hi-C, PacBio Kinnex, and Illumina WGS for all samples

Highlight of my year ... by far ... has been welcoming Melissa and her lab to the NIH. After a slightly(!) rocky start, we're allowed to hire trainees again, so please reach out to her if you're interested. You won't find a better mentor!