Campolina: a deep neural framework for accurate segmentation of nanopore signals - Genome Biology Nanopore sequencing enables real-time, long-read analysis by processing raw signals as they are produced. A key step, segmentation of signals into events, is typically handled algorithmically, struggl...

Transformer-based AI has boosted
@nanoporetech.com
sequencing accuracy, but at a cost to portability due to GPU demands.
Our new work, spearheaded by
Sara Bakic, introduces Campolina link.springer.com/article/10.1... to improve nanopore signal segmentation for event-based mappers.

Absolutely thrilled to share the latest work from my lab focused on the variation and evolution of human centromeres among global populations! We assembled 2,110 human centromeres, identifying 226 new major haplotypes and 1,870 α-satellite HOR variants. www.biorxiv.org/content/10.6...

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-...

This is a highly collaborative effort with outstanding colleagues:
🙏 Dr. Seishi Ogawa, @yotarochi.bsky.social, @glennislogsdon.bsky.social, @thinks.lol, Masahiro Sugawa, Yoshitaka Sakamoto, and many others.
We hope this work helps reshape how we study centromere variation and its link to disease.

Finally, using ascairn, we analyzed 142 TCGA brain tumor whole genomes with 1p/19q co-deletion (class-defining centromere translocation).
We found that these events are dicentric, and that centromere haplogroups may influence the occurence of 1p/19q co-deletion!

We applied ascairn to over 3,300 WGS samples from the 1000 Genomes Project and Human Genome Diversity Project.
This revealed population-level differences in centromere haplogroups, providing new insights into human ancestry and migration. (4/n)

GitHub - friend1ws/ascairn: Centromere sequence analysis using rare k-mer markers Centromere sequence analysis using rare k-mer markers - friend1ws/ascairn

We developed a new algorithm, ascairn, to infer centromere haplogroups directly from short-read WGS data.
✅ Accuracy exceeds 95% for most chromosomes!
The tool is freely available here:
🔗 github.com/friend1ws/as...
(3/n)

We extracted rarely observed short nucleotide sequences (rare k-mers) from centromere assemblies generated by several pangenome consortia.
These rare k-mers act like “centromere SNPs”!
Rare k-mer profiles group centromere sequences into evolutionarily related haplogroups.
(2/n)

Rare k-mers reveal centromere haplogroups underlying human diversity and cancer translocations Centromeres are among the most diverse and dynamically evolving regions of the human genome and are commonly affected in various human cancers. However, organized into highly repetitive α-satellite hi...

🚨New preprint out!
🧬Short reads can now decode centromeres.
🌍We reveal population-scale centromere haplogroups and their links to disease.
biorxiv.org/content/10.1... (1/n)

Systematically developing a registry of splice-site creating variants utilizing massive publicly available transcriptome sequence data - Nature Communications Splice-site creating variants (SSCVs) are considered promising candidates for treatment with antisense oligonucleotides. Here, the authors present a novel framework to screen for SSCVs solely using tr...

SSCVs are genomic variants that create novel splice sites and alter splicing. This updated resource supports variant interpretation and drug target discovery, especially with antisense oligonucleotides.
Details in our paper 👉 www.nature.com/articles/s41...

🧬 SSCV DB updated!
We screened 525,323 RNA-seq samples (up from 310,699 at the time of our SSCV paper) and identified 48,569 splice-site creating variants (SSCVs).
👉 sscvdb.io

#RNAseq #splicing #ASO

New from the lab by algorithm geek Hajime Suzuki! Genome assembly in centromeric regions is still challenging. By focusing on k-mer periodicity, Hajime implemented a novel hashing approach (github.com/ocxtal/mm2-ivh), which dramatically improves assembly in repetitive regions like centromeres!

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

📢 HPRC Release 2 is here!

Now with phased genomes from 200+ individuals, a 5x increase from Release 1.

Explore sequencing data, assemblies, annotations & alignments in our interactive data explorer ⬇️:

humanpangenome.org/hprc-data-re...

The Betrayal of Itō Shiori: When Lawyers Do More Harm Than Good - Unseen Japan Itō Shiori's award-winning documentary BLACK BOX DIARIES still can't be screened in Japan. Is that truly in the interests of justice?

Itō Shiori's award-winning documentary BLACK BOX DIARIES still can't be screened in Japan. A group of lawyers - Itō's former attorneys - say she didn't get permission for some of the footage. But is that true? Why are attorneys undermining their own former client?