iiinova — where your digital self keeps evolving

Reposted by Floris Barthel

Adam Phillippy @aphillippy.bsky.social · 06/08/2026

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]

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Reposted by Floris Barthel

UC Santa Cruz Genomics Institute @ucscgenomics.bsky.social · 06/08/2026

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/

A quote from Prajna Hebbar, graduate student at UC Santa Cruz and lead author on the T2T marmoset paper, reads "Routine T2T genomics is making findings easier... It's great to be in an era where we're not stuck with the technical problems- we can go into the biology and make discoveries relevant to human health." A small monkey is pictured on the side.

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Reposted by Floris Barthel

Floris Barthel @florisbarthel.bsky.social · 28/07/2026

Excited to share a big KaryoScope update this past week: the HKS k-mer backend is now integrated, and you can build databases for any features of interest. The complete @humanpangenome.bsky.social HG002 assembly (~6.3 Gbp) now annotates in 21 minutes on a MacBook Pro. 🧵

Macbook laptop showing KaryoScope actively running alongside the final output karyotype plots

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Floris Barthel @florisbarthel.bsky.social · 28/07/2026

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Reposted by Floris Barthel

bioRxiv Genomics @biorxiv-genomic.bsky.social · 22/07/2026

HPRC2: A human pangenome reference with near-complete coverage of common genetic variation www.biorxiv.org/content/10.64898/20…

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Reposted by Floris Barthel

bioRxiv Bioinfo @biorxiv-bioinfo.bsky.social · 28/05/2026

Fast Set Operations for Compact k-mer Sets www.biorxiv.org/content/10.64898/20…

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Floris Barthel @florisbarthel.bsky.social · 26/05/2026

Busy month at the lab. We've refreshed our site with four new preprints: arm-specific telomeres in astrocytoma (Jehangir), pancreatic cancer assembly (Wagner), telomere crisis in astrocytes (Mbegbu) and KaryoScope (Ranallo-Benavidez). Plus new(-ish) lab members Shea, Nick, Daniel, Griffin, and Divy.

barthel-lab.org

the barthel laboratory - studying telomere dysfunction in gliomagenesis and evolution at TGen

The Barthel Laboratory studies how telomere dysfunction drives structural genome evolution and shapes the molecular trajectory of cancer. Based at TGen in Phoenix, Arizona, we combine cytogenetics and...

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Floris Barthel @florisbarthel.bsky.social · 22/05/2026

Telomere crisis is an engine of genomic instability, driving the structural evolution of cancer genomes. Our new preprint finds this damage isn't random: it converges on the nucleolus and the chromosomes that build it. 🧵 www.biorxiv.org/content/10.6...

two multicolor FISH karyograms of crisis cells

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Floris Barthel @florisbarthel.bsky.social · 17/05/2026

The human genome's most variable and clinically important regions (centromeres, telomeres, and acrocentric short arms) have been hardest to study at scale. Thrilled to share KaryoScope, our new preprint that brings them within reach. 🧵 www.biorxiv.org/content/10.6...

KaryoScope karyotype of the HG002 diploid assembly. All 22 autosomes plus X and Y, each shown as paired haplotypes (h1, h2). Each chromosome has a full-length track colored by chromosome of origin, a centromere zoom panel showing satellite composition, and a subtelomere zoom panel. Legends map chromosomes, satellite families, and subtelomeric features to colors.

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Floris Barthel @florisbarthel.bsky.social · 08/05/2026

🧵 Excited to contribute to a new preprint led by Justin Zook & the NIST/GIAB team: "A complete human pancreatic cancer genome": the first near-complete, haplotype-resolved tumor cell line assembly (HG008-T, hypodiploid PDAC). 📄 www.biorxiv.org/content/10.6...

Side-by-side computational and traditional multi-color karyotype for HG008T

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Floris Barthel @florisbarthel.bsky.social · 29/04/2026

Very excited for our lab's first paper to be printed!

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Floris Barthel @florisbarthel.bsky.social · 23/04/2026

New preprint! We used Oxford Nanopore long-read sequencing to ask: does chromosome-arm-specific telomere length shape how IDH-mutant astrocytoma genomes evolve? Short answer: yes, and in two opposite directions. 🔗 www.biorxiv.org/content/10.6...

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Reposted by Floris Barthel

Edoardo Gianni @edogia.bsky.social · 13/02/2026

How could a simple self-replicating system emerge at the origins of life? RNA polymerase ribozymes can replicate RNA, but existing ones are so large that their self-replication seems impossible. Could they be smaller? Excited to share our latest work in @science.org on a new small polymerase. 1/n

science.org

A small polymerase ribozyme that can synthesize itself and its complementary strand

The emergence of a chemical system capable of self-replication and evolution is a critical event in the origin of life. RNA polymerase ribozymes can replicate RNA, but their large size and structural ...

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Reposted by Floris Barthel

Andrea Guarracino @andreaguarracino.bsky.social · 06/02/2026

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

guarracinolab.github.io

Guarracino Lab | Pangenome Research

We develop methods to build and analyze pangenomes, with applications in cancer and complex disease. Translational Genomics Research Institute, Phoenix, AZ.

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Reposted by Floris Barthel

Adam Phillippy @aphillippy.bsky.social · 02/02/2026

Time for a thread on our Christmas preprint “Origin and evolution of acrocentric chromosomes in human and great apes”. I had so much fun with this project and paper. It will be hard to summarize in a thread, but I’ll try www.biorxiv.org/content/10.6... [1/21]

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Reposted by Floris Barthel

Adam Phillippy @aphillippy.bsky.social · 29/01/2026

New tool from @alexsweeten.bsky.social to find and classify all your satellites: "AniAnn's: alignment-free annotation of tandem repeat arrays using fast average nucleotide identity estimates" 📄 www.biorxiv.org/content/10.6... 📦 github.com/marbl/anianns

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Reposted by Floris Barthel

Eunhee Yi @eunhee-yi.bsky.social · 20/11/2025

It was a great pleasure to learn about a recent discovery in ecDNA biology that answers the most critical question on ecDNA maintenance! @nature.com Are you a non-scientist? No worries! My team wrote a lay-audience-friendly summary about this exciting research finding! Check it out! rdcu.be/eQMvM

rdcu.be

Circular DNA has a ticket to ride chromosomes | Nature

How circular extrachromosomal DNA is inherited during cell division is a puzzle. Key sequences enabling this DNA to journey with chromosomes have been identified. How circular extrachromosomal DNA is inherited during cell division is a puzzle. Key sequences enabling this DNA to journey with chromosomes have been identified.

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Reposted by Floris Barthel

Noam Teyssier @noamteyssier.bsky.social · 14/11/2025

BINSEQ is a high-performance format for sequencing data and bqtools is a CLI tool that lets you create and manipulate these files in the style of samtools. Excited to release a tutorial with @robert.bio showcasing how to use it to encode, decode, and grep sequences in the browser on sandbox.bio!

sandbox.bio

Efficient sequence analysis with bqtools

Interactive bqtools tutorial: learn to analyse sequence data efficiently with BINSEQ files using a command-line interface in your browser.

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Reposted by Floris Barthel

Dave Keating @davekeating.substack.com · 31/10/2025

Breaking: it's now official, the pro-EU D66 party came first in the Dutch election. Their best result ever. The National Press Agency has just announced the final vote count. It’s a narrow victory with D66 just 15,155 votes ahead of the far-right PVV of Geert Wilders.

davekeating.substack.com

The most pro-EU party just won big in the Dutch election

D66 had a surprise surge, tripling their seats in yesterday's Netherlands election—and its openly gay leader Rob Jetten is set to become prime minister.

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Floris Barthel @florisbarthel.bsky.social · 17/10/2025

Yi-An Chen presenting his work on the telomeric interactome #ASHG2025, now also on biorxiv: www.biorxiv.org/content/10.1...

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Floris Barthel @florisbarthel.bsky.social · 16/10/2025

Ogechukwu (Mimi) Mbegbu, super star RA and resident FISH-ing expert showcasing her cytogenetic analysis of astrocytes undergoing telomere dysfunction at #ASHG2025. Lots of chromosomal chaos observed and a 3-fold bias towards acrocentric abnormalities?! Stay tuned for the mechanism

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Floris Barthel @florisbarthel.bsky.social · 15/10/2025

I had the opportunity to write an editorial for a piece in Neuro-Oncology (@neuroonc.bsky.social) executing a genomic analysis on perhaps the largest cohort of extracranial metastases of adult gliomas to date. Congratulations to the authors on this terrific piece of work! bit.ly/494Pz8s

bit.ly

Uncommon Territory: The Clinical and Molecular Profile of Metastatic Gliomas

Floris P Barthel; Uncommon Territory: The Clinical and Molecular Profile of Metastatic Gliomas, Neuro-Oncology, , noaf244, https://doi.org/10.1093/neuonc/n

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Reposted by Floris Barthel

Mike Schatz @mikeschatz.bsky.social · 14/10/2025

Getting excited for #ASHG25. The must see talk is tomorrow at 1:30 by Qiuhui (Iris) Li presenting the first large-scale integration of long-read genome sequencing with electronic health record data across >1000 All of Us participants meetings.ashg.org/event/ASHG25...

meetings.ashg.org

PheedLoop

PheedLoop: Hybrid, In-Person & Virtual Event Software

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Floris Barthel @florisbarthel.bsky.social · 14/10/2025

This 7-year journey has reached a first milestone! 🥳 Excited to share our preprint (3rd of 2025) on the 3D telomeric interactome, a project that started with a K99 in 2018. Thanks to Yi-An Chen, first postdoc in our lab and first author who worked tirelessly to realize this dream. bit.ly/3W3wuMk

bit.ly

Mapping the Telomeric 3D Interactome with Telomere-C Reveals Repetitive Element Hubs Associated with Telomere Maintenance

Telomeres are essential for genome integrity, but the accurate, high-resolution mapping of their three-dimensional (3D) chromatin interactions, a process thought to mediate gene regulation and telomer...

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Reposted by Floris Barthel

bioRxiv Genomics @biorxiv-genomic.bsky.social · 11/10/2025

Mapping the Telomeric 3D Interactome with Telomere-C Reveals Repetitive Element Hubs Associated with Telomere Maintenance www.biorxiv.org/content/10.1101/202…

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Reposted by Floris Barthel

Andre Kahles @akkah21.bsky.social · 08/10/2025

After years of research and continuous refinement, we’re thrilled to share that our paper on the MetaGraph framework — enabling Petabase-scale search across sequencing data — has been published today in Nature (www.nature.com/articles/s41...)

nature.com

Efficient and accurate search in petabase-scale sequence repositories - Nature

MetaGraph enables scalable indexing of large sets of DNA, RNA or protein sequences using annotated de Bruijn graphs.

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Reposted by Floris Barthel

Camille Marchet ⚡ @camillemrcht.bsky.social · 18/06/2025

This is going to be a cool event, invited talk by Jana Ebler + discussion panel and latest research activities in graphs+pangenomics!

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Reposted by Floris Barthel

bioRxiv Bioinfo @biorxiv-bioinfo.bsky.social · 17/06/2025

REINDEER2: practical abundance index at scale www.biorxiv.org/content/10.1101/202…

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Reposted by Floris Barthel

Bede Constantinides @bede.im · 13/06/2025

New preprint! Deacon is a versatile tool for filtering FASTA/FASTQ files and streams at hundreds of megabases per second using minimizers, built with rapid metagenomic host depletion in mind, but equally useful for search. github.com/bede/deacon

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Reposted by Floris Barthel

Human Pangenome Reference Consortium @humanpangenome.bsky.social · 12/05/2025

📢 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...

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Reposted by Floris Barthel

Emre Kocakavuk @ekocakavuk.bsky.social · 07/05/2025

🧪 We’re Hiring: Lab Technician 🧪 I’m happy to share that our newly established Emmy Noether Group in Essen is looking for a Lab Technician to join our team! 🔗 Apply here: karriere.ume.de/job-finder/?... 📅 Start: At the earliest possible date 💻 Homepage: kocakavuklab.vercel.app/overview

karriere.ume.de

Job Finder - Karriereportal - Universitätsklinikum Essen

Finden Sie eine Stelle am Universitätsklinikum Essen

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Reposted by Floris Barthel

Noam Teyssier @noamteyssier.bsky.social · 29/04/2025

Extracting @NCBI SRA files with fasterq-dump can require 17x the size of the accession while decompressing. Our new tool xsra extracts sequences at 5x throughput with significantly less disk usage, built-in compression, and optional BINSEQ outputs github.com/arcInstitute...

github.com

GitHub - ArcInstitute/xsra: An efficient CLI to extract sequences from the SRA

An efficient CLI to extract sequences from the SRA - ArcInstitute/xsra

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Reposted by Floris Barthel

Camille Marchet ⚡ @camillemrcht.bsky.social · 23/04/2025

1/ We made a tool called Vizitig to explore sequencing datasets visually, interactively, and with metadata. It uses a colored de Bruijn graph under the hood.

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Floris Barthel @florisbarthel.bsky.social · 16/04/2025

🚨 Pre-print alert! 🚨 We generated chromosome-scale diploid genome assemblies for the widely used fibroblast lines BJ and IMR-90. These models of replicative senescence and telomere shortening now have fully resolved telomeres, subtelomeres, and centromeres. 🧬 🧵👇

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