Fast Set Operations for Compact k-mer Sets https://www.biorxiv.org/content/10.64898/2026.05.24.727514v1

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.

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...

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...

🧵 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...

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

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...

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

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

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]

*Mic drop* 🎤

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

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

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!

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.

Grateful to @mishakolmogorov.bsky.social @benedictpaten.bsky.social @acarroll.bsky.social @kishwar.bsky.social and team for the opportunity to contribute.

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

Thanks for sharing, @samiramin.com! See our first pre-print on this topic here: www.biorxiv.org/content/10.1.... More to follow :)

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

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

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...

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

Mapping the Telomeric 3D Interactome with Telomere-C Reveals Repetitive Element Hubs Associated with Telomere Maintenance https://www.biorxiv.org/content/10.1101/2025.10.09.681516v1

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...)

Thrilled to share our preprint led by the lab's incredible first PhD student, @sharvarimankame.bsky.social! 🎉 We've explored the longitudinal consequences of temozolomide (TMZ) treatment & host co-culture in #Glioblastoma using cell-free DNA (cfDNA) sequencing. A deep dive into therapeutic impact..

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

REINDEER2: practical abundance index at scale https://www.biorxiv.org/content/10.1101/2025.06.16.659990v1

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

Mechanisms and timing of programmed DNA elimination in songbirds www.biorxiv.org/content/10.1...

📢 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...

🧪 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

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...

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.

🚨 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. 🧬 🧵👇