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. 🧬 🧵👇