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Floris Barthel @florisbarthel.bsky.social · Aug 7

Fully on board with this as you know and happy to contribute my 2 cents. Coordinates/position, be gone!

Floris Barthel @florisbarthel.bsky.social · Jul 14

P.s. this is a repost of a deleted post from earlier today, where the link to the pre-print was not working. An update to BlueSky allowing post editing would be welcomed :)

Floris Barthel @florisbarthel.bsky.social · Jul 14

This was pre-print number two of 2025 from our lab. Several more scheduled for public release later this year... Stay tuned!!

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Floris Barthel @florisbarthel.bsky.social · Jul 14

We're actively developing a novel high-sensitive method for #cfDNA analysis and anticipate a preprint on that approach very soon. Exciting times ahead for #LiquidBiopsy in #GBM research! Kudo's to @tgenresearch.bsky.social for supporting this work and #PrecisionMedicine in general!

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Floris Barthel @florisbarthel.bsky.social · Jul 14

This preprint marks a significant milestone for our lab and especially for Sharvari. Her dedication and scientific rigor shine through in this comprehensive study. Incredibly proud of her accomplishments and grateful for the opportunity to mentor her! 👩‍🔬

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Floris Barthel @florisbarthel.bsky.social · Jul 14

What's next? @sharvarimankame.bsky.social is currently evaluating cfDNA in plasma and CSF samples from #Glioblastoma patients, translating these exciting in vitro findings to the clinic.

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Floris Barthel @florisbarthel.bsky.social · Jul 14

We observed specific cfDNA fragmentation signatures associated with TMZ sensitivity and resistance. These patterns could serve as valuable biomarkers for predicting treatment response.

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Floris Barthel @florisbarthel.bsky.social · Jul 14

@sharvarimankame.bsky.social's work leverages cfDNA as a non-invasive window into the complex interplay between treatment, tumor evolution, and the host. This brings us closer to developing more effective monitoring strategies for #GBM patients.

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Floris Barthel @florisbarthel.bsky.social · Jul 14

Some key findings: co-culturing glioblastoma cells with host cells significantly alters cfDNA fragmentation patterns. This highlights the vital role of the tumor microenvironment in shaping cfDNA characteristics.

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Floris Barthel @florisbarthel.bsky.social · Jul 14

Our study reveals how TMZ treatment drives dynamic changes in cfDNA profiles, reflecting tumor response and resistance mechanisms. This is crucial for understanding how #GBM adapts to therapy over time.

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Floris Barthel @florisbarthel.bsky.social · Jul 14

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..

Cell-Free DNA Reveals the Longitudinal Effects of Temozolomide Treatment and Host Co-Culture in Glioblastoma Models

Glioblastoma (GBM) is a highly aggressive brain tumor with limited options for longitudinal monitoring. We evaluated the potential of cell-free DNA (cfDNA) as a real-time biomarker of tumor burden und...

doi.org

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Floris Barthel @florisbarthel.bsky.social · Jul 14

This preprint marks a significant milestone for our lab and especially for Sharvari. Her dedication and scientific rigor shine through in this comprehensive study. Incredibly proud to have the opportunity to mentor her in our lab! 👩‍🔬

Floris Barthel @florisbarthel.bsky.social · Jul 14

We observed specific cfDNA fragmentation signatures associated with TMZ sensitivity and resistance. These patterns could serve as valuable biomarkers for predicting treatment response.

1

Floris Barthel @florisbarthel.bsky.social · Jul 14

Sharvari's work leverages cfDNA as a non-invasive window into the complex interplay between treatment, tumor evolution, and the host. This brings us closer to developing more effective monitoring strategies for #GBM patients.

1

Floris Barthel @florisbarthel.bsky.social · Jul 14

A key finding: co-culturing glioblastoma cells with host cells significantly alters cfDNA fragmentation patterns. This highlights the vital role of the tumor microenvironment in shaping cfDNA characteristics.

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Floris Barthel @florisbarthel.bsky.social · Jul 14

Our study reveals how TMZ treatment drives dynamic changes in cfDNA profiles, reflecting tumor response and resistance mechanisms. This is crucial for understanding how #GBM adapts to therapy over time.

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Reposted by Floris Barthel

Camille Marchet ⚡ @camillemrcht.bsky.social · Jun 18

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

Bonsai Sequence Bioinformatics @bonsaiseqbioinfo.bsky.social · Jun 18

Also check the pangenomics mini-symposium, TBA a flash talk by @imartayan.bsky.social 🧬

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Reposted by Floris Barthel

bioRxiv Bioinfo @biorxiv-bioinfo.bsky.social · Jun 17

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

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Reposted by Floris Barthel

Bede Constantinides @bedec.bsky.social · Jun 13

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

bioRxiv Bioinfo @biorxiv-bioinfo.bsky.social · Jun 13

Deacon: fast sequence filtering and contaminant depletion https://www.biorxiv.org/content/10.1101/2025.06.09.658732v1

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Reposted by Floris Barthel

Jack Bateman @jbateman01.bsky.social · Jun 1

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

Mechanisms and timing of programmed DNA elimination in songbirds

It is commonly assumed that multicellular organisms contain the same genetic information in all the cells of an individual. However, there is a growing list of species in which parts of the genome are...

www.biorxiv.org

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Reposted by Floris Barthel

Human Pangenome Reference Consortium @humanpangenome.bsky.social · May 12

📢 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 · May 7

🧪 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

Job Finder - Karriereportal - Universitätsklinikum Essen

Finden Sie eine Stelle am Universitätsklinikum Essen

karriere.ume.de

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Reposted by Floris Barthel

Noam Teyssier @noamteyssier.bsky.social · Apr 29

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

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

github.com

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Reposted by Floris Barthel

Camille Marchet ⚡ @camillemrcht.bsky.social · Apr 23

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.

bioRxiv Bioinfo @biorxiv-bioinfo.bsky.social · Apr 22

Vizitig: context-rich exploration of sequencing datasets https://www.biorxiv.org/content/10.1101/2025.04.19.649656v1

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Floris Barthel @florisbarthel.bsky.social · Apr 16

But mostly, massive credit to first authors @trhyker.bsky.social + @yuehao.bsky.social , and co-authors @pedalheadphx.bsky.social @mishakolmogorov.bsky.social @benedictpaten.bsky.social @mitchiela.bsky.social @msstephkayb.bsky.social + others not on here (yet) 🙏

🔗 www.biorxiv.org/content/10.1...

Diploid genome assembly of human fibroblast cell lines enables clone specific variant calling, improved read mapping and accurate phasing

Human cell lines are fundamental tools in biomedical research and are widely used in disease modeling, drug development, and many other domains. Here, we present chromosome-level, phased diploid genom...

www.biorxiv.org

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