Floris Barthel
@florisbarthel.bsky.social
Assistant professor @TGen | Postdoc @jacksonlab @MDAndersonNews | Genomics | Cancer | Gliomas | Telomeres
Reposted by Floris Barthel
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!
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!
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.
sandbox.bio
November 14, 2025 at 6:12 PM
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!
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!
Reposted by Floris Barthel
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.
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.
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.
davekeating.substack.com
October 31, 2025 at 12:54 PM
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.
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.
@tgenresearch.bsky.social partners to release new technology with @googleresearch.bsky.social and @ucscgenomics.bsky.social: DeepSomatic 🧑🏽💻 This #machinelearning method is a major leap forward for #cancer mutation #detection. More at bit.ly/4nYDDJY and lnkd.in/gQA4frVa
#Research #Genomics
#Research #Genomics
October 24, 2025 at 4:19 PM
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...
October 17, 2025 at 7:51 PM
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 :)
October 17, 2025 at 7:48 PM
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
October 16, 2025 at 9:44 PM
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
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
bit.ly
October 15, 2025 at 6:13 PM
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
Reposted by Floris Barthel
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...
PheedLoop
PheedLoop: Hybrid, In-Person & Virtual Event Software
meetings.ashg.org
October 14, 2025 at 5:40 PM
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
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...
bit.ly
October 13, 2025 at 11:21 PM
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
Reposted by Floris Barthel
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
October 11, 2025 at 12:33 AM
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
Reposted by Floris Barthel
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...)
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.
www.nature.com
October 8, 2025 at 8:56 PM
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..
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
July 14, 2025 at 7:24 PM
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..
Reposted by Floris Barthel
This is going to be a cool event, invited talk by Jana Ebler + discussion panel and latest research activities in graphs+pangenomics!
Also check the pangenomics mini-symposium, TBA a flash talk by @imartayan.bsky.social 🧬
June 18, 2025 at 7:48 AM
This is going to be a cool event, invited talk by Jana Ebler + discussion panel and latest research activities in graphs+pangenomics!
Reposted by Floris Barthel
REINDEER2: practical abundance index at scale https://www.biorxiv.org/content/10.1101/2025.06.16.659990v1
June 17, 2025 at 1:46 PM
REINDEER2: practical abundance index at scale https://www.biorxiv.org/content/10.1101/2025.06.16.659990v1
Reposted by Floris Barthel
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
github.com/bede/deacon
Deacon: fast sequence filtering and contaminant depletion https://www.biorxiv.org/content/10.1101/2025.06.09.658732v1
June 13, 2025 at 1:25 PM
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
github.com/bede/deacon
Reposted by Floris Barthel
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
June 1, 2025 at 9:24 PM
Mechanisms and timing of programmed DNA elimination in songbirds www.biorxiv.org/content/10.1...
Reposted by Floris Barthel
📢 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...
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...
May 12, 2025 at 1:15 PM
📢 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...
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...
Reposted by Floris Barthel
🧪 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
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
May 7, 2025 at 8:32 PM
🧪 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
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
Reposted by Floris Barthel
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/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
April 29, 2025 at 9:03 PM
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/arcInstitute...
Reposted by Floris Barthel
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.
It uses a colored de Bruijn graph under the hood.
Vizitig: context-rich exploration of sequencing datasets https://www.biorxiv.org/content/10.1101/2025.04.19.649656v1
April 23, 2025 at 9:43 AM
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.
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. 🧬
🧵👇
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. 🧬
🧵👇
April 16, 2025 at 6:05 PM
🚨 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. 🧬
🧵👇
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. 🧬
🧵👇