@florisbarthel

Assistant professor @TGenResearch | Postdoc @jacksonlab @MDAndersonNews | Evolutionary cancer genomics | Glioma | Telomere dysfunction | Tweets are my own

 Phoenix, AZ
barthel-lab.com
Joined November 2009
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Glioblastoma is monitored mostly by MRI, which can miss early changes. Cell-free DNA (cfDNA) in blood is a promising alternative, but we know little about what governs its release. Our new paper in Neuro-Oncology, led by @SharvariMankame, dissects it. 🧵 doi.org/10.1093/neuonc/noag2…
Top: a five-step workflow schematic: cfDNA extraction from GBM43 and GBM12 cultures sampled at 24, 48, 72, 96 and 120 hours, library preparation, targeted sequencing, quality control, and variant calling. Bottom: brightfield micrographs of the two patient-derived glioblastoma lines. GBM43 grows as adherent, spindle-shaped cells and GBM12 as rounded neurospheres (scale bars 300 µm).

ALT Top: a five-step workflow schematic: cfDNA extraction from GBM43 and GBM12 cultures sampled at 24, 48, 72, 96 and 120 hours, library preparation, targeted sequencing, quality control, and variant calling. Bottom: brightfield micrographs of the two patient-derived glioblastoma lines. GBM43 grows as adherent, spindle-shaped cells and GBM12 as rounded neurospheres (scale bars 300 µm).

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Replying to @florisbarthel @SharvariMankame
Huge credit to @SharvariMankame, who led this work, and to Hersh Nanda, Maria Kyriakidou, Mimi Mbegbu, Nanyun Tang and Michael Berens at @TGen. Angad Beniwal, Matthew Dufault and Nhan Tran ran the mouse studies at @MayoClinic Arizona.
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Supported by a @theABTA Discovery Award, the Ivy Foundation, the Lane Spyrow GBM Fellowship and Students Supporting Brain Tumor Research. 📄 Open access in Neuro-Oncology (@NeuroOnc): doi.org/10.1093/neuonc/noag2…

Cell-free DNA sequencing captures tumor dynamics, microenvironment interactions, and treatment...

AbstractBackground. Glioblastoma (GBM) is a highly aggressive brain tumor for which cell-free DNA (cfDNA) has shown promise as a minimally invasive biomark

academic.oup.com
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Floris Barthel retweeted
Peter Ly@PeterLyLabOct 2
That’s a wrap for FASEB Aneuploidy 2026! Thanks to all the attendees for making it a special meeting. The science was so out-of-this-world that NASA even launched a spaceship for us. 🚀 See you again in 2029! #ANESRC
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BryanRoth
@zenbrainestAug 14
Replying to @JacquesCarolan
@JacquesCarolan @MWCvitkovic
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Bob Schmitz@Schmitz_LabAug 6
Here is a neat story led by Alex Tadros on the history of Arabidopsis laboratory stocks. They can be diverged by over 100 generations! Genetic and epigenetic divergence among Arabidopsis thaliana Col-0 laboratory lineages since the 1950s biorxiv.org/content/10.64898…

Genetic and epigenetic divergence among Arabidopsis thaliana Col-0 laboratory lineages since the...

The model plant Arabidopsis thaliana has been a workhorse of plant biology since the 1950s, when the Columbia-0 (Col-0) accession was widely adopted by the research community as a reference genotype....

biorxiv.org
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Floris Barthel retweeted
Lior Pachter@lpachterJul 29
One of the major pains of academia is having to click through labyrinths of webpages to submit papers. Now, thanks to @Josephmrich (and AI), problem solved! His tool is called PaperPush and is available at github.com/pachterlab/paperp… It's super easy to use! 1/🧵

GitHub - pachterlab/paperpush: 📝 Automated manuscript validation and submission portal completion

📝 Automated manuscript validation and submission portal completion - pachterlab/paperpush

github.com
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Floris Barthel@florisbarthelJul 28
Excited to share a big KaryoScope update from this past week: the HKS k-mer backend is now integrated, and you can build databases for any features of interest. The complete HG002 diploid assembly (~6.3 Gbp, 46 chromosomes) now annotates in 21 minutes on a MacBook Pro. 🧵
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Excited to share a big KaryoScope update from this past week: the HKS k-mer backend is now integrated, and you can build databases for any features of interest. The complete HG002 diploid assembly (~6.3 Gbp, 46 chromosomes) now annotates in 21 minutes on a MacBook Pro. 🧵
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The improved HKS index was developed by @jnalanko, @CamilleMrcht and S Puglisi. KaryoScope and its KMC-derived data structure were developed by Rhyker Ranallo-Benavidez, with support from co-authors and @HumanPangenome. HKS: biorxiv.org/content/10.64898… github.com/jnalanko/HKS

Hierarchical genomic feature annotation with variable-length queries

K -mer-based methods are widely used for sequence classification in metagenomics, pangenomics, and RNA-seq analysis, but existing tools face important limitations: they typically require a fixed k...

biorxiv.org
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If you build a KaryoScope database for your organism of interest, we would love to hear about it. 📄 biorxiv.org/content/10.64898… 💻 github.com/barthel-lab/Karyo…

KaryoScope: rapid, alignment-free sequence annotation for the pangenome era

The pangenome era is producing long-read sequencing data and complete genome assemblies ([1][1]–[3][2]) at a pace that current annotation methods cannot match. Existing tools were each built for a...

biorxiv.org
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