Floris Barthel

@florisbarthel.bsky.social

250 Followers 568 Following

Assistant professor @TGen | Postdoc @jacksonlab @MDAndersonNews | Genomics | Cancer | Gliomas | Telomeres

control vs dnTRF2 nucleolar necklace
KaryoScope Hi-C inter-chromosomal contact maps and the log2 fold-change map with the chr13 row/column in blue
UBF/fibrillarin immunofluorescence, compact vs necklace nucleoli
DAPI metaphase spreads with arrowheaded translocations, plus pie charts of shifting translocation composition
chromosomal abnormality catalog organized by type (deletions / translocations / fusions) across four clones showing an abundance of acrocentric involvement
the longitudinal growth curve showing the senescence and crisis growth plateaus
two multicolor FISH karyograms of crisis cells
Four-panel performance scaling of KaryoScope across CPU thread counts. Top left: feature-ID lookup throughput (Mb/s) for KMC (red) and HKS (blue) k-mer backends. Bottom left: peak memory (GB) for each backend. Top right: smoothing-step runtime (minutes) comparing Python (red) and Rust (blue) implementations. Bottom right: smoothing-step memory. HKS and Rust each scale substantially better than KMC and Python.
KaryoScope karyotype of the HG008 pancreatic tumor assembly. Each chromosome is shown as a track colored by chromosome of origin, revealing complex rearrangements: derivative chromosomes from reciprocal translocations, dicentric chromosomes, and chromoplexy-like patterns where blocks of one chromosome's sequence appear within another.
Pangenome-scale centromere structural variation. Panel A: dendrogram of centromere haplotype cluster representatives across chromosomes 1–22 and X, each row showing a KaryoScope satellite composition profile (major haplotypes gray, minor red). Panel B: FISH validation of three minor centromere subtypes — chr3 HSat1A deletion in GM21144, chr5 HSat3 loss in HG00558, chr9 HSat3 inversion in HG02630 — on metaphase chromosome spreads. Panels C and D: haplotype frequencies per chromosome and diploid major/minor pairing tables.
Pangenome-scale D4Z4 macrosatellite catalog from KaryoScope. Panels A and C–F: KaryoScope tracks (satellites, genes, repeats, subtelomere, D4Z4 arrays) for representative haplotypes across chromosomes 4q and 10q, including canonical, multi-array, and mixed configurations. Waffle charts (B) show D4Z4 structural category frequencies across 249 chr4 and 333 chr10 haplotypes. Contingency tables (G) summarize diploid combinations. Scatterplot (H) compares repeat-unit counts between haplotypes within individuals.
KaryoScope annotation of three Robertsonian translocation assemblies (top: rob(14;21), middle: rob(13;14) in GM03786, bottom: rob(13;14) in GM04890). Each row shows six progressively zooming panels from full contig (~130–200 Mb) down to 200 kb at the fusion site. Tracks per panel show chromosome of origin, genes, repeats, satellites, and acrocentric features. The SST1 satellite block (green) is visible at every fusion point.
Schematic comparing FISH (fluorescence in situ hybridization) and KaryoScope workflows side by side in four parallel steps: feature definition (cloning vectors vs. genomic feature sets), fragmentation (vector processing vs. k-mer enumeration), label assignment (fluorescent probes vs. labeled k-mer sets), and query (in situ probe binding vs. k-mer database lookup). KaryoScope is presented as a computational analog of FISH.
KaryoScope karyotype of the HG002 diploid assembly. All 22 autosomes plus X and Y, each shown as paired haplotypes (h1, h2). Each chromosome has a full-length track colored by chromosome of origin, a centromere zoom panel showing satellite composition, and a subtelomere zoom panel. Legends map chromosomes, satellite families, and subtelomeric features to colors.
KaryoScope visualization of two reciprocal translocations
CenMAP visualization of the 7p-6p dicentric chromosome
Chromoplexy causing a complex series of events linking chromosomes 3, 6, 7, and 11 in three hybrid tumor chromosomes
Side-by-side computational and traditional multi-color karyotype for HG008T
Side-by-side computational and traditional multi-color karyotype for HG008T