Danilo Dubocanin

The paper introduces GBZ-base and GAF-base, indexed pangenome file formats for efficient subgraph and alignment extraction.

The paper introduces scE2G models to predict enhancer-gene regulatory interactions from single-cell data and demonstrates their performance across multiple cell types and perturbations.

460 haplotypes from 230 genomes, selected to maximize common-variant coverage, capture 99.43% of All of Us common small variants and halve structurally unreliable regions and base errors versus HPRC1.

This paper presents near-complete, haplotype-resolved assemblies of a pancreatic cancer genome and normal tissue, identifying extensive somatic variants and epigenetic changes in previously excluded regions.

The paper constructs an atlas of telomere variation across humans using long-read sequencing and reveals heritable telomere variant repeats and telomerase-independent extension mechanisms.

The paper analyzes chromosome 22q11.2 haplotypes to show how structural variations in specific regions correlate with microdeletion and inversion risks across populations.

The paper uses a complete diploid human genome to study centromeric chromatin organization, revealing that DNA methylation regulates centromere structure and plasticity.

The paper characterizes the genetic diversity and regulatory features of human-specific NOTCH2NL duplications using long-read sequencing and organoid models.

The paper uses long-read sequencing to identify pathogenic variants in autism cases, finding three pathogenic mutations and nine candidate structural variants missed by short-read sequencing.

The paper investigates how heterochromatin boundaries maintain centromere position, size, and number through specific histone modifications and methyltransferases.

The paper maps somatic mutation burden and functional impact across the cancer genome using telomere-to-telomere sequencing, revealing novel mutation hotspots and regulatory rewiring mechanisms.

The paper uses Fiber-seq to study paternal chromatin repackaging in sperm, finding that protamine lacunae and nucleosome retention play distinct roles in epigenetic inheritance.

This study shows plasmids can form chromatin structures in mammalian cells and uses plasmid Fiber-seq to map these structures and their functional consequences.

The paper uses Fiber-seq to show that regional centromeres have dichromatin organization, with accessible and compacted chromatin, which is conserved across species despite DNA sequence differences.

The paper identifies centromeric transposable elements and epigenetic features in the eastern hoolock gibbon that contribute to karyotypic variation and chromosomal instability.

This paper introduces FiberFold, a deep learning model that predicts haplotype-specific 3D chromatin organization using Fiber-seq data, revealing changes in TADs in a Mendelian disease.

This paper introduces fibertools, a toolkit for DNA-m6A detection and integration of long-read genetic and epigenetic data, achieving high accuracy and speed.

The paper identifies HSat3 DNA as a platform for transcription factor binding, showing it enhances nucleolar RNA Polymerase I activity through Hippo pathway interactions.

The paper introduces FIRE to comprehensively map haplotype-selective chromatin accessibility in diploid human genomes, revealing somatic epimutations that contribute to non-genetic chromatin alterations.

The paper uses long-read single-molecule accessibility mapping to reveal that human mtDNA undergoes all-or-none global compaction, with most nucleoids in an inaccessible state.

This study links transcription factor binding to gene expression by analyzing chromatin configurations using single-molecule footprinting in human cells.

The paper uses Fiber-seq to study RNA polymerase interactions with chromatin fibers, showing Pol II pausing affects nucleosomes and coordination between nearby transcriptional elements.

Mandalorion v4 improves isoform identification and quantification from full-length transcriptome sequencing data, showing high precision and recall even without genome annotation.

The paper uses single-molecule chromatin fiber sequencing to detail the structure and function of human telomeric DNA and chromatin.