Jane Ranchalis

A near-complete human pancreatic cancer genome

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.

Genetic diversity and regulatory features of human-specific NOTCH2NL duplications

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

Protamine lacunae preserve the paternal chromatin landscape in sperm

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.

Conservation of dichromatin organization along regional centromeres

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.

DNA-m6A calling and integrated long-read epigenetic and genetic analysis with fibertools

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

Resolving the chromatin impact of mosaic variants with targeted Fiber-seq

This study uses targeted Fiber-seq to analyze the chromatin impact of mosaic variants, showing that pathogenic DMPK CTG expansions disrupt regulatory elements and that base editing can alter chromatin accessibility.

RNA polymerases reshape chromatin and coordinate transcription on individual fibers

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.

Full-length isoform sequencing for resolving the molecular basis of Charcot-Marie-Tooth 2A

The paper uses full-length isoform sequencing to identify a splicing defect in MFN2 causing CMT2A in a patient with undiagnosed neuropathy.

Single-molecule architecture and heterogeneity of human telomeric DNA and chromatin

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