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Articles by Jane E. Ranchalis
Long-read transcriptome analysis using IsoRanker for identifying pathogenic variants in Mendelian conditions
Keywords long-read transcript IsoRanker Mendelian HARS1 rare disease variant interpretation splicing RNA transcriptomics functional genomics Get full text access Log in, subscribe or purchase for full access. References 1. Yang, Y. ∙ Muzny, D.M. ∙ Reid, J.G. ... Clinical whole-exome sequencing for the diagnosis of mendelian disorders N. Engl. J. Med. 2013; 369:1502-1511 2. Kurosaki, T. ∙ Maquat, L.E. Nonsense-mediated mRNA decay in humans at a glance J. Cell Sci. 2016; 129:461-467 3. Wang, G.-S.
A haplotype-resolved view of human gene regulation
Abstract Diploid human cells contain two non-identical genomes, and differences in their regulation underlie human development and disease. We present Fiber-seq Inferred Regulatory Elements (FIRE) and show that FIRE provides a more comprehensive and quantitative snapshot of the accessible chromatin landscape across the 6 Gbp diploid human genome, overcoming previously known and unknown biases afflicting our existing regulatory element catalog.
RNA polymerases reshape chromatin and coordinate transcription on individual fibers
Abstract During eukaryotic transcription, RNA polymerases must initiate and pause within a crowded, complex environment, surrounded by nucleosomes and other transcriptional activity. This environment creates a spatial arrangement along individual chromatin fibers ripe for both competition and coordination, yet these relationships remain largely unknown owing to the inherent limitations of traditional structural and sequencing methodologies.
DNA-m6A calling and integrated long-read epigenetic and genetic analysis with fibertools
Abstract Long-read DNA sequencing has recently emerged as a powerful tool for studying both genetic and epigenetic architectures at single-molecule and single-nucleotide resolution. Long-read epigenetic studies encompass both the direct identification of native cytosine methylation as well as the identification of exogenously placed DNA N6-methyladenine (DNA-m6A).
Fibertools: fast and accurate DNA-m6A calling using single-molecule long-read sequencing
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Conservation of chromatin organization within human and primate centromeres
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