John M. Franklin

The paper introduces Centrolign, a tool for aligning centromeric regions, revealing mutation dynamics and enabling variant calling in human centromeres.

This study identifies nuclear stress bodies in Drosophila germline that mediate a stress response by delaying Hsf-dependent transcription and enabling selective expression of molecular chaperones over transposable elements.

DiMeLo-cito improves DiMeLo-seq by eliminating wash steps, enabling mitotic protein-DNA interaction analysis in diploid human cells and revealing CTCF bookmarking.

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.

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

NuSeT improves nuclear segmentation in microscopy images by combining U-Net and RPN with watershed, reducing false positives and handling complex overlaps.