Ketrin Gjoni

Nov 7, 2024 | biorxiv.org | Ketrin Gjoni |Xingjie Ren |Amanda Everitt |Yin Shen

AbstractThree-dimensional genome organization plays a critical role in gene regulation, and disruptions can lead to developmental disorders by altering the contact between genes and their distal regulatory elements. Structural variants (SVs) can disturb local genome organization, such as the merging of topologically associating domains upon boundary deletion. Testing large numbers of SVs experimentally for their effects on chromatin structure and gene expression is time and cost prohibitive.

Nov 5, 2023 | biorxiv.org | Ketrin Gjoni |Katherine S. Pollard

AbstractComputationally editing genome sequences is a common bioinformatics task, but current approaches have limitations, such as incompatibility with structural variants, challenges in identifying responsible sequence perturbations, and the need for vcf file inputs and phased data. To address these bottlenecks, we present Sequence Mutator for Predictive Models (SuPreMo), a scalable and comprehensive tool for performing in silico mutagenesis.

Apr 5, 2023 | biorxiv.org | Evonne McArthur |Laura M Gunsalus |Ketrin Gjoni |Shuzhen Kuang

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