Quinn E. Eberhard

The paper introduces hmSEEKR, a k-mer-based hidden Markov model that identifies non-linear sequence similarities in transcriptomes, revealing functional RNA domains with biological relevance.

The paper identifies how Xist Repeat A recruits SPEN via SR proteins to induce gene silencing, revealing a role for splicing factors in this process.

The paper introduces new functions in SEEKR to calculate p-values and visualize k-mer similarity, applying them to identify chromatin-enriched lncRNAs with XIST-like fragments.

The paper shows that Airn lncRNA can deposit Polycomb with potency comparable to Xist when expressed at similar levels, but Xist is more potent when promoter activation is equal.

This study identifies SAFB-associated RNAs in mouse embryonic stem cells and shows SAFB promotes gene expression by binding purine-rich regions in nascent transcripts.