Kaitlin U. Laverty

Identification of methylation-sensitive human transcription factors using meSMiLE-seq

This study identifies DNA binding motifs for 98 human transcription factors using meSMiLE-seq, revealing methylation-sensitive binding preferences for some TFs.

GHT-SELEX demonstrates unexpectedly high intrinsic sequence specificity and complex DNA binding of many human transcription factors

The paper uses GHT-SELEX to show many human TFs have high intrinsic sequence specificity and complex DNA binding, often matching in vivo ChIP-seq results.

Cross-platform DNA motif discovery and benchmarking to explore binding specificities of poorly studied human transcription factors

The paper evaluates cross-platform DNA motif discovery tools using 4,237 experiments to identify reliable transcription factor binding motifs and highlights challenges in motif detection.

mRNABench: A curated benchmark for mature mRNA property and function prediction

mRNABench evaluates self-supervised mRNA foundation models using 13 datasets and 81 tasks to assess their ability to predict mRNA properties.

Extensive binding of nebulous human transcription factors to genomic dark matter

The paper identifies genomic binding sites of 166 poorly characterized human transcription factors, revealing that some bind to dark matter DNA and others to regulatory regions.

Codebook: sequence specificity and genomic binding of poorly-characterized human transcription factors

The paper systematically determines the sequence specificity of 332 poorly characterized human transcription factors, identifying over 4,000 experiments and revealing tens of thousands of new TF binding sites.

Reconstructing the sequence specificities of RNA-binding proteins across eukaryotes

The paper introduces EuPRI, a resource of RNA motifs for 34,736 RBPs across 690 eukaryotes, expanding motif knowledge and enabling functional and evolutionary insights.

Binding specificities of human RNA binding proteins towards structured and linear RNA sequences

The paper identifies binding specificities of human RNA-binding proteins using HTR-SELEX, revealing that 70% bind linear sequences and 30% bind structured motifs, with novel roles for ZC3H12A/B/C in viral transcript degradation.