Timothy R. Hughes

The paper benchmarks methods for inferring transcription factor binding specificities using a large community challenge and finds deep learning models outperform traditional methods, though positional weight matrices are competitive.

This study shows that Pumilio and Brain tumor regulate Smaug mRNA degradation during the Drosophila maternal-to-zygotic transition, preventing ectopic Smaug protein expression and ensuring proper mRNA clearance.

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

This study systematically investigates EBV transcriptional regulators' interactions with the human genome, identifying extensive gene expression alterations and chromatin changes.

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.

The paper identifies two distinct DNA-binding domains in Zelda that regulate its tissue-specific chromatin occupancy in Drosophila embryos and neuroblasts.

This study identifies At-RS31 as a plant-specific splicing factor that regulates alternative splicing and integrates TOR and ABA signaling pathways through its binding targets and interactions with other splicing factors.

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.

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.

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.

The paper uses deep learning to analyze chromatin accessibility in Drosophila embryos, revealing a two-phase process driven by pioneer TFs and enhancer-activating TFs.

The paper analyzes RELA-bound transposable elements across species to show their ancient and lineage-specific contributions to NF-κB binding and inflammation.

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.

This study identifies NHL-2 as a co-factor in C. elegans germline 22G-RNA pathways and shows it regulates gene expression through RNA binding and stability.

This study identifies ARGLU1 as a glucocorticoid receptor coactivator and splicing modulator, showing its role in stress hormone signaling and brain development through genetic and transcriptomic analyses.