David Landsman

The paper assesses the oncogenic potential of histone missense mutations using whole-exome sequencing data from over 12,000 cancer patients, finding that these mutations affect DNA repair interactions and increase mutagenesis.

The paper develops a computational method to predict cell-type-specific nucleosome-binding abilities of transcription factors using ChIP-seq, MNase-seq, and DNase-seq data, identifying new potential pioneer transcription factors.

This paper introduces GTax, a tool to detect and remove foreign RNA contamination in sequencing samples, and shows it reduces chimeric transcripts in tomato de novo transcriptome assembly.

The paper examines Mediator complex dynamics during heat shock in yeast, finding altered occupancy and interactions with PIC components at stress-responsive genes.

BAMscale processes DNA sequencing datasets to generate normalized peak scores and scaled coverage tracks for visualization.

The paper shows that Kin28 depletion increases Taf1 and Taf4 promoter occupancy in yeast, while TBP occupancy remains unchanged, suggesting uncoupling of Taf and TBP during transcription.

The paper investigates Mediator complex recruitment and dynamics in yeast, showing that Mediator lacking Med2-Med3-Med15 is associated with active promoters and that PIC components like TBP, Pol II, and Taf1 influence Mediator association.

This study shows that Mediator subunits regulate Ty1 retrotransposon mobility by altering the ratio of Ty1i to Ty1 transcripts, affecting retromobility without significantly changing genomic RNA or Gag levels.