Martha L. Bulyk

The paper investigates how histone modifications affect transcription factor binding to nucleosomes and finds that specific marks influence binding preferences and modes.

This paper characterizes FG214, a heme-binding one-component switch from Fimbriimonas ginsengisoli, showing heme redox state controls monomer-dimer transitions and DNA binding.

The paper investigates why many GWAS loci linked to immune-mediated diseases lack eQTL colocalization by analyzing chromatin accessibility QTLs in LCLs and other immune cell types.

This study systematically profiles 95 viral transcriptional regulators (vTRs) across multiple assays, revealing their diverse mechanisms of rewiring host pathways to promote viral replication and disease links.

The paper identifies non-DNA-contacting residues that determine mono- versus bispecific DNA binding in forkhead transcription factors using protein binding microarrays.

The paper identifies novel candidate genes and transcription factor variants associated with congenital heart defect and orofacial cleft through a gene burden analysis of parent-offspring trio cohorts.

The paper develops PIONEAR-seq to analyze TF binding to nucleosomes and finds that DNA flexibility, not TF intrinsic properties, determines binding preferences.

The paper investigates NKX2-5 mutations in congenital heart disease by analyzing their epigenomic, biochemical, and chromatin search functions in cardiomyocytes, revealing diverse loss and gain-of-function defects.

TF2TG integrates TF-DNA binding, protein-protein interactions, and transcriptomic data to identify and rank potential target genes for Drosophila transcription factors.

The paper identifies two categories of transcription factor isoforms with distinct molecular functions and shows they contribute to gene regulatory complexity.

The paper reanalyzes data to show H4K20me1 is not a mark of transcriptional silencers in Drosophila and human, and instead is associated with active transcription.

The paper identifies three novel candidate genes for ocular congenital cranial dysinnervation disorders using zebrafish CRISPR screening and protein binding microarrays to assess variant functionality.

The paper analyzes DNA binding effects of 92 human homeodomain mutants, identifying 14 novel specificity-determining residues and highlighting limitations of variant effect prediction tools.

The paper develops PADIT-seq to detect low-affinity TF-DNA interactions and shows overlapping binding sites modulate TF genomic occupancy.

The paper identifies 69 blood cell trait GWAS loci potentially driven by PU.1 occupancy variation and nominates 51 variants as causal through colocalization analysis with PU.1 bQTLs.

The paper identifies UNC-130 as a lineage-specific repressor that enables convergent differentiation in C. elegans by allowing proper specification of glial cells from distinct lineages.

The paper identifies BDNF-specific chromatin accessibility changes in neurons and links them to gene regulation and neurodevelopmental traits.

The paper identifies the DNA binding domain and sequence of SALL4, discovers its target genes in liver cancer cells, and reveals its mechanism of gene regulation.

The paper shows GA-repeats on mammalian X chromosomes support Ohno's hypothesis of dosage compensation by transcriptional upregulation through convergent evolution.

The paper identifies three classes of enhancers regulated by Bicoid and Orthodenticle in Drosophila embryos, revealing a feed-forward relay mechanism that coordinates gene expression timing.