Judith F. Kribelbauer-Swietek

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.

Multiscale regulation of nutrient stress responses in Escherichia coli from chromatin structure to small regulatory RNAs

The paper identifies nutrient stress response mechanisms in E. coli by integrating chromatin structure and small regulatory RNA data, revealing novel transcription factor-sRNA interactions.

EXTRA-seq: a genome-integrated extended massively parallel reporter assay to quantify enhancer-promoter communication

EXTRA-seq quantifies enhancer-promoter communication in endogenous contexts, revealing the TATA-box's role in modulating expression and improving gene expression prediction when integrated with deep learning models.

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.

Non-coding variants impact cis-regulatory coordination in a cell type-specific manner

The paper evaluates CM mapping tools, shows cell type-specific CRE interactions, and demonstrates how non-coding variants affect CM activity in a cell type-specific manner.

Context transcription factors establish cooperative environments and mediate enhancer communication

The paper identifies 'context-only' transcription factors that contribute to enhancer communication by forming cooperative environments with pioneer factors.

Probing molecular specificity with deep sequencing and biophysically interpretable machine learning

The paper introduces ProBound, a machine learning framework that quantifies biophysical parameters of protein-ligand interactions using NGS data, and couples it with Kd-seq to determine absolute affinities.

Context-dependent gene regulation by transcription factor complexes

The paper investigates how DNA sequence influences the formation of transcription factor complexes and shows that non-canonical binding sites arise from direct interactions with functionally bound sites.

SelexGLM differentiates androgen and glucocorticoid receptor DNA-binding preference over an extended binding site

This study identifies differences in DNA-binding preferences between androgen and glucocorticoid receptors using SELEX-seq and SelexGLM, revealing AR's greater sequence sensitivity and enthalpy-driven binding.