Khyati Dalal
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View article: Widespread low-affinity motifs enhance chromatin accessibility and regulatory potential in mESCs
Widespread low-affinity motifs enhance chromatin accessibility and regulatory potential in mESCs Open
Summary Low-affinity transcription factor (TF) motifs are an important element of the cis-regulatory code, yet they are notoriously difficult to map and mechanistically incompletely understood, limiting our ability to interpret non-coding …
View article: Interpreting regulatory mechanisms of Hippo signaling through a deep learning sequence model
Interpreting regulatory mechanisms of Hippo signaling through a deep learning sequence model Open
Signaling pathway components are well studied, but how they mediate cell-type-specific transcription responses is an unresolved problem. Using the Hippo pathway in mouse trophoblast stem cells as a model, we show that the DNA binding of si…
View article: Interpretable deep learning reveals the sequence rules of Hippo signaling
Interpretable deep learning reveals the sequence rules of Hippo signaling Open
Summary The response to signaling pathways is highly context-specific, and identifying the transcription factors and mechanisms that are responsible is very challenging. Using the Hippo pathway in mouse trophoblast stem cells as a model, w…
View article: A long-range chromatin interaction regulates SATB homeobox 1 gene expression in trophoblast stem cells
A long-range chromatin interaction regulates SATB homeobox 1 gene expression in trophoblast stem cells Open
SATB homeobox proteins are important regulators of developmental gene expression. Among the stem cell lineages determined during early embryonic development, trophoblast stem (TS) cells exhibit robust SATB expression. Both SATB1 and SATB2 …
View article: Base-resolution models of transcription factor binding reveal soft motif syntax
Base-resolution models of transcription factor binding reveal soft motif syntax Open
Summary The arrangement of transcription factor (TF) binding motifs (syntax) is an important part of the cis-regulatory code, yet remains elusive. We introduce a deep learning model, BPNet, that uses DNA sequence to predict base-resolution…