Intrinsically disordered regions direct transcription factor in vivo binding specificity
Transcription factors (TFs) that bind common DNA motifs in vitro occupy distinct sets of
promoters in vivo, raising the question of how binding specificity is achieved. TFs are …
promoters in vivo, raising the question of how binding specificity is achieved. TFs are …
Multiscale models quantifying yeast physiology: towards a whole-cell model
The yeast Saccharomyces cerevisiae is widely used as a cell factory and as an important
eukaryal model organism for studying cellular physiology related to human health and …
eukaryal model organism for studying cellular physiology related to human health and …
Simple biochemical features underlie transcriptional activation domain diversity and dynamic, fuzzy binding to Mediator
AL Sanborn, BT Yeh, JT Feigerle, CV Hao… - Elife, 2021 - elifesciences.org
Gene activator proteins comprise distinct DNA-binding and transcriptional activation
domains (ADs). Because few ADs have been described, we tested domains tiling all yeast …
domains (ADs). Because few ADs have been described, we tested domains tiling all yeast …
Global analysis of the yeast knockout phenome
Genome-wide phenotypic screens in the budding yeast Saccharomyces cerevisiae, enabled
by its knockout collection, have produced the largest, richest, and most systematic …
by its knockout collection, have produced the largest, richest, and most systematic …
From classical mendelian randomization to causal networks for systematic integration of multi-omics
A Yazdani, A Yazdani, R Mendez-Giraldez… - Frontiers in …, 2022 - frontiersin.org
The number of studies with information at multiple biological levels of granularity, such as
genomics, proteomics, and metabolomics, is increasing each year, and a biomedical …
genomics, proteomics, and metabolomics, is increasing each year, and a biomedical …
Inferring gene regulation from stochastic transcriptional variation across single cells at steady state
Regulatory relationships between transcription factors (TFs) and their target genes lie at the
heart of cellular identity and function; however, uncovering these relationships is often labor …
heart of cellular identity and function; however, uncovering these relationships is often labor …
Revisiting the model for coactivator recruitment: Med15 can select its target sites independent of promoter-bound transcription factors
Activation domains (ADs) within transcription factors (TFs) induce gene expression by
recruiting coactivators such as the Mediator complex. Coactivators lack DNA binding …
recruiting coactivators such as the Mediator complex. Coactivators lack DNA binding …
A genome‐scale yeast library with inducible expression of individual genes
The ability to switch a gene from off to on and monitor dynamic changes provides a powerful
approach for probing gene function and elucidating causal regulatory relationships. Here …
approach for probing gene function and elucidating causal regulatory relationships. Here …
Bayesian inference of sample-specific coexpression networks
Gene regulatory networks (GRNs) are effective tools for inferring complex interactions
between molecules that regulate biological processes and hence can provide insights into …
between molecules that regulate biological processes and hence can provide insights into …
[HTML][HTML] High-performance single-cell gene regulatory network inference at scale: the Inferelator 3.0
Results In this work, we present the Inferelator 3.0, which has been significantly updated to
integrate data from distinct cell types to learn context-specific regulatory networks and …
integrate data from distinct cell types to learn context-specific regulatory networks and …