ChIPping away at gene regulation

CE Massie, IG Mills - EMBO reports, 2008 - embopress.org
The coordinated regulation of gene expression in higher eukaryotes is complex and poorly
understood. Recent technological advances have allowed the first insights into these …

Coupling and coordination in gene expression processes: a systems biology view

S Komili, PA Silver - Nature Reviews Genetics, 2008 - nature.com
Genome-scale analyses have allowed us to progress beyond studying gene expression at
the level of individual components of a given process by providing global information about …

Backup in gene regulatory networks explains differences between binding and knockout results

A Gitter, Z Siegfried, M Klutstein, O Fornes… - Molecular systems …, 2009 - embopress.org
The complementarity of gene expression and protein–DNA interaction data led to several
successful models of biological systems. However, recent studies in multiple species raise …

Advances in analysis of transcriptional regulatory networks

TM Kim, PJ Park - Wiley Interdisciplinary Reviews: Systems …, 2011 - Wiley Online Library
A transcriptional regulatory network represents a molecular framework in which
developmental or environmental cues are transformed into differential expression of genes …

[HTML][HTML] Emergence of co-expression in gene regulatory networks

W Yin, L Mendoza, J Monzon-Sandoval, AO Urrutia… - PloS one, 2021 - journals.plos.org
Transcriptomes are known to organize themselves into gene co-expression clusters or
modules where groups of genes display distinct patterns of coordinated or synchronous …

A yeast one‐hybrid and microfluidics‐based pipeline to map mammalian gene regulatory networks

C Gubelmann, SM Waszak, A Isakova… - Molecular systems …, 2013 - embopress.org
The comprehensive mapping of gene promoters and enhancers has significantly improved
our understanding of how the mammalian regulatory genome is organized. An important …

[HTML][HTML] Regulating gene expression through control of transcription factor multivalent interactions

BT Donovan, DR Larson - Molecular Cell, 2022 - cell.com
Regulating gene expression through control of transcription factor multivalent interactions:
Molecular Cell Skip to Main Content Advertisement Molecular Cell This journal offers authors …

The evolution of gene regulatory interactions

DA Garfield, GA Wray - BioScience, 2010 - academic.oup.com
Abstract Changes in the timing and level at which genes are expressed are known to play
an important role in evolution, but the mechanisms underlying changes in gene expression …

[HTML][HTML] The ties that bind: mapping the dynamic enhancer-promoter interactome

CH Spurrell, DE Dickel, A Visel - Cell, 2016 - cell.com
Coupling chromosome conformation capture to molecular enrichment for promoter-
containing DNA fragments enables the systematic mapping of interactions between …

Computational approaches to study transcriptional regulation

MM Babu - Biochemical Society Transactions, 2008 - portlandpress.com
In recent years, a number of technical and experimental advances have allowed us to obtain
an unprecedented amount of information about living systems on a genomic scale. Although …