Perspectives on gene regulatory network evolution
MS Halfon - Trends in Genetics, 2017 - cell.com
Animal development proceeds through the activity of genes and their cis-regulatory modules
(CRMs) working together in sets of gene regulatory networks (GRNs). The emergence of …
(CRMs) working together in sets of gene regulatory networks (GRNs). The emergence of …
Identifying transcriptional cis‐regulatory modules in animal genomes
K Suryamohan, MS Halfon - Wiley Interdisciplinary Reviews …, 2015 - Wiley Online Library
Gene expression is regulated through the activity of transcription factors (TF s) and
chromatin‐modifying proteins acting on specific DNA sequences, referred to as cis …
chromatin‐modifying proteins acting on specific DNA sequences, referred to as cis …
Integrating diverse datasets improves developmental enhancer prediction
GD Erwin, N Oksenberg, RM Truty… - PLoS computational …, 2014 - journals.plos.org
Gene-regulatory enhancers have been identified using various approaches, including
evolutionary conservation, regulatory protein binding, chromatin modifications, and DNA …
evolutionary conservation, regulatory protein binding, chromatin modifications, and DNA …
Prediction of gene regulatory enhancers across species reveals evolutionarily conserved sequence properties
Genomic regions with gene regulatory enhancer activity turnover rapidly across mammals.
In contrast, gene expression patterns and transcription factor binding preferences are largely …
In contrast, gene expression patterns and transcription factor binding preferences are largely …
A new method for enhancer prediction based on deep belief network
Background Studies have shown that enhancers are significant regulatory elements to play
crucial roles in gene expression regulation. Since enhancers are unrelated to the orientation …
crucial roles in gene expression regulation. Since enhancers are unrelated to the orientation …
Short DNA sequence patterns accurately identify broadly active human enhancers
Background Enhancers are DNA regulatory elements that influence gene expression. There
is substantial diversity in enhancers' activity patterns: some enhancers drive expression in a …
is substantial diversity in enhancers' activity patterns: some enhancers drive expression in a …
[HTML][HTML] Machine and deep learning methods for predicting 3D genome organization
BPG Wall, M Nguyen, JC Harrell, MG Dozmorov - ArXiv, 2024 - ncbi.nlm.nih.gov
Abstract Three-Dimensional (3D) chromatin interactions, such as enhancer-promoter
interactions (EPIs), loops, Topologically Associating Domains (TADs), and A/B …
interactions (EPIs), loops, Topologically Associating Domains (TADs), and A/B …
A comprehensive review of computational prediction of genome-wide features
There are significant correlations among different types of genetic, genomic and epigenomic
features within the genome. These correlations make the in silico feature prediction possible …
features within the genome. These correlations make the in silico feature prediction possible …
Identification and computational analysis of gene regulatory elements
L Taher, L Narlikar… - Cold Spring Harbor …, 2015 - cshprotocols.cshlp.org
Over the last two decades, advances in experimental and computational technologies have
greatly facilitated genomic research. Next-generation sequencing technologies have made …
greatly facilitated genomic research. Next-generation sequencing technologies have made …
Mechanisms of evolutionary innovation point to genetic control logic as the key difference between prokaryotes and eukaryotes
W Bains, D Schulze-Makuch - Journal of Molecular Evolution, 2015 - Springer
The evolution of life from the simplest, original form to complex, intelligent animal life
occurred through a number of key innovations. Here we present a new tool to analyze these …
occurred through a number of key innovations. Here we present a new tool to analyze these …