Cicero predicts cis-regulatory DNA interactions from single-cell chromatin accessibility data
Linking regulatory DNA elements to their target genes, which may be located hundreds of
kilobases away, remains challenging. Here, we introduce Cicero, an algorithm that identifies …
kilobases away, remains challenging. Here, we introduce Cicero, an algorithm that identifies …
Progress and challenges in bioinformatics approaches for enhancer identification
D Kleftogiannis, P Kalnis, VB Bajic - Briefings in bioinformatics, 2016 - academic.oup.com
Enhancers are cis-acting DNA elements that play critical roles in distal regulation of gene
expression. Identifying enhancers is an important step for understanding distinct gene …
expression. Identifying enhancers is an important step for understanding distinct gene …
Recent advances in genetic engineering tools based on synthetic biology
Genome-scale engineering is a crucial methodology to rationally regulate microbiological
system operations, leading to expected biological behaviors or enhanced bioproduct yields …
system operations, leading to expected biological behaviors or enhanced bioproduct yields …
Combining transcription factor binding affinities with open-chromatin data for accurate gene expression prediction
F Schmidt, N Gasparoni, G Gasparoni… - Nucleic acids …, 2017 - academic.oup.com
The binding and contribution of transcription factors (TF) to cell specific gene expression is
often deduced from open-chromatin measurements to avoid costly TF ChIP-seq assays …
often deduced from open-chromatin measurements to avoid costly TF ChIP-seq assays …
Dynamic organization of lncRNA and circular RNA regulators collectively controlled cardiac differentiation in humans
Y Li, J Zhang, C Huo, N Ding, J Li, J Xiao, X Lin… - …, 2017 - thelancet.com
Advances in developmental cardiology have increased our understanding of the early
aspects of heart differentiation. However, understanding noncoding RNA (ncRNA) …
aspects of heart differentiation. However, understanding noncoding RNA (ncRNA) …
Integrative prediction of gene expression with chromatin accessibility and conformation data
Background Enhancers play a fundamental role in orchestrating cell state and development.
Although several methods have been developed to identify enhancers, linking them to their …
Although several methods have been developed to identify enhancers, linking them to their …
[HTML][HTML] The spatial binding model of the pioneer factor Oct4 with its target genes during cell reprogramming
Understanding the target regulation between pioneer factor and its binding genes is crucial
for improving the efficiency of TF-mediated reprogramming. Oct4 as the only one factor that …
for improving the efficiency of TF-mediated reprogramming. Oct4 as the only one factor that …
Automated identification of core regulatory genes in human gene regulatory networks
Human gene regulatory networks (GRN) can be difficult to interpret due to a tangle of edges
interconnecting thousands of genes. We constructed a general human GRN from extensive …
interconnecting thousands of genes. We constructed a general human GRN from extensive …
Predicting expression: the complementary power of histone modification and transcription factor binding data
Abstract Background Transcription factors (TFs) and histone modifications (HMs) play critical
roles in gene expression by regulating mRNA transcription. Modelling frameworks have …
roles in gene expression by regulating mRNA transcription. Modelling frameworks have …
Virtual reference environments: a simple way to make research reproducible
Abstract 'Reproducible research'has received increasing attention over the past few years as
bioinformatics and computational biology methodologies become more complex. Although …
bioinformatics and computational biology methodologies become more complex. Although …