Decoding enhancer complexity with machine learning and high-throughput discovery

GD Smith, WH Ching, P Cornejo-Páramo, ES Wong - Genome biology, 2023 - Springer
Enhancers are genomic DNA elements controlling spatiotemporal gene expression. Their
flexible organization and functional redundancies make deciphering their sequence-function …

Enhancer evolution and the origins of morphological novelty

M Rebeiz, M Tsiantis - Current Opinion in Genetics & Development, 2017 - Elsevier
Highlights•Genome-wide and single gene studies have revealed a variety of mechanisms by
which new expression patterns arise.•Studying newly evolved morphologies at the level of …

Genetics of schizophrenia: historical insights and prevailing evidence

J Van de Leemput, JL Hess, SJ Glatt, MT Tsuang - Advances in genetics, 2016 - Elsevier
Abstract Schizophrenia's (SZ's) heritability and familial transmission have been known for
several decades; however, despite the clear evidence for a genetic component, it has been …

Evolution of transcriptional enhancers and animal diversity

M Rubinstein, FSJ de Souza - … Transactions of the …, 2013 - royalsocietypublishing.org
Deciphering the genetic bases that drive animal diversity is one of the major challenges of
modern biology. Although four decades ago it was proposed that animal evolution was …

Gene regulatory network architecture in different developmental contexts influences the genetic basis of morphological evolution

S Kittelmann, AD Buffry, FA Franke, I Almudi… - PLoS …, 2018 - journals.plos.org
Convergent phenotypic evolution is often caused by recurrent changes at particular nodes in
the underlying gene regulatory networks (GRNs). The genes at such evolutionary 'hotspots' …

The functionality and evolution of eukaryotic transcriptional enhancers

AD Buffry, CC Mendes, AP McGregor - Advances in Genetics, 2016 - Elsevier
Enhancers regulate precise spatial and temporal patterns of gene expression in eukaryotes
and, moreover, evolutionary changes in these modular cis-regulatory elements may …

Comparative transcriptomics analysis pipeline for the meta-analysis of phylogenetically divergent datasets (CoRMAP)

Y Sheng, RA Ali, A Heyland - BMC bioinformatics, 2022 - Springer
Background Transcriptional regulation is a fundamental mechanism underlying biological
functions. In recent years, a broad array of RNA-Seq tools have been used to measure …

Mobile DNA is replete with hotspots for the de novo emergence of gene regulation

T Fuqua, A Wagner - bioRxiv, 2023 - biorxiv.org
ABSTRACT DNA mutations that create new gene expression are important raw materials for
Darwinian evolution. One potential source of new gene regulation is mobile DNA, which can …

The evolutionary origination of a novel expression pattern through an extreme heterochronic shift

T Pham, SM Day, WJ Glassford… - Evolution & …, 2017 - Wiley Online Library
The evolutionary origins of morphological structures are thought to often depend upon the
redeployment of old genes into new developmental settings. Although many examples of cis …

MuSERA: multiple sample enriched region assessment

V Jalili, M Matteucci, MJ Morelli… - Briefings in …, 2017 - academic.oup.com
Enriched region (ER) identification is a fundamental step in several next-generation
sequencing (NGS) experiment types. Yet, although NGS experimental protocols recommend …