Imperial College London


Faculty of MedicineInstitute of Clinical Sciences

Professor of Computational Biology



+44 (0)20 3313 8353b.lenhard Website




Mr Alastair Douglas Ivor Williams +44 (0)20 3313 4318




230ICTEM buildingHammersmith Campus






BibTex format

author = {Tan, G and Polychronopoulos, D and Lenhard, B},
doi = {10.1371/journal.pcbi.1006940},
journal = {PLoS Comput Biol},
title = {CNEr: A toolkit for exploring extreme noncoding conservation.},
url = {},
volume = {15},
year = {2019}

RIS format (EndNote, RefMan)

AB - Conserved Noncoding Elements (CNEs) are elements exhibiting extreme noncoding conservation in Metazoan genomes. They cluster around developmental genes and act as long-range enhancers, yet nothing that we know about their function explains the observed conservation levels. Clusters of CNEs coincide with topologically associating domains (TADs), indicating ancient origins and stability of TAD locations. This has suggested further hypotheses about the still elusive origin of CNEs, and has provided a comparative genomics-based method of estimating the position of TADs around developmentally regulated genes in genomes where chromatin conformation capture data is missing. To enable researchers in gene regulation and chromatin biology to start deciphering this phenomenon, we developed CNEr, a R/Bioconductor toolkit for large-scale identification of CNEs and for studying their genomic properties. We apply CNEr to two novel genome comparisons-fruit fly vs tsetse fly, and two sea urchin genomes-and report novel insights gained from their analysis. We also show how to reveal interesting characteristics of CNEs by coupling CNEr with existing Bioconductor packages. CNEr is available at Bioconductor ( and maintained at github (
AU - Tan,G
AU - Polychronopoulos,D
AU - Lenhard,B
DO - 10.1371/journal.pcbi.1006940
PY - 2019///
TI - CNEr: A toolkit for exploring extreme noncoding conservation.
T2 - PLoS Comput Biol
UR -
UR -
VL - 15
ER -