Conserved non-coding elements: developmental gene regulation meets genome organization
D Polychronopoulos, JWD King, AJ Nash… - Nucleic acids …, 2017 - academic.oup.com
Comparative genomics has revealed a class of non-protein-coding genomic sequences that
display an extraordinary degree of conservation between two or more organisms, regularly …
display an extraordinary degree of conservation between two or more organisms, regularly …
A genome alignment of 120 mammals highlights ultraconserved element variability and placenta-associated enhancers
Background Multiple alignments of mammalian genomes have been the basis of many
comparative genomic studies aiming at annotating genes, detecting regions under …
comparative genomic studies aiming at annotating genes, detecting regions under …
A transcribed ultraconserved noncoding RNA, Uc. 173, is a key molecule for the inhibition of lead-induced neuronal apoptosis
A Nan, X Zhou, L Chen, M Liu, N Zhang, L Zhang… - …, 2015 - pmc.ncbi.nlm.nih.gov
As a common toxic metal, lead has significant neurotoxicity to brain development. Long non-
coding RNAs (lncRNAs) function in multiple biological processes. However, whether …
coding RNAs (lncRNAs) function in multiple biological processes. However, whether …
Auto-and cross-regulation of the hnRNPs D and DL
K Kemmerer, S Fischer, JE Weigand - Rna, 2018 - rnajournal.cshlp.org
HnRNP D, better known as AUF1, is an extensively studied protein that controls a variety of
cellular pathways. Consequently, its expression has to be tightly regulated to prevent the …
cellular pathways. Consequently, its expression has to be tightly regulated to prevent the …
RNAdetector: a free user-friendly stand-alone and cloud-based system for RNA-Seq data analysis
Background RNA-Seq is a well-established technology extensively used for transcriptome
profiling, allowing the analysis of coding and non-coding RNA molecules. However, this …
profiling, allowing the analysis of coding and non-coding RNA molecules. However, this …
Multi-omics analysis in human retina uncovers ultraconserved cis-regulatory elements at rare eye disease loci
V Lopez Soriano, A Dueñas Rey, R Mukherjee… - Nature …, 2024 - nature.com
Cross-species genome comparisons have revealed a substantial number of ultraconserved
non-coding elements (UCNEs). Several of these elements have proved to be essential …
non-coding elements (UCNEs). Several of these elements have proved to be essential …
Computationally defined and in vitro validated putative genomic safe harbour loci for transgene expression in human cells
Selection of the target site is an inherent question for any project aiming for directed
transgene integration. Genomic safe harbour (GSH) loci have been proposed as safe sites …
transgene integration. Genomic safe harbour (GSH) loci have been proposed as safe sites …
Impact of genetic variation in gene regulatory sequences: A population genomics perspective
The unprecedented rise of high-throughput sequencing and assay technologies has
provided a detailed insight into the non-coding sequences and their potential role as gene …
provided a detailed insight into the non-coding sequences and their potential role as gene …
Frameshift alignment: statistics and post-genomic applications
Motivation: The alignment of DNA sequences to proteins, allowing for frameshifts, is a
classic method in sequence analysis. It can help identify pseudogenes (which accumulate …
classic method in sequence analysis. It can help identify pseudogenes (which accumulate …
Visual exploratory data analysis for copy number variation studies in biomedical research
Abstract The study of Copy Number Variations (CNVs) is recently emerging as a hot topic for
biomedical cancer research. While different data sources, websites, and tools concerning …
biomedical cancer research. While different data sources, websites, and tools concerning …