Towards a complete map of the human long non-coding RNA transcriptome

B Uszczynska-Ratajczak, J Lagarde… - Nature Reviews …, 2018 - nature.com
Gene maps, or annotations, enable us to navigate the functional landscape of our genome.
They are a resource upon which virtually all studies depend, from single-gene to genome …

Human long noncoding RNA interactome: detection, characterization and function

M Kazimierczyk, MK Kasprowicz, ME Kasprzyk… - International journal of …, 2020 - mdpi.com
The application of a new generation of sequencing techniques has revealed that most of the
genome has already been transcribed. However, only a small part of the genome codes …

GT-Scan: identifying unique genomic targets

A O'Brien, TL Bailey - Bioinformatics, 2014 - academic.oup.com
A number of technologies, including CRISPR/Cas, transcription activator-like effector
nucleases and zinc-finger nucleases, allow the user to target a chosen locus for genome …

Computational approaches for functional prediction and characterisation of long noncoding RNAs

B Signal, BS Gloss, ME Dinger - Trends in Genetics, 2016 - cell.com
Although a considerable portion of eukaryotic genomes is transcribed as long noncoding
RNAs (lncRNAs), the vast majority are functionally uncharacterised. The rapidly expanding …

Aid or antagonize: nuclear long noncoding RNAs regulate host responses and outcomes of viral infections

V Kulkarni, S Jayakumar, M Mohan, S Kulkarni - Cells, 2023 - mdpi.com
Long noncoding RNAs (lncRNAs) are transcripts measuring> 200 bp in length and devoid of
protein-coding potential. LncRNAs exceed the number of protein-coding mRNAs and …

TripDesign: a DNA triplex design approach based on interaction forces

L Sun, B Cao, Y Liu, P Shi, Y Zheng… - The Journal of …, 2022 - ACS Publications
A DNA triplex has the advantages of improved nanostructure stability and pH environment
responsiveness compared with single-stranded and double-stranded nucleic acids …

Prediction of lncRNAs and their interactions with nucleic acids: benchmarking bioinformatics tools

IV Antonov, E Mazurov, M Borodovsky… - Briefings in …, 2019 - academic.oup.com
The genomes of mammalian species are pervasively transcribed producing as many
noncoding as protein-coding RNAs. There is a growing body of evidence supporting their …

Deep learning based DNA: RNA triplex forming potential prediction

Y Zhang, Y Long, CK Kwoh - BMC bioinformatics, 2020 - Springer
Abstract Background Long non-coding RNAs (lncRNAs) can exert functions via forming
triplex with DNA. The current methods in predicting the triplex formation mainly rely on …

TTSBBC: triplex target site biomarkers and barcodes in cancer

M Ylagan, Q Xu, J Kowalski - Nucleic Acids Research, 2024 - academic.oup.com
The technology of triplex-forming oligonucleotides (TFOs) provides an approach to
manipulate genes at the DNA level. TFOs bind to specific sites on genomic DNA, creating a …

Biochemical methods to investigate lncRNA and the influence of lncRNA: protein complexes on chromatin

EJ McFadden, AE Hargrove - Biochemistry, 2016 - ACS Publications
Long noncoding RNAs (lncRNAs), defined as nontranslated transcripts greater than 200
nucleotides in length, are often differentially expressed throughout developmental stages …