Cargando…

ncOrtho: efficient and reliable identification of miRNA orthologs

MicroRNAs (miRNAs) are post-transcriptional regulators that finetune gene expression via translational repression or degradation of their target mRNAs. Despite their functional relevance, frameworks for the scalable and accurate detection of miRNA orthologs are missing. Consequently, there is still...

Descripción completa

Detalles Bibliográficos
Autores principales:	Langschied, Felix, Leisegang, Matthias S, Brandes, Ralf P, Ebersberger, Ingo
Formato:	Online Artículo Texto
Lenguaje:	English
Publicado:	Oxford University Press 2023
Materias:	Methods Online
Acceso en línea:	https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10359484/ https://www.ncbi.nlm.nih.gov/pubmed/37260093 http://dx.doi.org/10.1093/nar/gkad467

Ejemplares similares

Efficient large-scale protein sequence comparison and gene matching to identify orthologs and co-orthologs
por: Mahmood, Khalid, et al.
Publicado: (2012)

OrthoClust: an orthology-based network framework for clustering data across multiple species
por: Yan, Koon-Kiu, et al.
Publicado: (2014)

OrthoGNC: A Software for Accurate Identification of Orthologs Based on Gene Neighborhood Conservation
por: Jahangiri-Tazehkand, Soheil, et al.
Publicado: (2017)

Identification and classification of ncRNA molecules using graph properties
por: Childs, Liam, et al.
Publicado: (2009)

An approach of orthology detection from homologous sequences under minimum evolution
por: Kim, Kyung Mo, et al.
Publicado: (2008)

QuartetS: a fast and accurate algorithm for large-scale orthology detection
por: Yu, Chenggang, et al.
Publicado: (2011)

miRdentify: high stringency miRNA predictor identifies several novel animal miRNAs
por: Hansen, Thomas B., et al.
Publicado: (2014)

miRNA target enrichment analysis reveals directly active miRNAs in health and disease
por: Steinfeld, Israel, et al.
Publicado: (2013)

Polysome shift assay for direct measurement of miRNA inhibition by anti-miRNA drugs
por: Androsavich, John R., et al.
Publicado: (2016)

Lentivirus-mediated antagomir expression for specific inhibition of miRNA function
por: Scherr, Michaela, et al.
Publicado: (2007)

Locking-to-unlocking system is an efficient strategy to design DNA/silver nanoclusters (AgNCs) probe for human miRNAs
por: Shah, Pratik, et al.
Publicado: (2016)

Impact of probe annotation on the integration of miRNA–mRNA expression profiles for miRNA target detection
por: Sales, Gabriele, et al.
Publicado: (2010)

Wiring miRNAs to pathways: a topological approach to integrate miRNA and mRNA expression profiles
por: Calura, Enrica, et al.
Publicado: (2014)

TALEN/CRISPR-mediated engineering of a promoterless anti-viral RNAi hairpin into an endogenous miRNA locus
por: Senís, Elena, et al.
Publicado: (2017)

RNPomics: Defining the ncRNA transcriptome by cDNA library generation from ribonucleo-protein particles
por: Rederstorff, Mathieu, et al.
Publicado: (2010)

miSTAR: miRNA target prediction through modeling quantitative and qualitative miRNA binding site information in a stacked model structure
por: Van Peer, Gert, et al.
Publicado: (2017)

Subtractive hybridization identifies novel differentially expressed ncRNA species in EBV-infected human B cells
por: Mrázek, Jan, et al.
Publicado: (2007)

Vicinal: a method for the determination of ncRNA ends using chimeric reads from RNA-seq experiments
por: Lu, Zhipeng, et al.
Publicado: (2014)

Integrative analysis of gene and miRNA expression profiles with transcription factor–miRNA feed-forward loops identifies regulators in human cancers
por: Yan, Zhenyu, et al.
Publicado: (2012)

miRVaS: a tool to predict the impact of genetic variants on miRNAs
por: Cammaerts, Sophia, et al.
Publicado: (2016)

Integration of sequence-similarity and functional association information can overcome intrinsic problems in orthology mapping across bacterial genomes
por: Li, Guojun, et al.
Publicado: (2011)

MetaPhOrs: orthology and paralogy predictions from multiple phylogenetic evidence using a consistency-based confidence score
por: Pryszcz, Leszek P., et al.
Publicado: (2011)

Prioritizing and selecting likely novel miRNAs from NGS data
por: Backes, Christina, et al.
Publicado: (2016)

Multiplexed miRNA northern blots via hybridization chain reaction
por: Schwarzkopf, Maayan, et al.
Publicado: (2016)

sPARTA: a parallelized pipeline for integrated analysis of plant miRNA and cleaved mRNA data sets, including new miRNA target-identification software
por: Kakrana, Atul, et al.
Publicado: (2014)

miRspring: a compact standalone research tool for analyzing miRNA-seq data
por: Humphreys, David T., et al.
Publicado: (2013)

PanOCT: automated clustering of orthologs using conserved gene neighborhood for pan-genomic analysis of bacterial strains and closely related species
por: Fouts, Derrick E., et al.
Publicado: (2012)

A fast ab-initio method for predicting miRNA precursors in genomes
por: Tempel, Sébastien, et al.
Publicado: (2012)

Tandem affinity purification of miRNA target mRNAs (TAP-Tar)
por: Nonne, Nora, et al.
Publicado: (2010)

Sensitive and specific miRNA detection method using SplintR Ligase
por: Jin, Jingmin, et al.
Publicado: (2016)

Identification of active miRNA promoters from nuclear run-on RNA sequencing
por: Liu, Qi, et al.
Publicado: (2017)

Design and implementation of a synthetic pre-miR switch for controlling miRNA biogenesis in mammals
por: Atanasov, Janina, et al.
Publicado: (2017)

OrthoSNAP: A tree splitting and pruning algorithm for retrieving single-copy orthologs from gene family trees
por: Steenwyk, Jacob L., et al.
Publicado: (2022)

Rapid identification of regulatory microRNAs by miTRAP (miRNA trapping by RNA in vitro affinity purification)
por: Braun, Juliane, et al.
Publicado: (2014)

Identification of miRNA targets with stable isotope labeling by amino acids in cell culture
por: Vinther, Jeppe, et al.
Publicado: (2006)

A high throughput experimental approach to identify miRNA targets in human cells
por: Tan, Lu Ping, et al.
Publicado: (2009)

Heterogeneous ensemble approach with discriminative features and modified-SMOTEbagging for pre-miRNA classification
por: Lertampaiporn, Supatcha, et al.
Publicado: (2013)

3′LIFE: a functional assay to detect miRNA targets in high-throughput
por: Wolter, Justin M., et al.
Publicado: (2014)

RILES, a novel method for temporal analysis of the in vivo regulation of miRNA expression
por: Ezzine, Safia, et al.
Publicado: (2013)

Quantitative analysis of conditional gene inactivation using rationally designed, tetracycline-controlled miRNAs
por: Berger, Stefan M., et al.
Publicado: (2010)

Cannot write session to /tmp/vufind_sessions/sess_6cd86fqtv1rlb7qf0v2t6hps2i