Cargando…

Directed acyclic graph kernels for structural RNA analysis

BACKGROUND: Recent discoveries of a large variety of important roles for non-coding RNAs (ncRNAs) have been reported by numerous researchers. In order to analyze ncRNAs by kernel methods including support vector machines, we propose stem kernels as an extension of string kernels for measuring the si...

Descripción completa

Detalles Bibliográficos
Autores principales:	Sato, Kengo, Mituyama, Toutai, Asai, Kiyoshi, Sakakibara, Yasubumi
Formato:	Texto
Lenguaje:	English
Publicado:	BioMed Central 2008
Materias:	Methodology Article
Acceso en línea:	https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2515856/ https://www.ncbi.nlm.nih.gov/pubmed/18647390 http://dx.doi.org/10.1186/1471-2105-9-318

Ejemplares similares

Software.ncrna.org: web servers for analyses of RNA sequences
por: Asai, Kiyoshi, et al.
Publicado: (2008)

CentroidFold: a web server for RNA secondary structure prediction
por: Sato, Kengo, et al.
Publicado: (2009)

Predictions of RNA secondary structure by combining homologous sequence information
por: Hamada, Michiaki, et al.
Publicado: (2009)

A shortcut for multiple testing on the directed acyclic graph of gene ontology
por: Saunders, Garrett, et al.
Publicado: (2014)

Efficient representation of uncertainty in multiple sequence alignments using directed acyclic graphs
por: Herman, Joseph L, et al.
Publicado: (2015)

Prediction of Conserved Precursors of miRNAs and Their Mature Forms by Integrating Position-Specific Structural Features
por: Terai, Goro, et al.
Publicado: (2012)

Direct Inference of Base-Pairing Probabilities with Neural Networks Improves Prediction of RNA Secondary Structures with Pseudoknots
por: Akiyama, Manato, et al.
Publicado: (2022)

Assessing causal relationships in genomics: From Bradford-Hill criteria to complex gene-environment interactions and directed acyclic graphs
por: Geneletti, Sara, et al.
Publicado: (2011)

A directed acyclic graph for interactions
por: Nilsson, Anton, et al.
Publicado: (2020)

Genome-wide searching with base-pairing kernel functions for noncoding RNAs: computational and expression analysis of snoRNA families in Caenorhabditis elegans
por: Morita, Kensuke, et al.
Publicado: (2009)

RNA secondary structure prediction using deep learning with thermodynamic integration
por: Sato, Kengo, et al.
Publicado: (2021)

Reducing bias through directed acyclic graphs
por: Shrier, Ian, et al.
Publicado: (2008)

Phasertng: directed acyclic graphs for crystallographic phasing
por: McCoy, Airlie J., et al.
Publicado: (2021)

Discovery of short pseudogenes derived from messenger RNAs
por: Terai, Goro, et al.
Publicado: (2010)

Evidence synthesis for constructing directed acyclic graphs (ESC-DAGs): a novel and systematic method for building directed acyclic graphs
por: Ferguson, Karl D, et al.
Publicado: (2020)

Corrigendum to: Evidence synthesis for constructing directed acyclic graphs (ESC-DAGs): a novel and systematic method for building directed acyclic graphs
por: Ferguson, Karl D, et al.
Publicado: (2019)

Directed acyclic graphs for clinical research: a tutorial
por: Byeon, Sangmin, et al.
Publicado: (2023)

Improved Measurements of RNA Structure Conservation with Generalized Centroid Estimators
por: Okada, Yohei, et al.
Publicado: (2011)

Enumerating consistent sub-graphs of directed acyclic graphs: an insight into biomedical ontologies
por: Peng, Yisu, et al.
Publicado: (2018)

Directed Acyclic Graphs: a Tool for Causal Studies in Pediatrics
por: Williams, Thomas C, et al.
Publicado: (2018)

Inference for a Large Directed Acyclic Graph with Unspecified Interventions
por: Li, Chunlin, et al.
Publicado: (2023)

Statistical Tests for Associations between Two Directed Acyclic Graphs
por: Hoehndorf, Robert, et al.
Publicado: (2010)

Reducing bias in experimental ecology through directed acyclic graphs
por: Arif, Suchinta, et al.
Publicado: (2023)

A Max-Margin Model for Predicting Residue—Base Contacts in Protein–RNA Interactions
por: Kashiwagi, Shunya, et al.
Publicado: (2021)

The dawn of directed acyclic graphs in primary care research and education
por: Iwata, Hiroyoshi, et al.
Publicado: (2023)

The Functional RNA Database 3.0: databases to support mining and annotation of functional RNAs
por: Mituyama, Toutai, et al.
Publicado: (2009)

Fast and accurate clustering of noncoding RNAs using ensembles of sequence alignments and secondary structures
por: Saito, Yutaka, et al.
Publicado: (2011)

Acyclic Matching in Some Subclasses of Graphs
por: Panda, B. S., et al.
Publicado: (2020)

Learning directed acyclic graphs from large-scale genomics data
por: Nikolay, Fabio, et al.
Publicado: (2017)

Directed acyclic graphs and causal thinking in clinical risk prediction modeling
por: Piccininni, Marco, et al.
Publicado: (2020)

Detection of differentially methylated regions from bisulfite-seq data by hidden Markov models incorporating genome-wide methylation level distributions
por: Saito, Yutaka, et al.
Publicado: (2015)

Using Directed Acyclic Graphs in Epidemiological Research in Psychosis: An Analysis of the Role of Bullying in Psychosis
por: Moffa, Giusi, et al.
Publicado: (2017)

Estimating and testing direct genetic effects in directed acyclic graphs using estimating equations
por: Konigorski, Stefan, et al.
Publicado: (2017)

Representing and extending ensembles of parsimonious evolutionary histories with a directed acyclic graph
por: Dumm, Will, et al.
Publicado: (2023)

MetaVelvet-SL: an extension of the Velvet assembler to a de novo metagenomic assembler utilizing supervised learning
por: Afiahayati,, et al.
Publicado: (2015)

An extended genovo metagenomic assembler by incorporating paired-end information
por: , Afiahayati, et al.
Publicado: (2013)

Bisulfighter: accurate detection of methylated cytosines and differentially methylated regions
por: Saito, Yutaka, et al.
Publicado: (2014)

Inferring Regulatory Networks From Mixed Observational Data Using Directed Acyclic Graphs
por: Zhong, Wujuan, et al.
Publicado: (2020)

A Framework for the Optimization of Complex Cyber-Physical Systems via Directed Acyclic Graph
por: Castejón-Limas, Manuel, et al.
Publicado: (2022)

Using Causal Loop Diagrams (CLDs) to inform the development of Directed Acyclic Graphs (DAGs)
por: Avila-Palencia, I
Publicado: (2023)

Cannot write session to /tmp/vufind_sessions/sess_d4j6h6mdsmbi7e9gjmob91hlif