Cargando…

Robust detection of alternative splicing in a population of single cells

Single cell RNA-seq experiments provide valuable insight into cellular heterogeneity but suffer from low coverage, 3′ bias and technical noise. These unique properties of single cell RNA-seq data make study of alternative splicing difficult, and thus most single cell studies have restricted analysis...

Descripción completa

Detalles Bibliográficos
Autores principales:	Welch, Joshua D., Hu, Yin, Prins, Jan F.
Formato:	Online Artículo Texto
Lenguaje:	English
Publicado:	Oxford University Press 2016
Materias:	Methods Online
Acceso en línea:	https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4856971/ https://www.ncbi.nlm.nih.gov/pubmed/26740580 http://dx.doi.org/10.1093/nar/gkv1525

Ejemplares similares

DiffSplice: the genome-wide detection of differential splicing events with RNA-seq
por: Hu, Yin, et al.
Publicado: (2013)

SplicePie: a novel analytical approach for the detection of alternative, non-sequential and recursive splicing
por: Pulyakhina, Irina, et al.
Publicado: (2015)

Analysis of alternative splicing of cassette exons at single-cell level using two fluorescent proteins
por: Gurskaya, Nadya G., et al.
Publicado: (2012)

MARVEL: an integrated alternative splicing analysis platform for single-cell RNA sequencing data
por: Wen, Wei Xiong, et al.
Publicado: (2023)

EASI—enrichment of alternatively spliced isoforms
por: Venables, Julian P., et al.
Publicado: (2006)

A sensitive procedure to detect alternatively spliced mRNA in pooled-tissue samples
por: Leparc, Germán Gastón, et al.
Publicado: (2007)

SpliceTools, a suite of downstream RNA splicing analysis tools to investigate mechanisms and impact of alternative splicing
por: Flemington, Erik K, et al.
Publicado: (2023)

A bichromatic fluorescent reporter for cell-based screens of alternative splicing
por: Orengo, James P., et al.
Publicado: (2006)

MapSplice: Accurate mapping of RNA-seq reads for splice junction discovery
por: Wang, Kai, et al.
Publicado: (2010)

psichomics: graphical application for alternative splicing quantification and analysis
por: Saraiva-Agostinho, Nuno, et al.
Publicado: (2019)

MATS: a Bayesian framework for flexible detection of differential alternative splicing from RNA-Seq data
por: Shen, Shihao, et al.
Publicado: (2012)

Freddie: annotation-independent detection and discovery of transcriptomic alternative splicing isoforms using long-read sequencing
por: Orabi, Baraa, et al.
Publicado: (2022)

Comprehensive exon array data processing method for quantitative analysis of alternative spliced variants
por: Chen, Ping, et al.
Publicado: (2011)

Robust gene expression control in human cells with a novel universal TetR aptamer splicing module
por: Mol, Adam A, et al.
Publicado: (2019)

Overestimation of alternative splicing caused by variable probe characteristics in exon arrays
por: Gaidatzis, Dimos, et al.
Publicado: (2009)

Single molecule analysis of combinatorial splicing
por: Conze, Tim, et al.
Publicado: (2010)

A computational method for studying the relation between alternative splicing and DNA methylation
por: Zheng, Zejun, et al.
Publicado: (2016)

Robust lineage reconstruction from high-dimensional single-cell data
por: Giecold, Gregory, et al.
Publicado: (2016)

Single cell measurement of telomerase expression and splicing using microfluidic emulsion cultures
por: Novak, Richard, et al.
Publicado: (2015)

MATCHER: manifold alignment reveals correspondence between single cell transcriptome and epigenome dynamics
por: Welch, Joshua D., et al.
Publicado: (2017)

SLICER: inferring branched, nonlinear cellular trajectories from single cell RNA-seq data
por: Welch, Joshua D., et al.
Publicado: (2016)

Alternative-splicing-based bicistronic vectors for ratio-controlled protein expression and application to recombinant antibody production
por: Fallot, Stéphanie, et al.
Publicado: (2009)

Towards more robust methods of alien gene detection
por: Azad, Rajeev K., et al.
Publicado: (2011)

Detection and visualization of differential splicing in RNA-Seq data with JunctionSeq
por: Hartley, Stephen W., et al.
Publicado: (2016)

FineSplice, enhanced splice junction detection and quantification: a novel pipeline based on the assessment of diverse RNA-Seq alignment solutions
por: Gatto, Alberto, et al.
Publicado: (2014)

Robustly detecting differential expression in RNA sequencing data using observation weights
por: Zhou, Xiaobei, et al.
Publicado: (2014)

A FRET-based assay for characterization of alternative splicing events using peptide nucleic acid fluorescence in situ hybridization
por: Blanco, Ana M., et al.
Publicado: (2009)

Detection of alternative lengthening of telomeres by telomere quantitative PCR
por: Lau, Loretta M. S., et al.
Publicado: (2013)

High-throughput alternative splicing quantification by primer extension and matrix-assisted laser desorption/ionization time-of-flight mass spectrometry
por: McCullough, Ron M., et al.
Publicado: (2005)

A cell-based splicing reporter system to identify regulators of cis-splicing between adjacent genes
por: Chwalenia, Katarzyna, et al.
Publicado: (2019)

Robust detection of chromosomal interactions from small numbers of cells using low-input Capture-C
por: Oudelaar, A. Marieke, et al.
Publicado: (2017)

UnSplicer: mapping spliced RNA-seq reads in compact genomes and filtering noisy splicing
por: Burns, Paul D., et al.
Publicado: (2014)

Latent cellular analysis robustly reveals subtle diversity in large-scale single-cell RNA-seq data
por: Cheng, Changde, et al.
Publicado: (2019)

BlackOPs: increasing confidence in variant detection through mappability filtering
por: Cabanski, Christopher R., et al.
Publicado: (2013)

Human Splicing Finder: an online bioinformatics tool to predict splicing signals
por: Desmet, François-Olivier, et al.
Publicado: (2009)

TrueSight: a new algorithm for splice junction detection using RNA-seq
por: Li, Yang, et al.
Publicado: (2013)

A robust PCR primer design platform applied to the detection of Acidobacteria Group 1 in soil
por: Gans, Jason D., et al.
Publicado: (2012)

CoolMPS for robust sequencing of single-nuclear RNAs captured by droplet-based method
por: Hahn, Oliver, et al.
Publicado: (2020)

Splice-Break: exploiting an RNA-seq splice junction algorithm to discover mitochondrial DNA deletion breakpoints and analyses of psychiatric disorders
por: Hjelm, Brooke E, et al.
Publicado: (2019)

Analysis of splicing patterns by pyrosequencing
por: Méreau, Agnès, et al.
Publicado: (2009)

Cannot write session to /tmp/vufind_sessions/sess_crre8ikk2jbhi5ccbdmonc1vua