(Q49025200)

English

SQANTI: extensive characterization of long-read transcript sequences for quality control in full-length transcriptome identification and quantification.

scientific article published on 9 February 2018

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scholarly article

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Europe PubMed Central

PMC publication ID

30 June 2018

http://europepmc.org/abstract/PMC/5848618

SQANTI: extensive characterization of long-read transcript sequences for quality control in full-length transcriptome identification and quantification. (English)

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Europe PubMed Central

PMC publication ID

30 June 2018

http://europepmc.org/abstract/PMC/5848618

quality control

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Cristina Martí

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Cristina Marti

3

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Susana Rodriguez-Navarro

object named as

Susana Rodriguez-Navarro

17

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12

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Iakes Ezkurdia

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30 June 2018

Lennart Martens

16

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Lennart Martens

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Europe PubMed Central

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30 June 2018

http://europepmc.org/abstract/PMC/5848618

author name string

Manuel Tardaguila

1

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Europe PubMed Central

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30 June 2018

http://europepmc.org/abstract/PMC/5848618

Lorena de la Fuente

2

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30 June 2018

http://europepmc.org/abstract/PMC/5848618

Cécile Pereira

4

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Europe PubMed Central

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30 June 2018

http://europepmc.org/abstract/PMC/5848618

Francisco Jose Pardo-Palacios

5

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30 June 2018

http://europepmc.org/abstract/PMC/5848618

Hector Del Risco

6

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30 June 2018

http://europepmc.org/abstract/PMC/5848618

Marc Ferrell

7

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30 June 2018

http://europepmc.org/abstract/PMC/5848618

Maravillas Mellado

8

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30 June 2018

http://europepmc.org/abstract/PMC/5848618

Marissa Macchietto

9

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30 June 2018

http://europepmc.org/abstract/PMC/5848618

Kenneth Verheggen

10

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30 June 2018

http://europepmc.org/abstract/PMC/5848618

Mariola Edelmann

11

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Europe PubMed Central

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30 June 2018

http://europepmc.org/abstract/PMC/5848618

Jesus Vazquez

13

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Europe PubMed Central

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30 June 2018

http://europepmc.org/abstract/PMC/5848618

Michael Tress

14

1 reference

Europe PubMed Central

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30 June 2018

http://europepmc.org/abstract/PMC/5848618

Ali Mortazavi

15

1 reference

Europe PubMed Central

PMC publication ID

30 June 2018

http://europepmc.org/abstract/PMC/5848618

Victoria Moreno-Manzano

18

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Europe PubMed Central

PMC publication ID

30 June 2018

http://europepmc.org/abstract/PMC/5848618

Ana Conesa

19

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Europe PubMed Central

PMC publication ID

30 June 2018

http://europepmc.org/abstract/PMC/5848618

publication date

9 February 2018

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Europe PubMed Central

PMC publication ID

30 June 2018

http://europepmc.org/abstract/PMC/5848618

Genome Research

1 reference

Europe PubMed Central

PMC publication ID

30 June 2018

http://europepmc.org/abstract/PMC/5848618

Evaluation and comparison of computational tools for RNA-seq isoform quantification

1 reference

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1 reference

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The ribosome-engaged landscape of alternative splicing

1 reference

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Alternative Splicing May Not Be the Key to Proteome Complexity

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Benchmarking of the Oxford Nanopore MinION sequencing for quantitative and qualitative assessment of cDNA populations

1 reference

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Human Proteome Project Mass Spectrometry Data Interpretation Guidelines 2.1.

1 reference

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1 reference

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cDNA Library Enrichment of Full Length Transcripts for SMRT Long Read Sequencing.

1 reference

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Isoform prefiltering improves performance of count-based methods for analysis of differential transcript usage.

1 reference

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Cytoplasmic Rbfox1 Regulates the Expression of Synaptic and Autism-Related Genes.

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Cell type- and brain region-resolved mouse brain proteome.

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Pladipus Enables Universal Distributed Computing in Proteomics Bioinformatics.

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Characterization of glucose-related metabolic pathways in differentiated rat oligodendrocyte lineage cells

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Widespread Polycistronic Transcripts in Fungi Revealed by Single-Molecule mRNA Sequencing

1 reference

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Alternative Splicing in the Mammalian Nervous System: Recent Insights into Mechanisms and Functional Roles

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Comprehensive transcriptome analysis using synthetic long-read sequencing reveals molecular co-association of distant splicing events

1 reference

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Identification of protein coding regions in RNA transcripts

1 reference

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3 July 2018

Most highly expressed protein-coding genes have a single dominant isoform.

1 reference

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A highly conserved program of neuronal microexons is misregulated in autistic brains

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A comprehensive survey of non-canonical splice sites in the human transcriptome.

1 reference

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proovread: large-scale high-accuracy PacBio correction through iterative short read consensus

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3 July 2018

Defining a personal, allele-specific, and single-molecule long-read transcriptome

1 reference

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3 July 2018

Increasing the Coding Potential of Genomes Through Alternative Splicing: The Case of PARK2 Gene.

1 reference

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3 July 2018

Proteomic analysis of mouse astrocytes and their secretome by a combination of FASP and StageTip-based, high pH, reversed-phase fractionation

1 reference

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Alternative splicing in cancer: implications for biology and therapy

1 reference

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Characterization of the human ESC transcriptome by hybrid sequencing

1 reference

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3 July 2018

An approach to correlate tandem mass spectral data of peptides with amino acid sequences in a protein database

1 reference

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3 July 2018

Assessment of transcript reconstruction methods for RNA-seq

1 reference

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3 July 2018

A single-molecule long-read survey of the human transcriptome

1 reference

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3 July 2018

Aberrant alternative splicing is another hallmark of cancer

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3' UTR-isoform choice has limited influence on the stability and translational efficiency of most mRNAs in mouse fibroblasts

1 reference

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3 July 2018

Frac-seq reveals isoform-specific recruitment to polyribosomes

1 reference

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3 July 2018

Alternative RNA splicing and cancer

1 reference

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Control of alternative splicing in immune responses: many regulators, many predictions, much still to learn

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Accurate identification and analysis of human mRNA isoforms using deep long read sequencing

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CUG-BP, Elav-like family (CELF)-mediated alternative splicing regulation in the brain during health and disease.

1 reference

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iReckon: simultaneous isoform discovery and abundance estimation from RNA-seq data

1 reference

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3 July 2018

APPRIS: annotation of principal and alternative splice isoforms

1 reference

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3 July 2018

STAR: ultrafast universal RNA-seq aligner

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5848618

3 July 2018

Sequencing the unsequenceable: expanded CGG-repeat alleles of the fragile X gene

1 reference

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3 July 2018

Improving PacBio long read accuracy by short read alignment

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5848618

3 July 2018

Pacific biosciences sequencing technology for genotyping and variation discovery in human data

1 reference

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3 July 2018

Primer-BLAST: a tool to design target-specific primers for polymerase chain reaction

1 reference

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3 July 2018

The importance of identifying alternative splicing in vertebrate genome annotation

1 reference

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The human pancreatic islet transcriptome: expression of candidate genes for type 1 diabetes and the impact of pro-inflammatory cytokines

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3 July 2018

Fast gapped-read alignment with Bowtie 2

1 reference

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3 July 2018

SpliceGrapher: detecting patterns of alternative splicing from RNA-Seq data in the context of gene models and EST data

1 reference

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RSEM: accurate transcript quantification from RNA-Seq data with or without a reference genome

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The origins, evolution, and functional potential of alternative splicing in vertebrates

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Apparent non-canonical trans-splicing is generated by reverse transcriptase in vitro

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Function annotation of the rice transcriptome at single-nucleotide resolution by RNA-seq

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Gene ontology analysis for RNA-seq: accounting for selection bias

1 reference

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RNA-Seq: a revolutionary tool for transcriptomics

1 reference

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1 reference

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1 reference

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1 reference

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1 reference

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1 reference

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Mechanisms of alternative pre-messenger RNA splicing

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14 August 2018

PeptideShaker enables reanalysis of MS-derived proteomics data sets.

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LoRDEC: accurate and efficient long read error correction.

1 reference

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14 August 2018

SearchGUI: An open-source graphical user interface for simultaneous OMSSA and X!Tandem searches.

1 reference

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14 August 2018

Boosting neural networks.

1 reference

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14 August 2018

Identifiers

10.1101/GR.222976.117

1 reference

Europe PubMed Central

PMC publication ID

30 June 2018

http://europepmc.org/abstract/PMC/5848618

PMC publication ID

1 reference

Europe PubMed Central

PMC publication ID

30 June 2018

http://europepmc.org/abstract/PMC/5848618

PubMed publication ID

1 reference

Europe PubMed Central

PMC publication ID

30 June 2018

http://europepmc.org/abstract/PMC/5848618

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