(Q34508599)

English

De novo reconstruction of the Toxoplasma gondii transcriptome improves on the current genome annotation and reveals alternatively spliced transcripts and putative long non-coding RNAs

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scholarly article

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Europe PubMed Central

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:23231500%20AND%20SRC:MED&resulttype=core&format=json

20 February 2020

De novo reconstruction of the Toxoplasma gondii transcriptome improves on the current genome annotation and reveals alternatively spliced transcripts and putative long non-coding RNAs (English)

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Europe PubMed Central

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:23231500%20AND%20SRC:MED&resulttype=core&format=json

20 February 2020

Toxoplasma gondii

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genome annotation

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based on heuristic

inferred from title

1

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20 February 2020

2

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20 February 2020

5

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20 February 2020

author name string

Brian Haas

3

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20 February 2020

Kirk D C Jensen

4

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20 February 2020

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publication date

12 December 2012

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20 February 2020

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20 February 2020

13

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20 February 2020

696

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20 February 2020

Admixture and recombination among Toxoplasma gondii lineages explain global genome diversity

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3543268

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A simple strand-specific RNA-Seq library preparation protocol combining the Illumina TruSeq RNA and the dUTP methods

1 reference

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7 July 2018

Conditional mutagenesis of a novel choline kinase demonstrates plasticity of phosphatidylcholine biogenesis and gene expression in Toxoplasma gondii

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3543268

7 July 2018

Targeted disruption of Toxoplasma gondii serine protease inhibitor 1 increases bradyzoite cyst formation in vitro and parasite tissue burden in mice

1 reference

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7 July 2018

Conserved function of lincRNAs in vertebrate embryonic development despite rapid sequence evolution

1 reference

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7 July 2018

Systematic identification of long noncoding RNAs expressed during zebrafish embryogenesis

1 reference

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7 July 2018

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1 reference

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7 July 2018

Next-generation transcriptome assembly

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7 July 2018

Toxoplasma polymorphic effectors determine macrophage polarization and intestinal inflammation.

1 reference

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7 July 2018

Computational methods for transcriptome annotation and quantification using RNA-seq

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3543268

7 July 2018

Full-length transcriptome assembly from RNA-Seq data without a reference genome

1 reference

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7 July 2018

Comparative functional genomics of the fission yeasts

1 reference

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7 July 2018

Integrative genomics viewer

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7 July 2018

Analysis and design of RNA sequencing experiments for identifying isoform regulation

1 reference

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7 July 2018

Full-parasites: database of full-length cDNAs of apicomplexa parasites, 2010 update

1 reference

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7 July 2018

De novo assembly and analysis of RNA-seq data.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3543268

7 July 2018

Optimization of de novo transcriptome assembly from next-generation sequencing data

1 reference

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7 July 2018

Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation

1 reference

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7 July 2018

Ab initio reconstruction of cell type-specific transcriptomes in mouse reveals the conserved multi-exonic structure of lincRNAs

1 reference

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7 July 2018

BEDTools: a flexible suite of utilities for comparing genomic features

1 reference

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7 July 2018

RNA-Seq: a method for comprehensive transcriptome analysis

1 reference

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7 July 2018

A strand-specific RNA-Seq analysis of the transcriptome of the typhoid bacillus Salmonella typhi

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3543268

7 July 2018

Inconsistencies of genome annotations in apicomplexan parasites revealed by 5'-end-one-pass and full-length sequences of oligo-capped cDNAs

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3543268

7 July 2018

De novo transcriptome assembly with ABySS.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3543268

7 July 2018

SOAP2: an improved ultrafast tool for short read alignment

1 reference

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7 July 2018

Whole genome sequencing of a natural recombinant Toxoplasma gondii strain reveals chromosome sorting and local allelic variants

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3543268

7 July 2018

TopHat: discovering splice junctions with RNA-Seq

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3543268

7 July 2018

Ultrafast and memory-efficient alignment of short DNA sequences to the human genome

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3543268

7 July 2018

Evolution and functions of long noncoding RNAs

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3543268

7 July 2018

Ab initio construction of a eukaryotic transcriptome by massively parallel mRNA sequencing

1 reference

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7 July 2018

RNA-Seq: a revolutionary tool for transcriptomics

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3543268

7 July 2018

Alternative isoform regulation in human tissue transcriptomes

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3543268

7 July 2018

Population structure of Toxoplasma gondii: clonal expansion driven by infrequent recombination and selective sweeps

1 reference

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7 July 2018

Mapping and quantifying mammalian transcriptomes by RNA-Seq

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7 July 2018

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1 reference

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7 July 2018

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7 July 2018

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1 reference

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7 July 2018

ToxoDB: an integrated Toxoplasma gondii database resource

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3543268

7 July 2018

Bradyzoite-specific surface antigen SRS9 plays a role in maintaining Toxoplasma gondii persistence in the brain and in host control of parasite replication in the intestine

1 reference

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7 July 2018

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7 July 2018

1 reference

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7 July 2018

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1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3543268

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Improving the Arabidopsis genome annotation using maximal transcript alignment assemblies

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3543268

7 July 2018

Gene discovery in the apicomplexa as revealed by EST sequencing and assembly of a comparative gene database

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3543268

7 July 2018

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1 reference

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7 July 2018

Integrating genomic homology into gene structure prediction.

1 reference

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7 July 2018

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21 January 2018

Molecular characterisation of an expressed sequence tag locus of Toxoplasma gondii encoding the micronemal protein MIC2.

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21 January 2018

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27 October 2018

Advancing RNA-Seq analysis

1 reference

https://pubmed.ncbi.nlm.nih.gov/23231500

12 December 2020

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10.1186/1471-2164-13-696

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Europe PubMed Central

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20 February 2020

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Europe PubMed Central

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:23231500%20AND%20SRC:MED&resulttype=core&format=json

20 February 2020

1 reference

Europe PubMed Central

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:23231500%20AND%20SRC:MED&resulttype=core&format=json

20 February 2020

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