A serine–arginine-rich (SR) splicing factor modulates alternative splicing of over a thousand genes in Toxoplasma gondii

Alternative splicing in human tumour viruses: a therapeutic target?

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A dual-targeted aminoacyl-tRNA synthetase inPlasmodium falciparumcharges cytosolic and apicoplast tRNACys

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voom: precision weights unlock linear model analysis tools for RNA-seq read counts

(2014) Charity W Law et al.   GENOME BIOLOGY

GenBank

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TopHat2: accurate alignment of transcriptomes in the presence of insertions, deletions and gene fusions

(2013) Daehwan Kim et al.   GENOME BIOLOGY

Antimalarial Activity of the Anticancer Histone Deacetylase Inhibitor SB939

(2012) Subathdrage D. M. Sumanadasa et al.   ANTIMICROBIAL AGENTS AND CHEMOTHERAPY

SpliceSeq: a resource for analysis and visualization of RNA-Seq data on alternative splicing and its functional impacts

(2012) Michael C. Ryan et al.   BIOINFORMATICS

RNA-SeQC: RNA-seq metrics for quality control and process optimization

(2012) David S. DeLuca et al.   BIOINFORMATICS

Geneious Basic: An integrated and extendable desktop software platform for the organization and analysis of sequence data

(2012) M. Kearse et al.   BIOINFORMATICS

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

(2012) Musa A Hassan et al.   BMC GENOMICS

Integrative Genomics Viewer (IGV): high-performance genomics data visualization and exploration

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Detecting differential usage of exons from RNA-seq data

(2012) S. Anders et al.   GENOME RESEARCH

Differential analysis of gene regulation at transcript resolution with RNA-seq

(2012) Cole Trapnell et al.   NATURE BIOTECHNOLOGY

Fiji: an open-source platform for biological-image analysis

(2012) Johannes Schindelin et al.   NATURE METHODS

The spliceosome as a target of novel antitumour drugs

(2012) Sophie Bonnal et al.   NATURE REVIEWS DRUG DISCOVERY

DiffSplice: the genome-wide detection of differential splicing events with RNA-seq

(2012) Yin Hu et al.   NUCLEIC ACIDS RESEARCH

Ensembl 2013

(2012) Paul Flicek et al.   NUCLEIC ACIDS RESEARCH

A novel Plasmodium falciparum SR protein is an alternative splicing factor required for the parasites’ proliferation in human erythrocytes

(2012) Shiri Eshar et al.   NUCLEIC ACIDS RESEARCH

Alternative transcription and alternative splicing in cancer

(2012) Sharmistha Pal et al.   PHARMACOLOGY & THERAPEUTICS

ApicoAP: The First Computational Model for Identifying Apicoplast-Targeted Proteins in Multiple Species of Apicomplexa

(2012) Gokcen Cilingir et al.   PLoS One

SpliceTrap: a method to quantify alternative splicing under single cellular conditions

(2011) Jie Wu et al.   BIOINFORMATICS

Identification of novel transcripts in annotated genomes using RNA-Seq

(2011) A. Roberts et al.   BIOINFORMATICS

Directional gene expression and antisense transcripts in sexual and asexual stages of Plasmodium falciparum

(2011) María J López-Barragán et al.   BMC GENOMICS

Two nucleus-localized CDK-like kinases with crucial roles for malaria parasite erythrocytic replication are involved in phosphorylation of splicing factor

(2011) Shruti Agarwal et al.   JOURNAL OF CELLULAR BIOCHEMISTRY

Improved techniques for endogenous epitope tagging and gene deletion in Toxoplasma gondii

(2011) Rajendra Upadhya et al.   JOURNAL OF MICROBIOLOGICAL METHODS

Jumbled Genomes: Missing Apicomplexan Synteny

(2011) J. D. DeBarry et al.   MOLECULAR BIOLOGY AND EVOLUTION

Fast, scalable generation of high-quality protein multiple sequence alignments using Clustal Omega

(2011) F. Sievers et al.   Molecular Systems Biology

SignalP 4.0: discriminating signal peptides from transmembrane regions

(2011) Thomas Nordahl Petersen et al.   NATURE METHODS

RNA-Seq analysis of splicing in Plasmodium falciparum uncovers new splice junctions, alternative splicing and splicing of antisense transcripts

(2011) K. Sorber et al.   NUCLEIC ACIDS RESEARCH

Plant serine/arginine-rich proteins: roles in precursor messenger RNA splicing, plant development, and stress responses

(2011) Anireddy S. N. Reddy et al.   Wiley Interdisciplinary Reviews-RNA

A rational nomenclature for serine/arginine-rich protein splicing factors (SR proteins)

(2010) J. L. Manley et al.   GENES & DEVELOPMENT

Plastid-associated Porphobilinogen Synthase fromToxoplasma gondii

(2010) Dhanasekaran Shanmugam et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

PfSRPK1, a Novel Splicing-related Kinase fromPlasmodium falciparum

(2010) Aparna Dixit et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

New insights into the blood-stage transcriptome ofPlasmodium falciparumusing RNA-Seq

(2010) Thomas D. Otto et al.   MOLECULAR MICROBIOLOGY

Mitochondrial translation in absence of local tRNA aminoacylation and methionyl tRNAMet formylation in Apicomplexa

(2010) Paco Pino et al.   MOLECULAR MICROBIOLOGY

Alternative expression analysis by RNA sequencing

(2010) Malachi Griffith et al.   NATURE METHODS

Analysis and design of RNA sequencing experiments for identifying isoform regulation

(2010) Yarden Katz et al.   NATURE METHODS

Alternative splicing and evolution: diversification, exon definition and function

(2010) Hadas Keren et al.   NATURE REVIEWS GENETICS

Prediction of alternative isoforms from exon expression levels in RNA-Seq experiments

(2010) Hugues Richard et al.   NUCLEIC ACIDS RESEARCH

Coordinated Progression through Two Subtranscriptomes Underlies the Tachyzoite Cycle of Toxoplasma gondii

(2010) Michael S. Behnke et al.   PLoS One

New Algorithms and Methods to Estimate Maximum-Likelihood Phylogenies: Assessing the Performance of PhyML 3.0

(2010) Stéphane Guindon et al.   SYSTEMATIC BIOLOGY

Histone Deacetylases Play a Major Role in the Transcriptional Regulation of the Plasmodium falciparum Life Cycle

(2010) Balbir K. Chaal et al.   PLoS Pathogens

Concerted Action of Two Formins in Gliding Motility and Host Cell Invasion by Toxoplasma gondii

(2010) Wassim Daher et al.   PLoS Pathogens

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

A Novel Dynamin-Related Protein Has Been Recruited for Apicoplast Fission in Toxoplasma gondii

(2009) Giel G. van Dooren et al.   CURRENT BIOLOGY

Tagging of Endogenous Genes in aToxoplasma gondiiStrain Lacking Ku80

(2009) My-Hang Huynh et al.   EUKARYOTIC CELL

A small-scale systematic analysis of alternative splicing in Plasmodium falciparum

(2009) Hideyuki Iriko et al.   PARASITOLOGY INTERNATIONAL

The SR protein family

(2009) Peter J Shepard et al.   GENOME BIOLOGY

BioVenn – a web application for the comparison and visualization of biological lists using area-proportional Venn diagrams

(2008) Tim Hulsen et al.   BMC GENOMICS

Alternative isoform regulation in human tissue transcriptomes

(2008) Eric T. Wang et al.   NATURE

PlasmoDB: a functional genomic database for malaria parasites

(2008) C. Aurrecoechea et al.   NUCLEIC ACIDS RESEARCH

Toxoplasma gondii Tic20 is essential for apicoplast protein import

(2008) G. G. van Dooren et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA