In silico analysis of the sequence features responsible for alternatively spliced introns in the model green alga Chlamydomonas reinhardtii

Comparative Analyses between Retained Introns and Constitutively Spliced Introns in Arabidopsis thaliana Using Random Forest and Support Vector Machine

(2014) Rui Mao et al.   PLoS One

The Chlamydomonas genome project: a decade on

(2014) Ian K. Blaby et al.   TRENDS IN PLANT SCIENCE

Bioinformatics Analysis of Alternative Polyadenylation in Green Alga Chlamydomonas reinhardtii Using Transcriptome Sequences from Three Different Sequencing Platforms

(2014) Zhixin Zhao et al.   G3-Genes Genomes Genetics

The functional consequences of intron retention: Alternative splicing coupled to NMD as a regulator of gene expression

(2013) Ying Ge et al.   BIOESSAYS

Orchestrated Intron Retention Regulates Normal Granulocyte Differentiation

(2013) Justin J.-L. Wong et al.   CELL

Regulation of Axon Guidance by Compartmentalized Nonsense-Mediated mRNA Decay

(2013) Dilek Colak et al.   CELL

Software for Computing and Annotating Genomic Ranges

(2013) Michael Lawrence et al.   PLoS Computational Biology

Transcriptome survey reveals increased complexity of the alternative splicing landscape inArabidopsis

(2012) Yamile Marquez et al.   GENOME RESEARCH

On the physiological significance of alternative splicing events in higher plants

(2012) Raquel F. Carvalho et al.   PROTOPLASMA

Cotranscriptional splicing efficiency differs dramatically between Drosophila and mouse

(2012) Y. L. Khodor et al.   RNA

Alternative splicing in plants – coming of age

(2012) Naeem H. Syed et al.   TRENDS IN PLANT SCIENCE

Exon and intron definition in pre-mRNA splicing

(2012) Laura De Conti et al.   Wiley Interdisciplinary Reviews-RNA

Deciphering the Plant Splicing Code: Experimental and Computational Approaches for Predicting Alternative Splicing and Splicing Regulatory Elements

(2012) Anireddy S. N. Reddy et al.   Frontiers in Plant Science

Integrative genomics viewer

(2011) James T Robinson et al.   NATURE BIOTECHNOLOGY

Measurements of genomic GC content in plant genomes with flow cytometry: a test for reliability

(2011) Petr Šmarda et al.   NEW PHYTOLOGIST

Two splice variants of the IDD14 transcription factor competitively form nonfunctional heterodimers which may regulate starch metabolism

(2011) Pil Joon Seo et al.   Nature Communications

Genome-wide analysis of alternative splicing in Chlamydomonas reinhardtii

(2010) Adam Labadorf et al.   BMC GENOMICS

Transcriptome sequencing and comparative analysis of cucumber flowers with different sex types

(2010) Shaogui Guo et al.   BMC GENOMICS

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

(2010) T. Lu et al.   GENOME RESEARCH

Contrasting GC-content dynamics across 33 mammalian genomes: Relationship with life-history traits and chromosome sizes

(2010) J. Romiguier et al.   GENOME RESEARCH

Deep RNA sequencing at single base-pair resolution reveals high complexity of the rice transcriptome

(2010) G. Zhang et al.   GENOME RESEARCH

Alternative splicing and evolution: diversification, exon definition and function

(2010) Hadas Keren et al.   NATURE REVIEWS GENETICS

Evolution of an Expanded Sex-Determining Locus in Volvox

(2010) P. Ferris et al.   SCIENCE

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

Genome-wide mapping of alternative splicing in Arabidopsis thaliana

(2009) S. A. Filichkin et al.   GENOME RESEARCH

Genome-wide analyses of alternative splicing in plants: Opportunities and challenges

(2008) W. B. Barbazuk et al.   GENOME RESEARCH

Deep surveying of alternative splicing complexity in the human transcriptome by high-throughput sequencing

(2008) Qun Pan et al.   NATURE GENETICS

Genome level analysis of rice mRNA 3′-end processing signals and alternative polyadenylation

(2008) Yingjia Shen et al.   NUCLEIC ACIDS RESEARCH

A General Definition and Nomenclature for Alternative Splicing Events

(2008) Michael Sammeth et al.   PLoS Computational Biology