A genome-wide survey of maternal and embryonic transcripts during Xenopus tropicalis development

Characterization of small RNAs inXenopus tropicalisgastrulae

(2012) Fernando Faunes et al.   GENESIS

RNA sequencing reveals a diverse and dynamic repertoire of the Xenopus tropicalis transcriptome over development

(2012) M. H. Tan et al.   GENOME RESEARCH

The GENCODE v7 catalog of human long noncoding RNAs: Analysis of their gene structure, evolution, and expression

(2012) T. Derrien et al.   GENOME RESEARCH

Differential gene and transcript expression analysis of RNA-seq experiments with TopHat and Cufflinks

(2012) Cole Trapnell et al.   Nature Protocols

clusterProfiler: an R Package for Comparing Biological Themes Among Gene Clusters

(2012) Guangchuang Yu et al.   OMICS-A JOURNAL OF INTEGRATIVE BIOLOGY

The zebrafish transcriptome during early development

(2011) Liselotte Vesterlund et al.   BMC DEVELOPMENTAL BIOLOGY

HESX1- and TCF3-mediated repression of Wnt/ -catenin targets is required for normal development of the anterior forebrain

(2011) C. L. Andoniadou et al.   DEVELOPMENT

Siamois and Twin are redundant and essential in formation of the Spemann organizer

(2011) Sangwoo Bae et al.   DEVELOPMENTAL BIOLOGY

An essential role for transcription before the MBT in Xenopus laevis

(2011) Jennifer Skirkanich et al.   DEVELOPMENTAL BIOLOGY

Mapping Gene Expression in Two Xenopus Species: Evolutionary Constraints and Developmental Flexibility

(2011) Itai Yanai et al.   DEVELOPMENTAL CELL

Integrative annotation of human large intergenic noncoding RNAs reveals global properties and specific subclasses

(2011) M. N. Cabili et al.   GENES & DEVELOPMENT

Systematic identification of long noncoding RNAs expressed during zebrafish embryogenesis

(2011) A. Pauli et al.   GENOME RESEARCH

Zebrafish mRNA sequencing deciphers novelties in transcriptome dynamics during maternal to zygotic transition

(2011) Håvard Aanes et al.   GENOME RESEARCH

Non-coding RNAs as regulators of embryogenesis

(2011) Andrea Pauli et al.   NATURE REVIEWS GENETICS

Genomewide characterization of non-polyadenylated RNAs

(2011) Li Yang et al.   GENOME BIOLOGY

Fast and accurate long-read alignment with Burrows–Wheeler transform

(2010) Heng Li et al.   BIOINFORMATICS

Uncovering the Complexity of Transcriptomes with RNA-Seq

(2010) Valerio Costa et al.   JOURNAL OF BIOMEDICINE AND BIOTECHNOLOGY

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

(2010) Mitchell Guttman et al.   NATURE BIOTECHNOLOGY

TopHat: discovering splice junctions with RNA-Seq

(2009) Cole Trapnell et al.   BIOINFORMATICS

The Xenopus Irx genes are essential for neural patterning and define the border between prethalamus and thalamus through mutual antagonism with the anterior repressors Fezf and Arx

(2009) Elisa Rodríguez-Seguel et al.   DEVELOPMENTAL BIOLOGY

A Hierarchy of H3K4me3 and H3K27me3 Acquisition in Spatial Gene Regulation in Xenopus Embryos

(2009) Robert C. Akkers et al.   DEVELOPMENTAL CELL

Abundant and dynamically expressed miRNAs, piRNAs, and other small RNAs in the vertebrate Xenopus tropicalis

(2009) J. Armisen et al.   GENOME RESEARCH

Differential expression of the Brunol/CELF family genes during Xenopus laevis early development

(2009) Jingyang Wu et al.   INTERNATIONAL JOURNAL OF DEVELOPMENTAL BIOLOGY

Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources

(2009) Da Wei Huang et al.   Nature Protocols

Translational control by cytoplasmic polyadenylation in Xenopus oocytes

(2008) Helois E. Radford et al.   Biochimica et Biophysica Acta-Gene Regulatory Mechanisms

A deadenylation negative feedback mechanism governs meiotic metaphase arrest

(2008) Eulàlia Belloc et al.   NATURE

Mapping and quantifying mammalian transcriptomes by RNA-Seq

(2008) Ali Mortazavi et al.   NATURE METHODS

RNA-Seq: a revolutionary tool for transcriptomics

(2008) Zhong Wang et al.   NATURE REVIEWS GENETICS

Identification of CUG-BP1/EDEN-BP target mRNAs in Xenopus tropicalis

(2008) Antoine Graindorge et al.   NUCLEIC ACIDS RESEARCH

Performance and Scalability of Discriminative Metrics for Comparative Gene Identification in 12 Drosophila Genomes

(2008) Michael F. Lin et al.   PLoS Computational Biology