Comparative Transcriptomics of Steinernema and Caenorhabditis Single Embryos Reveals Orthologous Gene Expression Convergence during Late Embryogenesis

BUSCO: assessing genome assembly and annotation completeness with single-copy orthologs

(2015) Felipe A. Simão et al.   BIOINFORMATICS

Next maSigPro: updating maSigPro bioconductor package for RNA-seq time series

(2014) M. J. Nueda et al.   BIOINFORMATICS

The developmental hourglass model: a predictor of the basic body plan?

(2014) N. Irie et al.   DEVELOPMENT

Tn5 transposase and tagmentation procedures for massively scaled sequencing projects

(2014) Simone Picelli et al.   GENOME RESEARCH

Regulatory analysis of the C. elegans genome with spatiotemporal resolution

(2014) Carlos L. Araya et al.   NATURE

Full-length RNA-seq from single cells using Smart-seq2

(2014) Simone Picelli et al.   Nature Protocols

Developmental Milestones Punctuate Gene Expression in the Caenorhabditis Embryo

(2012) Michal Levin et al.   DEVELOPMENTAL CELL

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

(2011) Bo Li et al.   BMC BIOINFORMATICS

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

(2011) Itai Yanai et al.   DEVELOPMENTAL CELL

Transposase mediated construction of RNA-seq libraries

(2011) J. Gertz et al.   GENOME RESEARCH

Scaffolding a Caenorhabditis nematode genome with RNA-seq

(2010) A. Mortazavi et al.   GENOME RESEARCH

Gene expression divergence recapitulates the developmental hourglass model

(2010) Alex T. Kalinka et al.   NATURE

Integrative Analysis of the Caenorhabditis elegans Genome by the modENCODE Project

(2010) M. B. Gerstein et al.   SCIENCE

edgeR: a Bioconductor package for differential expression analysis of digital gene expression data

(2009) M. D. Robinson et al.   BIOINFORMATICS

The maternal-to-zygotic transition: a play in two acts

(2009) W. Tadros et al.   DEVELOPMENT

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

(2009) Ben Langmead et al.   GENOME BIOLOGY