RNAseq versus genome-predicted transcriptomes: a large population of novel transcripts identified in an Illumina-454 Hydra transcriptome

Oases: robust de novo RNA-seq assembly across the dynamic range of expression levels

(2012) Marcel H. Schulz et al.   BIOINFORMATICS

Hydra, a fruitful model system for 270 years

(2012) Brigitte Galliot   INTERNATIONAL JOURNAL OF DEVELOPMENTAL BIOLOGY

Molecular Signatures of the Three Stem Cell Lineages in Hydra and the Emergence of Stem Cell Function at the Base of Multicellularity

(2012) Georg Hemmrich et al.   MOLECULAR BIOLOGY AND EVOLUTION

Whole Transcriptome Analysis of the CoralAcropora milleporaReveals Complex Responses to CO2-driven Acidification during the Initiation of Calcification

(2012) A. MOYA et al.   MOLECULAR ECOLOGY

PANTHER in 2013: modeling the evolution of gene function, and other gene attributes, in the context of phylogenetic trees

(2012) Huaiyu Mi et al.   NUCLEIC ACIDS RESEARCH

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

(2011) Bo Li et al.   BMC BIOINFORMATICS

Using the Acropora digitifera genome to understand coral responses to environmental change

(2011) Chuya Shinzato et al.   NATURE

NCBI Reference Sequences (RefSeq): current status, new features and genome annotation policy

(2011) K. D. Pruitt et al.   NUCLEIC ACIDS RESEARCH

The Genome Portal of the Department of Energy Joint Genome Institute

(2011) I. V. Grigoriev et al.   NUCLEIC ACIDS RESEARCH

The genome of the fire ant Solenopsis invicta

(2011) Y. Wurm et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Pseudogenes: Pseudo-functional or key regulators in health and disease?

(2011) R. C. Pink et al.   RNA

Search and clustering orders of magnitude faster than BLAST

(2010) Robert C. Edgar   BIOINFORMATICS

Phylogeny and biogeography of Hydra (Cnidaria: Hydridae) using mitochondrial and nuclear DNA sequences

(2010) D.E. Martínez et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

The dynamic genome of Hydra

(2010) Jarrod A. Chapman et al.   NATURE

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

(2010) Cole Trapnell et al.   NATURE BIOTECHNOLOGY

Convergent origins and rapid evolution of spliced leader trans-splicing in Metazoa: Insights from the Ctenophora and Hydrozoa

(2010) R. Derelle et al.   RNA

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

(2010) Stéphane Guindon et al.   SYSTEMATIC BIOLOGY

New tricks with old genes: the genetic bases of novel cnidarian traits

(2010) Sylvain Forêt et al.   TRENDS IN GENETICS

TagDust--a program to eliminate artifacts from next generation sequencing data

(2009) T. Lassmann et al.   BIOINFORMATICS

TopHat: discovering splice junctions with RNA-Seq

(2009) Cole Trapnell et al.   BIOINFORMATICS

Sequencing and de novo analysis of a coral larval transcriptome using 454 GSFlx

(2009) Eli Meyer et al.   BMC GENOMICS

Phylogenomics Revives Traditional Views on Deep Animal Relationships

(2009) Hervé Philippe et al.   CURRENT BIOLOGY

The transcriptome of the colonial marine hydroid Hydractinia echinata

(2009) Jorge Soza-Ried et al.   FEBS Journal

Cellular stress and RNA splicing

(2009) Giuseppe Biamonti et al.   TRENDS IN BIOCHEMICAL SCIENCES

Improved base calling for the Illumina Genome Analyzer using machine learning strategies

(2009) Martin Kircher et al.   GENOME BIOLOGY

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

(2009) Ben Langmead et al.   GENOME BIOLOGY

Compagen, a comparative genomics platform for early branching metazoan animals, reveals early origins of genes regulating stem-cell differentiation

(2008) Georg Hemmrich et al.   BIOESSAYS

Velvet: Algorithms for de novo short read assembly using de Bruijn graphs

(2008) D. R. Zerbino et al.   GENOME RESEARCH

Accurate whole human genome sequencing using reversible terminator chemistry

(2008) David R. Bentley et al.   NATURE

Deciphering deuterostome phylogeny: molecular, morphological and palaeontological perspectives

(2008) B. J Swalla et al.   PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

The Ediacaran emergence of bilaterians: congruence between the genetic and the geological fossil records

(2008) K. J Peterson et al.   PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

Multigene Phylogeny of Choanozoa and the Origin of Animals

(2008) Kamran Shalchian-Tabrizi et al.   PLoS One

Automated eukaryotic gene structure annotation using EVidenceModeler and the Program to Assemble Spliced Alignments

(2008) Brian J Haas et al.   GENOME BIOLOGY