A de novo assembly of the newt transcriptome combined with proteomic validation identifies new protein families expressed during tissue regeneration

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

(2012) Marcel H. Schulz et al.   BIOINFORMATICS

Spiked-in Pulsed in Vivo Labeling Identifies a New Member of the CCN Family in Regenerating Newt Hearts

(2012) Mario Looso et al.   JOURNAL OF PROTEOME RESEARCH

De novo assembly and characterization of a maternal and developmental transcriptome for the emerging model crustacean Parhyale hawaiensis

(2011) Victor Zeng et al.   BMC GENOMICS

A de novo transcriptome of the Asian tiger mosquito, Aedes albopictus, to identify candidate transcripts for diapause preparation

(2011) Monica F Poelchau et al.   BMC GENOMICS

Dopamine Controls Neurogenesis in the Adult Salamander Midbrain in Homeostasis and during Regeneration of Dopamine Neurons

(2011) Daniel A. Berg et al.   Cell Stem Cell

The Cellular Basis for Animal Regeneration

(2011) Elly M. Tanaka et al.   DEVELOPMENTAL CELL

De novo assembly and validation of planaria transcriptome by massive parallel sequencing and shotgun proteomics

(2011) C. Adamidi et al.   GENOME RESEARCH

Andromeda: A Peptide Search Engine Integrated into the MaxQuant Environment

(2011) Jürgen Cox et al.   JOURNAL OF PROTEOME RESEARCH

SignalP 4.0: discriminating signal peptides from transmembrane regions

(2011) Thomas Nordahl Petersen et al.   NATURE METHODS

KEGG for integration and interpretation of large-scale molecular data sets

(2011) M. Kanehisa et al.   NUCLEIC ACIDS RESEARCH

The Pfam protein families database

(2011) M. Punta et al.   NUCLEIC ACIDS RESEARCH

Analysis of newly established EST databases reveals similarities between heart regeneration in newt and fish

(2010) Thilo Borchardt et al.   BMC GENOMICS

Efficient regeneration by activation of neurogenesis in homeostatically quiescent regions of the adult vertebrate brain

(2010) D. A. Berg et al.   DEVELOPMENT

Optimization of de novo transcriptome assembly from next-generation sequencing data

(2010) Y. Surget-Groba et al.   GENOME RESEARCH

Evidence for the Local Evolution of Mechanisms Underlying Limb Regeneration in Salamanders

(2010) A. Acely Garza-Garcia et al.   INTEGRATIVE AND COMPARATIVE BIOLOGY

Advanced Identification of Proteins in Uncharacterized Proteomes by Pulsedin VivoStable Isotope Labeling-based Mass Spectrometry

(2010) Mario Looso et al.   MOLECULAR & CELLULAR PROTEOMICS

Reactome: a database of reactions, pathways and biological processes

(2010) D. Croft et al.   NUCLEIC ACIDS RESEARCH

From fish to amphibians to mammals: in search of novel strategies to optimize cardiac regeneration

(2009) Simonetta Ausoni et al.   JOURNAL OF CELL BIOLOGY

PROSITE, a protein domain database for functional characterization and annotation

(2009) Christian J. A. Sigrist et al.   NUCLEIC ACIDS RESEARCH

Evolution of animal regeneration: re-emergence of a field

(2009) Alexandra E. Bely et al.   TRENDS IN ECOLOGY & EVOLUTION

An overview of the wcd EST clustering tool

(2008) Scott Hazelhurst et al.   BIOINFORMATICS

MaxQuant enables high peptide identification rates, individualized p.p.b.-range mass accuracies and proteome-wide protein quantification

(2008) Jürgen Cox et al.   NATURE BIOTECHNOLOGY

The GOA database in 2009--an integrated Gene Ontology Annotation resource

(2008) D. Barrell et al.   NUCLEIC ACIDS RESEARCH