Unusually Large Number of Mutations in Asexually Reproducing Clonal Planarian Dugesia japonica

Planarian shows decision-making behavior in response to multiple stimuli by integrative brain function

(2015) Takeshi Inoue et al.   Zoological Letters

Thermosensory Signaling by TRPM Is Processed by Brain Serotonergic Neurons to Produce Planarian Thermotaxis

(2014) T. Inoue et al.   JOURNAL OF NEUROSCIENCE

Informed and automated k-mer size selection for genome assembly

(2013) R. Chikhi et al.   BIOINFORMATICS

Innate sexuality determines the mechanisms of telomere maintenance

(2013) Kenta Tasaka et al.   INTERNATIONAL JOURNAL OF DEVELOPMENTAL BIOLOGY

Comparative transcriptome analysis between planarian Dugesia japonica and other platyhelminth species

(2012) Osamu Nishimura et al.   BMC GENOMICS

A survey of error-correction methods for next-generation sequencing

(2012) X. Yang et al.   BRIEFINGS IN BIOINFORMATICS

Integrative Genomics Viewer (IGV): high-performance genomics data visualization and exploration

(2012) H. Thorvaldsdottir et al.   BRIEFINGS IN BIOINFORMATICS

A program for annotating and predicting the effects of single nucleotide polymorphisms, SnpEff

(2012) Pablo Cingolani et al.   FLY

Fast gapped-read alignment with Bowtie 2

(2012) Ben Langmead et al.   NATURE METHODS

The Complete Mitochondrial Genome ofDugesia japonica(Platyhelminthes; Order Tricladida)

(2012) Masato Sakai et al.   ZOOLOGICAL SCIENCE

Transcriptome Analysis of the Planarian Eye Identifies ovo as a Specific Regulator of Eye Regeneration

(2012) Sylvain W. Lapan et al.   Cell Reports

SOAPdenovo2: an empirically improved memory-efficient short-read de novo assembler

(2012) Ruibang Luo et al.   GigaScience

Using Drosophila melanogaster as a Model for Genotoxic Chemical Mutational Studies with a New Program, SnpSift

(2012) Pablo Cingolani et al.   Frontiers in Genetics

Smed454 dataset: unravelling the transcriptome of Schmidtea mediterranea

(2011) Josep F Abril et al.   BMC GENOMICS

How to apply de Bruijn graphs to genome assembly

(2011) Phillip E C Compeau et al.   NATURE BIOTECHNOLOGY

Full-length transcriptome assembly from RNA-Seq data without a reference genome

(2011) Manfred G Grabherr et al.   NATURE BIOTECHNOLOGY

Computational methods for transcriptome annotation and quantification using RNA-seq

(2011) Manuel Garber et al.   NATURE METHODS

The head-regeneration transcriptome of the planarian Schmidtea mediterranea

(2011) Thomas Sandmann et al.   GENOME BIOLOGY

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

(2010) Heng Li et al.   BIOINFORMATICS

Cellular and molecular dissection of pluripotent adult somatic stem cells in planarians

(2010) Norito Shibata et al.   DEVELOPMENT GROWTH & DIFFERENTIATION

Single-cell gene profiling of planarian stem cells using fluorescent activated cell sorting and its “index sorting” function for stem cell research

(2010) Tetsutaro Hayashi et al.   DEVELOPMENT GROWTH & DIFFERENTIATION

The Genome Analysis Toolkit: A MapReduce framework for analyzing next-generation DNA sequencing data

(2010) A. McKenna et al.   GENOME RESEARCH

Djrho2 is involved in regeneration of visual nerves in Dugesia japonica

(2010) Changxin Ma et al.   Journal of Genetics and Genomics

A small scale expression screen identifies tissue specific markers in the Dugesia japonica strain Pek-1

(2010) Changxin Ma et al.   Journal of Genetics and Genomics

Galaxy: a comprehensive approach for supporting accessible, reproducible, and transparent computational research in the life sciences

(2010) Jeremy Goecks et al.   GENOME BIOLOGY

DEGseq: an R package for identifying differentially expressed genes from RNA-seq data

(2009) Likun Wang et al.   BIOINFORMATICS

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

A planarian p53 homolog regulates proliferation and self-renewal in adult stem cell lineages

(2009) Bret J. Pearson et al.   DEVELOPMENT

De novo assembly of human genomes with massively parallel short read sequencing

(2009) R. Li et al.   GENOME RESEARCH

Planarian Hedgehog/Patched establishes anterior–posterior polarity by regulating Wnt signaling

(2009) Shigenobu Yazawa et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Planarian PTEN homologs regulate stem cells and regeneration through TOR signaling

(2008) N. J. Oviedo et al.   Disease Models & Mechanisms

RNA-Seq: a revolutionary tool for transcriptomics

(2008) Zhong Wang et al.   NATURE REVIEWS GENETICS

Brain regeneration from pluripotent stem cells in planarian

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