Draft genome of Dugesia japonica provides insights into conserved regulatory elements of the brain restriction gene nou-darake in planarians

Inheritance of a Nuclear PIWI from Pluripotent Stem Cells by Somatic Descendants Ensures Differentiation by Silencing Transposons in Planarian

(2016) Norito Shibata et al.   DEVELOPMENTAL CELL

Multiple Neuropeptide-Coding Genes Involved in Planarian Pharynx Extension

(2016) Seira Shimoyama et al.   ZOOLOGICAL SCIENCE

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

(2015) Takeshi Inoue et al.   Zoological Letters

SSPACE-LongRead: scaffolding bacterial draft genomes using long read sequence information

(2014) Marten Boetzer et al.   BMC BIOINFORMATICS

L_RNA_scaffolder: scaffolding genomes with transcripts

(2013) Wei Xue et al.   BMC GENOMICS

Pseudo-Sanger sequencing: massively parallel production of long and near error-free reads using NGS technology

(2013) Jue Ruan et al.   BMC GENOMICS

De novo transcript sequence reconstruction from RNA-seq using the Trinity platform for reference generation and analysis

(2013) Brian J Haas et al.   Nature Protocols

GapFiller: a de novo assembly approach to fill the gap within paired reads

(2012) Francesca Nadalin et al.   BMC BIOINFORMATICS

Comparative transcriptome analysis between planarian Dugesia japonica and other platyhelminth species

(2012) Osamu Nishimura et al.   BMC GENOMICS

Toward almost closed genomes with GapFiller

(2012) Marten Boetzer et al.   GENOME BIOLOGY

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

(2012) Ruibang Luo et al.   GigaScience

A fast, lock-free approach for efficient parallel counting of occurrences of k-mers

(2011) Guillaume Marçais et al.   BIOINFORMATICS

Regeneration of dopaminergic neurons after 6-hydroxydopamine-induced lesion in planarian brain

(2011) Kaneyasu Nishimura et al.   JOURNAL OF NEUROCHEMISTRY

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

(2011) Manfred G Grabherr et al.   NATURE BIOTECHNOLOGY

Scaffolding pre-assembled contigs using SSPACE

(2010) Marten Boetzer et al.   BIOINFORMATICS

BEDTools: a flexible suite of utilities for comparing genomic features

(2010) Aaron R. Quinlan et al.   BIOINFORMATICS

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

High-quality draft assemblies of mammalian genomes from massively parallel sequence data

(2010) S. Gnerre et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

JBrowse: A next-generation genome browser

(2009) M. E. Skinner et al.   GENOME RESEARCH

JASPAR 2010: the greatly expanded open-access database of transcription factor binding profiles

(2009) Elodie Portales-Casamar et al.   NUCLEIC ACIDS RESEARCH

To Be or Not to Be a Flatworm: The Acoel Controversy

(2009) Bernhard Egger et al.   PLoS One

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

(2009) Ben Langmead et al.   GENOME BIOLOGY

The TRANSFAC project as an example of framework technology that supports the analysis of genomic regulation

(2008) E. Wingender   BRIEFINGS IN BIOINFORMATICS

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

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

Brain regeneration from pluripotent stem cells in planarian

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