Acoel genome reveals the regulatory landscape of whole-body regeneration

Analysis of sea star larval regeneration reveals conserved processes of whole-body regeneration across the metazoa

(2019) Gregory A. Cary et al.   BMC BIOLOGY

Minimap2: pairwise alignment for nucleotide sequences

(2018) Heng Li   BIOINFORMATICS

NanoPack: visualizing and processing long-read sequencing data

(2018) Wouter De Coster et al.   BIOINFORMATICS

NGmerge: merging paired-end reads via novel empirically-derived models of sequencing errors

(2018) John M. Gaspar   BMC BIOINFORMATICS

Orthogonal muscle fibres have different instructive roles in planarian regeneration

(2017) M. Lucila Scimone et al.   NATURE

chromVAR: inferring transcription-factor-associated accessibility from single-cell epigenomic data

(2017) Alicia N Schep et al.   NATURE METHODS

Differential analysis of RNA-seq incorporating quantification uncertainty

(2017) Harold Pimentel et al.   NATURE METHODS

Salmon provides fast and bias-aware quantification of transcript expression

(2017) Rob Patro et al.   NATURE METHODS

JASPAR 2018: update of the open-access database of transcription factor binding profiles and its web framework

(2017) Aziz Khan et al.   NUCLEIC ACIDS RESEARCH

Acoel regeneration mechanisms indicate an ancient role for muscle in regenerative patterning

(2017) Amelie A. Raz et al.   Nature Communications

(Neo)blast from the past: new insights into planarian stem cell lineages

(2016) Shu Jun Zhu et al.   CURRENT OPINION IN GENETICS & DEVELOPMENT

Pioneer transcription factors, chromatin dynamics, and cell fate control

(2016) Kenneth S Zaret et al.   CURRENT OPINION IN GENETICS & DEVELOPMENT

Neuregulin-1 signaling is essential for nerve-dependent axolotl limb regeneration

(2016) Johanna E. Farkas et al.   DEVELOPMENT

Egf Signaling Directs Neoblast Repopulation by Regulating Asymmetric Cell Division in Planarians

(2016) Kai Lei et al.   DEVELOPMENTAL CELL

Chromosome-scale shotgun assembly using an in vitro method for long-range linkage

(2016) Nicholas H. Putnam et al.   GENOME RESEARCH

Modulation of tissue repair by regeneration enhancer elements

(2016) Junsu Kang et al.   NATURE

New deep-sea species of Xenoturbella and the position of Xenacoelomorpha

(2016) Greg W. Rouse et al.   NATURE

Xenacoelomorpha is the sister group to Nephrozoa

(2016) Johanna Taylor Cannon et al.   NATURE

Localized epigenetic silencing of a damage-activated WNT enhancer limits regeneration in mature Drosophila imaginal discs

(2016) Robin E Harris et al.   eLife

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

(2015) Felipe A. Simão et al.   BIOINFORMATICS

A Generic and Cell-Type-Specific Wound Response Precedes Regeneration in Planarians

(2015) Omri Wurtzel et al.   DEVELOPMENTAL CELL

Nrg1 is an injury-induced cardiomyocyte mitogen for the endogenous heart regeneration program in zebrafish

(2015) Matthew Gemberling et al.   eLife

RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies

(2014) Alexandros Stamatakis   BIOINFORMATICS

Whole-Body Acoel Regeneration Is Controlled by Wnt and Bmp-Admp Signaling

(2014) Mansi Srivastava et al.   CURRENT BIOLOGY

egr-4 , a target of EGFR signaling, is required for the formation of the brain primordia and head regeneration in planarians

(2014) Susanna Fraguas et al.   DEVELOPMENT

Early and late response ofNematostella vectensistranscriptome to heavy metals

(2014) Ron Elran et al.   MOLECULAR ECOLOGY

Discovery of directional and nondirectional pioneer transcription factors by modeling DNase profile magnitude and shape

(2014) Richard I Sherwood et al.   NATURE BIOTECHNOLOGY

MAFFT Multiple Sequence Alignment Software Version 7: Improvements in Performance and Usability

(2013) K. Katoh et al.   MOLECULAR BIOLOGY AND EVOLUTION

Transposition of native chromatin for fast and sensitive epigenomic profiling of open chromatin, DNA-binding proteins and nucleosome position

(2013) Jason D Buenrostro et al.   NATURE METHODS

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

Follistatin antagonizes Activin signaling and acts with Notum to direct planarian head regeneration

(2013) Rachel H. Roberts-Galbraith et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

PRICE: Software for the Targeted Assembly of Components of (Meta) Genomic Sequence Data

(2013) J. Graham Ruby et al.   G3-Genes Genomes Genetics

Tissue absence initiates regeneration through Follistatin-mediated inhibition of Activin signaling

(2013) Michael A Gaviño et al.   eLife

REAPR: a universal tool for genome assembly evaluation

(2013) Martin Hunt et al.   GENOME BIOLOGY

A molecular wound response program associated with regeneration initiation in planarians

(2012) D. Wenemoser et al.   GENES & DEVELOPMENT

Fast gapped-read alignment with Bowtie 2

(2012) Ben Langmead et al.   NATURE METHODS

Activation and function of immediate-early genes in the nervous systemThis paper is one of a selection of papers in a Special Issue entitled 31st Annual International Asilomar Chromatin and Chromosomes Conference, and has undergone the Journal’s usual peer review process.

(2011) Beatriz Pérez-Cadahía et al.   Biochemistry and Cell Biology

Illumina mate-paired DNA sequencing-library preparation using Cre-Lox recombination

(2011) Filip Van Nieuwerburgh et al.   NUCLEIC ACIDS RESEARCH

Polarized notum Activation at Wounds Inhibits Wnt Function to Promote Planarian Head Regeneration

(2011) C. P. Petersen et al.   SCIENCE

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

Early growth response transcription factors and the modulation of immune response

(2009) Diana Gómez-Martín et al.   AUTOIMMUNITY REVIEWS

The sequence and de novo assembly of the giant panda genome

(2009) Ruiqiang Li et al.   NATURE

Evolution of animal regeneration: re-emergence of a field

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

Using native and syntenically mapped cDNA alignments to improve de novo gene finding

(2008) Mario Stanke et al.   BIOINFORMATICS

Model-based Analysis of ChIP-Seq (MACS)

(2008) Yong Zhang et al.   GENOME BIOLOGY

 -Catenin Defines Head Versus Tail Identity During Planarian Regeneration and Homeostasis

(2007) K. A. Gurley et al.   SCIENCE

Smed- catenin-1 Is Required for Anteroposterior Blastema Polarity in Planarian Regeneration

(2007) C. P. Petersen et al.   SCIENCE