Comparative Genomics of Flatworms (Platyhelminthes) Reveals Shared Genomic Features of Ecto- and Endoparastic Neodermata

How might flukes and tapeworms maintain genome integrity without a canonical piRNA pathway?

(2014) Danielle E. Skinner et al.   TRENDS IN PARASITOLOGY

Substantial Loss of Conserved and Gain of Novel MicroRNA Families in Flatworms

(2013) Bastian Fromm et al.   MOLECULAR BIOLOGY AND EVOLUTION

Inferring ancient divergences requires genes with strong phylogenetic signals

(2013) Leonidas Salichos et al.   NATURE

The genomes of four tapeworm species reveal adaptations to parasitism

(2013) Isheng J. Tsai et al.   NATURE

The genome of the hydatid tapeworm Echinococcus granulosus

(2013) Huajun Zheng et al.   NATURE GENETICS

Reconstructing mitochondrial genomes directly from genomic next-generation sequencing reads—a baiting and iterative mapping approach

(2013) Christoph Hahn et al.   NUCLEIC ACIDS RESEARCH

PhyloBayes MPI: Phylogenetic Reconstruction with Infinite Mixtures of Profiles in a Parallel Environment

(2013) Nicolas Lartillot et al.   SYSTEMATIC BIOLOGY

The Evolution of Intron Size in Amniotes: A Role for Powered Flight?

(2012) Qu Zhang et al.   Genome Biology and Evolution

Phylogenetic analysis of the Argonaute protein family in platyhelminths

(2012) Yadong Zheng   MOLECULAR PHYLOGENETICS AND EVOLUTION

Insights into bilaterian evolution from three spiralian genomes

(2012) Oleg Simakov et al.   NATURE

A beginner's guide to eukaryotic genome annotation

(2012) Mark Yandell et al.   NATURE REVIEWS GENETICS

Scaling metagenome sequence assembly with probabilistic de Bruijn graphs

(2012) J. Pell et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Simultaneous genome sequencing of symbionts and their hosts

(2012) Sujai Kumar et al.   SYMBIOSIS

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

(2012) Ruibang Luo et al.   GigaScience

The variant call format and VCFtools

(2011) P. Danecek et al.   BIOINFORMATICS

MAKER2: an annotation pipeline and genome-database management tool for second-generation genome projects

(2011) Carson Holt et al.   BMC BIOINFORMATICS

Fast, scalable generation of high-quality protein multiple sequence alignments using Clustal Omega

(2011) F. Sievers et al.   Molecular Systems Biology

Acoelomorph flatworms are deuterostomes related to Xenoturbella

(2011) Hervé Philippe et al.   NATURE

Resolving the evolutionary relationships of molluscs with phylogenomic tools

(2011) Stephen A. Smith et al.   NATURE

959 Nematode Genomes: a semantic wiki for coordinating sequencing projects

(2011) S. Kumar et al.   NUCLEIC ACIDS RESEARCH

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

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

The draft genome of the carcinogenic human liver fluke Clonorchis sinensis

(2011) Xiaoyun Wang et al.   GENOME BIOLOGY

The planarian flatworm: an in vivo model for stem cell biology and nervous system regeneration

(2010) L. Gentile et al.   Disease Models & Mechanisms

Closing the mitochondrial circle on paraphyly of the Monogenea (Platyhelminthes) infers evolution in the diet of parasitic flatworms

(2010) Elizabeth M. Perkins et al.   INTERNATIONAL JOURNAL FOR PARASITOLOGY

FASconCAT: Convenient handling of data matrices

(2010) Patrick Kück et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

Fast and accurate short read alignment with Burrows-Wheeler transform

(2009) H. Li et al.   BIOINFORMATICS

Prospects for a genetic management strategy to control Gyrodactylus salaris infection in wild Atlantic salmon (Salmo salar) stocks

(2009) Ragnar Salte et al.   CANADIAN JOURNAL OF FISHERIES AND AQUATIC SCIENCES

ABySS: A parallel assembler for short read sequence data

(2009) J. T. Simpson et al.   GENOME RESEARCH

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

(2009) R. Li et al.   GENOME RESEARCH

The Schistosoma japonicum genome reveals features of host–parasite interplay

(2009)   NATURE

The genome of the blood fluke Schistosoma mansoni

(2009) Matthew Berriman et al.   NATURE

The sequence and de novo assembly of the giant panda genome

(2009) Ruiqiang Li et al.   NATURE

Whole Genome Amplification and De novo Assembly of Single Bacterial Cells

(2009) Sébastien Rodrigue et al.   PLoS One

Assessing the root of bilaterian animals with scalable phylogenomic methods

(2009) A. Hejnol et al.   PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

A Monte Carlo Approach Successfully Identifies Randomness in Multiple Sequence Alignments : A More Objective Means of Data Exclusion

(2009) Bernhard Misof et al.   SYSTEMATIC BIOLOGY

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

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

Broad phylogenomic sampling improves resolution of the animal tree of life

(2008) Casey W. Dunn et al.   NATURE

Assessing the gene space in draft genomes

(2008) Genis Parra et al.   NUCLEIC ACIDS RESEARCH

High-throughput functional annotation and data mining with the Blast2GO suite

(2008) S. Gotz et al.   NUCLEIC ACIDS RESEARCH