The genome of the crustacean Parhyale hawaiensis, a model for animal development, regeneration, immunity and lignocellulose digestion

CRISPR/Cas9 Mutagenesis Reveals Versatile Roles of Hox Genes in Crustacean Limb Specification and Evolution

(2016) Arnaud Martin et al.   CURRENT BIOLOGY

Toll Genes Have an Ancestral Role in Axis Elongation

(2016) Matthew A. Benton et al.   CURRENT BIOLOGY

Non-insect crustacean models in developmental genetics including an encomium to Parhyale hawaiensis

(2016) Evangelia Stamataki et al.   CURRENT OPINION IN GENETICS & DEVELOPMENT

Comprehensive analysis of Hox gene expression in the amphipod crustacean Parhyale hawaiensis

(2016) Julia M. Serano et al.   DEVELOPMENTAL BIOLOGY

Mechanism and biological role of Dnmt2 in Nucleic Acid Methylation

(2016) Albert Jeltsch et al.   RNA Biology

Live imaging reveals the progenitors and cell dynamics of limb regeneration

(2016) Frederike Alwes et al.   eLife

Lignocellulose degradation mechanisms across the Tree of Life

(2015) Simon M Cragg et al.   CURRENT OPINION IN CHEMICAL BIOLOGY

C2H2 zinc finger proteins greatly expand the human regulatory lexicon

(2015) Hamed S Najafabadi et al.   NATURE BIOTECHNOLOGY

Ancient and Novel Small RNA Pathways Compensate for the Loss of piRNAs in Multiple Independent Nematode Lineages

(2015) Peter Sarkies et al.   PLOS BIOLOGY

Exploring genome characteristics and sequence quality without a reference

(2014) Jared T. Simpson   BIOINFORMATICS

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

(2014) Alexandros Stamatakis   BIOINFORMATICS

Cells from the Immune System Generate Adult-Born Neurons in Crayfish

(2014) Jeanne L. Benton et al.   DEVELOPMENTAL CELL

Efficient de novo assembly of highly heterozygous genomes from whole-genome shotgun short reads

(2014) Rei Kajitani et al.   GENOME RESEARCH

A first Glimpse at the genome of the Baikalian amphipodEulimnogammarus verrucosus

(2014) Lorena Rivarola-Duarte et al.   JOURNAL OF EXPERIMENTAL ZOOLOGY PART B-MOLECULAR AND DEVELOPMENTAL EVOLUTION

Genomic Sequence and Experimental Tractability of a New Decapod Shrimp Model, Neocaridina denticulata

(2014) Nathan Kenny et al.   Marine Drugs

Rfam 12.0: updates to the RNA families database

(2014) Eric P. Nawrocki et al.   NUCLEIC ACIDS RESEARCH

A Common Cellular Basis for Muscle Regeneration in Arthropods and Vertebrates

(2014) N. Konstantinides et al.   SCIENCE

The locust genome provides insight into swarm formation and long-distance flight

(2014) Xianhui Wang et al.   Nature Communications

Functional genetics for all: engineered nucleases, CRISPR and the gene editing revolution

(2014) Anna F Gilles et al.   EvoDevo

Analysis of the Wnt gene repertoire in an onychophoran provides new insights into the evolution of segmentation

(2014) Mattias Hogvall et al.   EvoDevo

The First Myriapod Genome Sequence Reveals Conservative Arthropod Gene Content and Genome Organisation in the Centipede Strigamia maritima

(2014) Ariel D. Chipman et al.   PLOS BIOLOGY

Ablation of a Single Cell From Eight-cell Embryos of the Amphipod Crustacean Parhyale hawaiensis

(2014) Anastasia R. Nast et al.   Jove-Journal of Visualized Experiments

Infernal 1.1: 100-fold faster RNA homology searches

(2013) E. P. Nawrocki et al.   BIOINFORMATICS

Planarian MBD2/3 is required for adult stem cell pluripotency independently of DNA methylation

(2013) Farah Jaber-Hijazi et al.   DEVELOPMENTAL BIOLOGY

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

RNA interference in the nucleus: roles for small RNAs in transcription, epigenetics and beyond

(2013) Stephane E. Castel et al.   NATURE REVIEWS GENETICS

Structural characterization of a unique marine animal family 7 cellobiohydrolase suggests a mechanism of cellulase salt tolerance

(2013) M. Kern et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

RNA-Guided Human Genome Engineering via Cas9

(2013) P. Mali et al.   SCIENCE

Multiplex Genome Engineering Using CRISPR/Cas Systems

(2013) L. Cong et al.   SCIENCE

STAR: ultrafast universal RNA-seq aligner

(2012) Alexander Dobin et al.   BIOINFORMATICS

Geneious Basic: An integrated and extendable desktop software platform for the organization and analysis of sequence data

(2012) M. Kearse et al.   BIOINFORMATICS

C. elegans piRNAs Mediate the Genome-wide Surveillance of Germline Transcripts

(2012) Heng-Chi Lee et al.   CELL

Independent migration of cell populations in the early gastrulation of the amphipod crustacean Parhyale hawaiensis

(2012) R. Crystal Chaw et al.   DEVELOPMENTAL BIOLOGY

Disease will limit future food supply from the global crustacean fishery and aquaculture sectors

(2012) G.D. Stentiford et al.   JOURNAL OF INVERTEBRATE PATHOLOGY

The scope of the crustacean immune system for disease control

(2012) Chris Hauton   JOURNAL OF INVERTEBRATE PATHOLOGY

Phylotranscriptomics to Bring the Understudied into the Fold: Monophyletic Ostracoda, Fossil Placement, and Pancrustacean Phylogeny

(2012) Todd H. Oakley et al.   MOLECULAR BIOLOGY AND EVOLUTION

The oyster genome reveals stress adaptation and complexity of shell formation

(2012) Guofan Zhang et al.   NATURE

Functions of DNA methylation: islands, start sites, gene bodies and beyond

(2012) Peter A. Jones   NATURE REVIEWS GENETICS

High Through-Put Sequencing of the Parhyale hawaiensis mRNAs and microRNAs to Aid Comparative Developmental Studies

(2012) Martin J. Blythe et al.   PLoS One

Evolution and function of the extended miR-2 microRNA family

(2012) Antonio Marco et al.   RNA Biology

A Programmable Dual-RNA-Guided DNA Endonuclease in Adaptive Bacterial Immunity

(2012) M. Jinek et al.   SCIENCE

Germline DNA Demethylation Dynamics and Imprint Erasure Through 5-Hydroxymethylcytosine

(2012) J. A. Hackett et al.   SCIENCE

The Evolution of the Wnt Pathway

(2012) T. W. Holstein   Cold Spring Harbor Perspectives in Biology

Vaccines and crustacean aquaculture—A mechanistic exploration

(2011) Andrew F. Rowley et al.   AQUACULTURE

Bismark: a flexible aligner and methylation caller for Bisulfite-Seq applications

(2011) Felix Krueger et al.   BIOINFORMATICS

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

(2011) Guillaume Marçais et al.   BIOINFORMATICS

MiRPara: a SVM-based software tool for prediction of most probable microRNA coding regions in genome scale sequences

(2011) Yonggan Wu et al.   BMC BIOINFORMATICS

Conservation, loss, and redeployment of Wnt ligands in protostomes: implications for understanding the evolution of segment formation

(2011) Ralf Janssen et al.   BMC EVOLUTIONARY BIOLOGY

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

Microbial diversity of cellulose hydrolysis

(2011) David B Wilson   CURRENT OPINION IN MICROBIOLOGY

A versatile strategy for gene trapping and trap conversion in emerging model organisms

(2011) Z. Kontarakis et al.   DEVELOPMENT

Patterns of cell lineage, movement, and migration from germ layer specification to gastrulation in the amphipod crustacean Parhyale hawaiensis

(2011) Frederike Alwes et al.   DEVELOPMENTAL BIOLOGY

The functional relationship between ectodermal and mesodermal segmentation in the crustacean, Parhyale hawaiensis

(2011) Roberta L. Hannibal et al.   DEVELOPMENTAL BIOLOGY

HomeoDB2: functional expansion of a comparative homeobox gene database for evolutionary developmental biology

(2011) Ying-fu Zhong et al.   EVOLUTION & DEVELOPMENT

Efficient de novo assembly of large genomes using compressed data structures

(2011) J. T. Simpson et al.   GENOME RESEARCH

Pancrustacean Phylogeny in the Light of New Phylogenomic Data: Support for Remipedia as the Possible Sister Group of Hexapoda

(2011) B. M. von Reumont et al.   MOLECULAR BIOLOGY AND EVOLUTION

Molecular phylogeny of Pholadoidea Lamarck, 1809 supports a single origin for xylotrophy (wood feeding) and xylotrophic bacterial endosymbiosis in Bivalvia

(2011) Daniel L. Distel et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

The Ecoresponsive Genome of Daphnia pulex

(2011) J. K. Colbourne et al.   SCIENCE

Scaffolding pre-assembled contigs using SSPACE

(2010) Marten Boetzer et al.   BIOINFORMATICS

Peptidoglycan activation of the proPO-system without a peptidoglycan receptor protein (PGRP)?

(2010) Haipeng Liu et al.   DEVELOPMENTAL AND COMPARATIVE IMMUNOLOGY

BAC library for the amphipod crustacean, Parhyale hawaiensis

(2010) Ronald J. Parchem et al.   GENOMICS

Evolutionary Dynamics of the wnt Gene Family: A Lophotrochozoan Perspective

(2010) S.-J. Cho et al.   MOLECULAR BIOLOGY AND EVOLUTION

A Phylogenomic Approach to Resolve the Arthropod Tree of Life

(2010) K. Meusemann et al.   MOLECULAR BIOLOGY AND EVOLUTION

Arthropod relationships revealed by phylogenomic analysis of nuclear protein-coding sequences

(2010) Jerome C. Regier et al.   NATURE

Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation

(2010) Cole Trapnell et al.   NATURE BIOTECHNOLOGY

Establishing, maintaining and modifying DNA methylation patterns in plants and animals

(2010) Julie A. Law et al.   NATURE REVIEWS GENETICS

Molecular insight into lignocellulose digestion by a marine isopod in the absence of gut microbes

(2010) A. J. King et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Conservation and divergence of methylation patterning in plants and animals

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

Phylogeny of Methylomes

(2010) A. Jeltsch   SCIENCE

Genome-Wide Evolutionary Analysis of Eukaryotic DNA Methylation

(2010) A. Zemach et al.   SCIENCE

The components of the Daphnia pulex immune system as revealed by complete genome sequencing

(2009) Seanna J McTaggart et al.   BMC GENOMICS

The putative invertebrate adaptive immune protein Litopenaeus vannamei Dscam (LvDscam) is the first reported Dscam to lack a transmembrane domain and cytoplasmic tail

(2009) Pin-Hsiang Chou et al.   DEVELOPMENTAL AND COMPARATIVE IMMUNOLOGY

Mesoderm and ectoderm lineages in the crustacean Parhyale hawaiensis display intra-germ layer compensation

(2009) Alivia L. Price et al.   DEVELOPMENTAL BIOLOGY

The deep evolution of metazoan microRNAs

(2009) Benjamin M. Wheeler et al.   EVOLUTION & DEVELOPMENT

Drosophila motor axons recognize and follow a Sidestep-labeled substrate pathway to reach their target fields

(2009) M. Siebert et al.   GENES & DEVELOPMENT

ABySS: A parallel assembler for short read sequence data

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

Review: Immunity mechanisms in crustaceans

(2009) Lorena Vazquez et al.   Innate Immunity

Isolation and partial characterization of novel genes encoding acidic cellulases from metagenomes of buffalo rumens

(2009) C.-J. Duan et al.   JOURNAL OF APPLIED MICROBIOLOGY

Cloning and Phylogenetic Analysis of Sid-1-Like Genes from Aphids

(2009) Weina Xu et al.   JOURNAL OF INSECT SCIENCE

Hemocyanin Suggests a Close Relationship of Remipedia and Hexapoda

(2009) B. Ertas et al.   MOLECULAR BIOLOGY AND EVOLUTION

Evidence for Multiple Independent Origins of trans-Splicing in Metazoa

(2009) V. Douris et al.   MOLECULAR BIOLOGY AND EVOLUTION

Distinct Argonaute-Mediated 22G-RNA Pathways Direct Genome Surveillance in the C. elegans Germline

(2009) Weifeng Gu et al.   MOLECULAR CELL

The origin and evolution of arthropods

(2009) Graham E. Budd et al.   NATURE

Rethinking how DNA methylation patterns are maintained

(2009) Peter A. Jones et al.   NATURE REVIEWS GENETICS

Probing the evolution of appendage specialization by Hox gene misexpression in an emerging model crustacean

(2009) A. Pavlopoulos et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Knockdown of Parhyale Ultrabithorax recapitulates evolutionary changes in crustacean appendage morphology

(2009) D. M. Liubicich et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Multiple Wnt Genes Are Required for Segmentation in the Short-Germ Embryo of Tribolium castaneum

(2008) Renata Bolognesi et al.   CURRENT BIOLOGY

Analysis of the Tribolium homeotic complex: insights into mechanisms constraining insect Hox clusters

(2008) Teresa D. Shippy et al.   DEVELOPMENT GENES AND EVOLUTION

Germ cells in the crustacean Parhyale hawaiensis depend on Vasa protein for their maintenance but not for their formation

(2008) Günes Özhan-Kizil et al.   DEVELOPMENTAL BIOLOGY

Passive protection of shrimp against white spot syndrome virus (WSSV) using specific antibody from egg yolk of chickens immunized with inactivated virus or a WSSV-DNA vaccine

(2008) Y LU et al.   FISH & SHELLFISH IMMUNOLOGY

Immunological responses of Penaeus monodon to DNA vaccine and its efficacy to protect shrimp against white spot syndrome virus (WSSV)

(2008) S. Rajesh Kumar et al.   FISH & SHELLFISH IMMUNOLOGY

A single Hox locus in Drosophila produces functional microRNAs from opposite DNA strands

(2008) A. Stark et al.   GENES & DEVELOPMENT

The Dscam Homologue of the Crustacean Daphnia Is Diversified by Alternative Splicing Like in Insects

(2008) Daniela Brites et al.   MOLECULAR BIOLOGY AND EVOLUTION

Early origins and evolution of microRNAs and Piwi-interacting RNAs in animals

(2008) Andrew Grimson et al.   NATURE

Mechanisms of post-transcriptional regulation by microRNAs: are the answers in sight?

(2008) Witold Filipowicz et al.   NATURE REVIEWS GENETICS

The Carbohydrate-Active EnZymes database (CAZy): an expert resource for Glycogenomics

(2008) B. L. Cantarel et al.   NUCLEIC ACIDS RESEARCH

“Vaccination” of shrimp against viral pathogens: Phenomenology and underlying mechanisms

(2008) Karyn N. Johnson et al.   VACCINE

Automated eukaryotic gene structure annotation using EVidenceModeler and the Program to Assemble Spliced Alignments

(2008) Brian J Haas et al.   GENOME BIOLOGY

Immunoglobulin superfamily members play an important role in the mosquito immune system

(2007) Lindsey S. Garver et al.   DEVELOPMENTAL AND COMPARATIVE IMMUNOLOGY