Transcriptomic analysis of Macrobrachium rosenbergii (giant fresh water prawn) post-larvae in response to M. rosenbergii nodavirus (MrNV) infection: de novo assembly and functional annotation

Transcriptome analysis of ‘Huanghai No. 2’ Fenneropenaeus chinensis response to WSSV using RNA-seq

(2018) Xiaoli Shi et al.   FISH & SHELLFISH IMMUNOLOGY

Transcriptome analysis of Macrobrachium rosenbergii intestines under the white spot syndrome virus and poly (I:C) challenges

(2018) Zhengfeng Ding et al.   PLoS One

De novo assembly, characterization, functional annotation and expression patterns of the black tiger shrimp (Penaeus monodon) transcriptome

(2018) Roger Huerlimann et al.   Scientific Reports

Molecular isolation and characterization of a spätzle gene from Macrobrachium rosenbergii

(2018) Akapon Vaniksampanna et al.   FISH & SHELLFISH IMMUNOLOGY

UniProt: a worldwide hub of protein knowledge

(2018)   NUCLEIC ACIDS RESEARCH

Hematopoietic tissue of Macrobrachium rosenbergii plays dual roles as a source of hemocyte hematopoiesis and as a defensive mechanism against Macrobrachium rosenbergii nodavirus infection

(2018) Pitchanee Jariyapong et al.   FISH & SHELLFISH IMMUNOLOGY

Gill transcriptomes reveal involvement of cytoskeleton remodeling and immune defense in ammonia stress response in the banana shrimp Fenneropenaeus merguiensis

(2017) Wei Wang et al.   FISH & SHELLFISH IMMUNOLOGY

Transcriptome profiling of the Macrobrachium rosenbergii lymphoid organ under the white spot syndrome virus challenge

(2017) Jun Cao et al.   FISH & SHELLFISH IMMUNOLOGY

Short versus long double-stranded RNA activation of a post-transcriptional gene knockdown pathway

(2017) Nir Shpak et al.   RNA Biology

A Tissue-Mapped Axolotl De Novo Transcriptome Enables Identification of Limb Regeneration Factors

(2017) Donald M. Bryant et al.   Cell Reports

De novo assembly and transcriptome characterization of major growth-related genes in various tissues of Penaeus monodon

(2016) Cuong Nguyen et al.   AQUACULTURE

MultiQC: summarize analysis results for multiple tools and samples in a single report

(2016) Philip Ewels et al.   BIOINFORMATICS

Differentially expressed transcripts in stomach of Penaeus monodon in response to AHPND infection

(2016) Wipasiri Soonthornchai et al.   DEVELOPMENTAL AND COMPARATIVE IMMUNOLOGY

Toll receptor response to white spot syndrome virus challenge in giant freshwater prawns ( Macrobrachium rosenbergii )

(2016) Jinling Feng et al.   FISH & SHELLFISH IMMUNOLOGY

A transcriptome study on Macrobrachium rosenbergii hepatopancreas experimentally challenged with white spot syndrome virus (WSSV)

(2016) Rama Rao et al.   JOURNAL OF INVERTEBRATE PATHOLOGY

A comparison of physiological and transcriptome responses to water deprivation and salt loading in the rat supraoptic nucleus

(2015) Michael P. Greenwood et al.   AMERICAN JOURNAL OF PHYSIOLOGY-REGULATORY INTEGRATIVE AND COMPARATIVE PHYSIOLOGY

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

(2015) Felipe A. Simão et al.   BIOINFORMATICS

Characterization of two novel ADP ribosylation factors from giant freshwater prawn Macrobrachium rosenbergii and their responses to WSSV challenge

(2015) Zheng-Feng Ding et al.   DEVELOPMENTAL AND COMPARATIVE IMMUNOLOGY

Function of a novel C-type lectin with two CRD domains from Macrobrachium rosenbergii in innate immunity

(2015) Xin Huang et al.   DEVELOPMENTAL AND COMPARATIVE IMMUNOLOGY

Involvement of Relish gene from Macrobrachium rosenbergii in the expression of anti-microbial peptides

(2015) Yan-Ru Shi et al.   DEVELOPMENTAL AND COMPARATIVE IMMUNOLOGY

Interaction study of a novel Macrobrachium rosenbergii effector caspase with B2 and capsid proteins of M. rosenbergii nodavirus reveals their roles in apoptosis

(2015) Supak Youngcharoen et al.   FISH & SHELLFISH IMMUNOLOGY

Macrobrachium rosenbergii mannose binding lectin: Synthesis of MrMBL-N20 and MrMBL-C16 peptides and their antimicrobial characterization, bioinformatics and relative gene expression analysis

(2015) Jesu Arockiaraj et al.   FISH & SHELLFISH IMMUNOLOGY

Identification and function of 11 Rab GTPases in giant freshwater prawn Macrobrachium rosenbergii

(2015) Ying Huang et al.   FISH & SHELLFISH IMMUNOLOGY

Transcriptome Profiles of Penaeus (Marsupenaeus) japonicus Animal and Vegetal Half-Embryos: Identification of Sex Determination, Germ Line, Mesoderm, and Other Developmental Genes

(2015) Melony J. Sellars et al.   MARINE BIOTECHNOLOGY

De-novo transcriptome analysis of the banana shrimp (Fenneropenaeus merguiensis) and identification of genes associated with reproduction and development

(2015) Daniel Powell et al.   Marine Genomics

RNA-seq analysis of Macrobrachium rosenbergii hepatopancreas in response to Vibrio parahaemolyticus infection

(2015) Rama Rao et al.   Gut Pathogens

Transcriptome and Molecular Pathway Analysis of the Hepatopancreas in the Pacific White Shrimp Litopenaeus vannamei under Chronic Low-Salinity Stress

(2015) Ke Chen et al.   PLoS One

Trimmomatic: a flexible trimmer for Illumina sequence data

(2014) Anthony M. Bolger et al.   BIOINFORMATICS

Cloning and characterization of two different ficolins from the giant freshwater prawn Macrobrachium rosenbergii

(2014) Xiao-Wen Zhang et al.   DEVELOPMENTAL AND COMPARATIVE IMMUNOLOGY

Molecular cloning and characterization of a Toll receptor gene from Macrobrachium rosenbergii

(2014) Chutima Srisuk et al.   FISH & SHELLFISH IMMUNOLOGY

A cytosolic glutathione s-transferase, GST-theta from freshwater prawn Macrobrachium rosenbergii: molecular and biochemical properties

(2014) Jesu Arockiaraj et al.   GENE

SNP Discovery in the Transcriptome of White Pacific Shrimp Litopenaeus vannamei by Next Generation Sequencing

(2014) Yang Yu et al.   PLoS One

Novel transcriptome assembly and improved annotation of the whiteleg shrimp (Litopenaeus vannamei), a dominant crustacean in global seafood mariculture

(2014) Noushin Ghaffari et al.   Scientific Reports

Quantitative assessment of single-cell RNA-sequencing methods

(2013) Angela R Wu 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

Transcriptome Analysis on Chinese Shrimp Fenneropenaeus chinensis during WSSV Acute Infection

(2013) Shihao Li et al.   PLoS One

Analysis of Expression, Cellular Localization, and Function of Three Inhibitors of Apoptosis (IAPs) from Litopenaeus vannamei during WSSV Infection and in Regulation of Antimicrobial Peptide Genes (AMPs)

(2013) Pei-Hui Wang et al.   PLoS One

Infections of MrNV (Macrobrachium rosenbergii nodavirus) in cultivated whiteleg shrimp Penaeus vannamei in Asia

(2012) Saengchan Senapin et al.   AQUACULTURE

Snakemake--a scalable bioinformatics workflow engine

(2012) J. Koster et al.   BIOINFORMATICS

Host defense against DNA virus infection in shrimp is mediated by the siRNA pathway

(2012) Tianzhi Huang et al.   EUROPEAN JOURNAL OF IMMUNOLOGY

Immunological role of thiol-dependent peroxiredoxin gene in Macrobrachium rosenbergii

(2012) Jesu Arockiaraj et al.   FISH & SHELLFISH IMMUNOLOGY

Transglutaminase regulates immune-related genes in shrimp

(2012) Fernand F. Fagutao et al.   FISH & SHELLFISH IMMUNOLOGY

Three different anti-lipopolysaccharide factors identified from giant freshwater prawn, Macrobrachium rosenbergii

(2012) Qian Ren et al.   FISH & SHELLFISH IMMUNOLOGY

Crustin, a WAP domain containing antimicrobial peptide from freshwater prawn Macrobrachium rosenbergii: Immune characterization

(2012) Jesu Arockiaraj et al.   FISH & SHELLFISH IMMUNOLOGY

Pattern recognition receptors acting in innate immune system of shrimp against pathogen infections

(2012) Xian-Wei Wang et al.   FISH & SHELLFISH IMMUNOLOGY

Molecular mechanisms of the shrimp clotting system

(2012) Mary Beth B. Maningas et al.   FISH & SHELLFISH IMMUNOLOGY

Functional Analysis of a Crustacean MicroRNA in Host-Virus Interactions

(2012) T. Huang et al.   JOURNAL OF VIROLOGY

Fast gapped-read alignment with Bowtie 2

(2012) Ben Langmead et al.   NATURE METHODS

Signature miRNAs Involved in the Innate Immunity of Invertebrates

(2012) Geng Yang et al.   PLoS One

Immunomodulatory effect of recombinant RNA-dependent RNA polymerase protein of Macrobrachium rosenbergii nodavirus in giant freshwater prawn M. rosenbergii

(2011) Pramoda Kumar Sahoo et al.   AQUACULTURE RESEARCH

RSEM: accurate transcript quantification from RNA-Seq data with or without a reference genome

(2011) Bo Li et al.   BMC BIOINFORMATICS

Identification and functional characterization of Dicer2 and five single VWC domain proteins of Litopenaeus vannamei

(2011) Yi-Hong Chen et al.   DEVELOPMENTAL AND COMPARATIVE IMMUNOLOGY

Molecular cloning, characterization and expression analysis of two novel Tolls (LvToll2 and LvToll3) and three putative Spätzle-like Toll ligands (LvSpz1–3) from Litopenaeus vannamei

(2011) Pei-Hui Wang et al.   DEVELOPMENTAL AND COMPARATIVE IMMUNOLOGY

Bioinformatic characterization and gene expression pattern of apoptosis inhibitor from Macrobrachium rosenbergii challenged with infectious hypodermal and hematopoietic necrosis virus

(2011) Jesu Arockiaraj et al.   FISH & SHELLFISH IMMUNOLOGY

Effect of infectious hypodermal and haematopoietic necrosis virus (IHHNV) infection on caspase 3c expression and activity in freshwater prawn Macrobrachium rosenbergii

(2011) Jesu Arockiaraj et al.   FISH & SHELLFISH IMMUNOLOGY

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

(2011) Manfred G Grabherr et al.   NATURE BIOTECHNOLOGY

Non-specific activation of antiviral immunity and induction of RNA interference may engage the same pathway in the Pacific white leg shrimp Litopenaeus vannamei

(2010) Yannick Labreuche et al.   DEVELOPMENTAL AND COMPARATIVE IMMUNOLOGY

Characterization of two novel ADP ribosylation factors from the shrimp Marsupenaeus japonicus

(2010) Jinyou Ma et al.   FISH & SHELLFISH IMMUNOLOGY

A Dicer-1 gene from white shrimp Litopenaeus vannamei: Expression pattern in the processes of immune response and larval development

(2010) Xuemei Yao et al.   FISH & SHELLFISH IMMUNOLOGY

Alternative expression analysis by RNA sequencing

(2010) Malachi Griffith et al.   NATURE METHODS

A scaling normalization method for differential expression analysis of RNA-seq data

(2010) Mark D Robinson et al.   GENOME BIOLOGY

Mechanisms of apoptosis in Crustacea: what conditions induce versus suppress cell death?

(2009) Michael A. Menze et al.   APOPTOSIS

edgeR: a Bioconductor package for differential expression analysis of digital gene expression data

(2009) M. D. Robinson et al.   BIOINFORMATICS

3' tag digital gene expression profiling of human brain and universal reference RNA using Illumina Genome Analyzer

(2009) Yan W Asmann et al.   BMC GENOMICS

Macrobrachium rosenbergii nodavirus disease (white tail disease) in Australia

(2009) L Owens et al.   DISEASES OF AQUATIC ORGANISMS

Identification and molecular characterization of a Spätzle-like protein from Chinese shrimp (Fenneropenaeus chinensis)

(2009) Xiu-Zhen Shi et al.   FISH & SHELLFISH IMMUNOLOGY

Identification and cloning of a selenium dependent glutathione peroxidase from giant freshwater prawn, Macrobrachium rosenbergii

(2009) Shinn-Pyng Yeh et al.   FISH & SHELLFISH IMMUNOLOGY

Molecular cloning and characterization of a class II ADP ribosylation factor from the shrimp Marsupenaeus japonicus

(2009) Mingchang Zhang et al.   FISH & SHELLFISH IMMUNOLOGY

Ran GTPase Regulates Hemocytic Phagocytosis of Shrimp by Interaction with Myosin

(2009) Weifeng Liu et al.   JOURNAL OF PROTEOME RESEARCH

Validation of reference genes for quantitative measurement of immune gene expression in shrimp

(2009) Arun K. Dhar et al.   MOLECULAR IMMUNOLOGY

Applications of next-generation sequencing technologies in functional genomics

(2008) Olena Morozova et al.   GENOMICS

Regulation of actin cytoskeleton dynamics by Arf-family GTPases

(2008) Kenneth R. Myers et al.   TRENDS IN CELL BIOLOGY

A key gene of the RNA interference pathway in the black tiger shrimp, Penaeus monodon: Identification and functional characterisation of Dicer-1

(2007) Jianguo Su et al.   FISH & SHELLFISH IMMUNOLOGY

Antiviral Phagocytosis Is Regulated by a Novel Rab-Dependent Complex in ShrimpPenaeus japonicus

(2007) Wenlin Wu et al.   JOURNAL OF PROTEOME RESEARCH