Silent Witness: Dual-Species Transcriptomics Reveals Epithelial Immunological Quiescence to Helminth Larval Encounter and Fostered Larval Development

WormBase ParaSite − a comprehensive resource for helminth genomics

(2017) Kevin L. Howe et al.   MOLECULAR AND BIOCHEMICAL PARASITOLOGY

Ensembl 2018

(2017) Daniel R Zerbino et al.   NUCLEIC ACIDS RESEARCH

Resolving host–pathogen interactions by dual RNA-seq

(2017) Alexander J. Westermann et al.   PLoS Pathogens

Pathogen-Reactive T Helper Cell Analysis in the Pig

(2017) Friederike Ebner et al.   Frontiers in Immunology

BlastKOALA and GhostKOALA: KEGG Tools for Functional Characterization of Genome and Metagenome Sequences

(2016) Minoru Kanehisa et al.   JOURNAL OF MOLECULAR BIOLOGY

Host parasite communications—Messages from helminths for the immune system

(2016) Gillian Coakley et al.   MOLECULAR AND BIOCHEMICAL PARASITOLOGY

Intestinal epithelial tuft cells initiate type 2 mucosal immunity to helminth parasites

(2016) François Gerbe et al.   NATURE

Expansion of the Gene Ontology knowledgebase and resources

(2016)   NUCLEIC ACIDS RESEARCH

UniProt: the universal protein knowledgebase

(2016)   NUCLEIC ACIDS RESEARCH

Environmental contamination and transmission of Ascaris suum in Danish organic pig farms

(2016) Kiran K. Katakam et al.   Parasites & Vectors

Tuft cells, taste-chemosensory cells, orchestrate parasite type 2 immunity in the gut

(2016) M. R. Howitt et al.   SCIENCE

Guidance for RNA-seq co-expression network construction and analysis: safety in numbers

(2015) S. Ballouz et al.   BIOINFORMATICS

Qualimap 2: advanced multi-sample quality control for high-throughput sequencing data

(2015) Konstantin Okonechnikov et al.   BIOINFORMATICS

The human hookworm vaccine: recent updates and prospects for success

(2015) M.E. Bottazzi   JOURNAL OF HELMINTHOLOGY

Serine Proteases of Parasitic Helminths

(2015) Yong Yang et al.   KOREAN JOURNAL OF PARASITOLOGY

Intestinal FoxO signaling is required to survive oral infection in Drosophila

(2015) C Fink et al.   Mucosal Immunology

limma powers differential expression analyses for RNA-sequencing and microarray studies

(2015) Matthew E. Ritchie et al.   NUCLEIC ACIDS RESEARCH

KEGG as a reference resource for gene and protein annotation

(2015) Minoru Kanehisa et al.   NUCLEIC ACIDS RESEARCH

The BioMart community portal: an innovative alternative to large, centralized data repositories

(2015) Damian Smedley et al.   NUCLEIC ACIDS RESEARCH

Genome analysis of Excretory/Secretory proteins in Taenia solium reveals their Abundance of Antigenic Regions (AAR)

(2015) Sandra Gomez et al.   Scientific Reports

Expression, purification, and characterization of theNecator americanusaspartic protease-1 (Na-APR-1 (M74)) antigen, a component of the bivalent human hookworm vaccine

(2015) Christopher A Seid et al.   Human Vaccines & Immunotherapeutics

Comparing Two Intestinal Porcine Epithelial Cell Lines (IPECs): Morphological Differentiation, Function and Metabolism

(2015) Constanze Nossol et al.   PLoS One

Trimmomatic: a flexible trimmer for Illumina sequence data

(2014) Anthony M. Bolger et al.   BIOINFORMATICS

InterProScan 5: genome-scale protein function classification

(2014) P. Jones et al.   BIOINFORMATICS

Comparative analysis of microRNA profiles between adult Ascaris lumbricoides and Ascaris suum

(2014) Chang-Chun Shao et al.   BMC Veterinary Research

Human intestinal epithelial cells respond to β-glucans via Dectin-1 and Syk

(2014) Sarit Cohen-Kedar et al.   EUROPEAN JOURNAL OF IMMUNOLOGY

Blockade of IL-33 release and suppression of type 2 innate lymphoid cell responses by helminth secreted products in airway allergy

(2014) H J McSorley et al.   Mucosal Immunology

The Global Burden of Disease Study 2010: Interpretation and Implications for the Neglected Tropical Diseases

(2014) Peter J. Hotez et al.   PLoS Neglected Tropical Diseases

Genome-Wide Tissue-Specific Gene Expression, Co-expression and Regulation of Co-expressed Genes in Adult Nematode Ascaris suum

(2014) Bruce A. Rosa et al.   PLoS Neglected Tropical Diseases

Kraken: ultrafast metagenomic sequence classification using exact alignments

(2014) Derrick E Wood et al.   GENOME BIOLOGY

Enzymology of the nematode cuticle: A potential drug target?

(2014) Antony P. Page et al.   International Journal for Parasitology-Drugs and Drug Resistance

Mucosal Inflammatory Response to Salmonella typhimurium Infection

(2014) Samir Patel et al.   Frontiers in Immunology

featureCounts: an efficient general purpose program for assigning sequence reads to genomic features

(2013) Y. Liao et al.   BIOINFORMATICS

Claudins and the Modulation of Tight Junction Permeability

(2013) Dorothee Günzel et al.   PHYSIOLOGICAL REVIEWS

Improved Cell Line IPEC-J2, Characterized as a Model for Porcine Jejunal Epithelium

(2013) Silke S. Zakrzewski et al.   PLoS One

The Human Hookworm Vaccine

(2013) Peter J. Hotez et al.   VACCINE

The Intestinal Expulsion of the Roundworm Ascaris suum Is Associated with Eosinophils, Intra-Epithelial T Cells and Decreased Intestinal Transit Time

(2013) Dries Masure et al.   PLoS Neglected Tropical Diseases

Proteomic Analysis of the Excretory-Secretory Products from Larval Stages of Ascaris suum Reveals High Abundance of Glycosyl Hydrolases

(2013) Tao Wang et al.   PLoS Neglected Tropical Diseases

TopHat2: accurate alignment of transcriptomes in the presence of insertions, deletions and gene fusions

(2013) Daehwan Kim et al.   GENOME BIOLOGY

Snakemake--a scalable bioinformatics workflow engine

(2012) J. Koster et al.   BIOINFORMATICS

Interleukin 33 as a Mechanically Responsive Cytokine Secreted by Living Cells

(2012) Rahul Kakkar et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Prolyl 4-Hydroxlase Activity Is Essential for Development and Cuticle Formation in the Human Infective Parasitic NematodeBrugia malayi

(2012) Alan D. Winter et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Differential analysis of gene regulation at transcript resolution with RNA-seq

(2012) Cole Trapnell et al.   NATURE BIOTECHNOLOGY

clusterProfiler: an R Package for Comparing Biological Themes Among Gene Clusters

(2012) Guangchuang Yu et al.   OMICS-A JOURNAL OF INTEGRATIVE BIOLOGY

Are Ascaris lumbricoides and Ascaris suum a single species?

(2012) Daniela Leles et al.   Parasites & Vectors

Neglected tropical diseases: diagnosis, clinical management, treatment and control

(2012) J Utzinger et al.   SWISS MEDICAL WEEKLY

Ascaris suum draft genome

(2011) Aaron R. Jex et al.   NATURE

SignalP 4.0: discriminating signal peptides from transmembrane regions

(2011) Thomas Nordahl Petersen et al.   NATURE METHODS

Ensembl BioMarts: a hub for data retrieval across taxonomic space

(2011) R. J. Kinsella et al.   Database-The Journal of Biological Databases and Curation

Developing vaccines to combat hookworm infection and intestinal schistosomiasis

(2010) Peter J. Hotez et al.   NATURE REVIEWS MICROBIOLOGY

BLAST+: architecture and applications

(2009) Christiam Camacho et al.   BMC BIOINFORMATICS

Identification of novel aspartic proteases from Strongyloides ratti and characterisation of their evolutionary relationships, stage-specific expression and molecular structure

(2009) Luciane V Mello et al.   BMC GENOMICS

Localized Th1-, Th2-, T Regulatory Cell-, and Inflammation-Associated Hepatic and Pulmonary Immune Responses in Ascaris suum-Infected Swine Are Increased by Retinoic Acid

(2009) H. Dawson et al.   INFECTION AND IMMUNITY

Helminth immunoregulation: The role of parasite secreted proteins in modulating host immunity

(2009) James P. Hewitson et al.   MOLECULAR AND BIOCHEMICAL PARASITOLOGY

Mapping identifiers for the integration of genomic datasets with the R/Bioconductor package biomaRt

(2009) Steffen Durinck et al.   Nature Protocols

On the hunt for helminths: innate immune cells in the recognition and response to helminth parasites

(2008) Jacqueline G. Perrigoue et al.   CELLULAR MICROBIOLOGY

Macrophage Migration Inhibitory Factor and Interleukin-8 Produced by Gastric Epithelial Cells during Helicobacter pylori Exposure Induce Expression and Activation of the Epidermal Growth Factor Receptor

(2008) E. J. Beswick et al.   INFECTION AND IMMUNITY

Alarming dendritic cells for Th2 induction

(2008) Andrew S. MacDonald et al.   JOURNAL OF EXPERIMENTAL MEDICINE

Necator americanus: The Na-ASP-2 protein secreted by the infective larvae induces neutrophil recruitment in vivo and in vitro

(2007) Molly A. Bower et al.   EXPERIMENTAL PARASITOLOGY

Innate immune recognition at the epithelial barrier drives adaptive immunity: APCs take the back seat

(2007) Jörg H. Fritz et al.   TRENDS IN IMMUNOLOGY