Genome and transcriptome of the porcine whipworm Trichuris suis

Infernal 1.1: 100-fold faster RNA homology searches

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

Efficient identification of Y chromosome sequences in the human andDrosophilagenomes

(2013) Antonio Bernardo Carvalho et al.   GENOME RESEARCH

WormBase 2014: new views of curated biology

(2013) Todd W. Harris et al.   NUCLEIC ACIDS RESEARCH

ShortStack: Comprehensive annotation and quantification of small RNA genes

(2013) M. J. Axtell   RNA

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

(2013) Daehwan Kim et al.   GENOME BIOLOGY

CD-HIT: accelerated for clustering the next-generation sequencing data

(2012) Limin Fu et al.   BIOINFORMATICS

Diversity in parasitic nematode genomes: the microRNAs of Brugia pahangi and Haemonchus contortus are largely novel

(2012) Alan D Winter et al.   BMC GENOMICS

Long noncoding RNAs in C. elegans

(2012) J.-W. Nam et al.   GENOME RESEARCH

Trichuris suis-induced modulation of human dendritic cell function is glycan-mediated

(2012) Elsenoor J. Klaver et al.   INTERNATIONAL JOURNAL FOR PARASITOLOGY

Whole-genome sequence of Schistosoma haematobium

(2012) Neil D Young et al.   NATURE GENETICS

Fast gapped-read alignment with Bowtie 2

(2012) Ben Langmead et al.   NATURE METHODS

Differential gene and transcript expression analysis of RNA-seq experiments with TopHat and Cufflinks

(2012) Cole Trapnell et al.   Nature Protocols

Rfam 11.0: 10 years of RNA families

(2012) Sarah W. Burge et al.   NUCLEIC ACIDS RESEARCH

Serine Protease(s) Secreted by the Nematode Trichuris muris Degrade the Mucus Barrier

(2012) Sumaira Z. Hasnain et al.   PLoS Neglected Tropical Diseases

FIMO: scanning for occurrences of a given motif

(2011) Charles E. Grant et al.   BIOINFORMATICS

Manipulation of vascular function by blood flukes?

(2011) Akram Da'dara et al.   BLOOD REVIEWS

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

(2011) Carson Holt et al.   BMC BIOINFORMATICS

Deep small RNA sequencing from the nematode Ascaris reveals conservation, functional diversification, and novel developmental profiles

(2011) J. Wang et al.   GENOME RESEARCH

Differential expression in RNA-seq: A matter of depth

(2011) S. Tarazona et al.   GENOME RESEARCH

Probiotic helminth administration in relapsing–remitting multiple sclerosis: a phase 1 study

(2011) JO Fleming et al.   Multiple Sclerosis Journal

Ascaris suum draft genome

(2011) Aaron R. Jex et al.   NATURE

The draft genome of the parasitic nematode Trichinella spiralis

(2011) Makedonka Mitreva et al.   NATURE GENETICS

miRDeep2 accurately identifies known and hundreds of novel microRNA genes in seven animal clades

(2011) Marc R. Friedländer et al.   NUCLEIC ACIDS RESEARCH

Identification and characterization of microRNAs in Trichinella spiralis by comparison with Brugia malayi and Caenorhabditis elegans

(2011) M. X. Chen et al.   PARASITOLOGY RESEARCH

Fast and accurate long-read alignment with Burrows–Wheeler transform

(2010) Heng Li et al.   BIOINFORMATICS

Long-term periodic anthelmintic treatments are associated with increased allergen skin reactivity

(2010) P. Endara et al.   CLINICAL AND EXPERIMENTAL ALLERGY

The ‘hygiene hypothesis’ for autoimmune and allergic diseases: an update

(2010) H. Okada et al.   CLINICAL AND EXPERIMENTAL IMMUNOLOGY

Mucin Gene Deficiency in Mice Impairs Host Resistance to an Enteric Parasitic Infection

(2010) Sumaira Z. Hasnain et al.   GASTROENTEROLOGY

Prediction and characterization of noncoding RNAs in C. elegans by integrating conservation, secondary structure, and high-throughput sequencing and array data

(2010) Z. J. Lu et al.   GENOME RESEARCH

Serine Protease-mediated Host Invasion by the Parasitic NematodeSteinernema carpocapsae

(2010) Duarte Toubarro et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

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

(2010) Cole Trapnell et al.   NATURE BIOTECHNOLOGY

Comprehensive discovery of endogenous Argonaute binding sites in Caenorhabditis elegans

(2010) Dimitrios G Zisoulis et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

SOAP2: an improved ultrafast tool for short read alignment

(2009) R. Li et al.   BIOINFORMATICS

An apoptosis-inducing serine protease secreted by the entomopathogenic nematode Steinernema carpocapsae

(2009) Duarte Toubarro et al.   INTERNATIONAL JOURNAL FOR PARASITOLOGY

Rescuing the bottom billion through control of neglected tropical diseases

(2009) Peter J Hotez et al.   LANCET

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

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

Small silencing RNAs: an expanding universe

(2009) Megha Ghildiyal et al.   NATURE REVIEWS GENETICS

MEROPS: the peptidase database

(2009) Neil D. Rawlings et al.   NUCLEIC ACIDS RESEARCH

Biochemical study andin vitroinsect immune suppression by a trypsin-like secreted protease from the nematodeSteinernema carpocapsae

(2009) N. BALASUBRAMANIAN et al.   PARASITE IMMUNOLOGY

Brugia malayi Excreted/Secreted Proteins at the Host/Parasite Interface: Stage- and Gender-Specific Proteomic Profiling

(2009) Sasisekhar Bennuru et al.   PLoS Neglected Tropical Diseases

Therapeutic options in inflammatory bowel disease: experimental evidence of a beneficial effect of kinin B1receptor blockade

(2008) F Marceau et al.   BRITISH JOURNAL OF PHARMACOLOGY

The secretome of the filarial parasite, Brugia malayi: Proteomic profile of adult excretory–secretory products

(2008) James P. Hewitson et al.   MOLECULAR AND BIOCHEMICAL PARASITOLOGY

A new class of anthelmintics effective against drug-resistant nematodes

(2008) Ronald Kaminsky et al.   NATURE

Alternative isoform regulation in human tissue transcriptomes

(2008) Eric T. Wang et al.   NATURE

Discovering microRNAs from deep sequencing data using miRDeep

(2008) Marc R Friedländer et al.   NATURE BIOTECHNOLOGY

Assessing the gene space in draft genomes

(2008) Genis Parra et al.   NUCLEIC ACIDS RESEARCH

The Transporter Classification Database: recent advances

(2008) M. H. Saier et al.   NUCLEIC ACIDS RESEARCH

Direct Identification of the Meloidogyne incognita Secretome Reveals Proteins with Host Cell Reprogramming Potential

(2008) Stéphane Bellafiore et al.   PLoS Pathogens