Long-read RNA sequencing of human and animal filarial parasites improves gene models and discovers operons

Deep neural networks for interpreting RNA-binding protein target preferences

(2020) Mahsa Ghanbari et al.   GENOME RESEARCH

The full-length transcriptome of C. elegans using direct RNA sequencing

(2020) Nathan P. Roach et al.   GENOME RESEARCH

Genetic and functional diversification of chemosensory pathway receptors in mosquito-borne filarial nematodes

(2020) Nicolas J. Wheeler et al.   PLOS BIOLOGY

Apollo: Democratizing genome annotation

(2019) Nathan A. Dunn et al.   PLoS Computational Biology

Graph-based genome alignment and genotyping with HISAT2 and HISAT-genotype

(2019) Daehwan Kim et al.   NATURE BIOTECHNOLOGY

FLAM-seq: full-length mRNA sequencing reveals principles of poly(A) tail length control

(2019) Ivano Legnini et al.   NATURE METHODS

Emodepside has sex-dependent immobilizing effects on adult Brugia malayi due to a differentially spliced binding pocket in the RCK1 region of the SLO-1 K channel

(2019) Sudhanva S. Kashyap et al.   PLoS Pathogens

Minimap2: pairwise alignment for nucleotide sequences

(2018) Heng Li   BIOINFORMATICS

Improving eukaryotic genome annotation using single molecule mRNA sequencing

(2018) Vincent Magrini et al.   BMC GENOMICS

Mining Filarial Genomes for Diagnostic and Therapeutic Targets

(2018) Sasisekhar Bennuru et al.   TRENDS IN PARASITOLOGY

Clinical validation of molecular markers of macrocyclic lactone resistance in Dirofilaria immitis

(2018) Cristina Ballesteros et al.   International Journal for Parasitology-Drugs and Drug Resistance

Targeted enrichment outperforms other enrichment techniques and enables more multi-species RNA-Seq analyses

(2018) Matthew Chung et al.   Scientific Reports

Global, regional, and national incidence, prevalence, and years lived with disability for 354 diseases and injuries for 195 countries and territories, 1990–2017: a systematic analysis for the Global Burden of Disease Study 2017

(2018) Spencer L James et al.   LANCET

Comparative genomics of the major parasitic worms

(2018)   NATURE GENETICS

Comparative genome analysis of programmed DNA elimination in nematodes

(2017) Jianbin Wang et al.   GENOME RESEARCH

WormBase ParaSite − a comprehensive resource for helminth genomics

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

Nextflow enables reproducible computational workflows

(2017) Paolo Di Tommaso et al.   NATURE BIOTECHNOLOGY

Short poly(A) tails are a conserved feature of highly expressed genes

(2017) Sarah Azoubel Lima et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Short poly(A) tails are a conserved feature of highly expressed genes

(2017) Sarah Azoubel Lima et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

The genomic basis of parasitism in the Strongyloides clade of nematodes

(2016) Vicky L Hunt et al.   NATURE GENETICS

Yeast-Based High-Throughput Screens to Identify Novel Compounds Active against Brugia malayi

(2016) Elizabeth Bilsland et al.   PLoS Neglected Tropical Diseases

The genome of Onchocerca volvulus, agent of river blindness

(2016) James A. Cotton et al.   Nature Microbiology

cDNA Library Enrichment of Full Length Transcripts for SMRT Long Read Sequencing

(2016) Maria Cartolano et al.   PLoS One

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

(2015) Felipe A. Simão et al.   BIOINFORMATICS

Establishment of macrocyclic lactone resistant Dirofilaria immitis isolates in experimentally infected laboratory dogs

(2014) Cassan N Pulaski et al.   Parasites & Vectors

The transcription start site landscape of C. elegans

(2013) T. L. Saito et al.   GENOME RESEARCH

BEDOPS: high-performance genomic feature operations

(2012) Shane Neph et al.   BIOINFORMATICS

Integrative Genomics Viewer (IGV): high-performance genomics data visualization and exploration

(2012) H. Thorvaldsdottir et al.   BRIEFINGS IN BIOINFORMATICS

Human and Animal Dirofilariasis: the Emergence of a Zoonotic Mosaic

(2012) F. Simon et al.   CLINICAL MICROBIOLOGY REVIEWS

The genome of the heartworm, Dirofilaria immitis, reveals drug and vaccine targets

(2012) Christelle Godel et al.   FASEB JOURNAL

Methods and strategies for gene structure curation in WormBase

(2011) G. W. Williams et al.   Database-The Journal of Biological Databases and Curation

The NIH-NIAID Filariasis Research Reagent Resource Center

(2011) Michelle L. Michalski et al.   PLoS Neglected Tropical Diseases

BEDTools: a flexible suite of utilities for comparing genomic features

(2010) Aaron R. Quinlan et al.   BIOINFORMATICS

Discovery of veterinary antiparasitic agents in the 21st Century: A view from industry

(2010) Debra J. Woods et al.   INTERNATIONAL JOURNAL FOR PARASITOLOGY

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

Biopython: freely available Python tools for computational molecular biology and bioinformatics

(2009) P. J. A. Cock et al.   BIOINFORMATICS

BLAST+: architecture and applications

(2009) Christiam Camacho et al.   BMC BIOINFORMATICS

Functional analysis of putative operons in Brugia malayi

(2009) Canhui Liu et al.   INTERNATIONAL JOURNAL FOR PARASITOLOGY

An Ivermectin-Sensitive Glutamate-Gated Chloride Channel from the Parasitic Nematode Haemonchus contortus

(2009) S. McCavera et al.   MOLECULAR PHARMACOLOGY

WormBase: a comprehensive resource for nematode research

(2009) Todd W. Harris et al.   NUCLEIC ACIDS RESEARCH