Published in BMC Genomics on January 04, 2012
Ancient and novel small RNA pathways compensate for the loss of piRNAs in multiple independent nematode lineages. PLoS Biol (2015) 1.50
Genome and transcriptome of the porcine whipworm Trichuris suis. Nat Genet (2014) 0.96
Detection of circulating parasite-derived microRNAs in filarial infections. PLoS Negl Trop Dis (2014) 0.95
Toxocara canis: molecular basis of immune recognition and evasion. Vet Parasitol (2012) 0.92
Identification of Dirofilaria immitis miRNA using illumina deep sequencing. Vet Res (2013) 0.92
Novel insights into the transcriptome of Dirofilaria immitis. PLoS One (2012) 0.88
Functional diversification of Argonautes in nematodes: an expanding universe. Biochem Soc Trans (2013) 0.87
microRNA profiling in the zoonotic parasite Echinococcus canadensis using a high-throughput approach. Parasit Vectors (2015) 0.85
Diversity and expression of microRNAs in the filarial parasite, Brugia malayi. PLoS One (2014) 0.84
microRNAs of parasitic helminths - Identification, characterization and potential as drug targets. Int J Parasitol Drugs Drug Resist (2014) 0.82
Rendering the Intractable More Tractable: Tools from Caenorhabditis elegans Ripe for Import into Parasitic Nematodes. Genetics (2015) 0.80
Application of small RNA technology for improved control of parasitic helminths. Vet Parasitol (2015) 0.79
Identification of MicroRNAs in Meloidogyne incognita Using Deep Sequencing. PLoS One (2015) 0.79
Identification of conserved and novel microRNAs in the Pacific oyster Crassostrea gigas by deep sequencing. PLoS One (2014) 0.78
A novel member of the let-7 microRNA family is associated with developmental transitions in filarial nematode parasites. BMC Genomics (2015) 0.78
Nematode endogenous small RNA pathways. Worm (2014) 0.78
Identification and characterisation of microRNAs in young adults of Angiostrongylus cantonensis via a deep-sequencing approach. Mem Inst Oswaldo Cruz (2013) 0.76
MicroRNAs of Toxocara canis and their predicted functional roles. Parasit Vectors (2016) 0.76
Functional analysis of microRNA activity in Brugia malayi. Int J Parasitol (2015) 0.75
Perusal of parasitic nematode 'omics in the post-genomic era. Mol Biochem Parasitol (2016) 0.75
Basic local alignment search tool. J Mol Biol (1990) 659.07
tRNAscan-SE: a program for improved detection of transfer RNA genes in genomic sequence. Nucleic Acids Res (1997) 142.55
Accurate whole human genome sequencing using reversible terminator chemistry. Nature (2008) 90.20
The C. elegans heterochronic gene lin-4 encodes small RNAs with antisense complementarity to lin-14. Cell (1993) 64.62
The 21-nucleotide let-7 RNA regulates developmental timing in Caenorhabditis elegans. Nature (2000) 39.31
miRBase: tools for microRNA genomics. Nucleic Acids Res (2007) 38.61
Most mammalian mRNAs are conserved targets of microRNAs. Genome Res (2008) 37.16
SILVA: a comprehensive online resource for quality checked and aligned ribosomal RNA sequence data compatible with ARB. Nucleic Acids Res (2007) 35.65
Posttranscriptional regulation of the heterochronic gene lin-14 by lin-4 mediates temporal pattern formation in C. elegans. Cell (1993) 33.79
MicroRNAs modulate hematopoietic lineage differentiation. Science (2003) 30.05
Biogenesis of small RNAs in animals. Nat Rev Mol Cell Biol (2009) 19.99
A microRNA component of the p53 tumour suppressor network. Nature (2007) 19.25
Serum response factor regulates a muscle-specific microRNA that targets Hand2 during cardiogenesis. Nature (2005) 17.17
MicroRNA expression in zebrafish embryonic development. Science (2005) 15.52
Large-scale sequencing reveals 21U-RNAs and additional microRNAs and endogenous siRNAs in C. elegans. Cell (2006) 15.12
A pancreatic islet-specific microRNA regulates insulin secretion. Nature (2004) 15.02
Small silencing RNAs: an expanding universe. Nat Rev Genet (2009) 13.88
An oligonucleotide microchip for genome-wide microRNA profiling in human and mouse tissues. Proc Natl Acad Sci U S A (2004) 13.66
The RIN: an RNA integrity number for assigning integrity values to RNA measurements. BMC Mol Biol (2006) 13.13
A microRNA controlling left/right neuronal asymmetry in Caenorhabditis elegans. Nature (2003) 12.93
A molecular evolutionary framework for the phylum Nematoda. Nature (1998) 10.64
Application of massively parallel sequencing to microRNA profiling and discovery in human embryonic stem cells. Genome Res (2008) 10.18
Discovering microRNAs from deep sequencing data using miRDeep. Nat Biotechnol (2008) 10.17
Searching protein sequence libraries: comparison of the sensitivity and selectivity of the Smith-Waterman and FASTA algorithms. Genomics (1991) 9.65
A cellular microRNA mediates antiviral defense in human cells. Science (2005) 8.48
Helminth infections: the great neglected tropical diseases. J Clin Invest (2008) 6.92
Early origins and evolution of microRNAs and Piwi-interacting RNAs in animals. Nature (2008) 6.81
MicroRNA-143 regulates adipocyte differentiation. J Biol Chem (2004) 6.78
The let-7 family of microRNAs. Trends Cell Biol (2008) 6.24
The let-7 MicroRNA family members mir-48, mir-84, and mir-241 function together to regulate developmental timing in Caenorhabditis elegans. Dev Cell (2005) 5.90
Most Caenorhabditis elegans microRNAs are individually not essential for development or viability. PLoS Genet (2007) 5.33
MicroRNAs act sequentially and asymmetrically to control chemosensory laterality in the nematode. Nature (2004) 5.31
Draft genome of the filarial nematode parasite Brugia malayi. Science (2007) 5.28
A MicroRNA targeting dicer for metastasis control. Cell (2010) 4.81
Strategies and tools for the control/elimination of lymphatic filariasis. Bull World Health Organ (1997) 4.76
Mechanisms of miRNA-mediated post-transcriptional regulation in animal cells. Curr Opin Cell Biol (2009) 4.56
Comprehensive discovery of endogenous Argonaute binding sites in Caenorhabditis elegans. Nat Struct Mol Biol (2010) 4.22
Antisense-mediated depletion reveals essential and specific functions of microRNAs in Drosophila development. Cell (2005) 3.95
The deep evolution of metazoan microRNAs. Evol Dev (2009) 3.56
Piwi and piRNAs act upstream of an endogenous siRNA pathway to suppress Tc3 transposon mobility in the Caenorhabditis elegans germline. Mol Cell (2008) 3.37
The biogenesis and function of PIWI proteins and piRNAs: progress and prospect. Annu Rev Cell Dev Biol (2009) 3.21
Many families of C. elegans microRNAs are not essential for development or viability. Curr Biol (2010) 2.90
Dynamic expression of small non-coding RNAs, including novel microRNAs and piRNAs/21U-RNAs, during Caenorhabditis elegans development. Genome Biol (2009) 2.81
Abundant primary piRNAs, endo-siRNAs, and microRNAs in a Drosophila ovary cell line. Genome Res (2009) 2.68
A phylogenetic analysis of filarial nematodes: comparison with the phylogeny of Wolbachia endosymbionts. Parasitology (2001) 2.53
Genome-scale spatiotemporal analysis of Caenorhabditis elegans microRNA promoter activity. Genome Res (2008) 2.52
The microRNA miR-1 regulates a MEF-2-dependent retrograde signal at neuromuscular junctions. Cell (2008) 2.19
Modulated microRNA expression during adult lifespan in Caenorhabditis elegans. Aging Cell (2006) 2.14
MicroRNA evolution by arm switching. EMBO Rep (2011) 2.12
Characterization of the Melanoma miRNAome by Deep Sequencing. PLoS One (2010) 2.08
Emerging paradigms of regulated microRNA processing. Genes Dev (2010) 2.06
Loss of individual microRNAs causes mutant phenotypes in sensitized genetic backgrounds in C. elegans. Curr Biol (2010) 2.02
MicroRNAs both promote and antagonize longevity in C. elegans. Curr Biol (2010) 1.99
Analysis of microRNA transcriptome by deep sequencing of small RNA libraries of peripheral blood. BMC Genomics (2010) 1.84
Identification and characterization of novel amphioxus microRNAs by Solexa sequencing. Genome Biol (2009) 1.82
Repertoire and evolution of miRNA genes in four divergent nematode species. Genome Res (2009) 1.64
Conserved microRNA targeting in Drosophila is as widespread in coding regions as in 3'UTRs. Proc Natl Acad Sci U S A (2010) 1.62
Deep small RNA sequencing from the nematode Ascaris reveals conservation, functional diversification, and novel developmental profiles. Genome Res (2011) 1.57
High-resolution profiling and discovery of planarian small RNAs. Proc Natl Acad Sci U S A (2009) 1.53
CID-miRNA: a web server for prediction of novel miRNA precursors in human genome. Biochem Biophys Res Commun (2008) 1.25
RNAi effector diversity in nematodes. PLoS Negl Trop Dis (2011) 1.24
Genome-wide identification of Schistosoma japonicum microRNAs using a deep-sequencing approach. PLoS One (2009) 1.20
A novel member of the transforming growth factor-beta (TGF-beta) superfamily from the filarial nematodes Brugia malayi and B. pahangi. Exp Parasitol (1998) 1.16
Xenopus microRNA genes are predominantly located within introns and are differentially expressed in adult frog tissues via post-transcriptional regulation. Genome Res (2007) 1.14
The conserved miR-51 microRNA family is redundantly required for embryonic development and pharynx attachment in Caenorhabditis elegans. Genetics (2010) 1.06
Cloning and bioinformatic identification of small RNAs in the filarial nematode, Brugia malayi. Mol Biochem Parasitol (2009) 1.02
The genome of Brugia malayi - all worms are not created equal. Parasitol Int (2008) 0.99
On the adult morphology of Wuchereria sp. (malayi?) from a monkey (Macaca irus) and from cats in Malaya, and on Wuchereria pahangi n.sp. from a dog and a cat. J Helminthol (1956) 0.98
The microRNAs of Caenorhabditis elegans. Semin Cell Dev Biol (2010) 0.89
The expression of the Mr 30,000 antigen in the third stage larvae of Brugia pahangi. Parasite Immunol (1991) 0.88
Annotation of two large contiguous regions from the Haemonchus contortus genome using RNA-seq and comparative analysis with Caenorhabditis elegans. PLoS One (2011) 0.84
A genome sequence survey of the filarial nematode Brugia malayi: repeats, gene discovery, and comparative genomics. Mol Biochem Parasitol (2004) 0.81
Inferring the phylogenetic position of Brugia pahangi using 18S ribosomal RNA (18S rRNA) gene sequence. Trop Biomed (2008) 0.80
Differential transcript expression between the microfilariae of the filarial nematodes, Brugia malayi and B. pahangi. BMC Genomics (2010) 0.79
Genome sequence of the human malaria parasite Plasmodium falciparum. Nature (2002) 37.89
ACT: the Artemis Comparison Tool. Bioinformatics (2005) 17.91
Amplification-free Illumina sequencing-library preparation facilitates improved mapping and assembly of (G+C)-biased genomes. Nat Methods (2009) 10.41
Artemis and ACT: viewing, annotating and comparing sequences stored in a relational database. Bioinformatics (2008) 9.17
The genome of the kinetoplastid parasite, Leishmania major. Science (2005) 8.64
Genomic sequence of the pathogenic and allergenic filamentous fungus Aspergillus fumigatus. Nature (2005) 8.55
GeneDB: a resource for prokaryotic and eukaryotic organisms. Nucleic Acids Res (2004) 6.30
A comprehensive survey of the Plasmodium life cycle by genomic, transcriptomic, and proteomic analyses. Science (2005) 5.99
Evolution of pathogenicity and sexual reproduction in eight Candida genomes. Nature (2009) 5.90
Improving draft assemblies by iterative mapping and assembly of short reads to eliminate gaps. Genome Biol (2010) 5.79
DNAPlotter: circular and linear interactive genome visualization. Bioinformatics (2008) 5.49
Comparative genomics of trypanosomatid parasitic protozoa. Science (2005) 5.37
Multiple populations of artemisinin-resistant Plasmodium falciparum in Cambodia. Nat Genet (2013) 5.22
ABACAS: algorithm-based automatic contiguation of assembled sequences. Bioinformatics (2009) 4.98
GOtcha: a new method for prediction of protein function assessed by the annotation of seven genomes. BMC Bioinformatics (2004) 4.76
Comparative genomic analysis of three Leishmania species that cause diverse human disease. Nat Genet (2007) 4.58
Analysis of Plasmodium falciparum diversity in natural infections by deep sequencing. Nature (2012) 4.37
Artemis: an integrated platform for visualization and analysis of high-throughput sequence-based experimental data. Bioinformatics (2011) 4.31
Iterative Correction of Reference Nucleotides (iCORN) using second generation sequencing technology. Bioinformatics (2010) 4.18
Assemblathon 2: evaluating de novo methods of genome assembly in three vertebrate species. Gigascience (2013) 4.11
High-throughput phenotyping using parallel sequencing of RNA interference targets in the African trypanosome. Genome Res (2011) 4.09
WormBase 2012: more genomes, more data, new website. Nucleic Acids Res (2011) 3.87
TriTrypDB: a functional genomic resource for the Trypanosomatidae. Nucleic Acids Res (2009) 3.79
Genome variation and evolution of the malaria parasite Plasmodium falciparum. Nat Genet (2006) 3.68
RATT: Rapid Annotation Transfer Tool. Nucleic Acids Res (2011) 3.29
BamView: viewing mapped read alignment data in the context of the reference sequence. Bioinformatics (2010) 3.24
A post-assembly genome-improvement toolkit (PAGIT) to obtain annotated genomes from contigs. Nat Protoc (2012) 3.17
An ancestral oomycete locus contains late blight avirulence gene Avr3a, encoding a protein that is recognized in the host cytoplasm. Proc Natl Acad Sci U S A (2005) 3.06
REAPR: a universal tool for genome assembly evaluation. Genome Biol (2013) 3.05
A human-curated annotation of the Candida albicans genome. PLoS Genet (2005) 3.04
New insights into the blood-stage transcriptome of Plasmodium falciparum using RNA-Seq. Mol Microbiol (2010) 2.76
Genome sequence of Theileria parva, a bovine pathogen that transforms lymphocytes. Science (2005) 2.71
Genomic-scale prioritization of drug targets: the TDR Targets database. Nat Rev Drug Discov (2008) 2.58
Genome of the host-cell transforming parasite Theileria annulata compared with T. parva. Science (2005) 2.55
High-throughput decoding of antitrypanosomal drug efficacy and resistance. Nature (2012) 2.55
WormBase 2014: new views of curated biology. Nucleic Acids Res (2013) 2.39
A systematically improved high quality genome and transcriptome of the human blood fluke Schistosoma mansoni. PLoS Negl Trop Dis (2012) 2.32
Comparative genomics of the fungal pathogens Candida dubliniensis and Candida albicans. Genome Res (2009) 2.24
Telomeric expression sites are highly conserved in Trypanosoma brucei. PLoS One (2008) 2.22
Whole genome sequencing of multiple Leishmania donovani clinical isolates provides insights into population structure and mechanisms of drug resistance. Genome Res (2011) 2.21
Plasmodium falciparum variant surface antigen expression patterns during malaria. PLoS Pathog (2005) 2.13
Genomic insights into the origin of parasitism in the emerging plant pathogen Bursaphelenchus xylophilus. PLoS Pathog (2011) 2.09
Just one cross appears capable of dramatically altering the population biology of a eukaryotic pathogen like Toxoplasma gondii. Proc Natl Acad Sci U S A (2006) 1.95
Chromosome and gene copy number variation allow major structural change between species and strains of Leishmania. Genome Res (2011) 1.90
Plasmodium falciparum var gene expression is modified by host immunity. Proc Natl Acad Sci U S A (2009) 1.86
The genome sequence of Trypanosoma brucei gambiense, causative agent of chronic human african trypanosomiasis. PLoS Negl Trop Dis (2010) 1.83
GeneDB--an annotation database for pathogens. Nucleic Acids Res (2011) 1.82
Assembly of the Candida albicans genome into sixteen supercontigs aligned on the eight chromosomes. Genome Biol (2007) 1.79
Schistosoma mansoni genome: closing in on a final gene set. Exp Parasitol (2007) 1.57
A comprehensive evaluation of assembly scaffolding tools. Genome Biol (2014) 1.55
Silencing of germline-expressed genes by DNA elimination in somatic cells. Dev Cell (2012) 1.54
The genome and life-stage specific transcriptomes of Globodera pallida elucidate key aspects of plant parasitism by a cyst nematode. Genome Biol (2014) 1.51
Vector transmission regulates immune control of Plasmodium virulence. Nature (2013) 1.50
Comparative genomics of the apicomplexan parasites Toxoplasma gondii and Neospora caninum: Coccidia differing in host range and transmission strategy. PLoS Pathog (2012) 1.44
The genome and transcriptome of Haemonchus contortus, a key model parasite for drug and vaccine discovery. Genome Biol (2013) 1.44
Identification of attractive drug targets in neglected-disease pathogens using an in silico approach. PLoS Negl Trop Dis (2010) 1.39
Gene synteny and evolution of genome architecture in trypanosomatids. Mol Biochem Parasitol (2004) 1.36
An insight into the sialome of Glossina morsitans morsitans. BMC Genomics (2010) 1.34
The DNA sequence of chromosome I of an African trypanosome: gene content, chromosome organisation, recombination and polymorphism. Nucleic Acids Res (2003) 1.33
The genetic map and comparative analysis with the physical map of Trypanosoma brucei. Nucleic Acids Res (2005) 1.33
A comprehensive evaluation of rodent malaria parasite genomes and gene expression. BMC Biol (2014) 1.31
Common inheritance of chromosome Ia associated with clonal expansion of Toxoplasma gondii. Genome Res (2006) 1.28
A deep sequencing approach to comparatively analyze the transcriptome of lifecycle stages of the filarial worm, Brugia malayi. PLoS Negl Trop Dis (2011) 1.23
Protein variation in blood-dwelling schistosome worms generated by differential splicing of micro-exon gene transcripts. Genome Res (2010) 1.22
Differential var gene expression in the organs of patients dying of falciparum malaria. Mol Microbiol (2007) 1.22
Antigenic diversity is generated by distinct evolutionary mechanisms in African trypanosome species. Proc Natl Acad Sci U S A (2012) 1.22
RNA interference in parasitic nematodes of animals: a reality check? Trends Parasitol (2007) 1.20
A new, expressed multigene family containing a hot spot for insertion of retroelements is associated with polymorphic subtelomeric regions of Trypanosoma brucei. Eukaryot Cell (2002) 1.19
Heat shock factor functions at the convergence of the stress response and developmental pathways in Caenorhabditis elegans. FASEB J (2003) 1.14
'Oming in on schistosomes: prospects and limitations for post-genomics. Trends Parasitol (2006) 1.11
Sequencing and analysis of chromosome 1 of Eimeria tenella reveals a unique segmental organization. Genome Res (2007) 1.10
Using RNA-seq to determine the transcriptional landscape and the hypoxic response of the pathogenic yeast Candida parapsilosis. BMC Genomics (2011) 1.10
Alteration of host cell phenotype by Theileria annulata and Theileria parva: mining for manipulators in the parasite genomes. Int J Parasitol (2005) 1.09
A cell-surface phylome for African trypanosomes. PLoS Negl Trop Dis (2013) 1.09
Differences between Trypanosoma brucei gambiense groups 1 and 2 in their resistance to killing by trypanolytic factor 1. PLoS Negl Trop Dis (2011) 1.09
Patterns of evolution in the unique tRNA gene arrays of the genus Entamoeba. Mol Biol Evol (2007) 1.09
Testing the efficacy of RNA interference in Haemonchus contortus. Int J Parasitol (2006) 1.08
BamView: visualizing and interpretation of next-generation sequencing read alignments. Brief Bioinform (2012) 1.08
B cells play a regulatory role in mice infected with the L3 of Brugia pahangi. Int Immunol (2005) 1.07
Genetic and molecular basis of drug resistance and species-specific drug action in schistosome parasites. Science (2013) 1.07
Infection with Brugia microfilariae induces apoptosis of CD4(+) T lymphocytes: a mechanism of immune unresponsiveness in filariasis. Eur J Immunol (2002) 1.05
Germline transgenesis and insertional mutagenesis in Schistosoma mansoni mediated by murine leukemia virus. PLoS Pathog (2012) 1.05
Transcriptome analysis of reproductive tissue and intrauterine developmental stages of the tsetse fly (Glossina morsitans morsitans). BMC Genomics (2010) 1.05
The ingi and RIME non-LTR retrotransposons are not randomly distributed in the genome of Trypanosoma brucei. Mol Biol Evol (2003) 1.03
Epidemiological analysis of tick-borne diseases in Zambia. Vet Parasitol (2010) 1.02
An unusual cause of fever and rash in an adult. Eur J Intern Med (2007) 1.02
Cultivar and growing region determine the antioxidant polyphenolic concentration and composition of apples grown in New Zealand. J Agric Food Chem (2005) 1.02
TGF-b2 induction regulates invasiveness of Theileria-transformed leukocytes and disease susceptibility. PLoS Pathog (2010) 1.00