Published in J Nematol on June 01, 2012
The draft genome and transcriptome of Panagrellus redivivus are shaped by the harsh demands of a free-living lifestyle. Genetics (2013) 1.04
Comparative genomics of Steinernema reveals deeply conserved gene regulatory networks. Genome Biol (2015) 0.98
Variation in the susceptibility of Drosophila to different entomopathogenic nematodes. Infect Immun (2015) 0.90
Origin and evolution of dishevelled. G3 (Bethesda) (2013) 0.83
Mechanisms of host seeking by parasitic nematodes. Mol Biochem Parasitol (2016) 0.81
All the microbiology nematodes can teach us. FEMS Microbiol Ecol (2016) 0.75
A transcriptomic insight into the infective juvenile stage of the insect parasitic nematode, Heterorhabditis indica. BMC Genomics (2016) 0.75
Velvet: algorithms for de novo short read assembly using de Bruijn graphs. Genome Res (2008) 151.16
tRNAscan-SE: a program for improved detection of transfer RNA genes in genomic sequence. Nucleic Acids Res (1997) 142.55
Mapping and quantifying mammalian transcriptomes by RNA-Seq. Nat Methods (2008) 126.81
Next-generation DNA sequencing methods. Annu Rev Genomics Hum Genet (2008) 68.81
Genome sequence of the nematode C. elegans: a platform for investigating biology. Science (1998) 61.48
The Pfam protein families database. Nucleic Acids Res (2004) 56.46
MUSCLE: a multiple sequence alignment method with reduced time and space complexity. BMC Bioinformatics (2004) 50.89
SOAP2: an improved ultrafast tool for short read alignment. Bioinformatics (2009) 39.47
InterProScan--an integration platform for the signature-recognition methods in InterPro. Bioinformatics (2001) 28.35
Distinguishing homologous from analogous proteins. Syst Zool (1970) 25.10
BLAST: improvements for better sequence analysis. Nucleic Acids Res (2006) 9.77
AUGUSTUS: a web server for gene finding in eukaryotes. Nucleic Acids Res (2004) 5.53
A genetic mapping system in Caenorhabditis elegans based on polymorphic sequence-tagged sites. Genetics (1992) 5.37
Draft genome of the filarial nematode parasite Brugia malayi. Science (2007) 5.28
Interacting genes in nematode dauer larva formation. Nature (1981) 5.21
WormBase: a comprehensive resource for nematode research. Nucleic Acids Res (2009) 5.20
Genome sequence of the metazoan plant-parasitic nematode Meloidogyne incognita. Nat Biotechnol (2008) 5.19
Revisiting the protein-coding gene catalog of Drosophila melanogaster using 12 fly genomes. Genome Res (2007) 4.73
The Pristionchus pacificus genome provides a unique perspective on nematode lifestyle and parasitism. Nat Genet (2008) 3.93
Construction of a general human chromosome jumping library, with application to cystic fibrosis. Science (1987) 3.87
Phylum-wide analysis of SSU rDNA reveals deep phylogenetic relationships among nematodes and accelerated evolution toward crown Clades. Mol Biol Evol (2006) 3.22
Sequence and genetic map of Meloidogyne hapla: A compact nematode genome for plant parasitism. Proc Natl Acad Sci U S A (2008) 2.85
The natural history of Caenorhabditis elegans. Curr Biol (2010) 2.75
Ecology of Caenorhabditis species. WormBook (2006) 2.25
Endogenous cellulases in animals: isolation of beta-1, 4-endoglucanase genes from two species of plant-parasitic cyst nematodes. Proc Natl Acad Sci U S A (1998) 2.21
Ontology annotation: mapping genomic regions to biological function. Curr Opin Chem Biol (2007) 2.21
Engineering broad root-knot resistance in transgenic plants by RNAi silencing of a conserved and essential root-knot nematode parasitism gene. Proc Natl Acad Sci U S A (2006) 2.18
Ascaris suum draft genome. Nature (2011) 2.16
Microsporidia are natural intracellular parasites of the nematode Caenorhabditis elegans. PLoS Biol (2008) 2.14
Genomic insights into the origin of parasitism in the emerging plant pathogen Bursaphelenchus xylophilus. PLoS Pathog (2011) 2.09
Caenorhabditis elegans is a nematode. Science (1998) 2.08
The draft genome of the parasitic nematode Trichinella spiralis. Nat Genet (2011) 2.03
Divergence times in Caenorhabditis and Drosophila inferred from direct estimates of the neutral mutation rate. Mol Biol Evol (2008) 2.02
Operons in eukaryotes. Brief Funct Genomic Proteomic (2004) 1.98
Apomictic, polyphagous root-knot nematodes: exceptionally successful and damaging biotrophic root pathogens. Annu Rev Phytopathol (2001) 1.95
The drugs we have and the drugs we need against major helminth infections. Adv Parasitol (2010) 1.93
Nematodes of the genus Pristionchus are closely associated with scarab beetles and the Colorado potato beetle in Western Europe. Zoology (Jena) (2006) 1.75
Scaffolding a Caenorhabditis nematode genome with RNA-seq. Genome Res (2010) 1.73
Ingestion of double-stranded RNA by preparasitic juvenile cyst nematodes leads to RNA interference. Mol Plant Microbe Interact (2002) 1.69
Adaptation in the age of ecological genomics: insights from parallelism and convergence. Trends Ecol Evol (2011) 1.67
Metazoan operons accelerate recovery from growth-arrested states. Cell (2011) 1.64
Convergent evolution of antifreeze glycoproteins in Antarctic notothenioid fish and Arctic cod. Proc Natl Acad Sci U S A (1997) 1.62
Genetic flexibility in the convergent evolution of hermaphroditism in Caenorhabditis nematodes. Dev Cell (2006) 1.53
Horizontal gene transfer of microbial cellulases into nematode genomes is associated with functional assimilation and gene turnover. BMC Evol Biol (2011) 1.51
A sensory code for host seeking in parasitic nematodes. Curr Biol (2011) 1.47
Common trends in mutualism revealed by model associations between invertebrates and bacteria. FEMS Microbiol Rev (2010) 1.38
Degradation of plant cell walls by a nematode. Nature (2000) 1.32
Use of RNA interference to investigate gene function in the human filarial nematode parasite Brugia malayi. Mol Biochem Parasitol (2003) 1.32
Analysis of protein domain families in Caenorhabditis elegans. Genomics (1997) 1.30
Detecting heterozygosity in shotgun genome assemblies: Lessons from obligately outcrossing nematodes. Genome Res (2009) 1.27
Host-generated double stranded RNA induces RNAi in plant-parasitic nematodes and protects the host from infection. Mol Biochem Parasitol (2006) 1.24
RNAi effector diversity in nematodes. PLoS Negl Trop Dis (2011) 1.24
flp gene disruption in a parasitic nematode reveals motor dysfunction and unusual neuronal sensitivity to RNA interference. FASEB J (2007) 1.23
Chromosome jumping from D4S10 (G8) toward the Huntington disease gene. Proc Natl Acad Sci U S A (1988) 1.20
Ecological genomics: understanding gene and genome function in the natural environment. Heredity (Edinb) (2007) 1.19
Quantitative sequence-function relationships in proteins based on gene ontology. BMC Bioinformatics (2007) 1.19
Isolation of naturally associated bacteria of necromenic Pristionchus nematodes and fitness consequences. J Exp Biol (2008) 1.19
Natural variation in Pristionchus pacificus dauer formation reveals cross-preference rather than self-preference of nematode dauer pheromones. Proc Biol Sci (2011) 1.17
RNAi and functional genomics in plant parasitic nematodes. Annu Rev Phytopathol (2009) 1.13
How the worm was won. The C. elegans genome sequencing project. Trends Genet (1999) 1.12
Postembryonic RNAi in Heterorhabditis bacteriophora: a nematode insect parasite and host for insect pathogenic symbionts. BMC Dev Biol (2007) 1.09
Short interfering RNA-mediated gene silencing in Globodera pallida and Meloidogyne incognita infective stage juveniles. Int J Parasitol (2009) 1.08
959 Nematode Genomes: a semantic wiki for coordinating sequencing projects. Nucleic Acids Res (2011) 1.04
Nematodes: the worm and its relatives. PLoS Biol (2011) 0.99
Systemic RNAi mediated gene silencing in the anhydrobiotic nematode Panagrolaimus superbus. BMC Mol Biol (2008) 0.99
Titration-free 454 sequencing using Y adapters. Nat Protoc (2011) 0.97
Pathogenicity of Steinernema scapterisci to Selected Invertebrates. J Nematol (1991) 0.94
Serine protease-mediated host invasion by the parasitic nematode Steinernema carpocapsae. J Biol Chem (2010) 0.89
Genomic organization of eukaryotic tRNAs. BMC Genomics (2010) 0.89
Unusual cleavage and gastrulation in a freshwater nematode: developmental and phylogenetic implications. Dev Genes Evol (2004) 0.89
Resolving tylenchid evolutionary relationships through multiple gene analysis derived from EST data. Mol Phylogenet Evol (2005) 0.85
Trichinella spiralis: the worm that would be virus. Parasitol Today (1990) 0.85
RNAi mediated gene knockdown and transgenesis by microinjection in the necromenic Nematode Pristionchus pacificus. J Vis Exp (2011) 0.81
Steinernema cholashanense n. sp. (Rhabditida, Steinernematidae) a new species of entomopathogenic nematode from the province of Sichuan, Chola Shan Mountains, China. J Invertebr Pathol (2007) 0.81
Comparative genomics: mammalian alignments reveal human functional elements. Nat Rev Genet (2011) 0.76
Nematode postembryonic cell lineages. J Nematol (1982) 0.76
Steinernema ichnusae sp. n. (Nematoda: Steinernematidae) a new entomopathogenic nematode from Sardinia Island (Italy). J Invertebr Pathol (2008) 0.76
Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation. Nat Biotechnol (2010) 75.21
Genome-wide mapping of in vivo protein-DNA interactions. Science (2007) 64.92
Landscape of transcription in human cells. Nature (2012) 20.18
Computation for ChIP-seq and RNA-seq studies. Nat Methods (2009) 16.11
Textpresso: an ontology-based information retrieval and extraction system for biological literature. PLoS Biol (2004) 15.72
Extensive promoter-centered chromatin interactions provide a topological basis for transcription regulation. Cell (2012) 8.41
WormBase: better software, richer content. Nucleic Acids Res (2006) 6.78
WormBase: a comprehensive resource for nematode research. Nucleic Acids Res (2009) 5.20
The neuroscience information framework: a data and knowledge environment for neuroscience. Neuroinformatics (2008) 4.60
Genome-wide prediction of C. elegans genetic interactions. Science (2006) 4.15
An encyclopedia of mouse DNA elements (Mouse ENCODE). Genome Biol (2012) 4.15
WormBase: a multi-species resource for nematode biology and genomics. Nucleic Acids Res (2004) 4.14
WormBase: new content and better access. Nucleic Acids Res (2006) 4.01
Federated access to heterogeneous information resources in the Neuroscience Information Framework (NIF). Neuroinformatics (2008) 3.94
WormBase 2012: more genomes, more data, new website. Nucleic Acids Res (2011) 3.87
WormBase: a comprehensive data resource for Caenorhabditis biology and genomics. Nucleic Acids Res (2005) 3.82
WormBase 2007. Nucleic Acids Res (2007) 3.69
A blend of small molecules regulates both mating and development in Caenorhabditis elegans. Nature (2008) 3.45
Automatic document classification of biological literature. BMC Bioinformatics (2006) 3.27
A C. elegans stretch receptor neuron revealed by a mechanosensitive TRP channel homologue. Nature (2006) 3.20
Lensless high-resolution on-chip optofluidic microscopes for Caenorhabditis elegans and cell imaging. Proc Natl Acad Sci U S A (2008) 2.88
Optofluidic microscopy--a method for implementing a high resolution optical microscope on a chip. Lab Chip (2006) 2.80
FOS-1 promotes basement-membrane removal during anchor-cell invasion in C. elegans. Cell (2005) 2.77
Semi-automated curation of protein subcellular localization: a text mining-based approach to Gene Ontology (GO) Cellular Component curation. BMC Bioinformatics (2009) 2.74
A C. elegans model of nicotine-dependent behavior: regulation by TRP-family channels. Cell (2006) 2.68
A shortcut to identifying small molecule signals that regulate behavior and development in Caenorhabditis elegans. Proc Natl Acad Sci U S A (2009) 2.64
RNA Pol II accumulates at promoters of growth genes during developmental arrest. Science (2009) 2.63
An automated system for measuring parameters of nematode sinusoidal movement. BMC Genet (2005) 2.57
Textpresso for neuroscience: searching the full text of thousands of neuroscience research papers. Neuroinformatics (2008) 2.39
WormBase 2014: new views of curated biology. Nucleic Acids Res (2013) 2.39
A modular library of small molecule signals regulates social behaviors in Caenorhabditis elegans. PLoS Biol (2012) 2.38
Dynamic transformations of genome-wide epigenetic marking and transcriptional control establish T cell identity. Cell (2012) 2.38
C. elegans LIN-18 is a Ryk ortholog and functions in parallel to LIN-17/Frizzled in Wnt signaling. Cell (2004) 2.35
DAF-16/FOXO regulates transcription of cki-1/Cip/Kip and repression of lin-4 during C. elegans L1 arrest. Curr Biol (2006) 2.33
A unified nomenclature for protein subunits of mediator complexes linking transcriptional regulators to RNA polymerase II. Mol Cell (2004) 2.27
Anchor cell invasion into the vulval epithelium in C. elegans. Dev Cell (2003) 2.23
RNA editing in the human ENCODE RNA-seq data. Genome Res (2012) 2.18
Ascaris suum draft genome. Nature (2011) 2.16
Ascaroside signaling is widely conserved among nematodes. Curr Biol (2012) 2.15
Overview of the Alliance for Cellular Signaling. Nature (2002) 2.15
Effects of sequence variation on differential allelic transcription factor occupancy and gene expression. Genome Res (2012) 1.99
Acute carbon dioxide avoidance in Caenorhabditis elegans. Proc Natl Acad Sci U S A (2008) 1.97
Transgene-free genome editing in Caenorhabditis elegans using CRISPR-Cas. Genetics (2013) 1.95
Ror receptor tyrosine kinases: orphans no more. Trends Cell Biol (2008) 1.82
An imaging system for standardized quantitative analysis of C. elegans behavior. BMC Bioinformatics (2004) 1.81
Epidermal growth factor signaling induces behavioral quiescence in Caenorhabditis elegans. Nat Neurosci (2007) 1.74
Scaffolding a Caenorhabditis nematode genome with RNA-seq. Genome Res (2010) 1.73
WormBook: the online review of Caenorhabditis elegans biology. Nucleic Acids Res (2006) 1.71
Comparative metabolomics reveals biogenesis of ascarosides, a modular library of small-molecule signals in C. elegans. J Am Chem Soc (2012) 1.70
Opposing Wnt pathways orient cell polarity during organogenesis. Cell (2008) 1.70
Worm Phenotype Ontology: integrating phenotype data within and beyond the C. elegans community. BMC Bioinformatics (2011) 1.69
Evidence of a mate-finding cue in the hermaphrodite nematode Caenorhabditis elegans. Proc Natl Acad Sci U S A (2002) 1.68
Metazoan operons accelerate recovery from growth-arrested states. Cell (2011) 1.64
The L-type cyclin CYL-1 and the heat-shock-factor HSF-1 are required for heat-shock-induced protein expression in Caenorhabditis elegans. Genetics (2004) 1.64
Conservation rules, their breakdown, and optimality in Caenorhabditis sinusoidal locomotion. J Theor Biol (2006) 1.64
Systems level circuit model of C. elegans undulatory locomotion: mathematical modeling and molecular genetics. J Comput Neurosci (2007) 1.63
SynMuv genes redundantly inhibit lin-3/EGF expression to prevent inappropriate vulval induction in C. elegans. Dev Cell (2006) 1.61
Issues in the design of a pilot concept-based query interface for the neuroinformatics information framework. Neuroinformatics (2008) 1.53
Automated data integration for developmental biological research. Development (2007) 1.51
A sensory code for host seeking in parasitic nematodes. Curr Biol (2011) 1.47
Genome annotation by high-throughput 5' RNA end determination. Proc Natl Acad Sci U S A (2004) 1.42
Receptor-type guanylate cyclase is required for carbon dioxide sensation by Caenorhabditis elegans. Proc Natl Acad Sci U S A (2010) 1.42
Nematodes, bacteria, and flies: a tripartite model for nematode parasitism. Curr Biol (2007) 1.42
The genome and developmental transcriptome of the strongylid nematode Haemonchus contortus. Genome Biol (2013) 1.37
Tissue-specific regulation of the LIM homeobox gene lin-11 during development of the Caenorhabditis elegans egg-laying system. Dev Biol (2002) 1.37
Toward an interactive article: integrating journals and biological databases. BMC Bioinformatics (2011) 1.37
Ascaroside expression in Caenorhabditis elegans is strongly dependent on diet and developmental stage. PLoS One (2011) 1.35
A C. elegans sperm TRP protein required for sperm-egg interactions during fertilization. Cell (2003) 1.34
Caenorhabditis elegans cog-1 locus encodes GTX/Nkx6.1 homeodomain proteins and regulates multiple aspects of reproductive system development. Dev Biol (2002) 1.32
An entomopathogenic nematode by any other name. PLoS Pathog (2012) 1.32
The C. elegans ROR receptor tyrosine kinase, CAM-1, non-autonomously inhibits the Wnt pathway. Development (2007) 1.30
A cell-specific enhancer that specifies lin-3 expression in the C. elegans anchor cell for vulval development. Development (2003) 1.28
cis-Regulatory control of three cell fate-specific genes in vulval organogenesis of Caenorhabditis elegans and C. briggsae. Dev Biol (2003) 1.28
Automatic categorization of diverse experimental information in the bioscience literature. BMC Bioinformatics (2012) 1.27
Olfaction shapes host-parasite interactions in parasitic nematodes. Proc Natl Acad Sci U S A (2012) 1.25
A practical, bioinformatic workflow system for large data sets generated by next-generation sequencing. Nucleic Acids Res (2010) 1.22
Caenorhabditis elegans inositol 5-phosphatase homolog negatively regulates inositol 1,4,5-triphosphate signaling in ovulation. Mol Biol Cell (2002) 1.20
The small ubiquitin-like modifier (SUMO) is required for gonadal and uterine-vulval morphogenesis in Caenorhabditis elegans. Genes Dev (2004) 1.20
Transcriptional network underlying Caenorhabditis elegans vulval development. Proc Natl Acad Sci U S A (2005) 1.19
Genetic dissection of developmental pathways. WormBook (2006) 1.19
Text mining in the biocuration workflow: applications for literature curation at WormBase, dictyBase and TAIR. Database (Oxford) (2012) 1.19
The epidermal growth factor system in Caenorhabditis elegans. Exp Cell Res (2003) 1.15
The versatile worm: genetic and genomic resources for Caenorhabditis elegans research. Nat Rev Genet (2007) 1.14
The draft genome sequence of the nematode Caenorhabditis briggsae, a companion to C. elegans. Genome Biol (2003) 1.14
Pharmacist-managed vaccination program increased influenza vaccination rates in cardiovascular patients enrolled in a secondary prevention lipid clinic. Pharmacotherapy (2007) 1.14
Percutaneous intervention for the treatment of hypoplastic aortoiliac syndrome. Catheter Cardiovasc Interv (2003) 1.13
Massively parallel sequencing and analysis of the Necator americanus transcriptome. PLoS Negl Trop Dis (2010) 1.12
A lover and a fighter: the genome sequence of an entomopathogenic nematode Heterorhabditis bacteriophora. PLoS One (2013) 1.11
Targeted metabolomics reveals a male pheromone and sex-specific ascaroside biosynthesis in Caenorhabditis elegans. ACS Chem Biol (2012) 1.11
Gene expression markers for Caenorhabditis elegans vulval cells. Mech Dev (2002) 1.10
Sex-specific mating pheromones in the nematode Panagrellus redivivus. Proc Natl Acad Sci U S A (2012) 1.10
Postembryonic RNAi in Heterorhabditis bacteriophora: a nematode insect parasite and host for insect pathogenic symbionts. BMC Dev Biol (2007) 1.09
A component of the transcriptional mediator complex inhibits RAS-dependent vulval fate specification in C. elegans. Development (2003) 1.08
C. elegans EVI1 proto-oncogene, EGL-43, is necessary for Notch-mediated cell fate specification and regulates cell invasion. Development (2007) 1.07
Nematode-bacterium symbioses--cooperation and conflict revealed in the "omics" age. Biol Bull (2012) 1.05
The C. elegans LIM homeobox gene lin-11 specifies multiple cell fates during vulval development. Development (2003) 1.05
Phospholipase Cepsilon regulates ovulation in Caenorhabditis elegans. Dev Biol (2004) 1.05
The draft genome and transcriptome of Panagrellus redivivus are shaped by the harsh demands of a free-living lifestyle. Genetics (2013) 1.04