Reference health
Recompleting the <i>Caenorhabditis elegans</i> genome
102/102 checkable references clean · checked 2026-07-22
Every reference with a DOI in the deposited reference list resolved to a known work in Crossref or DataCite at the dated check, and none carried a retraction, withdrawal, or removal notice.
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The 102 checked references that resolve
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The plant parasite Pratylenchus coffeae carries a minimal nematode genome
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Genome Sequence of the Nematode
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Mapping single molecule sequencing reads using basic local alignment with successive refinement (BLASR): application and theory
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Resolving the complexity of the human genome using single-molecule sequencing
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Hidden genetic variation shapes the structure of functional elements in Drosophila
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Heterochromatin-Enriched Assemblies Reveal the Sequence and Organization of the
<i>Drosophila melanogaster</i>
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THE EVOLUTION OF RESTRICTED RECOMBINATION AND THE ACCUMULATION OF REPEATED DNA SEQUENCES
resolves10.1038/nmeth.2474
Nonhybrid, finished microbial genome assemblies from long-read SMRT sequencing data
resolves10.1016/S0091-679X(08)61402-8
Chapter 22 The Physical Map of the Caenorhabditis elegans Genome
resolves10.1371/journal.pcbi.1003998
Extensive Error in the Number of Genes Inferred from Draft Genome Assemblies
resolves10.1534/genetics.115.186197
Next-Generation Sequencing-Based Approaches for Mutation Mapping and Identification in<i>Caenorhabditis elegans</i>
resolves10.1186/s12915-017-0473-4
De novo assembly of the complex genome of Nippostrongylus brasiliensis using MinION long reads
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A NEW GENERATION OF HOMOLOGY SEARCH TOOLS BASED ON PROBABILISTIC INFERENCE
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Whole-Genome Profiling of Mutagenesis in<i>Caenorhabditis elegans</i>
resolves10.1093/bioinformatics/bts565
CD-HIT: accelerated for clustering the next-generation sequencing data
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Linear plasmid vector for cloning of repetitive or unstable sequences in Escherichia coli
resolves10.1101/gr.191395.115
Oxford Nanopore sequencing, hybrid error correction, and de novo assembly of a eukaryotic genome
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GenomeTools: A Comprehensive Software Library for Efficient Processing of Structured Genome Annotations
resolves10.1101/gr.3729105
Genomics in <i>C. elegans</i>: So many genes, such a little worm: Table 1.
resolves10.1038/s41467-017-01982-7
Centromere evolution and CpG methylation during vertebrate speciation
resolves10.1101/gr.5560806
Flexibility and constraint in the nucleosome core landscape of
<i>Caenorhabditis elegans</i>
chromatin
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A Combined Transmembrane Topology and Signal Peptide Prediction Method
resolves10.1093/nar/gkx1038
Rfam 13.0: shifting to a genome-centric resource for non-coding RNA families
resolves10.1073/pnas.1932072100
Evolution's cauldron: Duplication, deletion, and rearrangement in the mouse and human genomes
resolves10.1074/jbc.M302192200
Sequence-specific Binding to Telomeric DNA by CEH-37, a Homeodomain Protein in the Nematode Caenorhabditis elegans
resolves10.1038/nbt.2280
Hybrid error correction and de novo assembly of single-molecule sequencing reads
resolves10.1101/gr.215087.116
Canu: scalable and accurate long-read assembly via adaptive
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Making sense of genomes of parasitic worms: Tackling bioinformatic challenges
resolves10.1073/pnas.0710982105
Selective aluminum passivation for targeted immobilization of single DNA polymerase molecules in zero-mode waveguide nanostructures
resolves10.1093/bioinformatics/btm039
Gepard: a rapid and sensitive tool for creating dotplots on genome scale
resolves10.1126/science.1079700
Zero-Mode Waveguides for Single-Molecule Analysis at High Concentrations
resolves10.1093/bioinformatics/btw152
Minimap and miniasm: fast mapping and de novo assembly for noisy long sequences
resolves10.1038/srep10814
Illumina Synthetic Long Read Sequencing Allows Recovery of Missing Sequences even in the “Finished” C. elegans Genome
resolves10.1038/nmeth.3444
A complete bacterial genome assembled de novo using only nanopore sequencing data
resolves10.1073/pnas.0702207104
The frailty of adaptive hypotheses for the origins of organismal complexity
resolves10.1016/0378-1119(85)90224-0
Genes coding for 5S ribosomal RNA of the nematode Caenorhabditis elegans
resolves10.1101/011650
<b>FusionCatcher</b>
– a tool for finding somatic fusion genes in paired-end RNA-sequencing data
resolves10.1038/nmeth.3454
Assembly and diploid architecture of an individual human genome via single-molecule technologies
resolves10.1093/bioinformatics/btq033
BEDTools: a flexible suite of utilities for comparing genomic features
resolves10.1038/nrmicro2790
Genome evolution in filamentous plant pathogens: why bigger can be better
resolves10.1371/journal.pgen.1000419
Recombinational Landscape and Population Genomics of Caenorhabditis elegans
resolves10.1038/ncb1685
Developmentally regulated transcription of mammalian telomeres by DNA-dependent RNA polymerase II
resolves10.1016/0092-8674(84)90301-5
Separation of yeast chromosome-sized DNAs by pulsed field gradient gel electrophoresis
resolves10.1186/1471-2164-11-465
Distributed probing of chromatin structure in vivo reveals pervasive chromatin accessibility for expressed and non-expressed genes during tissue differentiation in C. elegans
resolves10.1534/g3.117.300141
Intricate and Cell Type-Specific Populations of Endogenous Circular DNA (eccDNA) in
<i>Caenorhabditis elegans</i>
and
<i>Homo sapiens</i>
resolves10.1534/g3.118.200162
Rapid Low-Cost Assembly of the
<i>Drosophila melanogaster</i>
Reference Genome Using Low-Coverage, Long-Read Sequencing
resolves10.1093/bioinformatics/btn013
Using native and syntenically mapped cDNA alignments to improve <i>de novo</i> gene finding
resolves10.1101/gr.221184.117
MinION-based long-read sequencing and assembly extends the
<i>Caenorhabditis elegans</i>
reference genome
resolves10.1038/nature15714
Single-molecule sequencing of the desiccation-tolerant grass Oropetium thomaeum
resolves10.1186/1471-2164-10-329
Polymorphic segmental duplication in the nematode Caenorhabditis elegans
resolves10.1371/journal.pone.0112963
Pilon: An Integrated Tool for Comprehensive Microbial Variant Detection and Genome Assembly Improvement
resolves10.1093/molbev/msx319
BUSCO Applications from Quality Assessments to Gene Prediction and Phylogenomics
resolves10.1038/88878
Rapid gene mapping in Caenorhabditis elegans using a high density polymorphism map
resolves10.1073/pnas.93.17.8983
Telomeric repeats (TTAGGC)n are sufficient for chromosome capping function in Caenorhabditis elegans.
resolves10.1016/0097-8485(94)85023-2
Non-globular domains in protein sequences: Automated segmentation using complexity measures
resolves10.1126/science.aao0827
Rapid genome shrinkage in a self-fertile nematode reveals sperm competition proteins
The 1 reference without a DOI — listed, not checked
no DOI — not checkedEfficient local alignment discovery amongst noisy long reads
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