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Comparative genomics of ten new Caenorhabditis species
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What this work says
Outgoing claims: the papers this work cites, builds on, or argues with.
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lin-12, a nematode homeotic gene, is homologous to a set of mammalian proteins that includes epidermal growth factor
inferredcites →https://doi.org/10.1016/0092-8674(89)90436-4openalex-snapshot
glp-1 and lin-12, genes implicated in distinct cell-cell interactions in C. elegans, encode similar transmembrane proteins
inferredcites →https://doi.org/10.1016/0092-8674(91)90064-6openalex-snapshot
Specific EGF repeats of Notch mediate interactions with Delta and serrate: Implications for notch as a multifunctional receptor
inferredcites →https://doi.org/10.1016/j.cub.2010.09.050openalex-snapshot
The natural history of Caenorhabditis elegans
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Mystery of intron gain: new data and new models
inferredcites →https://doi.org/10.1016/j.tig.2012.02.007openalex-snapshot
Causes and consequences of the evolution of reproductive mode in Caenorhabditis nematodes
inferredcites →https://doi.org/10.1016/j.ympev.2014.08.013openalex-snapshot
Phylogenetic analysis at deep timescales: Unreliable gene trees, bypassed hidden support, and the coalescence/concatalescence conundrum
inferredcites →https://doi.org/10.1038/335547a0openalex-snapshot
The Caenorhabditis elegans lin-12 gene encodes a transmembrane protein with overall similarity to Drosophila Notch
inferredcites →https://doi.org/10.1038/s41467-018-05712-5openalex-snapshot
Biology and genome of a newly discovered sibling species of Caenorhabditis elegans
inferredcites →https://doi.org/10.1046/j.1525-142x.2002.02027.xopenalex-snapshot
Evolution of discrete Notch‐like receptors from a distant gene duplication in Caenorhabditis
inferredcites →https://doi.org/10.1073/pnas.0308192101openalex-snapshot
Origins of recently gained introns in Caenorhabditis
inferredcites →https://doi.org/10.1073/pnas.0403094101openalex-snapshot
Caenorhabditis phylogeny predicts convergence of hermaphroditism and extensive intron loss
inferredcites →https://doi.org/10.1073/pnas.1720115115openalex-snapshot
Earth BioGenome Project: Sequencing life for the future of life
inferredcites →https://doi.org/10.1080/10635150601146041openalex-snapshot
Inconsistency of Phylogenetic Estimates from Concatenated Data under Coalescence
inferredcites →https://doi.org/10.1093/bioinformatics/btm071openalex-snapshot
CEGMA: a pipeline to accurately annotate core genes in eukaryotic genomes
inferredcites →https://doi.org/10.1093/bioinformatics/btp348openalex-snapshot
trimAl: a tool for automated alignment trimming in large-scale phylogenetic analyses
inferredcites →https://doi.org/10.1093/bioinformatics/btr010openalex-snapshot
A novel hybrid gene prediction method employing protein multiple sequence alignments
inferredcites →https://doi.org/10.1093/bioinformatics/bts635openalex-snapshot
STAR: ultrafast universal RNA-seq aligner
inferredcites →https://doi.org/10.1093/bioinformatics/btt310openalex-snapshot
Informed and automated k -mer size selection for genome assembly
inferredcites →https://doi.org/10.1093/bioinformatics/btt702openalex-snapshot
NextClip: an analysis and read preparation tool for Nextera Long Mate Pair libraries
inferredcites →https://doi.org/10.1093/bioinformatics/btu031openalex-snapshot
InterProScan 5: genome-scale protein function classification
inferredcites →https://doi.org/10.1093/bioinformatics/btu033openalex-snapshot
RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies
inferredcites →https://doi.org/10.1093/bioinformatics/btu462openalex-snapshot
ASTRAL: genome-scale coalescent-based species tree estimation
inferredcites →https://doi.org/10.1093/bioinformatics/btv234openalex-snapshot
ASTRAL-II: coalescent-based species tree estimation with many hundreds of taxa and thousands of genes
inferredcites →https://doi.org/10.1093/bioinformatics/btv351openalex-snapshot
BUSCO: assessing genome assembly and annotation completeness with single-copy orthologs
inferredcites →https://doi.org/10.1093/bioinformatics/btv661openalex-snapshot
BRAKER1: Unsupervised RNA-Seq-Based Genome Annotation with GeneMark-ET and AUGUSTUS
inferredcites →https://doi.org/10.1093/molbev/msh112openalex-snapshot
A Bayesian Mixture Model for Across-Site Heterogeneities in the Amino-Acid Replacement Process
inferredcites →https://doi.org/10.1093/molbev/msl098openalex-snapshot
Smoke Without Fire: Most Reported Cases of Intron Gain in Nematodes Instead Reflect Intron Losses
inferredcites →https://doi.org/10.1093/molbev/msw046openalex-snapshot
ETE 3: Reconstruction, Analysis, and Visualization of Phylogenomic Data
inferredcites →https://doi.org/10.1093/nar/26.4.1107openalex-snapshot
GeneMark.hmm: new solutions for gene finding
inferredcites →https://doi.org/10.1093/nar/gks1067openalex-snapshot
New and continuing developments at PROSITE
inferredcites →https://doi.org/10.1093/nar/gkw290openalex-snapshot
Interactive tree of life (iTOL) v3: an online tool for the display and annotation of phylogenetic and other trees
inferredcites →https://doi.org/10.1093/nar/gkw893openalex-snapshot
CeNDR, the Caenorhabditis elegans natural diversity resource
inferredcites →https://doi.org/10.1093/nar/gkx998openalex-snapshot
WormBase 2017: molting into a new stage
inferredcites →https://doi.org/10.1093/sysbio/syt022openalex-snapshot
PhyloBayes MPI: Phylogenetic Reconstruction with Infinite Mixtures of Profiles in a Parallel Environment
inferredcites →https://doi.org/10.1093/sysbio/syv016openalex-snapshot
On the Robustness to Gene Tree Estimation Error (or lack thereof) of Coalescent-Based Species Tree Methods
inferredcites →https://doi.org/10.1101/gr.074492.107openalex-snapshot
Velvet: Algorithms for de novo short read assembly using de Bruijn graphs
inferredcites →https://doi.org/10.1101/gr.10.8.1115openalex-snapshot
Conservation, Regulation, Synteny, and Introns in a Large-scale C. briggsae–C. elegans Genomic Alignment
inferredcites →https://doi.org/10.1101/gr.111021.110openalex-snapshot
Scaffolding a Caenorhabditis nematode genome with RNA-seq
inferredcites →https://doi.org/10.1101/gr.170720.113openalex-snapshot
Efficient de novo assembly of highly heterozygous genomes from whole-genome shotgun short reads
inferredcites →https://doi.org/10.1101/gr.2639304openalex-snapshot
A Phylogeny of Caenorhabditis Reveals Frequent Loss of Introns During Nematode Evolution
inferredcites →https://doi.org/10.1101/gr.8.5.449openalex-snapshot
Two Large Families of Chemoreceptor Genes in the NematodesCaenorhabditis elegans and Caenorhabditis briggsae Reveal Extensive Gene Duplication, Diversification, Movement, and Intron Loss
inferredcites →https://doi.org/10.1111/j.1439-0469.1996.tb00827.xopenalex-snapshot
Phylogeny of Rhabditis subgenus Caenorhabditis (Rhabditidae, Nematoda)*
inferredcites →https://doi.org/10.1126/science.282.5396.2012openalex-snapshot
Genome Sequence of the Nematode C. elegans : A Platform for Investigating Biology
inferredcites →https://doi.org/10.1126/science.284.5415.770openalex-snapshot
Notch Signaling: Cell Fate Control and Signal Integration in Development
inferredcites →https://doi.org/10.1126/science.aao0827openalex-snapshot
Rapid genome shrinkage in a self-fertile nematode reveals sperm competition proteins
inferredcites →https://doi.org/10.1159/000084979openalex-snapshot
Repbase Update, a database of eukaryotic repetitive elements
inferredcites →https://doi.org/10.1163/156854102321122557openalex-snapshot
Description of Caenorhabditis japonica n. sp. (Nematoda: Rhabditida) associated with the burrower bug Parastrachia japonensis (Heteroptera: Cydnidae) in Japan
inferredcites →https://doi.org/10.11646/zootaxa.1456.1.2openalex-snapshot
Comparison of the cryptic nematode species Caenorhabditis brenneri sp. n. and C. remanei (Nematoda: Rhabditidae) with the stem species pattern of the Caenorhabditis Elegans group
inferredcites →https://doi.org/10.1186/1471-2105-10-421openalex-snapshot
BLAST+: architecture and applications
inferredcites →https://doi.org/10.1186/1471-2105-15-182openalex-snapshot
Skewer: a fast and accurate adapter trimmer for next-generation sequencing paired-end reads
inferredcites →https://doi.org/10.1186/1471-2148-11-339openalex-snapshot
A phylogeny and molecular barcodes for Caenorhabditis, with numerous new species from rotting fruits
inferredcites →https://doi.org/10.1186/1741-7007-10-59openalex-snapshot
Population dynamics and habitat sharing of natural populations of Caenorhabditis elegans and C. briggsae
inferredcites →https://doi.org/10.1186/gb-2014-15-3-r46openalex-snapshot
Kraken: ultrafast metagenomic sequence classification using exact alignments
inferredcites →https://doi.org/10.1186/s12864-017-3860-xopenalex-snapshot
Genome analysis of Diploscapter coronatus: insights into molecular peculiarities of a nematode with parthenogenetic reproduction
inferredcites →https://doi.org/10.1186/s12898-017-0150-zopenalex-snapshot
Ephemeral-habitat colonization and neotropical species richness of Caenorhabditis nematodes
inferredcites →https://doi.org/10.1186/s13059-015-0721-2openalex-snapshot
OrthoFinder: solving fundamental biases in whole genome comparisons dramatically improves orthogroup inference accuracy
inferredcites →https://doi.org/10.1186/s40850-017-0013-2openalex-snapshot
Caenorhabditis monodelphis sp. n.: defining the stem morphology and genomics of the genus Caenorhabditis
inferredcites →https://doi.org/10.1242/dev.112.1.231openalex-snapshot
Two homologous regulatory genes, lin-12 and glp-1 , have overlapping functions
inferredcites →https://doi.org/10.1242/dev.119.4.1019openalex-snapshot
glp-1 can substitute for lin-12 in specifying cell fate decisions in Caenorhabditis elegans
inferredcites →https://doi.org/10.12688/f1000research.12232.1openalex-snapshot
BlobTools: Interrogation of genome assemblies
inferredcites →https://doi.org/10.1371/journal.pbio.0000045openalex-snapshot
The Genome Sequence of Caenorhabditis briggsae: A Platform for Comparative Genomics
inferredcites →https://doi.org/10.1371/journal.pcbi.1000392openalex-snapshot
Fast Statistical Alignment
inferredcites →https://doi.org/10.1371/journal.pgen.1005323openalex-snapshot
Reproductive Mode and the Evolution of Genome Size and Structure in Caenorhabditis Nematodes
inferredcites →https://doi.org/10.1371/journal.pone.0094723openalex-snapshot
A Streamlined System for Species Diagnosis in Caenorhabditis (Nematoda: Rhabditidae) with Name Designations for 15 Distinct Biological Species
inferredcites →https://doi.org/10.1371/journal.pone.0110957openalex-snapshot
Description of Caenorhabditis sinica sp. n. (Nematoda: Rhabditidae), a Nematode Species Used in Comparative Biology for C. elegans
inferredcites →https://doi.org/10.1534/genetics.116.191148openalex-snapshot
The Genetic Basis of Natural Variation in Caenorhabditis elegans Telomere Length
inferredcites →https://doi.org/10.1534/genetics.116.195511openalex-snapshot
The Natural Biotic Environment of Caenorhabditis elegans
inferredcites →https://doi.org/10.1895/wormbook.1.115.2openalex-snapshot
Isolation of C. elegans and related nematodes
inferredcites →https://doi.org/10.32614/r.manualsopenalex-snapshot
R: A Language and Environment for Statistical Computing
inferredcites →https://doi.org/10.4137/ebo.s12813openalex-snapshot
PhyloTreePruner: A Phylogenetic Tree-Based Approach for selection of Orthologous sequences for phylogenomics
What points at this work
Incoming claims: where this work appears in other papers’ reference lists and arguments.
inferred← citeshttps://doi.org/10.1093/molbev/msaa107openalex-snapshot
Degradation of the Repetitive Genomic Landscape in a Close Relative of Caenorhabditis elegans
inferred← citeshttps://doi.org/10.1101/627620openalex-snapshot
Patterns of putative gene loss suggest rampant developmental system drift in nematodes
inferred← citeshttps://doi.org/10.1101/694414openalex-snapshot
A genetic pathway encoding double-stranded RNA transporters and interactors regulates growth and plasticity in Caenorhabditis elegans
inferred← citeshttps://doi.org/10.1101/gr.246082.118openalex-snapshot
Long-read sequencing reveals intra-species tolerance of substantial structural variations and new subtelomere formation in C. elegans
inferred← citeshttps://doi.org/10.7554/elife.50465openalex-snapshot
Deep sampling of Hawaiian Caenorhabditis elegans reveals high genetic diversity and admixture with global populations
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