WormBook Archives

In March 2016, GENETICS launched WormBook, a comprehensive compendium of review articles presenting the current state of knowledge in C. elegans research. WormBook articles span the breadth of the biology, genetics, genomics, and evolutionary biology of C. elegans. Find historical WormBook articles published as the online companion to WormBase here. This page contains the full list of all historical and GSA-published WormBook articles, organized by section.

Frequently Asked Questions

Introduction

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A transparent window into biology: A primer on Caenorhabditis elegans

Additional articles

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Wormbook: Wormbiology for the 21st century
Notch and the awesome power of genetics
Pathway to RAS
One lucky XX male: Isolation of the first Caenorhabditis elegans sex-determination mutants
Worm spadework
Joy of the worm
Early worms

Biochemistry

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Ascaroside signaling in C. elegans
Carbohydrates and glycosylation
Intermediary metabolism

Cell and organelle biology

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Conserved components of the macroautophagy machinery in Caenorhabditis elegans
The Caenorhabditis elegans cuticle and precuticle: A model for studying dynamic apical extracellular matrices in vivo
Extracellular vesicles
Mitotic cell division in Caenorhabditis elegans
Invading, leading and navigating cells in Caenorhabditis elegans: Insights into cell movement in vivo
Cell biology of the mitochondrion
Cell biology of the Caenorhabditis elegans nucleus
The Caenorhabditis elegans excretory system: A model for tubulogenesis, cell fate specification, and plasticity

Cell biology

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Autophagy in C. elegans
Basement membranes
The cadherin superfamily
Carbohydrates and glycosylation
C. elegans as a model for membrane traffic
Cell cycle regulation
Cell division
Cell fusions
The cuticle
The C. elegans eggshell
Development, structure, and maintenance of C. elegans body wall muscle
Epidermal morphogenesis
Epithelial junctions, cytoskeleton, and polarity
Gastrulation in C. elegans
Membrane ion transport in non-excitable tissues
Mitochondrial genetics
Polarity establishment, asymmetric division and segregation of fate determinants in early C. elegans embryos
Potassium channels in C. elegans
Programmed cell death
Sarcomere assembly in C. elegans muscle
The sensory cilia of Caenorhabditis elegans
Nematode sperm motility
Spermatogenesis
Synaptogenesis
Tubulins in C. elegans

Cell fate, signaling, and development

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Neurogenesis in Caenorhabditis elegans
Mechanisms of lineage specification in Caenorhabditis elegans
Caenorhabditis elegans gastrulation: A model for understanding how cells polarize, change shape, and journey toward the center of an embryo
Biology of the Caenorhabditis elegans germline stem cell system
Developmental plasticity and cellular reprogramming in Caenorhabditis elegans
Tor signaling in Caenorhabditis elegans development, metabolism, and aging
Developmental control of the cell cycle: Insights from Caenorhabditis elegans
Programmed cell death during Caenorhabditis elegans development

Developmental control

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The C. elegans intestine
The C. elegans pharynx: A model for organogenesis
Development and migration of the C. elegans Q neuroblasts and their descendants
Embryological variation during nematode development
Epidermal morphogenesis
Gastrulation in C. elegans
Hermaphrodite cell-fate specification
Notch signaling in the C. elegans embryo
Polarity establishment, asymmetric division, and segregation of fate determinants in early C. elegans embryos
Programmed cell death
Translational control of maternal RNAs

Disease models and drug discovery

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C. elegans and volatile anesthetics
Anthelmintic drugs and nematicides: Studies in Caenorhabditis elegans
Obesity and the regulation of fat metabolism

Evolution and ecology

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Introduction to nematode evolution and ecology
A quick tour of nematode diversity and the backbone of nematode phylogeny
Ecology of Caenorhabditis species
Evolution of development in nematodes related to C. elegans
The evolution of nematode sex determination: C. elegans as a reference point for comparative biology
Interactions with microbial pathogens
Molecular evolution inferences from the C. elegans genome
Natural variation and population genetics of C. elegans
Nematode genome evolution
The phylogenetic relationships of Caenorhabditis and other rhabditids
Life history in Caenorhabditis elegans: from molecular genetics to evolutionary ecology
Natural genetic variation as a tool for discovery in Caenorhabditis nematodes
Males, outcrossing, and sexual selection in Caenorhabditis nematodes
From “the worm” to “the worms” and back again: The evolutionary developmental biology of nematodes
Experimental evolution with Caenorhabditis nematodes
The natural biotic environment of Caenorhabditis elegans

Evolution and ecology (Biology and genomes of nematodes other than C. elegans)

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Genomics and biology of the nematode Caenorhabditis briggsae
The biology and genome of Heterorhabditis bacteriophora
The biology of Strongyloides spp.
Oscheius tipulae
Pristionchus pacificus
Biology and genome of Trichinella spiralis

Gene and genome regulatory mechanisms

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Nematode chromosomes
Germ granules and gene regulation in the Caenorhabditis elegans germline
Mechanisms of sex determination and X-chromosome dosage compensation
DNA repair, recombination, and damage signaling
mRNA editing, processing and quality control in Caenorhabditis elegans
Recent molecular genetic explorations of Caenorhabditis elegans microRNAs
Repressive chromatin in Caenorhabditis elegans: Establishment, composition, and function

Genetics and genomics

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Introduction to genetics and genomics
Caenorhabditis nomenclature

Genetics and genomics (Genetics)

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Complementation
Essential genes
Gene duplications and genetic redundancy in C. elegans
Genetic enhancers
Genetic mosaics
Genetic suppression
Karyotype, ploidy and gene dosage
Natural variation and population genetics of C. elegans

Genetics and genomics (Genomics)

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C. elegans network biology: A beginning
C. elegans noncoding RNA genes
Genomic classification of protein-coding gene families
Germline genomics
Mitochondrial genetics
Nematode genome evolution
Overview of gene structure in C. elegans
Transposons in C. elegans

Metabolism, physiology, and aging

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Mitochondrial dysfunction, aging, and the mitochondrial unfolded protein response in Caenorhabditis elegans
Starvation responses throughout the Caenorhabditis elegans life cycle
Organismal protein homeostasis mechanisms
Lipid and carbohydrate metabolism in Caenorhabditis elegans

Molecular biology

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C. elegans microRNAs
C. elegans noncoding RNA genes
Endogenous RNAi pathways in C. elegans
Gene expression changes associated with aging in C. elegans
Genomic classification of protein-coding gene families
Germline chromatin
Mechanism and regulation of translation in C. elegans
Operon and non-operon gene clusters in the C. elegans genome
Overview of gene structure in C. elegans
Pre-mRNA splicing and its regulation in Caenorhabditis elegans
Replication and repair
RNA-binding proteins
Roles of chromatin factors in C. elegans development
Transcription mechanisms
Transcriptional regulation of gene expression in C. elegans
Translational control of maternal RNAs
Trans-splicing and operons in C. elegans
Transposons in C. elegans
Ubiquitin-mediated pathways in C. elegans
X-chromosome dosage compensation

Nematodes other than C. elegans (Biology and genomes)

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Genomics and biology of the nematode Caenorhabditis briggsae
The biology and genome of Heterorhabditis bacteriophora
The biology of Strongyloides spp.
Oscheius tipulae
Pristionchus pacificus
Biology and genome of Trichinella spiralis

Nematodes other than C. elegans (Evolution and ecology)

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Evolution of development in nematodes related to C. elegans
A quick tour of nematode diversity and the backbone of nematode phylogeny
Ecology of Caenorhabditis species
The evolution of nematode sex determination
Interactions with microbial pathogens
Molecular evolution inferences from the C. elegans genome
Natural variation and population genetics of C. elegans
Introduction to nematode evolution and ecology
Nematode genome evolution
The phylogenetic relationships of Caenorhabditis and other rhabditids

Neurobiology and behavior

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Behavioral plasticity
Dendrite morphogenesis in Caenorhabditis elegans
Synaptogenesis: Unmasking molecular mechanisms using Caenorhabditis elegans
Chemosensory signal transduction in Caenorhabditis elegans
Behavioral states
How Caenorhabditis elegans senses mechanical stress, temperature, and other physical stimuli
Sexual dimorphism and sex differences in Caenorhabditis elegans neuronal development and behavior
The genetics of axon guidance and axon regeneration in Caenorhabditis elegans

Neurobiology and behavior (Behavior)

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Egg-laying
Male mating behavior

Neurobiology and behavior (Development)

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Neurogenesis in the nematode Caenorhabditis elegans
Synaptogenesis

Neurobiology and behavior (Function)

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The neuronal genome of Caenorhabditis elegans
Potassium channels in C. elegans
The putative chemoreceptor families of C. elegans
Synaptic function
The sensory cilia of Caenorhabditis elegans

Neurobiology and behavior (History)

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Getting into the mind of the worm—a personal view

Neurobiology and behavior (Neurotransmitters)

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Acetylcholine
Biogenic amine neurotransmitters in C. elegans
Ethanol
GABA
Ionotropic glutamate receptors: Genetics, behavior and electrophysiology
Neuropeptides

Neurobiology and behavior (Sensory modalities)

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Chemosensation in C. elegans
Mechanosensation

Post-embryonic development

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Dauer
Evolution of development in nematodes related to C. elegans
Gene expression changes associated with aging in C. elegans
Hermaphrodite cell-fate specification
Male development
The measurement and analysis of age-related changes in Caenorhabditis elegans
Morphogenesis of the vulva and the vulval-uterine connection
Roles of chromatin factors in C. elegans development
Vulval development

Post-embryonic development (Behavior)

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C. elegans feeding

Sex determination

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Introduction to sex determination
Hermaphrodite cell-fate specification
Male development
Morphogenesis of the vulva and the vulval-uterine connection
Sex determination in the germ line
Somatic sex determination
The evolution of nematode sex determination: C. elegans as a reference point for comparative biology
Vulval development
X-chromosome dosage compensation

Signal transduction

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Introduction to signal transduction
Genomic overview of protein kinases
Canonical RTK-Ras-ERK signaling and related alternative pathways
Eph receptor signaling in C. elegans
Heterotrimeric G proteins in C. elegans
Neurotransmitter signaling through heterotrimeric G proteins: Insights from studies in C. elegans
Homologs of the HH signalling network in C. elegans
Insulin/insulin-like growth factor signaling in C. elegans
Notch signaling: Genetics and structure
Nuclear receptor signal transduction in C. elegans
Signaling in the innate immune response
Small GTPases
TGF-β signaling in C. elegans
The putative chemoreceptor families of C. elegans
WNT signaling in C. elegans

The germ line

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Introduction to the germ line
Control of oocyte meiotic maturation and fertilization
Germline chromatin
Germline genomics
Germline proliferation and its control
Germline survival and apoptosis
Meiosis
Specification of the germ line
Spermatogenesis

WormHistory

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Getting into the mind of the worm
History of research on C. elegans and other free-living nematodes as model organisms

WormHistory (From GENETICS, Perspectives)

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Early Worms
One Lucky XX Male
Joy of the worm
Notch and the Awesome Power of Genetics
Pathway to RAS
Worm Spadework

WormHistory (From The Journal of Cell Biology, People & Ideas)

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The broad scope of micrornas
Observing and making connections
Using aging research to probe biology
Breaking out new ideas on molting
Cell biology by way of development
On the trail of mitochondrial dysfunction
From unlikely scientist to royal society fellow
Building new models and communities
How to stay young at heart, body, and mind
New perspectives on q cell biology
Invasive procedures
Transcriptional mapmaker
Changing avenues without losing focus

WormHistory (Other topics)

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The beginning of connectomics

WormMethods

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Detecting gene expression in Caenorhabditis elegans
Visualizing and quantifying molecular and cellular processes in Caenorhabditis elegans using light microscopy
Methods for analyzing neuronal structure and activity in Caenorhabditis elegans
The Caenorhabditis elegans transgenic toolbox
Next-generation sequencing-based approaches for mutation mapping and identification in Caenorhabditis elegans
CRISPR-based methods for Caenorhabditis elegans genome engineering

WormMethods (Basic methods for C. elegans)

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Maintenance of C. elegans
Nomarski images for learning the anatomy, with tips for mosaic analysis
A biologist’s guide to statistical thinking and analysis
Web resources for C. elegans studies
An introduction to the UCSC genome browser

WormMethods (Behavioral assays)

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Behavior
Assaying mechanosensation
Methods for measuring pharyngeal behaviors
Thermotaxis navigation behavior
Working with dauer larvae

WormMethods (Cell and molecular biology)

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Biochemistry and molecular biology
Methods in cell biology
Cell isolation and culture
Mass spectrometry-based shotgun proteomic analysis of C. elegans protein complexes
Modern techniques for the analysis of chromatin and nuclear organization in C. elegans

WormMethods (Forward and reverse genetics)

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Classical genetic methods
Forward and reverse mutagenesis in C. elegans
Genetic balancers
Genetic dissection of developmental pathways
Reverse genetics

WormMethods (Measuring and monitoring gene expression)

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Immunohistochemistry
RNA in situ hybridization of dissected gonads
In situ hybridization on whole mount embryos of C. elegans
Protocols for large scale in situ hybridization on C. elegans larvae
Reporter gene fusions
DNA microarrays
Single molecule fluorescent in situ hybridization (smFISH) of C. elegans worms and embryos

WormMethods (Methods for nematode species other than C. elegans)

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Caenorhabditis briggsae methods
Isolation of C. elegans and related nematodes
Pristionchus pacificus protocols
Pristionchus pacificus genomics: From genetics to genome sequence
Strongyloides stercoralis: A model for translational research on parasitic nematode biology
Transgenesis in animal parasitic nematodes: Strongyloides spp. and Brugia spp.

WormMethods (Microinjection and transformation)

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C. elegans gene transformation by microparticle bombardment
Transformation and microinjection
Transgenic solutions for the germline
Keeping track of worm trackers
Microfluidics as a tool for C. elegans research

WormMethods (Microscopy and other instrumentation)

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Keeping track of worm trackers
Microfluidics as a tool for C. elegans research

WormMethods (Neurophysiological methods)

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Neurophysiological methods in C. elegans: An introduction
Culture of embryonic C. elegans cells for electrophysiological and pharmacological analyses
Electrophysiological recordings from the neuromuscular junction of C. elegans
Electrophysiological recordings from the pharynx
Heterologous expression of C. elegans ion channels in xenopus oocytes
Imaging the activity of neurons and muscles