Transcriptome analysis of adult Caenorhabditis elegans cells reveals tissue-specific gene and isoform expression

Cell type-specific transcriptome profiling in C. elegans using the Translating Ribosome Affinity Purification technique

(2017) Xicotencatl Gracida et al.   METHODS

Comprehensive single-cell transcriptional profiling of a multicellular organism

(2017) Junyue Cao et al.   SCIENCE

In vivo mapping of tissue- and subcellular-specific proteomes in Caenorhabditis elegans

(2017) Aaron W. Reinke et al.   Science Advances

Tissue enrichment analysis for C. elegans genomics

(2016) David Angeles-Albores et al.   BMC BIOINFORMATICS

A gene‐centered C. elegans protein–DNA interaction network provides a framework for functional predictions

(2016) Juan I Fuxman Bass et al.   Molecular Systems Biology

g:Profiler—a web server for functional interpretation of gene lists (2016 update)

(2016) Jüri Reimand et al.   NUCLEIC ACIDS RESEARCH

The glyoxylate shunt is essential for desiccation tolerance in C. elegans and budding yeast

(2016) Cihan Erkut et al.   eLife

Comparative RNA-Seq analysis reveals pervasive tissue-specific alternative polyadenylation in Caenorhabditis elegans intestine and muscles

(2015) Stephen M Blazie et al.   BMC BIOLOGY

Caenorhabditis elegans OSM-11 signaling regulates SKN-1/Nrf during embryonic development and adult longevity and stress response

(2015) Arne Dresen et al.   DEVELOPMENTAL BIOLOGY

Structural Damage in the C. elegans Epidermis Causes Release of STA-2 and Induction of an Innate Immune Response

(2015) Yun Zhang et al.   IMMUNITY

The C. elegans adult neuronal IIS/FOXO transcriptome reveals adult phenotype regulators

(2015) Rachel Kaletsky et al.   NATURE

Genome-wide Functional Analysis of CREB/Long-Term Memory-Dependent Transcription Reveals Distinct Basal and Memory Gene Expression Programs

(2015) Vanisha Lakhina et al.   NEURON

RSAT 2015: Regulatory Sequence Analysis Tools

(2015) Alejandra Medina-Rivera et al.   NUCLEIC ACIDS RESEARCH

mTORC2-SGK-1 acts in two environmentally responsive pathways with opposing effects on longevity

(2014) Masaki Mizunuma et al.   AGING CELL

subSeq: Determining Appropriate Sequencing Depth Through Efficient Read Subsampling

(2014) David G. Robinson et al.   BIOINFORMATICS

Dauer-independent insulin/IGF-1-signalling implicates collagen remodelling in longevity

(2014) Collin Y. Ewald et al.   NATURE

Isolation of Specific Neurons from C. elegans Larvae for Gene Expression Profiling

(2014) W. Clay Spencer et al.   PLoS One

footprintDB: a database of transcription factors with annotated cis elements and binding interfaces

(2013) Alvaro Sebastian et al.   BIOINFORMATICS

featureCounts: an efficient general purpose program for assigning sequence reads to genomic features

(2013) Y. Liao et al.   BIOINFORMATICS

PQM-1 Complements DAF-16 as a Key Transcriptional Regulator of DAF-2-Mediated Development and Longevity

(2013) Ronald G. Tepper et al.   CELL

Direct and Indirect Gene Regulation by a Life-Extending FOXO Protein in C. elegans: Roles for GATA Factors and Lipid Gene Regulators

(2013) Peichuan Zhang et al.   Cell Metabolism

Complex expression dynamics and robustness in C. elegans insulin networks

(2013) A. D. Ritter et al.   GENOME RESEARCH

Single-cell transcriptomics reveals bimodality in expression and splicing in immune cells

(2013) Alex K. Shalek et al.   NATURE

WormBase 2014: new views of curated biology

(2013) Todd W. Harris et al.   NUCLEIC ACIDS RESEARCH

CELF Family RNA–Binding Protein UNC-75 Regulates Two Sets of Mutually Exclusive Exons of the unc-32 Gene in Neuron-Specific Manners in Caenorhabditis elegans

(2013) Hidehito Kuroyanagi et al.   PLoS Genetics

RSeQC: quality control of RNA-seq experiments

(2012) Liguo Wang et al.   BIOINFORMATICS

STAR: ultrafast universal RNA-seq aligner

(2012) Alexander Dobin et al.   BIOINFORMATICS

A survey of putative secreted and transmembrane proteins encoded in the C. elegans genome

(2012) Jinkyo Suh et al.   BMC GENOMICS

Inactivation of Conserved C. elegans Genes Engages Pathogen- and Xenobiotic-Associated Defenses

(2012) Justine A. Melo et al.   CELL

Detecting differential usage of exons from RNA-seq data

(2012) S. Anders et al.   GENOME RESEARCH

An image analysis toolbox for high-throughput C. elegans assays

(2012) Carolina Wählby et al.   NATURE METHODS

PDF-1 neuropeptide signaling modulates a neural circuit for mate-searching behavior in C. elegans

(2012) Arantza Barrios et al.   NATURE NEUROSCIENCE

DBL-1, a TGF- , is essential for Caenorhabditis elegans aversive olfactory learning

(2012) X. Zhang et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

The Caenorhabditis elegans epidermis as a model skin. I: development, patterning, and growth

(2012) Andrew D. Chisholm et al.   Wiley Interdisciplinary Reviews-Developmental Biology

Catalase activity and innate immune response ofCaenorhabditis elegansagainst the heavy metal toxin lead

(2011) Balasubramanian Vigneshkumar et al.   ENVIRONMENTAL TOXICOLOGY

Contribution of sams-1 and pmt-1 to lipid homoeostasis in adult Caenorhabditis elegans

(2011) Yingxiu Li et al.   JOURNAL OF BIOCHEMISTRY

Iron metabolism and the innate immune response to infection

(2011) Erin E. Johnson et al.   MICROBES AND INFECTION

CREB and the CRTC co-activators: sensors for hormonal and metabolic signals

(2011) Judith Y. Altarejos et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

REVIGO Summarizes and Visualizes Long Lists of Gene Ontology Terms

(2011) Fran Supek et al.   PLoS One

A flexible R package for nonnegative matrix factorization

(2010) Renaud Gaujoux et al.   BMC BIOINFORMATICS

TGF-β and Insulin Signaling Regulate Reproductive Aging via Oocyte and Germline Quality Maintenance

(2010) Shijing Luo et al.   CELL

A global analysis of C. elegans trans-splicing

(2010) M. A. Allen et al.   GENOME RESEARCH

A spatial and temporal map of C. elegans gene expression

(2010) W. C. Spencer et al.   GENOME RESEARCH

The genetics of ageing

(2010) Cynthia J. Kenyon   NATURE

Insulin Signaling and Dietary Restriction Differentially Influence the Decline of Learning and Memory with Age

(2010) Amanda L. Kauffman et al.   PLOS BIOLOGY

edgeR: a Bioconductor package for differential expression analysis of digital gene expression data

(2009) M. D. Robinson et al.   BIOINFORMATICS

C. elegans Major Fats Are Stored in Vesicles Distinct from Lysosome-Related Organelles

(2009) Eyleen J. O'Rourke et al.   Cell Metabolism

Caenorhabditis elegans as an emerging model for studying the basic biology of obesity

(2009) K. T. Jones et al.   Disease Models & Mechanisms

The signal pathway of gonadotrophins-induced mammalian oocyte meiotic resumption

(2009) M. Zhang et al.   MOLECULAR HUMAN REPRODUCTION

Global Prediction of Tissue-Specific Gene Expression and Context-Dependent Gene Networks in Caenorhabditis elegans

(2009) Maria D. Chikina et al.   PLoS Computational Biology

TGF-ß Sma/Mab Signaling Mutations Uncouple Reproductive Aging from Somatic Aging

(2009) Shijing Luo et al.   PLoS Genetics

Human Protein Reference Database--2009 update

(2008) T. S. Keshava Prasad et al.   NUCLEIC ACIDS RESEARCH