1. Corrigendum: Regulatory analysis of the C. elegans genome with spatiotemporal resolution.

    Nature 528(7580):152 (2015) PMID 26560031

  2. Remarkably Divergent Regions Punctuate the Genome Assembly of the Caenorhabditis elegans Hawaiian Strain CB4856.

    Genetics 200(3):975 (2015) PMID 25995208 PMCID PMC4512556

    The Hawaiian strain (CB4856) of Caenorhabditis elegans is one of the most divergent from the canonical laboratory strain N2 and has been widely used in developmental, population, and evolutionary studies. To enhance the utility of the strain, we have generated a draft sequence of the CB4856 geno...
  3. Regulatory analysis of the C. elegans genome with spatiotemporal resolution.

    Nature 512(7515):400 (2014) PMID 25164749 PMCID PMC4530805

    Discovering the structure and dynamics of transcriptional regulatory events in the genome with cellular and temporal resolution is crucial to understanding the regulatory underpinnings of development and disease. We determined the genomic distribution of binding sites for 92 transcription factor...
  4. Comparative analysis of regulatory information and circuits across distant species.

    Nature 512(7515):453 (2014) PMID 25164757 PMCID PMC4336544

    Despite the large evolutionary distances between metazoan species, they can show remarkable commonalities in their biology, and this has helped to establish fly and worm as model organisms for human biology. Although studies of individual elements and factors have explored similarities in gene r...
  5. Isolation of specific neurons from C. elegans larvae for gene expression profiling.

    PLoS ONE 9(11):e112102 (2014) PMID 25372608 PMCID PMC4221280

    The simple and well-described structure of the C. elegans nervous system offers an unprecedented opportunity to identify the genetic programs that define the connectivity and function of individual neurons and their circuits. A correspondingly precise gene expression map of C. elegans neurons wo...
  6. The million mutation project: a new approach to genetics in Caenorhabditis elegans.

    Genome Research 23(10):1749 (2013) PMID 23800452 PMCID PMC3787271

    We have created a library of 2007 mutagenized Caenorhabditis elegans strains, each sequenced to a target depth of 15-fold coverage, to provide the research community with mutant alleles for each of the worm's more than 20,000 genes. The library contains over 800,000 unique single nucleotide vari...
  7. A high-fidelity cell lineage tracing method for obtaining systematic spatiotemporal gene expression patterns in Caenorhabditis elegans.

    G3: Genes, Genomes, Genetics 3(5):851 (2013) PMID 23550142 PMCID PMC3656732

    Advances in microscopy and fluorescent reporters have allowed us to detect the onset of gene expression on a cell-by-cell basis in a systemic fashion. This information, however, is often encoded in large repositories of images, and developing ways to extract this spatiotemporal expression data i...
  8. Genetic control of vulval development in Caenorhabditis briggsae.

    G3: Genes, Genomes, Genetics 2(12):1625 (2012) PMID 23275885 PMCID PMC3516484

    The nematode Caenorhabditis briggsae is an excellent model organism for the comparative analysis of gene function and developmental mechanisms. To study the evolutionary conservation and divergence of genetic pathways mediating vulva formation, we screened for mutations in C. briggsae that cause...
  9. A genome-scale resource for in vivo tag-based protein function exploration in C. elegans.

    Cell 150(4):855 (2012) PMID 22901814 PMCID PMC3979301

    Understanding the in vivo dynamics of protein localization and their physical interactions is important for many problems in biology. To enable systematic protein function interrogation in a multicellular context, we built a genome-scale transgenic platform for in vivo expression of fluorescent-...
  10. Multidimensional regulation of gene expression in the C. elegans embryo.

    Genome Research 22(7):1282 (2012) PMID 22508763 PMCID PMC3396369

    How cells adopt different expression patterns is a fundamental question of developmental biology. We quantitatively measured reporter expression of 127 genes, primarily transcription factors, in every cell and with high temporal resolution in C. elegans embryos. Embryonic cells are highly distin...
  11. Evidence for compensatory upregulation of expressed X-linked genes in mammals, Caenorhabditis elegans and Drosophila melanogaster.

    Nature Genetics 43(12):1179 (2011) PMID 22019781 PMCID PMC3576853

    Many animal species use a chromosome-based mechanism of sex determination, which has led to the coordinate evolution of dosage-compensation systems. Dosage compensation not only corrects the imbalance in the number of X chromosomes between the sexes but also is hypothesized to correct dosage imb...
  12. Prediction and characterization of noncoding RNAs in C. elegans by integrating conservation, secondary structure, and high-throughput sequencing and array data.

    Genome Research 21(2):276 (2011) PMID 21177971 PMCID PMC3032931

    We present an integrative machine learning method, incRNA, for whole-genome identification of noncoding RNAs (ncRNAs). It combines a large amount of expression data, RNA secondary-structure stability, and evolutionary conservation at the protein and nucleic-acid level. Using the incRNA model and...
  13. Diverse transcription factor binding features revealed by genome-wide ChIP-seq in C. elegans.

    Genome Research 21(2):245 (2011) PMID 21177963 PMCID PMC3032928

    Regulation of gene expression by sequence-specific transcription factors is central to developmental programs and depends on the binding of transcription factors with target sites in the genome. To date, most such analyses in Caenorhabditis elegans have focused on the interactions between a sing...
  14. A global analysis of C. elegans trans-splicing.

    Genome Research 21(2):255 (2011) PMID 21177958 PMCID PMC3032929

    Trans-splicing of one of two short leader RNAs, SL1 or SL2, occurs at the 5' ends of pre-mRNAs of many C. elegans genes. We have exploited RNA-sequencing data from the modENCODE project to analyze the transcriptome of C. elegans for patterns of trans-splicing. Transcripts of ∼70% of genes are tr...
  15. A comprehensive analysis of gene expression changes provoked by bacterial and fungal infection in C. elegans.

    PLoS ONE 6(5):e19055 (2011) PMID 21602919 PMCID PMC3094335

    While Caenorhabditis elegans specifically responds to infection by the up-regulation of certain genes, distinct pathogens trigger the expression of a common set of genes. We applied new methods to conduct a comprehensive and comparative study of the transcriptional response of C. elegans to bact...
  16. Integrative analysis of the Caenorhabditis elegans genome by the modENCODE project.
    Mark B Gerstein, Zhi John Lu, Eric L Van Nostrand, Chao Cheng, Bradley I Arshinoff, Tao Liu, Kevin Yip, Rebecca Robilotto, Andreas Rechtsteiner, Kohta Ikegami, Pedro Alves, Aurelien Chateigner, Marc Perry, Mitzi Morris, Raymond K Auerbach, Xin Feng, Jing Leng, Anne Vielle, Wei Niu, Kahn Rhrissorrakrai, Ashish Agarwal, Roger P Alexander, Galt Barber, Cathleen M Brdlik, Jennifer Brennan, Jeremy Jean Brouillet, Adrian Carr, Ming-Sin Cheung, Hiram Clawson, Sergio Contrino, Luke O Dannenberg, Abby F Dernburg, Arshad Desai, Lindsay Dick, Andréa C Dosé, Jiang Du, Thea Egelhofer, Sevinc Ercan, Ghia Euskirchen, Brent Ewing, Elise A Feingold, Reto Gassmann, Peter J Good, Phil Green, Francois Gullier, Michelle Gutwein, Mark S Guyer, Lukas Habegger, Ting Han, Jorja G Henikoff, Stefan R Henz, Angie Hinrichs, Heather Holster, Tony Hyman, A Leo Iniguez, Judith Janette, Morten Jensen, Masaomi Kato, W James Kent, Ellen Kephart, Vishal Khivansara, Ekta Khurana, John Kim, Paulina Kolasinska-Zwierz, Eric C Lai, Isabel Latorre, Amber Leahey, Suzanna Lewis, Paul Lloyd, Lucas Lochovsky, Rebecca F Lowdon, Yaniv Lubling, Rachel Lyne, Michael MacCoss, Sebastian D Mackowiak, Marco Mangone, Sheldon McKay, Desirea Mecenas, Gennifer Merrihew, David Miller, Andrew Muroyama, John I Murray, Siew-Loon Ooi, Hoang Pham, Taryn Phippen, Elicia A Preston, Nikolaus Rajewsky, Gunnar Rätsch, Heidi Rosenbaum, Joel Rozowsky, Kim Rutherford, Peter Ruzanov, Mihail Sarov, Rajkumar Sasidharan, Andrea Sboner, Paul Scheid, Eran Segal, Hyunjin Shin, Chong Shou, Frank J Slack, Cindie Slightam, Richard Smith, William C Spencer, E O Stinson, Scott Taing, Teruaki Takasaki, Dionne Vafeados, Ksenia Voronina, Guilin Wang, Nicole L Washington, Christina M Whittle, Beijing Wu, Yan, Georg Zeller, Zheng Zha, Mei Zhong, Xingliang Zhou, Julie Ahringer, Susan Strome, Kristin C Gunsalus, Gos Micklem, X Shirley Liu, Valerie Reinke, Stuart Kim, LaDeana W Hillier, Steven Henikoff, Fabio Piano, Michael Snyder, Lincoln Stein, Jason D Lieb, and Robert H Waterston

    Science 330(6012):1775 (2010) PMID 21177976 PMCID PMC3142569

    We systematically generated large-scale data sets to improve genome annotation for the nematode Caenorhabditis elegans, a key model organism. These data sets include transcriptome profiling across a developmental time course, genome-wide identification of transcription factor-binding sites, and ...
  17. A negative regulatory loop between microRNA and Hox gene controls posterior identities in Caenorhabditis elegans.

    PLoS Genetics 6(9):e1001089 (2010) PMID 20824072 PMCID PMC2932687

    MicroRNAs (miRNAs) have been found to regulate gene expression across eukaryotic species, but the function of most miRNA genes remains unknown. Here we describe how the analysis of the expression patterns of a well-conserved miRNA gene, mir-57, at cellular resolution for every minute during earl...
  18. New tools for investigating the comparative biology of Caenorhabditis briggsae and C. elegans.

    Genetics 184(3):853 (2010) PMID 20008572 PMCID PMC2845351

    Comparative studies of Caenorhabditis briggsae and C. elegans have provided insights into gene function and developmental control in both organisms. C. elegans is a well developed model organism with a variety of molecular and genetic tools to study gene functions. In contrast, there are only ve...
  19. Genome-wide identification of binding sites defines distinct functions for Caenorhabditis elegans PHA-4/FOXA in development and environmental response.

    PLoS Genetics 6(2):e1000848 (2010) PMID 20174564 PMCID PMC2824807

    Transcription factors are key components of regulatory networks that control development, as well as the response to environmental stimuli. We have established an experimental pipeline in Caenorhabditis elegans that permits global identification of the binding sites for transcription factors usi...
  20. Using machine learning to speed up manual image annotation: application to a 3D imaging protocol for measuring single cell gene expression in the developing C. elegans embryo.

    BMC Bioinformatics 11:84 (2010) PMID 20146825 PMCID PMC2838868

    Image analysis is an essential component in many biological experiments that study gene expression, cell cycle progression, and protein localization. A protocol for tracking the expression of individual C. elegans genes was developed that collects image samples of a developing embryo by 3-D time...