1. ICeE an interface for C. elegans experiments.

    Worm 3(3):e959420 (2014) PMID 26430546 PMCID PMC4588384

    An increasing number of laboratories are using the COPAS Biosort™ to implement high-throughput approaches to tackle diverse biological problems. While providing a powerful tool for generating quantitative data, the utility of the Biosort is currently limited by the absence of resources for data ...
  2. EDGEdb: a transcription factor-DNA interaction database for the analysis of C. elegans differential gene expression.

    BMC Genomics 8:21 (2007) PMID 17233892 PMCID PMC1790901

    Transcription regulatory networks are composed of protein-DNA interactions between transcription factors and their target genes. A long-term goal in genome biology is to map protein-DNA interaction networks of all regulatory regions in a genome of interest. Both transcription factor -and gene-ce...
  3. High-throughput expression of C. elegans proteins.

    Genome Research 14(10B):2102 (2004) PMID 15489332 PMCID PMC528926

    Proteome-scale studies of protein three-dimensional structures should provide valuable information for both investigating basic biology and developing therapeutics. Critical for these endeavors is the expression of recombinant proteins. We selected Caenorhabditis elegans as our model organism in...
  4. Systematic interactome mapping and genetic perturbation analysis of a C. elegans TGF-beta signaling network.

    Molecular Cell 13(4):469 (2004) PMID 14992718

    To initiate a system-level analysis of C. elegans DAF-7/TGF-beta signaling, we combined interactome mapping with single and double genetic perturbations. Yeast two-hybrid (Y2H) screens starting with known DAF-7/TGF-beta pathway components defined a network of 71 interactions among 59 proteins. C...
  5. Structure-based drug design targeting an inactive RNA conformation: exploiting the flexibility of HIV-1 TAR RNA.

    Journal of Molecular Biology 336(3):625 (2004) PMID 15095977

    The targeting of RNA for the design of novel anti-viral compounds represents an area of vast potential. We have used NMR and computational methods to model the interaction of a series of synthetic inhibitors of the in vitro RNA binding activities of a peptide derived from the transcriptional act...
  6. A map of the interactome network of the metazoan C. elegans.

    Science 303(5657):540 (2004) PMID 14704431 PMCID PMC1698949

    To initiate studies on how protein-protein interaction (or "interactome") networks relate to multicellular functions, we have mapped a large fraction of the Caenorhabditis elegans interactome network. Starting with a subset of metazoan-specific proteins, more than 4000 interactions were identifi...
  7. Structure-based Drug Design Targeting an Inactive RNA Conformation: Exploiting the Flexibility of HIV-1 TAR RNA

    Journal of Molecular Biology 336(3):625 (2004)

    The targeting of RNA for the design of novel anti-viral compounds represents an area of vast potential. We have used NMR and computational methods to model the interaction of a series of synthetic inhibitors of the in vitro RNA binding activities of a peptide derived from the transcr...
  8. Systematic Interactome Mapping and Genetic Perturbation Analysis of aC. elegansTGF-β Signaling Network

    Molecular Cell 13(4):469 (2004)

    To initiate a system-level analysis of C. elegans DAF-7/TGF-β signaling, we combined interactome mapping with single and double genetic perturbations. Yeast two-hybrid (Y2H) screens starting with known DAF-7/TGF-β pathway components defined a network of 71 interactions among 59 prote...
  9. BTB proteins are substrate-specific adaptors in an SCF-like modular ubiquitin ligase containing CUL-3.

    Nature 425(6955):316 (2003) PMID 13679922

    Programmed destruction of regulatory proteins through the ubiquitin-proteasome system is a widely used mechanism for controlling signalling pathways. Cullins are proteins that function as scaffolds for modular ubiquitin ligases typified by the SCF (Skp1-Cul1-F-box) complex. The substrate selecti...
  10. Functional cdc25C dual-specificity phosphatase is required for S-phase entry in human cells.

    Molecular Biology of the Cell 14(7):2984 (2003) PMID 12857880 PMCID PMC165692

    In view of the common regulatory mechanism that induces transcription of the mitotic phosphatase cdc25C and cyclin A at the beginning of S-phase, we investigated whether cdc25C was required for S-phase transit. Here, we show that in both nontransformed human fibroblasts and HeLa cells, cdc25C pr...
  11. C. elegans ORFeome version 1.1: experimental verification of the genome annotation and resource for proteome-scale protein expression.

    Nature Genetics 34(1):35 (2003) PMID 12679813

    To verify the genome annotation and to create a resource to functionally characterize the proteome, we attempted to Gateway-clone all predicted protein-encoding open reading frames (ORFs), or the 'ORFeome,' of Caenorhabditis elegans. We successfully cloned approximately 12,000 ORFs (ORFeome 1.1)...
  12. WorfDB: the Caenorhabditis elegans ORFeome Database.

    Nucleic Acids Research 31(1):237 (2003) PMID 12519990 PMCID PMC165539

    WorfDB (Worm ORFeome DataBase; http://worfdb.dfci.harvard.edu) was created to integrate and disseminate the data from the cloning of complete set of approximately 19 000 predicted protein-encoding Open Reading Frames (ORFs) of Caenorhabditis elegans (also referred to as the 'worm ORFeome'). Worf...
  13. Integrating interactome, phenome, and transcriptome mapping data for the C. elegans germline.

    Current Biology 12(22):1952 (2002) PMID 12445390

    By integrating functional genomic and proteomic mapping approaches, biological hypotheses should be formulated with increasing levels of confidence. For example, yeast interactome and transcriptome data can be correlated in biologically meaningful ways. Here, we combine interactome mapping data ...
  14. Combined functional genomic maps of the C. elegans DNA damage response.

    Science 295(5552):127 (2002) PMID 11778048

    Many human cancers originate from defects in the DNA damage response (DDR). Although much is known about this process, it is likely that additional DDR genes remain to be discovered. To identify such genes, we used a strategy that combines protein-protein interaction mapping and large-scale phen...
  15. Mapping the residues of protein kinase CK2 α subunit responsible for responsiveness to polyanionic inhibitors

    FEBS Letters 380(1):25 (1996)

    The quadruple mutation of the whole basic cluster, K 74KKK 77 conserved in the catalytic subunits of protein kinase CK2 and implicated in substrate recognition, not only abolishes inhibition by heparin but even induces with some peptide substrates an up to 5-fold stimulation by ...