1. 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...
  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. 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...
  5. 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...
  6. 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...
  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) 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...
  8. 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...
  9. 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...
  10. 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...
  11. 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...
  12. 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...
  13. 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...
  14. 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...
  15. 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...
  16. 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...
  17. 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...
  18. 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...
  19. 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)...
  20. 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)...