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Marc Vidal, PhD


Researcher

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Researcher

  • Professor of Genetics, Harvard Medical School and Dana-Farber Cancer Institute
  • Director of Center for Cancer Systems Biology - CCSB

Contact Information

  • Office Phone Number617-632-5114
  • Fax617-632-5739

Bio

Dr. Vidal received his PhD in 1991 from Gembloux University (Belgium) for work performed at Northwestern University. He identified the yeast genes SIN3 and RPD3, and demonstrated that they encode global transcriptional regulators. During postdoctoral training at the Massachusetts General Hospital Cancer Center, he developed the reverse two-hybrid system to genetically characterize protein-protein interactions. In 2000, he joined DFCI, where his research focuses on understanding global and local properties of interactome networks.

Recent Awards:

  • Abbott Bioresearch Award, Boston, MA 2003
  • Chercheur Qualifié du Fonds National de la Recherche Scientifique (Belgium), Permanent Position 1997
  • Chaire Francqui, Fondation Francqui, Belgium 2005

Research

A Systems Approach to Cancer Biology

Physical interactions mediated by proteins are critical for cellular function, constituting in toto complex macromolecular "interactome" networks. Systematic mapping of protein-protein, protein-DNA, protein-RNA and protein-metabolite interactions at the scale of the whole proteome advances understanding of interactome networks. Applications range from functional characterization of single proteins to discoveries on local and global systems properties of cellular networks. We generate and improve comprehensive interactome maps for multiple organisms (currently human, the model unicellular eukaryote yeast S. cerevisiae, and the model metazoan D. melanogaster). To ensure that the interactome maps we release are of the highest possible quality we carry out all experimental steps thoroughly and carefully, verifying all interacting pairs and validating them by independent, orthogonal assays.

Classical forward genetics and modern functional genomics (i.e. reverse genetics) have assigned potential functions to thousands of genes across dozens of organisms. The availability of genome sequences and the development of automated phenotypic analyses makes reverse genetics strategies based on null or nearly null alleles a major source of gene function information. Functional interpretation of (nearly) null alleles is often complicated because gene products do not operate in isolation but instead act on each other within complex and dynamic interactome networks. In interactome graphs, knockouts or knockdowns eliminate a node and ALL its edges. We have been developing alternatives to generate alleles that perturb a single interaction, or edge at a time, while maintaining all others unperturbed. Such “edgetic” alleles allow precise evaluation of the in vivo roles of individual interactions. We have provided proof-of-principle of an integrated strategy based on reverse yeast two-hybrid to isolate edgetic alleles and functionally characterize them in vivo. This strategy could be readily implemented for other biological pathways in other model organisms.

Many mutations responsible for human disease might also be edgetic. Edgetic mutations would be different in their effects and properties than the complete losses of gene products (node removal) generally accepted as primarily responsible for disease. Conventional node removal models for disease cannot reconcile with the increasingly appreciated prevalence of complex genotype-to-phenotype associations for even simple Mendelian disorders, particularly the confounding influence of allelic heterogeneity, locus heterogeneity, incomplete penetrance, and variable expressivity. We have delineated clear distinctions of mutations corresponding to node removal versus edgetic perturbations in the full set of mutations associated with human Mendelian disorders. Mutations associated with recessive disorders are more likely node removal, whereas mutations associated with dominant disorders are more likely edgetic. We have developed and tested an experimental platform that can characterize, at high throughput, edgetic interaction profiles of mutant disease proteins. We are currently using this platform at high throughput to edgetically profile cancer mutations, both the set of mutations already identified as well as the vaster set of cancer mutations being identified by cancer genome projects.

To learn more about the Vidal Lab or the Center for Cancer Systems Biology, please visit http://ccsb.dfci.harvard.edu.

A comprehensive library of human transcription factors for cell fate engineering. Nat Biotechnol. 2021 04; 39(4):510-519.
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Interrogation of kinase genetic interactions provides a global view of PAK1-mediated signal transduction pathways. J Biol Chem. 2020 12 11; 295(50):16906-16919.
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A massively parallel barcoded sequencing pipeline enables generation of the first ORFeome and interactome map for rice. Proc Natl Acad Sci U S A. 2020 05 26; 117(21):11836-11842.
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ORF Capture-Seq as a versatile method for targeted identification of full-length isoforms. Nat Commun. 2020 05 11; 11(1):2326.
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Yeast-Based Genetic Interaction Analysis of Human Kinome. Cells. 2020 05 07; 9(5).
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A reference map of the human binary protein interactome. Nature. 2020 04; 580(7803):402-408.
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Precision medicine - networks to the rescue. Curr Opin Biotechnol. 2020 06; 63:177-189.
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A proactive genotype-to-patient-phenotype map for cystathionine beta-synthase. Genome Med. 2020 01 30; 12(1):13.
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Maximizing binary interactome mapping with a minimal number of assays. Nat Commun. 2019 08 29; 10(1):3907.
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A genome-wide positioning systems network algorithm for in silico drug repurposing. Nat Commun. 2019 08 02; 10(1):3476.
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Global Analysis of Intercellular Homeodomain Protein Transfer. Cell Rep. 2019 07 16; 28(3):712-722.e3.
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Network-based prediction of protein interactions. Nat Commun. 2019 03 18; 10(1):1240.
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APID database: redefining protein-protein interaction experimental evidences and binary interactomes. Database (Oxford). 2019 01 01; 2019.
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Controllability in an islet specific regulatory network identifies the transcriptional factor NFATC4, which regulates Type 2 Diabetes associated genes. NPJ Syst Biol Appl. 2018; 4:25.
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How many human proteoforms are there? Nat Chem Biol. 2018 02 14; 14(3):206-214.
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Network Analysis of UBE3A/E6AP-Associated Proteins Provides Connections to Several Distinct Cellular Processes. J Mol Biol. 2018 03 30; 430(7):1024-1050.
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Protein Interactomics by Two-Hybrid Methods. Methods Mol Biol. 2018; 1794:1-14.
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A framework for exhaustively mapping functional missense variants. Mol Syst Biol. 2017 12 21; 13(12):957.
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Challenges and recommendations for epigenomics in precision health. Nat Biotechnol. 2017 12 08; 35(12):1128-1132.
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Domain-based prediction of the human isoform interactome provides insights into the functional impact of alternative splicing. PLoS Comput Biol. 2017 Aug; 13(8):e1005717.
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Yeast genetic interaction screen of human genes associated with amyotrophic lateral sclerosis: identification of MAP2K5 kinase as a potential drug target. Genome Res. 2017 09; 27(9):1487-1500.
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Dynamic Role of trans Regulation of Gene Expression in Relation to Complex Traits. Am J Hum Genet. 2017 06 01; 100(6):985-986.
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Identifying pathogenicity of human variants via paralog-based yeast complementation. PLoS Genet. 2017 May; 13(5):e1006779.
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Dynamic Role of trans Regulation of Gene Expression in Relation to Complex Traits. Am J Hum Genet. 2017 Apr 06; 100(4):571-580.
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Proteome-Scale Human Interactomics. Trends Biochem Sci. 2017 05; 42(5):342-354.
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HSP90 Shapes the Consequences of Human Genetic Variation. Cell. 2017 Feb 23; 168(5):856-866.e12.
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Genome-Scale Networks Link Neurodegenerative Disease Genes to a-Synuclein through Specific Molecular Pathways. Cell Syst. 2017 02 22; 4(2):157-170.e14.
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In Situ Peroxidase Labeling and Mass-Spectrometry Connects Alpha-Synuclein Directly to Endocytic Trafficking and mRNA Metabolism in Neurons. Cell Syst. 2017 02 22; 4(2):242-250.e4.
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Proteome-scale Binary Interactomics in Human Cells. Mol Cell Proteomics. 2016 Dec; 15(12):3624-3639.
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Playing Hide-and-Seek with Yeast. Cell. 2016 Aug 25; 166(5):1069-1073.
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Mapping transcription factor interactome networks using HaloTag protein arrays. Proc Natl Acad Sci U S A. 2016 07 19; 113(29):E4238-47.
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The transcription factor ERG recruits CCR4-NOT to control mRNA decay and mitotic progression. Nat Struct Mol Biol. 2016 07; 23(7):663-72.
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How much of the human protein interactome remains to be mapped? Sci Signal. 2016 05 10; 9(427):eg7.
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An inter-species protein-protein interaction network across vast evolutionary distance. Mol Syst Biol. 2016 Apr 22; 12(4):865.
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Pooled-matrix protein interaction screens using Barcode Fusion Genetics. Mol Syst Biol. 2016 Apr 22; 12(4):863.
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Survey of variation in human transcription factors reveals prevalent DNA binding changes. Science. 2016 Mar 25; 351(6280):1450-1454.
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An extended set of yeast-based functional assays accurately identifies human disease mutations. Genome Res. 2016 05; 26(5):670-80.
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A Zebrafish Genetic Screen Identifies Neuromedin U as a Regulator of Sleep/Wake States. Neuron. 2016 Feb 17; 89(4):842-56.
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Widespread Expansion of Protein Interaction Capabilities by Alternative Splicing. Cell. 2016 Feb 11; 164(4):805-17.
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Network-based in silico drug efficacy screening. Nat Commun. 2016 Feb 01; 7:10331.
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MECP2 Is a Frequently Amplified Oncogene with a Novel Epigenetic Mechanism That Mimics the Role of Activated RAS in Malignancy. Cancer Discov. 2016 Jan; 6(1):45-58.
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Global Edgetic Rewiring in Cancer Networks. Cell Syst. 2015 Oct 28; 1(4):251-3.
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Widespread macromolecular interaction perturbations in human genetic disorders. Cell. 2015 Apr 23; 161(3):647-660.
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Human gene-centered transcription factor networks for enhancers and disease variants. Cell. 2015 Apr 23; 161(3):661-673.
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Protein domain-level landscape of cancer-type-specific somatic mutations. PLoS Comput Biol. 2015 Mar; 11(3):e1004147.
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Disease networks. Uncovering disease-disease relationships through the incomplete interactome. Science. 2015 Feb 20; 347(6224):1257601.
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A disease module in the interactome explains disease heterogeneity, drug response and captures novel pathways and genes in asthma. Hum Mol Genet. 2015 Jun 01; 24(11):3005-20.
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Selecting causal genes from genome-wide association studies via functionally coherent subnetworks. Nat Methods. 2015 Feb; 12(2):154-9.
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The yeast two-hybrid assay: still finding connections after 25 years. Nat Methods. 2014 Dec; 11(12):1203-6.
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A proteome-scale map of the human interactome network. Cell. 2014 Nov 20; 159(5):1212-1226.
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A chaperome subnetwork safeguards proteostasis in aging and neurodegenerative disease. Cell Rep. 2014 Nov 06; 9(3):1135-50.
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Multiplex single-molecule interaction profiling of DNA-barcoded proteins. Nature. 2014 Nov 27; 515(7528):554-7.
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Convergent targeting of a common host protein-network by pathogen effectors from three kingdoms of life. Cell Host Microbe. 2014 Sep 10; 16(3):364-75.
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Systematic screening reveals a role for BRCA1 in the response to transcription-associated DNA damage. Genes Dev. 2014 Sep 01; 28(17):1957-75.
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Protein interaction network of alternatively spliced isoforms from brain links genetic risk factors for autism. Nat Commun. 2014 Apr 11; 5:3650.
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Systematic identification of pathological lamin A interactors. Mol Biol Cell. 2014 May; 25(9):1493-510.
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Edgotype: a fundamental link between genotype and phenotype. Curr Opin Genet Dev. 2013 Dec; 23(6):649-57.
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Mycobacterium tuberculosis type VII secreted effector EsxH targets host ESCRT to impair trafficking. PLoS Pathog. 2013 Oct; 9(10):e1003734.
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Mapping differential interactomes by affinity purification coupled with data-independent mass spectrometry acquisition. Nat Methods. 2013 Dec; 10(12):1239-45.
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SH3 interactome conserves general function over specific form. Mol Syst Biol. 2013; 9:652.
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Protein interactions of the transcription factor Hoxa1. BMC Dev Biol. 2012 Oct 22; 12:29.
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Identification of FAM111A as an SV40 host range restriction and adenovirus helper factor. PLoS Pathog. 2012; 8(10):e1002949.
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Comparative analysis of virus-host interactomes with a mammalian high-throughput protein complementation assay based on Gaussia princeps luciferase. Methods. 2012 Dec; 58(4):349-59.
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Interpreting cancer genomes using systematic host network perturbations by tumour virus proteins. Nature. 2012 Jul 26; 487(7408):491-5.
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Proto-genes and de novo gene birth. Nature. 2012 Jul 19; 487(7407):370-4.
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The human proteome - a scientific opportunity for transforming diagnostics, therapeutics, and healthcare. Clin Proteomics. 2012 Jul 03; 9(1):6.
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Viral perturbations of host networks reflect disease etiology. PLoS Comput Biol. 2012; 8(6):e1002531.
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CKIP-1 regulates mammalian and zebrafish myoblast fusion. J Cell Sci. 2012 Aug 15; 125(Pt 16):3790-800.
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Host-pathogen interactome mapping for HTLV-1 and -2 retroviruses. Retrovirology. 2012 Mar 29; 9:26.
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Evidence for transcript networks composed of chimeric RNAs in human cells. PLoS One. 2012; 7(1):e28213.
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Interplay between BRCA1 and RHAMM regulates epithelial apicobasal polarization and may influence risk of breast cancer. PLoS Biol. 2011 Nov; 9(11):e1001199.
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A systematic screen for CDK4/6 substrates links FOXM1 phosphorylation to senescence suppression in cancer cells. Cancer Cell. 2011 Nov 15; 20(5):620-34.
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Organization of the synaptonemal complex during meiosis in Caenorhabditis elegans. Genetics. 2011 Oct; 189(2):411-21.
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Evidence for network evolution in an Arabidopsis interactome map. Science. 2011 Jul 29; 333(6042):601-7.
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A public genome-scale lentiviral expression library of human ORFs. Nat Methods. 2011 Jun 26; 8(8):659-61.
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Next-generation sequencing to generate interactome datasets. Nat Methods. 2011 Jun; 8(6):478-80.
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Interactome networks and human disease. Cell. 2011 Mar 18; 144(6):986-98.
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Knocking out multigene redundancies via cycles of sexual assortment and fluorescence selection. Nat Methods. 2011 Feb; 8(2):159-64.
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Protein-protein interactions and networks: forward and reverse edgetics. Methods Mol Biol. 2011; 759:197-213.
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A global protein-lipid interactome map. Mol Syst Biol. 2010 Nov 30; 6:443.
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COT drives resistance to RAF inhibition through MAP kinase pathway reactivation. Nature. 2010 Dec 16; 468(7326):968-72.
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An antibiotic selection marker for nematode transgenesis. Nat Methods. 2010 Sep; 7(9):721-3.
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A genome-wide gene function prediction resource for Drosophila melanogaster. PLoS One. 2010 Aug 12; 5(8):e12139.
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RNAi screening implicates a SKN-1-dependent transcriptional response in stress resistance and longevity deriving from translation inhibition. PLoS Genet. 2010 Aug 05; 6(8).
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The landscape of C. elegans 3'UTRs. Science. 2010 Jul 23; 329(5990):432-5.
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Interactome mapping of the phosphatidylinositol 3-kinase-mammalian target of rapamycin pathway identifies deformed epidermal autoregulatory factor-1 as a new glycogen synthase kinase-3 interactor. Mol Cell Proteomics. 2010 Jul; 9(7):1578-93.
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TACC3-TSC2 maintains nuclear envelope structure and controls cell division. . 2010 Mar 15; 9(6):1143-55.
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High-quality binary interactome mapping. Methods Enzymol. 2010; 470:281-315.
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Pharmacological inhibition of gut-derived serotonin synthesis is a potential bone anabolic treatment for osteoporosis. Nat Med. 2010 Mar; 16(3):308-12.
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A unifying view of 21st century systems biology. FEBS Lett. 2009 Dec 17; 583(24):3891-4.
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Edgetic perturbation models of human inherited disorders. Mol Syst Biol. 2009; 5:321.
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'Edgetic' perturbation of a C. elegans BCL2 ortholog. Nat Methods. 2009 Nov; 6(11):843-9.
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Autophagy induction by the pathogen receptor CD46. . 2009 Oct 22; 6(4):354-66.
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Bayesian modeling of the yeast SH3 domain interactome predicts spatiotemporal dynamics of endocytosis proteins. PLoS Biol. 2009 Oct; 7(10):e1000218.
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Large-scale RACE approach for proactive experimental definition of C. elegans ORFeome. Genome Res. 2009 Dec; 19(12):2334-42.
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Multimodal assessment of protein functional deficiency supports pathogenicity of BRCA1 p.V1688del. Cancer Res. 2009 Sep 01; 69(17):7030-7.
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Metabolic network analysis integrated with transcript verification for sequenced genomes. Nat Methods. 2009 Aug; 6(8):589-92.
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Analysis of the human E2 ubiquitin conjugating enzyme protein interaction network. Genome Res. 2009 Oct; 19(10):1905-11.
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[Systems biology: from yesterday's concepts to tomorrow's discoveries]. Med Sci (Paris). 2009 Jun-Jul; 25(6-7):578-84.
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Shifted Transversal Design smart-pooling for high coverage interactome mapping. Genome Res. 2009 Jul; 19(7):1262-9.
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NuMA-related LIN-5, ASPM-1, calmodulin and dynein promote meiotic spindle rotation independently of cortical LIN-5/GPR/Galpha. Nat Cell Biol. 2009 Mar; 11(3):269-77.
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Array MAPPIT: high-throughput interactome analysis in mammalian cells. J Proteome Res. 2009 Feb; 8(2):877-86.
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Literature-curated protein interaction datasets. Nat Methods. 2009 Jan; 6(1):39-46.
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Empirically controlled mapping of the Caenorhabditis elegans protein-protein interactome network. Nat Methods. 2009 Jan; 6(1):47-54.
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An experimentally derived confidence score for binary protein-protein interactions. Nat Methods. 2009 Jan; 6(1):91-7.
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An empirical framework for binary interactome mapping. Nat Methods. 2009 Jan; 6(1):83-90.
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VirusMINT: a viral protein interaction database. Nucleic Acids Res. 2009 Jan; 37(Database issue):D669-73.
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High-quality binary protein interaction map of the yeast interactome network. Science. 2008 Oct 03; 322(5898):104-10.
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A protein domain-based interactome network for C. elegans early embryogenesis. Cell. 2008 Aug 08; 134(3):534-45.
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Genome-wide coactivation analysis of PGC-1alpha identifies BAF60a as a regulator of hepatic lipid metabolism. Cell Metab. 2008 Aug; 8(2):105-17.
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Networking metabolites and diseases. Proc Natl Acad Sci U S A. 2008 Jul 22; 105(29):9849-50.
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A mitochondrial protein compendium elucidates complex I disease biology. Cell. 2008 Jul 11; 134(1):112-23.
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2020 vision for biology: the role of plants in addressing grand challenges in biology. Mol Plant. 2008 Jul; 1(4):561-3.
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Isoform discovery by targeted cloning, 'deep-well' pooling and parallel sequencing. Nat Methods. 2008 Jul; 5(7):597-600.
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Efficient targeted transcript discovery via array-based normalization of RACE libraries. Nat Methods. 2008 Jul; 5(7):629-35.
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Revisiting the Saccharomyces cerevisiae predicted ORFeome. Genome Res. 2008 Aug; 18(8):1294-303.
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Systems engineering to systems biology. Mol Syst Biol. 2008; 4:185.
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Broadening the horizon--level 2.5 of the HUPO-PSI format for molecular interactions. BMC Biol. 2007 Oct 09; 5:44.
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Network modeling links breast cancer susceptibility and centrosome dysfunction. Nat Genet. 2007 Nov; 39(11):1338-49.
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Drug-target network. Nat Biotechnol. 2007 Oct; 25(10):1119-26.
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The minimum information required for reporting a molecular interaction experiment (MIMIx). Nat Biotechnol. 2007 Aug; 25(8):894-8.
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Fas-activated serine/threonine phosphoprotein (FAST) is a regulator of alternative splicing. Proc Natl Acad Sci U S A. 2007 Jul 03; 104(27):11370-5.
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Integrative genomic approaches identify IKBKE as a breast cancer oncogene. Cell. 2007 Jun 15; 129(6):1065-79.
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Confirmation of organized modularity in the yeast interactome. PLoS Biol. 2007 Jun; 5(6):e153.
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The human disease network. Proc Natl Acad Sci U S A. 2007 May 22; 104(21):8685-90.
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Genome-scale analysis of in vivo spatiotemporal promoter activity in Caenorhabditis elegans. Nat Biotechnol. 2007 Jun; 25(6):663-8.
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Epstein-Barr virus and virus human protein interaction maps. Proc Natl Acad Sci U S A. 2007 May 01; 104(18):7606-11.
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Large-scale RNAi screens identify novel genes that interact with the C. elegans retinoblastoma pathway as well as splicing-related components with synMuv B activity. BMC Dev Biol. 2007 Apr 06; 7:30.
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Insight into transcription factor gene duplication from Caenorhabditis elegans Promoterome-driven expression patterns. BMC Genomics. 2007 Jan 23; 8:27.
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hORFeome v3.1: a resource of human open reading frames representing over 10,000 human genes. Genomics. 2007 Mar; 89(3):307-15.
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Association of Dishevelled with the clathrin AP-2 adaptor is required for Frizzled endocytosis and planar cell polarity signaling. Dev Cell. 2007 Jan; 12(1):129-41.
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InSite: a computational method for identifying protein-protein interaction binding sites on a proteome-wide scale. Genome Biol. 2007; 8(9):R192.
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QUICKstep and GS-TAP: new moves for protein-interaction analysis. Nat Methods. 2006 Dec; 3(12):975-6.
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The 14-3-3 protein FTT-2 regulates DAF-16 in Caenorhabditis elegans. Dev Biol. 2007 Jan 01; 301(1):82-91.
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C. elegans network biology: a beginning. WormBook. 2006 Aug 21; 1-20.
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C. elegans GLA-3 is a novel component of the MAP kinase MPK-1 signaling pathway required for germ cell survival. Genes Dev. 2006 Aug 15; 20(16):2279-92.
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Intrinsic disorder is a common feature of hub proteins from four eukaryotic interactomes. PLoS Comput Biol. 2006 Aug 04; 2(8):e100.
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A protein-protein interaction network for human inherited ataxias and disorders of Purkinje cell degeneration. Cell. 2006 May 19; 125(4):801-14.
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From genome to proteome: developing expression clone resources for the human genome. Hum Mol Genet. 2006 Apr 15; 15 Spec No 1:R31-43.
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[Network "interactome"]. Bull Mem Acad R Med Belg. 2006; 161(3-4):199-210; discussion 210-2.
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Towards a proteome-scale map of the human protein-protein interaction network. Nature. 2005 Oct 20; 437(7062):1173-8.
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Interactome: gateway into systems biology. Hum Mol Genet. 2005 Oct 15; 14 Spec No. 2:R171-81.
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Pooled ORF expression technology (POET): using proteomics to screen pools of open reading frames for protein expression. Mol Cell Proteomics. 2005 Nov; 4(11):1647-52.
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Predictive models of molecular machines involved in Caenorhabditis elegans early embryogenesis. Nature. 2005 Aug 11; 436(7052):861-5.
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Systematic analysis of genes required for synapse structure and function. Nature. 2005 Jul 28; 436(7050):510-7.
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lin-8, which antagonizes Caenorhabditis elegans Ras-mediated vulval induction, encodes a novel nuclear protein that interacts with the LIN-35 Rb protein. Genetics. 2005 Nov; 171(3):1017-31.
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Local modeling of global interactome networks. Bioinformatics. 2005 Sep 01; 21(17):3548-57.
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Effect of sampling on topology predictions of protein-protein interaction networks. Nat Biotechnol. 2005 Jul; 23(7):839-44.
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Perturbing interactions. Nat Methods. 2005 Jun; 2(6):412-4.
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Biochemical clustering of monomeric GTPases of the Ras superfamily. Mol Cell Proteomics. 2005 Jul; 4(7):936-44.
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Closing in on the C. elegans ORFeome by cloning TWINSCAN predictions. Genome Res. 2005 Apr; 15(4):577-82.
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Functional genomic analysis of RNA interference in C. elegans. Science. 2005 May 20; 308(5725):1164-7.
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A gene expression fingerprint of C. elegans embryonic motor neurons. BMC Genomics. 2005 Mar 21; 6:42.
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Interactome modeling. FEBS Lett. 2005 Mar 21; 579(8):1834-8.
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New genes with roles in the C. elegans embryo revealed using RNAi of ovary-enriched ORFeome clones. Genome Res. 2005 Feb; 15(2):250-9.
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Combining biological networks to predict genetic interactions. Proc Natl Acad Sci U S A. 2004 Nov 02; 101(44):15682-7.
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A gateway-compatible yeast one-hybrid system. Genome Res. 2004 Oct; 14(10B):2093-101.
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Feasibility of genome-scale construction of promoter::reporter gene fusions for expression in Caenorhabditis elegans using a multisite gateway recombination system. Genome Res. 2004 Oct; 14(10B):2070-5.
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Generation of the Brucella melitensis ORFeome version 1.1. Genome Res. 2004 Oct; 14(10B):2201-6.
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Toward improving Caenorhabditis elegans phenome mapping with an ORFeome-based RNAi library. Genome Res. 2004 Oct; 14(10B):2162-8.
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ORFeome cloning and systems biology: standardized mass production of the parts from the parts-list. Genome Res. 2004 Oct; 14(10B):2001-9.
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C. elegans ORFeome version 3.1: increasing the coverage of ORFeome resources with improved gene predictions. Genome Res. 2004 Oct; 14(10B):2064-9.
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Academia-industry collaboration: an integral element for building "omic" resources. Genome Res. 2004 Oct; 14(10B):2010-4.
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Human ORFeome version 1.1: a platform for reverse proteomics. Genome Res. 2004 Oct; 14(10B):2128-35.
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High-throughput expression of C. elegans proteins. Genome Res. 2004 Oct; 14(10B):2102-10.
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A first version of the Caenorhabditis elegans Promoterome. Genome Res. 2004 Oct; 14(10B):2169-75.
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Evidence for dynamically organized modularity in the yeast protein-protein interaction network. Nature. 2004 Jul 01; 430(6995):88-93.
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Annotation transfer between genomes: protein-protein interologs and protein-DNA regulogs. Genome Res. 2004 Jun; 14(6):1107-18.
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Identification of critical domains and putative partners for the Caenorhabditis elegans spindle component LIN-5. Mol Genet Genomics. 2004 Jun; 271(5):532-44.
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Increasing specificity in high-throughput yeast two-hybrid experiments. Methods. 2004 Apr; 32(4):363-70.
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Systematic interactome mapping and genetic perturbation analysis of a C. elegans TGF-beta signaling network. Mol Cell. 2004 Feb 27; 13(4):469-82.
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Role for the pleckstrin homology domain-containing protein CKIP-1 in phosphatidylinositol 3-kinase-regulated muscle differentiation. Mol Cell Biol. 2004 Feb; 24(3):1245-55.
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The HUPO PSI's molecular interaction format--a community standard for the representation of protein interaction data. Nat Biotechnol. 2004 Feb; 22(2):177-83.
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ORFeome projects: gateway between genomics and omics. Curr Opin Chem Biol. 2004 Feb; 8(1):20-5.
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BRCA1/BARD1 orthologs required for DNA repair in Caenorhabditis elegans. Curr Biol. 2004 Jan 06; 14(1):33-9.
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A map of the interactome network of the metazoan C. elegans. Science. 2004 Jan 23; 303(5657):540-3.
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Integrating 'omic' information: a bridge between genomics and systems biology. Trends Genet. 2003 Oct; 19(10):551-60.
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RNAi on the apoptosis TRAIL: the mammalian cell genetic screen comes of age. Dev Cell. 2003 Oct; 5(4):534-5.
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BTB proteins are substrate-specific adaptors in an SCF-like modular ubiquitin ligase containing CUL-3. Nature. 2003 Sep 18; 425(6955):316-21.
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High-throughput expression, purification, and characterization of recombinant Caenorhabditis elegans proteins. Biochem Biophys Res Commun. 2003 Aug 08; 307(4):928-34.
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C. elegans ORFeome version 1.1: experimental verification of the genome annotation and resource for proteome-scale protein expression. Nat Genet. 2003 May; 34(1):35-41.
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WorfDB: the Caenorhabditis elegans ORFeome Database. Nucleic Acids Res. 2003 Jan 01; 31(1):237-40.
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Caenorhabditis elegans HUS-1 is a DNA damage checkpoint protein required for genome stability and EGL-1-mediated apoptosis. Curr Biol. 2002 Nov 19; 12(22):1908-18.
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Integrating interactome, phenome, and transcriptome mapping data for the C. elegans germline. Curr Biol. 2002 Nov 19; 12(22):1952-8.
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Structural genomics: a pipeline for providing structures for the biologist. Protein Sci. 2002 Apr; 11(4):723-38.
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MEX-3 interacting proteins link cell polarity to asymmetric gene expression in Caenorhabditis elegans. Development. 2002 Feb; 129(3):747-59.
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Combined functional genomic maps of the C. elegans DNA damage response. Science. 2002 Jan 04; 295(5552):127-31.
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Integrated version of reverse two-hybrid system for the postproteomic era. Methods Enzymol. 2002; 350:525-45.
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Correlation between transcriptome and interactome mapping data from Saccharomyces cerevisiae. Nat Genet. 2001 Dec; 29(4):482-6.
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Identification of potential interaction networks using sequence-based searches for conserved protein-protein interactions or "interologs". Genome Res. 2001 Dec; 11(12):2120-6.
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Evidence that HAX-1 is an interleukin-1 alpha N-terminal binding protein. Cytokine. 2001 Aug 07; 15(3):122-37.
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Histone deacetylase-dependent transcriptional repression by pRB in yeast occurs independently of interaction through the LXCXE binding cleft. Proc Natl Acad Sci U S A. 2001 Jul 17; 98(15):8720-5.
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High-throughput yeast two-hybrid assays for large-scale protein interaction mapping. Methods. 2001 Jul; 24(3):297-306.
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Open-reading-frame sequence tags (OSTs) support the existence of at least 17,300 genes in C. elegans. Nat Genet. 2001 Mar; 27(3):332-6.
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A biological atlas of functional maps. Cell. 2001 Feb 09; 104(3):333-9.
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Use of protein-interaction maps to formulate biological questions. Curr Opin Chem Biol. 2001 Feb; 5(1):57-62.
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Protein interaction maps for model organisms. Nat Rev Mol Cell Biol. 2001 Jan; 2(1):55-62.
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Yeast two-hybrid systems and protein interaction mapping projects for yeast and worm. Yeast. 2000 Jun 30; 17(2):88-94.
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Cables links Cdk5 and c-Abl and facilitates Cdk5 tyrosine phosphorylation, kinase upregulation, and neurite outgrowth. Neuron. 2000 Jun; 26(3):633-46.
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Protein interaction mapping in C. elegans using proteins involved in vulval development. Science. 2000 Jan 07; 287(5450):116-22.
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A green fluorescent protein-based reverse two-hybrid system: application to the characterization of large numbers of potential protein-protein interactions. Methods Enzymol. 2000; 328:74-88.
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GATEWAY recombinational cloning: application to the cloning of large numbers of open reading frames or ORFeomes. Methods Enzymol. 2000; 328:575-92.
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A genetic strategy to eliminate self-activator baits prior to high-throughput yeast two-hybrid screens. Genome Res. 1999 Nov; 9(11):1128-34.
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Prospects for drug screening using the reverse two-hybrid system. Trends Biotechnol. 1999 Sep; 17(9):374-81.
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Yeast forward and reverse 'n'-hybrid systems. Nucleic Acids Res. 1999 Feb 15; 27(4):919-29.
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A model of elegance. Am J Hum Genet. 1998 Oct; 63(4):955-61.
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A novel human DnaJ protein, hTid-1, a homolog of the Drosophila tumor suppressor protein Tid56, can interact with the human papillomavirus type 16 E7 oncoprotein. Virology. 1998 Jul 20; 247(1):74-85.
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Human papillomavirus 16 E6 oncoprotein binds to interferon regulatory factor-3 and inhibits its transcriptional activity. Genes Dev. 1998 Jul 01; 12(13):2061-72.
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Two classes of human papillomavirus type 16 E1 mutants suggest pleiotropic conformational constraints affecting E1 multimerization, E2 interaction, and interaction with cellular proteins. J Virol. 1997 Aug; 71(8):5942-51.
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Mapping and characterization of the interaction domains of human papillomavirus type 16 E1 and E2 proteins. J Virol. 1997 Feb; 71(2):891-9.
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A novel member of the RING finger family, KRIP-1, associates with the KRAB-A transcriptional repressor domain of zinc finger proteins. Proc Natl Acad Sci U S A. 1996 Dec 24; 93(26):15299-304.
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Reverse two-hybrid and one-hybrid systems to detect dissociation of protein-protein and DNA-protein interactions. Proc Natl Acad Sci U S A. 1996 Sep 17; 93(19):10315-20.
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Genetic characterization of a mammalian protein-protein interaction domain by using a yeast reverse two-hybrid system. Proc Natl Acad Sci U S A. 1996 Sep 17; 93(19):10321-6.
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RBF, a novel RB-related gene that regulates E2F activity and interacts with cyclin E in Drosophila. Genes Dev. 1996 May 15; 10(10):1206-18.
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Truncated WT1 mutants alter the subnuclear localization of the wild-type protein. Proc Natl Acad Sci U S A. 1995 Dec 19; 92(26):11960-4.
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E2F-4 and E2F-5, two members of the E2F family, are expressed in the early phases of the cell cycle. Proc Natl Acad Sci U S A. 1995 Mar 14; 92(6):2403-7.
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A functional assay for heterozygous mutations in the GTPase activating protein related domain of the neurofibromatosis type 1 gene. Oncogene. 1995 Mar 02; 10(5):841-7.
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The retinoblastoma protein binds to a family of E2F transcription factors. Mol Cell Biol. 1993 Dec; 13(12):7813-25.
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Screening patients for heterozygous p53 mutations using a functional assay in yeast. Nat Genet. 1993 Oct; 5(2):124-9.
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A cDNA encoding a pRB-binding protein with properties of the transcription factor E2F. Cell. 1992 Jul 24; 70(2):337-50.
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