MARC contact VIDAL

Summary

Affiliation: Harvard University
Country: USA

Publications

  1. pmc An experimentally derived confidence score for binary protein-protein interactions
    Pascal Braun
    Center for Cancer Systems Biology and Department of Cancer Biology, Dana Farber Cancer Institute, 44 Binney Street, Boston, MA 02115, USA
    Nat Methods 6:91-7. 2009
  2. pmc An empirical framework for binary interactome mapping
    Kavitha Venkatesan
    Center for Cancer Systems Biology and Department of Cancer Biology, Dana Farber Cancer Institute, 1 Jimmy Fund Way, Boston, MA 02115, USA
    Nat Methods 6:83-90. 2009
  3. pmc Edgetic perturbation models of human inherited disorders
    Quan Zhong
    Center for Cancer Systems Biology CCSB and Department of Cancer Biology, Dana Farber Cancer Institute, Boston, MA 02115, USA
    Mol Syst Biol 5:321. 2009
  4. pmc Systems engineering to systems biology
    Muhammed A Yildirim
    Center for Cancer Systems Biology CCSB, Dana Farber Cancer Institute, Harvard Medical School, Boston, MA, USA
    Mol Syst Biol 4:185. 2008
  5. pmc 'Edgetic' perturbation of a C. elegans BCL2 ortholog
    Matija Dreze
    Center for Cancer Systems Biology CCSB and Department of Cancer Biology, Dana Farber Cancer Institute, Boston, Massachusetts, USA
    Nat Methods 6:843-9. 2009
  6. pmc Proto-genes and de novo gene birth
    Anne Ruxandra Carvunis
    Center for Cancer Systems Biology and Department of Cancer Biology, Dana Farber Cancer Institute, Boston, Massachusetts 02215, USA
    Nature 487:370-4. 2012
  7. pmc Viral perturbations of host networks reflect disease etiology
    Natali Gulbahce
    Center for Complex Networks Research CCNR and Department of Physics, Northeastern University, Boston, Massachusetts, United States of America
    PLoS Comput Biol 8:e1002531. 2012
  8. pmc A public genome-scale lentiviral expression library of human ORFs
    Xiaoping Yang
    RNA interference RNAi Platform, Broad Institute of Harvard and Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
    Nat Methods 8:659-61. 2011
  9. pmc The human proteome - a scientific opportunity for transforming diagnostics, therapeutics, and healthcare
    Marc Vidal
    University of Michigan, Ann Arbor, MI, USA
    Clin Proteomics 9:6. 2012
  10. pmc Protein interactions of the transcription factor Hoxa1
    Barbara Lambert
    Molecular and Cellular Animal Embryology Group, Life Sciences Institute ISV, Universite Catholique de Louvain, Louvain la Neuve, 1348, Belgium
    BMC Dev Biol 12:29. 2012

Detail Information

Publications87

  1. pmc An experimentally derived confidence score for binary protein-protein interactions
    Pascal Braun
    Center for Cancer Systems Biology and Department of Cancer Biology, Dana Farber Cancer Institute, 44 Binney Street, Boston, MA 02115, USA
    Nat Methods 6:91-7. 2009
    ..This general approach will allow a systematic and empirical assignment of confidence scores to all individual protein-protein interactions in interactome networks...
  2. pmc An empirical framework for binary interactome mapping
    Kavitha Venkatesan
    Center for Cancer Systems Biology and Department of Cancer Biology, Dana Farber Cancer Institute, 1 Jimmy Fund Way, Boston, MA 02115, USA
    Nat Methods 6:83-90. 2009
    ....
  3. pmc Edgetic perturbation models of human inherited disorders
    Quan Zhong
    Center for Cancer Systems Biology CCSB and Department of Cancer Biology, Dana Farber Cancer Institute, Boston, MA 02115, USA
    Mol Syst Biol 5:321. 2009
    ..Edgetic network perturbation models might improve both the understanding of dissemination of disease alleles in human populations and the development of molecular therapeutic strategies...
  4. pmc Systems engineering to systems biology
    Muhammed A Yildirim
    Center for Cancer Systems Biology CCSB, Dana Farber Cancer Institute, Harvard Medical School, Boston, MA, USA
    Mol Syst Biol 4:185. 2008
  5. pmc 'Edgetic' perturbation of a C. elegans BCL2 ortholog
    Matija Dreze
    Center for Cancer Systems Biology CCSB and Department of Cancer Biology, Dana Farber Cancer Institute, Boston, Massachusetts, USA
    Nat Methods 6:843-9. 2009
    ..This approach is amenable to higher throughput and is particularly applicable to interactome network analysis in organisms for which transgenesis is straightforward...
  6. pmc Proto-genes and de novo gene birth
    Anne Ruxandra Carvunis
    Center for Cancer Systems Biology and Department of Cancer Biology, Dana Farber Cancer Institute, Boston, Massachusetts 02215, USA
    Nature 487:370-4. 2012
    ..Our work illustrates that evolution exploits seemingly dispensable sequences to generate adaptive functional innovation...
  7. pmc Viral perturbations of host networks reflect disease etiology
    Natali Gulbahce
    Center for Complex Networks Research CCNR and Department of Physics, Northeastern University, Boston, Massachusetts, United States of America
    PLoS Comput Biol 8:e1002531. 2012
    ..The topological proximity found between cellular targets of viral proteins and disease genes was exploited to uncover a novel pathway linking HPV to Fanconi anemia...
  8. pmc A public genome-scale lentiviral expression library of human ORFs
    Xiaoping Yang
    RNA interference RNAi Platform, Broad Institute of Harvard and Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
    Nat Methods 8:659-61. 2011
    ..Using this ORFeome resource, we created a genome-scale expression collection in a lentiviral vector, thereby enabling both targeted experiments and high-throughput screens in diverse cell types...
  9. pmc The human proteome - a scientific opportunity for transforming diagnostics, therapeutics, and healthcare
    Marc Vidal
    University of Michigan, Ann Arbor, MI, USA
    Clin Proteomics 9:6. 2012
    ..This executive summary and the following full report describe the main discussions and outcomes of the workshop...
  10. pmc Protein interactions of the transcription factor Hoxa1
    Barbara Lambert
    Molecular and Cellular Animal Embryology Group, Life Sciences Institute ISV, Universite Catholique de Louvain, Louvain la Neuve, 1348, Belgium
    BMC Dev Biol 12:29. 2012
    ..Their mode of action remains scantily documented. While other families of transcription factors, like Smad or Stat, are known cell signaling transducers, such a function has never been squarely addressed for Hox proteins...
  11. pmc Host-pathogen interactome mapping for HTLV-1 and -2 retroviruses
    Nicolas Simonis
    Center for Cancer Systems Biology CCSB and Department of Cancer Biology, Dana Farber Cancer Institute, 450 Brookline Ave, Boston, MA 02215, USA
    Retrovirology 9:26. 2012
    ..Identifying shared and distinct host-pathogen protein interaction profiles for these two viruses would enlighten how they exploit distinctive or common strategies to subvert cellular pathways toward disease progression...
  12. pmc InSite: a computational method for identifying protein-protein interaction binding sites on a proteome-wide scale
    Haidong Wang
    Computer Science Department, Stanford University, Serra Mall, Stanford, CA 94305, USA
    Genome Biol 8:R192. 2007
    ..Several regions containing disease-causing mutations or cancer polymorphisms in human are predicted to be binding for protein pairs related to the disease, which suggests novel mechanistic hypotheses for several diseases...
  13. pmc A gene expression fingerprint of C. elegans embryonic motor neurons
    Rebecca M Fox
    Department of Cell and Developmental Biology, Vanderbilt University, Nashville, TN 37232 8240, USA
    BMC Genomics 6:42. 2005
    ..Here we describe a powerful strategy, Micro-Array Profiling of C. elegans cells (MAPCeL), and confirm that this approach provides a comprehensive gene expression profile of unc-4::GFP motor neurons in vivo...
  14. pmc Insight into transcription factor gene duplication from Caenorhabditis elegans Promoterome-driven expression patterns
    John S Reece-Hoyes
    Institute of Integrative and Comparative Biology, Faculty of Biological Sciences, University of Leeds, Clarendon Way, Leeds, LS2 9JT, West Yorkshire, UK
    BMC Genomics 8:27. 2007
    ..elegans transcription factor genes was examined, in vivo, with a reporter gene approach...
  15. pmc 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
    Julian Ceron
    Massachusetts General Hospital Cancer Center and Harvard Medical School, Charlestown, MA 02129, USA
    BMC Dev Biol 7:30. 2007
    ..For instance, lin-35 Rb is a synthetic multivulva (synMuv) class B gene, which causes a multivulva phenotype when inactivated simultaneously with a class A or C synMuv gene...
  16. pmc Broadening the horizon--level 2.5 of the HUPO-PSI format for molecular interactions
    Samuel Kerrien
    European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, UK
    BMC Biol 5:44. 2007
    ....
  17. ncbi request reprint Interactome modeling
    Marc Vidal
    Center for Cancer Systems Biology and Department of Cancer Biology, Dana Farber Cancer Institute, Harvard Medical School, 44 Binney Street, Boston, MA 02115, USA
    FEBS Lett 579:1834-8. 2005
    ..This review focuses on an early attempt at mapping a multicellular interactome network and on the lessons learned from that attempt...
  18. doi request reprint A unifying view of 21st century systems biology
    Marc Vidal
    Center for Cancer Systems Biology CCSB and Department of Cancer Biology, Dana Farber Cancer Institute, Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
    FEBS Lett 583:3891-4. 2009
    ....
  19. pmc Interactome networks and human disease
    Marc Vidal
    Center for Cancer Systems Biology and Department of Cancer Biology, Dana Farber Cancer Institute, Boston, MA 02215, USA
    Cell 144:986-98. 2011
    ....
  20. pmc C. elegans ORFeome version 3.1: increasing the coverage of ORFeome resources with improved gene predictions
    Philippe Lamesch
    Center for Cancer Systems Biology and Department of Cancer Biology, Dana Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts 02115, USA
    Genome Res 14:2064-9. 2004
    ..elegans ORFeome, and likely the ORFeomes of other multicellular organisms, needs to be an iterative process that requires multiple rounds of experimental validation together with gradually improving gene predictions...
  21. ncbi request reprint C. elegans ORFeome version 1.1: experimental verification of the genome annotation and resource for proteome-scale protein expression
    Jerome Reboul
    Dana Farber Cancer Institute and Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115, USA
    Nat Genet 34:35-41. 2003
    ..We suggest that similar ORFeome projects will be valuable for other organisms, including humans...
  22. pmc A map of the interactome network of the metazoan C. elegans
    Siming Li
    Dana Farber Cancer Institute and Department of Genetics, Harvard Medical School, 44 Binney Street, Boston, MA 02115, USA
    Science 303:540-3. 2004
    ..Topological and biological features of this interactome network, as well as its integration with phenome and transcriptome data sets, lead to numerous biological hypotheses...
  23. ncbi request reprint Combined functional genomic maps of the C. elegans DNA damage response
    Simon J Boulton
    Dana Farber Cancer Institute and Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
    Science 295:127-31. 2002
    ..Thus, the combination of functional genomic mapping approaches in model organisms may facilitate the identification and characterization of genes involved in cancer and, perhaps, other human diseases...
  24. ncbi request reprint hORFeome v3.1: a resource of human open reading frames representing over 10,000 human genes
    Philippe Lamesch
    Center for Cancer Systems Biology and Department of Cancer Biology, Dana Farber Cancer Institute, and Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
    Genomics 89:307-15. 2007
    ..dfci.harvard.edu). This expansion of the original ORFeome resource greatly increases the potential experimental search space for large-scale proteomics studies, which will lead to the generation of more comprehensive datasets...
  25. ncbi request reprint Network modeling links breast cancer susceptibility and centrosome dysfunction
    Miguel Angel Pujana
    Center for Cancer Systems Biology CCSB, Dana Farber Cancer Institute and Department of Genetics, Harvard Medical School, 44 Binney St, Boston, Massachusetts 02115, USA
    Nat Genet 39:1338-49. 2007
    ..Our network modeling strategy should be useful for the discovery of additional cancer-associated genes...
  26. pmc High-quality binary protein interaction map of the yeast interactome network
    Haiyuan Yu
    Center for Cancer Systems Biology CCSB, Dana Farber Cancer Institute, Boston, MA 02115, USA
    Science 322:104-10. 2008
    ..Rather than correlating with essentiality, protein connectivity correlates with genetic pleiotropy...
  27. ncbi request reprint Functional genomic analysis of RNA interference in C. elegans
    John K Kim
    Department of Molecular Biology, Massachusetts General Hospital, Boston, MA 02114, USA
    Science 308:1164-7. 2005
    ..We demonstrate that some of these genes are also required for germline and somatic transgene silencing. Moreover, the physical interactions among these potential RNAi factors suggest links to other RNA-dependent gene regulatory pathways...
  28. ncbi request reprint Systematic interactome mapping and genetic perturbation analysis of a C. elegans TGF-beta signaling network
    Muneesh Tewari
    Center for Cancer Systems Biology, Dana Farber Cancer Institute, Boston, Massachusetts 02115, USA
    Mol Cell 13:469-82. 2004
    ..Integrating interactome maps with systematic genetic perturbations may be useful for developing a systems biology approach to this and other signaling modules...
  29. ncbi request reprint Increasing specificity in high-throughput yeast two-hybrid experiments
    Pierre Olivier Vidalain
    Dana Farber Cancer Institute and Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
    Methods 32:363-70. 2004
    ..Contaminating plasmids are eliminated by extended culture of yeast cells under positive selection for the interaction, allowing the identification of the true interaction partner...
  30. doi request reprint [Systems biology: from yesterday's concepts to tomorrow's discoveries]
    Anne Ruxandra Carvunis
    Center for Cancer Systems Biology, Department of Cancer Biology, Dana Farber Cancer Institute, 1, Jimmy Fund Way, Boston, Massachusetts 02115, USA
    Med Sci (Paris) 25:578-84. 2009
    ....
  31. pmc Literature-curated protein interaction datasets
    Michael E Cusick
    Center for Cancer Systems Biology and Department of Cancer Biology, Dana Farber Cancer Institute, 44 Binney Street, Boston, Massachusetts 02115, USA
    Nat Methods 6:39-46. 2009
    ..In an evaluation of existing curation of protein interaction experiments reported in the literature, we found that curation can be error-prone and possibly of lower quality than commonly assumed...
  32. pmc Multimodal assessment of protein functional deficiency supports pathogenicity of BRCA1 p.V1688del
    Arcangela De Nicolo
    Department of Cancer Biology, Dana Farber Cancer Institute, Boston, MA 02115, USA
    Cancer Res 69:7030-7. 2009
    ..Multimodal analyses like ours could advance understanding of tumor suppression by BRCA1 and ultimately contribute to developing efficient strategies for screening and characterization of VUS...
  33. pmc Isoform discovery by targeted cloning, 'deep-well' pooling and parallel sequencing
    Kourosh Salehi-Ashtiani
    Center for Cancer Systems Biology, Department of Cancer Biology, Dana Farber Cancer Institute, 44 Binney Street, Boston, Massachusetts 02115, USA
    Nat Methods 5:597-600. 2008
    ..This ORFeome discovery pipeline will be applicable to any eukaryotic species with a sequenced genome...
  34. pmc Large-scale RACE approach for proactive experimental definition of C. elegans ORFeome
    Kourosh Salehi-Ashtiani
    Center for Cancer Systems Biology CCSB and Department of Cancer Biology, Dana Farber Cancer Institute, and Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115, USA
    Genome Res 19:2334-42. 2009
    ..Our results show that as much as 20% of the C. elegans genome may be incorrectly annotated. Many annotation errors could be corrected proactively with our large-scale RACE platform...
  35. pmc Networking metabolites and diseases
    Pascal Braun
    Center for Cancer Systems Biology and Department of Cancer Biology, Dana Farber Cancer Institute, 44 Binney Street, Boston, MA 02115, USA
    Proc Natl Acad Sci U S A 105:9849-50. 2008
  36. ncbi request reprint Integrating 'omic' information: a bridge between genomics and systems biology
    Hui Ge
    Dana Farber Cancer Institute and Department of Genetics, Harvard Medical School, SM858, 44 Binney Street, Boston, MA 02115, USA
    Trends Genet 19:551-60. 2003
    ..Here, we review the recent development of strategies for such integration and we argue that these will be important for a systems approach to modular biology...
  37. ncbi request reprint Towards a proteome-scale map of the human protein-protein interaction network
    Jean François Rual
    Center for Cancer Systems Biology and Department of Cancer Biology, Dana Farber Cancer Institute, Harvard Medical School, 44 Binney Street, Boston, Massachusetts 02115, USA
    Nature 437:1173-8. 2005
    ..This work represents an important step towards a systematic and comprehensive human interactome project...
  38. ncbi request reprint Interactome: gateway into systems biology
    Michael E Cusick
    Center for Cancer Systems Biology and Department of Cancer Biology, Dana Farber Cancer Institute, 44 Binney Street, Boston, MA 02115, USA
    Hum Mol Genet 14:R171-81. 2005
    ..Such maps are also a useful resource to predict the function(s) of thousands of genes...
  39. pmc Human ORFeome version 1.1: a platform for reverse proteomics
    Jean François Rual
    Center for Cancer Systems Biology and Department of Cancer Biology, Dana Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts 02115, USA
    Genome Res 14:2128-35. 2004
    ..1 represents a central resource for the cloning of large sets of human ORFs in various settings for functional proteomics of many types, and will serve as the foundation for subsequent improved versions of the human ORFeome...
  40. ncbi request reprint Academia-industry collaboration: an integral element for building "omic" resources
    David E Hill
    Center for Cancer Systems Biology, Department of Cancer Biology, Dana Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts 02115, USA
    Genome Res 14:2010-4. 2004
  41. pmc A first version of the Caenorhabditis elegans Promoterome
    Denis Dupuy
    Center for Cancer Systems Biology and Department of Cancer Biology, Dana Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts 02115, USA
    Genome Res 14:2169-75. 2004
    ....
  42. ncbi request reprint Effect of sampling on topology predictions of protein-protein interaction networks
    Jing Dong J Han
    Center for Cancer Systems Biology and Department of Cancer Biology, Dana Farber Cancer Institute, Boston, Massachusetts 02115, USA
    Nat Biotechnol 23:839-44. 2005
    ..We conclude that given the current limited coverage levels, the observed scale-free topology of existing interactome maps cannot be confidently extrapolated to complete interactomes...
  43. ncbi request reprint Integrating interactome, phenome, and transcriptome mapping data for the C. elegans germline
    Albertha J M Walhout
    Dana Farber Cancer Institute and Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
    Curr Biol 12:1952-8. 2002
    ..Similar integration of interactome, phenome, and transcriptome data should be possible for other biological processes in the nematode and for other organisms, including humans...
  44. pmc WorfDB: the Caenorhabditis elegans ORFeome Database
    Philippe Vaglio
    Department of Cancer Biology, Dana Farber Cancer Institute and Harvard Medical School, Smith 858, 1 Jimmy Fund Way, Boston, MA 02115, USA
    Nucleic Acids Res 31:237-40. 2003
    ..The database contains this OST information along with data pertinent to the cloning process. WorfDB could serve as a model database for other metazoan ORFeome cloning projects...
  45. pmc Empirically controlled mapping of the Caenorhabditis elegans protein-protein interactome network
    Nicolas Simonis
    Center for Cancer Systems Biology and Department of Cancer Biology, Dana Farber Cancer Institute, 44 Binney Street, Boston, MA 02115, USA
    Nat Methods 6:47-54. 2009
    ..Comparison with other types of functional genomic data shows the complementarity of distinct experimental approaches in predicting different functional relationships between genes or proteins..
  46. pmc Toward improving Caenorhabditis elegans phenome mapping with an ORFeome-based RNAi library
    Jean François Rual
    Center for Cancer Systems Biology and Department of Cancer Biology, Dana Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts 02115, USA
    Genome Res 14:2162-8. 2004
    ..The versatility inherent to the Gateway system suggests that additional HT-RNAi libraries can now be readily generated to perform gene knockdowns under various conditions, increasing the possibilities for phenome mapping in C. elegans...
  47. ncbi request reprint Genome-scale analysis of in vivo spatiotemporal promoter activity in Caenorhabditis elegans
    Denis Dupuy
    Center for Cancer Systems Biology, Department of Cancer Biology, Dana Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts 02115, USA
    Nat Biotechnol 25:663-8. 2007
    ..Moreover, integration of this data set with C. elegans protein-protein interactome data sets enables prediction of anatomical and temporal interaction territories between protein partners...
  48. ncbi request reprint ORFeome projects: gateway between genomics and omics
    Jean François Rual
    Center for Cancer Systems Biology and Department of Cancer Biology, Dana Farber Cancer Institute and Department of Genetics, Harvard Medical School, 44 Binney Street, Boston, MA 02115, USA
    Curr Opin Chem Biol 8:20-5. 2004
    ..The creation of such ORFeome resources using novel technologies for cloning and expressing entire proteomes constitutes an effective gateway from whole genome sequencing efforts to downstream 'omics' applications...
  49. ncbi request reprint Drug-target network
    Muhammed A Yildirim
    Center for Cancer Systems Biology CCSB, Harvard Medical School, 44 Binney St, Boston, Massachusetts 02115, USA
    Nat Biotechnol 25:1119-26. 2007
    ..Significant differences in distance were found between etiological and palliative drugs. A recent trend toward more rational drug design was observed...
  50. ncbi request reprint Integrative genomic approaches identify IKBKE as a breast cancer oncogene
    Jesse S Boehm
    Department of Medical Oncology, Dana Farber Cancer Institute, Boston, MA 02115, USA
    Cell 129:1065-79. 2007
    ..These observations suggest a mechanism for NF-kappaB activation in breast cancer, implicate the NF-kappaB pathway as a downstream mediator of PI3K, and provide a framework for integrated genomic approaches in oncogene discovery...
  51. pmc Association of Dishevelled with the clathrin AP-2 adaptor is required for Frizzled endocytosis and planar cell polarity signaling
    Anan Yu
    Department of Cell Biology and CBR Institute for Biomedical Research, Harvard Medical School, Boston, MA 02115, USA
    Dev Cell 12:129-41. 2007
    ..We suggest that the direct interaction of Dvl2 with AP-2 is important for Frizzled internalization and Frizzled/PCP signaling...
  52. pmc Revisiting the Saccharomyces cerevisiae predicted ORFeome
    Qian Ru Li
    Center for Cancer Systems Biology CCSB and Department of Cancer Biology, Dana Farber Cancer Institute, Harvard Medical School, Boston, MA 02115, USA
    Genome Res 18:1294-303. 2008
    ..Rather, such ORFs might be important for micro-evolutionary divergence between species...
  53. ncbi request reprint Local modeling of global interactome networks
    Denise Scholtens
    Department of Biostatistics, Harvard School of Public Health, Boston, MA 02115, USA
    Bioinformatics 21:3548-57. 2005
    ..Static graphs currently used to model Y2H and AP-MS data neglect dynamic and spatial aspects of macromolecular complexes and pleiotropic protein function...
  54. ncbi request reprint Systematic analysis of genes required for synapse structure and function
    Derek Sieburth
    Department of Molecular Biology, Massachusetts General Hospital, Boston, Massachusetts 02114, USA
    Nature 436:510-7. 2005
    ..Twenty-four genes encoded proteins that were localized to presynaptic specializations. Loss-of-function mutations in 12 genes caused defects in presynaptic structure...
  55. pmc A protein domain-based interactome network for C. elegans early embryogenesis
    Mike Boxem
    Center for Cancer Systems Biology and Department of Cancer Biology, Dana Farber Cancer Institute, Harvard Medical School, Boston, MA 02115, USA
    Cell 134:534-45. 2008
    ..This interactome modeling strategy revealed insights into C. elegans centrosome function and is applicable to other biological processes in this and other organisms...
  56. pmc Combining biological networks to predict genetic interactions
    Sharyl L Wong
    Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, 250 Longwood Avenue, Boston, MA 02115, USA
    Proc Natl Acad Sci U S A 101:15682-7. 2004
    ....
  57. pmc A mitochondrial protein compendium elucidates complex I disease biology
    David J Pagliarini
    Center for Human Genetic Research, Massachusetts General Hospital, Boston, MA 02114, USA
    Cell 134:112-23. 2008
    ..Our results have important implications for understanding CI function and pathogenesis and, more generally, illustrate how our compendium can serve as a foundation for systematic investigations of mitochondria...
  58. ncbi request reprint Evidence for dynamically organized modularity in the yeast protein-protein interaction network
    Jing Dong J Han
    Center for Cancer Systems Biology and Department of Cancer Biology, Dana Farber Cancer Institute, and Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115, USA
    Nature 430:88-93. 2004
    ....
  59. pmc Fas-activated serine/threonine phosphoprotein (FAST) is a regulator of alternative splicing
    Maria Simarro
    Division of Rheumatology, Immunology, and Allergy, Brigham and Women s Hospital, Harvard Medical School, Boston, MA 02115, USA
    Proc Natl Acad Sci U S A 104:11370-5. 2007
    ..Mutational analysis reveals that FAST-mediated alternative splicing is separable from the survival effects of FAST. Our data reveal that nuclear FAST can regulate the splicing of FGFR2 transcripts...
  60. pmc Epstein-Barr virus and virus human protein interaction maps
    Michael A Calderwood
    Program in Virology, Department of Medicine, The Channing Laboratory, Harvard Medical School and Brigham and Women s Hospital, Boston, MA 02115, USA
    Proc Natl Acad Sci U S A 104:7606-11. 2007
    ..Targeting of hubs might be an efficient mechanism for EBV reorganization of cellular processes...
  61. pmc A genome-wide gene function prediction resource for Drosophila melanogaster
    Han Yan
    Department of Cancer Biology, Center for Cancer Systems Biology CCSB, Dana Farber Cancer Institute, Boston, Massachusetts, United States of America
    PLoS ONE 5:e12139. 2010
    ..The resulting resource of prioritized associations between Drosophila genes and their potential functions offers a guide for experimental investigations...
  62. ncbi request reprint BRCA1/BARD1 orthologs required for DNA repair in Caenorhabditis elegans
    Simon J Boulton
    DNA Damage Response Laboratory, Cancer Research UK, The London Research Institute, Clare Hall Laboratories, EN6 3LD, South Mimms, United Kingdom
    Curr Biol 14:33-9. 2004
    ..Our findings support a shared role for Ce-BRC-1 and Ce-BRD-1 in C. elegans DNA repair processes, and this role will permit studies of the BRCA1 pathway in an organism amenable to rapid genetic and biochemical analysis...
  63. pmc Structural genomics: a pipeline for providing structures for the biologist
    Mark R Chance
    Center for Synchrotron Biosciences, Albert Einstein College of Medicine, Bronx, New York 10461, USA
    Protein Sci 11:723-38. 2002
  64. ncbi request reprint Integrated version of reverse two-hybrid system for the postproteomic era
    Hideki Endoh
    Enanta Pharmaceuticals Inc, Cambridge, Massachusetts 02139, USA
    Methods Enzymol 350:525-45. 2002
  65. pmc Annotation transfer between genomes: protein-protein interologs and protein-DNA regulogs
    Haiyuan Yu
    Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut 06520, USA
    Genome Res 14:1107-18. 2004
    ..We test a number of these in two-hybrid experiments and are able to verify 45 overlaps, which we show to be statistically significant...
  66. ncbi request reprint Caenorhabditis elegans HUS-1 is a DNA damage checkpoint protein required for genome stability and EGL-1-mediated apoptosis
    E Randal Hofmann
    Cold Spring Harbor Laboratory, 1 Bungtown Road, Cold Spring Harbor, NY 11724, USA
    Curr Biol 12:1908-18. 2002
    ..However, in metazoans, DNA damage can induce apoptosis as well. How DNA damage activates the apoptotic machinery is not fully understood...
  67. ncbi request reprint The HUPO PSI's molecular interaction format--a community standard for the representation of protein interaction data
    Henning Hermjakob
    European Bioinformatics Institute, EBI Hinxton, Wellcome Trust Genome Campus, Hinxton, Cambridge, UK
    Nat Biotechnol 22:177-83. 2004
    ....
  68. ncbi request reprint BTB proteins are substrate-specific adaptors in an SCF-like modular ubiquitin ligase containing CUL-3
    Lai Xu
    Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, One Baylor Plaza, Houston, Texas 77030, USA
    Nature 425:316-21. 2003
    ..elegans CUL-3. Biochemical studies using the BTB protein MEL-26 and its genetic target MEI-1 (refs 12, 13) indicate that BTB proteins merge the functional properties of Skp1 and F-box proteins into a single polypeptide...
  69. ncbi request reprint A protein-protein interaction network for human inherited ataxias and disorders of Purkinje cell degeneration
    Janghoo Lim
    Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
    Cell 125:801-14. 2006
    ..This interactome thus provides a tool for understanding pathogenic mechanisms common for this class of neurodegenerative disorders and for identifying candidate genes for inherited ataxias...
  70. ncbi request reprint ORFeome cloning and systems biology: standardized mass production of the parts from the parts-list
    Michael A Brasch
    Atto Bioscience, Rockville, Maryland 20850, USA
    Genome Res 14:2001-9. 2004
    ..Here we discuss the use of a recombinational cloning system that allows efficiency, adaptability, and compatibility in the generation of ORFeome, promoterome, and other resources...
  71. pmc Feasibility of genome-scale construction of promoter::reporter gene fusions for expression in Caenorhabditis elegans using a multisite gateway recombination system
    Ian A Hope
    School of Biology, University of Leeds, Leeds, LS2 9JT, UK
    Genome Res 14:2070-5. 2004
    ..The recombinational cloning involved in the Gateway system, which permits the highly efficient and precise transfer of DNA segments between plasmid vectors, makes this technology ideal for genomics research programs...
  72. ncbi request reprint From genome to proteome: developing expression clone resources for the human genome
    Gary Temple
    Mammalian Gene Collection, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892, USA
    Hum Mol Genet 15:R31-43. 2006
    ....
  73. pmc New genes with roles in the C. elegans embryo revealed using RNAi of ovary-enriched ORFeome clones
    Anita G Fernandez
    Department of Biology, New York University, New York, New York 10003, USA
    Genome Res 15:250-9. 2005
    ..Furthermore, we discovered a striking direct relationship between phylogenetic distribution and the penetrance level of embryonic lethality elicited by RNAi...
  74. ncbi request reprint Predictive models of molecular machines involved in Caenorhabditis elegans early embryogenesis
    Kristin C Gunsalus
    Center for Comparative Functional Genomics, Department of Biology, New York University, New York, New York 10003, USA
    Nature 436:861-5. 2005
    ..We assessed the overall predictive value of such molecular machine models by dynamic localization of ten previously uncharacterized proteins within the living embryo...
  75. ncbi request reprint Pooled ORF expression technology (POET): using proteomics to screen pools of open reading frames for protein expression
    William K Gillette
    Protein Expression Laboratory, Research Technology Program, SAIC Frederick, Inc NCI, National Institutes of Health, Frederick, Maryland 21702, USA
    Mol Cell Proteomics 4:1647-52. 2005
    ..Using POET, pools of ORFs can be constructed, and the pools of the resulting proteins can be analyzed and manipulated to rapidly acquire information about the attributes of hundreds of proteins simultaneously...
  76. pmc Closing in on the C. elegans ORFeome by cloning TWINSCAN predictions
    Chaochun Wei
    Laboratory for Computational Genomics and Department of Computer Science and Engineering, Washington University, St Louis, Missouri 63130, USA
    Genome Res 15:577-82. 2005
    ..The results also suggest that this technology can significantly improve our knowledge of the "parts list" for even the best-studied model organisms...
  77. ncbi request reprint The minimum information required for reporting a molecular interaction experiment (MIMIx)
    Sandra Orchard
    European Molecular Biology Laboratory EMBL European Bioinformatics Institute, Wellcome Trust Genome Campus, Cambridge, UK
    Nat Biotechnol 25:894-8. 2007
    ....
  78. pmc Efficient targeted transcript discovery via array-based normalization of RACE libraries
    Sarah Djebali
    Grup de Recerca en Informàtica Biomèdica, Institut Municipal d Investigació Mèdica Universitat Pompeu Fabra, Dr Aiguader 88, 08003 Barcelona, Spain
    Nat Methods 5:629-35. 2008
    ....
  79. pmc Intrinsic disorder is a common feature of hub proteins from four eukaryotic interactomes
    Chad Haynes
    Laboratory of Statistical Genetics, The Rockefeller University, New York, New York, USA
    PLoS Comput Biol 2:e100. 2006
    ..The results of this study demonstrate that intrinsic structural disorder is a distinctive and common characteristic of eukaryotic hub proteins, and that disorder may serve as a determinant of protein interactivity...
  80. pmc High-throughput expression of C. elegans proteins
    Chi Hao Luan
    Center for Biophysical Sciences and Engineering, Southeast Collaboratory for Structural Genomics, University of Alabama at Birmingham, Birmingham, Alabama 35294, USA
    Genome Res 14:2102-10. 2004
    ..The pipeline described here is applicable to high-throughput expression of recombinant proteins for other species, both prokaryotic and eukaryotic, provided that ORFeome resources become available...
  81. pmc A gateway-compatible yeast one-hybrid system
    Bart Deplancke
    Program in Gene Function and Expression, University of Massachusetts Medical School, Worcester, Massachusetts 01605, USA
    Genome Res 14:2093-101. 2004
    ..Taken together, the Gateway-compatible Y1H system will allow the high-throughput identification of protein-DNA interactions and may be a valuable tool to decipher transcription regulatory networks...
  82. pmc C. elegans GLA-3 is a novel component of the MAP kinase MPK-1 signaling pathway required for germ cell survival
    Ekaterini A Kritikou
    Institute of Molecular Biology, University of Zurich, 8057 Zurich, Switzerland
    Genes Dev 20:2279-92. 2006
    ..elegans germline and functions as a negative regulator of the MAPK signaling pathway during vulval development and in muscle cells...
  83. ncbi request reprint MEX-3 interacting proteins link cell polarity to asymmetric gene expression in Caenorhabditis elegans
    Nancy N Huang
    Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA 02138, USA
    Development 129:747-59. 2002
    ..We propose that MEX-6 and SPN-4 act with MEX-3 to translate the temporal and spatial information provided by the early acting par genes into the asymmetric expression of the cell fate determinant PAL-1...
  84. ncbi request reprint Perturbing interactions
    Stuart Milstein
    Nat Methods 2:412-4. 2005
  85. ncbi request reprint High-throughput expression, purification, and characterization of recombinant Caenorhabditis elegans proteins
    Raymond Y Huang
    Center for Synchrotron Biosciences, Albert Einstein College of Medicine, Bronx, NY 10461, USA
    Biochem Biophys Res Commun 307:928-34. 2003
    ..The ZipTip purified proteins can be further analyzed under both native and denaturing conditions for functional proteomics efforts...
  86. pmc Confirmation of organized modularity in the yeast interactome
    Nicolas Bertin
    PLoS Biol 5:e153. 2007
  87. pmc Genome-wide coactivation analysis of PGC-1alpha identifies BAF60a as a regulator of hepatic lipid metabolism
    Siming Li
    Life Sciences Institute and Department of Cell and Developmental Biology, University of Michigan Medical Center, Ann Arbor, MI 48109, USA
    Cell Metab 8:105-17. 2008
    ..These results define a role for the SWI/SNF complexes in the regulation of lipid homeostasis...

Research Grants21

  1. Rewiring Pathways and Networks by Environmental Perturbations
    Marc Vidal; Fiscal Year: 2009
    ....
  2. Generation of a C. elegans Protein Interaction Database
    Marc Vidal; Fiscal Year: 2002
    ....
  3. The C. elegans Interactome Project
    Marc Vidal; Fiscal Year: 2005
    ....
  4. Conference on Systems & Biology
    Marc Vidal; Fiscal Year: 2005
    ..abstract_text> ..
  5. The C. elegans Interactome Project
    Marc Vidal; Fiscal Year: 2006
    ....
  6. Generation of a C. elegans Protein Interaction Database
    Marc Vidal; Fiscal Year: 2004
    ....
  7. GENERATION OF A C ELEGANS PROTEIN INTERACTION DATASET
    Marc Vidal; Fiscal Year: 2000
    ..This work should help in developing the tools and the strategies needed to generate and interpret a comprehensive human-protein interaction database. ..
  8. Mapping the Human Binary Interactome Network
    Marc Vidal; Fiscal Year: 2009
    ..Our modified specific aims are to: i) Provide an expanded high-confidence/high-coverage version of the human binary interactome map ii) Validate human binary interaction data iii) Analyze the expanded human interactome model ..
  9. Rewiring Pathways and Networks by Environmental Perturbations
    Marc Vidal; Fiscal Year: 2010
    ....
  10. Rewiring Pathways and Networks by Environmental Perturbations
    Marc Vidal; Fiscal Year: 2007
    ....
  11. Genomic Analysis of Network Perturbations in Human Disease
    Marc Vidal; Fiscal Year: 2007
    ....
  12. The C. elegans Interactome Project
    Marc Vidal; Fiscal Year: 2007
    ....
  13. Integrated interactome mapping
    Marc Vidal; Fiscal Year: 2006
    ..abstract_text> ..
  14. A C. elegans localization-of-expression mapping project
    Marc Vidal; Fiscal Year: 2005
    ..Using a complete set of worm promoters, we then propose to develop high-throughput methods to localize gene expression in vivo and initiate a protein-DNA interaction mapping project (R33). ..
  15. Generation of a C. elegans Protein Interaction Database
    Marc Vidal; Fiscal Year: 2003
    ....
  16. Generation of a C. elegans Protein Interaction Database
    Marc Vidal; Fiscal Year: 2001
    ....
  17. Mapping the Human Binary Interactome Network
    MARC contact VIDAL; Fiscal Year: 2010
    ..Our modified specific aims are to: i) Provide an expanded high-confidence/high-coverage version of the human binary interactome map ii) Validate human binary interaction data iii) Analyze the expanded human interactome model ..