Charles Auffray

Summary

Country: France

Publications

  1. pmc Bridging the gap between systems biology and medicine
    Gilles Clermont
    Department of Critical Care Medicine and CRISMA laboratory, University of Pittsburgh School of Medicine, Scaife 602, 3550 Terrace, Pittsburgh, PA 15261, USA
    Genome Med 1:88. 2009
  2. pmc Sharing knowledge: a new frontier for public-private partnerships in medicine
    Charles Auffray
    Functional Genomics and Systems Biology for Health, CNRS Institute of Biological Sciences, 7 Rue Guy Moquet BP8, 94801 Villejuif, France
    Genome Med 1:29. 2009
  3. pmc Computational disease modeling - fact or fiction?
    Jesper N Tegnér
    Computational Medicine group, Department of Medicine, Center for Molecular Medicine, Karolinska University Hospital, Solna, Stockholm, Sweden
    BMC Syst Biol 3:56. 2009
  4. doi An integrative systems biology approach to understanding pulmonary diseases
    Charles Auffray
    Functional Genomics and Systems Biology for Health, CNRS Institute of Biological Sciences, 7 Rue Guy Moquet BP8, 94801 Villejuif Cedex, France
    Chest 137:1410-6. 2010
  5. ncbi From functional genomics to systems biology: concepts and practices
    Charles Auffray
    Genexpress, Functional Genomics and Systemic Biology for Health, CNRS FRE 2571, 7, rue Guy Moquet, BP 8, 94801 Villejuif Cedex, France
    C R Biol 326:879-92. 2003
  6. ncbi Self-organized living systems: conjunction of a stable organization with chaotic fluctuations in biological space-time
    Charles Auffray
    Genexpress, Functional Genomics and Systemic Biology for Health, CNRS FRE 2571, 7 rue Guy Moquet, BP8, 94801 Villejuif Cedex, France
    Philos Trans A Math Phys Eng Sci 361:1125-39. 2003
  7. pmc A functional and regulatory network associated with PIP expression in human breast cancer
    Marie Anne Debily
    Array s IMAGE, Genexpress, Functional Genomics and Systems Biology for Health, LGN UMR 7091 CNRS and Pierre and Marie Curie University, Paris VI, Villejuif, France
    PLoS ONE 4:e4696. 2009
  8. pmc Deciphering cellular states of innate tumor drug responses
    Esther Graudens
    Array s IMAGE, Genexpress, Functional Genomics and Systems Biology for Health, LGN UMR 7091 CNRS and Pierre and Marie Curie University, Paris VI, Villejuif, France
    Genome Biol 7:R19. 2006
  9. pmc The cytoskeleton-associated PDZ-LIM protein, ALP, acts on serum response factor activity to regulate muscle differentiation
    Pascal Pomies
    Centre National de la Recherche Scientifique Unité Mixte de Recherche 5237, Centre de Recherches de Biochimie Macromoleculaire, 34293 Montpellier, France
    Mol Biol Cell 18:1723-33. 2007
  10. ncbi Characterization of tissue expression and full-length coding sequence of a novel human gene mapping at 3q12.1 and transcribed in oligodendrocytes
    Nicole Adeline Fayein
    Genexpress, CNRS, FRE 2376, 19 rue Guy Moquet, BP8, F 94801 Villejuif Cedex, France
    Gene 289:119-29. 2002

Detail Information

Publications39

  1. pmc Bridging the gap between systems biology and medicine
    Gilles Clermont
    Department of Critical Care Medicine and CRISMA laboratory, University of Pittsburgh School of Medicine, Scaife 602, 3550 Terrace, Pittsburgh, PA 15261, USA
    Genome Med 1:88. 2009
    ....
  2. pmc Sharing knowledge: a new frontier for public-private partnerships in medicine
    Charles Auffray
    Functional Genomics and Systems Biology for Health, CNRS Institute of Biological Sciences, 7 Rue Guy Moquet BP8, 94801 Villejuif, France
    Genome Med 1:29. 2009
    ....
  3. pmc Computational disease modeling - fact or fiction?
    Jesper N Tegnér
    Computational Medicine group, Department of Medicine, Center for Molecular Medicine, Karolinska University Hospital, Solna, Stockholm, Sweden
    BMC Syst Biol 3:56. 2009
    ..On the other hand, the physics-inspired top-down modeling strategy identifies and selects features of (presumably) essential relevance to the phenomena of interest and combines available data in models of modest complexity...
  4. doi An integrative systems biology approach to understanding pulmonary diseases
    Charles Auffray
    Functional Genomics and Systems Biology for Health, CNRS Institute of Biological Sciences, 7 Rue Guy Moquet BP8, 94801 Villejuif Cedex, France
    Chest 137:1410-6. 2010
    ..This can be tested and validated in prospective clinical trials...
  5. ncbi From functional genomics to systems biology: concepts and practices
    Charles Auffray
    Genexpress, Functional Genomics and Systemic Biology for Health, CNRS FRE 2571, 7, rue Guy Moquet, BP 8, 94801 Villejuif Cedex, France
    C R Biol 326:879-92. 2003
    ..Galactose utilization in yeast, and sea urchin development are two examples of emerging systems biology...
  6. ncbi Self-organized living systems: conjunction of a stable organization with chaotic fluctuations in biological space-time
    Charles Auffray
    Genexpress, Functional Genomics and Systemic Biology for Health, CNRS FRE 2571, 7 rue Guy Moquet, BP8, 94801 Villejuif Cedex, France
    Philos Trans A Math Phys Eng Sci 361:1125-39. 2003
    ....
  7. pmc A functional and regulatory network associated with PIP expression in human breast cancer
    Marie Anne Debily
    Array s IMAGE, Genexpress, Functional Genomics and Systems Biology for Health, LGN UMR 7091 CNRS and Pierre and Marie Curie University, Paris VI, Villejuif, France
    PLoS ONE 4:e4696. 2009
    ....
  8. pmc Deciphering cellular states of innate tumor drug responses
    Esther Graudens
    Array s IMAGE, Genexpress, Functional Genomics and Systems Biology for Health, LGN UMR 7091 CNRS and Pierre and Marie Curie University, Paris VI, Villejuif, France
    Genome Biol 7:R19. 2006
    ....
  9. pmc The cytoskeleton-associated PDZ-LIM protein, ALP, acts on serum response factor activity to regulate muscle differentiation
    Pascal Pomies
    Centre National de la Recherche Scientifique Unité Mixte de Recherche 5237, Centre de Recherches de Biochimie Macromoleculaire, 34293 Montpellier, France
    Mol Biol Cell 18:1723-33. 2007
    ..Collectively, these results suggest a critical role of ALP on muscle differentiation, likely via cytoskeletal regulation of SRF...
  10. ncbi Characterization of tissue expression and full-length coding sequence of a novel human gene mapping at 3q12.1 and transcribed in oligodendrocytes
    Nicole Adeline Fayein
    Genexpress, CNRS, FRE 2376, 19 rue Guy Moquet, BP8, F 94801 Villejuif Cedex, France
    Gene 289:119-29. 2002
    ..This work supports further investigations aimed at determining the role of the C3orf4 gene in myelinating cells...
  11. ncbi 'The 39 steps' in gene expression profiling: critical issues and proposed best practices for microarray experiments
    Sandrine Imbeaud
    Array s IMAGE, Genexpress, Functional Genomics and Systems Biology for Health, LGN UMR 7091, CNRS and Pierre and Marie Curie University, Paris VI, Villejuif, France
    Drug Discov Today 10:1175-82. 2005
    ....
  12. pmc Towards standardization of RNA quality assessment using user-independent classifiers of microcapillary electrophoresis traces
    Sandrine Imbeaud
    Array s IMAGE, Genexpress, Functional Genomics and Systems Biology for Health LGN UMR 7091, CNRS and Pierre and Marie Curie University of Paris 6, 7, rue Guy Moquet, 94801 Villejuif, France
    Nucleic Acids Res 33:e56. 2005
    ....
  13. ncbi A transgenic mouse model engineered to investigate human brain-derived neurotrophic factor in vivo
    Fabrice Guillemot
    Genexpress, Génomique Fonctionnelle et Biologie Systémique pour la Santé, CNRS et Université Pierre et Marie Curie Paris VI, LGN, UMR 7091, 7 rue Guy Moquet, BP8, 94801 Villejuif, France
    Transgenic Res 16:223-37. 2007
    ..This line constitutes an exploitable system for investigating human BDNF gene regulation in vivo...
  14. ncbi Foreword: from the TRANSCRIPTOME conferences to the SYSTEMOSCOPE international consortium
    Charles Auffray
    Genexpress, Functional Genomics and Systemic Biology for Health, CNRS FRE 2571, 7, rue Guy Moquet, BP 8, 94801 Villejuif Cedex, France
    C R Biol 326:867-75. 2003
    ....
  15. pmc Systems medicine: the future of medical genomics and healthcare
    Charles Auffray
    Functional Genomics and Systems Biology for Health, LGN UMR 7091, CNRS and Pierre and Marie Curie University of Paris VI, 7 rue Guy Moquet, 94801 Villejuif, France
    Genome Med 1:2. 2009
    ....
  16. pmc Identification of genes involved in ceramide-dependent neuronal apoptosis using cDNA arrays
    Charles Decraene
    Genexpress, CNRS FRE 2376, BP8, 94801 Villejuif, France
    Genome Biol 3:RESEARCH0042. 2002
    ..Elevated ceramide levels have been shown to induce apoptosis in primary neuronal cultures and neuronally differentiated PC 12 cells...
  17. pmc Origins of systems biology in William Harvey's masterpiece on the movement of the heart and the blood in animals
    Charles Auffray
    Functional Genomics and Systems Biology for Health, CNRS Institute of Biological Sciences, 7 rue Guy Moquet, BP8, 94801 Villejuif, France
    Int J Mol Sci 10:1658-69. 2009
    ....
  18. ncbi Scale relativity theory and integrative systems biology: 1. Founding principles and scale laws
    Charles Auffray
    Functional Genomics and Systems Biology for Health, UMR 7091 LGN, CNRS Pierre and Marie Curie University Paris VI, 7 rue Guy Moquet BP 8, 94801 Villejuif Cedex, France
    Prog Biophys Mol Biol 97:79-114. 2008
    ..Initial applications of these laws to the study of species evolution, embryogenesis and cell confinement are discussed...
  19. pmc Predictive, preventive, personalized and participatory medicine: back to the future
    Charles Auffray
    Functional Genomics and Systems Biology for Health, CNRS Institute of Biological Sciences, 7 rue Guy Moquet, BP8, 94801 Villejuif Cedex, France
    Genome Med 2:57. 2010
    ....
  20. ncbi Modifications in the myogenic program induced by in vivo and in vitro aging
    Sylvie Bortoli
    Genexpress, CNRS FRE 2571, 19 rue Guy Moquet, BP 8, 94801 Villejuif Cedex, France
    Gene 347:65-72. 2005
    ....
  21. ncbi Alternative usage of 5' exons in the chicken nerve growth factor gene: refined characterization of a weakly expressed gene
    Odile Bertaux
    Génomique Fonctionnelle et Biologie Systémique en Santé CNRS FRE 2571, 19 rue Guy Moquet, BP 8, Villejuif cedex F 94 801, France
    Gene 334:83-97. 2004
    ..Complementary data are published as a Web supplement available at...
  22. ncbi Gene expression profiling of human satellite cells during muscular aging using cDNA arrays
    Sylvie Bortoli
    Genexpress, CNRS FRE 2571, 19 rue Guy Moquet, BP 8, 94801 Villejuif Cedex, France
    Gene 321:145-54. 2003
    ..Finally, we have identified four potential new markers of presenescence for human myoblasts, which could be useful in developing therapeutic strategies...
  23. ncbi Sex-linked recombination variation and distribution of disease-related genes
    Claude Chelala
    Genexpress, Functional Genomics and Systems Biology for Health, CNRS UMR 7091 7, rue Guy Moquet, BP8, 94801 Villejuif Cedex, France
    Gene 346:29-39. 2005
    ....
  24. ncbi Transforming growth factor-beta1-modulated cerebral gene expression
    Sylvain Lesne
    Universite de Caen, UMR CNRS 6551, France
    J Cereb Blood Flow Metab 22:1114-23. 2002
    ..The authors' observations enlarge the repertoire of known TGF-beta1-modulated genes and their possible involvement in neurodegenerative processes...
  25. ncbi Complementary DNA arrays identify CD63 tetraspanin and alpha3 integrin chain as differentially expressed in low and high metastatic human colon carcinoma cells
    Isabelle Sordat
    Experimental and Molecular Pathology Unit, Swiss Institute for Experimental Cancer Research, Epalinges, Switzerland
    Lab Invest 82:1715-24. 2002
    ..Our results suggest that changes in the expression of surface CD63 and alpha3beta1 integrin interacting with LN-5 could affect migratory signals and the progression of the metastatic disease...
  26. ncbi ALP and MLP distribution during myofibrillogenesis in cultured cardiomyocytes
    James R Henderson
    Department of Biology Huntsman Cancer Institute, University of Utah, Salt Lake City, Utah 84112 0840, USA
    Cell Motil Cytoskeleton 54:254-65. 2003
    ..The subcellular distribution pattern of MLP during myofibrillogenesis suggests that it functions during differentiation prior to the establishment of costameres...
  27. ncbi Transcriptome analysis of two bovine muscles during ontogenesis
    Karine Sudre
    INRA, Unite de Recherches sur les Herbivores, Theix, 63122 Saint Genes Champanelle, France
    J Biochem 133:745-56. 2003
    ..Among these genes, 33% have unknown biological functions. Taken together, the results reported here underline the importance of the last three months of gestation in muscle myogenesis, and highlight new genes involved in this process...
  28. pmc Systems analysis of transcriptome and proteome in retinoic acid/arsenic trioxide-induced cell differentiation/apoptosis of promyelocytic leukemia
    Pei Zheng Zheng
    State Key Laboratory of Medical Genomics, Ruijin Hospital, Shanghai Second Medical University, 197 Rui Jin Road II, Shanghai 200025, China
    Proc Natl Acad Sci U S A 102:7653-8. 2005
    ..Hence, this investigation has provided not only a detailed understanding of the combined therapeutic effects of RA/ATO in APL but also a road map to approach hematopoietic malignancies at the systems level...
  29. ncbi Scale relativity theory and integrative systems biology: 2. Macroscopic quantum-type mechanics
    Laurent Nottale
    LUTH, CNRS, Observatoire de Paris and Paris Diderot University Paris VII, 5 place Jules Janssen, 92190 Meudon, France
    Prog Biophys Mol Biol 97:115-57. 2008
    ....
  30. pmc Functional Annotation: extracting functional and regulatory order from microarrays
    Sandrine Imbeaud
    Mol Syst Biol 1:2005.0009. 2005
  31. pmc The Human Anatomic Gene Expression Library (H-ANGEL), the H-Inv integrative display of human gene expression across disparate technologies and platforms
    Motohiko Tanino
    Integrated Database Group, Japan Biological Information Research Center, Japan Biological Informatics Consortium, Time24 Building 10F, 2 45 Aomi, Koto ku, Tokyo 135 0064, Japan
    Nucleic Acids Res 33:D567-72. 2005
    ..In future editions, we will incorporate the capability for expression data updates from existing and new platforms. H-ANGEL is accessible at http://www.jbirc.aist.go.jp/hinv/h-angel/...
  32. ncbi Matching gene expression with hypometabolism after cerebral ischemia in the nonhuman primate
    Julien Chuquet
    UMR CNRS 6551, University of Caen, IFR 47, Center Cyceron, Caen, France
    J Cereb Blood Flow Metab 22:1165-9. 2002
    ..These patterns of coordinated modifications in gene expression could define molecular checkpoints for the development of an ischemic infarct and a molecular definition of the penumbra...
  33. ncbi Drug specific resistance to oxaliplatin is associated with apoptosis defect in a cellular model of colon carcinoma
    Isabelle Gourdier
    CNRS UMR 5094, Faculte de Pharmacie, 15 Avenue Charles Flahaut, P O Box 14491, 34093 Montpellier, France
    FEBS Lett 529:232-6. 2002
    ..Taken together, these findings suggest that altered mitochondrial-mediated apoptosis could play a role in oxaliplatin resistance...
  34. pmc Integrative annotation of 21,037 human genes validated by full-length cDNA clones
    Tadashi Imanishi
    Integrated Database Group, Biological Information Research Center, National Institute of Advanced Industrial Science and Technology, Tokyo, Japan
    PLoS Biol 2:e162. 2004
    ..The H-InvDB platform represents a substantial contribution to resources needed for the exploration of human biology and pathology...
  35. ncbi Characterization of a new human isoform of the enigma homolog family specifically expressed in skeletal muscle
    Nicolas Niederlander
    CNRS FRE2593, Centre de Recherche de Biochimie Macromoleculaire, Montpellier, France
    Biochem Biophys Res Commun 325:1304-11. 2004
    ..Two additional new ENH4 partners of about 34 and 54kDa were also identified. These results bring new lights on the ENH protein family members...
  36. ncbi HNF1alpha inactivation promotes lipogenesis in human hepatocellular adenoma independently of SREBP-1 and carbohydrate-response element-binding protein (ChREBP) activation
    Sandra Rebouissou
    INSERM, U674, Génomique fonctionnelle des tumeurs solides, Paris Cedex, France
    J Biol Chem 282:14437-46. 2007
    ..Finally, our findings have potential clinical implications since lipogenesis can be efficiently inhibited by targeted therapies...
  37. pmc Protein subnetwork markers improve prediction of cancer outcome
    Charles Auffray
    Mol Syst Biol 3:141. 2007
  38. doi The beta-catenin pathway is activated in focal nodular hyperplasia but not in cirrhotic FNH-like nodules
    Sandra Rebouissou
    INSERM, U674, Génomique fonctionnelle des tumeurs solides, 27 rue Juliette Dodu, Paris F 75010, France
    J Hepatol 49:61-71. 2008
    ..In contrast, FNH-like lesions/nodules occur in cirrhotic liver but share similar histopathological features. We conducted a transcriptome analysis to identify biological pathways deregulated in FNH...
  39. pmc The H-Invitational Database (H-InvDB), a comprehensive annotation resource for human genes and transcripts
    Chisato Yamasaki
    Japan Biological Information Research Center, Japan Biological Informatics Consortium, Japan
    Nucleic Acids Res 36:D793-9. 2008
    ....