Research Topics
Genomes and Genes | Charles AuffraySummaryCountry: France Publications
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Publications
Bridging the gap between systems biology and medicineGilles 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....- Sharing knowledge: a new frontier for public-private partnerships in medicineCharles 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.... - 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... 
Self-organized living systems: conjunction of a stable organization with chaotic fluctuations in biological space-timeCharles 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....- From functional genomics to systems biology: concepts and practicesCharles 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... 
An integrative systems biology approach to understanding pulmonary diseasesCharles 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...- Deciphering cellular states of innate tumor drug responsesEsther 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..The demonstrated power of this research strategy makes it generally applicable to other physiological and pathological situations... - A functional and regulatory network associated with PIP expression in human breast cancerMarie 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.... - The cytoskeleton-associated PDZ-LIM protein, ALP, acts on serum response factor activity to regulate muscle differentiationPascal 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... - Characterization of tissue expression and full-length coding sequence of a novel human gene mapping at 3q12.1 and transcribed in oligodendrocytesNicole 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... - 'The 39 steps' in gene expression profiling: critical issues and proposed best practices for microarray experimentsSandrine 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.... - A transgenic mouse model engineered to investigate human brain-derived neurotrophic factor in vivoFabrice 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... - Towards standardization of RNA quality assessment using user-independent classifiers of microcapillary electrophoresis tracesSandrine 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.... - Foreword: from the TRANSCRIPTOME conferences to the SYSTEMOSCOPE international consortiumCharles 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.... - Systems medicine: the future of medical genomics and healthcareCharles 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.... - Identification of genes involved in ceramide-dependent neuronal apoptosis using cDNA arraysCharles Decraene
Genexpress, CNRS FRE 2376, BP8, 94801 Villejuif, France
Genome Biol 3:RESEARCH0042. 2002..The remaining 209 genes, with or without known functions, constitute a pool of genes potentially implicated in the regulation of neuronal cell death... - Predictive, preventive, personalized and participatory medicine: back to the futureCharles 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.... - Scale relativity theory and integrative systems biology: 1. Founding principles and scale lawsCharles 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... - Modifications in the myogenic program induced by in vivo and in vitro agingSylvie Bortoli
Genexpress, CNRS FRE 2571, 19 rue Guy Moquet, BP 8, 94801 Villejuif Cedex, France
Gene 347:65-72. 2005.... - Alternative usage of 5' exons in the chicken nerve growth factor gene: refined characterization of a weakly expressed geneOdile 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... - Gene expression profiling of human satellite cells during muscular aging using cDNA arraysSylvie 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... - Sex-linked recombination variation and distribution of disease-related genesClaude 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.... - Transforming growth factor-beta1-modulated cerebral gene expressionSylvain 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... - Complementary DNA arrays identify CD63 tetraspanin and alpha3 integrin chain as differentially expressed in low and high metastatic human colon carcinoma cellsIsabelle 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... - ALP and MLP distribution during myofibrillogenesis in cultured cardiomyocytesJames 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... - Transcriptome analysis of two bovine muscles during ontogenesisKarine Sudre
INRA, , Theix, , France
J Biochem (Tokyo) 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... - Scale relativity theory and integrative systems biology: 2. Macroscopic quantum-type mechanicsLaurent 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.... - Systems analysis of transcriptome and proteome in retinoic acid/arsenic trioxide-induced cell differentiation/apoptosis of promyelocytic leukemiaPei-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... - Functional Annotation: extracting functional and regulatory order from microarraysSandrine Imbeaud
Mol Syst Biol 1:2005.0009. 2005 - The H-Invitational Database (H-InvDB), a comprehensive annotation resource for human genes and transcriptsChisato Yamasaki
Japan Biological Information Research Center, Japan Biological Informatics Consortium, Japan
Nucleic Acids Res 36:D793-9. 2008.... - The beta-catenin pathway is activated in focal nodular hyperplasia but not in cirrhotic FNH-like nodulesSandra 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... - Integrative annotation of 21,037 human genes validated by full-length cDNA clonesTadashi 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... - HNF1alpha inactivation promotes lipogenesis in human hepatocellular adenoma independently of SREBP-1 and carbohydrate-response element-binding protein (ChREBP) activationSandra 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... - Characterization of a new human isoform of the enigma homolog family specifically expressed in skeletal muscleNicolas 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... - Drug specific resistance to oxaliplatin is associated with apoptosis defect in a cellular model of colon carcinomaIsabelle Gourdier
CNRS UMR 5094, , 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... - Matching gene expression with hypometabolism after cerebral ischemia in the nonhuman primateJulien 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... - The Human Anatomic Gene Expression Library (H-ANGEL), the H-Inv integrative display of human gene expression across disparate technologies and platformsMotohiko 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/... - Protein subnetwork markers improve prediction of cancer outcomeCharles Auffray
Mol Syst Biol 3:141. 2007