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Charles Auffray
Functional Genomics and Systems Biology for Health, Centre National de la Recherche Scientifique (CNRS) - Institute of Biological Sciences, Villejuif, France

Faculty Member: Physiology > Physiogenomics [ since 9 March 2005 ]
[ Sponsorship ] [ Biography ] [ Homepage ] [ Evaluations ]
Sponsorship

Charles Auffray sponsors free access to F1000 for Centre de Biotechnologie de Sfax (Tunisia - HINARI), Sfax, Tunisia. Supporting F1000's initiative to make itself available to scientists in all countries, including free access to developing countries (more details).

Biography

Dr. Charles Auffray, Research Director at CNRS, heads the Genexpress team in Functional Genomics and Systems Biology for Health, located in Villejuif, France, affiliated with the CNRS Institute of Biological Sciences.

Dr. Charles Auffray obtained the Agrégation in Physiology and Biochemistry at Ecole Normale Supérieure de Cachan in 1975, his phD in Molecular Immunology and Genetic Engineering at Pierre & Marie Curie University of Paris VI and Pasteur Institute, Paris in 1981. From 1981-1983 he was a Post-doctoral Fellow and Junior Faculty at the Department of Biochemistry and Molecular Biology of Harvard University in Cambridge, USA; from 1983-1991 a Group Leader at the Institute of Embryology, CNRS and Collège de France, Nogent s/Marne; from 1991-1995 the Scientific Director of the Genexpress Program at Généthon in Evry, concurrently Head of the CNRS Research Unit in Molecular Genetics and Developmental Biology, then Functional Genomics and Systems Biology for Health in Villejuif (1991-2003).

Dr. Charles Auffray develops a systems approach to cancer and the physio-pathology of the immune, neuro-muscular and respiratory systems by integrating functional genomics tools with mathematical, physical and computational approaches. He is actively involved in the development of open-access reagent, instrumentation and information platforms, in partnership with academic and industrial groups. He co-founded the IMAGE and SYSTEMOSCOPE International Consortia to also tackle related ethical, legal, and social issues with emphasis on interdisciplinarity and public education. Dr. Charles Auffray is the co-author of 237 original publications, including 175 in peer-reviewed scientific journals and 10 books, which have received over 12,000 citations. He is a member of several international societies, review committees, and editorial boards, and the co-organizer of a series of international conferences on Functional Genomics and Systems Biology.

Home page

http://www.vjf.cnrs.fr/genexpress/

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Evaluations

Listening to the noise: random fluctuations reveal gene network parameters.
Munsky B, Trinh B, Khammash M
Mol Syst Biol 2009 5:318 [abstract on PubMed] [related articles] [full text] [order article]
Selected by | Charles Auffray
Evaluated 17 Dec 2009

Single-molecule sequencing of an individual human genome.
Pushkarev D, Neff NF, Quake SR
Nat Biotechnol 2009 Aug 10 [abstract on PubMed] [related articles] [full text]
Selected by | Charles Auffray
Evaluated 10 Sep 2009

A systems approach to prion disease.
Hwang D, Lee IY, …, Carlson GA, Hood LE
Mol Syst Biol 2009 5:252 [abstract on PubMed] [related articles] [FREE full text]
Selected by | Charles Auffray
Evaluated 26 May 2009

On reliable discovery of molecular signatures.
Nilsson R, Björkegren J, Tegnér J
BMC Bioinformatics 2009 10:38 [abstract on PubMed] [related articles] [FREE full text]
Selected by | Charles Auffray / Panayiotis (Takis) Benos
Evaluated 13 May 2009

A global view of gene activity and alternative splicing by deep sequencing of the human transcriptome.
Sultan M, Schulz MH, …, Lehrach H, Yaspo ML
Science 2008 Aug 15 321(5891):956-60 [abstract on PubMed] [related articles] [full text] [order article]
Selected by | Charles Auffray
Evaluated 2 Feb 2009

DNA sequencing of a cytogenetically normal acute myeloid leukaemia genome.
Ley TJ, Mardis ER, …, DiPersio JF, Wilson RK
Nature 2008 Nov 6 456(7218):66-72 [abstract on PubMed] [related articles] [full text] [order article]
Selected by | Charles Auffray / Peter Wiernik
Evaluated 21 Nov 2008

High-Quality Binary Protein Interaction Map of the Yeast Interactome Network.
Yu H, Braun P, …, Hill DE, Vidal M
Science 2008 Aug 21 [abstract on PubMed] [related articles] [full text]
Selected by | Hunter Fraser / Charles Auffray
Evaluated 25 Sep 2008

Combined analysis reveals a core set of cycling genes.
Lu Y, Mahony S, …, Breeden LL, Bar-Joseph Z
Genome Biol 2007 8(7):R146 [abstract on PubMed] [related articles] [FREE full text]
Selected by | Charles Auffray
Evaluated 15 Jul 2008

High throughput gene expression measurement with real time PCR in a microfluidic dynamic array.
Spurgeon SL, Jones RC, Ramakrishnan R
PLoS ONE 2008 3(2):e1662 [abstract on PubMed] [related articles] [FREE full text]
Selected by | Charles Auffray
Evaluated 15 Jul 2008

Direct multiplexed measurement of gene expression with color-coded probe pairs.
Geiss GK, Bumgarner RE, …, Davidson EH, Hood L
Nat Biotechnol 2008 Mar 26(3):317-25 [abstract on PubMed] [related articles] [full text] [order article]
Selected by | Charles Auffray
Evaluated 29 Apr 2008

Global regulatory logic for specification of an embryonic cell lineage.
Oliveri P, Tu Q, Davidson EH
Proc Natl Acad Sci U S A 2008 Apr 22 105(16):5955-62 [abstract on PubMed] [related articles] [full text] [order article]
Selected by | Charles Auffray
Evaluated 29 Apr 2008

Profiling essential genes in human mammary cells by multiplex RNAi screening.
Silva JM, Marran K, …, Hannon GJ, Chang K
Science 2008 Feb 1 319(5863):617-20 [abstract on PubMed] [related articles] [full text] [order article]
Selected by | Stephen Jackson / Charles Auffray
Evaluated 28 Mar 2008

Cancer proliferation gene discovery through functional genomics.
Schlabach MR, Luo J, …, Hannon GJ, Elledge SJ
Science 2008 Feb 1 319(5863):620-4 [abstract on PubMed] [related articles] [full text] [order article]
Selected by | Stephen Jackson / Paul Workman / Charles Auffray
Evaluated 28 Mar 2008

Rapid appearance and local toxicity of amyloid-beta plaques in a mouse model of Alzheimer's disease.
Meyer-Luehmann M, Spires-Jones TL, …, Bacskai BJ, Hyman BT
Nature 2008 Feb 7 451(7179):720-4 [abstract on PubMed] [related articles] [full text] [order article]
Selected by | Charles Auffray
Evaluated 15 Feb 2008


Rapid cognitive improvement in Alzheimer's disease following perispinal etanercept administration.
Tobinick EL, Gross H
J Neuroinflammation 2008 Jan 9 5(1):2 [abstract on PubMed] [related articles] [FREE full text]
Selected by | Charles Auffray
Evaluated 21 Jan 2008

A predictive model for transcriptional control of physiology in a free living cell.
Bonneau R, Facciotti MT, …, Hood L, Baliga NS
Cell 2007 Dec 28 131(7):1354-65 [abstract on PubMed] [related articles] [full text] [order article]
Selected by | Charles Auffray
Evaluated 11 Jan 2008

The PowerAtlas: a power and sample size atlas for microarray experimental design and research.
Page GP, Edwards JW, …, Trivedi P, Allison DB
BMC Bioinformatics 2006 7:84 [abstract on PubMed] [related articles] [FREE full text]
Selected by | Charles Auffray
Evaluated 1 Oct 2007

A top-down systems biology view of microbiome-mammalian metabolic interactions in a mouse model.
Martin FP, Dumas ME, …, Holmes E, Nicholson JK
Mol Syst Biol 2007 3:112 [abstract on PubMed] [related articles] [FREE full text]
Selected by | Charles Auffray
Evaluated 6 Aug 2007

Advancing translational research with the Semantic Web.
Ruttenberg A, Clark T, …, Herman I, Cheung KH
BMC Bioinformatics 2007 8 Suppl 3:S2 [abstract on PubMed] [related articles] [FREE full text]
Selected by | Charles Auffray
Evaluated 29 May 2007

Critical review of published microarray studies for cancer outcome and guidelines on statistical analysis and reporting.
Dupuy A, Simon RM
J Natl Cancer Inst 2007 Jan 17 99(2):147-57 [abstract on PubMed] [related articles] [full text] [order article]
Selected by | Charles Auffray
Evaluated 4 Apr 2007

An integrative genomics approach to infer causal associations between gene expression and disease.
Schadt EE, Lamb J, …, Sachs A, Lusis AJ
Nat Genet 2005 Jul 37(7):710-7 [abstract on PubMed] [related articles] [full text] [order article]
Selected by | Joshua Plotkin / Charles Auffray
Evaluated 11 Jan 2007

Maternal serotonin is crucial for murine embryonic development.
Côté F, Fligny C, …, Mallet J, Vodjdani G
Proc Natl Acad Sci U S A 2007 Jan 2 104:329-334 [abstract on PubMed] [related articles] [FREE full text]
Selected by | Charles Auffray / Marc Caron / Jonathan Flint
Evaluated 5 Jan 2007

An assessment of recently published gene expression data analyses: reporting experimental design and statistical factors.
Jafari P, Azuaje F
BMC Med Inform Decis Mak 2006 6:27 [abstract on PubMed] [related articles] [FREE full text]
Selected by | Charles Auffray
Evaluated 10 Oct 2006

Tumor stem cells derived from glioblastomas cultured in bFGF and EGF more closely mirror the phenotype and genotype of primary tumors than do serum-cultured cell lines.
Lee J, Kotliarova S, …, Park JK, Fine HA
Cancer Cell 2006 May 9(5):391-403 [abstract on PubMed] [related articles] [full text] [order article]
Selected by | Robert Abraham / Charles Auffray / Brent Cochran
Evaluated 13 Jul 2006


Short blocks from the noncoding parts of the human genome have instances within nearly all known genes and relate to biological processes.
Rigoutsos I, Huynh T, …, McHardy A, Platt D
Proc Natl Acad Sci U S A 2006 Apr 25 103(17):6605-10 [abstract on PubMed] [related articles] [FREE full text]
Selected by | Charles Auffray
Evaluated 12 May 2006

Evolving gene/transcript definitions significantly alter the interpretation of GeneChip data.
Dai M, Wang P, …, Watson SJ, Meng F
Nucleic Acids Res 2005 33(20):e175 [abstract on PubMed] [related articles] [FREE full text]
Selected by | Brent Cochran / Charles Auffray
Evaluated 28 Mar 2006

An interactive power analysis tool for microarray hypothesis testing and generation.
Seo J, Gordish-Dressman H, Hoffman EP
Bioinformatics 2006 Apr 1 22(7):808-14 [abstract on PubMed] [related articles] [FREE full text]
Selected by | Charles Auffray
Evaluated 27 Mar 2006

ARACNE: an algorithm for the reconstruction of gene regulatory networks in a mammalian cellular context.
Margolin AA, Nemenman I, …, Dalla Favera R, Califano A
BMC Bioinformatics 2006 7 Suppl 1:S7 [abstract on PubMed] [related articles] [FREE full text]
Selected by | Charles Auffray
Evaluated 27 Mar 2006

A data integration methodology for systems biology: experimental verification.
Hwang D, Smith JJ, …, Aitchison JD, Hood L
Proc Natl Acad Sci U S A 2005 Nov 29 102(48):17302-7 [abstract on PubMed] [related articles] [FREE full text]
Selected by | Charles Auffray
Evaluated 24 Jan 2006

A data integration methodology for systems biology.
Hwang D, Rust AG, …, Siegel AF, Bolouri H
Proc Natl Acad Sci U S A 2005 Nov 29 102(48):17296-301 [abstract on PubMed] [related articles] [FREE full text]
Selected by | Charles Auffray
Evaluated 24 Jan 2006

Towards a proteome-scale map of the human protein-protein interaction network.
Rual JF, Venkatesan K, …, Roth FP, Vidal M
Nature 2005 Oct 20 437(7062):1173-8 [abstract on PubMed] [related articles] [full text] [order article]
Selected by | Charles Auffray
Evaluated 24 Jan 2006

Fundamental issues in systems biology.
O'Malley MA, Dupré J
Bioessays 2005 Dec 27(12):1270-6 [abstract on PubMed] [related articles] [full text] [order article]
Selected by | Charles Auffray
Evaluated 5 Dec 2005

An index to quantify an individual's scientific research output.
Hirsch JE
Proc Natl Acad Sci U S A 2005 Nov 15 102(46):16569-72 [abstract on PubMed] [related articles] [FREE full text]
Selected by | Marjori Matzke / Charles Auffray
Evaluated 1 Dec 2005

A fine-scale map of recombination rates and hotspots across the human genome.
Myers S, Bottolo L, …, McVean G, Donnelly P
Science 2005 Oct 14 310(5746):321-4 [abstract on PubMed] [related articles] [FREE full text]
Selected by | Richard L Stevens / Charles Auffray / Nicolas Galtier
Evaluated 24 Nov 2005

Eukaryotic cells are dynamically ordered or critical but not chaotic.
Shmulevich I, Kauffman SA, Aldana M
Proc Natl Acad Sci U S A 2005 Sep 20 102(38):13439-44 [abstract on PubMed] [related articles] [FREE full text]
Selected by | Charles Auffray
Evaluated 7 Oct 2005

Uncertainty principle of genetic information in a living cell.
Strippoli P, Canaider S, …, Zannotti M, Frabetti F
Theor Biol Med Model 2005 Sep 30 2:40 [abstract on PubMed] [related articles] [FREE full text]
Selected by | Charles Auffray
Evaluated 6 Oct 2005

Why most published research findings are false.
Ioannidis JP
PLoS Med 2005 Aug 2(8):e124 [abstract on PubMed] [related articles] [FREE full text]
Selected by | Marjori Matzke / Andreas Wagner / Charles Auffray / Andrew Hector
Dissenters | David Sassoon
Author Response | John Ioannidis
Evaluated 20 Sep 2005



Search for a prion-specific nucleic acid.
Safar JG, Kellings K, …, Prusiner SB, Riesner D
J Virol 2005 Aug 79(16):10796-806 [abstract on PubMed] [related articles] [FREE full text]
Selected by | Marjori Matzke / Charles Auffray
Evaluated 8 Sep 2005

Vector-capping: a simple method for preparing a high-quality full-length cDNA library.
Kato S, Ohtoko K, Ohtake H, Kimura T
DNA Res 2005 Feb 28 12(1):53-62 [abstract on PubMed] [related articles] [FREE full text]
Selected by | Charles Auffray
Evaluated 6 Sep 2005

Transcriptional maps of 10 human chromosomes at 5-nucleotide resolution.
Cheng J, Kapranov P, …, Gerhard DS, Gingeras TR
Science 2005 May 20 308(5725):1149-54 [abstract on PubMed] [related articles] [FREE full text]
Selected by | Michael Roth / Charles Auffray / Albert La Spada
Evaluated 28 Jul 2005

Reproducible research: a bioinformatics case study.
Gentleman R
Stat Appl Genet Mol Biol 2005 4(1):Article2 [abstract on PubMed] [related articles] [full text] [order article]
Selected by | Daniel Weeks / Charles Auffray
Evaluated 27 Jul 2005

Extension of a genetic network model by iterative experimentation and mathematical analysis.
Locke JC, Southern MM, …, Turner MS, Millar AJ
Mol Syst Biol 2005 1:2005.0013 [abstract on PubMed] [related articles] [FREE full text]
Selected by | Lee Sweetlove / Charles Auffray / Elena Alvarez-Buylla
Evaluated 27 Jul 2005

MicroRNA expression profiles classify human cancers.
Lu J, Getz G, …, Horvitz HR, Golub TR
Nature 2005 Jun 9 435(7043):834-8 [abstract on PubMed] [related articles] [full text] [order article]
Selected by | Julie Ahringer / Frank Lyko / Fritz Eckstein / Charles Auffray / Miles Wilkinson
Evaluated 27 Jul 2005

Epigenetic differences arise during the lifetime of monozygotic twins.
Fraga MF, Ballestar E, …, Plass C, Esteller M
Proc Natl Acad Sci U S A 2005 Jul 26 102(30):10604-9 [abstract on PubMed] [related articles] [FREE full text]
Selected by | Alain Ghysen / Charles Auffray / Stephen Scherer / Thomas Jenuwein
Evaluated 27 Jul 2005

Interpreting expression profiles of cancers by genome-wide survey of breadth of expression in normal tissues.
Ge X, Yamamoto S, …, Wang SM, Aburatani H
Genomics 2005 Aug 86(2):127-41 [abstract on PubMed] [related articles] [full text] [order article]
Selected by | Charles Auffray
Evaluated 27 Jul 2005

An evolutionary and functional assessment of regulatory network motifs.
Mazurie A, Bottani S, Vergassola M
Genome Biol 2005 6(4):R35 [abstract on PubMed] [related articles] [FREE full text]
Selected by | Arcady Mushegian / Charles Auffray
Evaluated 6 Jun 2005

Reductionism and complexity in molecular biology. Scientists now have the tools to unravel biological and overcome the limitations of reductionism.
Van Regenmortel MH
EMBO Rep 2004 Nov 5(11):1016-20 [abstract on PubMed] [related articles] [FREE full text]
Selected by | Michele Pagano / Charles Auffray
Evaluated 25 Apr 2005

Complex trait analysis of gene expression uncovers polygenic and pleiotropic networks that modulate nervous system function.
Chesler EJ, Lu L, …, Manly KF, Williams RW
Nat Genet 2005 Mar 37(3):233-42 [abstract on PubMed] [related articles] [full text] [order article]
Selected by | David P Wolfer / Charles Auffray
Evaluated 15 Apr 2005

Assessing natural variations in gene expression in humans by comparing with monozygotic twins using microarrays.
Sharma A, Sharma VK, …, Ramachandran S, Brahmachari SK
Physiol Genomics 2005 Mar 21 21(1):117-23 [abstract on PubMed] [related articles] [FREE full text]
Selected by | Charles Auffray
Evaluated 4 Apr 2005

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