C. Auffray - Academia.edu (original) (raw)

Papers by C. Auffray

Research paper thumbnail of Novel gene transcripts preferentially expressed in human muscles revealed by quantitative hybridization of a high density cDNA array

Genome Research, 1996

A set of 1091 human skeletal muscle cDNA clone inserts representing more than 800 human gene tran... more A set of 1091 human skeletal muscle cDNA clone inserts representing more than 800 human gene transcripts were spotted as PCR products at high density on nylon membranes. Replicas of the filters were hybridized in stringent conditions with 33P-radiolabeled cDNA probes transcribed from skeletal muscle poly(A)+ RNA. Hybridization signals were collected on phosphor screens and processed using a software specifically adapted for this application to identify and quantitate each spot. Parameters likely to influence the hybridization signal intensity were assessed to eliminate artifacts. Each clone was assigned to one of four intensity classes reflecting the steady-state level of transcription of the corresponding gene in skeletal muscle. Differential expression of specific gene transcripts was detected using complex cDNA probes derived from nine different tissues, allowing assessment of their tissue specificity. This made it possible to identify 48 novel gene transcripts (including 7 homol...

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Research paper thumbnail of Towards a European health research and innovation cloud (HRIC)

Genome Medicine, 2020

The European Union (EU) initiative on the Digital Transformation of Health and Care (Digicare) ai... more The European Union (EU) initiative on the Digital Transformation of Health and Care (Digicare) aims to provide the conditions necessary for building a secure, flexible, and decentralized digital health infrastructure. Creating a European Health Research and Innovation Cloud (HRIC) within this environment should enable data sharing and analysis for health research across the EU, in compliance with data protection legislation while preserving the full trust of the participants. Such a HRIC should learn from and build on existing data infrastructures, integrate best practices, and focus on the concrete needs of the community in terms of technologies, governance, management, regulation, and ethics requirements. Here, we describe the vision and expected benefits of digital data sharing in health research activities and present a roadmap that fosters the opportunities while answering the challenges of implementing a HRIC. For this, we put forward five specific recommendations and action p...

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Research paper thumbnail of Identification of a cDNA clone coding for the acetylcholine binding subunit of Torpedo marmorata acetylcholine receptor

The EMBO Journal, 1982

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Research paper thumbnail of LATE-BREAKING ABSTRACT: Transcriptomic fingerprinting in severe adult-onset asthma shows type2-high and inflammatory-cell gene signatures in the U-BIOPRED cohort

European Respiratory Journal, 2015

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Research paper thumbnail of Faculty of 1000 evaluation for Genome-wide dFOXO targets and topology of the transcriptomic response to stress and insulin signalling

F1000 - Post-publication peer review of the biomedical literature, 2011

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Research paper thumbnail of Flash - pour un libre accès aux informations sur le génome

médecine/sciences, 1992

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Research paper thumbnail of Typing of MHC haplotypes in OS chicken by means of RFLP analysis

Progress in clinical and biological research, 1989

For the analysis of the genetic background of autoimmune thyroiditis we used the Obese strain (OS... more For the analysis of the genetic background of autoimmune thyroiditis we used the Obese strain (OS) chicken model which develops a SAT. Practically all animals from this strain show severe lymphoid infiltration of the thyroid gland and circulating autoantibodies against thyroglobulin (Tg-AAb) within a few weeks after hatching. Of the 3 MHC haplotypes (B5, B13, B15) present in the OS, B13 was mostly associated with severe thyroid infiltration. Haplotypes B5 and B15 were associated both with severe, as well as with mild infiltration. To clarify these controversial results published by different groups and to further assess the role of the MHC in the development of SAT, we selected by appropriate breeding sublines with high and low levels of Tg-AAb. With the help of serological methods and GvH assays we were not able to find additional differences in the MHC antigens of that line. Therefore, for further characterization of these haplotypes, RFLP analysis was applied in the present study...

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Research paper thumbnail of Isolation and characterization of three class II MHC genomic clones from the chicken

Journal of immunology (Baltimore, Md. : 1950), Jan 15, 1989

A genomic library was constructed from sperm DNA from an individual of the inbred chicken line G-... more A genomic library was constructed from sperm DNA from an individual of the inbred chicken line G-B2, MHC haplotype B6. The library was screened with a chicken class II probe (beta 2 exon specific) and three MHC class II beta chain genomic clones were isolated. The restriction maps of the three clones showed that each of the three clones was unique. The position of the beta chain sequence was located in each of the three genomic clones by Southern blot hybridization. Subclones containing the beta chain gene were produced from each of the genomic clones and the orientation of the leader peptide, beta 1, beta 2, transmembrane, and cytoplasmic exons was determined by Southern blot hybridization and nucleotide sequencing. The complete nucleotide sequence of two of the three subclones was determined. Comparison of the nucleotide and predicted amino acid sequences of the two subclones with other class II beta chain sequences showed that the B6 chicken beta chain genes are evolutionarily re...

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Research paper thumbnail of Identification of 16 Chicken Microchromosomes by Molecular Markers Using Two-colour Fluorescence In Situ Hybridization (FISH)

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Research paper thumbnail of Faculty of 1000 evaluation for Identification of aberrant pathways and network activities from high-throughput data

F1000 - Post-publication peer review of the biomedical literature, 2012

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Research paper thumbnail of A physical map of 30,000 human genes

Science, 1998

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Research paper thumbnail of 088 Bioénergétique de l’atteinte musculaire squelettique au cours de la bronchopneumopathie chronique obstructive (BPCO) : une étude de biologie systémique

Revue des Maladies Respiratoires, 2007

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Research paper thumbnail of The rat vitamin-D-dependent calcium-binding protein (9-kDa CaBP) gene. Complete nucleotide sequence and structural organization

European Journal of Biochemistry, 1988

The structural organization of the entire rat vitamin-D-dependent calcium-binding protein (9-kDa ... more The structural organization of the entire rat vitamin-D-dependent calcium-binding protein (9-kDa CaBP) gene was determined by analysis of overlapping genomic clones isolated from a rat genomic library using the rat 9-kDa CaBP cDNA [Desplan C., Heidmann O., Lillie J., Auffray C. and Thomasset M. (1983) J. Biol. Chem. 258, 13502-13505]. These clones together span 30 kbp of rat genomic DNA, with the rat 9-kDa CaBP gene lying in the middle. The 9-kDa CaBP gene is 2.5 kbp long and contains three exons interrupted by two introns. The first exon contains almost the entire 5' untranslated region. The second exon codes for the calcium-binding site I, the third exon codes for site II and the 3' untranslated region. Therefore each of the calcium-binding domains is encoded by single, separate exons. The transcription initiation site was identified by S1 nuclease mapping and primer extension. A consensus sequence TATAAA is localized 31 bp upstream from the cap site and the 'CCAAT-box' lies upstream from the transcription start. Single (AC)25 and (AG)23 repeats are present in the second intron together with an Alu-like sequence. Repetitive elements are present 5 kbp upstream from the cap site and in the 3' flanking region. Comparison of the known rat CaBP sequences (9-kDa CaBP, 28-kDa CaBP, S100 protein) shows that the 9-kDa CaBP is more closely related to the S100 protein than to the 28-kDa CaBP. There is no evidence to indicate that 9-kDa CaBP has arisen from the 28-kDa CaBP.

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Research paper thumbnail of Gene organization of DC and DX subregions of the human major histocompatibility complex

Proceedings of the National Academy of Sciences, 1985

The DC and DX subregions of the human major histocompatibility complex (MHC) have been cloned fro... more The DC and DX subregions of the human major histocompatibility complex (MHC) have been cloned from a cosmid library made from a human B-cell line, Priess. The DC subregion, 48 kilobases, includes the DC alpha and DC beta genes. A second DC-like region, the DX subregion, 35 kilobases, contains the DX alpha gene and a newly found beta gene termed DX beta. Since the DC and DX genes are highly homologous in nucleotide sequence, gene size, exon-intron organization, and direction of transcription, the DC and DX subregions were presumably generated by duplication of an ancestral alpha-beta gene pair. Nucleotide sequencing indicates that all four genes have intact coding sequences and promoter regions. Homology between the upstream promoter sequences of these four genes and seven other class II genes at nucleotides -69 to -78 and -98 to -110 highlights these previously described conserved elements. Moreover, a striking conservation of flanking alpha-gene-specific and beta-gene-specific sequ...

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Research paper thumbnail of M19 Modulates Skeletal Muscle Differentiation and Insulin Secretion in Pancreatic β-Cells through Modulation of Respiratory Chain Activity

PLoS ONE, 2012

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Research paper thumbnail of DNA sequences

Nature, 1992

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Research paper thumbnail of Preface: Integrative Statistical and Computational Methods for Genomics Studies

Journal of Biological Systems, 2002

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Research paper thumbnail of A prioritization analysis of disease association by data-mining of functional annotation of human genes

Genomics, 2012

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Research paper thumbnail of Integrated Physical, Genetic, and Genic Map Covering 3 Mb Around the Human NGF Gene (NGFB) at 1p13

Genomics, 1996

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Research paper thumbnail of Bridging the gap between systems biology and medicine

Genome Medicine, 2009

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Research paper thumbnail of Novel gene transcripts preferentially expressed in human muscles revealed by quantitative hybridization of a high density cDNA array

Genome Research, 1996

A set of 1091 human skeletal muscle cDNA clone inserts representing more than 800 human gene tran... more A set of 1091 human skeletal muscle cDNA clone inserts representing more than 800 human gene transcripts were spotted as PCR products at high density on nylon membranes. Replicas of the filters were hybridized in stringent conditions with 33P-radiolabeled cDNA probes transcribed from skeletal muscle poly(A)+ RNA. Hybridization signals were collected on phosphor screens and processed using a software specifically adapted for this application to identify and quantitate each spot. Parameters likely to influence the hybridization signal intensity were assessed to eliminate artifacts. Each clone was assigned to one of four intensity classes reflecting the steady-state level of transcription of the corresponding gene in skeletal muscle. Differential expression of specific gene transcripts was detected using complex cDNA probes derived from nine different tissues, allowing assessment of their tissue specificity. This made it possible to identify 48 novel gene transcripts (including 7 homol...

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Research paper thumbnail of Towards a European health research and innovation cloud (HRIC)

Genome Medicine, 2020

The European Union (EU) initiative on the Digital Transformation of Health and Care (Digicare) ai... more The European Union (EU) initiative on the Digital Transformation of Health and Care (Digicare) aims to provide the conditions necessary for building a secure, flexible, and decentralized digital health infrastructure. Creating a European Health Research and Innovation Cloud (HRIC) within this environment should enable data sharing and analysis for health research across the EU, in compliance with data protection legislation while preserving the full trust of the participants. Such a HRIC should learn from and build on existing data infrastructures, integrate best practices, and focus on the concrete needs of the community in terms of technologies, governance, management, regulation, and ethics requirements. Here, we describe the vision and expected benefits of digital data sharing in health research activities and present a roadmap that fosters the opportunities while answering the challenges of implementing a HRIC. For this, we put forward five specific recommendations and action p...

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Research paper thumbnail of Identification of a cDNA clone coding for the acetylcholine binding subunit of Torpedo marmorata acetylcholine receptor

The EMBO Journal, 1982

Bookmarks Related papers MentionsView impact

Research paper thumbnail of LATE-BREAKING ABSTRACT: Transcriptomic fingerprinting in severe adult-onset asthma shows type2-high and inflammatory-cell gene signatures in the U-BIOPRED cohort

European Respiratory Journal, 2015

Bookmarks Related papers MentionsView impact

Research paper thumbnail of Faculty of 1000 evaluation for Genome-wide dFOXO targets and topology of the transcriptomic response to stress and insulin signalling

F1000 - Post-publication peer review of the biomedical literature, 2011

Bookmarks Related papers MentionsView impact

Research paper thumbnail of Flash - pour un libre accès aux informations sur le génome

médecine/sciences, 1992

Bookmarks Related papers MentionsView impact

Research paper thumbnail of Typing of MHC haplotypes in OS chicken by means of RFLP analysis

Progress in clinical and biological research, 1989

For the analysis of the genetic background of autoimmune thyroiditis we used the Obese strain (OS... more For the analysis of the genetic background of autoimmune thyroiditis we used the Obese strain (OS) chicken model which develops a SAT. Practically all animals from this strain show severe lymphoid infiltration of the thyroid gland and circulating autoantibodies against thyroglobulin (Tg-AAb) within a few weeks after hatching. Of the 3 MHC haplotypes (B5, B13, B15) present in the OS, B13 was mostly associated with severe thyroid infiltration. Haplotypes B5 and B15 were associated both with severe, as well as with mild infiltration. To clarify these controversial results published by different groups and to further assess the role of the MHC in the development of SAT, we selected by appropriate breeding sublines with high and low levels of Tg-AAb. With the help of serological methods and GvH assays we were not able to find additional differences in the MHC antigens of that line. Therefore, for further characterization of these haplotypes, RFLP analysis was applied in the present study...

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Research paper thumbnail of Isolation and characterization of three class II MHC genomic clones from the chicken

Journal of immunology (Baltimore, Md. : 1950), Jan 15, 1989

A genomic library was constructed from sperm DNA from an individual of the inbred chicken line G-... more A genomic library was constructed from sperm DNA from an individual of the inbred chicken line G-B2, MHC haplotype B6. The library was screened with a chicken class II probe (beta 2 exon specific) and three MHC class II beta chain genomic clones were isolated. The restriction maps of the three clones showed that each of the three clones was unique. The position of the beta chain sequence was located in each of the three genomic clones by Southern blot hybridization. Subclones containing the beta chain gene were produced from each of the genomic clones and the orientation of the leader peptide, beta 1, beta 2, transmembrane, and cytoplasmic exons was determined by Southern blot hybridization and nucleotide sequencing. The complete nucleotide sequence of two of the three subclones was determined. Comparison of the nucleotide and predicted amino acid sequences of the two subclones with other class II beta chain sequences showed that the B6 chicken beta chain genes are evolutionarily re...

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Research paper thumbnail of Identification of 16 Chicken Microchromosomes by Molecular Markers Using Two-colour Fluorescence In Situ Hybridization (FISH)

Bookmarks Related papers MentionsView impact

Research paper thumbnail of Faculty of 1000 evaluation for Identification of aberrant pathways and network activities from high-throughput data

F1000 - Post-publication peer review of the biomedical literature, 2012

Bookmarks Related papers MentionsView impact

Research paper thumbnail of A physical map of 30,000 human genes

Science, 1998

Bookmarks Related papers MentionsView impact

Research paper thumbnail of 088 Bioénergétique de l’atteinte musculaire squelettique au cours de la bronchopneumopathie chronique obstructive (BPCO) : une étude de biologie systémique

Revue des Maladies Respiratoires, 2007

Bookmarks Related papers MentionsView impact

Research paper thumbnail of The rat vitamin-D-dependent calcium-binding protein (9-kDa CaBP) gene. Complete nucleotide sequence and structural organization

European Journal of Biochemistry, 1988

The structural organization of the entire rat vitamin-D-dependent calcium-binding protein (9-kDa ... more The structural organization of the entire rat vitamin-D-dependent calcium-binding protein (9-kDa CaBP) gene was determined by analysis of overlapping genomic clones isolated from a rat genomic library using the rat 9-kDa CaBP cDNA [Desplan C., Heidmann O., Lillie J., Auffray C. and Thomasset M. (1983) J. Biol. Chem. 258, 13502-13505]. These clones together span 30 kbp of rat genomic DNA, with the rat 9-kDa CaBP gene lying in the middle. The 9-kDa CaBP gene is 2.5 kbp long and contains three exons interrupted by two introns. The first exon contains almost the entire 5' untranslated region. The second exon codes for the calcium-binding site I, the third exon codes for site II and the 3' untranslated region. Therefore each of the calcium-binding domains is encoded by single, separate exons. The transcription initiation site was identified by S1 nuclease mapping and primer extension. A consensus sequence TATAAA is localized 31 bp upstream from the cap site and the 'CCAAT-box' lies upstream from the transcription start. Single (AC)25 and (AG)23 repeats are present in the second intron together with an Alu-like sequence. Repetitive elements are present 5 kbp upstream from the cap site and in the 3' flanking region. Comparison of the known rat CaBP sequences (9-kDa CaBP, 28-kDa CaBP, S100 protein) shows that the 9-kDa CaBP is more closely related to the S100 protein than to the 28-kDa CaBP. There is no evidence to indicate that 9-kDa CaBP has arisen from the 28-kDa CaBP.

Bookmarks Related papers MentionsView impact

Research paper thumbnail of Gene organization of DC and DX subregions of the human major histocompatibility complex

Proceedings of the National Academy of Sciences, 1985

The DC and DX subregions of the human major histocompatibility complex (MHC) have been cloned fro... more The DC and DX subregions of the human major histocompatibility complex (MHC) have been cloned from a cosmid library made from a human B-cell line, Priess. The DC subregion, 48 kilobases, includes the DC alpha and DC beta genes. A second DC-like region, the DX subregion, 35 kilobases, contains the DX alpha gene and a newly found beta gene termed DX beta. Since the DC and DX genes are highly homologous in nucleotide sequence, gene size, exon-intron organization, and direction of transcription, the DC and DX subregions were presumably generated by duplication of an ancestral alpha-beta gene pair. Nucleotide sequencing indicates that all four genes have intact coding sequences and promoter regions. Homology between the upstream promoter sequences of these four genes and seven other class II genes at nucleotides -69 to -78 and -98 to -110 highlights these previously described conserved elements. Moreover, a striking conservation of flanking alpha-gene-specific and beta-gene-specific sequ...

Bookmarks Related papers MentionsView impact

Research paper thumbnail of M19 Modulates Skeletal Muscle Differentiation and Insulin Secretion in Pancreatic β-Cells through Modulation of Respiratory Chain Activity

PLoS ONE, 2012

Bookmarks Related papers MentionsView impact

Research paper thumbnail of DNA sequences

Nature, 1992

Bookmarks Related papers MentionsView impact

Research paper thumbnail of Preface: Integrative Statistical and Computational Methods for Genomics Studies

Journal of Biological Systems, 2002

Bookmarks Related papers MentionsView impact

Research paper thumbnail of A prioritization analysis of disease association by data-mining of functional annotation of human genes

Genomics, 2012

Bookmarks Related papers MentionsView impact

Research paper thumbnail of Integrated Physical, Genetic, and Genic Map Covering 3 Mb Around the Human NGF Gene (NGFB) at 1p13

Genomics, 1996

Bookmarks Related papers MentionsView impact

Research paper thumbnail of Bridging the gap between systems biology and medicine

Genome Medicine, 2009

Bookmarks Related papers MentionsView impact