16 results on '"Atragene"'
Search Results
2. Modulazione genica e funzionale di cellule endoteliali arteriose e venose infettate in modo persistente da coxsackievirus B: possibile ruolo nei processi di trombogenesi e aterosclerosi
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Ferioli, Elena, Favaro, E., Bottelli, Antonella, Atragene, Daniela, Zanone, M. M., and Conaldi, PIER GIULIO
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- 2004
3. H9c2 cardiac muscle cells express insulin-like growth factor binding protein-3 (IGFBP-3)
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Riccarda GRANATA, Gauna, C., Arnolfo, E., Atragene, D., Broglio, F., Ponti, R., Ricotti, E., and Ghigo, E.
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Insulin-Like Growth Factor Binding Protein 3 ,Blotting, Western ,Animals ,Apoptosis ,Papillary Muscles ,Embryo, Mammalian ,Flow Cytometry ,Culture Media, Serum-Free ,Cell Line ,Rats - Published
- 2003
4. Artemisinin inhibits inducible nitric oxide synthase and nuclear factor NF-kB activation
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Loredana Bergandi, Dario Ghigo, Amalia Bosia, Daniela Atragene, Elisabetta Aldieri, Costanzo Costamagna, and Chiara Riganti
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Lipopolysaccharides ,DNA, Complementary ,Antiparasitic ,medicine.drug_class ,Biophysics ,Nitric Oxide Synthase Type II ,Pharmacology ,Biochemistry ,Nitric oxide ,Cell Line ,Parthenolide ,chemistry.chemical_compound ,Antimalarials ,Mice ,Structural Biology ,parasitic diseases ,Genetics ,medicine ,Animals ,Humans ,NF-kB ,Artemisinin ,Enzyme Inhibitors ,Molecular Biology ,IkB-α ,Natural product ,biology ,Base Sequence ,NF-kappa B ,Cell Biology ,NFKB1 ,Artemisinins ,Malaria ,Nitric oxide synthase ,chemistry ,Cell culture ,biology.protein ,Cytokines ,Nitric Oxide Synthase ,Neuroglia ,Sesquiterpenes ,medicine.drug - Abstract
Artemisinin is a natural product used as an alternative drug in the treatment of severe and multidrug-resistant malaria. In the present work we show that artemisinin shares with other sesquiterpene lactones the ability to inhibit the activation of the nuclear factor NF-kB: by this mechanism, artemisinin, as well as parthenolide, inhibits nitric oxide synthesis in cytokine-stimulated human astrocytoma T67 cells. These results suggest that artemisinin, in addition to its antiparasitic properties, could also exert a therapeutic effect on neurological complications of malaria.
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- 2003
5. Discrete analysis of camelid variable domains: sequences, structures, and in-silico structure prediction: Sequence-structure characteristics of VHH domains
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Melarkode Vattekatte, Akhila, Shinada, Nicolas Ken, Narwani, Tarun, Noël, Floriane, Bertrand, Olivier, Meyniel, Jean-Philippe, Malpertuy, Alain, Gelly, Jean-Christophe, Cadet, Frédéric, De Brevern, Alexandre, Université de La Réunion - Faculté des Sciences et Technologies (FST), Université de La Réunion (UR), Laboratoire d'Excellence : Biogenèse et pathologies du globule rouge (Labex Gr-Ex), Université Sorbonne Paris Cité (USPC)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Université de Paris (UP), Dynamique des Structures et Interactions des Macromolécules Biologiques - Pôle de La Réunion (DSIMB Réunion), Biologie Intégrée du Globule Rouge (BIGR (UMR_S_1134 / U1134)), Institut National de la Transfusion Sanguine [Paris] (INTS)-Université Paris Diderot - Paris 7 (UPD7)-Université de La Réunion (UR)-Université des Antilles (UA)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut National de la Transfusion Sanguine [Paris] (INTS)-Université Paris Diderot - Paris 7 (UPD7)-Université de La Réunion (UR)-Université des Antilles (UA)-Institut National de la Santé et de la Recherche Médicale (INSERM), Institut National de la Transfusion Sanguine [Paris] (INTS)-Université de La Réunion (UR)-Institut National de la Santé et de la Recherche Médicale (INSERM)-CHU Pointe-à-Pitre/Abymes [Guadeloupe] -Université des Antilles (UA)-Université de Paris (UP), Services and solutions for Research Informatics [Paris] (Discngine), Discngine S.A.S [Paris], Institut National de la Transfusion Sanguine [Paris] (INTS), Immunité et cancer (U932), Institut Curie [Paris]-Institut National de la Santé et de la Recherche Médicale (INSERM), ISoft, Atragene (Atragene), Atragene, GR-Ex, Laboratoire d'Excellence, GR-Ex, PEACCEL, Ministry of Research (France)., University Paris Diderot, Sorbonne, Paris Cité (France)., Discngine, Paris, France., ANRT, France., Conseil Régional de la Réunion., The European Social Fund EU (ESF)., French National Computing Centre CINES under grant no. A0010707621 by the GENCI (Grand Equipement National de Calcul Intensif)., French National Computing Centre CINES under grant no. A0040710426 by the GENCI (Grand Equipement National de Calcul Intensif)., University of La Réunion, Réunion Island (France)., National Institute for Blood Transfusion (INTS, France)., National Institute for Health and Medical Research (INSERM, France)., Indo-French Centre for the Promotion of Advanced Research/CEFIPRA: 5302-2., ANR-18-IDEX-0001,Université de Paris,Université de Paris(2018), and ANR-11-IDEX-0005,USPC,Université Sorbonne Paris Cité(2011)
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Frameworks ,Structural alphabet ,[SDV]Life Sciences [q-bio] ,complementarity determining regions ,Bioinformatics Keywords Secondary structure ,Sequence structure relationship ,[SDV.BBM]Life Sciences [q-bio]/Biochemistry, Molecular Biology ,secondary structure ,Subjects Biochemistry ,[SDV.BIBS]Life Sciences [q-bio]/Quantitative Methods [q-bio.QM] ,nanobodies ,Antibodies - Abstract
International audience; Antigen binding by antibodies requires precise orientation of the complementarity- determining region (CDR) loops in the variable domain to establish the correct contact surface. Members of the family Camelidae have a modified form of immunoglobulin gamma (IgG) with only heavy chains, called Heavy Chain only Antibodies (HCAb). Antigen binding in HCAbs is mediated by only 3 CDR loops from the single variable domain (VHH) at the N-terminus of each heavy chain. This feature of the VHH, along with other important features, e.g. easy expression, small size, thermo-stability and hydrophilicity, made them promising candidates for therapeutics and diagnostics. Thus, to design better VHH domains, it is important to thoroughly understand their sequence and structure characteristics and relationships. In this study sequence, characteristics of VHH have been analysed in depth, along with their structural features using innovative approaches, namely a structural alphabet. An elaborate summary of various studies proposing structural models of VHHs showed diversity in the algorithms used. Finally, a case study to elucidate the differences in structural models from single and multiple templates is presented. In this case study, along with the above-mentioned aspects of VHH, an exciting view of various factors in structure prediction of VHH, like template framework selection, is also discussed.
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- 2020
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6. Discrete analysis of camelid variable domains: sequences, structures, and in-silico structure prediction
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Frédéric Cadet, Nicolas K. Shinada, Olivier Bertrand, Floriane Noël, Alexandre G. de Brevern, Alain Malpertuy, Jean-Christophe Gelly, Jean-Philippe Meyniel, Tarun Jairaj Narwani, Akhila Melarkode Vattekatte, Université de La Réunion - Faculté des Sciences et Technologies (FST), Université de La Réunion (UR), Laboratoire d'Excellence : Biogenèse et pathologies du globule rouge (Labex Gr-Ex), Université Sorbonne Paris Cité (USPC)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Université de Paris (UP), Dynamique des Structures et Interactions des Macromolécules Biologiques - Pôle de La Réunion (DSIMB Réunion), Biologie Intégrée du Globule Rouge (BIGR (UMR_S_1134 / U1134)), Institut National de la Transfusion Sanguine [Paris] (INTS)-Université Paris Diderot - Paris 7 (UPD7)-Université de La Réunion (UR)-Université des Antilles (UA)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut National de la Transfusion Sanguine [Paris] (INTS)-Université Paris Diderot - Paris 7 (UPD7)-Université de La Réunion (UR)-Université des Antilles (UA)-Institut National de la Santé et de la Recherche Médicale (INSERM), Institut National de la Transfusion Sanguine [Paris] (INTS)-Université de La Réunion (UR)-Institut National de la Santé et de la Recherche Médicale (INSERM)-CHU Pointe-à-Pitre/Abymes [Guadeloupe] -Université des Antilles (UA)-Université de Paris (UP), Services and solutions for Research Informatics [Paris] (Discngine), Discngine S.A.S [Paris], Institut National de la Transfusion Sanguine [Paris] (INTS), Immunité et cancer (U932), Institut Curie [Paris]-Institut National de la Santé et de la Recherche Médicale (INSERM), ISoft, Atragene (Atragene), Atragene, GR-Ex, Laboratoire d'Excellence, GR-Ex, PEACCEL, Ministry of Research (France)., University Paris Diderot, Sorbonne, Paris Cité (France)., Discngine, Paris, France., ANRT, France., Conseil Régional de la Réunion., The European Social Fund EU (ESF)., French National Computing Centre CINES under grant no. A0010707621 by the GENCI (Grand Equipement National de Calcul Intensif)., French National Computing Centre CINES under grant no. A0040710426 by the GENCI (Grand Equipement National de Calcul Intensif)., University of La Réunion, Réunion Island (France)., National Institute for Blood Transfusion (INTS, France)., National Institute for Health and Medical Research (INSERM, France)., Indo-French Centre for the Promotion of Advanced Research/CEFIPRA: 5302-2., ANR-18-IDEX-0001,Université de Paris,Université de Paris(2018), and ANR-11-IDEX-0005,USPC,Université Sorbonne Paris Cité(2011)
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Bioinformatics ,Computer science ,[SDV]Life Sciences [q-bio] ,Structural alphabet ,In silico ,Bioinformatics Keywords Secondary structure ,Discrete analysis ,lcsh:Medicine ,Complementarity determining region ,Computational biology ,Subjects Biochemistry ,Biochemistry ,Antibodies ,General Biochemistry, Genetics and Molecular Biology ,03 medical and health sciences ,Secondary structure ,[SDV.BBM]Life Sciences [q-bio]/Biochemistry, Molecular Biology ,Protein secondary structure ,Complementarity determining regions ,030304 developmental biology ,0303 health sciences ,Heavy chain ,Frameworks ,General Neuroscience ,lcsh:R ,030302 biochemistry & molecular biology ,General Medicine ,[SDV.BIBS]Life Sciences [q-bio]/Quantitative Methods [q-bio.QM] ,3. Good health ,Template ,Complementarity (molecular biology) ,Sequence structure relationship ,Nanobodies ,General Agricultural and Biological Sciences - Abstract
Antigen binding by antibodies requires precise orientation of the complementarity- determining region (CDR) loops in the variable domain to establish the correct contact surface. Members of the family Camelidae have a modified form of immunoglobulin gamma (IgG) with only heavy chains, called Heavy Chain only Antibodies (HCAb). Antigen binding in HCAbs is mediated by only three CDR loops from the single variable domain (VHH) at the N-terminus of each heavy chain. This feature of the VHH, along with their other important features, e.g., easy expression, small size, thermo-stability and hydrophilicity, made them promising candidates for therapeutics and diagnostics. Thus, to design better VHH domains, it is important to thoroughly understand their sequence and structure characteristics and relationship. In this study, sequence characteristics of VHH domains have been analysed in depth, along with their structural features using innovative approaches, namely a structural alphabet. An elaborate summary of various studies proposing structural models of VHH domains showed diversity in the algorithms used. Finally, a case study to elucidate the differences in structural models from single and multiple templates is presented. In this case study, along with the above-mentioned aspects of VHH, an exciting view of various factors in structure prediction of VHH, like template framework selection, is also discussed.
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- 2020
- Full Text
- View/download PDF
7. Trends in IT Innovation to Build a Next Generation Bioinformatics Solution to Manage and Analyse Biological Big Data Produced by NGS Technologies
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de Brevern, Alexandre G., Meyniel, Jean-Philippe, Fairhead, Cecile, Neuvéglise, Cécile, Malpertuy, Alain, Université Paris Diderot - Paris 7 (UPD7), ISoft, Institut de génétique et microbiologie [Orsay] (IGM), Université Paris-Sud - Paris 11 (UP11)-Centre National de la Recherche Scientifique (CNRS), MICrobiologie de l'ALImentation au Service de la Santé (MICALIS), Institut National de la Recherche Agronomique (INRA)-AgroParisTech, Atragene, Ministry of Research (France), University Paris Diderot, Sorbonne, Paris Cite (France), National Institute for Blood Transfusion (INTS, France), National Institute for Health and Medical Research (INSERM, France), labex GR-Ex, University Paris Sud, CNRS, INRA, AgroParisTech, ISOFT, ATRAGENE, and program 'Investissements d'avenir' of the French National Research Agency [11-LABX-0051, ANR-11-IDEX-0005-02]
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Databases, Factual ,[SDV]Life Sciences [q-bio] ,lcsh:R ,lcsh:Medicine ,Computational Biology ,High-Throughput Nucleotide Sequencing ,Humans ,Review Article ,Genomics ,Software - Abstract
International audience; Sequencing the human genome began in 1994, and 10 years of work were necessary in order to provide a nearly complete sequence. Nowadays, NGS technologies allow sequencing of a whole human genome in a few days. This deluge of data challenges scientists in many ways, as they are faced with data management issues and analysis and visualization drawbacks due to the limitations of current bioinformatics tools. In this paper, we describe how the NGS Big Data revolution changes the way of managing and analysing data. We present how biologists are confronted with abundance of methods, tools, and data formats. To overcome these problems, focus on Big Data Information Technology innovations from web and business intelligence. We underline the interest of NoSQL databases, which are much more efficient than relational databases. Since Big Data leads to the loss of interactivity with data during analysis due to high processing time, we describe solutions from the Business Intelligence that allow one to regain interactivity whatever the volume of data is. We illustrate this point with a focus on the Amadea platform. Finally, we discuss visualization challenges posed by Big Data and present the latest innovations with JavaScript graphic libraries.
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- 2015
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8. Influence of microarrays experiments missing values on the stability of gene groups by hierarchical clustering
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Alexandre G, de Brevern, Serge, Hazout, Alain, Malpertuy, Bioinformatique génomique et moléculaire ((U 726)), Institut National de la Santé et de la Recherche Médicale (INSERM)-Université Paris Diderot - Paris 7 (UPD7), Atragene (Atragene), Atragene, This work was supported by grants from the Ministry for Research, Institute for Health and Medical Care (INSERM) and Genopole®. AdB was supported by the Fondation de la Recherche Médicale., Université Paris Diderot - Paris 7 (UPD7)-Institut National de la Santé et de la Recherche Médicale (INSERM), and de Brevern, Alexandre G.
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[SDV.BIO]Life Sciences [q-bio]/Biotechnology ,MESH: Sacc ,Genes, Fungal ,Saccharomyces cerevisiae ,[SDV.GEN] Life Sciences [q-bio]/Genetics ,MESH: Research Support, Non-U.S. Gov't ,lcsh:Computer applications to medicine. Medical informatics ,MESH: Gene Expression Profiling ,Reference Values ,Gene Expression Regulation, Fungal ,Databases, Genetic ,[SDV.BBM] Life Sciences [q-bio]/Biochemistry, Molecular Biology ,Cluster Analysis ,[SDV.BBM]Life Sciences [q-bio]/Biochemistry, Molecular Biology ,lcsh:QH301-705.5 ,MESH: Databases, Genetic ,Oligonucleotide Array Sequence Analysis ,[SDV.GEN]Life Sciences [q-bio]/Genetics ,Gene Expression Profiling ,MESH: Research Design ,MESH: Reference Values ,Computational Biology ,MESH: Cluster Analysis ,[SDV.BIO] Life Sciences [q-bio]/Biotechnology ,lcsh:Biology (General) ,Research Design ,MESH: Oligonucleotide Array Sequence Analysis ,lcsh:R858-859.7 ,MESH: Genes, Fungal ,MESH: Gene Expression Regulation, Fungal ,Research Article ,MESH: Computational Biology - Abstract
Background Microarray technologies produced large amount of data. The hierarchical clustering is commonly used to identify clusters of co-expressed genes. However, microarray datasets often contain missing values (MVs) representing a major drawback for the use of the clustering methods. Usually the MVs are not treated, or replaced by zero or estimated by the k-Nearest Neighbor (kNN) approach. The topic of the paper is to study the stability of gene clusters, defined by various hierarchical clustering algorithms, of microarrays experiments including or not MVs. Results In this study, we show that the MVs have important effects on the stability of the gene clusters. Moreover, the magnitude of the gene misallocations is depending on the aggregation algorithm. The most appropriate aggregation methods (e.g. complete-linkage and Ward) are highly sensitive to MVs, and surprisingly, for a very tiny proportion of MVs (e.g. 1%). In most of the case, the MVs must be replaced by expected values. The MVs replacement by the kNN approach clearly improves the identification of co-expressed gene clusters. Nevertheless, we observe that kNN approach is less suitable for the extreme values of gene expression. Conclusion The presence of MVs (even at a low rate) is a major factor of gene cluster instability. In addition, the impact depends on the hierarchical clustering algorithm used. Some methods should be used carefully. Nevertheless, the kNN approach constitutes one efficient method for restoring the missing expression gene values, with a low error level. Our study highlights the need of statistical treatments in microarray data to avoid misinterpretation.
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- 2004
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9. Global analysis of VHHs framework regions with a structural alphabet
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Noël, Floriane, Malpertuy, Alain, De Brevern, Alexandre, Biologie Intégrée du Globule Rouge (BIGR (UMR_S_1134 / U1134)), Institut National de la Transfusion Sanguine [Paris] (INTS)-Université Paris Diderot - Paris 7 (UPD7)-Université de La Réunion (UR)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Université des Antilles (UA), Atragene Informatics, and This work was supported by grants from the French Ministry of Research, University Paris Diderot, Sorbonne Paris Cité, French National Institute for Blood Transfusion (INTS), French Institute for Health and Medical Research (INSERM). AdB also acknowledges the Indo-French Centre for the Promotion of Advanced Research / CEFIPRA for collaborative grants (numbers 5302-2). This study was supported by grants from the Laboratory of Excellence GR-Ex, reference ANR-11-LABX-0051. The labex GR-Ex is funded by the programme 'Investissements d’avenir' of the French National Research Agency, reference ANR-11-IDEX-0005-02. Calculations were performed on an SGI cluster granted by Conseil Régional Ile de France and INTS (SESAME Grant).
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[SDV.IMM]Life Sciences [q-bio]/Immunology ,[SDV.BBM]Life Sciences [q-bio]/Biochemistry, Molecular Biology ,MESH: secondary structure ,sequence structure relationship ,structural alphabet ,antibodies ,frameworks ,VHHs ,nanobodies ,[SDV.BIBS]Life Sciences [q-bio]/Quantitative Methods [q-bio.QM] - Abstract
International audience; The VHHs are antigen-binding region/domain of camelid heavy chain antibodies (HCAb). They have many interesting biotechnological and biomedical properties due to their small size, high solubility and stability, and high affinity and specificity for their antigens. HCAb and classical IgGs are evolutionary related and share a common fold. VHHs are composed of regions considered as constant, called the frameworks (FRs) connected by Complementarity Determining Regions (CDRs), a highly variable region that provide interaction with the epitope. Actually, no systematic structural analyses had been performed on VHH structures despite a significant number of structures. This work is the first study to analyse the structural diversity of FRs of VHHs. Using a structural alphabet that allows approximating the local conformation, we show that each of the four FRs do not have a unique structure but exhibit many structural variant patterns. Moreover, no direct simple link between the local conformational change and amino acid composition can be detected. These results indicate that long-range interactions affect the local conformation of FRs and impact the building of structural models.
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- 2016
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10. Le cahier de laboratoire électronique (CLE)
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Amiard, Anabelle, Baczynski, Céline, Blanchet, Christophe, de Brevern, Alexandre, Dorlanne-Messiaen, Emmanuelle, Grognard, Eric, Kisselova, Galina, Malpertuy, Alain, Menez Jamet, Jeanne, Racle, Ivan, Rouger, Céline, de Brevern, Alexandre G., Sanofi, Fovea Pharmaceuticals/Vision Institute, SANOFI Recherche, Novo Nordisk Production SAS, Novo Nordisk, Agilent Technologies France, DSIMB, U 665, Dynamique des Structures et Interactions des Macromolécules Biologiques (DSIMB), Institut National de la Transfusion Sanguine [Paris] (INTS)-Université Paris Diderot - Paris 7 (UPD7)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut National de la Transfusion Sanguine [Paris] (INTS)-Université Paris Diderot - Paris 7 (UPD7)-Institut National de la Santé et de la Recherche Médicale (INSERM), ProductLife (ProductLife), ProductLife, Cambridgesoft, Ipsen, IPSEN, Atragene Informatics, Vaxon Biotech, I. Racle, Bayer Santé familiale SAS, Bayer HealthCare SAS, and Laboratoires Expanscience
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[SPI.OTHER]Engineering Sciences [physics]/Other ,Information sharing ,Intellectual property ,Electronic signature ,Archives ,[SPI.OTHER] Engineering Sciences [physics]/Other ,GLP ,[INFO.INFO-SE] Computer Science [cs]/Software Engineering [cs.SE] ,[INFO.INFO-SE]Computer Science [cs]/Software Engineering [cs.SE] ,Regulatory ,Electronic laboratory notebook (eLN) ,[SDV.BBM] Life Sciences [q-bio]/Biochemistry, Molecular Biology ,[SDV.BBM]Life Sciences [q-bio]/Biochemistry, Molecular Biology ,LIMS ,Patent ,Legal ,Law ,21CFR Part 11 - Abstract
International audience; The laboratory notebook is an essential tool in the company and in the laboratory. It allows durable follow-up of experiments; it is also an essential legal tool. Its electronic versions have become increasingly efficient over recent years, providing new functions, more rapid access to data and aid to decision-making, but they also raise new questions concerning their ease of use and their possible limitations. This article is designed to summarize the specificities and advantages of the electronic laboratory notebook as well as its current limitations.
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- 2011
11. Comparative analysis of missing value imputation methods to improve clustering and interpretation of microarray experiments
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Gaëlle Lelandais, Magalie Celton, Alexandre G. de Brevern, Alain Malpertuy, Sciences Pour l'Oenologie (SPO), Institut National de la Recherche Agronomique (INRA)-Université de Montpellier (UM)-Université Montpellier 1 (UM1)-Institut de Recherche pour le Développement (IRD [Nouvelle-Calédonie])-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), Bioinformatique génomique et moléculaire ((U 726)), Université Paris Diderot - Paris 7 (UPD7)-Institut National de la Santé et de la Recherche Médicale (INSERM), Atragene Informatics, Dynamique des Structures et Interactions des Macromolécules Biologiques (DSIMB), Institut National de la Transfusion Sanguine [Paris] (INTS)-Université Paris Diderot - Paris 7 (UPD7)-Institut National de la Santé et de la Recherche Médicale (INSERM), This work was supported by grants from the Ministère de la Recherche, from French Institute for Health and Medical Research (INSERM), Université Paris Diderot - Paris 7, Institut National de Transfusion Sanguine (INTS) and Genopole®., Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro), Institut National de la Santé et de la Recherche Médicale (INSERM)-Université Paris Diderot - Paris 7 (UPD7), Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Université Montpellier 1 (UM1)-Université de Montpellier (UM)-Institut National de la Recherche Agronomique (INRA), Université Montpellier 1 (UM1)-Institut National de la Recherche Agronomique (INRA)-Université de Montpellier (UM)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), and BMC, Ed.
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lcsh:QH426-470 ,lcsh:Biotechnology ,MESH: Algorithms ,Biotechnologies ,Saccharomyces cerevisiae ,Biology ,computer.software_genre ,03 medical and health sciences ,MESH: Gene Expression Profiling ,0302 clinical medicine ,lcsh:TP248.13-248.65 ,[SDV.BBM.GTP]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Genomics [q-bio.GN] ,Gene cluster ,Genetics ,Cluster Analysis ,Humans ,Imputation (statistics) ,Cluster analysis ,030304 developmental biology ,Oligonucleotide Array Sequence Analysis ,0303 health sciences ,MESH: Humans ,Gene Expression Profiling ,Computational Biology ,cluster de gènes ,Maximization ,Missing data ,MESH: Cluster Analysis ,MESH: Saccharomyces cerevisiae ,Hierarchical clustering ,Gene expression profiling ,lcsh:Genetics ,biopuce ,030220 oncology & carcinogenesis ,MESH: Oligonucleotide Array Sequence Analysis ,[SDV.BBM.GTP] Life Sciences [q-bio]/Biochemistry, Molecular Biology/Genomics [q-bio.GN] ,Data mining ,DNA microarray ,computer ,Algorithms ,Biotechnology ,MESH: Computational Biology ,Research Article - Abstract
BMC Genomics ISI Document Delivery No.: 565GZ Times Cited: 11 Cited Reference Count: 84 Celton, Magalie Malpertuy, Alain Lelandais, Gaelle de Brevern, Alexandre G. Ministere de la Recherche; French Institute for Health and Medical Research (INSERM); Universite - Paris Diderot Paris 7; Institut National de Transfusion Sanguine (INTS) and Genopole(R); Clustering Agreement Ration (CAR) We would like to thanks all the scientists who have deposited their experiments and make them freely available to the scientific community. In the same way, we would like to thanks all the scientists who have developed and distributed missing value replacement methods. This work was supported by grants from the Ministere de la Recherche, from French Institute for Health and Medical Research (INSERM), Universite - Paris Diderot Paris 7, Institut National de Transfusion Sanguine (INTS) and Genopole (R). Clustering Agreement Ration (CAR) was proposed by late Pr. Serge Hazout. Biomed central ltd London; International audience; BACKGROUND: Microarray technologies produced large amount of data. In a previous study, we have shown the interest of k-Nearest Neighbour approach for restoring the missing gene expression values, and its positive impact of the gene clustering by hierarchical algorithm. Since, numerous replacement methods have been proposed to impute missing values (MVs) for microarray data. In this study, we have evaluated twelve different usable methods, and their influence on the quality of gene clustering. Interestingly we have used several datasets, both kinetic and non kinetic experiments from yeast and human. RESULTS: We underline the excellent efficiency of approaches proposed and implemented by Bo and co-workers and especially one based on expected maximization (EM_array). These improvements have been observed also on the imputation of extreme values, the most difficult predictable values. We showed that the imputed MVs have still important effects on the stability of the gene clusters. The improvement on the clustering obtained by hierarchical clustering remains limited and, not sufficient to restore completely the correct gene associations. However, a common tendency can be found between the quality of the imputation method and the gene cluster stability. Even if the comparison between clustering algorithms is a complex task, we observed that k-means approach is more efficient to conserve gene associations. CONCLUSIONS: More than 6.000.000 independent simulations have assessed the quality of 12 imputation methods on five very different biological datasets. Important improvements have so been done since our last study. The EM_array approach constitutes one efficient method for restoring the missing expression gene values, with a lower estimation error level. Nonetheless, the presence of MVs even at a low rate is a major factor of gene cluster instability. Our study highlights the need for a systematic assessment of imputation methods and so of dedicated benchmarks. A noticeable point is the specific influence of some biological dataset.
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- 2009
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12. Discrete analysis of camelid variable domains: sequences, structures, and in-silico structure prediction.
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Melarkode Vattekatte A, Shinada NK, Narwani TJ, Noël F, Bertrand O, Meyniel JP, Malpertuy A, Gelly JC, Cadet F, and de Brevern AG
- Abstract
Antigen binding by antibodies requires precise orientation of the complementarity- determining region (CDR) loops in the variable domain to establish the correct contact surface. Members of the family Camelidae have a modified form of immunoglobulin gamma (IgG) with only heavy chains, called Heavy Chain only Antibodies (HCAb). Antigen binding in HCAbs is mediated by only three CDR loops from the single variable domain (V
H H) at the N-terminus of each heavy chain. This feature of the VH H, along with their other important features, e.g., easy expression, small size, thermo-stability and hydrophilicity, made them promising candidates for therapeutics and diagnostics. Thus, to design better VH H domains, it is important to thoroughly understand their sequence and structure characteristics and relationship. In this study, sequence characteristics of VH H domains have been analysed in depth, along with their structural features using innovative approaches, namely a structural alphabet. An elaborate summary of various studies proposing structural models of VH H domains showed diversity in the algorithms used. Finally, a case study to elucidate the differences in structural models from single and multiple templates is presented. In this case study, along with the above-mentioned aspects of VH H, an exciting view of various factors in structure prediction of VH H, like template framework selection, is also discussed., Competing Interests: Frederic Cadet is associated with PEACCEL, Paris, France. Jean-Christophe Gelly and Alexandre G. de Brevern are associated with IBL, Paris, France. Jean-Philippe Meyneil is employed by ISoft, Paris, France. Alain Malpertuy is employed by Atragene, Paris, France. Nicolas K. Shinada is sponsored by Discngine, Paris, France and ANRT, France. All other authors declare no competing interests., (©2020 Melarkode Vattekatte et al.)- Published
- 2020
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13. Global analysis of VHHs framework regions with a structural alphabet.
- Author
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Noël F, Malpertuy A, and de Brevern AG
- Subjects
- Amino Acid Sequence, Animals, Binding Sites, Antibody genetics, Binding Sites, Antibody immunology, Camelids, New World genetics, Camelids, New World immunology, Camelus genetics, Camelus immunology, Complementarity Determining Regions genetics, Complementarity Determining Regions immunology, Crystallography, X-Ray, Immunoglobulin Heavy Chains genetics, Immunoglobulin Heavy Chains immunology, Immunoglobulin Variable Region genetics, Immunoglobulin Variable Region immunology, Models, Molecular, Sequence Homology, Amino Acid, Species Specificity, Complementarity Determining Regions chemistry, Immunoglobulin Heavy Chains chemistry, Immunoglobulin Variable Region chemistry, Protein Domains, Protein Structure, Secondary
- Abstract
The VHHs are antigen-binding region/domain of camelid heavy chain antibodies (HCAb). They have many interesting biotechnological and biomedical properties due to their small size, high solubility and stability, and high affinity and specificity for their antigens. HCAb and classical IgGs are evolutionary related and share a common fold. VHHs are composed of regions considered as constant, called the frameworks (FRs) connected by Complementarity Determining Regions (CDRs), a highly variable region that provide interaction with the epitope. Actually, no systematic structural analyses had been performed on VHH structures despite a significant number of structures. This work is the first study to analyse the structural diversity of FRs of VHHs. Using a structural alphabet that allows approximating the local conformation, we show that each of the four FRs do not have a unique structure but exhibit many structural variant patterns. Moreover, no direct simple link between the local conformational change and amino acid composition can be detected. These results indicate that long-range interactions affect the local conformation of FRs and impact the building of structural models., (Copyright © 2016 Elsevier B.V. and Société Française de Biochimie et Biologie Moléculaire (SFBBM). All rights reserved.)
- Published
- 2016
- Full Text
- View/download PDF
14. Trends in IT Innovation to Build a Next Generation Bioinformatics Solution to Manage and Analyse Biological Big Data Produced by NGS Technologies.
- Author
-
de Brevern AG, Meyniel JP, Fairhead C, Neuvéglise C, and Malpertuy A
- Subjects
- Databases, Factual trends, Genomics trends, Humans, Computational Biology trends, High-Throughput Nucleotide Sequencing trends, Software
- Abstract
Sequencing the human genome began in 1994, and 10 years of work were necessary in order to provide a nearly complete sequence. Nowadays, NGS technologies allow sequencing of a whole human genome in a few days. This deluge of data challenges scientists in many ways, as they are faced with data management issues and analysis and visualization drawbacks due to the limitations of current bioinformatics tools. In this paper, we describe how the NGS Big Data revolution changes the way of managing and analysing data. We present how biologists are confronted with abundance of methods, tools, and data formats. To overcome these problems, focus on Big Data Information Technology innovations from web and business intelligence. We underline the interest of NoSQL databases, which are much more efficient than relational databases. Since Big Data leads to the loss of interactivity with data during analysis due to high processing time, we describe solutions from the Business Intelligence that allow one to regain interactivity whatever the volume of data is. We illustrate this point with a focus on the Amadea platform. Finally, we discuss visualization challenges posed by Big Data and present the latest innovations with JavaScript graphic libraries.
- Published
- 2015
- Full Text
- View/download PDF
15. [Gene regulation and bioinformatics].
- Author
-
Bichet A, Polverari D, and Malpertuy A
- Subjects
- Conserved Sequence, Humans, Algorithms, Computational Biology methods, Gene Expression Regulation genetics, Genomics methods
- Abstract
Gene regulation networks control differentiation and function of hundreds of cell types. Dysfunctions of transcription factors, which are key elements in the regulation pathways, are involved in numerous pathologies. The recent development of genomics technologies allows the study of gene regulation mechanisms and help us understand their impact on the cells. Bioinformatic tools are needed to fully exploit data obtained by genomics approaches. Thus, bioinformatics play an essential role in the characterisation of the transcription factors binding sites and their target genes. In this review we will introduce the main breakthroughs in bioinformatics area for the comprehension of regulation mechanisms. We will insist on i) the approaches "with a priori" for the genome annotation based on known transcription factors binding sites, ii) the approaches "without a priori" for the discovery of new binding sites and iii) the functional annotation of the target genes of those transcription factors. Finally, we will present recent examples of the fruitful use of in silico studies for the comprehension of regulation mechanisms and of the consequences of their dysfunction.
- Published
- 2005
16. H9c2 cardiac muscle cells express insulin-like growth factor binding protein-3 (IGFBP-3).
- Author
-
Granata R, Gauna C, Arnolfo E, Atragene D, Broglio F, Ponti R, Ricotti E, and Ghigo E
- Subjects
- Animals, Apoptosis, Blotting, Western, Cell Line, Culture Media, Serum-Free pharmacology, Embryo, Mammalian, Flow Cytometry, Papillary Muscles cytology, Papillary Muscles drug effects, Papillary Muscles physiology, Rats, Insulin-Like Growth Factor Binding Protein 3 metabolism, Papillary Muscles metabolism
- Published
- 2002
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