LIVIVO - The Search Portal for Life Sciences

zur deutschen Oberfläche wechseln
Advanced search

Search results

Result 1 - 9 of total 9

Search options

  1. Article ; Online: Single cell transcriptome sequencing of stimulated and frozen human peripheral blood mononuclear cells

    Céline Derbois / Marie-Ange Palomares / Jean-François Deleuze / Eric Cabannes / Eric Bonnet

    Scientific Data, Vol 10, Iss 1, Pp 1-

    2023  Volume 11

    Abstract: Abstract Peripheral blood mononuclear cells (PBMCs) are blood cells that are a critical part of the immune system used to fight off infection, defending our bodies from harmful pathogens. In biomedical research, PBMCs are commonly used to study global ... ...

    Abstract Abstract Peripheral blood mononuclear cells (PBMCs) are blood cells that are a critical part of the immune system used to fight off infection, defending our bodies from harmful pathogens. In biomedical research, PBMCs are commonly used to study global immune response to disease outbreak and progression, pathogen infections, for vaccine development and a multitude of other clinical applications. Over the past few years, the revolution in single-cell RNA sequencing (scRNA-seq) has enabled an unbiased quantification of gene expression in thousands of individual cells, which provides a more efficient tool to decipher the immune system in human diseases. In this work, we generate scRNA-seq data from human PBMCs at high sequencing depth (>100,000 reads/cell) for more than 30,000 cells, in resting, stimulated, fresh and frozen conditions. The data generated can be used for benchmarking batch correction and data integration methods, and to study the effect of freezing-thawing cycles on the quality of immune cell populations and their transcriptomic profiles.
    Keywords Science ; Q
    Subject code 610
    Language English
    Publishing date 2023-07-01T00:00:00Z
    Publisher Nature Portfolio
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

    Full text online

    More links

    Kategorien

    Inter-library loan at ZB MED

    Your chosen title can be delivered directly to ZB MED Cologne location if you are registered as a user at ZB MED Cologne.

  2. Article ; Online: New and emerging agents in the management of lipodystrophy in HIV-infected patients

    Eric Bonnet

    HIV/AIDS : Research and Palliative Care, Vol 2010, Iss default, Pp 167-

    2010  Volume 178

    Abstract: Eric BonnetService des Maladies Infectieuses, Hôpital Purpan, Toulouse, FranceAbstract: Lipodystrophy remains a major long-term complication in human immunodeficiency virus-infected patients under antiretroviral (ARV) therapy. Patients may present with ... ...

    Abstract Eric BonnetService des Maladies Infectieuses, Hôpital Purpan, Toulouse, FranceAbstract: Lipodystrophy remains a major long-term complication in human immunodeficiency virus-infected patients under antiretroviral (ARV) therapy. Patients may present with lipoatrophy or lipohypertrophy or both. The choice of treatments to improve fat redistribution depends on the form of lipodystrophy and its duration. Measures known to improve lipoatrophy are switches in ARV therapy (stavudine or zidovudine to abacavir or tenofovir) and filling interventions. Pioglitazone may be added to these measures, although any benefits appear small. Uridine and leptin were found to be disappointing so far. Regarding lipohypertrophy, diet and exercise, recombinant human growth hormone, and metformin may reduce visceral fat, but may worsen subcutaneous lipoatrophy. Surgical therapy may be required. Attractive pharmacologic treatments include growth hormone-releasing factor and leptin. Adiponectin and adiponectin receptors are promising therapeutic targets to explore.Keywords: lipoatrophy, lipohypertrophy, lipodystrophy, treatment, HIV, AIDS
    Keywords Immunologic diseases. Allergy ; RC581-607 ; Specialties of internal medicine ; RC581-951 ; Internal medicine ; RC31-1245 ; Medicine ; R ; DOAJ:Allergy and Immunology ; DOAJ:Medicine (General) ; DOAJ:Health Sciences ; Medicine (General) ; R5-920
    Subject code 610
    Language English
    Publishing date 2010-09-01T00:00:00Z
    Publisher Dove Medical Press
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

    Full text online

    More links

    Kategorien

    Inter-library loan at ZB MED

    Your chosen title can be delivered directly to ZB MED Cologne location if you are registered as a user at ZB MED Cologne.

  3. Article ; Online: DEVEA

    Solène Brohard / Carole Escartin / Eric Bonnet / Fernando Perez-Sanz / Jean-François Deleuze / Miriam Riquelme-Perez

    F1000Research, Vol

    an interactive shiny application for Differential Expression analysis, data Visualization and Enrichment Analysis of transcriptomics data [version 2; peer review: 2 approved]

    2023  Volume 11

    Abstract: We are at a time of considerable growth in transcriptomics studies and subsequent in silico analysis. RNA sequencing (RNA-Seq) is the most widely used approach to analyse the transcriptome and is integrated in many studies. The processing of ... ...

    Abstract We are at a time of considerable growth in transcriptomics studies and subsequent in silico analysis. RNA sequencing (RNA-Seq) is the most widely used approach to analyse the transcriptome and is integrated in many studies. The processing of transcriptomic data typically requires a noteworthy number of steps, statistical knowledge, and coding skills, which are not accessible to all scientists. Despite the development of a plethora of software applications over the past few years to address this concern, there is still room for improvement. Here we present DEVEA, an R shiny application tool developed to perform differential expression analysis, data visualization and enrichment pathway analysis mainly from transcriptomics data, but also from simpler gene lists with or without statistical values. The intuitive and easy-to-manipulate interface facilitates gene expression exploration through numerous interactive figures and tables, and statistical comparisons of expression profile levels between groups. Further meta-analysis such as enrichment analysis is also possible, without the need for prior bioinformatics expertise. DEVEA performs a comprehensive analysis from multiple and flexible data sources representing distinct analytical steps. Consequently, it produces dynamic graphs and tables, to explore the expression levels and statistical results from differential expression analysis. Moreover, it generates a comprehensive pathway analysis to extend biological insights. Finally, a complete and customizable HTML report can be extracted to enable the scientists to explore results beyond the application. DEVEA is freely accessible at https://shiny.imib.es/devea/ and the source code is available on our GitHub repository https://github.com/MiriamRiquelmeP/DEVEA.
    Keywords Bioinformatics ; transcriptomics ; RNA sequencing ; differential expression analysis ; enrichment analysis ; visualization ; eng ; Medicine ; R ; Science ; Q
    Subject code 306
    Language English
    Publishing date 2023-03-01T00:00:00Z
    Publisher F1000 Research Ltd
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

    Full text online

    More links

    Kategorien

    Inter-library loan at ZB MED

    Your chosen title can be delivered directly to ZB MED Cologne location if you are registered as a user at ZB MED Cologne.

  4. Article ; Online: Integrative multi-omics module network inference with Lemon-Tree.

    Eric Bonnet / Laurence Calzone / Tom Michoel

    PLoS Computational Biology, Vol 11, Iss 2, p e

    2015  Volume 1003983

    Abstract: Module network inference is an established statistical method to reconstruct co-expression modules and their upstream regulatory programs from integrated multi-omics datasets measuring the activity levels of various cellular components across different ... ...

    Abstract Module network inference is an established statistical method to reconstruct co-expression modules and their upstream regulatory programs from integrated multi-omics datasets measuring the activity levels of various cellular components across different individuals, experimental conditions or time points of a dynamic process. We have developed Lemon-Tree, an open-source, platform-independent, modular, extensible software package implementing state-of-the-art ensemble methods for module network inference. We benchmarked Lemon-Tree using large-scale tumor datasets and showed that Lemon-Tree algorithms compare favorably with state-of-the-art module network inference software. We also analyzed a large dataset of somatic copy-number alterations and gene expression levels measured in glioblastoma samples from The Cancer Genome Atlas and found that Lemon-Tree correctly identifies known glioblastoma oncogenes and tumor suppressors as master regulators in the inferred module network. Novel candidate driver genes predicted by Lemon-Tree were validated using tumor pathway and survival analyses. Lemon-Tree is available from http://lemon-tree.googlecode.com under the GNU General Public License version 2.0.
    Keywords Biology (General) ; QH301-705.5
    Subject code 006
    Language English
    Publishing date 2015-02-01T00:00:00Z
    Publisher Public Library of Science (PLoS)
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

    Full text online

    More links

    Kategorien

    Inter-library loan at ZB MED

    Your chosen title can be delivered directly to ZB MED Cologne location if you are registered as a user at ZB MED Cologne.

  5. Article ; Online: Systematic analysis of TruSeq, SMARTer and SMARTer Ultra-Low RNA-seq kits for standard, low and ultra-low quantity samples

    Marie-Ange Palomares / Cyril Dalmasso / Eric Bonnet / Céline Derbois / Solène Brohard-Julien / Christophe Ambroise / Christophe Battail / Jean-François Deleuze / Robert Olaso

    Scientific Reports, Vol 9, Iss 1, Pp 1-

    2019  Volume 12

    Abstract: Abstract High-throughput RNA-sequencing has become the gold standard method for whole-transcriptome gene expression analysis, and is widely used in numerous applications to study cell and tissue transcriptomes. It is also being increasingly used in a ... ...

    Abstract Abstract High-throughput RNA-sequencing has become the gold standard method for whole-transcriptome gene expression analysis, and is widely used in numerous applications to study cell and tissue transcriptomes. It is also being increasingly used in a number of clinical applications, including expression profiling for diagnostics and alternative transcript detection. However, despite its many advantages, RNA sequencing can be challenging in some situations, for instance in cases of low input amounts or degraded RNA samples. Several protocols have been proposed to overcome these challenges, and many are available as commercial kits. In this study, we systematically test three recent commercial technologies for RNA-seq library preparation (TruSeq, SMARTer and SMARTer Ultra-Low) on human biological reference materials, using standard (1 mg), low (100 ng and 10 ng) and ultra-low (<1 ng) input amounts, and for mRNA and total RNA, stranded and unstranded. The results are analyzed using read quality and alignment metrics, gene detection and differential gene expression metrics. Overall, we show that the TruSeq kit performs well with an input amount of 100 ng, while the SMARTer kit shows decreased performance for inputs of 100 and 10 ng, and the SMARTer Ultra-Low kit performs relatively well for input amounts <1 ng. All the results are discussed in detail, and we provide guidelines for biologists for the selection of an RNA-seq library preparation kit.
    Keywords Medicine ; R ; Science ; Q
    Subject code 621
    Language English
    Publishing date 2019-05-01T00:00:00Z
    Publisher Nature Publishing Group
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

    Full text online

    More links

    Kategorien

    Inter-library loan at ZB MED

    Your chosen title can be delivered directly to ZB MED Cologne location if you are registered as a user at ZB MED Cologne.

  6. Article ; Online: zt

    Yves Van de Peer / Eric Bonnet

    Journal of Statistical Software, Vol 7, Iss

    A Sofware Tool for Simple and Partial Mantel Tests

    2002  Volume 10

    Keywords Statistics ; HA1-4737 ; Social Sciences ; H ; DOAJ:Statistics ; DOAJ:Mathematics and Statistics
    Language English
    Publishing date 2002-01-01T00:00:00Z
    Publisher University of California at Los Angeles, Department of Statistics
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

    Full text online

    More links

    Kategorien

    Inter-library loan at ZB MED

    Your chosen title can be delivered directly to ZB MED Cologne location if you are registered as a user at ZB MED Cologne.

  7. Article ; Online: zt

    Eric Bonnet / Yves Van de Peer

    Journal of Statistical Software, Vol 7, Iss 1, Pp 1-

    A Sofware Tool for Simple and Partial Mantel Tests

    2002  Volume 12

    Abstract: Different methods of data analysis (e.g. clustering and ordination) are based on distance matrices. In some cases, researchers may wish to compare several distance matrices with one another in order to test a hypothesis concerning a possible relationship ...

    Abstract Different methods of data analysis (e.g. clustering and ordination) are based on distance matrices. In some cases, researchers may wish to compare several distance matrices with one another in order to test a hypothesis concerning a possible relationship between these matrices. However, this is not always self-evident. Usually, values in distance matrices are, in some way, correlated and therefore the usual assumption of independence between objects is violated in the classical tests approach. Furthermore, often, spurious correlations can be observed when comparing two distances matrices. A classic example is the comparison between genetic and environmental distances. Colonies that are in close proximity of each other tend to have similar environments and therefore there will be a positive correlation between environmental and geographical distances. Such colonies will also be more likely to exchange migrants so that genetic distances will be positively correlated with spatial distances. The consequence is that an observed positive association between genetic and environmental distances may be simply due to spatial effects. The most widely used method to account for distance correlations is a procedure known as the Mantel test (Mantel, 1967; Mantel and Valand, 1970 following the pioneering work of Daniels, 1944

    Daniels and Kendall 1947). The simple Mantel test considers two matrices while an extension known as the partial Mantel test considers three matrices. These tools are widely used in different fields of research such as population genetics, ecology, anthropology, psychometrics and sociology.
    Keywords Statistics ; HA1-4737 ; Social Sciences ; H
    Subject code 310
    Language English
    Publishing date 2002-10-01T00:00:00Z
    Publisher University of California, Los Angeles
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

    Full text online

    More links

    Kategorien

    Inter-library loan at ZB MED

    Your chosen title can be delivered directly to ZB MED Cologne location if you are registered as a user at ZB MED Cologne.

  8. Article: Hot topics in the diagnosis and management of skin and soft-tissue infections

    Esposito, Silvano / Ata Nevzat Yalcin / David Chien Lye / Emilio Bouza / Eric Bonnet / Giuseppe De Simone / Ian Gould / John Segreti / Kordo Saeed / Matteo Bassetti / Matthew Dryden / Monica Chan / Serhat Unal

    International journal of antimicrobial agents. 2016 July, v. 48, no. 1

    2016  

    Abstract: Eighteen hot topics regarding the diagnosis and management of skin and soft-tissue infections (SSTIs) were selected and reviewed by members of the SSTI Working Group of the International Society of Chemotherapy (ISC). Despite the large amount of ... ...

    Abstract Eighteen hot topics regarding the diagnosis and management of skin and soft-tissue infections (SSTIs) were selected and reviewed by members of the SSTI Working Group of the International Society of Chemotherapy (ISC). Despite the large amount of literature available on the issue selected, there are still many unknowns with regard to many of them and further studies are required to answer these challenging issues that face clinicians on a daily basis.
    Keywords anti-infective agents ; disease control ; disease diagnosis ; skin (animal)
    Language English
    Dates of publication 2016-07
    Size p. 19-26.
    Publishing place Elsevier B.V.
    Document type Article
    ZDB-ID 1093977-5
    ISSN 1872-7913 ; 0924-8579
    ISSN (online) 1872-7913
    ISSN 0924-8579
    DOI 10.1016/j.ijantimicag.2016.04.011
    Database NAL-Catalogue (AGRICOLA)

    More links

    Kategorien

    In stock of ZB MED Cologne/Königswinter

    Zs.A 3368: Show issues Location:
    Je nach Verfügbarkeit (siehe Angabe bei Bestand)
    bis Jg. 1994: Bestellungen von Artikeln über das Online-Bestellformular
    Jg. 1995 - 2021: Lesesall (2.OG)
    ab Jg. 2022: Lesesaal (EG)
    Zs.MO 500: Show issues

    Order via subito

    This service is chargeable due to the Delivery terms set by subito. Orders including an article and supplementary material will be classified as separate orders. In these cases, fees will be demanded for each order.

  9. Article ; Online: Module network inference from a cancer gene expression data set identifies microRNA regulated modules.

    Eric Bonnet / Marianthi Tatari / Anagha Joshi / Tom Michoel / Kathleen Marchal / Geert Berx / Yves Van de Peer

    PLoS ONE, Vol 5, Iss 4, p e

    2010  Volume 10162

    Abstract: BACKGROUND: MicroRNAs (miRNAs) are small RNAs that recognize and regulate mRNA target genes. Multiple lines of evidence indicate that they are key regulators of numerous critical functions in development and disease, including cancer. However, defining ... ...

    Abstract BACKGROUND: MicroRNAs (miRNAs) are small RNAs that recognize and regulate mRNA target genes. Multiple lines of evidence indicate that they are key regulators of numerous critical functions in development and disease, including cancer. However, defining the place and function of miRNAs in complex regulatory networks is not straightforward. Systems approaches, like the inference of a module network from expression data, can help to achieve this goal. METHODOLOGY/PRINCIPAL FINDINGS: During the last decade, much progress has been made in the development of robust and powerful module network inference algorithms. In this study, we analyze and assess experimentally a module network inferred from both miRNA and mRNA expression data, using our recently developed module network inference algorithm based on probabilistic optimization techniques. We show that several miRNAs are predicted as statistically significant regulators for various modules of tightly co-expressed genes. A detailed analysis of three of those modules demonstrates that the specific assignment of miRNAs is functionally coherent and supported by literature. We further designed a set of experiments to test the assignment of miR-200a as the top regulator of a small module of nine genes. The results strongly suggest that miR-200a is regulating the module genes via the transcription factor ZEB1. Interestingly, this module is most likely involved in epithelial homeostasis and its dysregulation might contribute to the malignant process in cancer cells. CONCLUSIONS/SIGNIFICANCE: Our results show that a robust module network analysis of expression data can provide novel insights of miRNA function in important cellular processes. Such a computational approach, starting from expression data alone, can be helpful in the process of identifying the function of miRNAs by suggesting modules of co-expressed genes in which they play a regulatory role. As shown in this study, those modules can then be tested experimentally to further investigate and refine the function of the miRNA in the regulatory network.
    Keywords Medicine ; R ; Science ; Q
    Subject code 006
    Language English
    Publishing date 2010-01-01T00:00:00Z
    Publisher Public Library of Science (PLoS)
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

    Full text online

    More links

    Kategorien

    Inter-library loan at ZB MED

    Your chosen title can be delivered directly to ZB MED Cologne location if you are registered as a user at ZB MED Cologne.

To top