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  1. Book ; Online: jvanheld/touret_sars-cov-2_inhibitors

    Jacques van Helden

    Touret sars-cov-2 inhibitors - hit selection with FDR + arbidol control

    2020  

    Abstract: Fixed a bug with the exported excel sheets with the selected hits (the full table was already OK in the previous release). ...

    Abstract Fixed a bug with the exported excel sheets with the selected hits (the full table was already OK in the previous release).
    Keywords covid19
    Publishing date 2020-04-20
    Publishing country eu
    Document type Book ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  2. Book ; Online: jvanheld/touret_sars-cov-2_inhibitors

    Jacques van Helden

    two-criteria selection of hits

    2020  

    Abstract: Selection of molecules inhibiting cell infection by SARS-CoV-2 from an in vitro screening covering 1520 antiviral molecules. Combination of two selection criteria: Plate-wise P-value, corrected for multiple testing (FDR) Relative viability above a ... ...

    Abstract Selection of molecules inhibiting cell infection by SARS-CoV-2 from an in vitro screening covering 1520 antiviral molecules. Combination of two selection criteria: Plate-wise P-value, corrected for multiple testing (FDR) Relative viability above a control level estimated from a duplicate of Arbidol treatments (broad spectrum antiviral). The analysis is done in R markdown, with a report exported in pdf and html. Result tables are exported in xlsx format.
    Keywords covid19
    Publishing date 2020-04-17
    Publishing country eu
    Document type Book ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  3. Book ; Online: jvanheld/SARS-CoV-2_origins

    Jacques van Helden / Erwan Sallard

    MedecineSciences-preprint

    2020  

    Abstract: Version of the code used to generate the results and figures of the article "Retrouver les origines du SARS-COV-2 dans les phylogénies de coronavirus", to be published in the Aug-Sept 2020 issue of the journal Médecine & Sciences. The article has also ... ...

    Abstract Version of the code used to generate the results and figures of the article "Retrouver les origines du SARS-COV-2 dans les phylogénies de coronavirus", to be published in the Aug-Sept 2020 issue of the journal Médecine & Sciences. The article has also been fully translated to English under the title "Tracing the origins of SARS-COV-2 in coronavirus phylogenies", that will become available in HAL (https://hal.archives-ouvertes.fr/).
    Keywords covid19
    Publishing date 2020-07-06
    Publishing country eu
    Document type Book ; Online
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  4. Article ; Online: In vitro screening of a FDA approved chemical library reveals potential inhibitors of SARS-CoV-2 replication

    Franck Touret / Magali Gilles / Karine Barral / Antoine Nougairède / Jacques van Helden / Etienne Decroly / Xavier de Lamballerie / Bruno Coutard

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

    2020  Volume 8

    Abstract: Abstract A novel coronavirus, named SARS-CoV-2, emerged in 2019 in China and rapidly spread worldwide. As no approved therapeutics exists to treat COVID-19, the disease associated to SARS-Cov-2, there is an urgent need to propose molecules that could ... ...

    Abstract Abstract A novel coronavirus, named SARS-CoV-2, emerged in 2019 in China and rapidly spread worldwide. As no approved therapeutics exists to treat COVID-19, the disease associated to SARS-Cov-2, there is an urgent need to propose molecules that could quickly enter into clinics. Repurposing of approved drugs is a strategy that can bypass the time-consuming stages of drug development. In this study, we screened the PRESTWICK CHEMICAL LIBRARY composed of 1,520 approved drugs in an infected cell-based assay. The robustness of the screen was assessed by the identification of drugs that already demonstrated in vitro antiviral effect against SARS-CoV-2. Thereby, 90 compounds were identified as positive hits from the screen and were grouped according to their chemical composition and their known therapeutic effect. Then EC50 and CC50 were determined for a subset of 15 compounds from a panel of 23 selected drugs covering the different groups. Eleven compounds such as macrolides antibiotics, proton pump inhibitors, antiarrhythmic agents or CNS drugs emerged showing antiviral potency with 2 < EC50 ≤ 20 µM. By providing new information on molecules inhibiting SARS-CoV-2 replication in vitro, this study provides information for the selection of drugs to be further validated in vivo. Disclaimer: This study corresponds to the early stages of antiviral development and the results do not support by themselves the use of the selected drugs to treat SARS-CoV-2 infection.
    Keywords Medicine ; R ; Science ; Q ; covid19
    Subject code 540
    Language English
    Publishing date 2020-08-01T00:00:00Z
    Publisher Nature Publishing Group
    Document type Article ; Online
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  5. Article: Sub-microscopic Plasmodium falciparum infections in matched peripheral, placental and umbilical cord blood samples from asymptomatic Congolese women at delivery

    Mbouamboua, Yvon / Félix Koukouikila-Koussounda / Francine Ntoumi / Selorme Adukpo / Michael Kombo / Christevy Vouvoungui / Jacques van Helden / Simon Charles Kobawila

    Acta tropica. 2019 May, v. 193

    2019  

    Abstract: In malaria-endemic areas, most pregnant women are susceptible to asymptomatic Plasmodium falciparum infections. We present here the results of a cross-sectional study conducted in Madibou, a southern district of Brazzaville in the Republic of Congo, ... ...

    Abstract In malaria-endemic areas, most pregnant women are susceptible to asymptomatic Plasmodium falciparum infections. We present here the results of a cross-sectional study conducted in Madibou, a southern district of Brazzaville in the Republic of Congo, between March 2014 and April 2015. The main aim was to characterize P. falciparum infections. Blood samples corresponding to peripheral, placental and cord from 370 asymptomatic malaria women at delivery were diagnosed for plasmodium infection by thick blood smears (microscopic infection). Sub-microscopic infection was detected by PCR, using the MSP-2 gene as marker. Microscopic infections were detected in peripheral, placental and cord blood samples with a prevalence of respectively 7.3% (27/370), 2.7% (10/370) and 0%. The negative samples were submitted to sub-microscopic detection, with respective prevalence of 25.4% (87/343), 16.7% (60/360) and 9.4% (35/370) (P < 0.001). We further investigated the genetic diversity of the parasite by characterizing MSP2 allelic families 3D7 (24 distinct alleles) and FC27 (20 distinct alleles). The total number of alleles for these two families were 31, 25 and 19 in peripheral, placental and cord samples respectively. The 3D7 MSP-2 was the predominant allelic family. The multiplicity of infections (MOI) in peripheral (mean 1.4 ± 0.01; range 1–4), placental (mean 1.2 ± 0.01; range 1–3) and cord samples (1.4 ± 0.01; range 1–3) were similar (P = 0.9) and are unaffected by age, gravidity or sulfadoxine-pyrimethamine. These results shown a high prevalence of sub-microscopic infection and a high genetic diversity of Plasmodium falciparum strains in Congo. Age, gravidity and doses of preventive treatment based on sulfadoxine-pyrimethamine do not interfere with the multiplicity of infections.
    Keywords Plasmodium falciparum ; alleles ; blood ; blood sampling ; cross-sectional studies ; genetic variation ; malaria ; parasites ; polymerase chain reaction ; pregnant women ; umbilical cord ; Republic of the Congo
    Language English
    Dates of publication 2019-05
    Size p. 142-147.
    Publishing place Elsevier B.V.
    Document type Article
    ZDB-ID 210415-5
    ISSN 1873-6254 ; 0001-706X
    ISSN (online) 1873-6254
    ISSN 0001-706X
    DOI 10.1016/j.actatropica.2019.03.001
    Database NAL-Catalogue (AGRICOLA)

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  6. Article ; Online: Coordinated response of the Desulfovibrio desulfuricans 27774 transcriptome to nitrate, nitrite and nitric oxide

    Ian T. Cadby / Matthew Faulkner / Jeanne Cheneby / Justine Long / Jacques van Helden / Alain Dolla / Jeffrey A. Cole

    Scientific Reports, Vol 7, Iss 1, Pp 1-

    2017  Volume 16

    Abstract: Abstract The sulfate reducing bacterium Desulfovibrio desulfuricans inhabits both the human gut and external environments. It can reduce nitrate and nitrite as alternative electron acceptors to sulfate to support growth. Like other sulphate reducing ... ...

    Abstract Abstract The sulfate reducing bacterium Desulfovibrio desulfuricans inhabits both the human gut and external environments. It can reduce nitrate and nitrite as alternative electron acceptors to sulfate to support growth. Like other sulphate reducing bacteria, it can also protect itself against nitrosative stress caused by NO generated when nitrite accumulates. By combining in vitro experiments with bioinformatic and RNA-seq data, metabolic responses to nitrate or NO and how nitrate and nitrite reduction are coordinated with the response to nitrosative stress were revealed. Although nitrate and nitrite reduction are tightly regulated in response to substrate availability, the global responses to nitrate or NO were largely regulated independently. Multiple NADH dehydrogenases, transcription factors of unknown function and genes for iron uptake were differentially expressed in response to electron acceptor availability or nitrosative stress. Amongst many fascinating problems for future research, the data revealed a YtfE orthologue, Ddes_1165, that is implicated in the repair of nitrosative damage. The combined data suggest that three transcription factors coordinate this regulation in which NrfS-NrfR coordinates nitrate and nitrite reduction to minimize toxicity due to nitrite accumulation, HcpR1 serves a global role in regulating the response to nitrate, and HcpR2 regulates the response to nitrosative stress.
    Keywords Medicine ; R ; Science ; Q
    Subject code 580
    Language English
    Publishing date 2017-11-01T00:00:00Z
    Publisher Nature Publishing Group
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  7. Article ; Online: Fine-tuning enhancer models to predict transcriptional targets across multiple genomes.

    Stein Aerts / Jacques van Helden / Olivier Sand / Bassem A Hassan

    PLoS ONE, Vol 2, Iss 11, p e

    2007  Volume 1115

    Abstract: Networks of regulatory relations between transcription factors (TF) and their target genes (TG)- implemented through TF binding sites (TFBS)- are key features of biology. An idealized approach to solving such networks consists of starting from a ... ...

    Abstract Networks of regulatory relations between transcription factors (TF) and their target genes (TG)- implemented through TF binding sites (TFBS)- are key features of biology. An idealized approach to solving such networks consists of starting from a consensus TFBS or a position weight matrix (PWM) to generate a high accuracy list of candidate TGs for biological validation. Developing and evaluating such approaches remains a formidable challenge in regulatory bioinformatics. We perform a benchmark study on 34 Drosophila TFs to assess existing TFBS and cis-regulatory module (CRM) detection methods, with a strong focus on the use of multiple genomes. Particularly, for CRM-modelling we investigate the addition of orthologous sites to a known PWM to construct phyloPWMs and we assess the added value of phylogenentic footprinting to predict contextual motifs around known TFBSs. For CRM-prediction, we compare motif conservation with network-level conservation approaches across multiple genomes. Choosing the optimal training and scoring strategies strongly enhances the performance of TG prediction for more than half of the tested TFs. Finally, we analyse a 35(th) TF, namely Eyeless, and find a significant overlap between predicted TGs and candidate TGs identified by microarray expression studies. In summary we identify several ways to optimize TF-specific TG predictions, some of which can be applied to all TFs, and others that can be applied only to particular TFs. The ability to model known TF-TG relations, together with the use of multiple genomes, results in a significant step forward in solving the architecture of gene regulatory networks.
    Keywords Medicine ; R ; Science ; Q
    Language English
    Publishing date 2007-01-01T00:00:00Z
    Publisher Public Library of Science (PLoS)
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  8. Article: Deciphering the adaptation strategies of Desulfovibrio piezophilus to hydrostatic pressure through metabolic and transcriptional analyses

    Amrani, Amira / Jacques van Helden / Aurélie Bergon / Aicha Aouane / Wajdi Ben Hania / Christian Tamburini / Béatrice Loriod / Jean Imbert / Bernard Ollivier / Nathalie Pradel / Alain Dolla

    Environmental microbiology reports. 2016 Aug., v. 8, no. 4

    2016  

    Abstract: Desulfovibrio piezophilus strain C1TLV30ᵀ is a mesophilic piezophilic sulfate‐reducer isolated from Wood Falls at 1700 m depth in the Mediterranean Sea. In this study, we analysed the effect of the hydrostatic pressure on this deep‐sea living ... ...

    Abstract Desulfovibrio piezophilus strain C1TLV30ᵀ is a mesophilic piezophilic sulfate‐reducer isolated from Wood Falls at 1700 m depth in the Mediterranean Sea. In this study, we analysed the effect of the hydrostatic pressure on this deep‐sea living bacterium at the physiologic and transcriptomic levels. Our results showed that lactate oxidation and energy metabolism were affected by the hydrostatic pressure. Especially, acetyl‐CoA oxidation pathway and energy conservation through hydrogen and formate recycling would be more important when the hydrostatic pressure is above (26 MPa) than below (0.1 MPa) the optimal one (10 MPa). This work underlines also the role of the amino acid glutamate as a piezolyte for the Desulfovibrio genus. The transcriptomic analysis revealed 146 differentially expressed genes emphasizing energy production and conversion, amino acid transport and metabolism and cell motility and signal transduction mechanisms as hydrostatic pressure responding processes. This dataset allowed us to identify a sequence motif upstream of a subset of differentially expressed genes as putative pressure‐dependent regulatory element.
    Keywords Desulfovibrio ; acetyl coenzyme A ; bacteria ; cell movement ; data collection ; energy ; energy conservation ; energy metabolism ; formates ; gene expression ; gene expression regulation ; glutamic acid ; hydrogen ; oxidation ; signal transduction ; transcription (genetics) ; transcriptomics ; wood ; Mediterranean Sea
    Language English
    Dates of publication 2016-08
    Size p. 520-526.
    Publishing place John Wiley & Sons, Ltd
    Document type Article
    Note JOURNAL ARTICLE
    ISSN 1758-2229
    DOI 10.1111/1758-2229.12427
    Database NAL-Catalogue (AGRICOLA)

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  9. Article ; Online: The bio.tools registry of software tools and data resources for the life sciences

    Jon Ison / Hans Ienasescu / Piotr Chmura / Emil Rydza / Hervé Ménager / Matúš Kalaš / Veit Schwämmle / Björn Grüning / Niall Beard / Rodrigo Lopez / Severine Duvaud / Heinz Stockinger / Bengt Persson / Radka Svobodová Vařeková / Tomáš Raček / Jiří Vondrášek / Hedi Peterson / Ahto Salumets / Inge Jonassen /
    Rob Hooft / Tommi Nyrönen / Alfonso Valencia / Salvador Capella / Josep Gelpí / Federico Zambelli / Babis Savakis / Brane Leskošek / Kristoffer Rapacki / Christophe Blanchet / Rafael Jimenez / Arlindo Oliveira / Gert Vriend / Olivier Collin / Jacques van Helden / Peter Løngreen / Søren Brunak

    Genome Biology, Vol 20, Iss 1, Pp 1-

    2019  Volume 4

    Abstract: Abstract Bioinformaticians and biologists rely increasingly upon workflows for the flexible utilization of the many life science tools that are needed to optimally convert data into knowledge. We outline a pan-European enterprise to provide a catalogue ( ... ...

    Abstract Abstract Bioinformaticians and biologists rely increasingly upon workflows for the flexible utilization of the many life science tools that are needed to optimally convert data into knowledge. We outline a pan-European enterprise to provide a catalogue (https://bio.tools) of tools and databases that can be used in these workflows. bio.tools not only lists where to find resources, but also provides a wide variety of practical information.
    Keywords Biology (General) ; QH301-705.5 ; Genetics ; QH426-470
    Language English
    Publishing date 2019-08-01T00:00:00Z
    Publisher BMC
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  10. Article: Integrating sequence, evolution and functional genomics in regulatory genomics

    Vingron, Martin / Alvis Brazma / Esko Ukkonen / Jacques van Helden / Kimmo Palin / Olivier Sand / Richard Coulson / Thomas Manke

    Genome biology. 2009 Jan., v. 10, no. 1

    2009  

    Abstract: With genome analysis expanding from the study of genes to the study of gene regulation, 'regulatory genomics' utilizes sequence information, evolution and functional genomics measurements to unravel how regulatory information is encoded in the genome. ...

    Abstract With genome analysis expanding from the study of genes to the study of gene regulation, 'regulatory genomics' utilizes sequence information, evolution and functional genomics measurements to unravel how regulatory information is encoded in the genome.
    Keywords evolution ; genes ; genomics ; sequence analysis
    Language English
    Dates of publication 2009-01
    Size p. 2084.
    Publishing place Springer-Verlag
    Document type Article
    ZDB-ID 2040529-7
    ISSN 1474-760X ; 1465-6914 ; 1465-6906
    ISSN (online) 1474-760X ; 1465-6914
    ISSN 1465-6906
    DOI 10.1186/gb-2009-10-1-202
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