Search

Your search keyword '"Biologie Computationnelle (ex C3BI)"' showing total 3 results
Start Over Author "Biologie Computationnelle (ex C3BI)"
3 results on '"Biologie Computationnelle (ex C3BI)"'

1. The iPPI-DB initiative: a community-centered database of protein–protein interaction modulators

Author

Torchet, Rachel, Druart, Karen, Ruano, Luis Checa, Moine-Franel, Alexandra, Borges, Hélène, Doppelt-Azeroual, Olivia, Brancotte, Bryan, Mareuil, Fabien, Nilges, Michael, Ménager, Hervé, Sperandio, Olivier, Hub Bioinformatique et Biostatistique - Bioinformatics and Biostatistics HUB, Institut Pasteur [Paris] (IP)-Centre National de la Recherche Scientifique (CNRS), Département de Biologie structurale et Chimie - Department of Structural Biology and Chemistry, Institut Pasteur [Paris] (IP), none declared, This work used the computational and storage services (TARS cluster, VMHosting) provided by the IT department at Institut Pasteur, Paris. The authorswish to acknowledge in particular the help and technical advice of Eric Deveaud,Emmanuel Guichard, Thomas Me ́nard and Youssef Ghorbal (IT Department,Institut Pasteur). They also want to acknowledge the technical help of Tru Huynh(Structural Bioinformatics Unit, Institut Pasteur). They thank Jon Ison, BenjaminBardiaux and Pascal Campagne for their proofreading of the paper.Marvin JS (20.5.0, 2020, http://www.chemaxon.com) is used for drawingand displaying chemical structures in both Query mode and Contributionmode of iPPI-DB. Pipeline Pilot (server 19.1) is used to prepare the DrugBankdatabase from a SDF file prior to chemical similarity search 202 (2020), Institut Pasteur [Paris]-Centre National de la Recherche Scientifique (CNRS), Institut Pasteur [Paris], Génomique métabolique (UMR 8030), Genoscope - Centre national de séquençage [Evry] (GENOSCOPE), Université Paris-Saclay-Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université d'Évry-Val-d'Essonne (UEVE)-Centre National de la Recherche Scientifique (CNRS), Spectrométrie de Masse pour la Biologie – Mass Spectrometry for Biology (UTechS MSBio), Centre National de la Recherche Scientifique (CNRS)-Centre de Ressources et de Recherche Technologique - Center for Technological Resources and Research (C2RT), Institut Pasteur [Paris]-Institut Pasteur [Paris], Centre de Bioinformatique, Biostatistique et Biologie Intégrative (C3BI), Etude de la dynamique des protéomes (EDyP), BioSanté (UMR BioSanté), Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut de Recherche Interdisciplinaire de Grenoble (IRIG), Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Grenoble Alpes (UGA)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut de Recherche Interdisciplinaire de Grenoble (IRIG), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Grenoble Alpes (UGA), Biologie Computationnelle (ex C3BI), Bioinformatique structurale - Structural Bioinformatics, and Druart, Karen

Subjects
[SDV.BIBS] Life Sciences [q-bio]/Quantitative Methods [q-bio.QM], [INFO.INFO-DB]Computer Science [cs]/Databases [cs.DB], AcademicSubjects/SCI01060, Databases and Ontologies, [SDV.BBM] Life Sciences [q-bio]/Biochemistry, Molecular Biology, [INFO.INFO-DB] Computer Science [cs]/Databases [cs.DB], [SDV.BBM]Life Sciences [q-bio]/Biochemistry, Molecular Biology, Original Papers, [SDV.BIBS]Life Sciences [q-bio]/Quantitative Methods [q-bio.QM], [CHIM.CHEM]Chemical Sciences/Cheminformatics
Abstract

International audience; Abstract Motivation One avenue to address the paucity of clinically testable targets is to reinvestigate the druggable genome by tackling complicated types of targets such as Protein-Protein Interactions (PPIs). Given the challenge to target those interfaces with small chemical compounds, it has become clear that learning from successful examples of PPI modulation is a powerful strategy. Freely accessible databases of PPI modulators that provide the community with tractable chemical and pharmacological data, as well as powerful tools to query them, are therefore essential to stimulate new drug discovery projects on PPI targets. Results Here, we present the new version iPPI-DB, our manually curated database of PPI modulators. In this completely redesigned version of the database, we introduce a new web interface relying on crowdsourcing for the maintenance of the database. This interface was created to enable community contributions, whereby external experts can suggest new database entries. Moreover, the data model, the graphical interface, and the tools to query the database have been completely modernized and improved. We added new PPI modulators, new PPI targets and extended our focus to stabilizers of PPIs as well. Availability and implementation The iPPI-DB server is available at https://ippidb.pasteur.fr The source code for this server is available at https://gitlab.pasteur.fr/ippidb/ippidb-web/ and is distributed under GPL licence (http://www.gnu.org/licences/gpl). Queries can be shared through persistent links according to the FAIR data standards. Data can be downloaded from the website as csv files. Supplementary information Supplementary data are available at Bioinformatics online.

Published
2021
Full Text
View/download PDF

2. TbD1 deletion as a driver of the evolutionary success of modern epidemic Mycobacterium tuberculosis lineages

Author

Laurence Ma, Varun Khanna, Christiane Bouchier, Roland Brosch, Mariagrazia Di Luca, Valérie Barbe, David Hardy, Sophie Mangenot, Wafa Frigui, Fadel Sayes, Alexandre Pawlik, Marina Zoppo, Arianna Tavanti, Mickael Orgeur, Gerald Larrouy-Maumus, Claudine Médigue, Dalila Spadoni, Daria Bottai, University of Pisa - Università di Pisa, Pathogénomique mycobactérienne intégrée - Integrated Mycobacterial Pathogenomics, Institut Pasteur [Paris] (IP)-Centre National de la Recherche Scientifique (CNRS), Neuropathologie expérimentale - Experimental neuropathology, Institut Pasteur [Paris] (IP)-Université Paris Descartes - Paris 5 (UPD5), Genoscope - Centre national de séquençage [Evry] (GENOSCOPE), Université Paris-Saclay-Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA), Université d'Évry-Val-d'Essonne (UEVE), Analyse Bio-Informatique pour la Génomique et le Métabolisme (LABGeM), Génomique métabolique (UMR 8030), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université d'Évry-Val-d'Essonne (UEVE)-Centre National de la Recherche Scientifique (CNRS)-Genoscope - Centre national de séquençage [Evry] (GENOSCOPE), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université d'Évry-Val-d'Essonne (UEVE)-Centre National de la Recherche Scientifique (CNRS), Génomique (Plate-Forme) - Genomics Platform, Institut Pasteur [Paris] (IP), Imperial College London, This work was supported in part by the French National Research Council ANR (ANR-10-LABX-62-IBEID, ANR-16-CE35-0009, ANR-16-CE15-0003), the Fondation pour la Recherche Médicale (DEQ20130326471 and SPF20160936136) and the European Union’s Horizon 2020 Research and Innovation Program (643381)., We are grateful to Professor Denis Mitchison, passed away in July 2018 aged 98, who initially enabled this study by kindly providing us with some of his original South Indian Mtb strains. We also thank Cristina Gutierrez for sharing selected Mtb clinical isolates, Dick van Soolingen for providing Mtb Tb36 strain, William R. Jacobs for the gift of vector pYUB412 and Graham F. Hatfull for providing vector pJV53. We thank Fabien Le Chevalier, Laleh Majlessi, Alexander Pym, Paul Wheeler, Stephen Gordon for help and stimulating discussions, Magali Tichit, Sabine Maurin and Johan Bedel from the histology service of the Institut Pasteur for their technical support, Alessandro Massolo for helpful advice in statistical analyses, and Jean Jaubert for help with the setup of the C3HeB/FeJ model, ANR-10-LABX-0062,IBEID,Integrative Biology of Emerging Infectious Diseases(2010), ANR-16-CE35-0009,TBemerg,Naissance d'un tueur: facteurs génétiques et adaptations métaboliques impliquées dans l'émergence des bacilles tuberculeux épidémiques(2016), ANR-16-CE15-0003,MTBLipVir,Analyse multi-échelle et multidisciplinaire des mécanismes intimes d'action des lipides de virulence de l'enveloppe de Mycobacterium tuberculosis(2016), European Project: 643381,H2020,H2020-PHC-2014-single-stage,TBVAC2020(2015), Institut Pasteur [Paris]-Centre National de la Recherche Scientifique (CNRS), Institut Pasteur [Paris]-Université Paris Descartes - Paris 5 (UPD5), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Centre National de la Recherche Scientifique (CNRS)-Université d'Évry-Val-d'Essonne (UEVE)-Genoscope - Centre national de séquençage [Evry] (GENOSCOPE), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Centre National de la Recherche Scientifique (CNRS)-Université d'Évry-Val-d'Essonne (UEVE), Institut Pasteur [Paris], Institut de Biologie François JACOB (JACOB), Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Génomique (Plate-Forme), ANR-10-LABX-62-IBEID,IBEID,Laboratoire d'Excellence 'Integrative Biology of Emerging Infectious Diseases'(2010), Biologie Computationnelle (ex C3BI), Institut Pasteur [Paris]-Université de Paris (UP), Bioanalyse génomique (Plate-Forme), and University College of London [London] (UCL)

Subjects
0301 basic medicine, Tuberculosis, Science, 030106 microbiology, Guinea Pigs, General Physics and Astronomy, Virulence, chemical and pharmacologic phenomena, Biology, General Biochemistry, Genetics and Molecular Biology, Article, Mycobacterium tuberculosis, Evolution, Molecular, 03 medical and health sciences, Mice, Phylogenetics, Epidemic spread, [SDV.BC.IC]Life Sciences [q-bio]/Cellular Biology/Cell Behavior [q-bio.CB], medicine, East africa, Animals, Humans, South east asia, [SDV.BBM.BC]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Biochemistry [q-bio.BM], lcsh:Science, Phylogeny, Sequence Deletion, Genetics, Mice, Inbred C3H, Multidisciplinary, Phylogenetic tree, [SDV.BID.EVO]Life Sciences [q-bio]/Biodiversity/Populations and Evolution [q-bio.PE], General Chemistry, respiratory system, bacterial infections and mycoses, biology.organism_classification, medicine.disease, [SDV.MP.BAC]Life Sciences [q-bio]/Microbiology and Parasitology/Bacteriology, 3. Good health, [SDV.BBM.BC]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Biomolecules [q-bio.BM], 030104 developmental biology, Infectious diseases, lcsh:Q, Pathogens
Abstract

Mycobacterium tuberculosis (Mtb) strains are classified into different phylogenetic lineages (L), three of which (L2/L3/L4) emerged from a common progenitor after the loss of the MmpS6/MmpL6-encoding Mtb-specific deletion 1 region (TbD1). These TbD1-deleted “modern” lineages are responsible for globally-spread tuberculosis epidemics, whereas TbD1-intact “ancestral” lineages tend to be restricted to specific geographical areas, such as South India and South East Asia (L1) or East Africa (L7). By constructing and characterizing a panel of recombinant TbD1-knock-in and knock-out strains and comparison with clinical isolates, here we show that deletion of TbD1 confers to Mtb a significant increase in resistance to oxidative stress and hypoxia, which correlates with enhanced virulence in selected cellular, guinea pig and C3HeB/FeJ mouse infection models, the latter two mirroring in part the development of hypoxic granulomas in human disease progression. Our results suggest that loss of TbD1 at the origin of the L2/L3/L4 Mtb lineages was a key driver for their global epidemic spread and outstanding evolutionary success., Mycobacterium tuberculosis (Mtb) modern strains emerged from a common progenitor after the loss of Mtb-specific deletion 1 region (TbD1). Here, the authors show that deletion of TbD1 correlates with enhanced Mtb virulence in animal models, mirroring the development of hypoxic granulomas in human disease progression.

Published
2020
Full Text
View/download PDF

3. Origin, evolution and global spread of SARS-CoV-2

Author

Zhukova, Anna, Blassel, Luc, Lemoine, Frédéric, Morel, Marie, Voznica, Jakub, Gascuel, Olivier, Biologie Computationnelle (ex C3BI), Institut Pasteur [Paris]-Centre National de la Recherche Scientifique (CNRS), Bioinformatique évolutive - Evolutionary Bioinformatics, Hub Bioinformatique et Biostatistique - Bioinformatics and Biostatistics HUB, Ecole Doctorale Complexité du Vivant (ED515), Sorbonne Université (SU), Université de Paris (UP), Centre National de la Recherche Scientifique (CNRS), Institut Pasteur [Paris] (IP)-Centre National de la Recherche Scientifique (CNRS), and Université Paris Cité (UPCité)

Subjects
Foyers épidémiques, [SDV.GEN]Life Sciences [q-bio]/Genetics, COVID19, Evolution, SARS-CoV-2, [SDV]Life Sciences [q-bio], [SDV.BID.EVO]Life Sciences [q-bio]/Biodiversity/Populations and Evolution [q-bio.PE], viruses, Origine, Évolution, [SDV.BIBS]Life Sciences [q-bio]/Quantitative Methods [q-bio.QM], Clusters, Origin, Transmission, [SDV.SPEE]Life Sciences [q-bio]/Santé publique et épidémiologie, [INFO.INFO-BI]Computer Science [cs]/Bioinformatics [q-bio.QM]
Abstract

International audience; SARS-CoV-2 is the virus responsible for the global COVID19 pandemic. We review what is known about the origin of this virus, detected in China at the end of December 2019. The genome of this virus mainly evolves under the effect of point mutations. These are generally neutral and have no impact on virulence and severity, but some appear to influence infectivity, notably the D614G mutation of the Spike protein. To date (30/09/2020) no recombination of the virus has been documented in the human host, and very few insertions and deletions. The worldwide spread of the virus was the subject of controversies that we summarize, before proposing a new approach free from the limitations of previous methods. The results show a complex scenario with, for example, numerous introductions to the USA and returns of the virus from the USA to certain countries including France.; Le SARS-CoV-2 est le virus responsable de la pandémie mondiale de COVID19. On dresse ici un bilan de ce qui est connu sur l’origine de ce virus, détecté en Chine fin décembre 2019. Le génome de ce virus évolue sous l’effet de mutations ponctuelles. Celles-ci sont généralement neutres et sans impact sur la virulence et la sévérité, mais certaines semblent influer sur l’infectiosité, notamment la mutation D614G de la protéine Spike. A l’inverse, on n’a à ce jour (30/09/2020) documenté aucune recombinaison du virus chez l’hôte humain, et très peu d’insertions et de délétions. La propagation mondiale du virus a fait l’objet de polémiques sur lesquelles nous revenons, avant de proposer une nouvelle approche débarrassée des limites des méthodes précédentes. Les résultats montrent une propagation complexe avec, par exemple, de très nombreuses introductions aux USA et des retours du virus depuis les USA vers certains pays dont la France.

Published
2020
Full Text
View/download PDF

Catalog

Books, media, physical & digital resources
See catalog results