Livrables
Report on the expected programme for users and developers.
Report on the use of MuG VRE on the integration of DNA simulation dataFinal Exploitation plan based on market knowledge
Report about the Final Exploitation plan based on market knowledge
Project HandbookContains general operational information including contact details, reporting processes, communication protocols, document templates and numbering methods, logos, etcetera.
Design of computational architecture of software modulesThe deliverable will report the general specification of the architecture of the software modules encapsulating analysis tools, and how these are interfaced with the data management and de computational infrastructure.
Computational infrastructure components implementationThis deliverable will describe how the different components required in the computational infrastructure (programming models, storage, deployment and test) will be implemented. This deliverable will detail also the links with WP4.
Computational infrastructure set-up zComputational infrastructure set-up
Data access API specification & implementationProject’s outputs
A summary report of project’s outputs, with links to institutional repositories and other open access resources produced by the partners
Report on the use of MuG VRE on the senescence projectBenchmarks & documentation
A requirement specification document with the data types, processing and data models needed
Pipelines design & implementation
Report on the use of MuG VRE on integration of whole yeast genome data
Database and ETL design & implementation
Database and ETL design &implementation
Plan for Dissemination and Use of KnowledgeThe initial Plan for Dissemination and Use of Knowledge will contain the approaches for the dissemination activities, including all the outcomes (website, newsletter and social media tools) and the Use of Knowledge and IPR Management Strategy
Quality PlanQA Plan includes information about technical quality control, procedures for risk monitoring, decision-making and conflict resolution, and procedures to evaluate the achievements of the project according to its objectives
Data Management PlanMonitoring of the Plan for Dissemination and Use of Knowledge
Follow-up and report on the Plan for Dissemination and Use of Knowledge execution
Initial Exploitation plan based on market knowledgeReport about the Initial Exploitation plan based on market knowledge
A first prototype of analysis tools for mining of the data provided by the browser
A browser-track that implements and connects all the 2D data from a genome or a genomic domain
Tailored Implementation of browser to support pilot projects in WP7, including the interface with the Yeast Genome viewer
Final computational infrastructure and its components
This deliverable will report on the resulting computational infrastructure including the description of the components that conforms it
A browser-track that implements and connects all the 1D data from a genome or a genomic domainA 3D genome browser connecting all the 1D-2D-3D tracks. The browser will allow different renderings of the upload coordinates
Preliminary browser-track that implements and connects all the 3D data from a genome or a genomic domain
Software tools of Protein-DNA interactions
The deliverable will provide a full description of adopted software and of its interfaces with data management and computational infrastructure
Software tools on 3C interaction dataSoftware tools linking multiresolution structural & simulation data
The Fact Sheet will outline the project's objectives, specify its technical baseline and intended target groups and application domains, and detail intermediate and final outputs
Project WebsiteA high quality multimedia website, with an intranet section with restricted access containing project files such as deliverables, internal partner working documents, etc.
Publications
Auteurs:
Pablo D Dans, Jürgen Walther, Hansel Gómez, Modesto Orozco
Publié dans:
Current Opinion in Structural Biology, Numéro 37, 2016, Page(s) 29-45, ISSN 0959-440X
Éditeur:
Elsevier BV
DOI:
10.1016/j.sbi.2015.11.011
Auteurs:
Quentin Szabo, Daniel Jost, Jia-Ming Chang, Diego I. Cattoni, Giorgio L. Papadopoulos, Boyan Bonev, Tom Sexton, Julian Gurgo, Caroline Jacquier, Marcelo Nollmann, Frédéric Bantignies, Giacomo Cavalli
Publié dans:
Science Advances, Numéro 4/2, 2018, Page(s) eaar8082, ISSN 2375-2548
Éditeur:
American Association for the advancement of science
DOI:
10.1126/sciadv.aar8082
Auteurs:
Arka Chakraborty, Sébastien Lyonnais, Federica Battistini, Adam Hospital, Giorgio Medici, Rafel Prohens, Modesto Orozco, Josep Vilardell, Maria Solà
Publié dans:
Nucleic Acids Research, Numéro 45/2, 2017, Page(s) 951-967, ISSN 0305-1048
Éditeur:
Oxford University Press
DOI:
10.1093/nar/gkw1147
Auteurs:
Boyan Bonev, Netta Mendelson Cohen, Quentin Szabo, Lauriane Fritsch, Giorgio L. Papadopoulos, Yaniv Lubling, Xiaole Xu, Xiaodan Lv, Jean-Philippe Hugnot, Amos Tanay, Giacomo Cavalli
Publié dans:
Cell, Numéro 171/3, 2017, Page(s) 557-572.e24, ISSN 0092-8674
Éditeur:
Cell Press
DOI:
10.1016/j.cell.2017.09.043
Auteurs:
Mike Goodstadt, Marc A. Marti-Renom
Publié dans:
FEBS Letters, Numéro 591/17, 2017, Page(s) 2505-2519, ISSN 0014-5793
Éditeur:
Elsevier BV
DOI:
10.1002/1873-3468.12778
Auteurs:
Jinsen Li, Jared M. Sagendorf, Tsu-Pei Chiu, Marco Pasi, Alberto Perez, Remo Rohs
Publié dans:
Nucleic Acids Research, Numéro 45/22, 2017, Page(s) 12877-12887, ISSN 0305-1048
Éditeur:
Oxford University Press
DOI:
10.1093/nar/gkx1145
Auteurs:
Pablo D. Dans, Ivan Ivani, Adam Hospital, Guillem Portella, Carlos González, Modesto Orozco
Publié dans:
Nucleic Acids Research, 2017, Page(s) gkw1355, ISSN 0305-1048
Éditeur:
Oxford University Press
DOI:
10.1093/nar/gkw1355
Auteurs:
Bernd Schuettengruber, Henri-Marc Bourbon, Luciano Di Croce, Giacomo Cavalli
Publié dans:
Cell, Numéro 171/1, 2017, Page(s) 34-57, ISSN 0092-8674
Éditeur:
Cell Press
DOI:
10.1016/j.cell.2017.08.002
Auteurs:
Yuki Ogiyama, Bernd Schuettengruber, Giorgio L. Papadopoulos, Jia-Ming Chang, Giacomo Cavalli
Publié dans:
Molecular Cell, Numéro 71/1, 2018, Page(s) 73-88.e5, ISSN 1097-2765
Éditeur:
Cell Press
DOI:
10.1016/j.molcel.2018.05.032
Auteurs:
Glòria Mas, Enrique Blanco, Cecilia Ballaré, Miriam Sansó, Yannick G. Spill, Deqing Hu, Yuki Aoi, François Le Dily, Ali Shilatifard, Marc A. Marti-Renom, Luciano Di Croce
Publié dans:
Nature Genetics, Numéro 50/10, 2018, Page(s) 1452-1462, ISSN 1061-4036
Éditeur:
Nature Publishing Group
DOI:
10.1038/s41588-018-0218-5
Auteurs:
Justina Jankauskaitė, Brian Jiménez-García, Justas Dapkūnas, Juan Fernández-Recio, Iain H Moal
Publié dans:
Bioinformatics, 2018, ISSN 1367-4803
Éditeur:
Oxford University Press
DOI:
10.1093/bioinformatics/bty635
Auteurs:
Aleksandar Kojic, Ana Cuadrado, Magali De Koninck, Daniel Giménez-Llorente, Miriam Rodríguez-Corsino, Gonzalo Gómez-López, François Le Dily, Marc A. Marti-Renom, Ana Losada
Publié dans:
Nature Structural & Molecular Biology, Numéro 25/6, 2018, Page(s) 496-504, ISSN 1545-9993
Éditeur:
Nature Publishing Group
DOI:
10.1038/s41594-018-0070-4
Auteurs:
Thierry Cheutin, Giacomo Cavalli
Publié dans:
Nature Communications, Numéro 9/1, 2018, ISSN 2041-1723
Éditeur:
Nature Publishing Group
DOI:
10.1038/s41467-018-05945-4
Auteurs:
Laura Pascual-Reguant, Enrique Blanco, Silvia Galan, François Le Dily, Yasmina Cuartero, Gemma Serra-Bardenys, Valerio Di Carlo, Ane Iturbide, Joan Pau Cebrià-Costa, Lara Nonell, Antonio García de Herreros, Luciano Di Croce, Marc A. Marti-Renom, Sandra Peiró
Publié dans:
Nature Communications, Numéro 9/1, 2018, ISSN 2041-1723
Éditeur:
Nature Publishing Group
DOI:
10.1038/s41467-018-05912-z
Auteurs:
Diego I. Cattoni, Andrés M. Cardozo Gizzi, Mariya Georgieva, Marco Di Stefano, Alessandro Valeri, Delphine Chamousset, Christophe Houbron, Stephanie Déjardin, Jean-Bernard Fiche, Inma González, Jia-Ming Chang, Thomas Sexton, Marc A. Marti-Renom, Frédéric Bantignies, Giacomo Cavalli, Marcelo Nollmann
Publié dans:
Nature Communications, Numéro 8/1, 2017, ISSN 2041-1723
Éditeur:
Nature Publishing Group
DOI:
10.1038/s41467-017-01962-x
Auteurs:
Bartomeu Mir, Israel Serrano, Diana Buitrago, Modesto Orozco, Núria Escaja, Carlos González
Publié dans:
Journal of the American Chemical Society, Numéro 139/40, 2017, Page(s) 13985-13988, ISSN 0002-7863
Éditeur:
American Chemical Society
DOI:
10.1021/jacs.7b07383
Auteurs:
Alexandra Balaceanu, Alberto Pérez, Pablo D Dans, Modesto Orozco
Publié dans:
Nucleic Acids Research, Numéro 46/15, 2018, Page(s) 7554-7565, ISSN 0305-1048
Éditeur:
Oxford University Press
DOI:
10.1093/nar/gky549
Auteurs:
Marc A. Marti-Renom, Genevieve Almouzni, Wendy A. Bickmore, Kerstin Bystricky, Giacomo Cavalli, Peter Fraser, Susan M. Gasser, Luca Giorgetti, Edith Heard, Mario Nicodemi, Marcelo Nollmann, Modesto Orozco, Ana Pombo, Maria-Elena Torres-Padilla
Publié dans:
Nature Genetics, Numéro 50/10, 2018, Page(s) 1352-1358, ISSN 1061-4036
Éditeur:
Nature Publishing Group
DOI:
10.1038/s41588-018-0236-3
Auteurs:
Adam Hospital, Pau Andrio, Cesare Cugnasco, Laia Codo, Yolanda Becerra, Pablo D. Dans, Federica Battistini, Jordi Torres, Ramón Goñi, Modesto Orozco, Josep Ll. Gelpí
Publié dans:
Nucleic Acids Research, Numéro 44/D1, 2016, Page(s) D272-D278, ISSN 0305-1048
Éditeur:
Oxford University Press
DOI:
10.1093/nar/gkv1301
Auteurs:
Pablo D. Dans, Linda Danilāne, Ivan Ivani, Tomáš Dršata, Filip Lankaš, Adam Hospital, Jürgen Walther, Ricard Illa Pujagut, Federica Battistini, Josep Lluis Gelpí, Richard Lavery, Modesto Orozco
Publié dans:
Nucleic Acids Research, Numéro 44/9, 2016, Page(s) 4052-4066, ISSN 0305-1048
Éditeur:
Oxford University Press
DOI:
10.1093/nar/gkw264
Auteurs:
François Le Dily, François Serra, Marc A. Marti-Renom
Publié dans:
Wiley Interdisciplinary Reviews: Computational Molecular Science, 2017, Page(s) e1308, ISSN 1759-0876
Éditeur:
John Wiley & Sons Inc.
DOI:
10.1002/wcms.1308
Auteurs:
Alexandra Balaceanu, Marco Pasi, Pablo D. Dans, Adam Hospital, Richard Lavery, Modesto Orozco
Publié dans:
The Journal of Physical Chemistry Letters, Numéro 8/1, 2017, Page(s) 21-28, ISSN 1948-7185
Éditeur:
American Chemical Society
DOI:
10.1021/acs.jpclett.6b02451
Auteurs:
Yuri B. Schwartz, Giacomo Cavalli
Publié dans:
Genetics, Numéro 205/1, 2017, Page(s) 5-24, ISSN 0016-6731
Éditeur:
Genetics Society of America
DOI:
10.1534/genetics.115.185132
Auteurs:
Filippo Ciabrelli, Federico Comoglio, Simon Fellous, Boyan Bonev, Maria Ninova, Quentin Szabo, Anne Xuéreb, Christophe Klopp, Alexei Aravin, Renato Paro, Frédéric Bantignies, Giacomo Cavalli
Publié dans:
Nature Genetics, 2017, ISSN 1061-4036
Éditeur:
Nature Publishing Group
DOI:
10.1038/ng.3848
Auteurs:
Vincent Loubiere, Anna Delest, Aubin Thomas, Boyan Bonev, Bernd Schuettengruber, Satish Sati, Anne-Marie Martinez, Giacomo Cavalli
Publié dans:
Nature Genetics, Numéro 48/11, 2016, Page(s) 1436-1442, ISSN 1061-4036
Éditeur:
Nature Publishing Group
DOI:
10.1038/ng.3671
Auteurs:
Boyan Bonev, Giacomo Cavalli
Publié dans:
Nature Reviews Genetics, Numéro 17/11, 2016, Page(s) 661-678, ISSN 1471-0056
Éditeur:
Nature Publishing Group
DOI:
10.1038/nrg.2016.112
Auteurs:
Darré, Leonardo; Ivani, Ivan; Dans, Pablo D.; Gómez, Hansel; Hospital, Adam; Orozco, Modesto
Publié dans:
Journal of the American Chemical Society, Numéro 4, 2016, ISSN 0002-7863
Éditeur:
American Chemical Society
DOI:
10.1021/jacs.6b09471
Auteurs:
V?ctor L?pez-Ferrando, Andrea Gazzo, Xavier de?la?Cruz, Modesto Orozco, Josep Ll Gelp?
Publié dans:
Nucleic Acids Research, 2017, ISSN 0305-1048
Éditeur:
Oxford University Press
DOI:
10.1093/nar/gkx313
Auteurs:
Radoslaw Pluta, D. Roeland Boer, Fabián Lorenzo-Díaz, Silvia Russi, Hansel Gómez, Cris Fernández-López, Rosa Pérez-Luque, Modesto Orozco, Manuel Espinosa, Miquel Coll
Publié dans:
Proceedings of the National Academy of Sciences, Numéro 114/32, 2017, Page(s) E6526-E6535, ISSN 0027-8424
Éditeur:
National Academy of Sciences
DOI:
10.1073/pnas.1702971114
Auteurs:
Anton, Victor; Ramon-Cortes, Cristian; Ejarque, Jorge; Badia, Rosa M.
Publié dans:
Numéro 1, 2017
Éditeur:
IEEE
DOI:
10.1109/PDP.2017.26
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