Multi-Scale Complex Genomics

Leistungen

Report on the expected programme for users and developers.

Report on the use of MuG VRE on the integration of DNA simulation data
Final Exploitation plan based on market knowledge

Report about the Final Exploitation plan based on market knowledge

Project Handbook

Contains general operational information including contact details, reporting processes, communication protocols, document templates and numbering methods, logos, etcetera.

Design of computational architecture of software modules

The 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 implementation

This 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 z

Computational infrastructure set-up

Data access API specification & implementation
Project’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 project
Benchmarks & 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 Knowledge

The 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 Plan

QA 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 Plan
Monitoring 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 knowledge

Report about the Initial Exploitation plan based on market knowledge

A critical evaluation of the problems on data structure the browser has to solve
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 domain
A 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 linking multiresolution structural and simulation data
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 data
Software tools linking multiresolution structural & simulation data

Project Fact Sheet

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 Website

A high quality multimedia website, with an intranet section with restricted access containing project files such as deliverables, internal partner working documents, etc.

Veröffentlichungen

Multiscale simulation of DNA

Autoren: Pablo D Dans, Jürgen Walther, Hansel Gómez, Modesto Orozco
Veröffentlicht in: Current Opinion in Structural Biology, Ausgabe 37, 2016, Seite(n) 29-45, ISSN 0959-440X
Herausgeber: Elsevier BV
DOI: 10.1016/j.sbi.2015.11.011

TADs are 3D structural units of higher-order chromosome organization in Drosophila

Autoren: 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
Veröffentlicht in: Science Advances, Ausgabe 4/2, 2018, Seite(n) eaar8082, ISSN 2375-2548
Herausgeber: American Association for the advancement of science
DOI: 10.1126/sciadv.aar8082

DNA structure directs positioning of the mitochondrial genome packaging protein Abf2p

Autoren: Arka Chakraborty, Sébastien Lyonnais, Federica Battistini, Adam Hospital, Giorgio Medici, Rafel Prohens, Modesto Orozco, Josep Vilardell, Maria Solà
Veröffentlicht in: Nucleic Acids Research, Ausgabe 45/2, 2017, Seite(n) 951-967, ISSN 0305-1048
Herausgeber: Oxford University Press
DOI: 10.1093/nar/gkw1147

Multiscale 3D Genome Rewiring during Mouse Neural Development

Autoren: 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
Veröffentlicht in: Cell, Ausgabe 171/3, 2017, Seite(n) 557-572.e24, ISSN 0092-8674
Herausgeber: Cell Press
DOI: 10.1016/j.cell.2017.09.043

Challenges for visualizing three-dimensional data in genomic browsers

Autoren: Mike Goodstadt, Marc A. Marti-Renom
Veröffentlicht in: FEBS Letters, Ausgabe 591/17, 2017, Seite(n) 2505-2519, ISSN 0014-5793
Herausgeber: Elsevier BV
DOI: 10.1002/1873-3468.12778

Expanding the repertoire of DNA shape features for genome-scale studies of transcription factor binding

Autoren: Jinsen Li, Jared M. Sagendorf, Tsu-Pei Chiu, Marco Pasi, Alberto Perez, Remo Rohs
Veröffentlicht in: Nucleic Acids Research, Ausgabe 45/22, 2017, Seite(n) 12877-12887, ISSN 0305-1048
Herausgeber: Oxford University Press
DOI: 10.1093/nar/gkx1145

How accurate are accurate force-fields for B-DNA?

Autoren: Pablo D. Dans, Ivan Ivani, Adam Hospital, Guillem Portella, Carlos González, Modesto Orozco
Veröffentlicht in: Nucleic Acids Research, 2017, Seite(n) gkw1355, ISSN 0305-1048
Herausgeber: Oxford University Press
DOI: 10.1093/nar/gkw1355

Genome Regulation by Polycomb and Trithorax: 70 Years and Counting

Autoren: Bernd Schuettengruber, Henri-Marc Bourbon, Luciano Di Croce, Giacomo Cavalli
Veröffentlicht in: Cell, Ausgabe 171/1, 2017, Seite(n) 34-57, ISSN 0092-8674
Herausgeber: Cell Press
DOI: 10.1016/j.cell.2017.08.002

Polycomb-Dependent Chromatin Looping Contributes to Gene Silencing during Drosophila Development

Autoren: Yuki Ogiyama, Bernd Schuettengruber, Giorgio L. Papadopoulos, Jia-Ming Chang, Giacomo Cavalli
Veröffentlicht in: Molecular Cell, Ausgabe 71/1, 2018, Seite(n) 73-88.e5, ISSN 1097-2765
Herausgeber: Cell Press
DOI: 10.1016/j.molcel.2018.05.032

Promoter bivalency favors an open chromatin architecture in embryonic stem cells

Autoren: 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
Veröffentlicht in: Nature Genetics, Ausgabe 50/10, 2018, Seite(n) 1452-1462, ISSN 1061-4036
Herausgeber: Nature Publishing Group
DOI: 10.1038/s41588-018-0218-5

SKEMPI 2.0: an updated benchmark of changes in protein–protein binding energy, kinetics and thermodynamics upon mutation

Autoren: Justina Jankauskaitė, Brian Jiménez-García, Justas Dapkūnas, Juan Fernández-Recio, Iain H Moal
Veröffentlicht in: Bioinformatics, 2018, ISSN 1367-4803
Herausgeber: Oxford University Press
DOI: 10.1093/bioinformatics/bty635

Distinct roles of cohesin-SA1 and cohesin-SA2 in 3D chromosome organization

Autoren: 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
Veröffentlicht in: Nature Structural & Molecular Biology, Ausgabe 25/6, 2018, Seite(n) 496-504, ISSN 1545-9993
Herausgeber: Nature Publishing Group
DOI: 10.1038/s41594-018-0070-4

Loss of PRC1 induces higher-order opening of Hox loci independently of transcription during Drosophila embryogenesis

Autoren: Thierry Cheutin, Giacomo Cavalli
Veröffentlicht in: Nature Communications, Ausgabe 9/1, 2018, ISSN 2041-1723
Herausgeber: Nature Publishing Group
DOI: 10.1038/s41467-018-05945-4

Lamin B1 mapping reveals the existence of dynamic and functional euchromatin lamin B1 domains

Autoren: 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
Veröffentlicht in: Nature Communications, Ausgabe 9/1, 2018, ISSN 2041-1723
Herausgeber: Nature Publishing Group
DOI: 10.1038/s41467-018-05912-z

Single-cell absolute contact probability detection reveals chromosomes are organized by multiple low-frequency yet specific interactions

Autoren: 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
Veröffentlicht in: Nature Communications, Ausgabe 8/1, 2017, ISSN 2041-1723
Herausgeber: Nature Publishing Group
DOI: 10.1038/s41467-017-01962-x

Prevalent Sequences in the Human Genome Can Form Mini i-Motif Structures at Physiological pH

Autoren: Bartomeu Mir, Israel Serrano, Diana Buitrago, Modesto Orozco, Núria Escaja, Carlos González
Veröffentlicht in: Journal of the American Chemical Society, Ausgabe 139/40, 2017, Seite(n) 13985-13988, ISSN 0002-7863
Herausgeber: American Chemical Society
DOI: 10.1021/jacs.7b07383

Allosterism and signal transfer in DNA

Autoren: Alexandra Balaceanu, Alberto Pérez, Pablo D Dans, Modesto Orozco
Veröffentlicht in: Nucleic Acids Research, Ausgabe 46/15, 2018, Seite(n) 7554-7565, ISSN 0305-1048
Herausgeber: Oxford University Press
DOI: 10.1093/nar/gky549

Challenges and guidelines toward 4D nucleome data and model standards

Autoren: 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
Veröffentlicht in: Nature Genetics, Ausgabe 50/10, 2018, Seite(n) 1352-1358, ISSN 1061-4036
Herausgeber: Nature Publishing Group
DOI: 10.1038/s41588-018-0236-3

BIGNASim: a NoSQL database structure and analysis portal for nucleic acids simulation data

Autoren: Adam Hospital, Pau Andrio, Cesare Cugnasco, Laia Codo, Yolanda Becerra, Pablo D. Dans, Federica Battistini, Jordi Torres, Ramón Goñi, Modesto Orozco, Josep Ll. Gelpí
Veröffentlicht in: Nucleic Acids Research, Ausgabe 44/D1, 2016, Seite(n) D272-D278, ISSN 0305-1048
Herausgeber: Oxford University Press
DOI: 10.1093/nar/gkv1301

Long-timescale dynamics of the Drew–Dickerson dodecamer

Autoren: 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
Veröffentlicht in: Nucleic Acids Research, Ausgabe 44/9, 2016, Seite(n) 4052-4066, ISSN 0305-1048
Herausgeber: Oxford University Press
DOI: 10.1093/nar/gkw264

3D modeling of chromatin structure: is there a way to integrate and reconcile single cell and population experimental data?

Autoren: François Le Dily, François Serra, Marc A. Marti-Renom
Veröffentlicht in: Wiley Interdisciplinary Reviews: Computational Molecular Science, 2017, Seite(n) e1308, ISSN 1759-0876
Herausgeber: John Wiley & Sons Inc.
DOI: 10.1002/wcms.1308

The Role of Unconventional Hydrogen Bonds in Determining BII Propensities in B-DNA

Autoren: Alexandra Balaceanu, Marco Pasi, Pablo D. Dans, Adam Hospital, Richard Lavery, Modesto Orozco
Veröffentlicht in: The Journal of Physical Chemistry Letters, Ausgabe 8/1, 2017, Seite(n) 21-28, ISSN 1948-7185
Herausgeber: American Chemical Society
DOI: 10.1021/acs.jpclett.6b02451

Three-Dimensional Genome Organization and Function in Drosophila

Autoren: Yuri B. Schwartz, Giacomo Cavalli
Veröffentlicht in: Genetics, Ausgabe 205/1, 2017, Seite(n) 5-24, ISSN 0016-6731
Herausgeber: Genetics Society of America
DOI: 10.1534/genetics.115.185132

Stable Polycomb-dependent transgenerational inheritance of chromatin states in Drosophila

Autoren: Filippo Ciabrelli, Federico Comoglio, Simon Fellous, Boyan Bonev, Maria Ninova, Quentin Szabo, Anne Xuéreb, Christophe Klopp, Alexei Aravin, Renato Paro, Frédéric Bantignies, Giacomo Cavalli
Veröffentlicht in: Nature Genetics, 2017, ISSN 1061-4036
Herausgeber: Nature Publishing Group
DOI: 10.1038/ng.3848

Coordinate redeployment of PRC1 proteins suppresses tumor formation during Drosophila development

Autoren: Vincent Loubiere, Anna Delest, Aubin Thomas, Boyan Bonev, Bernd Schuettengruber, Satish Sati, Anne-Marie Martinez, Giacomo Cavalli
Veröffentlicht in: Nature Genetics, Ausgabe 48/11, 2016, Seite(n) 1436-1442, ISSN 1061-4036
Herausgeber: Nature Publishing Group
DOI: 10.1038/ng.3671

Organization and function of the 3D genome

Autoren: Boyan Bonev, Giacomo Cavalli
Veröffentlicht in: Nature Reviews Genetics, Ausgabe 17/11, 2016, Seite(n) 661-678, ISSN 1471-0056
Herausgeber: Nature Publishing Group
DOI: 10.1038/nrg.2016.112

Small Details Matter: The 2'-Hydroxyl as a Conformational Switch in RNA

Autoren: Darré, Leonardo; Ivani, Ivan; Dans, Pablo D.; Gómez, Hansel; Hospital, Adam; Orozco, Modesto
Veröffentlicht in: Journal of the American Chemical Society, Ausgabe 4, 2016, ISSN 0002-7863
Herausgeber: American Chemical Society
DOI: 10.1021/jacs.6b09471

PMut: a web-based tool for the annotation of pathological variants on proteins, 2017 update

Autoren: V?ctor L?pez-Ferrando, Andrea Gazzo, Xavier de?la?Cruz, Modesto Orozco, Josep Ll Gelp?
Veröffentlicht in: Nucleic Acids Research, 2017, ISSN 0305-1048
Herausgeber: Oxford University Press
DOI: 10.1093/nar/gkx313

Structural basis of a histidine-DNA nicking/joining mechanism for gene transfer and promiscuous spread of antibiotic resistance

Autoren: Radoslaw Pluta, D. Roeland Boer, Fabián Lorenzo-Díaz, Silvia Russi, Hansel Gómez, Cris Fernández-López, Rosa Pérez-Luque, Modesto Orozco, Manuel Espinosa, Miquel Coll
Veröffentlicht in: Proceedings of the National Academy of Sciences, Ausgabe 114/32, 2017, Seite(n) E6526-E6535, ISSN 0027-8424
Herausgeber: National Academy of Sciences
DOI: 10.1073/pnas.1702971114

Transparent Execution of Task-Based Parallel Applications in Docker with COMP Superscalar

Autoren: Anton, Victor; Ramon-Cortes, Cristian; Ejarque, Jorge; Badia, Rosa M.
Veröffentlicht in: Ausgabe 1, 2017
Herausgeber: IEEE
DOI: 10.1109/PDP.2017.26

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