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MuG

Multi-Scale Complex Genomics

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EC-Contrib. €

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Project "MuG" data sheet

The following table provides information about the project.

Coordinator
FUNDACIO INSTITUT DE RECERCA BIOMEDICA (IRB BARCELONA) 

Organization address
address: CARRER BALDIRI REIXAC 10-12 PARC SCIENTIFIC DE BARCELONA
city: BARCELONA
postcode: 8028
website: www.irbbarcelona.org

contact info
title: n.a.
name: n.a.
surname: n.a.
function: n.a.
email: n.a.
telephone: n.a.
fax: n.a.

 Coordinator Country Spain [ES]
 Project website http://www.multiscalegenomics.eu
 Total cost 2˙961˙163 €
 EC max contribution 2˙961˙163 € (100%)
 Programme 1. H2020-EU.1.4.1.3. (Development, deployment and operation of ICT-based e-infrastructures)
 Code Call H2020-EINFRA-2015-1
 Funding Scheme RIA
 Starting year 2015
 Duration (year-month-day) from 2015-11-01   to  2018-10-31

 Partnership

Take a look of project's partnership.

# participants  country  role  EC contrib. [€] 
1    FUNDACIO INSTITUT DE RECERCA BIOMEDICA (IRB BARCELONA) ES (BARCELONA) coordinator 668˙625.00
2    EUROPEAN MOLECULAR BIOLOGY LABORATORY DE (HEIDELBERG) participant 567˙955.00
3    FUNDACIO CENTRE DE REGULACIO GENOMICA ES (BARCELONA) participant 510˙695.00
4    BARCELONA SUPERCOMPUTING CENTER - CENTRO NACIONAL DE SUPERCOMPUTACION ES (BARCELONA) participant 470˙250.00
5    CENTRE NATIONAL DE LA RECHERCHE SCIENTIFIQUE CNRS FR (PARIS) participant 408˙091.00
6    THE UNIVERSITY OF NOTTINGHAM UK (NOTTINGHAM) participant 335˙547.00

Map

 Project objective

Genomics is probably the fastest evolving field in current science. A decade ago our main concern was to obtain the sequence (the 1D code) of the genome; but today the big challenges are to determine how genotype information is transferred into phenotype, and how pathological phenotypic changes can be predicted from genome alterations. While investigating these points, we have realized that a part of the regulation of gene expression is implicitly coded in the way in which chromatin is folded. As technology has advanced and information of the folded state of chromatin has emerged, a new branch of genomics (3D/4D genomics) has emerged. Hundreds of laboratories are now defining a young and active community that, though in the end concerned with the same scientific problem, uses many different approaches to study it that individually target radically different length and timescales. The community faces severe practical problems related to: i) how huge, noisy, and diverse data related to widely different size and time scales can be integrated, ii) the lack of standardized analysis and simulation tools, iii) the complete disconnection of associated informatics databases, and iv) the lack of validated and flexible visualization engines. MuG is born at the critical point in the evolution of the field, in a bottom-up approach from the biologist who are suffering severe IT problemes. MuG, supported by European leaders in the field, join three different expertise: biologist with interest in chromatin structure, methods developers and HPC facilities with strong history of supporting Bio-computational problems. We believe that MuG will be a steep-forward in approaching the potential of High Performance Computing to the development of 3D/4D genomics, and will contribute to give a structure to this new and exciting field.

 Deliverables

List of deliverables.
Project Handbook Documents, reports 2019-06-29 10:36:49
A critical evaluation of the problems on data structure the browser has to solve Demonstrators, pilots, prototypes 2019-06-29 10:36:48
Software tools of Protein-DNA interactions Other 2019-06-29 10:36:49
A browser-track that implements and connects all the 2D data from a genome or a genomic domain Demonstrators, pilots, prototypes 2019-06-29 10:36:49
Pipelines design & implementation Documents, reports 2019-06-29 10:36:48
Plan for Dissemination and Use of Knowledge Documents, reports 2019-06-29 10:36:48
Data Management Plan Documents, reports 2019-06-29 10:36:48
Project Fact Sheet Websites, patent fillings, videos etc. 2019-06-29 10:36:48
Database and ETL design & implementation Documents, reports 2019-06-29 10:36:48
Initial Exploitation plan based on market knowledge Documents, reports 2019-06-29 10:36:49
A requirement specification document with the data types, processing and data models needed Documents, reports 2019-06-29 10:36:48
Preliminary browser-track that implements and connects all the 3D data from a genome or a genomic domain Demonstrators, pilots, prototypes 2019-06-29 10:36:48
Monitoring of the Plan for Dissemination and Use of Knowledge Documents, reports 2019-06-29 10:36:49
Computational infrastructure set-up z Documents, reports 2019-06-29 10:36:49
A browser-track that implements and connects all the 1D data from a genome or a genomic domain Demonstrators, pilots, prototypes 2019-06-29 10:36:48
Quality Plan Documents, reports 2019-06-29 10:36:48
Project Website Websites, patent fillings, videos etc. 2019-06-29 10:36:49
Design of computational architecture of software modules Documents, reports 2019-06-29 10:36:48
Final Exploitation plan based on market knowledge Documents, reports 2019-06-29 10:36:47
Final computational infrastructure and its components Demonstrators, pilots, prototypes 2019-06-29 10:36:47
Report on the use of MuG VRE on the senescence project Documents, reports 2019-06-29 10:36:47
Project’s outputs Documents, reports 2019-06-29 10:36:47
Benchmarks & documentation Documents, reports 2019-06-29 10:36:47
A first prototype of analysis tools for mining of the data provided by the browser Demonstrators, pilots, prototypes 2019-06-29 10:36:47
Report on the MuG training programme Documents, reports 2019-06-29 10:36:47
Report on the use of MuG VRE on the integration of DNA simulation data Documents, reports 2019-06-29 10:36:47
Data access API specification & implementation Documents, reports 2019-06-29 10:36:47
Software tools linking multiresolution structural and simulation data Other 2019-06-29 10:36:47
A 3D genome browser connecting all the 1D-2D-3D tracks. The browser will allow different renderings of the upload coordinates Demonstrators, pilots, prototypes 2019-06-29 10:36:47
Report on the use of MuG VRE on integration of whole yeast genome data Documents, reports 2019-06-29 10:36:47
Tailored Implementation of browser to support pilot projects in WP7, including the interface with the Yeast Genome viewer Demonstrators, pilots, prototypes 2019-06-29 10:36:47
Software tools linking multiresolution structural & simulation data Other 2019-06-29 10:36:47
Computational infrastructure components implementation Documents, reports 2019-06-29 10:36:47
Software tools on 3C interaction data Other 2019-06-29 10:36:47

Take a look to the deliverables list in detail:  detailed list of MuG deliverables.

 Publications

year authors and title journal last update
List of publications.
2016 Pablo D Dans, Jürgen Walther, Hansel Gómez, Modesto Orozco
Multiscale simulation of DNA
published pages: 29-45, ISSN: 0959-440X, DOI: 10.1016/j.sbi.2015.11.011
Current Opinion in Structural Biology 37 2019-07-08
2016 Darré, Leonardo; Ivani, Ivan; Dans, Pablo D.; Gómez, Hansel; Hospital, Adam; Orozco, Modesto
Small Details Matter: The 2\'-Hydroxyl as a Conformational Switch in RNA
published pages: , ISSN: 0002-7863, DOI: 10.1021/jacs.6b09471
Journal of the American Chemical Society 4 2019-07-08
2017 Yuri B. Schwartz, Giacomo Cavalli
Three-Dimensional Genome Organization and Function in Drosophila
published pages: 5-24, ISSN: 0016-6731, DOI: 10.1534/genetics.115.185132
Genetics 205/1 2019-07-08
2017 Filippo Ciabrelli, Federico Comoglio, Simon Fellous, Boyan Bonev, Maria Ninova, Quentin Szabo, Anne Xuéreb, Christophe Klopp, Alexei Aravin, Renato Paro, Frédéric Bantignies, Giacomo Cavalli
Stable Polycomb-dependent transgenerational inheritance of chromatin states in Drosophila
published pages: , ISSN: 1061-4036, DOI: 10.1038/ng.3848
Nature Genetics 2019-07-08
2016 Adam Hospital, Pau Andrio, Cesare Cugnasco, Laia Codo, Yolanda Becerra, Pablo D. Dans, Federica Battistini, Jordi Torres, Ramón Goñi, Modesto Orozco, Josep Ll. Gelpí
BIGNASim: a NoSQL database structure and analysis portal for nucleic acids simulation data
published pages: D272-D278, ISSN: 0305-1048, DOI: 10.1093/nar/gkv1301
Nucleic Acids Research 44/D1 2019-07-08
2016 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
Long-timescale dynamics of the Drew–Dickerson dodecamer
published pages: 4052-4066, ISSN: 0305-1048, DOI: 10.1093/nar/gkw264
Nucleic Acids Research 44/9 2019-07-08
2016 Vincent Loubiere, Anna Delest, Aubin Thomas, Boyan Bonev, Bernd Schuettengruber, Satish Sati, Anne-Marie Martinez, Giacomo Cavalli
Coordinate redeployment of PRC1 proteins suppresses tumor formation during Drosophila development
published pages: 1436-1442, ISSN: 1061-4036, DOI: 10.1038/ng.3671
Nature Genetics 48/11 2019-07-08
2017 V?ctor L?pez-Ferrando, Andrea Gazzo, Xavier de?la?Cruz, Modesto Orozco, Josep Ll Gelp?
PMut: a web-based tool for the annotation of pathological variants on proteins, 2017 update
published pages: , ISSN: 0305-1048, DOI: 10.1093/nar/gkx313
Nucleic Acids Research 2019-07-08
2017 François Le Dily, François Serra, Marc A. Marti-Renom
3D modeling of chromatin structure: is there a way to integrate and reconcile single cell and population experimental data?
published pages: e1308, ISSN: 1759-0876, DOI: 10.1002/wcms.1308
Wiley Interdisciplinary Reviews: Computational Molecular Science 2019-07-08
2017 Anton, Victor; Ramon-Cortes, Cristian; Ejarque, Jorge; Badia, Rosa M.
Transparent Execution of Task-Based Parallel Applications in Docker with COMP Superscalar
published pages: , ISSN: , DOI: 10.1109/PDP.2017.26
1 2019-07-08
2017 Alexandra Balaceanu, Marco Pasi, Pablo D. Dans, Adam Hospital, Richard Lavery, Modesto Orozco
The Role of Unconventional Hydrogen Bonds in Determining BII Propensities in B-DNA
published pages: 21-28, ISSN: 1948-7185, DOI: 10.1021/acs.jpclett.6b02451
The Journal of Physical Chemistry Letters 8/1 2019-07-08
2016 Boyan Bonev, Giacomo Cavalli
Organization and function of the 3D genome
published pages: 661-678, ISSN: 1471-0056, DOI: 10.1038/nrg.2016.112
Nature Reviews Genetics 17/11 2019-07-08
2018 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
Challenges and guidelines toward 4D nucleome data and model standards
published pages: 1352-1358, ISSN: 1061-4036, DOI: 10.1038/s41588-018-0236-3
Nature Genetics 50/10 2019-06-29
2018 Thierry Cheutin, Giacomo Cavalli
Loss of PRC1 induces higher-order opening of Hox loci independently of transcription during Drosophila embryogenesis
published pages: , ISSN: 2041-1723, DOI: 10.1038/s41467-018-05945-4
Nature Communications 9/1 2019-06-29
2017 Bernd Schuettengruber, Henri-Marc Bourbon, Luciano Di Croce, Giacomo Cavalli
Genome Regulation by Polycomb and Trithorax: 70 Years and Counting
published pages: 34-57, ISSN: 0092-8674, DOI: 10.1016/j.cell.2017.08.002
Cell 171/1 2019-06-29
2017 Arka Chakraborty, Sébastien Lyonnais, Federica Battistini, Adam Hospital, Giorgio Medici, Rafel Prohens, Modesto Orozco, Josep Vilardell, Maria Solà
DNA structure directs positioning of the mitochondrial genome packaging protein Abf2p
published pages: 951-967, ISSN: 0305-1048, DOI: 10.1093/nar/gkw1147
Nucleic Acids Research 45/2 2019-06-29
2017 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
Multiscale 3D Genome Rewiring during Mouse Neural Development
published pages: 557-572.e24, ISSN: 0092-8674, DOI: 10.1016/j.cell.2017.09.043
Cell 171/3 2019-06-29
2018 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
TADs are 3D structural units of higher-order chromosome organization in Drosophila
published pages: eaar8082, ISSN: 2375-2548, DOI: 10.1126/sciadv.aar8082
Science Advances 4/2 2019-06-29
2017 Jinsen Li, Jared M. Sagendorf, Tsu-Pei Chiu, Marco Pasi, Alberto Perez, Remo Rohs
Expanding the repertoire of DNA shape features for genome-scale studies of transcription factor binding
published pages: 12877-12887, ISSN: 0305-1048, DOI: 10.1093/nar/gkx1145
Nucleic Acids Research 45/22 2019-06-29
2017 Mike Goodstadt, Marc A. Marti-Renom
Challenges for visualizing three-dimensional data in genomic browsers
published pages: 2505-2519, ISSN: 0014-5793, DOI: 10.1002/1873-3468.12778
FEBS Letters 591/17 2019-06-29
2017 Pablo D. Dans, Ivan Ivani, Adam Hospital, Guillem Portella, Carlos González, Modesto Orozco
How accurate are accurate force-fields for B-DNA?
published pages: gkw1355, ISSN: 0305-1048, DOI: 10.1093/nar/gkw1355
Nucleic Acids Research 2019-06-29
2017 Bartomeu Mir, Israel Serrano, Diana Buitrago, Modesto Orozco, Núria Escaja, Carlos González
Prevalent Sequences in the Human Genome Can Form Mini i-Motif Structures at Physiological pH
published pages: 13985-13988, ISSN: 0002-7863, DOI: 10.1021/jacs.7b07383
Journal of the American Chemical Society 139/40 2019-06-29
2017 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
Single-cell absolute contact probability detection reveals chromosomes are organized by multiple low-frequency yet specific interactions
published pages: , ISSN: 2041-1723, DOI: 10.1038/s41467-017-01962-x
Nature Communications 8/1 2019-06-29
2018 Yuki Ogiyama, Bernd Schuettengruber, Giorgio L. Papadopoulos, Jia-Ming Chang, Giacomo Cavalli
Polycomb-Dependent Chromatin Looping Contributes to Gene Silencing during Drosophila Development
published pages: 73-88.e5, ISSN: 1097-2765, DOI: 10.1016/j.molcel.2018.05.032
Molecular Cell 71/1 2019-06-29
2018 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
Distinct roles of cohesin-SA1 and cohesin-SA2 in 3D chromosome organization
published pages: 496-504, ISSN: 1545-9993, DOI: 10.1038/s41594-018-0070-4
Nature Structural & Molecular Biology 25/6 2019-06-29
2018 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
Lamin B1 mapping reveals the existence of dynamic and functional euchromatin lamin B1 domains
published pages: , ISSN: 2041-1723, DOI: 10.1038/s41467-018-05912-z
Nature Communications 9/1 2019-06-29
2018 Justina Jankauskaitė, Brian Jiménez-García, Justas Dapkūnas, Juan Fernández-Recio, Iain H Moal
SKEMPI 2.0: an updated benchmark of changes in protein–protein binding energy, kinetics and thermodynamics upon mutation
published pages: , ISSN: 1367-4803, DOI: 10.1093/bioinformatics/bty635
Bioinformatics 2019-06-29
2018 Alexandra Balaceanu, Alberto Pérez, Pablo D Dans, Modesto Orozco
Allosterism and signal transfer in DNA
published pages: 7554-7565, ISSN: 0305-1048, DOI: 10.1093/nar/gky549
Nucleic Acids Research 46/15 2019-06-29

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