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INFERNET SIGNED

New algorithms for inference and optimization from large-scale biological data

Total Cost €

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EC-Contrib. €

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Partnership

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Project "INFERNET" data sheet

The following table provides information about the project.

Coordinator
IIGM FOUNDATION 

Organization address
address: PIAZZA BERNINI 5
city: TORINO
postcode: 10138
website: http://www.hugef-torino.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 Italy [IT]
 Project website https://www.infernet.eu/
 Total cost 900˙000 €
 EC max contribution 900˙000 € (100%)
 Programme 1. H2020-EU.1.3.3. (Stimulating innovation by means of cross-fertilisation of knowledge)
 Code Call H2020-MSCA-RISE-2016
 Funding Scheme MSCA-RISE
 Starting year 2017
 Duration (year-month-day) from 2017-03-01   to  2021-02-28

 Partnership

Take a look of project's partnership.

# participants  country  role  EC contrib. [€] 
1    IIGM FOUNDATION IT (TORINO) coordinator 310˙500.00
2    BEATSON INSTITUTE FOR CANCER RESEARCH LBG UK (BEARSDEN) participant 297˙000.00
3    SORBONNE UNIVERSITE FR (PARIS) participant 292˙500.00
4    UNIVERSITE PIERRE ET MARIE CURIE - PARIS 6 FR (PARIS) participant 0.00
5    UNIVERSIDAD DE LA HABANA CU (PLAZA) partner 0.00
6    Universidad Nacional de General Sarmiento AR (Los Polvorines - Provincia de Buenos Aires) partner 0.00

Map

 Project objective

The tremendous technological advance underlying the ongoing genomic revolution in the life sciences has profoundly transformed biological research over the last 10-15 years. The grand challenge ahead is to leverage experimental progress like high-throughput sequencing by developing effective tools for large scale data-based inference and optimization. The goals of INFERNET rely on the transfer of ideas and methods developed in recent years at the boundary between statistical physics and information theory into the world of quantitative biology. We aim at setting up a consortium characterized by a proven track-record of high-quality research in order to implement a highly integrated program leading from the design of new algorithms to concrete biological applications. The consortium will provide the optimal environment to nurture a generation of researchers that will drive new developments at the forefront of these challenging fields.

The perimeter of each individual research activity will be delimited by: (a) the research themes characterized by the toolbox and methods developed and shared within INFERNET, (b) the choice of the application domains. Principal research themes covered by the consortium will be: (i) the inference of interaction networks from data, (ii) the analysis of static and dynamical processes on networks. Application domains can be broken down into four main areas: (i) the inference and modeling of multi-scale biological networks, (ii) the rational design of biological molecules, (iii) the quantitative study of cell energetics in proliferative regimes, (iv) the characterization of functional states of large-scale regulatory networks. Each individual research project will be a puzzle piece of the wider research project, as well as tailored to suit each researcher's scientific and professional development.

 Deliverables

List of deliverables.
International Workshop - Habana Other 2020-04-14 23:46:59
Reconstruction of regulatory and signaling networks Documents, reports 2020-04-14 23:46:59
Gold Standard Database. Deployment of algorithmic pipeline Documents, reports 2020-04-14 23:46:59
RepSeq database Documents, reports 2020-04-14 23:46:59
Integrative analysis of gene expression and cancer metabolism Documents, reports 2020-04-14 23:46:59
New inference techniques. Maximum inter-alignment matching Documents, reports 2020-04-14 23:46:59
International School - Paris Other 2020-04-14 23:46:58
Data management Plan (DMP) Other 2020-04-14 23:46:58
INFERNET website Other 2020-04-14 23:46:58
Progress report 1 Other 2020-04-14 23:46:58

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

 Publications

year authors and title journal last update
List of publications.
2019 Alfredo Braunstein, Anna Paola Muntoni, Andrea Pagnani, Mirko Pieropan
Compressed sensing reconstruction using Expectation Propagation
published pages: , ISSN: 1751-8113, DOI: 10.1088/1751-8121/ab3065
Journal of Physics A: Mathematical and Theoretical 2020-04-14
2019 Elena Facco, Andrea Pagnani, Elena Tea Russo, Alessandro Laio
The intrinsic dimension of protein sequence evolution
published pages: e1006767, ISSN: 1553-7358, DOI: 10.1371/journal.pcbi.1006767
PLOS Computational Biology 15/4 2020-04-14
2017 Jorge Fernandez-de-Cossio-Diaz, Andrea De Martino, Roberto Mulet
Microenvironmental cooperation promotes early spread and bistability of a Warburg-like phenotype
published pages: , ISSN: 2045-2322, DOI: 10.1038/s41598-017-03342-3
Scientific Reports 7/1 2020-04-14
2017 Jorge Fernandez-de-Cossio-Diaz, Kalet Leon, Roberto Mulet
Characterizing steady states of genome-scale metabolic networks in continuous cell cultures
published pages: e1005835, ISSN: 1553-7358, DOI: 10.1371/journal.pcbi.1005835
PLOS Computational Biology 13/11 2020-04-14
2017 Jorge Fernandez-de-Cossio-Diaz, Alexei Vazquez
Limits of aerobic metabolism in cancer cells
published pages: , ISSN: 2045-2322, DOI: 10.1038/s41598-017-14071-y
Scientific Reports 7/1 2020-04-14
2018 Hendrik Szurmant, Martin Weigt
Inter-residue, inter-protein and inter-family coevolution: bridging the scales
published pages: 26-32, ISSN: 0959-440X, DOI: 10.1016/j.sbi.2017.10.014
Current Opinion in Structural Biology 50 2020-04-14
2018 Irene Franco, Anna Johansson, Karl Olsson, Peter Vrtačnik, Pär Lundin, Hafdis T. Helgadottir, Malin Larsson, Gwladys Revêchon, Carla Bosia, Andrea Pagnani, Paolo Provero, Thomas Gustafsson, Helene Fischer, Maria Eriksson
Somatic mutagenesis in satellite cells associates with human skeletal muscle aging
published pages: , ISSN: 2041-1723, DOI: 10.1038/s41467-018-03244-6
Nature Communications 9/1 2020-04-14
2017 Jonathan Fiorentino, Andrea De Martino
Independent channels for miRNA biosynthesis ensure efficient static and dynamic control in the regulation of the early stages of myogenesis
published pages: 53-63, ISSN: 0022-5193, DOI: 10.1016/j.jtbi.2017.06.038
Journal of Theoretical Biology 430 2020-04-14
2018 Aurell, Erik; Domínguez, Eduardo; Machado, David; Mulet, Roberto
Exploring the diluted ferromagnetic p-spin model with a Cavity Master Equation
published pages: , ISSN: 2470-0053, DOI: 10.1103/PhysRevE.97.050103
Physical Review APS 1 2020-04-14
2018 Jorge Fernandez-de-Cossio-Diaz, Alexei Vazquez
A physical model of cell metabolism
published pages: , ISSN: 2045-2322, DOI: 10.1038/s41598-018-26724-7
Scientific Reports 8/1 2020-04-14
2018 Matteo Figliuzzi, Pierre Barrat-Charlaix, Martin Weigt
How Pairwise Coevolutionary Models Capture the Collective Residue Variability in Proteins?
published pages: 1018-1027, ISSN: 0737-4038, DOI: 10.1093/molbev/msy007
Molecular Biology and Evolution 35/4 2020-04-14
2017 Araks Martirosyan, Matteo Marsili, Andrea De Martino
Translating ceRNA Susceptibilities into Correlation Functions
published pages: 206-213, ISSN: 0006-3495, DOI: 10.1016/j.bpj.2017.05.042
Biophysical Journal 113/1 2020-04-14
2018 Andrea De Martino, Daniele De Martino
An introduction to the maximum entropy approach and its application to inference problems in biology
published pages: e00596, ISSN: 2405-8440, DOI: 10.1016/j.heliyon.2018.e00596
Heliyon 4/4 2020-04-14
2019 Jorge Fernandez-de-Cossio-Diaz, Roberto Mulet
Maximum entropy and population heterogeneity in continuous cell cultures
published pages: e1006823, ISSN: 1553-7358, DOI: 10.1371/journal.pcbi.1006823
PLOS Computational Biology 15/2 2020-04-14

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