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INFERNET SIGNED

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

Total Cost €

EC-Contrib. €

Partnership

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Outcomes and
results

INFERNET project word cloud

Explore the words cloud of the INFERNET project. It provides you a very rough idea of what is the project "INFERNET" about.

delimited domains underlying suit record nurture quality dynamical world covered sequencing ongoing shared modeling drive rational researcher data boundary tremendous last ahead proliferative experimental transfer infernet tools regulatory rely functional goals biological networks life environment track physics ideas regimes theory optimal quantitative statistical broken cell leverage optimization setting inference algorithms revolution individual generation molecules genomic profoundly throughput principal progress forefront transformed perimeter piece static professional interaction 15 energetics themes technological proven sciences toolbox grand scientific characterization puzzle biology

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 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.	IT (TORINO)	coordinator	310˙500.00
2	BEATSON INSTITUTE FOR CANCER RESEARCH LBG BEATSON INSTITUTE FOR CANCER RESEARCH LBG Organization address address: SWITCHBACK ROAD GARSCUBE ESTATE city: BEARSDEN postcode: G61 1BD website: http://www.beatson.gla.ac.uk/ contact info title: n.a. name: n.a. surname: n.a. function: n.a. email: n.a. telephone: n.a. fax: n.a.	UK (BEARSDEN)	participant	297˙000.00
3	SORBONNE UNIVERSITE SORBONNE UNIVERSITE Organization address address: 21 RUE DE L'ECOLE DE MEDECINE city: PARIS postcode: 75006 website: n.a. contact info title: n.a. name: n.a. surname: n.a. function: n.a. email: n.a. telephone: n.a. fax: n.a.	FR (PARIS)	participant	292˙500.00
4	UNIVERSITE PIERRE ET MARIE CURIE - PARIS 6 UNIVERSITE PIERRE ET MARIE CURIE - PARIS 6 Organization address address: Place Jussieu 4 city: PARIS postcode: 75252 website: www.upmc.fr contact info title: n.a. name: n.a. surname: n.a. function: n.a. email: n.a. telephone: n.a. fax: n.a.	FR (PARIS)	participant	0.00
5	UNIVERSIDAD DE LA HABANA UNIVERSIDAD DE LA HABANA Organization address address: COLINA UNIVERSITARIA SAN LAZARO Y L city: PLAZA postcode: 10400 website: n.a. contact info title: n.a. name: n.a. surname: n.a. function: n.a. email: n.a. telephone: n.a. fax: n.a.	CU (PLAZA)	partner	0.00
6	Universidad Nacional de General Sarmiento Universidad Nacional de General Sarmiento Organization address address: Juan M. Gutierrez 1150 city: Los Polvorines - Provincia de Buenos Aires postcode: B 1613 GSX website: www.ungs.edu.ar contact info title: n.a. name: n.a. surname: n.a. function: n.a. email: n.a. telephone: n.a. fax: n.a.	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

List of publications.
year	authors and title	journal	last update
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 VrtaÄnik, PÃ¤r Lundin, Hafdis T. Helgadottir, Malin Larsson, Gwladys RevÃªchon, 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; DomÃnguez, 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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