Deliverables
[Month 24] Development of novel inference techniques including prior knowledge as input to T2.1b. Study of the maximum inter-alignment matching of families with paralogs.. Message-passing method for sampling high-dimensional polytopes including prior knowledge.
[Month 24] Publication of the curated datasets (T3.1) on the project-portal.
[Month 24]. “Gold-Standard”: a list of multi-domain interacting proteins of known structure. Contact maps at different cutoffs will be available, together with the list of sequences in Pfam and Uniprot, and proposed seeds for the MSAs. Deployment of the algorithmic pipeline for maximizing the inter-alignment information developed as D1.2
[Month 24]: Algorithm for the efficient reconstruction/inference of regulatory networks integrating transcriptional and post-transcriptional data bases, expression data bases, sigalling networks and data bases for validated interactions.
[Month 24]: Algorithm for the efficient analysis of metabolism and gene expression at genome scale and in tissue.
[month 12] Progress Report 1
[month 24] International Workshop – Habana
[month 6 - revised version months 24, 48] Data Management Plan (DMP).
[month 3] INFERNET website
[month 16] International School – Paris.
Publications
Author(s): Jorge Fernandez-de-Cossio-Diaz, Alexei Vazquez
Published in: Scientific Reports, 7/1, 2017, ISSN 2045-2322
Publisher: Nature Publishing Group
DOI: 10.1038/s41598-017-14071-y
Author(s): Jorge Fernandez-de-Cossio-Diaz, Kalet Leon, Roberto Mulet
Published in: PLOS Computational Biology, 13/11, 2017, Page(s) e1005835, ISSN 1553-7358
Publisher: Jorge Fernandez-de-Cossio-Diaz
DOI: 10.1371/journal.pcbi.1005835
Author(s): Aurell, Erik; Domínguez, Eduardo; Machado, David; Mulet, Roberto
Published in: Physical Review APS, 1, 2018, ISSN 2470-0053
Publisher: Roberto Mulet
DOI: 10.1103/PhysRevE.97.050103
Author(s): Jonathan Fiorentino, Andrea De Martino
Published in: Journal of Theoretical Biology, 430, 2017, Page(s) 53-63, ISSN 0022-5193
Publisher: Academic Press
DOI: 10.1016/j.jtbi.2017.06.038
Author(s): 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
Published in: Nature Communications, 9/1, 2018, ISSN 2041-1723
Publisher: Nature Publishing Group
DOI: 10.1038/s41467-018-03244-6
Author(s): Hendrik Szurmant, Martin Weigt
Published in: Current Opinion in Structural Biology, 50, 2018, Page(s) 26-32, ISSN 0959-440X
Publisher: Elsevier BV
DOI: 10.1016/j.sbi.2017.10.014
Author(s): Jorge Fernandez-de-Cossio-Diaz, Andrea De Martino, Roberto Mulet
Published in: Scientific Reports, 7/1, 2017, ISSN 2045-2322
Publisher: Nature Publishing Group
DOI: 10.1038/s41598-017-03342-3
Author(s): Matteo Figliuzzi, Pierre Barrat-Charlaix, Martin Weigt
Published in: Molecular Biology and Evolution, 35/4, 2018, Page(s) 1018-1027, ISSN 0737-4038
Publisher: Oxford University Press
DOI: 10.1093/molbev/msy007
Author(s): Araks Martirosyan, Matteo Marsili, Andrea De Martino
Published in: Biophysical Journal, 113/1, 2017, Page(s) 206-213, ISSN 0006-3495
Publisher: Biophysical Society
DOI: 10.1016/j.bpj.2017.05.042
Author(s): Jorge Fernandez-de-Cossio-Diaz, Alexei Vazquez
Published in: Scientific Reports, 8/1, 2018, ISSN 2045-2322
Publisher: Nature Publishing Group
DOI: 10.1038/s41598-018-26724-7
Author(s): Andrea De Martino, Daniele De Martino
Published in: Heliyon, 4/4, 2018, Page(s) e00596, ISSN 2405-8440
Publisher: Helyon
DOI: 10.1016/j.heliyon.2018.e00596
Author(s): Jorge Fernandez-de-Cossio-Diaz, Roberto Mulet
Published in: PLOS Computational Biology, 15/2, 2019, Page(s) e1006823, ISSN 1553-7358
Publisher: Public Library of Science
DOI: 10.1371/journal.pcbi.1006823
Author(s): Elena Facco, Andrea Pagnani, Elena Tea Russo, Alessandro Laio
Published in: PLOS Computational Biology, 15/4, 2019, Page(s) e1006767, ISSN 1553-7358
Publisher: The Public Library of Science
DOI: 10.1371/journal.pcbi.1006767
Author(s): Alfredo Braunstein, Anna Paola Muntoni, Andrea Pagnani, Mirko Pieropan
Published in: Journal of Physics A: Mathematical and Theoretical, 2019, ISSN 1751-8113
Publisher: Institute of Physics Publishing
DOI: 10.1088/1751-8121/ab3065
Author(s): Giancarlo Croce, Thomas Gueudré, Maria Virginia Ruiz Cuevas, Victoria Keidel, Matteo Figliuzzi, Hendrik Szurmant, Martin Weigt
Published in: PLOS Computational Biology, 15/10, 2019, Page(s) e1006891, ISSN 1553-7358
Publisher: Public Library of Science
DOI: 10.1371/journal.pcbi.1006891
Author(s): Francesca Rizzato, Stefano Zamuner, Andrea Pagnani, Alessandro Laio
Published in: Scientific Reports, 9/1, 2019, ISSN 2045-2322
Publisher: Nature Publishing Group
DOI: 10.1038/s41598-019-53958-w
Author(s): Erik Aurell, Eduardo Domínguez, David Machado, Roberto Mulet
Published in: Physical Review Letters, 123/23, 2019, ISSN 0031-9007
Publisher: American Physical Society
DOI: 10.1103/physrevlett.123.230602
Author(s): Anna Paola Muntoni, Rafael Díaz Hernández Rojas, Alfredo Braunstein, Andrea Pagnani, Isaac Pérez Castillo
Published in: Physical Review E, 100/3, 2019, ISSN 2470-0045
Publisher: APS
DOI: 10.1103/PhysRevE.100.032134
Author(s): Kai Shimagaki, Martin Weigt
Published in: Physical Review E, 100/3, 2019, ISSN 2470-0045
Publisher: APS
DOI: 10.1103/PhysRevE.100.032128
Author(s): Guillaume Marmier, Martin Weigt, Anne-Florence Bitbol
Published in: PLOS Computational Biology, 15/10, 2019, Page(s) e1007179, ISSN 1553-7358
Publisher: Public Library of Science
DOI: 10.1371/journal.pcbi.1007179
Author(s): Julio A. Peraza-Goicolea, Eduardo Martínez-Montes, Eduardo Aubert, Pedro A. Valdés-Hernández, Roberto Mulet
Published in: Neural Networks, 123, 2020, Page(s) 52-69, ISSN 0893-6080
Publisher: Pergamon Press Ltd.
DOI: 10.1016/j.neunet.2019.11.014
Author(s): Alfredo Braunstein, Giovanni Catania, Luca Dall’Asta
Published in: Physical Review Letters, 123/2, 2019, ISSN 0031-9007
Publisher: American Physical Society
DOI: 10.1103/PhysRevLett.123.020604
Author(s): Jorge Fernandez-de-Cossio-Diaz, Roberto Mulet, Alexei Vazquez
Published in: Scientific Reports, 9/1, 2019, ISSN 2045-2322
Publisher: Nature Publishing Group
DOI: 10.1038/s41598-019-45882-w
Author(s): Edwin Rodriguez Horta, Pierre Barrat-Charlaix, Martin Weigt
Published in: Entropy, 21/11, 2019, Page(s) 1090, ISSN 1099-4300
Publisher: Multidisciplinary Digital Publishing Institute (MDPI)
DOI: 10.3390/e21111090
Author(s): Mattia Miotto, Enzo Marinari, Andrea De Martino
Published in: PLOS Computational Biology, 15/11, 2019, Page(s) e1007474, ISSN 1553-7358
Publisher: Public Library of Science
DOI: 10.1371/journal.pcbi.1007474
Author(s): Matteo Mori, Enzo Marinari, Andrea De Martino
Published in: npj Systems Biology and Applications, 5/1, 2019, ISSN 2056-7189
Publisher: Nature Publishing Group
DOI: 10.1038/s41540-019-0093-4
Author(s): Kristell Oizel, Jacqueline Tait-Mulder, Jorge Fernandez-de-Cossio-Diaz, Matthias Pietzke, Holly Brunton, Sandeep Dhayade, Dimitris Athineos, Sergio Lilla, Giovanny Rodriguez Blanco, David Sumpton, Gillian Mackay, Karen Blyth, Sara Zanivan, Johannes Meiser, Alexei Vazquez
Published in: SSRN Electronic Journal, 2019, ISSN 1556-5068
Publisher: Cell Press
DOI: 10.2139/ssrn.3456295
Author(s): Araks Martirosyan, Marco Del Giudice, Chiara Enrico Bena, Andrea Pagnani, Carla Bosia, Andrea De Martino
Published in: Computational Biology of Non-Coding RNA - Methods and Protocols, 1912, 2019, Page(s) 367-409, ISBN 978-1-4939-8981-2
Publisher: Springer New York
DOI: 10.1007/978-1-4939-8982-9_15