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

Deliverables

Documents, reports (5)

New inference techniques. Maximum inter-alignment matching

[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.

RepSeq database

[Month 24] Publication of the curated datasets (T3.1) on the project-portal.

Gold Standard Database. Deployment of algorithmic pipeline

[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

Reconstruction of regulatory and signaling networks

[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.

Integrative analysis of gene expression and cancer metabolism

[Month 24]: Algorithm for the efficient analysis of metabolism and gene expression at genome scale and in tissue.

Other (5)

Progress report 1

[month 12] Progress Report 1

International Workshop - Habana

[month 24] International Workshop – Habana

Data management Plan (DMP)

[month 6 - revised version months 24, 48] Data Management Plan (DMP).

INFERNET website

[month 3] INFERNET website

International School - Paris

[month 16] International School – Paris.

Publications

Peer reviewed articles (27)

Limits of aerobic metabolism in cancer cells

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

Characterizing steady states of genome-scale metabolic networks in continuous cell cultures

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

Exploring the diluted ferromagnetic p-spin model with a Cavity Master Equation

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

Independent channels for miRNA biosynthesis ensure efficient static and dynamic control in the regulation of the early stages of myogenesis

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

Somatic mutagenesis in satellite cells associates with human skeletal muscle aging

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

Inter-residue, inter-protein and inter-family coevolution: bridging the scales

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

Microenvironmental cooperation promotes early spread and bistability of a Warburg-like phenotype

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

How Pairwise Coevolutionary Models Capture the Collective Residue Variability in Proteins?

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

Translating ceRNA Susceptibilities into Correlation Functions

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

A physical model of cell metabolism

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

An introduction to the maximum entropy approach and its application to inference problems in biology

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

Maximum entropy and population heterogeneity in continuous cell cultures

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

The intrinsic dimension of protein sequence evolution

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

Compressed sensing reconstruction using Expectation Propagation

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

A multi-scale coevolutionary approach to predict interactions between protein domains

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

A common root for coevolution and substitution rate variability in protein sequence evolution

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

Theory of Nonequilibrium Local Search on Random Satisfaction Problems

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

Nonconvex image reconstruction via expectation propagation

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

Selection of sequence motifs and generative Hopfield-Potts models for protein families

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

Phylogenetic correlations can suffice to infer protein partners from sequences

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

Modeling functional resting-state brain networks through neural message passing on the human connectome

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

Loop Corrections in Spin Models through Density Consistency

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

Cell population heterogeneity driven by stochastic partition and growth optimality

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

Toward Inferring Potts Models for Phylogenetically Correlated Sequence Data

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

Competing endogenous RNA crosstalk at system level

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

A yield-cost tradeoff governs Escherichia coli’s decision between fermentation and respiration in carbon-limited growth

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

Formate Induces a Metabolic Switch in Nucleotide and Energy Metabolism

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

Book chapters (1)

Kinetic Modelling of Competition and Depletion of Shared miRNAs by Competing Endogenous RNAs

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