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

CORDIS fournit des liens vers les livrables publics et les publications des projets HORIZON.

Les liens vers les livrables et les publications des projets du 7e PC, ainsi que les liens vers certains types de résultats spécifiques tels que les jeux de données et les logiciels, sont récupérés dynamiquement sur OpenAIRE .

Livrables

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.

Functional modules

Month 58 Results for longrange effects and predictions on functional modules in the human posttranscriptional regulatory and signaling network Integrated regulatory networks for specific cell types

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.

Prediction highly neutralizing antibodies. Experimental validation

Month 40 Rational prediction o biomolecules from model inference Wetlab validation of the biomolecule phenotypes

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.

Bacterial core interactome based on proximity. Full bacterial interactome

Month 40 First predictions of the coevolutionary inferred Bacterial Core interactome based on operon based proximity Integration of T23 for predicting the whole bacterial interactome

Improved inference for graphical models

Month 36 Improved inference strategies for analyzing graphical models

Predictors of cell responses. Protocol of experimental design in-tissue experiments

Month 58 Analysis of different predictors of cellular responses to changes in the levels of key enzymes andor uptake systems relevant for proliferative regimes specifically for bacteria or cancer cells

Progress report 1

[month 12] Progress Report 1

International Workshop - Habana

[month 24] International Workshop – Habana

International Workshop - Buenos Aires

[month 36] International Workshop – Buenos Aires.

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.

Progress report 2

[month 36] Progress Report 2.

Final Conference - Turin

[month 28] Final conference – Turin.

Publications

A density consistency approach to the inverse Ising problem

Auteurs: Alfredo Braunstein; Giovanni Catania; Luca Dall'Asta; Luca Dall'Asta; Anna Paola Muntoni
Publié dans: Journal of Statistical Mechanics: Theory and Experiment, Numéro 26, 2021, ISSN 1742-5468
Éditeur: Institute of Physics
DOI: 10.48550/arxiv.2010.13746

Epistatic models predict mutable sites in SARS-CoV-2 proteins and epitopes

Auteurs: Juan Rodriguez-Rivas, Giancarlo Croce, Maureen Muscat, Martin Weigt
Publié dans: PNAS, 2022, ISSN 0027-8424
Éditeur: National Academy of Sciences
DOI: 10.1073/pnas.2113118119

Inference of metabolic fluxes in nutrient-limited continuous cultures: A Maximum Entropy approach with the minimum information

Auteurs: Jose A. Pereiro-Morejón; Jorge Fernández-de-Cossio-Díaz; R. Mulet;
Publié dans: iScience, 2022, ISSN 2589-0042
Éditeur: CellPress
DOI: 10.1016/j.isci.2022.105450

Contamination source detection in water distribution networks using belief propagation

Auteurs: Ernesto Ortega; Alfredo Braunstein; Alfredo Braunstein; Alejandro Lage-Castellanos
Publié dans: Stochastic Environmental Research and Risk Assessment, Numéro 29, 2020, ISSN 1436-3240
Éditeur: Springer Verlag
DOI: 10.48550/arxiv.1809.10626

Stochastic and parameter analysis for an integrative cancer model

Auteurs: Marcela V. Reale; David Hipólito Margarit; Ariel F. Scagliotti; Lilia M. Romanelli
Publié dans: Physica Scripta, Numéro 10, 2022, ISSN 0031-8949
Éditeur: Royal Swedish Academy of Sciences
DOI: 10.1088/1402-4896/aca566

Statistical mechanics of interacting metabolic networks.

Auteurs: Jorge Fernandez-de-Cossio-Diaz; Jorge Fernandez-de-Cossio-Diaz; Roberto Mulet
Publié dans: Physical Review E, Numéro 21, 2020, ISSN 1539-3755
Éditeur: American Physical Society
DOI: 10.1103/physreve.101.042401

Expectation propagation on the diluted Bayesian classifier.

Auteurs: Alfredo Braunstein; Alfredo Braunstein; Thomas Gueudré; Andrea Pagnani; Andrea Pagnani; Mirko Pieropan
Publié dans: Physical Review E, Numéro 39, 2021, ISSN 1539-3755
Éditeur: American Physical Society
DOI: 10.1103/physreve.103.043301

Path-integral solution of MacArthur’s resource-competition model for large ecosystems with random species-resources couplings

Auteurs: A. R. Batista-Tomás; Andrea De Martino; Roberto Mulet
Publié dans: Chaos, 2021, ISSN 1054-1500
Éditeur: American Institute of Physics
DOI: 10.1063/5.0046972

Sparse generative modeling via parameter reduction of Boltzmann machines: Application to protein-sequence families.

Auteurs: Pierre Barrat-Charlaix; Anna Paola Muntoni; Kai Shimagaki; Martin Weigt; Francesco Zamponi
Publié dans: Physical Review E, Numéro 5, 2021, ISSN 1539-3755
Éditeur: American Physical Society
DOI: 10.48550/arxiv.2011.11259

Efficient generative modeling of protein sequences using simple autoregressive models

Auteurs: Jeanne Trinquier; Jeanne Trinquier; Guido Uguzzoni; Andrea Pagnani; Francesco Zamponi; Martin Weigt
Publié dans: Nature Communications, Numéro 11, 2022, Page(s) 2021, ISSN 2041-1723
Éditeur: Nature Publishing Group
DOI: 10.48550/arxiv.2103.03292

Global multivariate model learning from hierarchically correlated data

Auteurs: Edwin Rodriguez Horta; Alejandro Lage-Castellanos; Martin Weigt; Pierre Barrat-Charlaix
Publié dans: Journal of Statistical Mechanics: Theory and Experiment, Numéro 29, 2021, ISSN 1742-5468
Éditeur: Institute of Physics
DOI: 10.1088/1742-5468/ac06c2

The cavity master equation: average and fixed point of the ferromagnetic model in random graphs

Auteurs: Eduardo Domínguez; David Machado; Roberto Mulet
Publié dans: Journal of Statistical Mechanics: Theory and Experiment, Numéro 6, 2020, ISSN 1742-5468
Éditeur: Institute of Physics
DOI: 10.48550/arxiv.2004.03674

FilterDCA: Interpretable supervised contact prediction using inter-domain coevolution

Auteurs: Maureen Muscat, Giancarlo Croce, Edoardo Sarti, Martin Weigt
Publié dans: Plos Computational Biology, 2020, ISSN 1553-734X
Éditeur: Public Library of Science
DOI: 10.1371/journal.pcbi.1007621

Loop Corrections in Spin Models through Density Consistency.

Auteurs: Alfredo Braunstein; Alfredo Braunstein; Giovanni Catania; Luca Dall'Asta; Luca Dall'Asta
Publié dans: Physical Review Letters, Numéro 15, 2019, ISSN 0031-9007
Éditeur: American Physical Society
DOI: 10.48550/arxiv.1810.10602

Evolution-based design of chorismate mutase enzymes

Auteurs: William P. Russ; Matteo Figliuzzi; Christian Stocker; Pierre Barrat-Charlaix; Michael Socolich; Pater Kast; Donald Hilvert; Rémi Monasson; Simona Cocco; Martin Weigt; Rama Ranganathan
Publié dans: Science, Numéro 20, 2020, ISSN 0036-8075
Éditeur: American Association for the Advancement of Science
DOI: 10.1101/2020.04.01.020487

Analysis of cell proliferation and tissue remodelling uncovers a KLF4 activity score associated with poor prognosis in colorectal cancer

Auteurs: Silvia Halim; Elke Markert; Alexei Vazquez
Publié dans: British Journal of Cancer, Numéro 5, 2018, ISSN 0007-0920
Éditeur: Nature Publishing Group
DOI: 10.1038/s41416-018-0253-0

An integrative model of cancer cell differentiation with immunotherapy*

Auteurs: David H Margarit; Nadia S González; Lilia M Romanelli; Alejandro J Fendrik; Ariel F Scagliotti; Marcela V Reale
Publié dans: Biophysical Journal, 2021, ISSN 1478-3967
Éditeur: Institute of Physics Publishing
DOI: 10.1088/1478-3975/ac2e72

Ancestral Sequence Reconstruction for Co-evolutionary models

Auteurs: Rodríguez-Horta, Edwin; Lage-Castellanos, Alejandro; Mulet, Roberto
Publié dans: Journal of Statistical Mechanics: Theory and Experiment, Numéro 9, 2022, ISSN 1742-5468
Éditeur: Institute of Physics
DOI: 10.48550/arxiv.2108.03801

Unsupervised Inference of Protein Fitness Landscape from Deep Mutational Scan

Auteurs: Jorge Fernandez-de-Cossio-Diaz; Guido Uguzzoni; Andrea Pagnani
Publié dans: Molecular Biology and Evolution, 2020, ISSN 0737-4038
Éditeur: Oxford University Press
DOI: 10.1093/molbev/msaa204

Initial cell density encodes proliferative potential in cancer cell populations

Auteurs: Chiara Enrico Bena; Marco Del Giudice; Alice Grob; Thomas Gueudré; Mattia Miotto; Dimitra Gialama; Matteo Osella; Emilia Turco; Francesca Ceroni; Andrea De Martino; Carla Bosia
Publié dans: Scientific Reports, Numéro 5, 2021, ISSN 2045-2322
Éditeur: Nature Publishing Group
DOI: 10.1038/s41598-021-85406-z

AMaLa: Analysis of Directed Evolution Experiments via Annealed Mutational Approximated Landscape

Auteurs: Luca Sesta; Guido Uguzzoni; Jorge Fernandez-de-Cossio-Diaz; Andrea Pagnani
Publié dans: International Journal of Molecular Sciences, Numéro 20, 2021, ISSN 1422-0067
Éditeur: Multidisciplinary Digital Publishing Institute (MDPI)
DOI: 10.3390/ijms222010908

Network reconstruction from infection cascades

Auteurs: Alfredo Braunstein; Alessandro Ingrosso; Anna Paola Muntoni; Anna Paola Muntoni; Anna Paola Muntoni
Publié dans: Journal of the Royal Society Interface, Numéro 9, 2019, ISSN 1742-5689
Éditeur: The Royal Society
DOI: 10.48550/arxiv.1609.00432

adabmDCA: adaptive Boltzmann machine learning for biological sequences.

Auteurs: Anna Paola Muntoni; Andrea Pagnani; Martin Weigt; Francesco Zamponi
Publié dans: BMC Bioinformatics, Numéro 11, 2021, ISSN 1471-2105
Éditeur: BioMed Central
DOI: 10.1186/s12859-021-04441-9

Exploration-exploitation tradeoffs dictate the optimal distributions of phenotypes for populations subject to fitness fluctuations.

Auteurs: "De Martino, Andrea; Gueudré , Thomas; Miotto, Mattia"
Publié dans: Physical Review E, Numéro 21, 2019, ISSN 1539-3755
Éditeur: American Physical Society
DOI: 10.48550/arxiv.1809.11030

Stochastic cell renewal process and lengthening of cell cycle

Auteurs: Alejandro Fendrik; Lilia Romanelli; Ernesto Rotondo
Publié dans: Physical Biology, 2019, ISSN 1478-3967
Éditeur: Institute of Physics Publishing
DOI: 10.1088/1478-3975/ab576c

Limits of aerobic metabolism in cancer cells

Auteurs: Jorge Fernandez-de-Cossio-Diaz, Alexei Vazquez
Publié dans: Scientific Reports, Numéro 7/1, 2017, ISSN 2045-2322
Éditeur: Nature Publishing Group
DOI: 10.1038/s41598-017-14071-y

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

Auteurs: Jorge Fernandez-de-Cossio-Diaz, Kalet Leon, Roberto Mulet
Publié dans: PLOS Computational Biology, Numéro 13/11, 2017, Page(s) e1005835, ISSN 1553-7358
Éditeur: Jorge Fernandez-de-Cossio-Diaz
DOI: 10.1371/journal.pcbi.1005835

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

Auteurs: Aurell, Erik; Domínguez, Eduardo; Machado, David; Mulet, Roberto
Publié dans: Physical Review E, Numéro 1, 2018, ISSN 2470-0053
Éditeur: 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

Auteurs: Jonathan Fiorentino, Andrea De Martino
Publié dans: Journal of Theoretical Biology, Numéro 430, 2017, Page(s) 53-63, ISSN 0022-5193
Éditeur: Academic Press
DOI: 10.1016/j.jtbi.2017.06.038

Somatic mutagenesis in satellite cells associates with human skeletal muscle aging

Auteurs: 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
Publié dans: Nature Communications, Numéro 9/1, 2018, ISSN 2041-1723
Éditeur: Nature Publishing Group
DOI: 10.1038/s41467-018-03244-6

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

Auteurs: Hendrik Szurmant, Martin Weigt
Publié dans: Current Opinion in Structural Biology, Numéro 50, 2018, Page(s) 26-32, ISSN 0959-440X
Éditeur: Elsevier BV
DOI: 10.1016/j.sbi.2017.10.014

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

Auteurs: Jorge Fernandez-de-Cossio-Diaz, Andrea De Martino, Roberto Mulet
Publié dans: Scientific Reports, Numéro 7/1, 2017, ISSN 2045-2322
Éditeur: Nature Publishing Group
DOI: 10.1038/s41598-017-03342-3

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

Auteurs: Matteo Figliuzzi, Pierre Barrat-Charlaix, Martin Weigt
Publié dans: Molecular Biology and Evolution, Numéro 35/4, 2018, Page(s) 1018-1027, ISSN 0737-4038
Éditeur: Oxford University Press
DOI: 10.1093/molbev/msy007

Translating ceRNA Susceptibilities into Correlation Functions

Auteurs: Araks Martirosyan, Matteo Marsili, Andrea De Martino
Publié dans: Biophysical Journal, Numéro 113/1, 2017, Page(s) 206-213, ISSN 0006-3495
Éditeur: Biophysical Society
DOI: 10.1016/j.bpj.2017.05.042

A physical model of cell metabolism

Auteurs: Jorge Fernandez-de-Cossio-Diaz, Alexei Vazquez
Publié dans: Scientific Reports, Numéro 8/1, 2018, ISSN 2045-2322
Éditeur: 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

Auteurs: Andrea De Martino, Daniele De Martino
Publié dans: Heliyon, Numéro 4/4, 2018, Page(s) e00596, ISSN 2405-8440
Éditeur: Helyon
DOI: 10.1016/j.heliyon.2018.e00596

Maximum entropy and population heterogeneity in continuous cell cultures

Auteurs: Jorge Fernandez-de-Cossio-Diaz, Roberto Mulet
Publié dans: PLOS Computational Biology, Numéro 15/2, 2019, Page(s) e1006823, ISSN 1553-7358
Éditeur: Public Library of Science
DOI: 10.1371/journal.pcbi.1006823

The intrinsic dimension of protein sequence evolution

Auteurs: Elena Facco, Andrea Pagnani, Elena Tea Russo, Alessandro Laio
Publié dans: PLOS Computational Biology, Numéro 15/4, 2019, Page(s) e1006767, ISSN 1553-7358
Éditeur: The Public Library of Science
DOI: 10.1371/journal.pcbi.1006767

Compressed sensing reconstruction using Expectation Propagation

Auteurs: Alfredo Braunstein, Anna Paola Muntoni, Andrea Pagnani, Mirko Pieropan
Publié dans: Journal of Physics A: Mathematical and Theoretical, 2019, ISSN 1751-8113
Éditeur: Institute of Physics Publishing
DOI: 10.1088/1751-8121/ab3065

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

Auteurs: Giancarlo Croce, Thomas Gueudré, Maria Virginia Ruiz Cuevas, Victoria Keidel, Matteo Figliuzzi, Hendrik Szurmant, Martin Weigt
Publié dans: PLOS Computational Biology, Numéro 15/10, 2019, Page(s) e1006891, ISSN 1553-7358
Éditeur: Public Library of Science
DOI: 10.1371/journal.pcbi.1006891

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

Auteurs: Francesca Rizzato, Stefano Zamuner, Andrea Pagnani, Alessandro Laio
Publié dans: Scientific Reports, Numéro 9/1, 2019, ISSN 2045-2322
Éditeur: Nature Publishing Group
DOI: 10.1038/s41598-019-53958-w

Theory of Nonequilibrium Local Search on Random Satisfaction Problems

Auteurs: Erik Aurell, Eduardo Domínguez, David Machado, Roberto Mulet
Publié dans: Physical Review Letters, Numéro 123/23, 2019, ISSN 0031-9007
Éditeur: American Physical Society
DOI: 10.1103/physrevlett.123.230602

Nonconvex image reconstruction via expectation propagation

Auteurs: Anna Paola Muntoni, Rafael Díaz Hernández Rojas, Alfredo Braunstein, Andrea Pagnani, Isaac Pérez Castillo
Publié dans: Physical Review E, Numéro 100/3, 2019, ISSN 2470-0045
Éditeur: APS
DOI: 10.1103/PhysRevE.100.032134

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

Auteurs: Kai Shimagaki, Martin Weigt
Publié dans: Physical Review E, Numéro 100/3, 2019, ISSN 2470-0045
Éditeur: APS
DOI: 10.1103/PhysRevE.100.032128

Phylogenetic correlations can suffice to infer protein partners from sequences

Auteurs: Guillaume Marmier, Martin Weigt, Anne-Florence Bitbol
Publié dans: PLOS Computational Biology, Numéro 15/10, 2019, Page(s) e1007179, ISSN 1553-7358
Éditeur: Public Library of Science
DOI: 10.1371/journal.pcbi.1007179

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

Auteurs: Julio A. Peraza-Goicolea, Eduardo Martínez-Montes, Eduardo Aubert, Pedro A. Valdés-Hernández, Roberto Mulet
Publié dans: Neural Networks, Numéro 123, 2020, Page(s) 52-69, ISSN 0893-6080
Éditeur: Pergamon Press Ltd.
DOI: 10.1016/j.neunet.2019.11.014

Cell population heterogeneity driven by stochastic partition and growth optimality

Auteurs: Jorge Fernandez-de-Cossio-Diaz, Roberto Mulet, Alexei Vazquez
Publié dans: Scientific Reports, Numéro 9/1, 2019, ISSN 2045-2322
Éditeur: Nature Publishing Group
DOI: 10.1038/s41598-019-45882-w

Toward Inferring Potts Models for Phylogenetically Correlated Sequence Data

Auteurs: Edwin Rodriguez Horta, Pierre Barrat-Charlaix, Martin Weigt
Publié dans: Entropy, Numéro 21/11, 2019, Page(s) 1090, ISSN 1099-4300
Éditeur: Multidisciplinary Digital Publishing Institute (MDPI)
DOI: 10.3390/e21111090

Competing endogenous RNA crosstalk at system level

Auteurs: Mattia Miotto, Enzo Marinari, Andrea De Martino
Publié dans: PLOS Computational Biology, Numéro 15/11, 2019, Page(s) e1007474, ISSN 1553-7358
Éditeur: Public Library of Science
DOI: 10.1371/journal.pcbi.1007474

Formate Induces a Metabolic Switch in Nucleotide and Energy Metabolism

Auteurs: 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
Publié dans: SSRN Electronic Journal, 2019, ISSN 1556-5068
Éditeur: Cell Press
DOI: 10.2139/ssrn.3456295

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

Auteurs: Matteo Mori; Enzo Marinari; Andrea De Martino
Publié dans: NPJ Systems Biology and Applications, Numéro 30, 2019, ISSN 2056-7189
Éditeur: Springer Nature
DOI: 10.1101/113183

Ancestral sequence reconstruction for co-evolutionary models

Auteurs: E Rodríguez-Horta; A Lage-Castellanos; R Mulet
Publié dans: Journal of Statistical Mechanics: Theory and Experiment, 2021, ISSN 1742-5468
Éditeur: Institute of Physics
DOI: 10.1088/1742-5468/ac3d93

Relationship between fitness and heterogeneity in exponentially growing microbial populations

Auteurs: Anna Paola Muntoni; Alfredo Braunstein; Andrea Pagnani; Daniele De Martino; Andrea De Martino
Publié dans: Biophysical Journal, Numéro 1, 2022, ISSN 0006-3495
Éditeur: Biophysical Society
DOI: 10.48550/arxiv.2104.02594

Statistical physics of interacting proteins: impact of dataset size and quality assessed in synthetic sequences

Auteurs: Carlos A. Gandarilla-Pérez; Carlos A. Gandarilla-Pérez; Pierre Mergny; Martin Weigt; Anne-Florence Bitbol; Anne-Florence Bitbol
Publié dans: Physical Review E, Numéro 18, 2020, ISSN 1539-3755
Éditeur: American Physical Society
DOI: 10.1101/2019.12.23.887307

Optimizing the Dilution Protocol in Continuous Cell Cultures

Auteurs: Barbara Ariane Perez Fernandez; Roberto Mulet
Publié dans: Revista Cubana de Fisica, 2021, ISSN 2224-7939
Éditeur: Sociedad Cubana de Fisica

Aligning biological sequences by exploiting residue conservation and coevolution.

Auteurs: Anna Paola Muntoni; Anna Paola Muntoni; Anna Paola Muntoni; Andrea Pagnani; Martin Weigt; Francesco Zamponi
Publié dans: Physical Review E, Numéro 15, 2020, ISSN 1539-3755
Éditeur: American Physical Society
DOI: 10.48550/arxiv.2005.08500

Probing Single-Cell Fermentation Fluxes and Exchange Networks via pH-Sensing Hybrid Nanofibers

Auteurs: Valentina Onesto, Stefania Forciniti, Francesco Alemanno, Krishnadev Narayanankutty Krishnadev Narayanankutty Biofisika Institutua (UPV/EHU, CSIC) and Fundación Biofísica Bizkaia, LeioaE-48940, Spain More by Krishnadev Narayanankutty Orcidhttps://orcid.org/0000-0001-7705-3213 , Anil Chandra, Saumya Prasad, Amalia Azzariti, Giuseppe Gigli, Adriano Barra, Andrea De Martino, Daniele De Martino, Lor
Publié dans: ACS Nano, 2022, ISSN 1936-0851
Éditeur: American Chemical Society
DOI: 10.1021/acsnano.2c06114

MicroRNAs organize intrinsic variation into stem cell states

Auteurs: Meenakshi Chakraborty; Meenakshi Chakraborty; Sofia Hu; Erica Visness; Marco Del Giudice; Andrea De Martino; Carla Bosia; Phillip A. Sharp; Salil Garg; Salil Garg
Publié dans: PNAS, Numéro 33, 2020, ISSN 0027-8424
Éditeur: National Academy of Sciences
DOI: 10.1073/pnas.1920695117

Dynamics of epidemics from cavity master equations: Susceptible-infectious-susceptible models

Auteurs: Ernesto Ortega; David Machado; Alejandro Lage-Castellanos
Publié dans: Physical Review E, Numéro 9, 2022, ISSN 1539-3755
Éditeur: American Physical Society
DOI: 10.1103/physreve.105.024308

Modeling sequence-space exploration and emergence of epistatic signals in protein evolution

Auteurs: Bisardi, Matteo; Rodriguez-Rivas, Juan; Zamponi, Francesco; Weigt, Martin
Publié dans: Molecular Biology and Evolution, Numéro 9, 2022, ISSN 0737-4038
Éditeur: Oxford University Press
DOI: 10.48550/arxiv.2106.02441

Predicting Interacting Protein Pairs by Coevolutionary Paralog Matching.

Auteurs: Thomas Gueudré; Carlo Baldassi; Andrea Pagnani; Martin Weigt
Publié dans: Protein-Protein Interaction Networks, Numéro 15, 2019, Page(s) 57–65, ISBN 978-1-4939-9872-2
Éditeur: Humana, New York, NY
DOI: 10.1007/978-1-4939-9873-9_5

Kinetic modelling of competition and depletion of shared miRNAs by competing endogenous RNAs

Auteurs: Martirosyan, Araks; Del Giudice, Marco; Bena, Chiara Enrico; Pagnani, Andrea; Bosia, Carla; De Martino, Andrea
Publié dans: Computational Biology of Non-Coding RNA, Numéro 15, 2019, Page(s) 367–409, ISBN 978-1-4939-8981-2
Éditeur: Humana Press, New York, NY
DOI: 10.48550/arxiv.1812.09538

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

Auteurs: Araks Martirosyan, Marco Del Giudice, Chiara Enrico Bena, Andrea Pagnani, Carla Bosia, Andrea De Martino
Publié dans: Computational Biology of Non-Coding RNA - Methods and Protocols, Numéro 1912, 2019, Page(s) 367-409, ISBN 978-1-4939-8981-2
Éditeur: Springer New York
DOI: 10.1007/978-1-4939-8982-9_15

Influence of settings and predictors in neural network model performance: a Buenos Aires air quality case

Auteurs: Ariel F. Scagliotti; David H. Margarit; Marcela V. Reale; Guillermo A. Jorge
Publié dans: Procedia Computer Science, 2022, ISSN 1877-0509
Éditeur: Elsevier
DOI: 10.1016/j.procs.2022.11.019

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