Jorge FERNANDEZ-DE-COSSIO-DIAZ

Identifiants chercheurs

IdHAL :

cossio

ORCID :

0000-0002-4476-805X

IdRef :

28327607X

arXiv :

fernandezdecossiodiaz_j_1

Présentation

I am a CNRS Junior Professor working at IPhT, interested in machine learning, statistical mechanics and biological sequence modeling.

Publications

Article dans une revue (25)

Designing molecular RNA switches with Restricted Boltzmann machines Jorge Fernandez-De-Cossio-Diaz,Pierre Hardouin,Francois-Xavier Lyonnet Du Moutier,Andrea Di Gioacchino,Bertrand Marchandet al. Nature Communications, In press, ⟨10.1038/s41467-025-66265-y⟩ Article dans une revue hal-04294884v1
Unsupervised modeling of mutational landscapes of adeno-associated viruses viability Matteo de Leonardis,Jorge Fernandez-De-Cossio-Diaz,Guido Uguzzoni,Andrea Pagnani BMC Bioinformatics, 2024, 25 (1), pp.229. ⟨10.1186/s12859-024-05823-5⟩ Article dans une revue hal-04733979v1
Inference and design of antibody specificity: From experiments to models and back Jorge Fernandez-De-Cossio-Diaz,Guido Uguzzoni,Kévin Ricard,Francesca Anselmi,Clément Nizaket al. PLoS Computational Biology, 2024, 20 (10), pp.e1012522. ⟨10.1371/journal.pcbi.1012522⟩ Article dans une revue hal-04778023v2
Inference of annealed protein fitness landscapes with AnnealDCA Luca Sesta,Andrea Pagnani,Jorge Fernandez-De-Cossio-Diaz,Guido Uguzzoni PLoS Computational Biology, 2024, 20 (2), pp.e1011812. ⟨10.1371/journal.pcbi.1011812⟩ Article dans une revue hal-04733981v1
HEK293 producing the extracellular domain HER1: Full datasets of continuous fermentation process and metabolites analysis Lisandra Calzadilla,Erick Hernández,Julio Dustet,Jorge Fernandez-De-Cossio-Diaz,Kalet Leónet al. Data in Brief, 2023, 50, pp.109604. ⟨10.1016/j.dib.2023.109604⟩ Article dans une revue (data paper) hal-04785695v1
Benchmarking solutions to the T-cell receptor epitope prediction problem: IMMREP22 workshop report Pieter Meysman,Justin Barton,Barbara Bravi,Liel Cohen-Lavi,Vadim Karnaukhovet al. ImmunoInformatics, 2023, 9, pp.100024. ⟨10.1016/j.immuno.2023.100024⟩ Article dans une revue hal-03854607v1
Disentangling Representations in Restricted Boltzmann Machines without Adversaries Jorge Fernandez-De-Cossio-Diaz,Simona Cocco,Rémi Monasson Physical Review X, 2023, 13 (2), pp.021003. ⟨10.1103/PhysRevX.13.021003⟩ Article dans une revue hal-04307038v1
A transfer-learning approach to predict antigen immunogenicity and T-cell receptor specificity Barbara Bravi,Andrea Di Gioacchino,Jorge Fernandez-De-Cossio-Diaz,Aleksandra Walczak,Thierry Moraet al. eLife, 2023, 12, pp.e.85126. ⟨10.7554/eLife.85126⟩ Article dans une revue hal-04252230v1
Multiple steady states and metabolic switches in continuous cultures of HEK293: Experimental evidences and metabolomics Lisandra Calzadilla,Erick Hernández,Julio Dustet,Jorge Fernandez-De-Cossio-Diaz,Kalet Leónet al. Biochemical Engineering Journal, 2023, 198, pp.109010. ⟨10.1016/j.bej.2023.109010⟩ Article dans une revue hal-04734126v1
Inference of metabolic fluxes in nutrient-limited continuous cultures: A Maximum Entropy approach with the minimum information José Antonio Pereiro-Morejon,Jorge Fernandez-De-Cossio-Diaz,Roberto Mulet iScience, 2022, 25 (12), pp.105450. ⟨10.1016/j.isci.2022.105450⟩ Article dans une revue hal-04622251v1
AMaLa: Analysis of Directed Evolution Experiments via Annealed Mutational Approximated Landscape Luca Sesta,Guido Uguzzoni,Jorge Fernandez-De-Cossio-Diaz,Andrea Pagnani International Journal of Molecular Sciences, 2021, 22 (20), pp.10908. ⟨10.3390/ijms222010908⟩ Article dans une revue hal-03405967v1
In‐silico media optimization for continuous cultures using genome scale metabolic networks: The case of CHO‐K1 Bárbara Pérez-Fernández,Jorge Fernandez-De-Cossio-Diaz,Tammy Boggiano,Kalet León,Roberto Mulet Biotechnology and Bioengineering, 2021, 118 (5), pp.1884-1897. ⟨10.1002/bit.27704⟩ Article dans une revue hal-04734127v1
Formate induces a metabolic switch in nucleotide and energy metabolism Kristell Oizel,Jacqueline Tait-Mulder,Jorge Fernandez-De-Cossio-Diaz,Matthias Pietzke,Holly Bruntonet al. Cell Death and Disease, 2020, 11 (5), pp.310. ⟨10.1038/s41419-020-2523-z⟩ Article dans une revue hal-04734134v1
Statistical mechanics of interacting metabolic networks Jorge Fernandez-De-Cossio-Diaz,Roberto Mulet Physical Review E , 2020, 101 (4), pp.042401. ⟨10.1103/PhysRevE.101.042401⟩ Article dans une revue hal-04734133v1
A self-consistent probabilistic formulation for inference of interactions Jorge Fernandez-De-Cossio,Jorge Fernandez-De-Cossio-Diaz,Yasser Perera-Negrin Scientific Reports, 2020, 10 (1), pp.21435. ⟨10.1038/s41598-020-78496-8⟩ Article dans une revue hal-04734130v1
Unsupervised Inference of Protein Fitness Landscape from Deep Mutational Scan Jorge Fernandez-De-Cossio-Diaz,Guido Uguzzoni,Andrea Pagnani Molecular Biology and Evolution, 2020, 38 (1), pp.318-328. ⟨10.1093/molbev/msaa204⟩ Article dans une revue hal-04734128v1
Maximum entropy and population heterogeneity in continuous cell cultures Jorge Fernandez-De-Cossio-Diaz,Roberto Mulet PLoS Computational Biology, 2019, 15 (2), pp.e1006823. ⟨10.1371/journal.pcbi.1006823⟩ Article dans une revue hal-04734137v1
Cell population heterogeneity driven by stochastic partition and growth optimality Jorge Fernandez-De-Cossio-Diaz,Roberto Mulet,Alexei Vazquez Scientific Reports, 2019, 9 (1), pp.9406. ⟨10.1038/s41598-019-45882-w⟩ Article dans une revue hal-04734135v1
A physical model of cell metabolism Jorge Fernandez-De-Cossio-Diaz,Alexei Vazquez Scientific Reports, 2018, 8 (1), pp.8349. ⟨10.1038/s41598-018-26724-7⟩ Article dans une revue hal-04734140v1
Characterizing steady states of genome-scale metabolic networks in continuous cell cultures Jorge Fernandez-De-Cossio-Diaz,Kalet Leon,Roberto Mulet PLoS Computational Biology, 2017, 13 (11), pp.e1005835. ⟨10.1371/journal.pcbi.1005835⟩ Article dans une revue hal-04734141v1
Microenvironmental cooperation promotes early spread and bistability of a Warburg-like phenotype Jorge Fernandez-De-Cossio-Diaz,Andrea de Martino,Roberto Mulet Scientific Reports, 2017, 7 (1), pp.3103. ⟨10.1038/s41598-017-03342-3⟩ Article dans une revue hal-04734143v1
Limits of aerobic metabolism in cancer cells Jorge Fernandez-De-Cossio-Diaz,Alexei Vazquez Scientific Reports, 2017, 7 (1), pp.13488. ⟨10.1038/s41598-017-14071-y⟩ Article dans une revue hal-04734142v1
Optimally Designed Quantum Transport across Disordered Networks Mattia Walschaers,Jorge Fernandez-De-Cossio Diaz,Roberto Mulet,Andreas Buchleitner Physical Review Letters, 2013, 111 (18), pp.180601. ⟨10.1103/PhysRevLett.111.180601⟩ Article dans une revue hal-04734147v1
Optimally Designed Quantum Transport across Disordered Networks Mattia Walschaers,Jorge Fernandez-De-Cossio Diaz,Roberto Mulet,Andreas Buchleitner Physical Review Letters, 2013, 111 (18), ⟨10.1103/PhysRevLett.111.180601⟩ Article dans une revue hal-03037452v1
Computation of Isotopic Peak Center-Mass Distribution by Fourier Transform Jorge Fernandez-De-Cossio Diaz,Jorge Fernandez-De-Cossio Analytical Chemistry, 2012, 84 (16), pp.7052-7056. ⟨10.1021/ac301296a⟩ Article dans une revue hal-04734148v1

Communication dans un congrès (1)

Accelerated Sampling with Stacked Restricted Boltzmann Machines Jorge Fernandez-De-Cossio-Diaz,Clément Roussel,Simona Cocco,Rémi Monasson The Twelfth International Conference on Learning Representations (ICLR 2024), May 2024, Vienna, Austria Communication dans un congrès hal-05355567v1

Chapitre d'ouvrage (1)

Generative Modeling of RNA Sequence Families with Restricted Boltzmann Machines Jorge Fernandez-De-Cossio-Diaz RNA Design, 2847, Springer US, pp.163-175, 2025, Methods in Molecular Biology, ⟨10.1007/978-1-0716-4079-1_11⟩ Chapitre d'ouvrage hal-04734117v1

Pré-publication, Document de travail (6)

Cross-individual translation of spontaneous zebrafish brain activity through a shared latent representation Mattéo Dommanget-Kott,Jorge Fernandez-De-Cossio-Diaz,Guillaume Faye-Bédrin,Georges Debrégeas,Volker Bormuth 2026 Pré-publication, Document de travail hal-05475874v1
Replica Theory of Spherical Boltzmann Machine Ensembles Thomas Tulinski,Jorge Fernandez-De-Cossio-Diaz,Simona Cocco,Rémi Monasson 2026 Pré-publication, Document de travail hal-05596208v2
A High-Order Cumulant Extension of Quasi-Linkage Equilibrium Kai Shimagaki,Jorge Fernandez-De-Cossio-Diaz,Mauro Pastore,Rémi Monasson,Simona Coccoet al. 2025 Pré-publication, Document de travail cea-05321646v1
Linking Brain and Behavior States in Zebrafish Larvae Locomotion using Hidden Markov Models Mattéo Dommanget-Kott,Jorge Fernandez-De-Cossio-Diaz,Monica Coraggioso,Volker Bormuth,Rémi Monassonet al. 2024 Pré-publication, Document de travail (preprint/prepublication) hal-04445557v2
Replica symmetry breaking and clustering phase transitions in undersampled restricted Boltzmann machines Jorge Fernandez-De-Cossio-Diaz,Thomas Tulinski,Simona Cocco,Rémi Monasson 2024 Pré-publication, Document de travail hal-04447899v1
Deep Tempering with Nested Restricted Boltzmann Machines Clément Roussel,Jorge Fernandez-De-Cossio-Diaz,Simona Cocco,Rémi Monasson 2023 Pré-publication, Document de travail hal-03919483v1