Jorge FERNANDEZ-DE-COSSIO-DIAZ

28
Documents
Affiliations actuelles
  • Institut de Physique Théorique - UMR CNRS 3681 (IPHT)
  • Université Paris-Saclay
  • Laboratoire de physique de l'ENS - ENS Paris (LPENS)
Contact

Présentation

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

Publications

Publications

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Designing molecular RNA switches with Restricted Boltzmann machines

Jorge Fernandez-De-Cossio-Diaz , Pierre Hardouin , Francois-Xavier Lyonnet Du Moutier , Andrea Di Gioacchino , Bertrand Marchand et al.
Nature Communications, In press
Article dans une revue hal-04294884 v1
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Inference and design of antibody specificity: From experiments to models and back

Jorge Fernandez-De-Cossio-Diaz , Guido Uguzzoni , Kévin Ricard , Francesca Anselmi , Clément Nizak et al.
PLoS Computational Biology, 2024, 20 (10), pp.e1012522. ⟨10.1371/journal.pcbi.1012522⟩
Article dans une revue hal-04778023 v2
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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-04733979 v1
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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-04733981 v1
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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 León et al.
Data in Brief, 2023, 50, pp.109604. ⟨10.1016/j.dib.2023.109604⟩
Article dans une revue (data paper) hal-04785695 v1
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Benchmarking solutions to the T-cell receptor epitope prediction problem: IMMREP22 workshop report

Pieter Meysman , Justin Barton , Barbara Bravi , Liel Cohen-Lavi , Vadim Karnaukhov et al.
ImmunoInformatics, 2023, 9, pp.100024. ⟨10.1016/j.immuno.2023.100024⟩
Article dans une revue hal-03854607 v1
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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 Mora et al.
eLife, 2023, 12, pp.e.85126. ⟨10.7554/eLife.85126⟩
Article dans une revue hal-04252230 v1
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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-04307038 v1

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 León et al.
Biochemical Engineering Journal, 2023, 198, pp.109010. ⟨10.1016/j.bej.2023.109010⟩
Article dans une revue hal-04734126 v1
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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-04622251 v1
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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-03405967 v1

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-04734127 v1
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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-04734128 v1

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-04734130 v1

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-04734133 v1

Formate induces a metabolic switch in nucleotide and energy metabolism

Kristell Oizel , Jacqueline Tait-Mulder , Jorge Fernandez-De-Cossio-Diaz , Matthias Pietzke , Holly Brunton et al.
Cell Death and Disease, 2020, 11 (5), pp.310. ⟨10.1038/s41419-020-2523-z⟩
Article dans une revue hal-04734134 v1

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-04734137 v1

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-04734135 v1

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-04734140 v1

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-04734143 v1

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-04734142 v1

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-04734141 v1

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, May 2024, Vienna, Austria. https://openreview.net/forum?id=kXNJ48Hvw1
Communication dans un congrès hal-05355567 v1