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In‐silico media optimization for continuous cultures using genome scale metabolic networks: The case of CHO‐K1

Biotechnology and bioengineering, 2021-05, Vol.118 (5), p.1884-1897

2021

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Optimally designed quantum transport across disordered networks

Physical review letters, 2013-11, Vol.111 (18), p.180601-180601, Article 180601

2013

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Limits of aerobic metabolism in cancer cells

Scientific reports, 2017-10, Vol.7 (1), p.13488-8, Article 13488

2017

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Maximum entropy and population heterogeneity in continuous cell cultures

PLoS computational biology, 2019-02, Vol.15 (2), p.e1006823

2019

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Unsupervised modeling of mutational landscapes of adeno-associated viruses viability

BMC bioinformatics, 2024-07, Vol.25 (1), p.229-19, Article 229

2024

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Inference of annealed protein fitness landscapes with AnnealDCA

PLoS computational biology, 2024-02, Vol.20 (2), p.e1011812-e1011812

2024

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Disentangling Representations in Restricted Boltzmann Machines without Adversaries

Physical review. X, 2023-04, Vol.13 (2), p.021003, Article 021003

2023

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

PLoS computational biology, 2017-11, Vol.13 (11), p.e1005835

2017

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

International journal of molecular sciences, 2021-10, Vol.22 (20), p.10908

2021

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A self-consistent probabilistic formulation for inference of interactions

Scientific reports, 2020-12, Vol.10 (1), p.21435-16, Article 21435

2020

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

Scientific reports, 2017-06, Vol.7 (1), p.3103-14, Article 3103

2017

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A transfer-learning approach to predict antigen immunogenicity and T-cell receptor specificity

eLife, 2023-09, Vol.12

2023

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Directed evolution of super-secreted variants from phage-displayed human Interleukin-2

Scientific reports, 2019-01, Vol.9 (1), p.800-800, Article 800

2019

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

iScience, 2022-12, Vol.25 (12), p.105450-105450, Article 105450

2022

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Computation of Isotopic Peak Center-Mass Distribution by Fourier Transform

Analytical chemistry (Washington), 2012-08, Vol.84 (16), p.7052-7056

2012

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HEK293 producing the extracellular domain HER1: Full datasets of continuous fermentation process and metabolites analysis

Data in brief, 2023-10, Vol.50, p.109604-109604, Article 109604

2023

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Generative Modeling of RNA Sequence Families with Restricted Boltzmann Machines

Methods in molecular biology (Clifton, N.J.), 2025, Vol.2847, p.163

Fernandez-de-Cossio-Diaz, Jorge

2025

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A physical model of cell metabolism

Scientific reports, 2018-05, Vol.8 (1), p.8349-13, Article 8349

2018

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Unsupervised Inference of Protein Fitness Landscape from Deep Mutational Scan

Molecular biology and evolution, 2021-01, Vol.38 (1), p.318-328

2021

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Cell population heterogeneity driven by stochastic partition and growth optimality

Scientific reports, 2019-06, Vol.9 (1), p.9406-7, Article 9406

2019

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Statistical mechanics of interacting metabolic networks

Physical review. E, 2020-04, Vol.101 (4-1), p.042401-042401, Article 042401

2020

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Multiple steady states and metabolic switches in continuous cultures of HEK293: Experimental evidences and metabolomics

Biochemical engineering journal, 2023-09, Vol.198, p.109010, Article 109010

2023

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Formate induces a metabolic switch in nucleotide and energy metabolism

Cell death & disease, 2020-05, Vol.11 (5), p.310-310, Article 310

2020

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Benchmarking solutions to the T-cell receptor epitope prediction problem: IMMREP22 workshop report

ImmunoInformatics, 2023-03, Vol.9, p.100024, Article 100024

2023

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Formate Induces a Metabolic Switch in Nucleotide and Energy Metabolism

SSRN Electronic Journal

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In‐silico media optimization for continuous cultures using genome scale metabolic networks: The case of CHO‐K1

Optimally designed quantum transport across disordered networks

Limits of aerobic metabolism in cancer cells

Maximum entropy and population heterogeneity in continuous cell cultures

Unsupervised modeling of mutational landscapes of adeno-associated viruses viability

Inference of annealed protein fitness landscapes with AnnealDCA

Disentangling Representations in Restricted Boltzmann Machines without Adversaries

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

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

A self-consistent probabilistic formulation for inference of interactions

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

A transfer-learning approach to predict antigen immunogenicity and T-cell receptor specificity

Directed evolution of super-secreted variants from phage-displayed human Interleukin-2

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

Computation of Isotopic Peak Center-Mass Distribution by Fourier Transform

HEK293 producing the extracellular domain HER1: Full datasets of continuous fermentation process and metabolites analysis

Generative Modeling of RNA Sequence Families with Restricted Boltzmann Machines

A physical model of cell metabolism

Unsupervised Inference of Protein Fitness Landscape from Deep Mutational Scan

Cell population heterogeneity driven by stochastic partition and growth optimality

Statistical mechanics of interacting metabolic networks

Multiple steady states and metabolic switches in continuous cultures of HEK293: Experimental evidences and metabolomics

Formate induces a metabolic switch in nucleotide and energy metabolism

Benchmarking solutions to the T-cell receptor epitope prediction problem: IMMREP22 workshop report

Formate Induces a Metabolic Switch in Nucleotide and Energy Metabolism

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