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Logistic PCA explains differences between genome-scale metabolic models in terms of metabolic pathways.
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- PLoS Computational Biology, 2024, v. 20, n. 6, p. 1, doi. 10.1371/journal.pcbi.1012236
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Costs of ribosomal RNA stabilization affect ribosome composition at maximum growth rate.
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- Communications Biology, 2024, v. 7, n. 1, p. N.PAG, doi. 10.1038/s42003-024-05815-4
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Publisher Correction: Costs of ribosomal RNA stabilization affect ribosome composition at maximum growth rate.
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- 2024
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- Correction Notice
PyCoMo: a python package for community metabolic model creation and analysis.
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- Bioinformatics, 2024, v. 40, n. 4, p. 1, doi. 10.1093/bioinformatics/btae153
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- Article
Costs of ribosomal RNA stabilization affect ribosome composition at maximum growth rate.
- Published in:
- Communications Biology, 2024, v. 7, n. 1, p. 1, doi. 10.1038/s42003-024-05815-4
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- Article
Publisher Correction: Costs of ribosomal RNA stabilization affect ribosome composition at maximum growth rate.
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- 2024
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- Correction Notice
Characterising the metabolic rewiring of extremely slow growing Komagataella phaffii.
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- Microbial Biotechnology, 2024, v. 17, n. 1, p. 1, doi. 10.1111/1751-7915.14386
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- Article
Sulfate limitation increases specific plasmid DNA yield and productivity in E. coli fed-batch processes.
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- Microbial Cell Factories, 2023, v. 22, n. 1, p. 1, doi. 10.1186/s12934-023-02248-2
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Environmental flexibility does not explain metabolic robustness.
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- NPJ Systems Biology & Applications, 2023, v. 6, n. 1, p. 1, doi. 10.1038/s41540-020-00155-5
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- Article
Optimizing VLP production in gene therapy: Opportunities and challenges for in silico modeling.
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- Biotechnology Journal, 2023, v. 18, n. 7, p. 1, doi. 10.1002/biot.202200636
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ecmtool: fast and memory-efficient enumeration of elementary conversion modes.
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- Bioinformatics, 2023, v. 39, n. 3, p. 1, doi. 10.1093/bioinformatics/btad095
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Probabilistic quotient's work and pharmacokinetics' contribution: countering size effect in metabolic time series measurements.
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- BMC Bioinformatics, 2022, v. 23, n. 1, p. 1, doi. 10.1186/s12859-022-04918-1
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- Article
Homologue series detection and management in LC-MS data with homologueDiscoverer.
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- Bioinformatics, 2022, v. 38, n. 22, p. 5139, doi. 10.1093/bioinformatics/btac647
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- Article
Probabilistic quotient's work and pharmacokinetics' contribution: countering size effect in metabolic time series measurements.
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- BMC Bioinformatics, 2022, v. 23, n. 1, p. 1, doi. 10.1186/s12859-022-04918-1
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- Article
Elementary vectors and autocatalytic sets for resource allocation in next-generation models of cellular growth.
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- PLoS Computational Biology, 2022, v. 18, n. 2, p. 1, doi. 10.1371/journal.pcbi.1009843
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EFMlrs: a Python package for elementary flux mode enumeration via lexicographic reverse search.
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- BMC Bioinformatics, 2021, v. 22, n. 1, p. 1, doi. 10.1186/s12859-021-04417-9
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- Article
Finger sweat analysis enables short interval metabolic biomonitoring in humans.
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- Nature Communications, 2021, v. 12, n. 1, p. 1, doi. 10.1038/s41467-021-26245-4
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- Article
Thermodynamic Genome-Scale Metabolic Modeling of Metallodrug Resistance in Colorectal Cancer.
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- Cancers, 2021, v. 13, n. 16, p. 4130, doi. 10.3390/cancers13164130
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- Article
Inclusion of maintenance energy improves the intracellular flux predictions of CHO.
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- PLoS Computational Biology, 2021, v. 17, n. 6, p. 1, doi. 10.1371/journal.pcbi.1009022
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- Article
Error propagation in constraint‐based modeling of Chinese hamster ovary cells.
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- Biotechnology Journal, 2021, v. 16, n. 4, p. 1, doi. 10.1002/biot.202000320
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- Article
Environmental flexibility does not explain metabolic robustness.
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- NPJ Systems Biology & Applications, 2020, v. 6, n. 1, p. N.PAG, doi. 10.1038/s41540-020-00155-5
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- Article
The sources and transmission routes of microbial populations throughout a meat processing facility.
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- NPJ Biofilms & Microbiomes, 2020, v. 6, n. 1, p. 1, doi. 10.1038/s41522-020-0136-z
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- Article
Key Challenges in Designing CHO Chassis Platforms.
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- Processes, 2020, v. 8, n. 6, p. 643, doi. 10.3390/pr8060643
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- Article
The secretome of Pichia pastoris in fed‐batch cultivations is largely independent of the carbon source but changes quantitatively over cultivation time.
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- Microbial Biotechnology, 2020, v. 13, n. 2, p. 479, doi. 10.1111/1751-7915.13499
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- Article
Genetic and Epigenetic Variation across Genes Involved in Energy Metabolism and Mitochondria of Chinese Hamster Ovary Cell Lines.
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- Biotechnology Journal, 2019, v. 14, n. 7, p. N.PAG, doi. 10.1002/biot.201800681
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- Article
Flux tope analysis: studying the coordination of reaction directions in metabolic networks.
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- Bioinformatics, 2019, v. 35, n. 2, p. 266, doi. 10.1093/bioinformatics/bty550
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- Article
Comprehensive assessment of measurement uncertainty in <sup>13</sup>C-based metabolic flux experiments.
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- Analytical & Bioanalytical Chemistry, 2018, v. 410, n. 14, p. 3337, doi. 10.1007/s00216-018-1017-7
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- Article
From elementary flux modes to elementary flux vectors: Metabolic pathway analysis with arbitrary linear flux constraints.
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- PLoS Computational Biology, 2017, v. 13, n. 4, p. 1, doi. 10.1371/journal.pcbi.1005409
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- Article
Optimal knockout strategies in genome-scale metabolic networks using particle swarm optimization.
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- BMC Bioinformatics, 2017, v. 18, p. 1, doi. 10.1186/s12859-017-1483-5
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- Article
CHOmine: an integrated data warehouse for CHO systems biology and modeling.
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- Database: The Journal of Biological Databases & Curation, 2017, v. 2017, n. 1, p. 1, doi. 10.1093/database/bax034
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- Article
Which sets of elementary flux modes form thermodynamically feasible flux distributions?
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- FEBS Journal, 2016, v. 283, n. 9, p. 1782, doi. 10.1111/febs.13702
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- Article
Exact quantification of cellular robustness in genome-scale metabolic networks.
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- Bioinformatics, 2016, v. 32, n. 5, p. 730, doi. 10.1093/bioinformatics/btv649
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- Article
ICT: isotope correction toolbox.
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- Bioinformatics, 2016, v. 32, n. 1, p. 154, doi. 10.1093/bioinformatics/btv514
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- Article
Designing minimal microbial strains of desired functionality using a genetic algorithm.
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- Algorithms for Molecular Biology, 2015, v. 10, p. 1, doi. 10.1186/s13015-015-0060-6
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- Article
tEFMA: computing thermodynamically feasible elementary flux modes in metabolic networks.
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- Bioinformatics, 2015, v. 31, n. 13, p. 2232, doi. 10.1093/bioinformatics/btv111
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- Article
Avoiding the Enumeration of Infeasible Elementary Flux Modes by Including Transcriptional Regulatory Rules in the Enumeration Process Saves Computational Costs.
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- PLoS ONE, 2015, v. 10, n. 6, p. 1, doi. 10.1371/journal.pone.0129840
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Metabolomics integrated elementary flux mode analysis in large metabolic networks.
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- Scientific Reports, 2015, p. 8930, doi. 10.1038/srep08930
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Design of Optimally Constructed Metabolic Networks of Minimal Functionality.
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- PLoS ONE, 2014, v. 9, n. 3, p. 1, doi. 10.1371/journal.pone.0092583
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Comparison and improvement of algorithms for computing minimal cut sets.
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- BMC Bioinformatics, 2013, v. 14, n. 1, p. 2, doi. 10.1186/1471-2105-14-318
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- Article
Elementary flux modes in a nutshell: Properties, calculation and applications.
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- Biotechnology Journal, 2013, v. 8, n. 9, p. 1009, doi. 10.1002/biot.201200269
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- Article
Quantitative modeling of triacylglycerol homeostasis in yeast – metabolic requirement for lipolysis to promote membrane lipid synthesis and cellular growth.
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- FEBS Journal, 2008, v. 275, n. 22, p. 5552, doi. 10.1111/j.1742-4658.2008.06681.x
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- Article