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An integrated computational-experimental approach reveals Yersinia pestis genes essential across a narrow or a broad range of environmental conditions.
- Published in:
- BMC Microbiology, 2017, v. 17, p. 1, doi. 10.1186/s12866-017-1073-8
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- Article
BioJazz: in silico evolution of cellular networks with unbounded complexity using rule-based modeling.
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- Nucleic Acids Research, 2015, v. 43, n. 19, p. 1A, doi. 10.1093/nar/gkv595
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- Article
Metabolic tinker: an online tool for guiding the design of synthetic metabolic pathways.
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- Nucleic Acids Research, 2013, v. 41, n. 11, p. e113, doi. 10.1093/nar/gkt234
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- Article
Mapping epigenetic changes to the host cell genome induced by Burkholderia pseudomallei reveals pathogen-specific and pathogen-generic signatures of infection.
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- Scientific Reports, 2016, p. 30861, doi. 10.1038/srep30861
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- Article
ChemChaste: Simulating spatially inhomogeneous biochemical reaction–diffusion systems for modeling cell–environment feedbacks.
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- GigaScience, 2022, v. 11, p. 1, doi. 10.1093/gigascience/giac051
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- Article
Campylobacter jejuni 11168H Exposed to Penicillin Forms Persister Cells and Cells With Altered Redox Protein Activity.
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- Frontiers in Cellular & Infection Microbiology, 2020, v. 10, p. N.PAG, doi. 10.3389/fcimb.2020.565975
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- Article
Biodiversity–function relationships in methanogenic communities.
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- Molecular Ecology, 2018, v. 27, n. 22, p. 4641, doi. 10.1111/mec.14895
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- Article
STRONG: metagenomics strain resolution on assembly graphs.
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- Genome Biology, 2021, v. 22, n. 1, p. 1, doi. 10.1186/s13059-021-02419-7
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- Article
Inhibiting the reproduction of SARS-CoV-2 through perturbations in human lung cell metabolic network.
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- Life Science Alliance, 2021, v. 4, n. 1, p. 1, doi. 10.26508/lsa.202000869
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- Article
Bistability in feedback circuits as a byproduct of evolution of evolvability.
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- Molecular Systems Biology, 2012, v. 8, n. 1, p. 1, doi. 10.1038/msb.2011.98
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- Article
Parasites lead to evolution of robustness against gene loss in host signaling networks.
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- Molecular Systems Biology, 2008, v. 4, n. 1, p. 1, doi. 10.1038/msb.2008.44
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- Article
Regulating the total level of a signaling protein can vary its dynamics in a range from switch like ultrasensitivity to adaptive responses.
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- FEBS Journal, 2009, v. 276, n. 12, p. 3290, doi. 10.1111/j.1742-4658.2009.07054.x
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- Article
Phosphate Sink Containing Two-Component Signaling Systems as Tunable Threshold Devices.
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- PLoS Computational Biology, 2014, v. 10, n. 10, p. 1, doi. 10.1371/journal.pcbi.1003890
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- Article
Phosphorelays Provide Tunable Signal Processing Capabilities for the Cell.
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- PLoS Computational Biology, 2013, v. 9, n. 11, p. 1, doi. 10.1371/journal.pcbi.1003322
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- Article
Split Histidine Kinases Enable Ultrasensitivity and Bistability in Two-Component Signaling Networks.
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- PLoS Computational Biology, 2013, v. 9, n. 3, p. 1, doi. 10.1371/journal.pcbi.1002949
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- Article
Evolution under Fluctuating Environments Explains Observed Robustness in Metabolic Networks.
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- PLoS Computational Biology, 2010, v. 6, n. 8, p. 1, doi. 10.1371/journal.pcbi.1000907
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- Article
Evolution of Taxis Responses in Virtual Bacteria: Non-Adaptive Dynamics.
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- PLoS Computational Biology, 2008, v. 4, n. 5, p. 1, doi. 10.1371/journal.pcbi.1000084
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- Article
Cooperation in microbial communities and their biotechnological applications.
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- Environmental Microbiology, 2017, v. 19, n. 8, p. 2949, doi. 10.1111/1462-2920.13767
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- Article
Dynamics of co-substrate pools can constrain and regulate metabolic fluxes.
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- eLife, 2023, p. 1, doi. 10.7554/eLife.84379
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- Article
Ultrasensitive Negative Feedback Control: A Natural Approach for the Design of Synthetic Controllers.
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- PLoS ONE, 2016, v. 11, n. 8, p. 1, doi. 10.1371/journal.pone.0161605
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- Article
Nonlinear Dynamics in Gene Regulation Promote Robustness and Evolvability of Gene Expression Levels.
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- PLoS ONE, 2016, v. 11, n. 4, p. 1, doi. 10.1371/journal.pone.0153295
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- Article
Enzyme Sequestration as a Tuning Point in Controlling Response Dynamics of Signalling Networks.
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- PLoS Computational Biology, 2016, v. 12, n. 5, p. 1, doi. 10.1371/journal.pcbi.1004918
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- Article
The Evolution of Connectivity in Metabolic Networks.
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- PLoS Biology, 2005, v. 3, n. 6, p. 1, doi. 10.1371/journal.pbio.0030228
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Evolutionary systems biology: What it is and why it matters.
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- BioEssays, 2013, v. 35, n. 8, p. 696, doi. 10.1002/bies.201300029
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- Article
Depicting a protein’s two faces: GPCR classification by phylogenetic tree-based HMMs
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- FEBS Letters, 2003, v. 554, n. 1/2, p. 95, doi. 10.1016/S0014-5793(03)01112-8
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- Article
Emergence and maintenance of functional modules in signaling pathways.
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- BMC Evolutionary Biology, 2007, v. 7, p. 205, doi. 10.1186/1471-2148-7-205
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MetQy—an R package to query metabolic functions of genes and genomes.
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- Bioinformatics, 2018, v. 34, n. 23, p. 4134, doi. 10.1093/bioinformatics/bty447
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- Article
The Promise of Evolutionary Systems Biology: Lessons from Bacterial Chemotaxis.
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- Science Signaling, 2010, v. 3, n. 128, p. 1, doi. 10.1126/scisignal.3128pe23
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- Article
Metabolic modelling in a dynamic evolutionary framework predicts adaptive diversification of bacteria in a long-term evolution experiment.
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- BMC Evolutionary Biology, 2016, v. 16, p. 1, doi. 10.1186/s12862-016-0733-x
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- Article