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Towards genome-scale signalling network reconstructions.
- Published in:
- 2010
- By:
- Publication type:
- journal article
iModulonMiner and PyModulon: Software for unsupervised mining of gene expression compendia.
- Published in:
- PLoS Computational Biology, 2024, v. 20, n. 10, p. 1, doi. 10.1371/journal.pcbi.1012546
- By:
- Publication type:
- Article
Modulating bacterial function utilizing A knowledge base of transcriptional regulatory modules.
- Published in:
- Nucleic Acids Research, 2024, v. 52, n. 18, p. 11362, doi. 10.1093/nar/gkae742
- By:
- Publication type:
- Article
OxyR Is a Convergent Target for Mutations Acquired during Adaptation to Oxidative Stress-Prone Metabolic States.
- Published in:
- Molecular Biology & Evolution, 2020, v. 37, n. 3, p. 660, doi. 10.1093/molbev/msz251
- By:
- Publication type:
- Article
Synthesizing Systems Biology Knowledge from Omics Using Genome‐Scale Models.
- Published in:
- Proteomics, 2020, v. 20, n. 17/18, p. 1, doi. 10.1002/pmic.201900282
- By:
- Publication type:
- Article
Modeling Red Blood Cell Metabolism in the Omics Era.
- Published in:
- Metabolites (2218-1989), 2023, v. 13, n. 11, p. 1145, doi. 10.3390/metabo13111145
- By:
- Publication type:
- Article
Differential Expression Analysis Utilizing Condition-Specific Metabolic Pathways.
- Published in:
- Metabolites (2218-1989), 2023, v. 13, n. 11, p. 1127, doi. 10.3390/metabo13111127
- By:
- Publication type:
- Article
Reconstruction and Validation of a Genome-Scale Metabolic Model of Streptococcus oralis (iCJ415), a Human Commensal and Opportunistic Pathogen.
- Published in:
- Frontiers in Genetics, 2020, p. 1, doi. 10.3389/fgene.2020.00116
- By:
- Publication type:
- Article
An atlas of human metabolism.
- Published in:
- Science Signaling, 2020, v. 13, n. 624, p. 1, doi. 10.1126/scisignal.aaz1482
- By:
- Publication type:
- Article
Multiple-omic data analysis of Klebsiella pneumoniae MGH 78578 reveals its transcriptional architecture and regulatory features.
- Published in:
- BMC Genomics, 2012, v. 13, n. 1, p. 679, doi. 10.1186/1471-2164-13-679
- By:
- Publication type:
- Article
Adaptations of Escherichia coli strains to oxidative stress are reflected in properties of their structural proteomes.
- Published in:
- BMC Bioinformatics, 2020, v. 21, n. 1, p. 1, doi. 10.1186/s12859-020-3505-y
- By:
- Publication type:
- Article
Positively charged mineral surfaces promoted the accumulation of organic intermediates at the origin of metabolism.
- Published in:
- PLoS Computational Biology, 2022, v. 18, n. 8, p. 1, doi. 10.1371/journal.pcbi.1010377
- By:
- Publication type:
- Article
A model-driven quantitative metabolomics analysis of aerobic and anaerobic metabolism in E. coli K-12 MG1655 that is biochemically and thermodynamically consistent.
- Published in:
- Biotechnology & Bioengineering, 2014, v. 111, n. 4, p. 803, doi. 10.1002/bit.25133
- By:
- Publication type:
- Article
Inferring the metabolism of human orphan metabolites from their metabolic network context affirms human gluconokinase activity.
- Published in:
- Biochemical Journal, 2013, v. 449, n. 2, p. 427, doi. 10.1042/BJ20120980
- By:
- Publication type:
- Article
Constraint-based models predict metabolic and associated cellular functions.
- Published in:
- Nature Reviews Genetics, 2014, v. 15, n. 2, p. 107, doi. 10.1038/nrg3643
- By:
- Publication type:
- Article
Systems biology analysis of the Clostridioides difficile core-genome contextualizes microenvironmental evolutionary pressures leading to genotypic and phenotypic divergence.
- Published in:
- NPJ Systems Biology & Applications, 2020, v. 6, n. 1, p. N.PAG, doi. 10.1038/s41540-020-00151-9
- By:
- Publication type:
- Article
Profiling the effect of nafcillin on HA-MRSA D712 using bacteriological and physiological media.
- Published in:
- Scientific Data, 2019, v. 6, n. 1, p. 1, doi. 10.1038/s41597-019-0331-z
- By:
- Publication type:
- Article
Characterization of CA-MRSA TCH1516 exposed to nafcillin in bacteriological and physiological media.
- Published in:
- Scientific Data, 2019, v. 6, n. 1, p. N.PAG, doi. 10.1038/s41597-019-0051-4
- By:
- Publication type:
- Article
Minimal cells, maximal knowledge.
- Published in:
- eLife, 2019, p. 1, doi. 10.7554/eLife.45379
- By:
- Publication type:
- Article
Network reconstruction of platelet metabolism identifies metabolic signature for aspirin resistance.
- Published in:
- Scientific Reports, 2014, p. 1, doi. 10.1038/srep03925
- By:
- Publication type:
- Article
Identification and Engineering of Transporters for Efficient Melatonin Production in Escherichia coli.
- Published in:
- Frontiers in Microbiology, 2022, p. 1, doi. 10.3389/fmicb.2022.880847
- By:
- Publication type:
- Article
Machine Learning Uncovers a Data-Driven Transcriptional Regulatory Network for the Crenarchaeal Thermoacidophile Sulfolobus acidocaldarius.
- Published in:
- Frontiers in Microbiology, 2021, v. 12, p. 1, doi. 10.3389/fmicb.2021.753521
- By:
- Publication type:
- Article
iCN718, an Updated and Improved Genome-Scale Metabolic Network Reconstruction of Acinetobacter baumannii AYE.
- Published in:
- Frontiers in Genetics, 2018, p. 1, doi. 10.3389/fgene.2018.00121
- By:
- Publication type:
- Article
Comparative Genome-Scale Metabolic Modeling of Metallo-Beta-Lactamase–Producing Multidrug-Resistant Klebsiella pneumoniae Clinical Isolates.
- Published in:
- Frontiers in Cellular & Infection Microbiology, 2019, v. 9, p. N.PAG, doi. 10.3389/fcimb.2019.00161
- By:
- Publication type:
- Article
A treasure trove of 1034 actinomycete genomes.
- Published in:
- Nucleic Acids Research, 2024, v. 52, n. 13, p. 7487, doi. 10.1093/nar/gkae523
- By:
- Publication type:
- Article
BGCFlow: systematic pangenome workflow for the analysis of biosynthetic gene clusters across large genomic datasets.
- Published in:
- Nucleic Acids Research, 2024, v. 52, n. 10, p. 5478, doi. 10.1093/nar/gkae314
- By:
- Publication type:
- Article
A multi-scale expression and regulation knowledge base for Escherichia coli.
- Published in:
- Nucleic Acids Research, 2023, v. 51, n. 19, p. 10176, doi. 10.1093/nar/gkad750
- By:
- Publication type:
- Article
The Escherichia coli Fur pan-regulon has few conserved but many unique regulatory targets.
- Published in:
- Nucleic Acids Research, 2023, v. 51, n. 8, p. 3618, doi. 10.1093/nar/gkad253
- By:
- Publication type:
- Article
Advanced transcriptomic analysis reveals the role of efflux pumps and media composition in antibiotic responses of Pseudomonas aeruginosa.
- Published in:
- Nucleic Acids Research, 2022, v. 50, n. 17, p. 9675, doi. 10.1093/nar/gkac743
- By:
- Publication type:
- Article
Machine learning from Pseudomonas aeruginosa transcriptomes identifies independently modulated sets of genes associated with known transcriptional regulators.
- Published in:
- Nucleic Acids Research, 2022, v. 50, n. 7, p. 3658, doi. 10.1093/nar/gkac187
- By:
- Publication type:
- Article
proChIPdb: a chromatin immunoprecipitation database for prokaryotic organisms.
- Published in:
- Nucleic Acids Research, 2022, v. 50, n. D1, p. D1077, doi. 10.1093/nar/gkab1043
- By:
- Publication type:
- Article
Unraveling the functions of uncharacterized transcription factors in Escherichia coli using ChIP-exo.
- Published in:
- Nucleic Acids Research, 2021, v. 49, n. 17, p. 9696, doi. 10.1093/nar/gkab735
- By:
- Publication type:
- Article
iModulonDB: a knowledgebase of microbial transcriptional regulation derived from machine learning.
- Published in:
- Nucleic Acids Research, 2021, v. 49, n. D1, p. D112, doi. 10.1093/nar/gkaa810
- By:
- Publication type:
- Article
The Bitome: digitized genomic features reveal fundamental genome organization.
- Published in:
- Nucleic Acids Research, 2020, v. 48, n. 18, p. 10157, doi. 10.1093/nar/gkaa774
- By:
- Publication type:
- Article
BiGG Models 2020: multi-strain genome-scale models and expansion across the phylogenetic tree.
- Published in:
- Nucleic Acids Research, 2020, v. 48, n. D1, p. D402, doi. 10.1093/nar/gkz1054
- By:
- Publication type:
- Article
Primary transcriptome and translatome analysis determines transcriptional and translational regulatory elements encoded in the Streptomyces clavuligerus genome.
- Published in:
- Nucleic Acids Research, 2019, v. 47, n. 12, p. 6114, doi. 10.1093/nar/gkz471
- By:
- Publication type:
- Article
y-ome defines the 35% of Escherichia coli genes that lack experimental evidence of function.
- Published in:
- Nucleic Acids Research, 2019, v. 47, n. 5, p. 2446, doi. 10.1093/nar/gkz030
- By:
- Publication type:
- Article
ALEdb 1.0: a database of mutations from adaptive laboratory evolution experimentation.
- Published in:
- Nucleic Acids Research, 2019, v. 47, n. D1, p. D1164, doi. 10.1093/nar/gky983
- By:
- Publication type:
- Article
Systems assessment of transcriptional regulation on central carbon metabolism by Cra and CRP.
- Published in:
- Nucleic Acids Research, 2018, v. 46, n. 6, p. 2901, doi. 10.1093/nar/gky069
- By:
- Publication type:
- Article
BiGG Models: A platform for integrating, standardizing and sharing genome-scale models.
- Published in:
- Nucleic Acids Research, 2016, v. 44, n. 1, p. D515, doi. 10.1093/nar/gkv1049
- By:
- Publication type:
- Article
A biochemically-interpretable machine learning classifier for microbial GWAS.
- Published in:
- Nature Communications, 2020, v. 11, n. 1, p. 1, doi. 10.1038/s41467-020-16310-9
- By:
- Publication type:
- Article
Multiplex secretome engineering enhances recombinant protein production and purity.
- Published in:
- Nature Communications, 2020, v. 11, n. 1, p. 1, doi. 10.1038/s41467-020-15866-w
- By:
- Publication type:
- Article
Genome-scale reconstructions of the mammalian secretory pathway predict metabolic costs and limitations of protein secretion.
- Published in:
- Nature Communications, 2020, v. 11, n. 1, p. 1, doi. 10.1038/s41467-019-13867-y
- By:
- Publication type:
- Article
The Escherichia coli transcriptome mostly consists of independently regulated modules.
- Published in:
- Nature Communications, 2019, v. 10, n. 1, p. 1, doi. 10.1038/s41467-019-13483-w
- By:
- Publication type:
- Article
Evolution and regulation of nitrogen flux through compartmentalized metabolic networks in a marine diatom.
- Published in:
- Nature Communications, 2019, v. 10, n. 1, p. N.PAG, doi. 10.1038/s41467-019-12407-y
- By:
- Publication type:
- Article
Decoding the jargon of bottom-up metabolic systems biology.
- Published in:
- BioEssays, 2015, v. 37, n. 6, p. 588, doi. 10.1002/bies.201400187
- By:
- Publication type:
- Article
DynamicME: dynamic simulation and refinement of integrated models of metabolism and protein expression.
- Published in:
- BMC Systems Biology, 2019, v. 13, n. 1, p. 1, doi. 10.1186/s12918-018-0675-6
- By:
- Publication type:
- Article
Reframing gene essentiality in terms of adaptive flexibility.
- Published in:
- BMC Systems Biology, 2018, v. 12, n. 1, p. N.PAG, doi. 10.1186/s12918-018-0653-z
- By:
- Publication type:
- Article
Escher-FBA: a web application for interactive flux balance analysis.
- Published in:
- BMC Systems Biology, 2018, v. 12, n. 1, p. N.PAG, doi. 10.1186/s12918-018-0607-5
- By:
- Publication type:
- Article
<italic>Escherichia coli</italic> B2 strains prevalent in inflammatory bowel disease patients have distinct metabolic capabilities that enable colonization of intestinal mucosa.
- Published in:
- BMC Systems Biology, 2018, v. 12, n. 1, p. N.PAG, doi. 10.1186/s12918-018-0587-5
- By:
- Publication type:
- Article