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Systems biology of the structural proteome.
- Published in:
- BMC Systems Biology, 2016, v. 11, p. 1, doi. 10.1186/s12918-016-0271-6
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- Article
Cerebrospinal fluid and plasma metabolomics of acute endurance exercise.
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- FASEB Journal, 2022, v. 36, n. 7, p. 1, doi. 10.1096/fj.202200509R
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- Article
Metabolic network analysis of pre-ASD newborns and 5-year-old children with autism spectrum disorder.
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- Communications Biology, 2024, v. 7, n. 1, p. 1, doi. 10.1038/s42003-024-06102-y
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- Article
Constraint-based models predict metabolic and associated cellular functions.
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- Nature Reviews Genetics, 2014, v. 15, n. 2, p. 107, doi. 10.1038/nrg3643
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- Article
Reduced Production of Bacterial Membrane Vesicles Predicts Mortality in ST45/USA600 Methicillin-Resistant Staphylococcus aureus Bacteremia.
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- Antibiotics (2079-6382), 2020, v. 9, n. 1, p. 2, doi. 10.3390/antibiotics9010002
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- Article
Model-driven discovery of synergistic inhibitors against E. coli and S. enterica serovar Typhimurium targeting a novel synthetic lethal pair, aldA and prpC.
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- Frontiers in Microbiology, 2015, p. 1, doi. 10.3389/fmicb.2015.00958
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- Article
Model-driven discovery of synergistic inhibitors against E. coli and S. enterica serovar Typhimurium targeting a novel synthetic lethal pair, aldA and prpC.
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- Frontiers in Microbiology, 2015, p. 1
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- Article
Rapid resistance development to three antistaphylococcal therapies in antibiotic-tolerant staphylococcus aureus bacteremia.
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- PLoS ONE, 2021, v. 16, n. 10, p. 1, doi. 10.1371/journal.pone.0258592
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- Article
596. Distinct, Segregated Daptomycin-Susceptible and Daptomycin-Nonsusceptible Staphylococcus aureus Populations Associated with Tricuspid-Valve Infective Endocarditis.
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- Open Forum Infectious Diseases, 2019, v. 6, p. S280, doi. 10.1093/ofid/ofz360.665
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Profiling the effect of nafcillin on HA-MRSA D712 using bacteriological and physiological media.
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- Scientific Data, 2019, v. 6, n. 1, p. 1, doi. 10.1038/s41597-019-0331-z
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- Article
Metabolic features of treatment-refractory major depressive disorder with suicidal ideation.
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- Translational Psychiatry, 2023, v. 13, n. 1, p. 1, doi. 10.1038/s41398-023-02696-9
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- Article
Genome-Scale Metabolic Model of Xanthomonas phaseoli pv. manihotis : An Approach to Elucidate Pathogenicity at the Metabolic Level.
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- Frontiers in Genetics, 2020, v. 11, p. N.PAG, doi. 10.3389/fgene.2020.00837
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Machine learning and structural analysis of Mycobacterium tuberculosis pan-genome identifies genetic signatures of antibiotic resistance.
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- Nature Communications, 2018, v. 9, n. 1, p. 1, doi. 10.1038/s41467-018-06634-y
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- Article
Genome-scale metabolic reconstructions of multiple Salmonella strains reveal serovar-specific metabolic traits.
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- Nature Communications, 2018, v. 9, n. 1, p. 1, doi. 10.1038/s41467-018-06112-5
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- Article
A workflow for generating multi-strain genome-scale metabolic models of prokaryotes.
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- Nature Protocols, 2020, v. 15, n. 1, p. 1, doi. 10.1038/s41596-019-0254-3
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- Article
Optimizing genome-scale network reconstructions.
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- Nature Biotechnology, 2014, v. 32, n. 5, p. 447, doi. 10.1038/nbt.2870
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- Article
<italic>Escherichia coli</italic> B2 strains prevalent in inflammatory bowel disease patients have distinct metabolic capabilities that enable colonization of intestinal mucosa.
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- BMC Systems Biology, 2018, v. 12, n. 1, p. N.PAG, doi. 10.1186/s12918-018-0587-5
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- Article
Updated and standardized genome-scale reconstruction of <italic>Mycobacterium tuberculosis</italic> H37Rv, iEK1011, simulates flux states indicative of physiological conditions.
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- BMC Systems Biology, 2018, v. 12, p. 1, doi. 10.1186/s12918-018-0557-y
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- Article
ssbio: a Python framework for structural systems biology.
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- Bioinformatics, 2018, v. 34, n. 12, p. 2155, doi. 10.1093/bioinformatics/bty077
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- Article
Transmission of Klebsiella strains and plasmids within and between grey‐headed flying fox colonies.
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- Environmental Microbiology, 2022, v. 24, n. 9, p. 4425, doi. 10.1111/1462-2920.16047
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High‐quality genome‐scale metabolic modelling of Pseudomonas putida highlights its broad metabolic capabilities.
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- Environmental Microbiology, 2020, v. 22, n. 1, p. 255, doi. 10.1111/1462-2920.14843
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What Makes a Bacterial Species Pathogenic?:Comparative Genomic Analysis of the Genus Leptospira.
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- PLoS Neglected Tropical Diseases, 2016, v. 10, n. 2, p. 1, doi. 10.1371/journal.pntd.0004403
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High-Quality Genome-Scale Models From Error-Prone, Long-Read Assemblies.
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- Frontiers in Microbiology, 2020, v. 11, p. N.PAG, doi. 10.3389/fmicb.2020.596626
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Metabolic and behavioral features of acute hyperpurinergia and the maternal immune activation mouse model of autism spectrum disorder.
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- PLoS ONE, 2021, v. 16, n. 3, p. 1, doi. 10.1371/journal.pone.0248771
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Pangenome analysis of Enterobacteria reveals richness of secondary metabolite gene clusters and their associated gene sets.
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- Synthetic & Systems Biotechnology, 2022, v. 7, n. 3, p. 900, doi. 10.1016/j.synbio.2022.04.011
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Identifying the effect of vancomycin on health care–associated methicillin-resistant Staphylococcus aureus strains using bacteriological and physiological media.
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- GigaScience, 2021, v. 10, n. 1, p. 1, doi. 10.1093/gigascience/giaa156
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Metagenomics-Based, Strain-Level Analysis of Escherichia coli From a Time-Series of Microbiome Samples From a Crohn's Disease Patient.
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- Frontiers in Microbiology, 2018, p. 1, doi. 10.3389/fmicb.2018.02559
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Global pathogenomic analysis identifies known and candidate genetic antimicrobial resistance determinants in twelve species.
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- Nature Communications, 2023, v. 14, n. 1, p. 1, doi. 10.1038/s41467-023-43549-9
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- Article
High-quality genome-scale metabolic network reconstruction of probiotic bacterium Escherichia coli Nissle 1917.
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- BMC Bioinformatics, 2022, v. 23, n. 1, p. 1, doi. 10.1186/s12859-022-05108-9
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- Article
Impact of insertion sequences on convergent evolution of Shigella species.
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- PLoS Genetics, 2020, v. 16, n. 7, p. 1, doi. 10.1371/journal.pgen.1008931
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Machine learning in computational biology to accelerate high-throughput protein expression.
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- Bioinformatics, 2017, v. 33, n. 16, p. 2487, doi. 10.1093/bioinformatics/btx207
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How can we overcome health inequalities in psychiatry?
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- BJPsych Bulletin, 2023, v. 47, n. 4, p. 228, doi. 10.1192/bjb.2023.49
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- Article
Reconstruction and Validation of a Genome-Scale Metabolic Model of Streptococcus oralis (iCJ415), a Human Commensal and Opportunistic Pathogen.
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- Frontiers in Genetics, 2020, p. 1, doi. 10.3389/fgene.2020.00116
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- Article
Comparative Genome-Scale Metabolic Modeling of Metallo-Beta-Lactamase–Producing Multidrug-Resistant Klebsiella pneumoniae Clinical Isolates.
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- Frontiers in Cellular & Infection Microbiology, 2019, v. 9, p. N.PAG, doi. 10.3389/fcimb.2019.00161
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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
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- Article
Metabolic features of Gulf War illness.
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- PLoS ONE, 2019, v. 14, n. 7, p. 1, doi. 10.1371/journal.pone.0219531
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- Article
Machine learning with random subspace ensembles identifies antimicrobial resistance determinants from pan-genomes of three pathogens.
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- PLoS Computational Biology, 2020, v. 16, n. 3, p. 1, doi. 10.1371/journal.pcbi.1007608
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Systems-level analysis of NalD mutation, a recurrent driver of rapid drug resistance in acute Pseudomonas aeruginosa infection.
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- PLoS Computational Biology, 2019, v. 15, n. 12, p. N.PAG, doi. 10.1371/journal.pcbi.1007562
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- Article
BOFdat: Generating biomass objective functions for genome-scale metabolic models from experimental data.
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- PLoS Computational Biology, 2019, v. 15, n. 4, p. 1, doi. 10.1371/journal.pcbi.1006971
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- Article
A computational knowledge-base elucidates the response of Staphylococcus aureus to different media types.
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- PLoS Computational Biology, 2019, v. 15, n. 01, p. 1, doi. 10.1371/journal.pcbi.1006644
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Systems biology analysis of the Clostridioides difficile core-genome contextualizes microenvironmental evolutionary pressures leading to genotypic and phenotypic divergence.
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- NPJ Systems Biology & Applications, 2020, v. 6, n. 1, p. N.PAG, doi. 10.1038/s41540-020-00151-9
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- Article
Bactabolize is a tool for high-throughput generation of bacterial strain-specific metabolic models.
- Published in:
- eLife, 2023, p. 1, doi. 10.7554/eLife.87406
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A systems approach discovers the role and characteristics of seven LysR type transcription factors in Escherichia coli.
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- Scientific Reports, 2022, v. 12, n. 1, p. 1, doi. 10.1038/s41598-022-11134-7
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- Article
Improved Dried Blood Spot-Based Metabolomics: A Targeted, Broad-Spectrum, Single-Injection Method.
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- Metabolites (2218-1989), 2020, v. 10, n. 3, p. 82, doi. 10.3390/metabo10030082
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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
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iML1515, a knowledgebase that computes Escherichia coli traits.
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- Nature Biotechnology, 2017, v. 35, n. 10, p. 904, doi. 10.1038/nbt.3956
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- Article
Comparative pangenomics: analysis of 12 microbial pathogen pangenomes reveals conserved global structures of genetic and functional diversity.
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- BMC Genomics, 2022, v. 23, n. 1, p. 1, doi. 10.1186/s12864-021-08223-8
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- Article
Adaptations of Escherichia coli strains to oxidative stress are reflected in properties of their structural proteomes.
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- BMC Bioinformatics, 2020, v. 21, n. 1, p. 1, doi. 10.1186/s12859-020-3505-y
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- 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
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- Article
Predicting the primary infection source of Escherichia coli bacteremia using virulence-associated genes.
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- European Journal of Clinical Microbiology & Infectious Diseases, 2024, v. 43, n. 4, p. 641, doi. 10.1007/s10096-024-04754-6
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- Article