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A treasure trove of 1034 actinomycete genomes.
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- Nucleic Acids Research, 2024, v. 52, n. 13, p. 7487, doi. 10.1093/nar/gkae523
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- Article
Proteome allocation is linked to transcriptional regulation through a modularized transcriptome.
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- Nature Communications, 2024, v. 15, n. 1, p. 1, doi. 10.1038/s41467-024-49231-y
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- Article
BGCFlow: systematic pangenome workflow for the analysis of biosynthetic gene clusters across large genomic datasets.
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- Nucleic Acids Research, 2024, v. 52, n. 10, p. 5478, doi. 10.1093/nar/gkae314
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- Article
Escherichia coli non-coding regulatory regions are highly conserved.
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- NAR Genomics & Bioinformatics, 2024, v. 6, n. 2, p. 1, doi. 10.1093/nargab/lqae041
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- Article
Advancing the scale of synthetic biology via cross-species transfer of cellular functions enabled by iModulon engraftment.
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- Nature Communications, 2024, v. 15, p. 1, doi. 10.1038/s41467-024-46486-3
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- Article
StressME: Unified computing framework of Escherichia coli metabolism, gene expression, and stress responses.
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- PLoS Computational Biology, 2024, v. 20, n. 2, p. 1, doi. 10.1371/journal.pcbi.1011865
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- Article
Inferred regulons are consistent with regulator binding sequences in E. coli.
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- PLoS Computational Biology, 2024, v. 20, n. 1, p. 1, doi. 10.1371/journal.pcbi.1011824
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- Article
Experimental promoter identification of a foodborne pathogen Salmonella enterica subsp. enterica serovar Typhimurium with near single base-pair resolution.
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- Frontiers in Microbiology, 2024, p. 1, doi. 10.3389/fmicb.2023.1271121
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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
Functional annotation of enzyme-encoding genes using deep learning with transformer layers.
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- Nature Communications, 2023, v. 14, n. 1, p. 1, doi. 10.1038/s41467-023-43216-z
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- Article
Differential Expression Analysis Utilizing Condition-Specific Metabolic Pathways.
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- Metabolites (2218-1989), 2023, v. 13, n. 11, p. 1127, doi. 10.3390/metabo13111127
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Modeling Red Blood Cell Metabolism in the Omics Era.
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- Metabolites (2218-1989), 2023, v. 13, n. 11, p. 1145, doi. 10.3390/metabo13111145
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- Article
A multi-scale expression and regulation knowledge base for Escherichia coli.
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- Nucleic Acids Research, 2023, v. 51, n. 19, p. 10176, doi. 10.1093/nar/gkad750
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- Article
Reconstruction of the last bacterial common ancestor from 183 pangenomes reveals a versatile ancient core genome.
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- Genome Biology, 2023, v. 24, n. 1, p. 1, doi. 10.1186/s13059-023-03028-2
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- Article
Empowering drug off-target discovery with metabolic and structural analysis.
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- Nature Communications, 2023, v. 14, n. 1, p. 1, doi. 10.1038/s41467-023-38859-x
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- Article
A model industrial workhorse: Bacillus subtilis strain 168 and its genome after a quarter of a century.
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- Microbial Biotechnology, 2023, v. 16, n. 6, p. 1203, doi. 10.1111/1751-7915.14257
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- Article
The Escherichia coli Fur pan-regulon has few conserved but many unique regulatory targets.
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- Nucleic Acids Research, 2023, v. 51, n. 8, p. 3618, doi. 10.1093/nar/gkad253
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- Article
Deep-learning optimized DEOCSU suite provides an iterable pipeline for accurate ChIP-exo peak calling.
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- Briefings in Bioinformatics, 2023, v. 24, n. 2, p. 1, doi. 10.1093/bib/bbad024
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- Article
Model-driven experimental design workflow expands understanding of regulatory role of Nac in Escherichia coli.
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- NAR Genomics & Bioinformatics, 2023, v. 5, n. 1, p. 1, doi. 10.1093/nargab/lqad006
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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
Integration of physiologically relevant photosynthetic energy flows into whole genome models of light‐driven metabolism.
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- Plant Journal, 2022, v. 112, n. 3, p. 603, doi. 10.1111/tpj.15965
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- Article
Advanced transcriptomic analysis reveals the role of efflux pumps and media composition in antibiotic responses of Pseudomonas aeruginosa.
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- Nucleic Acids Research, 2022, v. 50, n. 17, p. 9675, doi. 10.1093/nar/gkac743
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- Article
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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Positively charged mineral surfaces promoted the accumulation of organic intermediates at the origin of metabolism.
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- PLoS Computational Biology, 2022, v. 18, n. 8, p. 1, doi. 10.1371/journal.pcbi.1010377
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Laboratory evolution of synthetic electron transport system variants reveals a larger metabolic respiratory system and its plasticity.
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- Nature Communications, 2022, v. 13, n. 1, p. 1, doi. 10.1038/s41467-022-30877-5
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Identification and Engineering of Transporters for Efficient Melatonin Production in Escherichia coli.
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- Frontiers in Microbiology, 2022, p. 1, doi. 10.3389/fmicb.2022.880847
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- Article
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
Machine learning from Pseudomonas aeruginosa transcriptomes identifies independently modulated sets of genes associated with known transcriptional regulators.
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- Nucleic Acids Research, 2022, v. 50, n. 7, p. 3658, doi. 10.1093/nar/gkac187
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- Article
Is the kinetome conserved?
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- Molecular Systems Biology, 2022, v. 18, n. 2, p. 1, doi. 10.15252/msb.202110782
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- Article
Genome-scale analysis of genetic regulatory elements in Streptomyces avermitilis MA-4680 using transcript boundary information.
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- BMC Genomics, 2022, v. 23, n. 1, p. 1, doi. 10.1186/s12864-022-08314-0
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proChIPdb: a chromatin immunoprecipitation database for prokaryotic organisms.
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- Nucleic Acids Research, 2022, v. 50, n. D1, p. D1077, doi. 10.1093/nar/gkab1043
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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
Optimal dimensionality selection for independent component analysis of transcriptomic data.
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- BMC Bioinformatics, 2021, v. 22, n. 1, p. 1, doi. 10.1186/s12859-021-04497-7
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- Article
Machine Learning Uncovers a Data-Driven Transcriptional Regulatory Network for the Crenarchaeal Thermoacidophile Sulfolobus acidocaldarius.
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- Frontiers in Microbiology, 2021, v. 12, p. 1, doi. 10.3389/fmicb.2021.753521
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- Article
Unraveling the functions of uncharacterized transcription factors in Escherichia coli using ChIP-exo.
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- Nucleic Acids Research, 2021, v. 49, n. 17, p. 9696, doi. 10.1093/nar/gkab735
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- Article
Identification of a transcription factor, PunR, that regulates the purine and purine nucleoside transporter punC in E. coli.
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- Communications Biology, 2021, v. 4, n. 1, p. 1, doi. 10.1038/s42003-021-02516-0
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- Article
Genome‐scale metabolic modeling reveals key features of a minimal gene set.
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- Molecular Systems Biology, 2021, v. 17, n. 7, p. 1, doi. 10.15252/msb.202010099
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- Article
Environmental conditions dictate differential evolution of vancomycin resistance in Staphylococcus aureus.
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- Communications Biology, 2021, v. 4, n. 1, p. 1, doi. 10.1038/s42003-021-02339-z
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- Article
Computation of condition-dependent proteome allocation reveals variability in the macro and micro nutrient requirements for growth.
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- PLoS Computational Biology, 2021, v. 17, n. 6, p. 1, doi. 10.1371/journal.pcbi.1007817
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- Article
The quantitative metabolome is shaped by abiotic constraints.
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- Nature Communications, 2021, v. 12, n. 1, p. 1, doi. 10.1038/s41467-021-23214-9
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- Article
Discovery of novel secondary metabolites encoded in actinomycete genomes through coculture.
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- Journal of Industrial Microbiology & Biotechnology, 2021, v. 48, n. 3/4, p. 1, doi. 10.1093/jimb/kuaa001
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- Article
Discovery of novel secondary metabolites encoded in actinomycete genomes through coculture.
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- Journal of Industrial Microbiology & Biotechnology, 2021, p. 1, doi. 10.1093/jimb/kuaa001
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- Article
Independent component analysis recovers consistent regulatory signals from disparate datasets.
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- PLoS Computational Biology, 2021, v. 17, n. 2, p. 1, doi. 10.1371/journal.pcbi.1008647
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- Article
MASSpy: Building, simulating, and visualizing dynamic biological models in Python using mass action kinetics.
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- PLoS Computational Biology, 2021, v. 17, n. 1, p. 1, doi. 10.1371/journal.pcbi.1008208
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- Article
Bacterial fitness landscapes stratify based on proteome allocation associated with discrete aero-types.
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- PLoS Computational Biology, 2021, v. 17, n. 1, p. 1, doi. 10.1371/journal.pcbi.1008596
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- Article
iModulonDB: a knowledgebase of microbial transcriptional regulation derived from machine learning.
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- Nucleic Acids Research, 2021, v. 49, n. D1, p. D112, doi. 10.1093/nar/gkaa810
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- Article
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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Genome-scale determination of 5´ and 3´ boundaries of RNA transcripts in Streptomyces genomes.
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- Scientific Data, 2020, v. 7, n. 1, p. 1, doi. 10.1038/s41597-020-00775-w
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- Article
Machine learning uncovers independently regulated modules in the Bacillus subtilis transcriptome.
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- Nature Communications, 2020, v. 11, n. 1, p. 1, doi. 10.1038/s41467-020-20153-9
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- Article
The Expanding Computational Toolbox for Engineering Microbial Phenotypes at the Genome Scale.
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- Microorganisms, 2020, v. 8, n. 12, p. 2050, doi. 10.3390/microorganisms8122050
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- Article