Genome-scale determination of 5´ and 3´ boundaries of RNA transcripts in Streptomyces genomes

publication published on 15 December 2020

A Diverse Genetic Basis for Metabolic Reactions is Revealed Through Pangenome analysis

A multi-scale transcriptional regulatory network knowledge base forEscherichia coli

A novel transcription factor PunR and Nac are involved in purine and purine nucleoside transporter punC regulation in E. coli

A treasure trove of 1,034 actinomycete genomes

Advanced transcriptomic analysis reveals the role of efflux pumps and media composition in antibiotic responses ofPseudomonas aeruginosa

Aerobicity stimulon in Escherichia coli revealed using multi-scale computational systems biology of adapted respiratory variants

Alleleomes characterize the survivors of 3.5 billion years of bacterial evolution

BGCFlow: Systematic pangenome workflow for the analysis of biosynthetic gene clusters across large genomic datasets

Biological and Genetic Determinants of Glycolysis: Phosphofructokinase Isoforms Boost Energy Status of Stored Red Blood Cells and Transfusion Outcomes

Bottom-up parameterization of enzyme rate constants: Reconciling inconsistent data

Computation of condition-dependent proteome allocation reveals variability in the macro and micro nutrient requirements for growth

CyuR is a Dual Regulator for L-Cysteine Dependent Antimicrobial Resistance inEscherichia coli

Data-Driven Strain Design Towards Mitigating Biomanufacturing Stresses

Data-Driven Strain Design Using Aggregated Adaptive Laboratory Evolution Mutational Data

Data-driven modeling ofE. colitranscriptional regulation

Environmental conditions dictate differential evolution of vancomycin resistance inStaphylococcus aureus

Escher-FBA: A web application for interactive flux balance analysis

Establishing comprehensive quaternary structural proteomes from genome sequence

Establishing comprehensive quaternary structural proteomes from genome sequence

Establishing comprehensive quaternary structural proteomes from genome sequence

Establishing comprehensive quaternary structural proteomes from genome sequence

Evolution guided tolerance engineering of Pseudomonas putida KT2440 for production of the sustainable aviation fuel precursor isoprenol

Expanding the iModulon Knowledgebase for Bacillus subtilis: Updated Transcriptome Decomposition Reveals Novel Regulatory Mechanisms

Genetic variation of human G6PD impacts Red Blood Cell transfusion efficacy

Genomic insights intoLactobacillaceae: Analyzing the “Alleleome” of core pangenomes for enhanced understanding of strain diversity and revealing Phylogroup-specific unique variants

Global pathogenomic analysis identifies known and novel genetic antimicrobial resistance determinants in twelve species

Impact of insertion sequences on convergent evolution ofShigellaspecies

Integration of physiologically relevant photosynthetic energy flows into whole genome models of light-driven metabolism

Lab evolution, transcriptomics, and modeling reveal mechanisms of paraquat tolerance

Laboratory evolution of multipleE. colistrains reveals unifying principles of adaptation but diversity in driving genotypes

Laboratory evolution of synthetic electron transport system variants reveals a larger metabolic respiratory system and its plasticity

Laboratory evolution reveals a two-dimensional rate-yield tradeoff in microbial metabolism

Laboratory evolution reveals transcriptional mechanisms underlying thermal adaptation ofEscherichia coli

Laboratory-acquired mutations fall outside the wild-type alleleome of Escherichia coli

MASSpy: Building, simulating, and visualizing dynamic biological models in Python using mass action kinetics

Machine Learning Uncovers the Transcriptional Regulatory Network for the Production HostStreptomyces albidoflavus

Machine Learning of Pseudomonas aeruginosa transcriptomes identifies independently modulated sets of genes associated with known transcriptional regulators

Machine learning of all Mycobacterium tuberculosis H37Rv RNA-seq data reveals a structured interplay between metabolism, stress response, and infection

Machine learning uncovers independently regulated modules in the Bacillus subtilis transcriptome

Machine learning uncovers thePseudomonas syringaetranscriptome in microbial communities and during infection

Metabolic homeostasis and growth in abiotic cells

Mining all publicly available expression data to compute dynamic microbial transcriptional regulatory networks

Multi-scale reactor designs extend the physical limits of CO2fixation

Multi-strain Analysis of Pseudomonas putida Reveals the Metabolic and Genetic Diversity of the Species

Pan-genomic analysis of transcriptional modules acrossSalmonellaTyphimurium reveals the regulatory landscape of different strains

PanKB: An interactive microbial pangenome knowledgebase for research, biotechnological innovation, and knowledge mining

Pangenome analytics reveal two-component systems as conserved targets in ESKAPEE pathogens

Pangenome mining of theStreptomycesgenus redefines their biosynthetic potential

Pangenome reconstruction ofLactobacillaceaemetabolism predicts species-specific metabolic traits

QSProteome: A Community-Driven Interactive Platform for Large-Scale Exploration and Evaluation of Predicted Protein Complex Structures

RBC-GEM: a Knowledge Base for Systems Biology of Human Red Blood Cell Metabolism

Revealing Transcriptomic Responses in Escherichia coli During Early Antibiotic Exposure

Systems-level physiology of the human red blood cell is computed from metabolic and macromolecular mechanisms

The Pangenome ofEscherichia coli

The hallmarks of a tradeoff in transcriptomes that balances stress and growth functions

The y-ome defines the thirty-four percent ofEscherichia coligenes that lack experimental evidence of function

Trade-off Between Resistance and Persistence in High Cell DensityEscherichia ColiCultures

Using theE. coliAlleleome in Strain Design

iModulonDB: a knowledgebase of microbial transcriptional regulation derived from machine learning

ssbio: A Python Framework for Structural Systems Biology