| Positively charged mineral surfaces promoted the accumulation of organic intermediates at the origin of metabolism | 0 | 0.34 | 2022 |
| Independent Component Analysis Recovers Consistent Regulatory Signals From Disparate Datasets | 0 | 0.34 | 2021 |
| Imodulondb: A Knowledgebase Of Microbial Transcriptional Regulation Derived From Machine Learning | 0 | 0.34 | 2021 |
| Computation Of Condition-Dependent Proteome Allocation Reveals Variability In The Macro And Micro Nutrient Requirements For Growth | 0 | 0.34 | 2021 |
| Masspy: Building, Simulating, And Visualizing Dynamic Biological Models In Python Using Mass Action Kinetics | 0 | 0.34 | 2021 |
| Bacterial Fitness Landscapes Stratify Based On Proteome Allocation Associated With Discrete Aero-Types | 0 | 0.34 | 2021 |
| Scalable Computation Of Intracellular Metabolite Concentrations | 0 | 0.34 | 2021 |
| Adaptations of Escherichia coli strains to oxidative stress are reflected in properties of their structural proteomes. | 0 | 0.34 | 2020 |
| BiGG Models 2020: multi-strain genome-scale models and expansion across the phylogenetic tree. | 0 | 0.34 | 2020 |
| Machine learning with random subspace ensembles identifies antimicrobial resistance determinants from pan-genomes of three pathogens. | 0 | 0.34 | 2020 |
| Estimating Cellular Goals from High-Dimensional Biological Data | 1 | 0.35 | 2019 |
| A computational knowledge-base elucidates the response of Staphylococcus aureus to different media types. | 0 | 0.34 | 2019 |
| BOFdat: Generating biomass objective functions for genome-scale metabolic models from experimental data. | 0 | 0.34 | 2019 |
| ALEdb 1.0: a database of mutations from adaptive laboratory evolution experimentation. | 2 | 0.36 | 2019 |
| DynamicME: dynamic simulation and refinement of integrated models of metabolism and protein expression. | 0 | 0.34 | 2019 |
| Genome-scale estimation of cellular objectives. | 0 | 0.34 | 2018 |
| COBRAme: A computational framework for genome-scale models of metabolism and gene expression. | 4 | 0.45 | 2018 |
| Updated and standardized genome-scale reconstruction of <Emphasis Type="Italic">Mycobacterium tuberculosis</Emphasis> H37Rv, iEK1011, simulates flux states indicative of physiological conditions | 0 | 0.34 | 2018 |
| Escher-FBA: a web application for interactive flux balance analysis. | 0 | 0.34 | 2018 |
| Systems biology as an emerging paradigm in transfusion medicine. | 0 | 0.34 | 2018 |
| <Emphasis Type="Italic">Escherichia coli</Emphasis> B2 strains prevalent in inflammatory bowel disease patients have distinct metabolic capabilities that enable colonization of intestinal mucosa | 0 | 0.34 | 2018 |
| ssbio: a Python framework for structural systems biology. | 0 | 0.34 | 2018 |
| Functional interrogation of Plasmodium genus metabolism identifies species- and stage-specific differences in nutrient essentiality and drug targeting. | 0 | 0.34 | 2018 |
| Network-level allosteric effects are elucidated by detailing how ligand-binding events modulate utilization of catalytic potentials. | 0 | 0.34 | 2018 |
| Reframing gene essentiality in terms of adaptive flexibility. | 0 | 0.34 | 2018 |
| Biomarkers are used to predict quantitative metabolite concentration profiles in human red blood cells. | 1 | 0.43 | 2017 |
| Machine learning in computational biology to accelerate high-throughput protein expression. | 0 | 0.34 | 2017 |
| BiGG Models: A platform for integrating, standardizing and sharing genome-scale models. | 36 | 1.46 | 2016 |
| solveME: fast and reliable solution of nonlinear ME models. | 1 | 0.37 | 2016 |
| Evaluation of rate law approximations in bottom-up kinetic models of metabolism. | 2 | 0.45 | 2016 |
| Solving Puzzles With Missing Pieces: The Power of Systems Biology [Point of View] | 1 | 0.38 | 2016 |
| Systems biology of the structural proteome. | 2 | 0.39 | 2016 |
| Quantification and Classification of E. coli Proteome Utilization and Unused Protein Costs across Environments. | 0 | 0.34 | 2016 |
| A Multi-scale Computational Platform to Mechanistically Assess the Effect of Genetic Variation on Drug Responses in Human Erythrocyte Metabolism. | 0 | 0.34 | 2016 |
| Escher: A Web Application For Building, Sharing, And Embedding Data-Rich Visualizations Of Biological Pathways | 19 | 1.02 | 2015 |
| JSBML 1.0: providing a smorgasbord of options to encode systems biology models | 6 | 0.51 | 2015 |
| SBMLsqueezer 2: context-sensitive creation of kinetic equations in biochemical networks | 4 | 0.40 | 2015 |
| Reconstruction and modeling protein translocation and compartmentalization in Escherichia coli at the genome-scale. | 8 | 0.59 | 2014 |
| A Systems Approach To Predict Oncometabolites Via Context-Specific Genome-Scale Metabolic Networks | 2 | 0.39 | 2014 |
| GIM3E: condition-specific models of cellular metabolism developed from metabolomics and expression data. | 9 | 0.69 | 2013 |
| Antibacterial mechanisms identified through structural systems pharmacology. | 7 | 0.39 | 2013 |
| Predicting outcomes of steady-state 13C isotope tracing experiments using Monte Carlo sampling. | 9 | 0.94 | 2012 |
| Gap-filling analysis of the iJO1366 Escherichia coli metabolic network reconstruction for discovery of metabolic functions. | 10 | 0.66 | 2012 |
| An experimentally-supported genome-scale metabolic network reconstruction for Yersinia pestis CO92. | 9 | 0.45 | 2011 |
| iAB-RBC-283: A proteomically derived knowledge-base of erythrocyte metabolism that can be used to simulate its physiological and patho-physiological states. | 11 | 0.81 | 2011 |
| A community effort towards a knowledge-base and mathematical model of the human pathogen Salmonella Typhimurium LT2. | 22 | 1.00 | 2011 |
| A multi-tissue type genome-scale metabolic network for analysis of whole-body systems physiology. | 14 | 0.80 | 2011 |
| BiGG: a Biochemical Genetic and Genomic knowledgebase of large scale metabolic reconstructions. | 98 | 4.27 | 2010 |
| Drug Off-Target Effects Predicted Using Structural Analysis In The Context Of A Metabolic Network Model | 33 | 1.82 | 2010 |
| Decomposing complex reaction networks using random sampling, principal component analysis and basis rotation. | 11 | 0.71 | 2009 |
