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Bernhard O. Palsson, Ph.D.
BENG 212 2019
BENG 213 2019
COBRA Toolbox and COBRApy
Literature on Cobra Methods
Literature on Model-Driven Analysis
The Metabolism Disease Database
Coupled effects of polybrene and calf serum on the efficiency of retroviral transduction and the stability of retroviral vectors.
Assessment of the metabolic capabilities of Haemophilus influenzae Rd through a genome-scale pathway analysis.
The Escherichia coli MG1655 in silico metabolic genotype: its definition, characteristics, and capabilities.
Extension of osmolality-induced podia is observed from fluorescently labeled hematopoietic cell lines in hyperosmotic medium.
Intercellular adhesion can be visualized using fluorescently labeled fibrosarcoma HT1080 cells cocultured with hematopoietic cell lines or CD34(+) enriched human mobilized peripheral blood cells.
Metabolic flux balance analysis and the in silico analysis of Escherichia coli K-12 gene deletions.
Multiple steady states in kinetic models of red cell metabolism.
Robustness analysis of the Escherichia coli metabolic network.
Flux-balance analysis of mitochondrial energy metabolism: consequences of systemic stoichiometric constraints.
In silico predictions of Escherichia coli metabolic capabilities are consistent with experimental data.
Metabolic modeling of microbial strains in silico.
Combining pathway analysis with flux balance analysis for the comprehensive study of metabolic systems.
Dynamic simulation of the human red blood cell metabolic network.
Characterizing the metabolic phenotype: a phenotype phase plane analysis.
Theory for the systemic definition of metabolic pathways and their use in interpreting metabolic function from a pathway-oriented perspective.
In situ labeling of adherent cells with PKH26.
Key adhesion molecules are present on long podia extended by hematopoietic cells.
Moloney murine leukemia virus-derived retroviral vectors decay intracellularly with a half-life in the range of 5.5 to 7.5 hours.
Effective intercellular communication distances are determined by the relative time constants for cyto/chemokine secretion and diffusion.
The underlying pathway structure of biochemical reaction networks.
Two new pseudopod morphologies displayed by the human hematopoietic KG1a progenitor cell line and by primary human CD34(+) cells.
Tissue culture surface characteristics influence the expansion of human bone marrow cells.
Elemental balancing of biomass and medium composition enhances growth capacity in high-density Chlorella vulgaris cultures.
How will bioinformatics influence metabolic engineering?
Cell cycle dependence of retroviral transduction: An issue of overlapping time scales.
Toward metabolic phenomics: analysis of genomic data using flux balances.
Metabolic pathway analysis: basic concepts and scientific applications in the post-genomic era.
Systems properties of the Haemophilus influenzae Rd metabolic genotype.
Phototoxicity of the fluorescent membrane dyes PKH2 and PKH26 on the human hematopoietic KG1a progenitor cell line.
Symmetry of initial cell divisions among primitive hematopoietic progenitors is independent of ontogenic age and regulatory molecules.
Characterization and efficacy of PKH26 as a probe to study the replication history of the human hematopoietic KG1a progenitor cell line.
Determination of redundancy and systems properties of the metabolic network of Helicobacter pylori using genome-scale extreme pathway analysis.
Transcriptional regulation in constraints-based metabolic models of Escherichia coli.
Initial proteome analysis of model microorganism Haemophilus influenzae strain Rd KW20.
Scalable method to determine mutations that occur during adaptive evolution of Escherichia coli.
Systemic metabolic reactions are obtained by singular value decomposition of genome-scale stoichiometric matrices.
Reconstructing metabolic flux vectors from extreme pathways: defining the alpha-spectrum.
An expanded genome-scale model of Escherichia coli K-12 (iJR904 GSM/GPR).
Large-scale evaluation of in silico gene deletions in Saccharomyces cerevisiae.
Reconciling gene expression data with known genome-scale regulatory network structures.
Genome-scale analysis of the uses of the Escherichia coli genome: model-driven analysis of heterogeneous data sets.
Description and interpretation of adaptive evolution of Escherichia coli K-12 MG1655 by using a genome-scale in silico metabolic model.
Network-based analysis of metabolic regulation in the human red blood cell.
Saccharomyces cerevisiae phenotypes can be predicted by using constraint-based analysis of a genome-scale reconstructed metabolic network.
Identifying constraints that govern cell behavior: a key to converting conceptual to computational models in biology?
Topological analysis of mass-balanced signaling networks: a framework to obtain network properties including crosstalk.
The convex basis of the left null space of the stoichiometric matrix leads to the definition of metabolically meaningful pools.
Metabolic pathways in the post-genome era.
Development of network-based pathway definitions: the need to analyze real metabolic networks.
Description and analysis of metabolic connectivity and dynamics in the human red blood cell.
Extreme pathway analysis of human red blood cell metabolism.
Genome-scale metabolic model of Helicobacter pylori 26695.
Extreme pathways and Kirchhoff's second law.
Escherichia coli K-12 undergoes adaptive evolution to achieve in silico predicted optimal growth.
Sequence-based analysis of metabolic demands for protein synthesis in prokaryotes.
Extreme pathway lengths and reaction participation in genome-scale metabolic networks.
Analysis of metabolic capabilities using singular value decomposition of extreme pathway matrices.
Genome-scale reconstruction of the Saccharomyces cerevisiae metabolic network.
H. influenzae Consortium: integrative study of H. influenzae-human interactions.
Constraints-based models: regulation of gene expression reduces the steady-state solution space.
Genome-scale microbial in silico models: the constraints-based approach.
Thirteen years of building constraint-based in silico models of Escherichia coli.
Quantitative analysis of Escherichia coli metabolic phenotypes within the context of phenotypic phase planes.
Importance of parenchymal:stromal cell ratio for the ex vivo reconstitution of human hematopoiesis.
In silico method for modelling metabolism and gene product expression at genome scale
Optimal selection of metabolic fluxes for in vivo measurement. II. Application to Escherichia coli and hybridoma cell metabolism.
Replication of mini-F plasmids during the bacterial division cycle.
Replication of prophage P1 is cell-cycle specific.
A Macintosh software package for simulation of human red blood cell metabolism.
Cell Culture conditions determine the enhancement of specific monoclonal antibody productivity of calcium alginate-entrapped S3H5/gamma2bA2 hybridoma cells.
Expansion of human bone marrow progenitor cells in a high cell density continuous perfusion system.
Model complexity has a significant effect on the numerical value and interpretation of metabolic sensitivity coefficients.
Simultaneous enzymatic/electrochemical determination of glucose and L-glutamine in hybridoma media by flow-injection analysis.
Biochemical production capabilities of Escherichia coli.
Loss of antibody productivity is highly reproducible in multiple hybridoma subclones.
Large-scale expansion of human stem and progenitor cells from bone marrow mononuclear cells in continuous perfusion cultures.
Stoichiometric interpretation of Escherichia coli glucose catabolism under various oxygenation rates.
Review: tissue engineering: reconstitution of human hematopoiesis ex vivo.
Optimal selection of metabolic fluxes for in vivo measurement. I. Development of mathematical methods.
Continuous photoautotrophic cultures of the eukaryotic alga Chlorella vulgaris can exhibit stable oscillatory dynamics.
The challenges of integrating multi-omic data sets.
Gap-filling analysis of the iJO1366 Escherichia coli metabolic network reconstruction for discovery of metabolic functions.
Exploiting adaptive laboratory evolution of Streptomyces clavuligerus for antibiotic discovery and overproduction.
Detailing the optimality of photosynthesis in cyanobacteria through systems biology analysis.
Constraining the metabolic genotype-phenotype relationship using a phylogeny of in silico methods.
Regulation of gene expression in flux balance models of metabolism.
Murine Sca-1(+)/Lin(-) cells and human KG1a cells exhibit multiple pseudopod morphologies during migration.
Metabolic modelling of microbes: the flux-balance approach.
The genome-scale metabolic extreme pathway structure in Haemophilus influenzae shows significant network redundancy.
In silico model-driven assessment of the effects of single nucleotide polymorphisms (SNPs) on human red blood cell metabolism.
Decomposing complex reaction networks using random sampling, principal component analysis and basis rotation.
Constraint-based analysis of metabolic capacity of Salmonella typhimurium during host-pathogen interaction.
Three-dimensional structural view of the central metabolic network of Thermotoga maritima.
Metabolic systems biology.
Simultaneous determination of ammonia nitrogen and L-glutamine in bioreactor media using flow injection.
Stability of antibody productivity is improved when hybridoma cells are entrapped in calcium alginate beads.
Metabolic capabilities of Escherichia coli: I. synthesis of biosynthetic precursors and cofactors.
Consistent and high rates of gene transfer can be obtained using flow-through transduction over a wide range of retroviral titers.
Determination of specific oxygen uptake rates in human hematopoietic cultures and implications for bioreactor design.
Cell growth and differentiation on feeder layers is predicted to be influenced by bioreactor geometry.
Different measures of human hematopoietic cell culture performance are optimized under vastly different conditions.
Membrane adsorption characteristics determine the kinetics of flow-through transductions.
Retroviral infection is limited by Brownian motion.
Kinetics of retrovirus mediated gene transfer: the importance of intracellular half-life of retroviruses.
flt-3 ligand is more potent than c-kit ligand for the synergistic stimulation of ex vivo hematopoietic cell expansion.
Unilineage model of hematopoiesis predicts self-renewal of stem and progenitor cells based on ex vivo growth data.
Donor-to-donor variability in the expansion potential of human bone marrow cells is reduced by accessory cells but not by soluble growth factors.
Metabolic network analysis integrated with transcript verification for sequenced genomes.
Central role of the cell in microbial ecology.
Production of pilus-like filaments in Geobacter sulfurreducens in the absence of the type IV pilin protein PilA.
Flow cytometric analysis of human bone marrow perfusion cultures: erythroid development and relationship with burst-forming units-erythroid.
Retroviral-mediated gene transfer in human bone marrow cells growth in continuous perfusion culture vessels.
Growth factor consumption and production in perfusion cultures of human bone marrow correlate with specific cell production.
Monoclonal antibody production using free-suspended and entrapped hybridoma cells.
Enhanced specific antibody productivity of calcium alginate-entrapped hybridoma is cell line-specific.
Predictions for oxygen supply control to enhance population stability of engineered production strains.
Preface. Tissue engineering and cell therapies.
Preface: Tissue engineering and cell therapies: II.
Microencapsulated human bone marrow cultures: a potential culture system for the clonal outgrowth of hematopoietic progenitor cells.
Frequent harvesting from perfused bone marrow cultures results in increased overall cell and progenitor expansion.
Stoichiometric flux balance models quantitatively predict growth and metabolic by-product secretion in wild-type Escherichia coli W3110.
High-density algal photobioreactors using light-emitting diodes.
In vitro expansion of hematopoietic cells for clinical application.
Parametric sensitivity of stoichiometric flux balance models applied to wild-type Escherichia coli metabolism.
Bioreactor expansion of human bone marrow: comparison of unprocessed, density-separated, and CD34-enriched cells.
Long-term culture-initiating cell expansion is dependent on frequent medium exchange combined with stromal and other accessory cell effects.
What lies beyond bioinformatics?
Using metabolic flux data to further constrain the metabolic solution space and predict internal flux patterns: the Escherichia coli spectrum.
Investigating the metabolic capabilities of Mycobacterium tuberculosis H37Rv using the in silico strain iNJ661 and proposing alternative drug targets.
The growing scope of applications of genome-scale metabolic reconstructions using Escherichia coli.
Network-based prediction of human tissue-specific metabolism.
Genome-scale reconstruction and in silico analysis of the Clostridium acetobutylicum ATCC 824 metabolic network.
Top-down analysis of temporal hierarchy in biochemical reaction networks.
A genome-scale metabolic reconstruction of Pseudomonas putida KT2440: iJN746 as a cell factory.
A consensus yeast metabolic network reconstruction obtained from a community approach to systems biology.
Use of randomized sampling for analysis of metabolic networks.
Aerobic fermentation of D-glucose by an evolved cytochrome oxidase-deficient Escherichia coli strain.
Understanding human metabolic physiology: a genome-to-systems approach.
Genome-scale reconstruction of the Lrp regulatory network in Escherichia coli.
Reconstruction of biochemical networks in microorganisms.
Genome-scale network analysis of imprinted human metabolic genes.
Identification of potential pathway mediation targets in Toll-like receptor signaling.
Impact of individual mutations on increased fitness in adaptively evolved strains of Escherichia coli.
Context-specific metabolic networks are consistent with experiments.
Predicting gene essentiality using genome-scale in silico models.
In silico analysis of SNPs and other high-throughput data.
Genome-scale reconstruction of metabolic network in Bacillus subtilis based on high-throughput phenotyping and gene essentiality data.
A genome-scale metabolic reconstruction for Escherichia coli K-12 MG1655 that accounts for 1260 ORFs and thermodynamic information.
An evaluation of Comparative Genome Sequencing (CGS) by comparing two previously-sequenced bacterial genomes.
A genome-scale, constraint-based approach to systems biology of human metabolism.
Microbial regulatory and metabolic networks.
Systematic condition-dependent annotation of metabolic genes.
Estimation of the number of extreme pathways for metabolic networks.
Metabolic reconstruction and modeling of nitrogen fixation in Rhizobium etli.
Three factors underlying incorrect in silico predictions of essential metabolic genes.
Formulating genome-scale kinetic models in the post-genome era.
Genome-wide analysis of Fis binding in Escherichia coli indicates a causative role for A-/AT-tracts.
Genomewide identification of protein binding locations using chromatin immunoprecipitation coupled with microarray.
Genome-scale reconstruction of Escherichia coli's transcriptional and translational machinery: a knowledge base, its mathematical formulation, and its functional characterization.
Connecting extracellular metabolomic measurements to intracellular flux states in yeast.
Gene expression profiling and the use of genome-scale in silico models of Escherichia coli for analysis: providing context for content.
Adaptive evolution of Escherichia coli K-12 MG1655 during growth on a Nonnative carbon source, L-1,2-propanediol.
Functional characterization of alternate optimal solutions of Escherichia coli's transcriptional and translational machinery.
De Novo assembly of the complete genome of an enhanced electricity-producing variant of Geobacter sulfurreducens using only short reads.
Systematizing the generation of missing metabolic knowledge.
Structural and operational complexity of the Geobacter sulfurreducens genome.
Omic data from evolved E. coli are consistent with computed optimal growth from genome-scale models.
Deletion of genes encoding cytochrome oxidases and quinol monooxygenase blocks the aerobic-anaerobic shift in Escherichia coli K-12 MG1655.
Drug off-target effects predicted using structural analysis in the context of a metabolic network model.
A detailed genome-wide reconstruction of mouse metabolism based on human Recon 1.
Insight into human alveolar macrophage and M. tuberculosis interactions via metabolic reconstructions.
RNA polymerase mutants found through adaptive evolution reprogram Escherichia coli for optimal growth in minimal media.
Genetic basis of growth adaptation of Escherichia coli after deletion of pgi, a major metabolic gene.
Microbiology. Topping off a multiscale balancing act.
The biomass objective function.
BiGG: a Biochemical Genetic and Genomic knowledgebase of large scale metabolic reconstructions.
Reconstruction annotation jamborees: a community approach to systems biology.
Using in silico models to simulate dual perturbation experiments: procedure development and interpretation of outcomes.
Functional states of the genome-scale Escherichia coli transcriptional regulatory system.
Probing the basis for genotype-phenotype relationships.
Can the protein occupancy landscape show the topologically isolated chromosomal domains in the E. coli genome?: An exciting prospect.
Flux-concentration duality in dynamic nonequilibrium biological networks.
Model-driven evaluation of the production potential for growth-coupled products of Escherichia coli.
Whole-genome resequencing of Escherichia coli K-12 MG1655 undergoing short-term laboratory evolution in lactate minimal media reveals flexible selection of adaptive mutations.
The transcription unit architecture of the Escherichia coli genome.
Applications of genome-scale metabolic reconstructions.
A protocol for generating a high-quality genome-scale metabolic reconstruction.
Towards genome-scale signalling network reconstructions.
What is flux balance analysis?
Mass action stoichiometric simulation models: incorporating kinetics and regulation into stoichiometric models.
Large-scale in silico modeling of metabolic interactions between cell types in the human brain.
Metabolic characterization of Escherichia coli strains adapted to growth on lactate.
In silico biotechnology. Era of reconstruction and interrogation.
Hierarchical thinking in network biology: the unbiased modularization of biochemical networks.
Candidate metabolic network states in human mitochondria. Impact of diabetes, ischemia, and diet.
Properties of metabolic networks: structure versus function.
High-throughput mutation detection underlying adaptive evolution of Escherichia coli-K12.
Expa: a program for calculating extreme pathways in biochemical reaction networks.
k-Cone analysis: determining all candidate values for kinetic parameters on a network scale.
Reconstruction of cellular signalling networks and analysis of their properties.
Genome-scale reconstruction of the metabolic network in Staphylococcus aureus N315: an initial draft to the two-dimensional annotation.
Automated in situ measurement of cell-specific antibody secretion and laser-mediated purification for rapid cloning of highly-secreting producers.
In silico design and adaptive evolution of Escherichia coli for production of lactic acid.
Untangling the web of functional and physical interactions in yeast.
Expanded metabolic reconstruction of Helicobacter pylori (iIT341 GSM/GPR): an in silico genome-scale characterization of single- and double-deletion mutants.
Immobilization of Escherichia coli RNA polymerase and location of binding sites by use of chromatin immunoprecipitation and microarrays.
Genome-scale models of microbial cells: evaluating the consequences of constraints.
The evolution of molecular biology into systems biology.
Uniform sampling of steady-state flux spaces: means to design experiments and to interpret enzymopathies.
Reconstruction of microbial transcriptional regulatory networks.
In Silico Metabolic Model and Protein Expression of Haemophilus influenzae Strain Rd KW20 in Rich Medium.
Integrating high-throughput and computational data elucidates bacterial networks.
Monte Carlo sampling can be used to determine the size and shape of the steady-state flux space.
Flagellar biosynthesis in silico: building quantitative models of regulatory networks.
Reconstruction and validation of Saccharomyces cerevisiae iND750, a fully compartmentalized genome-scale metabolic model.
Reconstruction and functional characterization of the human mitochondrial metabolic network based on proteomic and biochemical data.
The JAK-STAT signaling network in the human B-cell: an extreme signaling pathway analysis.
Comparison of network-based pathway analysis methods.
Genome-scale in silico models of E. coli have multiple equivalent phenotypic states: assessment of correlated reaction subsets that comprise network states.
Integrated analysis of metabolic phenotypes in Saccharomyces cerevisiae.
High-throughput laser-mediated in situ cell purification with high purity and yield.
Metabolic gene-deletion strains of Escherichia coli evolve to computationally predicted growth phenotypes.
Parallel adaptive evolution cultures of Escherichia coli lead to convergent growth phenotypes with different gene expression states.
Latent pathway activation and increased pathway capacity enable Escherichia coli adaptation to loss of key metabolic enzymes.
The global transcriptional regulatory network for metabolism in Escherichia coli exhibits few dominant functional states.
Identification of genome-scale metabolic network models using experimentally measured flux profiles.
Transcriptional regulation of the fad regulon genes of Escherichia coli by ArcA.
Isotopomer analysis of myocardial substrate metabolism: a systems biology approach.
Building the power house: recent advances in mitochondrial studies through proteomics and systems biology.
Matrix formalism to describe functional states of transcriptional regulatory systems.
Systems biology as a foundation for genome-scale synthetic biology.
Experimental and computational assessment of conditionally essential genes in Escherichia coli.
Comparative genome sequencing of Escherichia coli allows observation of bacterial evolution on a laboratory timescale.
Systems approach to refining genome annotation.
Toward whole cell modeling and simulation: comprehensive functional genomics through the constraint-based approach.
Global reconstruction of the human metabolic network based on genomic and bibliomic data.
Systems analysis of energy metabolism elucidates the affected respiratory chain complex in Leigh's syndrome.
Quantitative prediction of cellular metabolism with constraint-based models: the COBRA Toolbox.
Systems biology of SNPs.
Metabolic analysis of adaptive evolution for in silico-designed lactate-producing strains.
Modeling methanogenesis with a genome-scale metabolic reconstruction of Methanosarcina barkeri.
The econometrics of evolution.
Long-range periodic patterns in microbial genomes indicate significant multi-scale chromosomal organization.
Towards multidimensional genome annotation.
PCR-based tandem epitope tagging system for Escherichia coli genome engineering.
Characterization of metabolism in the Fe(III)-reducing organism Geobacter sulfurreducens by constraint-based modeling.
The model organism as a system: integrating 'omics' data sets.
Metabolite coupling in genome-scale metabolic networks.
Optoinjection for efficient targeted delivery of a broad range of compounds and macromolecules into diverse cell types.
Network-level analysis of metabolic regulation in the human red blood cell using random sampling and singular value decomposition.
Systems biology of the human red blood cell.
Candidate states of Helicobacter pylori's genome-scale metabolic network upon application of "loop law" thermodynamic constraints.
Integrated analysis of regulatory and metabolic networks reveals novel regulatory mechanisms in Saccharomyces cerevisiae.
Iterative reconstruction of transcriptional regulatory networks: an algorithmic approach.
Crystal structure of a hyperactive Escherichia coli glycerol kinase mutant Gly230 --> Asp obtained using microfluidic crystallization devices.
COBRAme: A Computational Framework for Building and Manipulating Models of Metabolism and Gene Expression
Literature mining supports a next-generation modeling approach to predict cellular byproduct secretion.
A Consensus Genome-scale Reconstruction of Chinese Hamster Ovary Cell Metabolism.
The aldehyde dehydrogenase, AldA, is essential for L-1,2-propanediol utilization in laboratory-evolved Escherichia coli
Multi-omic data integration enables discovery of hidden biological regularities.
A Phaeodactylum tricornutum literature database for interactive annotation of content
Multi-omics Quantification of Species Variation of Escherichia coli Links Molecular Features with Strain Phenotypes.
solveME: fast and reliable solution of nonlinear ME models.
Biomarkers defining the metabolic age of red blood cells during cold storage.
Sharing and community curation of mass spectrometry data with Global Natural Products Social Molecular Networking.
Metabolic fate of adenine in red blood cells during storage in SAGM solution.
A Multi-scale Computational Platform to Mechanistically Assess the Effect of Genetic Variation on Drug Responses in Human Erythrocyte Metabolism.
Construction and Evaluation of an Organic Anion Transporter 1 (OAT1)-Centered Metabolic Network.
Quantification and Classification of E. coli Proteome Utilization and Unused Protein Costs across Environments.
Unique attributes of cyanobacterial metabolism revealed by improved genome-scale metabolic modeling and essential gene analysis.
Whole-Genome Sequencing of Invasion-Resistant Cells Identifies Laminin α2 as a Host Factor for Bacterial Invasion.
Reliable and efficient solution of genome-scale models of Metabolism and macromolecular Expression.
Topological and Kinetic Determinants of the Modal Matrices of Dynamic Models of Metabolism
Expanding The Computable Reactome In Pseudomonas putida Reveals Metabolic Cycles Providing Robustness
Revealing genome-scale transcriptional regulatory landscape of OmpR highlights its expanded regulatory roles under osmotic stress in Escherichia coli K-12 MG1655.
Laboratory Evolution to Alternating Substrate Environments Yields Distinct Phenotypic and Genetic Adaptive Strategies.
Machine Learning in Computational Biology to Accelerate High-Throughput Protein Expression.
Metabolomics comparison of red cells stored in four additive solutions reveals differences in citrate anticoagulant permeability and metabolism.
Elucidating dynamic metabolic physiology through network integration of quantitative time-course metabolomics.
Biomarkers are used to predict quantitative metabolite concentration profiles in human red blood cells.
Citrate metabolism in red blood cells stored in additive solution-3.
A Model for Designing Adaptive Laboratory Evolution Experiments.
Integrated Regulatory and Metabolic Networks of the Marine Diatom Phaeodactylum tricornutum Predict the Response to Rising CO2 Levels.
Systems biology analysis of drivers underlying hallmarks of cancer cell metabolism.
Increased production of L-serine in Escherichia coli through Adaptive Laboratory Evolution.
Quantitative feature extraction from the Chinese hamster ovary bioprocess bibliome using a novel meta-analysis workflow.
Genome-Scale Model Reveals Metabolic Basis of Biomass Partitioning in a Model Diatom.
Comparative genome-scale modelling of Staphylococcus aureus strains identifies strain-specific metabolic capabilities linked to pathogenicity.
TFpredict and SABINE: sequence-based prediction of structural and functional characteristics of transcription factors.
SBML qualitative models: a model representation format and infrastructure to foster interactions between qualitative modelling formalisms and tools.
Path2Models: large-scale generation of computational models from biochemical pathway maps.
Parkinson's disease: dopaminergic nerve cell model is consistent with experimental finding of increased extracellular transport of α-synuclein.
A Markov chain model for N-linked protein glycosylation - towards a low-parameter tool for model-driven glycoengineering.
Engineering of oleaginous organisms for lipid production.
Adaptive Evolution of Thermotoga maritima Reveals Plasticity of the ABC Transporter Network.
Investigating Moorella thermoacetica metabolism with a genome-scale constraint-based metabolic model.
Unraveling interactions in microbial communities - from co-cultures to microbiomes.
A logical data representation framework for electricity-driven bioproduction processes.
Do genome-scale models need exact solvers or clearer standards?
Systems biology-guided identification of synthetic lethal gene pairs and its potential use to discover antibiotic combinations
Personalized Whole-Cell Kinetic Models of Metabolism for Discovery in Genomics and Pharmacodynamics
The systems biology simulation core algorithm.
Optimizing eukaryotic cell hosts for protein production through systems biotechnology and genome-scale modeling.
Networks of energetic and metabolic interactions define dynamics in microbial communities.
Evaluation of rate law approximations in bottom-up kinetic models of metabolism.
What do cells actually want?
Characterizing Strain Variation in Engineered E. coli Using a Multi-Omics-Based Workflow.
Global Rebalancing of Cellular Resources by Pleiotropic Point Mutations Illustrates a Multi-scale Mechanism of Adaptive Evolution.
Acidithiobacillus ferrooxidans's comprehensive model driven analysis of the electron transfer metabolism and synthetic strain design for biomining applications
A modeling method for increased precision and scope of directly measurable fluxes at a genome-scale.
Evolution of E. coli on [U-13C]Glucose Reveals a Negligible Isotopic Influence on Metabolism and Physiology.
Systems biology of the structural proteome.
What Makes a Bacterial Species Pathogenic?:Comparative Genomic Analysis of the Genus Leptospira.
Solving puzzles with missing pieces: The power of systems biology
Identified metabolic signature for assessing red blood cell unit quality is associated with endothelial damage markers and clinical outcomes.
MID Max: LC-MS/MS Method for Measuring the Precursor and Product Mass Isotopomer Distributions of Metabolic Intermediates and Cofactors for Metabolic Flux Analysis Applications.
From random mutagenesis to systems biology in metabolic engineering of mammalian cells
BiGG Models: A platform for integrating, standardizing and sharing genome-scale models.
Systems assessment of transcriptional regulation on central carbon metabolism by Cra and CRP
Adaptive laboratory evolution of a genome-reduced Escherichia coli
Machine learning and structural analysis of Mycobacterium tuberculosis pan-genome identifies genetic signatures of antibiotic resistance
Characterizing posttranslational modifications in prokaryotic metabolism using a multiscale workflow
Thermodynamic favorability and pathway yield as evolutionary tradeoffs in biosynthetic pathway choice
Systems analysis of metabolism in platelet concentrates during storage in platelet additive solution.
Escher-FBA: a web application for interactive flux balance analysis
Basics of genome-scale metabolic modeling and applications on C1-utilization.
Genome-scale metabolic reconstructions of multiple Salmonella strains reveal serovar-specific metabolic traits.
Evolution of gene knockout strains of E. coli reveal regulatory architectures governed by metabolism.
Multiple optimal phenotypes overcome redox and glycolytic intermediate metabolite imbalances in knockout evolutions.
Systematic discovery of uncharacterized transcription factors in Escherichia coli K-12 MG1655.
Network-level allosteric effects are elucidated by detailing how ligand-binding events modulate utilization of catalytic potentials.
A unified resource for transcriptional regulation in Escherichia coli K-12 incorporating high-throughput-generated binding data into RegulonDB version 10.0
Growth Adaptation of gnd and sdhCB Escherichia coli Deletion Strains Diverges From a Similar Initial Perturbation of the Transcriptome
Identification of growth-coupled production strains considering protein costs and kinetic variability
Estimating Metabolic Equilibrium Constants: Progress and Future Challenges
Metagenomics-Based, Strain-Level Analysis of Escherichia coli From a Time-Series of Microbiome Samples From a Crohn's Disease Patient
Creation and analysis of biochemical constraint-based models using the COBRA Toolbox v.3.0.
Revealing Key Determinants of Clonal Variation in Transgene Expression in Recombinant CHO Cells Using Targeted Genome Editing.
Dataset on economic analysis of mass production of algae in LED-based photobioreactors.
The y-ome defines the 35% of Escherichia coli genes that lack experimental evidence of function
Pseudogene repair driven by selection pressure applied in experimental evolution.
A computational knowledge-base elucidates the response of Staphylococcus aureus to different media types.
Reframing gene essentiality in terms of adaptive flexibility.
ALEdb 1.0: a database of mutations from adaptive laboratory evolution experimentation.
Modeling genome-wide enzyme evolution predicts strong epistasis underlying catalytic turnover rates
Machine learning applied to enzyme turnover numbers reveals protein structural correlates and improves metabolic models
Gapless, Unambiguous Genome Sequence for Escherichia coli C, a Workhorse of Industrial Biology
Predicting the metabolic capabilities of Synechococcus elongatus PCC 7942 adapted to different light regimes.
Sugar-stimulated CO2 sequestration by the green microalga Chlorella vulgaris
COBRAme: A computational framework for genome-scale models of metabolism and gene expression.
Adaptive laboratory evolution resolves energy depletion to maintain high aromatic metabolite phenotypes in Escherichia coli strains lacking the Phosphotransferase System.
Escherichia coli B2 strains prevalent in inflammatory bowel disease patients have distinct metabolic capabilities that enable colonization of intestinal mucosa.
Metabolic Models of Protein Allocation Call for the Kinetome.
Dissecting the genetic and metabolic mechanisms of adaptation to the knockout of a major metabolic enzyme in Escherichia coli.
Antibiotic-Induced Changes to the Host Metabolic Environment Inhibit Drug Efficacy and Alter Immune Function.
Generation of a platform strain for ionic liquid tolerance using adaptive laboratory evolution.
Quantitative time-course metabolomics in human red blood cells reveal the temperature dependence of human metabolic networks.
iML1515, a knowledgebase that computes Escherichia coli traits.
Utilizing biomarkers to forecast quantitative metabolite concentration profiles in human red blood cells
Thermosensitivity of growth is determined by chaperone-mediated proteome reallocation
A Padawan Programmer’s Guide to Developing Software Libraries
Fast growth phenotype of E. coli K-12 from adaptive laboratory evolution does not require intracellular flux rewiring.
Global transcriptional regulatory network for Escherichia coli robustly connects gene expression to transcription factor activities.
Underground metabolism: network-level perspective and biotechnological potential
Mannose and fructose metabolism in red blood cells during cold storage in SAGM.
Functional interrogation of Plasmodium genus metabolism identifies species- and stage-specific differences in nutrient essentiality and drug targeting.
Modeling the multi-scale mechanisms of macromolecular resource allocation
Quantitative -omic data empowers bottom-up systems biology
Adaptation to the coupling of glycolysis to toxic methylglyoxal production in tpiA deletion strains of Escherichia coli requires synchronized and counterintuitive genetic changes.
Temperature-Dependent Estimation of Gibbs Energies Using an Updated Group-Contribution Method.
The Staphylococcus aureus Two-Component System AgrAC Displays Four Distinct Genomic Arrangements That Delineate Genomic Virulence Factor Signatures
ChIP-exo interrogation of Crp, DNA, and RNAP holoenzyme interactions.
High-Level dCas9 Expression Induces Abnormal Cell Morphology in Escherichia coli.
iCN718, an Updated and Improved Genome-Scale Metabolic Network Reconstruction of Acinetobacter baumannii AYE
Laboratory evolution reveals regulatory and metabolic trade-offs of glycerol utilization in Saccharomyces cerevisiae.
Systems biology as an emerging paradigm in transfusion medicine.
Updated and standardized genome-scale reconstruction of Mycobacterium tuberculosis H37Rv, iEK1011, simulates flux states indicative of physiological conditions.
Recon3D enables a three-dimensional view of gene variation in human metabolism.
ssbio: A Python Framework for Structural Systems Biology
Systems assessment of transcriptional regulation on central carbon metabolism by Cra and CRP.
Genome-scale analysis of Methicillin-resistant Staphylococcus aureus USA300 reveals a tradeoff between pathogenesis and drug resistance.
ChIP-exo interrogation of Crp, DNA, and RNAP holoenzyme interactions
SBMLsqueezer 2: context-sensitive creation of kinetic equations in biochemical networks.
Genome-scale models of metabolism and gene expression extend and refine growth phenotype prediction.
The microbiome extends to subepidermal compartments of normal skin.
Systems biology of stored blood cells: can it help to extend the expiration date?
Proteomic analysis of Chinese hamster ovary cells.
Sulfide-driven microbial electrosynthesis.
Analysis of omics data with genome-scale models of metabolism.
Inferring the metabolism of human orphan metabolites from their metabolic network context affirms human gluconokinase activity.
Anaerobic utilization of toluene by marine alpha- and gammaproteobacteria reducing nitrate.
UPLC-UV-MS(E) analysis for quantification and identification of major carotenoid and chlorophyll species in algae.
Multiple-omic data analysis of Klebsiella pneumoniae MGH 78578 reveals its transcriptional architecture and regulatory features.
Multiscale Modeling of Metabolism and Macromolecular Synthesis in E. coli and Its Application to the Evolution of Codon Usage.
Network context and selection in the evolution to enzyme specificity.
Comparative Analysis of Regulatory Elements between Escherichia coli and Klebsiella pneumoniae by Genome-Wide Transcription Start Site Profiling.
Adaptive Laboratory Evolution
Genomically and biochemically accurate metabolic reconstruction of Methanosarcina barkeri Fusaro, iMG746.
A community-driven global reconstruction of human metabolism.
Enhancement of carotenoid biosynthesis in the green microalga Dunaliella salina with light-emitting diodes and adaptive laboratory evolution.
Transcriptional regulation of the carbohydrate utilization network in Thermotoga maritima.
Optimizing Cofactor Specificity of Oxidoreductase Enzymes for the Generation of Microbial Production Strains—OptSwap
The genome organization of Thermotoga maritima reflects its lifestyle.
Reconciling a Salmonella enterica metabolic model with experimental data confirms that overexpression of the glyoxylate shunt can rescue a lethal ppc deletion mutant.
Multispecific Drug Transporter Oat3 (Slc22a8) Regulates Multiple Metabolic Pathways.
COBRApy: COnstraints-Based Reconstruction and Analysis for Python.
Genomic landscapes of Chinese hamster ovary cell lines as revealed by the Cricetulus griseus draft genome.
MS/MS networking guided analysis of molecule and gene cluster families.
Structural systems biology evaluation of metabolic thermotolerance in Escherichia coli.
Basic and applied uses of genome-scale metabolic network reconstructions of Escherichia coli.
Studying Salmonellae and Yersiniae host-pathogen interactions using integrated 'omics and modeling.
Characterizing the interplay between multiple levels of organization within bacterial sigma factor regulatory networks.
Salmonella modulates metabolism during growth under conditions that induce expression of virulence genes.
In situ to in silico and back: elucidating the physiology and ecology of Geobacter spp. using genome-scale modelling.
A c-type cytochrome and a transcriptional regulator responsible for enhanced extracellular electron transfer in Geobacter sulfurreducens revealed by adaptive evolution.
Microbial laboratory evolution in the era of genome-scale science.
A multi-tissue type genome-scale metabolic network for analysis of whole-body systems physiology.
Cumulative number of cell divisions as a meaningful timescale for adaptive laboratory evolution of Escherichia coli.
Elimination of thermodynamically infeasible loops in steady-state metabolic models.
Linkage of organic anion transporter-1 to metabolic pathways through integrated "omics"-driven network and functional analysis.
Monitoring metabolites consumption and secretion in cultured cells using ultra-performance liquid chromatography quadrupole-time of flight mass spectrometry (UPLC-Q-ToF-MS).
MODELING HOST-PATHOGEN INTERACTIONS: COMPUTATIONAL BIOLOGY AND BIOINFORMATICS FOR INFECTIOUS DISEASE RESEARCH.
Using the reconstructed genome-scale human metabolic network to study physiology and pathology.
Transcriptional regulation of central carbon and energy metabolism in bacteria by redox-responsive repressor Rex.
A road map for the development of community systems (CoSy) biology.
Raloxifene attenuates Pseudomonas aeruginosa pyocyanin production and virulence.
Predicting outcomes of steady-state ¹³C isotope tracing experiments using Monte Carlo sampling.
Model-driven multi-omic data analysis elucidates metabolic immunomodulators of macrophage activation.
Maximizing biomass productivity and cell density of Chlorella vulgaris by using light-emitting diode-based photobioreactor.
An experimentally-supported genome-scale metabolic network reconstruction for Yersinia pestis CO92.
A variational principle for computing nonequilibrium fluxes and potentials in genome-scale biochemical networks.
The human metabolic reconstruction Recon 1 directs hypotheses of novel human metabolic functions.
A comprehensive genome-scale reconstruction of Escherichia coli metabolism--2011.
A community effort towards a knowledge-base and mathematical model of the human pathogen Salmonella Typhimurium LT2.
Technologies and approaches to elucidate and model the virulence program of salmonella.
iAB-RBC-283: A proteomically derived knowledge-base of erythrocyte metabolism that can be used to simulate its physiological and patho-physiological states.
Quantitative prediction of cellular metabolism with constraint-based models: the COBRA Toolbox v2.0.
The genomic sequence of the Chinese hamster ovary (CHO)-K1 cell line.
Metabolic network reconstruction of Chlamydomonas offers insight into light-driven algal metabolism.
Sensitive and accurate identification of protein-DNA binding events in ChIP-chip assays using higher order derivative analysis.
An experimentally validated genome-scale metabolic reconstruction of Klebsiella pneumoniae MGH 78578, iYL1228.
Functional and metabolic effects of adaptive glycerol kinase (GLPK) mutants in Escherichia coli.
The role of cellular objectives and selective pressures in metabolic pathway evolution.
The PurR regulon in Escherichia coli K-12 MG1655.
Adaptive laboratory evolution--harnessing the power of biology for metabolic engineering.
Intracellular metabolite profiling of platelets: evaluation of extraction processes and chromatographic strategies.
The development of a fully-integrated immune response model (FIRM) simulator of the immune response through integration of multiple subset models.
Model-driven discovery of synergistic inhibitors against E. coli and S. enterica serovar Typhimurium targeting a novel synthetic lethal pair, aldA and prpC.
Multidimensional Analytical Approach Based on UHPLC-UV-Ion Mobility-MS for the Screening of Natural Pigments.
Next-generation genome-scale models for metabolic engineering.
Computing the functional proteome: recent progress and future prospects for genome-scale models.
Ion Mobility-Derived Collision Cross Section As an Additional Measure for Lipid Fingerprinting and Identification.
Model-driven discovery of underground metabolic functions in Escherichia coli.
Improving collaboration by standardization efforts in systems biology.
Discovery of key mutations enabling rapid growth of Escherichia coli K-12 MG1655 on glucose minimal media using adaptive laboratory evolution.
The Metabolic Impact of a NADH-producing Glucose-6-phosphate Dehydrogenase in Escherichia coli.
Supplementation of Saturated Long-chain Fatty Acids Maintains Intestinal Eubiosis and Reduces Ethanol-induced Liver Injury in Mice.
Fast Swinnex filtration (FSF): a fast and robust sampling and extraction method suitable for metabolomics analysis of cultures grown in complex media
A Systems Approach to Predict Oncometabolites via Context-Specific Genome-Scale Metabolic Networks.
Reconstruction and modeling protein translocation and compartmentalization in Escherichia coli at the genome-scale.
Deciphering Fur transcriptional regulatory network highlights its complex role beyond iron metabolism in Escherichia coli.
The architecture of ArgR-DNA complexes at the genome-scale in Escherichia coli.
How to set up collaborations between academia and industrial biotech companies.
Decoding the jargon of bottom-up metabolic systems biology.
Escher: A Web Application for Building, Sharing, and Embedding Data-Rich Visualizations of Biological Pathways.
Genome-wide Reconstruction of OxyR and SoxRS Transcriptional Regulatory Networks under Oxidative Stress in Escherichia coli K-12 MG1655.
Systems biology definition of the core proteome of metabolism and expression is consistent with high-throughput data.
Decoding genome-wide GadEWX-transcriptional regulatory networks reveals multifaceted cellular responses to acid stress in Escherichia coli.
CONDENSED VERSION--Pharmacogenomic and clinical data link non-pharmacokinetic metabolic dysregulation to drug side effect pathogenesis
Deciphering the transcriptional regulatory logic of amino acid metabolism.
Deciphering the transcriptional regulatory logic of amino acid metabolism.
A streamlined ribosome profiling protocol for the characterization of microorganisms.
JSBML 1.0: providing a smorgasbord of options to encode systems biology models.
Pharmacogenomic and clinical data link non-pharmacokinetic metabolic dysregulation to drug side effect pathogenesis.
Prediction of intracellular metabolic states from extracellular metabolomic data.
Using Genome-scale Models to Predict Biological Capabilities.
A pH and solvent optimized reverse-phase ion-paring-LC–MS/MS method that leverages multiple scan-types for targeted absolute quantification of intracellular metabolites
Systems glycobiology for glycoengineering.
Metabolomic analysis of platelets during storage: a comparison between apheresis- and buffy coat-derived platelet concentrates.
A Gapless, Unambiguous Genome Sequence of the Enterohemorrhagic Escherichia coli O157:H7 Strain EDL933.
Global metabolic network reorganization by adaptive mutations allows fast growth of Escherichia coli on glycerol.
Effects of abiotic stressors on lutein production in the green microalga Dunaliella salina.
Genome-scale reconstruction of the sigma factor network in Escherichia coli: topology and functional states.
Network reconstruction of platelet metabolism identifies metabolic signature for aspirin resistance.
Constraint-based models predict metabolic and associated cellular functions.
Capsule deletion via a lamda-Red knockout system perturbs biofilm formation and fimbriae expression in Klebsiella pneumoniae MGH 78578.
Characterization and modelling of interspecies electron transfer mechanisms and microbial community dynamics of a syntrophic association.
Characterizing acetogenic metabolism using a genome-scale metabolic reconstruction of Clostridium ljungdahlii.
A model-driven quantitative metabolomics analysis of aerobic and anaerobic metabolism in E. coli K-12 MG1655 that is biochemically and thermodynamically consistent.
Genome-scale metabolic reconstructions of multiple Escherichia coli strains highlight strain-specific adaptations to nutritional environments.
Systems biology and biotechnology of Streptomyces species for the production of secondary metabolites.
GIM3E: condition-specific models of cellular metabolism developed from metabolomics and expression data.
Single-cell genome and metatranscriptome sequencing reveal metabolic interactions of an alkane-degrading methanogenic community.
Determining the control circuitry of redox metabolism at the genome-scale.
Cofactory: Sequence-based prediction of cofactor specificity of Rossmann folds.
Ion mobility derived collision cross sections to support metabolomics applications.
Generation of an atlas for commodity chemical production in Escherichia coli and a novel pathway prediction algorithm, GEM-Path.
Evolution of Escherichia coli to 42 °C and Subsequent Genetic Engineering Reveals Adaptive Mechanisms and Novel Mutations.
The COMBREX project: design, methodology, and initial results.
Multi-Tissue Computational Modeling Analyzes Pathophysiology of Type 2 Diabetes in MKR Mice.
Minimal metabolic pathway structure is consistent with associated biomolecular interactions.
Predicting microbial growth.
Comprehensive metabolomic study of platelets reveals the expression of discrete metabolic phenotypes during storage.
Tracing Compartmentalized NADPH Metabolism in the Cytosol and Mitochondria of Mammalian Cells.
Optimal cofactor swapping can increase the theoretical yield for chemical production in Escherichia coli and Saccharomyces cerevisiae.
Biochemical Characterization of Human Gluconokinase and the Proposed Metabolic Impact of Gluconic Acid as Determined by Constraint Based Metabolic Network Analysis.
Engineering synergy in biotechnology.
Optimizing genome-scale network reconstructions.
Constraint-Based Modeling of Carbon Fixation and the Energetics of Electron Transfer in Geobacter metallireducens.
Antibacterial mechanisms identified through structural systems pharmacology.